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pyMez.Code.DataHandlers.NISTModels module

NISTModels is a module to handle data types found at NIST in Boulder, CO

#-----------------------------------------------------------------------------
# Name:        NISTModels
# Purpose:    To handle data generated at NIST Boulder
# Author:      Aric Sanders
# Created:     2/22/2016
# License:     MIT License
#-----------------------------------------------------------------------------
""" NISTModels is a module to handle data types found at NIST in Boulder, CO """

#-----------------------------------------------------------------------------
# Standard Imports
import os
import fnmatch
import datetime
#-----------------------------------------------------------------------------
# Third Party Imports
try:
    from pyMez.Code.Utils.Alias import *
    METHOD_ALIASES=1
except:
    print("The module pyMez.Code.Utils.Alias was not found")
    METHOD_ALIASES=0
    pass
try:
    from pyMez.Code.DataHandlers.GeneralModels import *
except:
    print("The module pyMez.Code.DataHandlers.GeneralModels was not found,"
          "please put it on the python path")
    raise ImportError
try:
    from pyMez.Code.DataHandlers.TouchstoneModels import *
except:
    print("The module pyMez.Code.DataHandlers.TouchstoneModels was not found,"
          "please put it on the python path")
    raise ImportError

try:
    import numpy as np
except:
    print("The module numpy was not found,"
          "please put it on the python path")
    raise ImportError
try:
    import matplotlib.pyplot as plt
except:
    print("The module matplotlib was not found,"
          "please put it on the python path")
#-----------------------------------------------------------------------------
# Module Constants
ONE_PORT_COLUMN_NAMES=["Frequency", "mag", "uMb", "uMa", "uMd", "uMg", "arg",
                                    "uAb", "uAa", "uAd", "uAg"]
#Note there are 2 power models!!! one with 4 error terms and one with 3
POWER_4TERM_COLUMN_NAMES=['Frequency','Efficiency','uEb', 'uEa','uEd','uEg',
                    'Calibration_Factor','uCb','uCa','uCd','uCg']
#todo: change this description to reflect the column names
POWER_4TERM_COLUMN_DESCRIPTIONS={"Frequency": "Frequency in GHz",
                                           "Efficiency":"Effective Efficiency",
                                           "uEs": "Uncertainty in efficiency due to standards",
                                           "uEc": "Uncertainty in efficiency for repeated connects",
                                           "uEe": "Total uncertainty in Efficiency",
                                           "Calibration_Factor": "Effective efficiency modified by reflection coefficient",
                                           "uCs": "Uncertainty in calibration factor due to standards",
                                           "uCc": "Uncertainty in calibration factor for repeated connects",
                                           "uCe": "Total uncertainty in calibration factor"}
POWER_3TERM_COLUMN_NAMES=['Frequency','Efficiency','uEs', 'uEc','uEe',
                    'Calibration_Factor','uCs','uCc','uCe']
POWER_3TERM_COLUMN_DESCRIPTIONS={"Frequency": "Frequency in GHz",
                                           "Efficiency":"Effective Efficiency",
                                           "uEs": "Uncertainty in efficiency due to standards",
                                           "uEc": "Uncertainty in efficiency for repeated connects",
                                           "uEe": "Total uncertainty in Efficiency",
                                           "Calibration_Factor": "Effective efficiency modified by reflection coefficient",
                                           "uCs": "Uncertainty in calibration factor due to standards",
                                           "uCc": "Uncertainty in calibration factor for repeated connects",
                                           "uCe": "Total uncertainty in calibration factor"}
#POWER_COLUMN_NAMES=POWER_3TERM_COLUMN_NAMES
# Constant that determines if S21 is in db-angle or mag-angle format true is in mag-angle
CONVERT_S21=True
# Constant that determines if 1-port raw files have S11 and S22 or just S11
COMBINE_S11_S22=True
#-----------------------------------------------------------------------------
# Module Functions
def asc_type(file_contents):
    """asc_type determines the type of asc file given it's contents, returns the class name of the appropriate model"""
    if type(file_contents) is StringType:
        contents=file_contents
    elif type(file_contents) is ListType:
        contents=string_list_collapse(file_contents)
    else:
        return None
    if re.search('table 1',contents,re.IGNORECASE) and re.search('table 2',contents,re.IGNORECASE) and re.search('table 3',contents,re.IGNORECASE):
        return 'TwoPortCalrepModel'
    elif re.search('table 1',contents,re.IGNORECASE) and re.search('table 2',contents,re.IGNORECASE):
        return 'PowerCalrepModel'
    elif re.search('table 1',contents,re.IGNORECASE):
        return 'OnePortCalrepModel'
    else:
        return None

def raw_type(file_contents):
    """Given the contents of a file in a list of lines or a single string returns the raw class name. It is assumed
    that the type of file is the 5th line of the header"""
    if type(file_contents) is StringType:
        lines=file_contents.splitlines()
    elif type(file_contents) is ListType:
        lines=file_contents
    #print("The value of {0} is {1}".format('lines[4]',lines[4]))
    out=None
    if re.search('1-port',lines[4],re.IGNORECASE):
        out='OnePortRawModel'
    elif re.search('2-port',lines[4],re.IGNORECASE) and not re.search('2-portNR',lines[4],re.IGNORECASE):
        out='TwoPortRawModel'
    elif re.search('2-portNR',lines[4],re.IGNORECASE):
        out='TwoPortNRRawModel'
    elif re.search('Thermistor|Dry Cal',lines[4],re.IGNORECASE):
        out='PowerRawModel'
    return out

def sparameter_power_type(file_path):
    """sparameter_power_type returns the class name of file given a file path"""
    extension=file_path.split('.')[-1]
    #print extension
    in_file=open(file_path,'r')
    lines=[]
    for line in in_file:
        lines.append(line)
    in_file.close()
    if re.match('asc',extension,re.IGNORECASE):
        #print("The value of {0} is {1}".format('extension',extension))
        # handle asc files
        out=asc_type(lines)
    elif re.match('[\w][\d]+_[\d]+',extension,re.IGNORECASE):
        #print("The value of {0} is {1}".format('extension',extension))
        out=raw_type(lines)
    return out

def calrep_to_benchmark(file_path):
    """Creates a benchmark list given a path to a calrep file, assumes column names are 2 lines after
    the occurrence of the last /"""
    in_file=open(file_path,'r')
    lines=[]
    for line in in_file:
        lines.append(line)
    block_end=re.compile('/')
    for index,line in enumerate(lines):
        if re.match(block_end,line):
            last_block_comment_line=index
    header=lines[0:last_block_comment_line+1]
    columns_line=last_block_comment_line+2
    column_names=lines[columns_line].split(' ')
    data=lines[columns_line+1:None]
    return [header,column_names,data]

def build_csv_from_raw(input_file_names_list,output_file_name,model_name):
    """Build csv from raw  takes a list of file names conforming to model and builds a single csv.
    It is intentioned to accept raw files from the sparameter power project that have been converted from bdat
    using Ron Ginely's converter (modified calrep program). The output is a single csv file with metadata added
    as extra columns (ie a denormalized table)"""
    try:
        # our current definition of metadata keys for all of the raw models
        metadata_keys=["System_Id","System_Letter","Connector_Type_Calibration","Connector_Type_Measurement",
              "Measurement_Type","Measurement_Date","Measurement_Time","Program_Used","Program_Revision","Operator",
              "Calibration_Name","Calibration_Date","Port_Used","Number_Connects","Number_Repeats","Nbs",
              "Number_Frequencies","Start_Frequency",
              "Device_Description","Device_Id"]
        # import the first file
        model=globals()[model_name]
        initial_file=model(input_file_names_list[0])
        # Add the metadata columns and replace any commas with -
        for column_name in metadata_keys:
            initial_file.add_column(column_name=column_name,column_type='str',
                            column_data=[initial_file.metadata[column_name].replace(',','-')
                                         for row in initial_file.data])
        # We also add a column at the end that is Measurement_Timestamp, that is
        # Measurement_Time+Measurement_Date in isoformat
        timestamp=initial_file.metadata["Measurement_Date"]+" "+initial_file.metadata["Measurement_Time"]
        datetime_timestamp=datetime.datetime.strptime(timestamp,'%d %b %Y %H:%M:%S')
        measurement_timestamp=datetime_timestamp.isoformat(' ')
        initial_file.add_column(column_name="Measurement_Timestamp",column_type='str',
                            column_data=[measurement_timestamp
                                         for row in initial_file.data])
        # now we save the intial file with its column names but not its header
        initial_file.header=None
        initial_file.save(output_file_name)

        # Now we re-open this file in the append mode and read-in each new file and append it. This seems to work
        # for very large data sets, where as keeping a single object in memory fails
        out_file=open(output_file_name,'a')
        # now we do the same thing over and over and add it to the out file
        for file_name in input_file_names_list[1:]:

            model=globals()[model_name]
            parsed_file=model(file_name)
            for column_name in metadata_keys:
                parsed_file.add_column(column_name=column_name,column_type='str',
                            column_data=[parsed_file.metadata[column_name].replace(',','-')
                                         for row in parsed_file.data])
            timestamp=parsed_file.metadata["Measurement_Date"]+" "+parsed_file.metadata["Measurement_Time"]
            datetime_timestamp=datetime.datetime.strptime(timestamp,'%d %b %Y %H:%M:%S')
            measurement_timestamp=datetime_timestamp.isoformat(' ')
            parsed_file.add_column(column_name="Measurement_Timestamp",column_type='str',
                            column_data=[measurement_timestamp
                                         for row in parsed_file.data])
            # add an endline before appending
            out_file.write('\n')
            # now we only want the data string
            data=parsed_file.get_data_string()
            out_file.write(data)
        # close the file after  loop
        out_file.close()
    # Catch any errors
    except:
            raise

#-----------------------------------------------------------------------------
# Module Classes
class OnePortCalrepModel(AsciiDataTable):
    def __init__(self,file_path,**options):
        "Intializes the OnePortCalrepModel Class, it is assumed that the file is of the .asc or table type"
        # This is a general pattern for adding a lot of options
        defaults= {"data_delimiter": ",", "column_names_delimiter": ",", "specific_descriptor": 'One_Port',
                   "general_descriptor": 'Sparameter', "extension": 'txt', "comment_begin": "#", "comment_end": "\n",
                   "column_types": ['float' for i in range(11)],
                   "column_descriptions": {"Frequency": "Frequency in GHz", "Magnitude": "Linear magnitude",
                                           "uMb": "Uncertainty in magnitude due to standards",
                                           "uMa": "Uncertainty in magnitude due to electronics",
                                           "uMd": "Uncertainty in magnitude for repeated connects",
                                           "uMg": "Total uncertainty in magnitude",
                                           "Phase": "Phase in degrees",
                                           "uPhb": "Uncertainty in phase due to standards",
                                           "uPha": "Uncertainty in phase due to electronics",
                                           "uPhd": "Uncertainty in phase for repeated connects",
                                           "uPhg": "Total uncertainty in phase"}, "header": None,
                   "column_names": ONE_PORT_COLUMN_NAMES, "column_names_end_token": "\n", "data": None,
                   "row_formatter_string": None, "data_table_element_separator": None,"row_begin_token":None,
                   "row_end_token":None,"escape_character":None,
                   "data_begin_token":None,"data_end_token":None}
        self.options={}
        for key,value in defaults.iteritems():
            self.options[key]=value
        for key,value in options.iteritems():
            self.options[key]=value
        # Define Method Aliases if they are available
        if METHOD_ALIASES:
            for command in alias(self):
                exec(command)
        if file_path is not None:
            self.path=file_path
            self.__read_and_fix__()

        #build the row_formatting string, the original files have 4 decimals of precision for freq/gamma and 2 for Phase
        row_formatter=""
        for i in range(11):
            if i<6:
                row_formatter=row_formatter+"{"+str(i)+":.4f}{delimiter}"
            elif i==10:
                row_formatter=row_formatter+"{"+str(i)+":.2f}"
            else:
                row_formatter=row_formatter+"{"+str(i)+":.2f}{delimiter}"
        self.options["row_formatter_string"]=row_formatter
        AsciiDataTable.__init__(self,None,**self.options)
        if file_path is not None:
            self.path=file_path

    def __read_and_fix__(self):
        """Reads in a 1 port ascii file and fixes any issues with inconsistent delimiters, etc"""
        lines=[]
        table_type=self.path.split(".")[-1]
        in_file=open(self.path,'r')
        for line in in_file:
            #if not re.match('[\s]+(?!\w+)',line):
                #print line
            lines.append(line)
        in_file.close()
        # Handle the cases in which it is the comma delimited table
        if re.match('txt',table_type,re.IGNORECASE):
            lines=strip_tokens(lines,*[self.options['data_begin_token'],
                                                    self.options['data_end_token']])
            self.options["data"]=strip_all_line_tokens(lines,begin_token=self.options["row_begin_token"],
                                            end_token=self.options["row_end_token"])
            self.options["data"]=split_all_rows(self.options["data"],delimiter=self.options["data_delimiter"],
                                     escape_character=self.options["escape_character"])
            self.options["data"]=convert_all_rows(self.options["data"],self.options["column_types"])
            #print self.options["data"]
            root_name_pattern=re.compile('(?P<root_name>\w+)[abc].txt',re.IGNORECASE)
            root_name_match=re.search(root_name_pattern,self.path)
            if root_name_match:
                root_name=root_name_match.groupdict()["root_name"]
            else:
                root_name=self.path.split('.')[0]
            self.options["header"]=["Device_Id = {0}".format(root_name)]

        elif re.match("asc",table_type,re.IGNORECASE):
            self.lines=lines
            data_begin_line=self.find_line("TABLE")+2
            # TODO: Replace with parse lines, it ignores blank lines
            data=np.loadtxt(self.path,skiprows=data_begin_line)
            self.options["data"]=data.tolist()
            self.options["header"]=lines[:self.find_line("TABLE")]
            #print("The {0} variable is {1}".format('data.tolist()',data.tolist()))

    def show(self):
        fig, (ax0, ax1) = plt.subplots(nrows=2, sharex=True)
        ax0.errorbar(self.get_column('Frequency'),self.get_column('mag'),
             yerr=self.get_column('uMg'),fmt='k--')
        ax0.set_title('Magnitude S11')
        ax1.errorbar(self.get_column('Frequency'),self.get_column('arg'),
             yerr=self.get_column('uAg'),fmt='ro')
        ax1.set_title('Phase S11')
        plt.show()

class PowerModel(AsciiDataTable):
    def __init__(self,file_path,**options):
        "Intializes the PowerModel Class, it is assumed that the file is of  table type"
        # This is a general pattern for adding a lot of options
        defaults= {"data_delimiter": ",", "column_names_delimiter": ",", "specific_descriptor": 'One_Port',
                   "general_descriptor": 'Power', "extension": 'txt', "comment_begin": "#", "comment_end": "\n",
                   "header": None,
                   "column_names":None, "column_names_end_token": "\n", "data": None,
                   "row_formatter_string": None, "data_table_element_separator": None,"row_begin_token":None,
                   "row_end_token":None,"escape_character":None,
                   "data_begin_token":None,"data_end_token":None}
        self.options={}
        for key,value in defaults.iteritems():
            self.options[key]=value
        for key,value in options.iteritems():
            self.options[key]=value
        # Define Method Aliases if they are available
        if METHOD_ALIASES:
            for command in alias(self):
                exec(command)
        if file_path is not None:
            self.power_4term_row_pattern=make_row_match_string(POWER_4TERM_COLUMN_NAMES)
            self.power_3term_row_pattern=make_row_match_string(POWER_3TERM_COLUMN_NAMES)
            self.path=file_path
            self.__read_and_fix__()
        #build the row_formatting string, the original files have 4 decimals of precision for freq/gamma and 2 for Phase
        row_formatter=""
        for i in range(len(self.options["column_names"])):
            if i<len(self.options["column_names"])-1:
                row_formatter=row_formatter+"{"+str(i)+":.4f}{delimiter}"
            elif i==len(self.options["column_names"])-1:
                row_formatter=row_formatter+"{"+str(i)+":.4f}"
        self.options["row_formatter_string"]=row_formatter
        AsciiDataTable.__init__(self,None,**self.options)
        if file_path is not None:
            self.path=file_path

    def __read_and_fix__(self):
        """Reads in a power ascii file and fixes any issues with inconsistent delimiters, etc"""
        lines=[]
        table_type=self.path.split(".")[-1]
        in_file=open(self.path,'r')
        for line in in_file:
            if not re.match('[\s]+(?!\w+)',line):
                #print line
                lines.append(line)
        # Handle the cases in which it is the comma delimited table
        # Does this need to be parse lines or numpy.loadtxt?
        if re.match('txt',table_type,re.IGNORECASE):
            lines=strip_tokens(lines,*[self.options['data_begin_token'],
                                                    self.options['data_end_token']])
            self.options["data"]=strip_all_line_tokens(lines,begin_token=self.options["row_begin_token"],
                                            end_token=self.options["row_end_token"])
            self.options["data"]=split_all_rows(self.options["data"],delimiter=self.options["data_delimiter"],
                                     escape_character=self.options["escape_character"])
            print("{0} is {1}".format("len(self.options['data'][0])",len(self.options['data'][0])))
            if len(self.options['data'][0])==9:
                self.power_pattern=self.power_3term_row_pattern
                self.options["column_names"]=POWER_3TERM_COLUMN_NAMES
                self.options["column_descriptions"]=POWER_3TERM_COLUMN_DESCRIPTIONS
            elif len(self.options['data'][0])==11:
                self.power_pattern=self.power_4term_row_pattern
                self.options["column_names"]=POWER_4TERM_COLUMN_NAMES
                self.options["column_descriptions"]=POWER_4TERM_COLUMN_DESCRIPTIONS
            self.options["column_types"]= ['float' for i in range(len(self.options["column_names"]))]
            self.options["data"]=convert_all_rows(self.options["data"],self.options["column_types"])
            #print self.options["data"]
            root_name_pattern=re.compile('(?P<root_name>\w+)[abc].txt',re.IGNORECASE)
            root_name_match=re.search(root_name_pattern,self.path)
            root_name=root_name_match.groupdict()["root_name"]
            self.options["header"]=["Device_Id = {0}".format(root_name)]



class OnePortRawModel(AsciiDataTable):
    """ Class that deals with the OnePort Raw Files after conversion to Ascii using Ron Ginley's converter.
    These files typically have header information seperated from data by !!
    Header format is:
    Line 1:		Spid$ - identification of type of system used
    Line 2:		Systemletter$ - letter name indicating which system was used
    Line 3:		Conncal$ - connector type from the system calibration
    Line 4:		Connectors$ - connector type used for the measurement
    Line 5:		Meastype$ - type of measurement (basically 1-port, 2-port or power)
    Line 6:		Datea$ - date of measurement
    Line 7:		Timea$ - time of measurement
    Line 8:		Programm$ - name of program used
    Line 9:		Rev$ - program revision
    Line 10:	Opr$ - operator
    Line 11:	Cfile$ - calibration name
    Line 12:	Cdate$ - calibration date
    Line 13:	Sport - identification of which port or direction was used for measurement
    Line 14:	Numconnects ? number of disconnect/reconnect cycles
    Line 15:	Numrepeats ? number of repeat measurements for each connect (usually 1)
    Line 16:	Nbs ? not sure
    Line 17:	Nfreq ? number of frequencies
    Line 18:	Startfreq ? data row pointer for bdat files
    Line 19:	Devicedescript$ - description of device being measured or of test being done
    Line 20:	Devicenum$ - Identifying number for device ? used for file names
    """
    def __init__(self,file_path=None,**options):
        """Initializes the OnePortRaw class, if a file_path is specified opens an existing file, else creates an
        empty container"""
        defaults= {"data_delimiter": ",", "column_names_delimiter": ",", "specific_descriptor": 'One_Port_Raw',
                   "general_descriptor": 'Sparameter', "extension": 'txt', "comment_begin": "#", "comment_end": "\n",
                   "column_types": ['float','int','int','float','float','float','float'],
                   "column_descriptions": {"Frequency":"Frequency in GHz",
                                           "Direction":"Direction of connects, may be unused",
                                           "Connect":"Connect number", "magS11":"Linear magnitude for port 1",
                                           "argS11":"Phase in degrees for port 1",
                                           "magS22":"Linear magnitude for port 2",
                                           "argS22":"Phase in degrees for port 2"}, "header": None,
                   "column_names": ["Frequency","Direction","Connect", "magS11",
                                    "argS11","magS22",  "argS22"],
                   "column_names_end_token": "\n", "data": None,
                   'row_formatter_string': "{0:.5f}{delimiter}{1}{delimiter}{2}{delimiter}"
                                           "{3:.4f}{delimiter}{4:.2f}{delimiter}{5:.4f}{delimiter}{6:.2f}",
                   "data_table_element_separator": None}
        self.options={}
        for key,value in defaults.iteritems():
            self.options[key]=value
        for key,value in options.iteritems():
            self.options[key]=value

        # Define Method Aliases if they are available
        if METHOD_ALIASES:
            for command in alias(self):
                exec(command)
        if file_path is not None:
            self.__read_and_fix__(file_path)
        if COMBINE_S11_S22:
            self.options['row_formatter_string']= "{0:.5f}{delimiter}{1}{delimiter}{2}{delimiter}{3:.4f}{delimiter}{4:.2f}"
            self.options["column_types"]= ['float','int','int','float','float']
            self.options["column_names"]=["Frequency","Direction","Connect", "mag","arg"]
            self.options["column_descriptions"]= {"Frequency":"Frequency in GHz",
                                           "Direction":"Direction of connects, may be unused",
                                           "Connect":"Connect number", "mag":"Linear magnitude",
                                           "arg":"Phase in degrees"}
        AsciiDataTable.__init__(self,None,**self.options)
        self.path=file_path
        self.structure_metadata()


    def __read_and_fix__(self,file_path=None):
        """Inputs in the raw OnePortRaw file and fixes any problems with delimiters,etc."""
        lines=[]
        in_file=open(file_path,'r')
        for index,line in enumerate(in_file):
            lines.append(line)
            if re.match("!!",line):
                data_begin_line=index+1
        self.lines=lines
        in_file.close()
        parse_options={"row_end_token":'\n',
                       "row_pattern":make_row_match_string(self.options["column_names"]),
                       "column_names":self.options["column_names"],"column_types":self.options["column_types"]}
        data=parse_lines(lines[data_begin_line:],**parse_options)
        self.options["data"]=data
        self.options["header"]=lines[:data_begin_line-1]
        if COMBINE_S11_S22:
            new_data=[]
            for index,row in enumerate(self.options["data"][:]):
                new_row=[row[0],row[1],row[2],row[3]+row[5],row[4]+row[6]]
                new_data.append(new_row)
            self.options["data"]=new_data



    def structure_metadata(self):
        """Returns a dictionary of key,value pairs extracted from the header"""
        keys=["System_Id","System_Letter","Connector_Type_Calibration","Connector_Type_Measurement",
              "Measurement_Type","Measurement_Date","Measurement_Time","Program_Used","Program_Revision","Operator",
              "Calibration_Name","Calibration_Date","Port_Used","Number_Connects","Number_Repeats","Nbs",
              "Number_Frequencies","Start_Frequency",
              "Device_Description","Device_Id"]
        self.metadata={}
        if self.header is None:
            pass
        else:
            for index,key in enumerate(keys):
                self.metadata[key]=self.header[index].rstrip().lstrip()
    def show(self):
        fig, (ax0, ax1) = plt.subplots(nrows=2, sharex=True)
        if COMBINE_S11_S22:
            ax0.plot(self.get_column('Frequency'),self.get_column('mag'),'k--')
            ax1.plot(self.get_column('Frequency'),self.get_column('arg'),'ro')
        else:
            ax0.plot(self.get_column('Frequency'),self.get_column('magS11'),'k--')
            ax0.plot(self.get_column('Frequency'),self.get_column('magS22'),'k--')
            ax1.plot(self.get_column('Frequency'),self.get_column('argS11'),'ro')
            ax1.plot(self.get_column('Frequency'),self.get_column('argS22'),'ro')
        ax0.set_title('Magnitude S11')
        ax1.set_title('Phase S11')
        plt.show()

class TwoPortRawModel(AsciiDataTable):
    """ Class that deals with the TwoPort Raw Files after conversion to Ascii using Ron Ginley's converter.
    These files typically have header information seperated from data by !!
    Header format is:
    Line 1:		Spid$ - identification of type of system used
    Line 2:		Systemletter$ - letter name indicating which system was used
    Line 3:		Conncal$ - connector type from the system calibration
    Line 4:		Connectors$ - connector type used for the measurement
    Line 5:		Meastype$ - type of measurement (basically 1-port, 2-port or power)
    Line 6:		Datea$ - date of measurement
    Line 7:		Timea$ - time of measurement
    Line 8:		Programm$ - name of program used
    Line 9:		Rev$ - program revision
    Line 10:	Opr$ - operator
    Line 11:	Cfile$ - calibration name
    Line 12:	Cdate$ - calibration date
    Line 13:	Sport - identification of which port or direction was used for measurement
    Line 14:	Numconnects ? number of disconnect/reconnect cycles
    Line 15:	Numrepeats ? number of repeat measurements for each connect (usually 1)
    Line 16:	Nbs ? not sure
    Line 17:	Nfreq ? number of frequencies
    Line 18:	Startfreq ? data row pointer for bdat files
    Line 19:	Devicedescript$ - description of device being measured or of test being done
    Line 20:	Devicenum$ - Identifying number for device ? used for file names
    """
    def __init__(self,file_path=None,**options):
        """Initializes the TwoPortRaw class, if a file_path is specified opens an existing file, else creates an
        empty container"""
        defaults= {"data_delimiter": ",", "column_names_delimiter": ",", "specific_descriptor": 'Two_Port_Raw',
                   "general_descriptor": 'Sparameter', "extension": 'txt', "comment_begin": "#", "comment_end": "\n",
                   "column_types": ['float','int','int','float','float','float','float','float','float'],
                   "column_descriptions": {"Frequency":"Frequency in GHz",
                                           "Direction":"Direction of connects, may be unused",
                                           "Connect":"Connect number", "magS11":"Linear magnitude for S11",
                                           "argS11":"Phase in degrees for S11",
                                           "magS21":"Linear magnitude for S21",
                                           "argS21":"Phase in degrees for S21",
                                           "magS22":"Linear magnitude for S22",
                                           "argS22":"Phase in degrees for S22"},
                   "header": None,
                   "column_names": ["Frequency","Direction","Connect", "magS11",
                                    "argS11","magS21","argS21","magS22","argS22"],
                   "column_names_end_token": "\n", "data": None,
                   'row_formatter_string': "{0:.5f}{delimiter}{1}{delimiter}{2}"
                                           "{delimiter}{3:.4f}{delimiter}{4:.2f}{delimiter}"
                                           "{5:.4f}{delimiter}{6:.2f}{delimiter}"
                                           "{7:.4f}{delimiter}{8:.2f}",
                   "data_table_element_separator": None}
        self.options={}
        for key,value in defaults.iteritems():
            self.options[key]=value
        for key,value in options.iteritems():
            self.options[key]=value
        # Define Method Aliases if they are available
        if METHOD_ALIASES:
            for command in alias(self):
                exec(command)
        if file_path is not None:
            self.__read_and_fix__(file_path)

        AsciiDataTable.__init__(self,None,**self.options)
        self.path=file_path
        self.structure_metadata()

    def __read_and_fix__(self,file_path=None):
        """Inputs in the raw OnePortRaw file and fixes any problems with delimiters,etc."""
        lines=[]
        in_file=open(file_path,'r')
        for index,line in enumerate(in_file):
            lines.append(line)
            if re.search("!!",line):
                data_begin_line=index+1
        self.lines=lines
        in_file.close()
        parse_options={"row_end_token":'\n',
                       "row_pattern":make_row_match_string(self.options["column_names"]),
                       "column_names":self.options["column_names"],"column_types":self.options["column_types"]}
        data=parse_lines(lines[data_begin_line:],**parse_options)
        self.options["data"]=data
        if CONVERT_S21:
            for row_index,row in enumerate(self.options["data"]):
                db_value=row[5]
                mag_value=10.**(-1*db_value/20.)
                self.options["data"][row_index][5]=mag_value

        self.options["header"]=lines[:data_begin_line-1]
        #print data


    def structure_metadata(self):
        """Returns a dictionary of key,value pairs extracted from the header"""
        keys=["System_Id","System_Letter","Connector_Type_Calibration","Connector_Type_Measurement",
              "Measurement_Type","Measurement_Date","Measurement_Time","Program_Used","Program_Revision","Operator",
              "Calibration_Name","Calibration_Date","Port_Used","Number_Connects","Number_Repeats","Nbs",
              "Number_Frequencies","Start_Frequency",
              "Device_Description","Device_Id"]
        self.metadata={}
        for index,key in enumerate(keys):
            self.metadata[key]=self.header[index].rstrip().lstrip()
    def show(self):
        fig, axes = plt.subplots(nrows=3, ncols=2)
        ax0, ax1, ax2, ax3, ax4, ax5 = axes.flat
        ax0.plot(self.get_column('Frequency'),self.get_column('magS11'),'k-o')
        ax0.set_title('Magnitude S11')
        ax1.plot(self.get_column('Frequency'),self.get_column('argS11'),'ro')
        ax1.set_title('Phase S11')
        ax2.plot(self.get_column('Frequency'),self.get_column('magS21'),'k-o')
        ax2.set_title('Magnitude S21')
        ax3.plot(self.get_column('Frequency'),self.get_column('argS21'),'ro')
        ax3.set_title('Phase S21')
        ax4.plot(self.get_column('Frequency'),self.get_column('magS22'),'k-o')
        ax4.set_title('Magnitude S22')
        ax5.plot(self.get_column('Frequency'),self.get_column('argS22'),'ro')
        ax5.set_title('Phase S22')
        plt.tight_layout()
        plt.show()
class TwoPortNRRawModel(AsciiDataTable):
    """ Class that deals with the TwoPort Raw Files after conversion to Ascii using Ron Ginley's converter.
    These files typically have header information seperated from data by !!
    Header format is:
    Line 1:		Spid$ - identification of type of system used
    Line 2:		Systemletter$ - letter name indicating which system was used
    Line 3:		Conncal$ - connector type from the system calibration
    Line 4:		Connectors$ - connector type used for the measurement
    Line 5:		Meastype$ - type of measurement (basically 1-port, 2-port or power)
    Line 6:		Datea$ - date of measurement
    Line 7:		Timea$ - time of measurement
    Line 8:		Programm$ - name of program used
    Line 9:		Rev$ - program revision
    Line 10:	Opr$ - operator
    Line 11:	Cfile$ - calibration name
    Line 12:	Cdate$ - calibration date
    Line 13:	Sport - identification of which port or direction was used for measurement
    Line 14:	Numconnects ? number of disconnect/reconnect cycles
    Line 15:	Numrepeats ? number of repeat measurements for each connect (usually 1)
    Line 16:	Nbs ? not sure
    Line 17:	Nfreq ? number of frequencies
    Line 18:	Startfreq ? data row pointer for bdat files
    Line 19:	Devicedescript$ - description of device being measured or of test being done
    Line 20:	Devicenum$ - Identifying number for device ? used for file names
    """
    def __init__(self,file_path=None,**options):
        """Initializes the TwoPortRaw class, if a file_path is specified opens an existing file, else creates an
        empty container"""
        defaults= {"data_delimiter": ",", "column_names_delimiter": ",", "specific_descriptor": 'Two_Port_NR_Raw',
                   "general_descriptor": 'Sparameter', "extension": 'txt', "comment_begin": "#", "comment_end": "\n",
                   "column_types": ['float','int','int','float','float','float','float',
                                    'float','float','float','float'],
                   "column_descriptions": {"Frequency":"Frequency in GHz",
                                           "Direction":"Direction of connects, may be unused",
                                           "Connect":"Connect number", "magS11":"Linear magnitude for S11",
                                           "argS11":"Phase in degrees for S11",
                                           "magS12":"Linear magnitude for S21",
                                           "argS12":"Phase in degrees for S21",
                                           "magS21":"Linear magnitude for S21",
                                           "argS21":"Phase in degrees for S21",
                                           "magS22":"Linear magnitude for S22",
                                           "argS22":"Phase in degrees for S22"},
                   "header": None,
                   "column_names": ["Frequency","Direction","Connect", "magS11",
                                    "argS11","magS12","argS12","magS21","argS21","magS22","argS22"],
                   "column_names_end_token": "\n", "data": None,
                   'row_formatter_string': "{0:.5f}{delimiter}{1}{delimiter}{2}"
                                           "{delimiter}{3:.4f}{delimiter}{4:.2f}{delimiter}"
                                           "{5:.4f}{delimiter}{6:.2f}{delimiter}"
                                           "{7:.4f}{delimiter}{8:.2f}{delimiter}"
                                           "{9:.4f}{delimiter}{10:.2f}",
                   "data_table_element_separator": None}
        self.options={}
        for key,value in defaults.iteritems():
            self.options[key]=value
        for key,value in options.iteritems():
            self.options[key]=value
        # Define Method Aliases if they are available
        if METHOD_ALIASES:
            for command in alias(self):
                exec(command)
        if file_path is not None:
            self.__read_and_fix__(file_path)

        AsciiDataTable.__init__(self,None,**self.options)
        self.path=file_path
        self.structure_metadata()

    def __read_and_fix__(self,file_path=None):
        """Inputs in the raw OnePortRaw file and fixes any problems with delimiters,etc."""
        lines=[]
        in_file=open(file_path,'r')
        for index,line in enumerate(in_file):
            lines.append(line)
            if re.search("!!",line):
                data_begin_line=index+1
        self.lines=lines
        in_file.close()
        parse_options={"row_end_token":'\n',
                       "row_pattern":make_row_match_string(self.options["column_names"]),
                       "column_names":self.options["column_names"],"column_types":self.options["column_types"]}
        data=parse_lines(lines[data_begin_line:],**parse_options)
        self.options["data"]=data
        if CONVERT_S21:
            for row_index,row in enumerate(self.options["data"]):
                db_value_S21=row[7]
                mag_value_S21=10.**(-1*db_value_S21/20.)
                db_value_S12=row[5]
                mag_value_S12=10.**(-1*db_value_S12/20.)
                self.options["data"][row_index][5]=mag_value_S12
                self.options["data"][row_index][7]=mag_value_S21
        self.options["header"]=lines[:data_begin_line-1]
        #print data


    def structure_metadata(self):
        """Returns a dictionary of key,value pairs extracted from the header"""
        keys=["System_Id","System_Letter","Connector_Type_Calibration","Connector_Type_Measurement",
              "Measurement_Type","Measurement_Date","Measurement_Time","Program_Used","Program_Revision","Operator",
              "Calibration_Name","Calibration_Date","Port_Used","Number_Connects","Number_Repeats","Nbs",
              "Number_Frequencies","Start_Frequency",
              "Device_Description","Device_Id"]
        self.metadata={}
        for index,key in enumerate(keys):
            self.metadata[key]=self.header[index].rstrip().lstrip()
    def show(self):
        fig, axes = plt.subplots(nrows=3, ncols=2)
        ax0, ax1, ax2, ax3, ax4, ax5 = axes.flat
        ax0.plot(self.get_column('Frequency'),self.get_column('magS11'),'k-o')
        ax0.set_title('Magnitude S11')
        ax1.plot(self.get_column('Frequency'),self.get_column('argS11'),'ro')
        ax1.set_title('Phase S11')
        ax2.plot(self.get_column('Frequency'),self.get_column('magS12'),'b-o')
        ax3.plot(self.get_column('Frequency'),self.get_column('argS12'),'bo')
        ax2.plot(self.get_column('Frequency'),self.get_column('magS21'),'k-o')
        ax2.set_title('Magnitude S21')
        ax3.plot(self.get_column('Frequency'),self.get_column('argS21'),'ro')
        ax3.set_title('Phase S21')
        ax4.plot(self.get_column('Frequency'),self.get_column('magS22'),'k-o')
        ax4.set_title('Magnitude S22')
        ax5.plot(self.get_column('Frequency'),self.get_column('argS22'),'ro')
        ax5.set_title('Phase S22')
        plt.tight_layout()
        plt.show()

class PowerRawModel(AsciiDataTable):
    """ Class that deals with the PowerRaw Files after conversion to Ascii using Ron Ginley's converter.
    These files typically have header information seperated from data by !!
    Header format is:
    Line 1:		Spid$ - identification of type of system used
    Line 2:		Systemletter$ - letter name indicating which system was used
    Line 3:		Conncal$ - connector type from the system calibration
    Line 4:		Connectors$ - connector type used for the measurement
    Line 5:		Meastype$ - type of measurement (basically 1-port, 2-port or power)
    Line 6:		Datea$ - date of measurement
    Line 7:		Timea$ - time of measurement
    Line 8:		Programm$ - name of program used
    Line 9:		Rev$ - program revision
    Line 10:	Opr$ - operator
    Line 11:	Cfile$ - calibration name
    Line 12:	Cdate$ - calibration date
    Line 13:	Sport - identification of which port or direction was used for measurement
    Line 14:	Numconnects ? number of disconnect/reconnect cycles
    Line 15:	Numrepeats ? number of repeat measurements for each connect (usually 1)
    Line 16:	Nbs ? not sure
    Line 17:	Nfreq ? number of frequencies
    Line 18:	Startfreq ? data row pointer for bdat files
    Line 19:	Devicedescript$ - description of device being measured or of test being done
    Line 20:	Devicenum$ - Identifying number for device ? used for file names
    """
    def __init__(self,file_path=None,**options):
        """Initializes the PowerRaw class, if a file_path is specified opens an existing file, else creates an
        empty container"""
        defaults= {"data_delimiter": ",", "column_names_delimiter": ",", "specific_descriptor": 'Raw',
                   "general_descriptor": 'Power', "extension": 'txt', "comment_begin": "#", "comment_end": "\n",
                   "column_types": ['float','int','int','float','float','float','float'],
                   "column_descriptions": {"Frequency":"Frequency in GHz",
                                           "Direction":"Direction of connects, may be unused",
                                           "Connect":"Connect number", "magS11":"Linear magnitude for S11",
                                           "argS11":"Phase in degrees for S11",
                                           "Efficiency":"Effective Efficiency",
                                           "Calibration_Factor":"Effective efficiency "
                                                                "modified by reflection coefficient"},
                   "header": None,
                   "column_names": ["Frequency","Direction","Connect", "magS11",
                                    "argS11","Efficiency","Calibration_Factor"],
                   "column_names_end_token": "\n", "data": None,
                   'row_formatter_string': "{0:.5g}{delimiter}{1}{delimiter}{2}"
                                           "{delimiter}{3:.5g}{delimiter}{4:.3f}{delimiter}"
                                           "{5:.5g}{delimiter}{6:.5g}",
                   "data_table_element_separator": None}
        self.options={}
        for key,value in defaults.iteritems():
            self.options[key]=value
        for key,value in options.iteritems():
            self.options[key]=value
        # Define Method Aliases if they are available
        if METHOD_ALIASES:
            for command in alias(self):
                exec(command)
        if file_path is not None:
            self.__read_and_fix__(file_path)

        AsciiDataTable.__init__(self,None,**self.options)
        self.path=file_path
        self.structure_metadata()

    def __read_and_fix__(self,file_path=None):
        """Inputs in the PowerRaw file and fixes any problems with delimiters,etc."""
        lines=[]
        in_file=open(file_path,'r')
        for index,line in enumerate(in_file):
            lines.append(line)
            if re.search("!!",line):
                data_begin_line=index+1
        self.lines=lines
        in_file.close()
        parse_options={"row_end_token":'\n',
                       "row_pattern":make_row_match_string(self.options["column_names"],delimiter_pattern='[\s|(),]+'),
                       "column_names":self.options["column_names"],"column_types":self.options["column_types"]}
        data=parse_lines(lines[data_begin_line:],**parse_options)
        self.options["data"]=data
        self.options["header"]=lines[:data_begin_line-1]
        #print data


    def structure_metadata(self):
        """Returns a dictionary of key,value pairs extracted from the header"""
        keys=["System_Id","System_Letter","Connector_Type_Calibration","Connector_Type_Measurement",
              "Measurement_Type","Measurement_Date","Measurement_Time","Program_Used","Program_Revision","Operator",
              "Calibration_Name","Calibration_Date","Port_Used","Number_Connects","Number_Repeats","Nbs",
              "Number_Frequencies","Start_Frequency",
              "Device_Description","Device_Id"]
        self.metadata={}
        for index,key in enumerate(keys):
            self.metadata[key]=self.header[index].rstrip().lstrip()

class TwoPortCalrepModel():
    """TwoPortCalrepModel is a model that holds data output by analyzing several datafiles using the HPBasic program
    Calrep. The data is stored in 3 tables: a S11 table, a S21 table and a S22 table. The data is in linear
    magnitude and angle in degrees. There are 2 types of files, one is a single file with .asc extension
    and 3 files with .txt extension"""

    def __init__(self,file_path=None,**options):
        """Intializes the TwoPortCalrepModel class, if a file path is specified it opens and reads the file"""
        defaults= {"specific_descriptor": 'Two_Port_Calrep'}
        self.options={}
        for key,value in defaults.iteritems():
            self.options[key]=value
        for key,value in options.iteritems():
            self.options[key]=value
        if file_path is None:
            pass
        elif re.match('asc',file_path.split(".")[-1],re.IGNORECASE):
            self.table_names=['header','S11','S22','S21']
            self.row_pattern=make_row_match_string(ONE_PORT_COLUMN_NAMES)
            self.path=file_path
            self.__read_and_fix__()

        elif re.match('txt',file_path.split(".")[-1],re.IGNORECASE) or type(file_path) is ListType:
            self.table_names=['S11','S22','S21']
            if type(file_path) is ListType:
                self.file_names=file_path
                self.tables=[]
                for index,table in enumerate(self.table_names):
                    if index==2:
                        #fixes a problem with the c tables, extra comma at the end
                        options={"row_end_token":',\n'}
                        self.tables.append(OnePortCalrepModel(self.file_names[index],**options))
                        self.tables[2].options["row_end_token"]=None
                    else:
                        self.tables.append(OnePortCalrepModel(self.file_names[index]))
            else:
                try:
                    root_name_pattern=re.compile('(?P<root_name>\w+)[abc].txt',re.IGNORECASE)
                    root_name_match=re.search(root_name_pattern,file_path)
                    root_name=root_name_match.groupdict()["root_name"]
                    directory=os.path.dirname(os.path.realpath(file_path))
                    self.file_names=[os.path.join(directory,root_name+end) for end in ['a.txt','b.txt','c.txt']]
                    self.tables=[]
                    for index,table in enumerate(self.table_names):
                        if index==2:
                            #fixes a problem with the c tables, extra comma at the end
                            options={"row_end_token":',\n'}
                            self.tables.append(OnePortCalrepModel(self.file_names[index],**options))
                            self.tables[2].options["row_end_token"]=None
                        else:
                            self.tables.append(OnePortCalrepModel(self.file_names[index]))

                except:
                    print("Could not import {0} please check that the a,b,c "
                          "tables are all in the same directory".format(file_path))
                    raise
            for index,table in enumerate(self.tables):
                column_names=[]
                for column_number,column in enumerate(table.column_names):
                    if column is not "Frequency":
                        column_names.append(column+self.table_names[index])
                    else:
                        column_names.append(column)
                #print column_names
                table.column_names=column_names
            if CONVERT_S21:
                for row_number,row in enumerate(self.tables[2].data):
                    new_S21=self.tables[2].data[row_number][1]
                    new_S21=10.**(-1*new_S21/20.)
                    new_value=[self.tables[2].data[row_number][i] for i in range(2,6)]
                    new_value=map(lambda x:abs((1/np.log10(np.e))*new_S21*x/20.),new_value)
                    self.tables[2].data[row_number][1]=new_S21
                    for i in range(2,6):
                        self.tables[2].data[row_number][i]=new_value[i-2]
            for key,value in self.options.iteritems():
                self.tables[0].options[key]=value
            self.joined_table=ascii_data_table_join("Frequency",self.tables[0],self.tables[2])
            self.joined_table=ascii_data_table_join("Frequency",self.joined_table,self.tables[1])

    def __read_and_fix__(self):
        in_file=open(self.path,'r')
        self.lines=[]
        table_locators=["Table 1","Table 2","Table 3"]
        begin_lines=[]
        for index,line in enumerate(in_file):
            self.lines.append(line)
            for table in table_locators:
                if re.search(table,line,re.IGNORECASE):
                    begin_lines.append(index)
        in_file.close()
        self.table_line_numbers=[]
        for index,begin_line in enumerate(begin_lines):
            if index == 0:
                header_begin_line=0
                header_end_line=begin_line-2
                table_1_begin_line=begin_line+3
                table_1_end_line=begin_lines[index+1]#-1
                self.table_line_numbers.append([header_begin_line,header_end_line])
                self.table_line_numbers.append([table_1_begin_line,table_1_end_line])

            elif index>0 and index<(len(begin_lines)-1):
                table_begin_line=begin_line+3
                table_end_line=begin_lines[index+1]#-1
                self.table_line_numbers.append([table_begin_line,table_end_line])

            elif index==(len(begin_lines)-1):
                table_begin_line=begin_line+3
                table_end_line=None
                self.table_line_numbers.append([table_begin_line,table_end_line])
        self.tables=[]
        for index,name in enumerate(self.table_names):
            self.table_lines=self.lines[self.table_line_numbers[index][0]:self.table_line_numbers[index][1]]
            self.tables.append(self.table_lines)
        for index,table in enumerate(self.table_names):
            if index==0:
                # by using parse_lines we get a list_list of strings instead of list_string
                # we can just remove end lines
                self.tables[index]=strip_all_line_tokens(self.tables[index],begin_token=None,end_token='\n')
            else:
                column_types=['float' for i in range(len(ONE_PORT_COLUMN_NAMES))]
                options={"row_pattern":self.row_pattern,"column_names":ONE_PORT_COLUMN_NAMES,"output":"list_list"}
                options["column_types"]=column_types
                self.tables[index]=parse_lines(self.tables[index],**options)

        # need to put S21 mag into linear magnitude
        if CONVERT_S21:
            for row_number,row in enumerate(self.tables[3]):
                new_S21=self.tables[3][row_number][1]
                new_S21=10.**(-1*new_S21/20.)
                new_value=[self.tables[3][row_number][i] for i in range(2,6)]
                new_value=map(lambda x:abs((1/np.log10(np.e))*new_S21*x/20),new_value)
                self.tables[3][row_number][1]=new_S21
                for i in range(2,6):
                    self.tables[3][row_number][i]=new_value[i-2]

        for index,table in enumerate(self.tables):
            #print("{0} is {1}".format("index",index))
            if index==0:
                pass
            else:
                table_options={"data":self.tables[index]}
                self.tables[index]=OnePortCalrepModel(None,**table_options)
                #print("{0} is {1}".format("self.tables[index].column_names",self.tables[index].column_names))
                column_names=[]
                for column_number,column in enumerate(self.tables[index].column_names):
                    if column is not "Frequency":
                        #print("{0} is {1}".format("self.table_names[index]",self.table_names[index]))
                        #print("{0} is {1}".format("column",column))
                        column_names.append(column+self.table_names[:][index])
                    else:
                        column_names.append(column)
                self.tables[index].column_names=column_names

        self.tables[1].header=self.tables[0]
        for key,value in self.options.iteritems():
            self.tables[1].options[key]=value
        self.joined_table=ascii_data_table_join("Frequency",self.tables[1],self.tables[3])
        self.joined_table=ascii_data_table_join("Frequency",self.joined_table,self.tables[2])

    def __str__(self):
        return self.joined_table.build_string()

    def show(self):
        fig, axes = plt.subplots(nrows=3, ncols=2)
        ax0, ax1, ax2, ax3, ax4, ax5 = axes.flat
        ax0.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('magS11'),
             yerr=self.joined_table.get_column('uMgS11'),fmt='k-o')
        ax0.set_title('Magnitude S11')
        ax1.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('argS11'),
             yerr=self.joined_table.get_column('uAgS11'),fmt='ro')
        ax1.set_title('Phase S11')
        ax2.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('magS21'),
             yerr=self.joined_table.get_column('uMgS21'),fmt='k-o')
        ax2.set_title('Magnitude S21')
        ax3.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('argS21'),
             yerr=self.joined_table.get_column('uAgS21'),fmt='ro')
        ax3.set_title('Phase S21')
        ax4.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('magS22'),
             yerr=self.joined_table.get_column('uMgS22'),fmt='k-o')
        ax4.set_title('Magnitude S22')
        ax5.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('argS22'),
             yerr=self.joined_table.get_column('uAgS22'),fmt='ro')
        ax5.set_title('Phase S22')
        plt.tight_layout()
        plt.show()

class PowerCalrepModel():
    """PowerCalrep is a model that holds data output by analyzing several datafiles using the HPBasic program
    Calrep. The data is stored in 2 tables: a S11 table, and a power table. The data is in linear
    magnitude and angle in degrees. There are 2 types of files, one is a single file with .asc extension
    and 2 files with .txt extension"""

    def __init__(self,file_path=None,**options):
        """Intializes the PowerCalrep class, if a file path is specified it opens and reads the file"""
        defaults= {}
        self.options={}
        for key,value in defaults.iteritems():
            self.options[key]=value
        for key,value in options.iteritems():
            self.options[key]=value
        if file_path is None:
            pass
        elif re.match('asc',file_path.split(".")[-1],re.IGNORECASE):
            self.table_names=['header','S11','Efficiency']
            self.row_pattern=make_row_match_string(ONE_PORT_COLUMN_NAMES)
            self.power_4term_row_pattern=make_row_match_string(POWER_4TERM_COLUMN_NAMES)
            self.power_3term_row_pattern=make_row_match_string(POWER_3TERM_COLUMN_NAMES)
            self.path=file_path
            self.__read_and_fix__()

        elif re.match('txt',file_path.split(".")[-1],re.IGNORECASE) or type(file_path) is ListType:
            self.table_names=['S11','Efficiency']
            if type(file_path) is ListType:
                self.file_names=file_path
                self.tables=[]
                for index,table in enumerate(self.table_names):
                    if index==0:
                        self.tables.append(PowerModel(self.file_names[index]))
                    elif index==1:
                        self.tables.append(OnePortCalrepModel(self.file_names[index]))
            else:
                try:
                    root_name_pattern=re.compile('(?P<root_name>\w+)[abc].txt',re.IGNORECASE)
                    root_name_match=re.search(root_name_pattern,file_path)
                    root_name=root_name_match.groupdict()["root_name"]
                    directory=os.path.dirname(os.path.realpath(file_path))
                    self.file_names=[os.path.join(directory,root_name+end) for end in ['a.txt','b.txt']]
                    self.tables=[]
                    for index,table in enumerate(self.table_names):
                        if index==0:
                            self.tables.append(OnePortCalrepModel(self.file_names[index]))
                        elif index==1:
                            self.tables.append(PowerModel(self.file_names[index]))
                except:
                    print("Could not import {0} please check that the a,b "
                          "tables are all in the same directory".format(file_path))
                    raise

            # for index,table in enumerate(self.tables):
            #     for column_number,column in enumerate(table.column_names):
            #         if column is not "Frequency":
            #             table.column_names[column_number]=self.table_names[index]+"_"+column

            self.joined_table=ascii_data_table_join("Frequency",self.tables[0],self.tables[1])
            #print self.joined_table

    def __read_and_fix__(self):
        in_file=open(self.path,'r')
        self.lines=[]
        table_locators=["Table 1","Table 2"]
        begin_lines=[]
        for index,line in enumerate(in_file):
            self.lines.append(line)
            for table in table_locators:
                if re.search(table,line,re.IGNORECASE):
                    begin_lines.append(index)
        in_file.close()
        self.table_line_numbers=[]
        for index,begin_line in enumerate(begin_lines):
            if index == 0:
                header_begin_line=0
                header_end_line=begin_line-1
                table_1_begin_line=begin_line+1
                table_1_end_line=begin_lines[index+1]
                self.table_line_numbers.append([header_begin_line,header_end_line])
                self.table_line_numbers.append([table_1_begin_line,table_1_end_line])
            elif index>0 and index<(len(begin_lines)-1):
                table_begin_line=begin_line+2
                print("{0} is {1}".format('begin_line',begin_line))
                table_end_line=begin_lines[index+1]
                self.table_line_numbers.append([table_begin_line,table_end_line])
            elif index==(len(begin_lines)-1):
                table_begin_line=begin_line+1
                table_end_line=None
                self.table_line_numbers.append([table_begin_line,table_end_line])
        self.tables=[]
        for index,name in enumerate(self.table_names):
            self.table_lines=self.lines[self.table_line_numbers[index][0]:self.table_line_numbers[index][1]]
            self.tables.append(self.table_lines)
        for index,table in enumerate(self.table_names):
            if index==0:
                # by using parse_lines we get a list_list of strings instead of list_string
                # we can just remove end lines
                self.tables[index]=strip_all_line_tokens(self.tables[index],begin_token=None,end_token='\n')
            elif index==1:
                column_types=['float' for i in range(len(ONE_PORT_COLUMN_NAMES))]
                options={"row_pattern":self.row_pattern,"column_names":ONE_PORT_COLUMN_NAMES,"output":"list_list"}
                options["column_types"]=column_types
                self.tables[index]=parse_lines(self.tables[index],**options)
                table_options={"data":self.tables[index]}
                self.tables[index]=OnePortCalrepModel(None,**table_options)
            elif index==2:
                # Here we need to test for the type of power model (how many columns)
                test_row=self.tables[index][2]
                if re.match(self.power_3term_row_pattern,test_row) and re.match(self.power_4term_row_pattern,test_row):
                    self.options["column_names"]=POWER_4TERM_COLUMN_NAMES
                    self.power_row_pattern=self.power_4term_row_pattern
                elif re.match(self.power_3term_row_pattern,test_row):
                    self.options["column_names"]=POWER_3TERM_COLUMN_NAMES
                    self.power_row_pattern=self.power_3term_row_pattern
                else:
                    raise ValueError("Power Table Does Not Conform")
                column_types=['float' for i in range(len(self.options["column_names"]))]
                table_options={"row_pattern":self.power_row_pattern,"column_names":self.options["column_names"],
                         "output":"list_list"}
                table_options["column_types"]=column_types
                self.tables[index]=parse_lines(self.tables[index],**table_options)
                table_options["data"]=self.tables[index]
                self.tables[index]=PowerModel(None,**table_options)

        # for table in self.tables:
        #     print table
        #print("Length of table 1 is {0}, Length of table 2 is {1}".format(len(self.tables[1].data),len(self.tables[2].data)))
        self.tables[1].header=self.tables[0]
        self.joined_table=ascii_data_table_join("Frequency",self.tables[1],self.tables[2])

    def __str__(self):
        return self.joined_table.build_string()

    def show(self):
        fig, axes = plt.subplots(nrows=2, ncols=2)
        ax0, ax1, ax2, ax3 = axes.flat
        ax0.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('mag'),
                     yerr=self.joined_table.get_column('uMg'),fmt='k--')
        ax0.set_title('Magnitude S11')
        ax1.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('arg'),
                     yerr=self.joined_table.get_column('uAg'),fmt='ro')
        ax1.set_title('Phase S11')
        ax2.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('Efficiency'),
                     yerr=self.joined_table.get_column('uEe'),fmt='k--')
        ax2.set_title('Effective Efficiency')
        ax3.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('Calibration_Factor'),
                     yerr=self.joined_table.get_column('uCe'),fmt='ro')
        ax3.set_title('Calibration Factor')
        plt.tight_layout()
        plt.show()


class JBSparameter(AsciiDataTable):
    """JBSparameter is a class that holds data taken and stored using Jim Booth's two port format.
     """

    def __init__(self,file_path=None,**options):
        """Initializes the JBSparameter class. JB Sparameter data is very close to s2p, but has # as a comment
         begin token, and space as a data delimiter. The first line has structured metadata that usually includes
         date and IFBW"""
        defaults={"header_begin_line":0,"data_end_line":None,"column_names_delimiter":' ',
                "column_names_begin_token":'#',"column_names_end_token":'\n',"data_table_element_separator":None,
                 "data_delimiter":' ',"comment_begin":"#",
                 "comment_end":"\n","row_end_token":'\n',"column_types":['float' for i in range(9)],
                 "column_descriptions":["Frequency in Hz",
                                        "Real part of S11",
                                        "Imaginary part of S11",
                                        "Real part of S21",
                                        "Imaginary part of S21",
                                        "Real part of S12",
                                        "Imaginary part of S12",
                                        "Real part of S22",
                                        "Imaginary part of S22"]}
        rfs=""
        for i in range(9):
            if i==8:
                rfs=rfs+"{%s:.6g}"%(str(i))
            else:
                rfs=rfs+"{%s:.6g}{delimiter}"%(str(i))
        options["row_formatter_string"]=rfs
        self.options={}
        for key,value in defaults.iteritems():
            self.options[key]=value
        for key,value in options.iteritems():
            self.options[key]=value
        # Define Method Aliases if they are available
        if METHOD_ALIASES:
            for command in alias(self):
                exec(command)

        if file_path is not None:
            column_name_line=0
            in_file=open(file_path,'r')
            for line in in_file:
                if line[0] is '#':
                    column_name_line+=1
            in_file.close()
            self.options["header_end_line"]=column_name_line-1
            self.options["column_names_begin_line"]=column_name_line-1
            self.options["column_names_end_line"]=column_name_line
            self.options["data_begin_line"]=column_name_line
            self.path=file_path
            AsciiDataTable.__init__(self,file_path,**self.options)
        else:
            AsciiDataTable.__init__(self,file_path,**self.options)
    def get_frequency_units(self):
        """Returns the frequency units by looking at the 0 index element of column names"""
        pattern='freq\((?P<Frequency_Units>\w+)\)'
        match=re.match(pattern,self.column_names[0])
        return match.groupdict()['Frequency_Units']




class SwitchTermsFR():
    pass
class SwitchTermsPort():
    pass
class NoiseCalRaw():
    pass
class ReverbChamber():
    pass
class RobotData():
    pass

#-----------------------------------------------------------------------------
# Module Scripts
def convert_all_two_ports_script(top_directory=None,output_directory=None):
    """Script reads all file names in all sub directories looking for ones that end in c, and tries to open
    file_name.asc and save it in the output directory"""
    TOP_DIRECTORY=r'C:\Share\ascii.dut'
    # This pattern will find any names that have c in them
    TWO_PORT_PATTERN=re.compile('(?P<two_port_name>\w+)c',re.IGNORECASE)
    # now we test the os.walk function
    # This has a memory leak I am not sure but I suspect it is jupyter's fault
    for root,directory,file_names in os.walk(TOP_DIRECTORY):
        #print file_names
        for file_name in file_names:
            file_name=file_name.split('.')[0]
            match=re.search(TWO_PORT_PATTERN,file_name)
            try:
                if match:
                    asc_file_name=match.groupdict()["two_port_name"]+".asc"
                    print asc_file_name
                    if asc_file_name in ['de.asc','00.asc','dir.asc','IL.asc',"L2.asc","L1.asc"]:raise
                    converted_file=TwoPortCalrepModel(os.path.join(root,asc_file_name))
                    #print converted_file.joined_table.header
                    del converted_file
            except:
                pass

def test_OnePortCalrepModel(file_path_1='700437.txt',file_path_2="700437.asc"):
    os.chdir(TESTS_DIRECTORY)
    print(" Import of {0} results in:".format(file_path_1))
    new_table_1=OnePortCalrepModel(file_path=file_path_1)
    print new_table_1
    print("-"*80)
    print("\n")
    print(" Import of {0} results in:".format(file_path_2))
    new_table_2=OnePortCalrepModel(file_path=file_path_2)
    print new_table_2
    print("{0} results in {1}:".format('new_table_1.get_column("Frequency")',new_table_1.get_column("Frequency")))
    print new_table_1.get_options()
    print new_table_1.data[-1]
    new_table_1.show()

def test_OnePortCalrepModel_Ctable(file_path_1='700437.txt'):
    """Tests the OnePortCalrepModel on ctables from 2 port """
    os.chdir(TESTS_DIRECTORY)
    print(" Import of {0} results in:".format(file_path_1))
    new_table_1=OnePortCalrepModel(file_path=file_path_1,**{"row_end_token":",\n"})
    print new_table_1
    print("-"*80)
    print("\n")
    new_table_1.show()


def test_OnePortRawModel(file_path='OnePortRawTestFile.txt'):
    os.chdir(TESTS_DIRECTORY)
    print(" Import of {0} results in:".format(file_path))
    new_table_1=OnePortRawModel(file_path=file_path)
    print new_table_1
    print("-"*80)
    print("{0} results in {1}:".format('new_table_1.get_column("Frequency")',new_table_1.get_column("Frequency")))
    print new_table_1.get_options()
    print new_table_1.metadata
    print new_table_1.column_names
    print('index' in new_table_1.column_names )
    new_table_1.show()

def test_TwoPortRawModel(file_path='TestFileTwoPortRaw.txt'):
    os.chdir(TESTS_DIRECTORY)
    print(" Import of {0} results in:".format(file_path))
    new_table_1=TwoPortRawModel(file_path=file_path)
    print new_table_1
    new_table_1.show()

def test_PowerRawModel(file_path='TestFilePowerRaw.txt'):
    os.chdir(TESTS_DIRECTORY)
    print(" Import of {0} results in:".format(file_path))
    new_table_1=PowerRawModel(file_path=file_path)
    print new_table_1
    #new_table_1.show()

def test_JBSparameter(file_path="ftest6_L1_g5_HF_air"):
    """Tests the JBSparameter class"""
    os.chdir(TESTS_DIRECTORY)
    # open an existing file
    new_table=JBSparameter(file_path=file_path)
    print new_table.column_names
    print new_table.get_frequency_units()
    old_prefix=new_table.get_frequency_units().replace('Hz','')
    #new_table.change_unit_prefix(column_selector=0,old_prefix='',new_prefix='G',unit='Hz')
    new_table.change_unit_prefix(column_selector=0,old_prefix=old_prefix,new_prefix='G',unit='Hz')
    print new_table.column_names
    print new_table.get_column(None,0)
    print new_table.get_frequency_units()
    print new_table.get_header_string()

def test_TwoPortCalrepModel(file_name="922729a.txt"):
    """Tests the TwoPortCalrepModel model type"""
    os.chdir(TESTS_DIRECTORY)
    new_two_port=TwoPortCalrepModel(file_name)
    for table in new_two_port.tables:
        print table
    print new_two_port.joined_table
    #new_two_port.joined_table.save()
    new_two_port.joined_table.path='N205RV.txt'
    new_two_port.joined_table.header=None
    new_two_port.joined_table.column_names=None
    #new_two_port.joined_table.save()

def test_PowerCalrepModel(file_name="700083.asc"):
    """Tests the TwoPortCalrepModel model type"""
    os.chdir(TESTS_DIRECTORY)
    new_power=PowerCalrepModel(file_name)
    for table in new_power.tables:
        print table
    print new_power.joined_table
    #print new_power.joined_table.data[-1]
    new_power.show()

def test_sparameter_power_type(file_list=None):
    """Tests the sparameter_power_type function. Each file's type is determined and it is imported using
     the appropriate model"""
    os.chdir(TESTS_DIRECTORY)
    if file_list is None:
        file_list=[r'CTNP11.L36_062399','CTN106.D4_091799','CTN208.A1_011613','700083.ASC',
                   '700437.asc','922729.asc']
    else:
        file_list=file_list
    for file_name in file_list:
        file_type=sparameter_power_type(file_name)
        print(" The model of {0} is {1}".format(file_name,file_type))
        try:
            model=globals()[file_type]
            table=model(file_name)
            print table
        except:
            print("There was an error opening {0}".format(file_name))



#-----------------------------------------------------------------------------
# Module Runner
if __name__ == '__main__':
    #test_OnePortCalrepModel()
    #test_OnePortCalrepModel('700437.asc')
    #test_OnePortCalrepModel_Ctable(file_path_1='922729c.txt')
    test_OnePortRawModel()
    test_OnePortRawModel('OnePortRawTestFile_002.txt')
    #test_TwoPortRawModel()
    #test_PowerRawModel()
    #test_JBSparameter()
    #test_JBSparameter('QuartzRefExample_L1_g10_HF')
    #test_TwoPortCalrepModel()
    #test_TwoPortCalrepModel('N205RV.asc')
    #test_PowerCalrepModel()
    #test_PowerCalrepModel('700083b.txt')
    #convert_all_two_ports_script()
    #test_sparameter_power_type()

Module variables

var COMBINE_S11_S22

var COMMENT_PATTERN

var CONVERT_S21

var DEFAULT_FILE_NAME

var FORMATS

var FREQUENCY_UNITS

var METHOD_ALIASES

var NUMBER_MATCH_STRING

var ONE_PORT_COLUMN_NAMES

var OPTION_LINE_PATTERN

var PARAMETERS

var POWER_3TERM_COLUMN_DESCRIPTIONS

var POWER_3TERM_COLUMN_NAMES

var POWER_4TERM_COLUMN_DESCRIPTIONS

var POWER_4TERM_COLUMN_NAMES

var S1P_DB_COLUMN_NAMES

var S1P_MA_COLUMN_NAMES

var S1P_RI_COLUMN_NAMES

var S2P_COMPLEX_COLUMN_NAMES

var S2P_DB_COLUMN_DESCRIPTION

var S2P_DB_COLUMN_NAMES

var S2P_MA_COLUMN_DESCRIPTION

var S2P_MA_COLUMN_NAMES

var S2P_NOISE_PARAMETER_COLUMN_NAMES

var S2P_RI_COLUMN_DESCRIPTION

var S2P_RI_COLUMN_NAMES

var SMITHPLOT

var StringTypes

var TESTS_DIRECTORY

var TOUCHSTONE_KEYWORDS

Functions

def asc_type(

file_contents)

asc_type determines the type of asc file given it's contents, returns the class name of the appropriate model

def asc_type(file_contents):
    """asc_type determines the type of asc file given it's contents, returns the class name of the appropriate model"""
    if type(file_contents) is StringType:
        contents=file_contents
    elif type(file_contents) is ListType:
        contents=string_list_collapse(file_contents)
    else:
        return None
    if re.search('table 1',contents,re.IGNORECASE) and re.search('table 2',contents,re.IGNORECASE) and re.search('table 3',contents,re.IGNORECASE):
        return 'TwoPortCalrepModel'
    elif re.search('table 1',contents,re.IGNORECASE) and re.search('table 2',contents,re.IGNORECASE):
        return 'PowerCalrepModel'
    elif re.search('table 1',contents,re.IGNORECASE):
        return 'OnePortCalrepModel'
    else:
        return None

def build_csv_from_raw(

input_file_names_list, output_file_name, model_name)

Build csv from raw takes a list of file names conforming to model and builds a single csv. It is intentioned to accept raw files from the sparameter power project that have been converted from bdat using Ron Ginely's converter (modified calrep program). The output is a single csv file with metadata added as extra columns (ie a denormalized table)

def build_csv_from_raw(input_file_names_list,output_file_name,model_name):
    """Build csv from raw  takes a list of file names conforming to model and builds a single csv.
    It is intentioned to accept raw files from the sparameter power project that have been converted from bdat
    using Ron Ginely's converter (modified calrep program). The output is a single csv file with metadata added
    as extra columns (ie a denormalized table)"""
    try:
        # our current definition of metadata keys for all of the raw models
        metadata_keys=["System_Id","System_Letter","Connector_Type_Calibration","Connector_Type_Measurement",
              "Measurement_Type","Measurement_Date","Measurement_Time","Program_Used","Program_Revision","Operator",
              "Calibration_Name","Calibration_Date","Port_Used","Number_Connects","Number_Repeats","Nbs",
              "Number_Frequencies","Start_Frequency",
              "Device_Description","Device_Id"]
        # import the first file
        model=globals()[model_name]
        initial_file=model(input_file_names_list[0])
        # Add the metadata columns and replace any commas with -
        for column_name in metadata_keys:
            initial_file.add_column(column_name=column_name,column_type='str',
                            column_data=[initial_file.metadata[column_name].replace(',','-')
                                         for row in initial_file.data])
        # We also add a column at the end that is Measurement_Timestamp, that is
        # Measurement_Time+Measurement_Date in isoformat
        timestamp=initial_file.metadata["Measurement_Date"]+" "+initial_file.metadata["Measurement_Time"]
        datetime_timestamp=datetime.datetime.strptime(timestamp,'%d %b %Y %H:%M:%S')
        measurement_timestamp=datetime_timestamp.isoformat(' ')
        initial_file.add_column(column_name="Measurement_Timestamp",column_type='str',
                            column_data=[measurement_timestamp
                                         for row in initial_file.data])
        # now we save the intial file with its column names but not its header
        initial_file.header=None
        initial_file.save(output_file_name)

        # Now we re-open this file in the append mode and read-in each new file and append it. This seems to work
        # for very large data sets, where as keeping a single object in memory fails
        out_file=open(output_file_name,'a')
        # now we do the same thing over and over and add it to the out file
        for file_name in input_file_names_list[1:]:

            model=globals()[model_name]
            parsed_file=model(file_name)
            for column_name in metadata_keys:
                parsed_file.add_column(column_name=column_name,column_type='str',
                            column_data=[parsed_file.metadata[column_name].replace(',','-')
                                         for row in parsed_file.data])
            timestamp=parsed_file.metadata["Measurement_Date"]+" "+parsed_file.metadata["Measurement_Time"]
            datetime_timestamp=datetime.datetime.strptime(timestamp,'%d %b %Y %H:%M:%S')
            measurement_timestamp=datetime_timestamp.isoformat(' ')
            parsed_file.add_column(column_name="Measurement_Timestamp",column_type='str',
                            column_data=[measurement_timestamp
                                         for row in parsed_file.data])
            # add an endline before appending
            out_file.write('\n')
            # now we only want the data string
            data=parsed_file.get_data_string()
            out_file.write(data)
        # close the file after  loop
        out_file.close()
    # Catch any errors
    except:
            raise

def calrep_to_benchmark(

file_path)

Creates a benchmark list given a path to a calrep file, assumes column names are 2 lines after the occurrence of the last /

def calrep_to_benchmark(file_path):
    """Creates a benchmark list given a path to a calrep file, assumes column names are 2 lines after
    the occurrence of the last /"""
    in_file=open(file_path,'r')
    lines=[]
    for line in in_file:
        lines.append(line)
    block_end=re.compile('/')
    for index,line in enumerate(lines):
        if re.match(block_end,line):
            last_block_comment_line=index
    header=lines[0:last_block_comment_line+1]
    columns_line=last_block_comment_line+2
    column_names=lines[columns_line].split(' ')
    data=lines[columns_line+1:None]
    return [header,column_names,data]

def convert_all_two_ports_script(

top_directory=None, output_directory=None)

Script reads all file names in all sub directories looking for ones that end in c, and tries to open file_name.asc and save it in the output directory

def convert_all_two_ports_script(top_directory=None,output_directory=None):
    """Script reads all file names in all sub directories looking for ones that end in c, and tries to open
    file_name.asc and save it in the output directory"""
    TOP_DIRECTORY=r'C:\Share\ascii.dut'
    # This pattern will find any names that have c in them
    TWO_PORT_PATTERN=re.compile('(?P<two_port_name>\w+)c',re.IGNORECASE)
    # now we test the os.walk function
    # This has a memory leak I am not sure but I suspect it is jupyter's fault
    for root,directory,file_names in os.walk(TOP_DIRECTORY):
        #print file_names
        for file_name in file_names:
            file_name=file_name.split('.')[0]
            match=re.search(TWO_PORT_PATTERN,file_name)
            try:
                if match:
                    asc_file_name=match.groupdict()["two_port_name"]+".asc"
                    print asc_file_name
                    if asc_file_name in ['de.asc','00.asc','dir.asc','IL.asc',"L2.asc","L1.asc"]:raise
                    converted_file=TwoPortCalrepModel(os.path.join(root,asc_file_name))
                    #print converted_file.joined_table.header
                    del converted_file
            except:
                pass

def raw_type(

file_contents)

Given the contents of a file in a list of lines or a single string returns the raw class name. It is assumed that the type of file is the 5th line of the header

def raw_type(file_contents):
    """Given the contents of a file in a list of lines or a single string returns the raw class name. It is assumed
    that the type of file is the 5th line of the header"""
    if type(file_contents) is StringType:
        lines=file_contents.splitlines()
    elif type(file_contents) is ListType:
        lines=file_contents
    #print("The value of {0} is {1}".format('lines[4]',lines[4]))
    out=None
    if re.search('1-port',lines[4],re.IGNORECASE):
        out='OnePortRawModel'
    elif re.search('2-port',lines[4],re.IGNORECASE) and not re.search('2-portNR',lines[4],re.IGNORECASE):
        out='TwoPortRawModel'
    elif re.search('2-portNR',lines[4],re.IGNORECASE):
        out='TwoPortNRRawModel'
    elif re.search('Thermistor|Dry Cal',lines[4],re.IGNORECASE):
        out='PowerRawModel'
    return out

def sparameter_power_type(

file_path)

sparameter_power_type returns the class name of file given a file path

def sparameter_power_type(file_path):
    """sparameter_power_type returns the class name of file given a file path"""
    extension=file_path.split('.')[-1]
    #print extension
    in_file=open(file_path,'r')
    lines=[]
    for line in in_file:
        lines.append(line)
    in_file.close()
    if re.match('asc',extension,re.IGNORECASE):
        #print("The value of {0} is {1}".format('extension',extension))
        # handle asc files
        out=asc_type(lines)
    elif re.match('[\w][\d]+_[\d]+',extension,re.IGNORECASE):
        #print("The value of {0} is {1}".format('extension',extension))
        out=raw_type(lines)
    return out

def test_JBSparameter(

file_path='ftest6_L1_g5_HF_air')

Tests the JBSparameter class

def test_JBSparameter(file_path="ftest6_L1_g5_HF_air"):
    """Tests the JBSparameter class"""
    os.chdir(TESTS_DIRECTORY)
    # open an existing file
    new_table=JBSparameter(file_path=file_path)
    print new_table.column_names
    print new_table.get_frequency_units()
    old_prefix=new_table.get_frequency_units().replace('Hz','')
    #new_table.change_unit_prefix(column_selector=0,old_prefix='',new_prefix='G',unit='Hz')
    new_table.change_unit_prefix(column_selector=0,old_prefix=old_prefix,new_prefix='G',unit='Hz')
    print new_table.column_names
    print new_table.get_column(None,0)
    print new_table.get_frequency_units()
    print new_table.get_header_string()

def test_OnePortCalrepModel(

file_path_1='700437.txt', file_path_2='700437.asc')

def test_OnePortCalrepModel(file_path_1='700437.txt',file_path_2="700437.asc"):
    os.chdir(TESTS_DIRECTORY)
    print(" Import of {0} results in:".format(file_path_1))
    new_table_1=OnePortCalrepModel(file_path=file_path_1)
    print new_table_1
    print("-"*80)
    print("\n")
    print(" Import of {0} results in:".format(file_path_2))
    new_table_2=OnePortCalrepModel(file_path=file_path_2)
    print new_table_2
    print("{0} results in {1}:".format('new_table_1.get_column("Frequency")',new_table_1.get_column("Frequency")))
    print new_table_1.get_options()
    print new_table_1.data[-1]
    new_table_1.show()

def test_OnePortCalrepModel_Ctable(

file_path_1='700437.txt')

Tests the OnePortCalrepModel on ctables from 2 port

def test_OnePortCalrepModel_Ctable(file_path_1='700437.txt'):
    """Tests the OnePortCalrepModel on ctables from 2 port """
    os.chdir(TESTS_DIRECTORY)
    print(" Import of {0} results in:".format(file_path_1))
    new_table_1=OnePortCalrepModel(file_path=file_path_1,**{"row_end_token":",\n"})
    print new_table_1
    print("-"*80)
    print("\n")
    new_table_1.show()

def test_OnePortRawModel(

file_path='OnePortRawTestFile.txt')

def test_OnePortRawModel(file_path='OnePortRawTestFile.txt'):
    os.chdir(TESTS_DIRECTORY)
    print(" Import of {0} results in:".format(file_path))
    new_table_1=OnePortRawModel(file_path=file_path)
    print new_table_1
    print("-"*80)
    print("{0} results in {1}:".format('new_table_1.get_column("Frequency")',new_table_1.get_column("Frequency")))
    print new_table_1.get_options()
    print new_table_1.metadata
    print new_table_1.column_names
    print('index' in new_table_1.column_names )
    new_table_1.show()

def test_PowerCalrepModel(

file_name='700083.asc')

Tests the TwoPortCalrepModel model type

def test_PowerCalrepModel(file_name="700083.asc"):
    """Tests the TwoPortCalrepModel model type"""
    os.chdir(TESTS_DIRECTORY)
    new_power=PowerCalrepModel(file_name)
    for table in new_power.tables:
        print table
    print new_power.joined_table
    #print new_power.joined_table.data[-1]
    new_power.show()

def test_PowerRawModel(

file_path='TestFilePowerRaw.txt')

def test_PowerRawModel(file_path='TestFilePowerRaw.txt'):
    os.chdir(TESTS_DIRECTORY)
    print(" Import of {0} results in:".format(file_path))
    new_table_1=PowerRawModel(file_path=file_path)
    print new_table_1

def test_TwoPortCalrepModel(

file_name='922729a.txt')

Tests the TwoPortCalrepModel model type

def test_TwoPortCalrepModel(file_name="922729a.txt"):
    """Tests the TwoPortCalrepModel model type"""
    os.chdir(TESTS_DIRECTORY)
    new_two_port=TwoPortCalrepModel(file_name)
    for table in new_two_port.tables:
        print table
    print new_two_port.joined_table
    #new_two_port.joined_table.save()
    new_two_port.joined_table.path='N205RV.txt'
    new_two_port.joined_table.header=None
    new_two_port.joined_table.column_names=None

def test_TwoPortRawModel(

file_path='TestFileTwoPortRaw.txt')

def test_TwoPortRawModel(file_path='TestFileTwoPortRaw.txt'):
    os.chdir(TESTS_DIRECTORY)
    print(" Import of {0} results in:".format(file_path))
    new_table_1=TwoPortRawModel(file_path=file_path)
    print new_table_1
    new_table_1.show()

def test_sparameter_power_type(

file_list=None)

Tests the sparameter_power_type function. Each file's type is determined and it is imported using the appropriate model

def test_sparameter_power_type(file_list=None):
    """Tests the sparameter_power_type function. Each file's type is determined and it is imported using
     the appropriate model"""
    os.chdir(TESTS_DIRECTORY)
    if file_list is None:
        file_list=[r'CTNP11.L36_062399','CTN106.D4_091799','CTN208.A1_011613','700083.ASC',
                   '700437.asc','922729.asc']
    else:
        file_list=file_list
    for file_name in file_list:
        file_type=sparameter_power_type(file_name)
        print(" The model of {0} is {1}".format(file_name,file_type))
        try:
            model=globals()[file_type]
            table=model(file_name)
            print table
        except:
            print("There was an error opening {0}".format(file_name))

Classes

class JBSparameter

JBSparameter is a class that holds data taken and stored using Jim Booth's two port format.

class JBSparameter(AsciiDataTable):
    """JBSparameter is a class that holds data taken and stored using Jim Booth's two port format.
     """

    def __init__(self,file_path=None,**options):
        """Initializes the JBSparameter class. JB Sparameter data is very close to s2p, but has # as a comment
         begin token, and space as a data delimiter. The first line has structured metadata that usually includes
         date and IFBW"""
        defaults={"header_begin_line":0,"data_end_line":None,"column_names_delimiter":' ',
                "column_names_begin_token":'#',"column_names_end_token":'\n',"data_table_element_separator":None,
                 "data_delimiter":' ',"comment_begin":"#",
                 "comment_end":"\n","row_end_token":'\n',"column_types":['float' for i in range(9)],
                 "column_descriptions":["Frequency in Hz",
                                        "Real part of S11",
                                        "Imaginary part of S11",
                                        "Real part of S21",
                                        "Imaginary part of S21",
                                        "Real part of S12",
                                        "Imaginary part of S12",
                                        "Real part of S22",
                                        "Imaginary part of S22"]}
        rfs=""
        for i in range(9):
            if i==8:
                rfs=rfs+"{%s:.6g}"%(str(i))
            else:
                rfs=rfs+"{%s:.6g}{delimiter}"%(str(i))
        options["row_formatter_string"]=rfs
        self.options={}
        for key,value in defaults.iteritems():
            self.options[key]=value
        for key,value in options.iteritems():
            self.options[key]=value
        # Define Method Aliases if they are available
        if METHOD_ALIASES:
            for command in alias(self):
                exec(command)

        if file_path is not None:
            column_name_line=0
            in_file=open(file_path,'r')
            for line in in_file:
                if line[0] is '#':
                    column_name_line+=1
            in_file.close()
            self.options["header_end_line"]=column_name_line-1
            self.options["column_names_begin_line"]=column_name_line-1
            self.options["column_names_end_line"]=column_name_line
            self.options["data_begin_line"]=column_name_line
            self.path=file_path
            AsciiDataTable.__init__(self,file_path,**self.options)
        else:
            AsciiDataTable.__init__(self,file_path,**self.options)
    def get_frequency_units(self):
        """Returns the frequency units by looking at the 0 index element of column names"""
        pattern='freq\((?P<Frequency_Units>\w+)\)'
        match=re.match(pattern,self.column_names[0])
        return match.groupdict()['Frequency_Units']

Ancestors (in MRO)

  • JBSparameter
  • pyMez.Code.DataHandlers.GeneralModels.AsciiDataTable

Instance variables

var options

Methods

def __init__(

self, file_path=None, **options)

Initializes the JBSparameter class. JB Sparameter data is very close to s2p, but has # as a comment begin token, and space as a data delimiter. The first line has structured metadata that usually includes date and IFBW

def __init__(self,file_path=None,**options):
    """Initializes the JBSparameter class. JB Sparameter data is very close to s2p, but has # as a comment
     begin token, and space as a data delimiter. The first line has structured metadata that usually includes
     date and IFBW"""
    defaults={"header_begin_line":0,"data_end_line":None,"column_names_delimiter":' ',
            "column_names_begin_token":'#',"column_names_end_token":'\n',"data_table_element_separator":None,
             "data_delimiter":' ',"comment_begin":"#",
             "comment_end":"\n","row_end_token":'\n',"column_types":['float' for i in range(9)],
             "column_descriptions":["Frequency in Hz",
                                    "Real part of S11",
                                    "Imaginary part of S11",
                                    "Real part of S21",
                                    "Imaginary part of S21",
                                    "Real part of S12",
                                    "Imaginary part of S12",
                                    "Real part of S22",
                                    "Imaginary part of S22"]}
    rfs=""
    for i in range(9):
        if i==8:
            rfs=rfs+"{%s:.6g}"%(str(i))
        else:
            rfs=rfs+"{%s:.6g}{delimiter}"%(str(i))
    options["row_formatter_string"]=rfs
    self.options={}
    for key,value in defaults.iteritems():
        self.options[key]=value
    for key,value in options.iteritems():
        self.options[key]=value
    # Define Method Aliases if they are available
    if METHOD_ALIASES:
        for command in alias(self):
            exec(command)
    if file_path is not None:
        column_name_line=0
        in_file=open(file_path,'r')
        for line in in_file:
            if line[0] is '#':
                column_name_line+=1
        in_file.close()
        self.options["header_end_line"]=column_name_line-1
        self.options["column_names_begin_line"]=column_name_line-1
        self.options["column_names_end_line"]=column_name_line
        self.options["data_begin_line"]=column_name_line
        self.path=file_path
        AsciiDataTable.__init__(self,file_path,**self.options)
    else:
        AsciiDataTable.__init__(self,file_path,**self.options)

def add_column(

self, column_name=None, column_type=None, column_data=None, format_string=None)

Adds a column with column_name, and column_type. If column data is supplied and it's length is the same as data(same number of rows) then it is added, else self.options['empty_character'] is added in each spot in the preceding rows

def add_column(self,column_name=None,column_type=None,column_data=None,format_string=None):
    """Adds a column with column_name, and column_type. If column data is supplied and it's length is the
    same as data(same number of rows) then it is added, else self.options['empty_character'] is added in each
    spot in the preceding rows"""
    original_column_names=self.column_names[:]
    try:
        self.column_names=original_column_names+[column_name]
        if self.options["column_types"]:
            old_column_types=self.options["column_types"][:]
            self.options["column_types"]=old_column_types+[column_type]
        if len(column_data) == len(self.data):
            for index,row in enumerate(self.data[:]):
                #print("{0} is {1}".format('self.data[index]',self.data[index]))
                #print("{0} is {1}".format('row',row))
                new_row=row[:]
                new_row.append(column_data[index])
                self.data[index]=new_row
        else:
            for index,row in enumerate(self.data[:]):
                self.data[index]=row.append(self.options['empty_value'])
                if column_data is not None:
                    for item in column_data:
                        empty_row=[self.options['empty_value'] for column in original_column_names]
                        empty_row.append(item)
                        self.add_row(empty_row)
        if self.options["row_formatter_string"] is None:
            pass
        else:
            if format_string is None:
                self.options["row_formatter_string"]=self.options["row_formatter_string"]+\
                                                             '{delimiter}'+"{"+str(len(self.column_names)-1)+"}"
            else:
                self.options["row_formatter_string"]=self.options["row_formatter_string"]+format_string
        #self.update_model()
    except:
        self.column_names=original_column_names
        print("Could not add columns")
        raise

def add_index(

self)

Adds a column with name index and values that are 0 referenced indices, does nothing if there is already a column with name index, always inserts it at the 0 position

def add_index(self):
    """Adds a column with name index and values that are 0 referenced indices, does nothing if there is
    already a column with name index, always inserts it at the 0 position"""
    if 'index' in self.column_names:
        print("Add Index passed")
        pass
    else:
        self.column_names.insert(0,'index')
        for index,row in enumerate(self.data):
            self.data[index].insert(0,index)
        if self.options['column_types']:
            self.options['column_types'].insert(0,'int')
        if self.options['row_formatter_string']:
            temp_formatter_list=self.options['row_formatter_string'].split("{delimiter}")
            iterated_row_formatter_list=[temp_formatter_list[i].replace(str(i),str(i+1))
                                         for i in range(len(temp_formatter_list))]
            new_formatter=string_list_collapse(iterated_row_formatter_list,string_delimiter="{delimiter}")
            self.options['row_formatter_string']='{0}{delimiter}'+new_formatter

def add_inline_comment(

self, comment='', line_number=None, string_position=None)

Adds an inline in the specified location

def add_inline_comment(self,comment="",line_number=None,string_position=None):
    "Adds an inline in the specified location"
    try:
        self.inline_comments.append([comment,line_number,string_position])
    except:pass

def add_row(

self, row_data)

Adds a single row given row_data which can be an ordered list/tuple or a dictionary with column names as keys

def add_row(self,row_data):
    """Adds a single row given row_data which can be an ordered list/tuple or a dictionary with
    column names as keys"""
    if len(row_data) not in [len(self.column_names),len(self.column_names)]:
        print(" could not add the row, dimensions do not match")
        return
    if type(row_data) in [ListType,np.ndarray]:
        self.data.append(row_data)
    elif type(row_data) in [DictionaryType]:
        data_list=[row_data[column_name] for column_name in self.column_names]
        self.data.append(data_list)

def build_string(

self, **temp_options)

Builds a string representation of the data table based on self.options, or temp_options. Passing temp_options does not permanently change the model

def build_string(self,**temp_options):
    """Builds a string representation of the data table based on self.options, or temp_options.
    Passing temp_options does not permanently change the model"""
    # store the original options to be put back after the string is made
    original_options=self.options
    for key,value in temp_options.iteritems():
        self.options[key]=value
    section_end=0
    next_section_begin=0
    if self.options['data_table_element_separator'] is None:
        inner_element_spacing=0
    else:
        inner_element_spacing=self.options['data_table_element_separator'].count('\n')-1
    string_out=""
    between_section=""
    if self.options['data_table_element_separator'] is not None:
        between_section=self.options['data_table_element_separator']
    if self.header is None:
        self.options['header_begin_line']=self.options['header_end_line']=None
        pass
    else:
        self.options["header_begin_line"]=0
        if self.data is None and self.column_names is None and self.footer is None:
            string_out=self.get_header_string()
            self.options["header_end_line"]=None
        else:
            string_out=self.get_header_string()+between_section
            last_header_line=self.get_header_string().count('\n')+1
            self.options["header_end_line"]=last_header_line
            next_section_begin=last_header_line+inner_element_spacing
    if self.column_names is None:
        self.options['column_names_begin_line']=self.options['column_names_end_line']=None
        pass
    else:
        self.options["column_names_begin_line"]=next_section_begin
        if self.data is None and self.footer is None:
            self.options["column_names_end_line"]=None
            string_out=string_out+self.get_column_names_string()
        else:
            string_out=string_out+self.get_column_names_string()+between_section
            last_column_names_line=self.get_column_names_string().count('\n')+\
                                   self.options["column_names_begin_line"]+1
            self.options["column_names_end_line"]=last_column_names_line
            next_section_begin=last_column_names_line+inner_element_spacing
    if self.data is None:
        self.options['data_begin_line']=self.options['data_end_line']=None
        pass
    else:
        self.options["data_begin_line"]=next_section_begin
        if self.footer is None:
            self.options["data_end_line"]=None
            string_out=string_out+self.get_data_string()
        else:
            string_out=string_out+self.get_data_string()+between_section
            last_data_line=self.get_data_string().count("\n")+\
                            self.options["data_begin_line"]+1
            self.options["data_end_line"]=last_data_line
            next_section_begin=last_data_line+inner_element_spacing
    if self.footer is None:
        self.options['footer_begin_line']=self.options['footer_end_line']=None
        pass
    else:
        self.options["footer_begin_line"]=next_section_begin
        string_out=string_out+self.get_footer_string()
        self.options['footer_end_line']=None
    # set the options back after the string has been made
    if self.inline_comments is None:
        pass
    else:
        lines=string_out.splitlines()
        for comment in self.inline_comments:
            lines=insert_inline_comment(lines,comment=comment[0],line_number=comment[1],
                                        string_position=comment[2],
                                        begin_token=self.options['inline_comment_begin'],
                                        end_token=self.options['inline_comment_end'])
        string_out=string_list_collapse(lines,string_delimiter='\n')
    self.options=original_options
    return string_out

def change_unit_prefix(

self, column_selector=None, old_prefix=None, new_prefix=None, unit='Hz')

Changes the prefix of the units of the column specified by column_selector (column name or index) example usage is self.change_unit_prefix(column_selector='Frequency',old_prefix=None,new_prefix='G',unit='Hz') to change a column from Hz to GHz. It updates the data values, column_descriptions, and column_units if they exist, see http://www.nist.gov/pml/wmd/metric/prefixes.cfm for possible prefixes

def change_unit_prefix(self,column_selector=None,old_prefix=None,new_prefix=None,unit='Hz'):
    """Changes the prefix of the units of the column specified by column_selector (column name or index)
    example usage is self.change_unit_prefix(column_selector='Frequency',old_prefix=None,new_prefix='G',unit='Hz')
    to change a column from Hz to GHz. It updates the data values, column_descriptions, and column_units if they
    exist, see http://www.nist.gov/pml/wmd/metric/prefixes.cfm for possible prefixes"""
    multipliers={"yotta":10.**24,"Y":10.**24,"zetta":10.**21,"Z":10.**21,"exa":10.**18,"E":10.**18,"peta":10.**15,
                 "P":10.**15,"tera":10.**12,"T":10.**12,"giga":10.**9,"G":10.**9,"mega":10.**6,"M":10.**6,
                 "kilo":10.**3,"k":10.**3,"hecto":10.**2,"h":10.**2,"deka":10.,"da":10.,None:1.,"":1.,
                 "deci":10.**-1,"d":10.**-1,"centi":10.**-2,"c":10.**-2,"milli":10.**-3,"m":10.**-3,
                 "micro":10.**-6,"mu":10.**-6,u"\u00B5":10.**-6,"nano":10.**-9,
                 "n":10.**-9,"pico":10.**-12,"p":10.**-12,"femto":10.**-15,
                 "f":10.**-15,"atto":10.**-18,"a":10.**-18,"zepto":10.**-21,"z":10.**-21,
                 "yocto":10.**-24,"y":10.**-24}
    # change column name into column index
    try:
        if old_prefix is None:
            old_prefix=""
        if new_prefix is None:
            new_prefix=""
        old_unit=old_prefix+unit
        new_unit=new_prefix+unit
        if column_selector in self.column_names:
            column_selector=self.column_names.index(column_selector)
        for index,row in enumerate(self.data):
            if type(self.data[index][column_selector]) in [FloatType,LongType]:
                #print "{0:e}".format(multipliers[old_prefix]/multipliers[new_prefix])
                self.data[index][column_selector]=\
                (multipliers[old_prefix]/multipliers[new_prefix])*self.data[index][column_selector]
            elif type(self.data[index][column_selector]) in [StringType,IntType]:
                self.data[index][column_selector]=\
                str((multipliers[old_prefix]/multipliers[new_prefix])*float(self.data[index][column_selector]))
            else:
                print type(self.data[index][column_selector])
                raise
        if self.options["column_descriptions"] is not None:
            old=self.options["column_descriptions"][column_selector]
            self.options["column_descriptions"][column_selector]=old.replace(old_unit,new_unit)
        if self.options["column_units"] is not None:
            old=self.options["column_units"][column_selector]
            self.options["column_units"][column_selector]=old.replace(old_unit,new_unit)
        if re.search(old_unit,self.column_names[column_selector]):
            old=self.column_names[column_selector]
            self.column_names[column_selector]=old.replace(old_unit,new_unit)
    except:
        print("Could not change the unit prefix of column {0}".format(column_selector))
        raise

def find_line(

self, begin_token)

Finds the first line that has begin token in it

def find_line(self,begin_token):
    """Finds the first line that has begin token in it"""
    for index,line in enumerate(self.lines):
        if re.search(begin_token,line,re.IGNORECASE):
            return index

def get_column(

self, column_name=None, column_index=None)

Returns a column as a list given a column name or column index

def get_column(self,column_name=None,column_index=None):
    """Returns a column as a list given a column name or column index"""
    if column_name is None:
        if column_index is None:
            return
        else:
            column_selector=column_index
    else:
        column_selector=self.column_names.index(column_name)
    out_list=[self.data[i][column_selector] for i in range(len(self.data))]
    return out_list

def get_column_names_string(

self)

Returns the column names as a string using options

def get_column_names_string(self):
    "Returns the column names as a string using options"
    string_out=""
    # This writes the column_names
    column_name_begin=""
    column_name_end=""
    if self.options["column_names_begin_token"] is None:
        column_name_begin=""
    else:
        column_name_begin=self.options["column_names_begin_token"]
    if self.options["column_names_end_token"] is None:
        column_name_end=""
    else:
        column_name_end=self.options["column_names_end_token"]
    if self.column_names is None:
        string_out=""
    else:
        if type(self.column_names) is StringType:
            string_out=self.column_names
        elif type(self.column_names) is ListType:
            string_out=list_to_string(self.column_names,
                                      data_delimiter=self.options["column_names_delimiter"],end="")
            #print("{0} is {1}".format('string_out',string_out))
        else:
            string_out=ensure_string(self.column_names)
    #print column_name_begin,string_out,column_name_end
    return column_name_begin+string_out+column_name_end

def get_data_dictionary_list(

self, use_row_formatter_string=True)

Returns a python list with a row dictionary of form {column_name:data_column}

def get_data_dictionary_list(self,use_row_formatter_string=True):
    """Returns a python list with a row dictionary of form {column_name:data_column}"""
    try:
        if self.options["row_formatter_string"] is None:
            use_row_formatter_string=False
        if use_row_formatter_string:
            list_formatter=[item.replace("{"+str(index),"{0")
                            for index,item in enumerate(self.options["row_formatter_string"].split("{delimiter}"))]
        else:
            list_formatter=["{0}" for i in self.column_names]
        #print self.column_names
        #print self.data
        #print list_formatter
        #print len(self.column_names)==len(self.data[0])
        #print len(list_formatter)==len(self.data[0])
        #print type(self.data[0])
        out_list=[{self.column_names[i]:list_formatter[i].format(value) for i,value in enumerate(line)}
                  for line in self.data]
        return out_list
    except:
        print("Could not form a data_dictionary_list, check that row_formatter_string is properly defined")
        #print(out_list)
        raise

def get_data_string(

self)

Returns the data as a string

def get_data_string(self):
    "Returns the data as a string"
    #Todo:refactor to cut out unused lines
    string_out=""
    if self.data is None:
        string_out= ""
    else:
        if type(self.data) is StringType:
            if self.options['data_begin_token'] is None:
                   if self.options['data_end_token'] is None:
                       string_out=self.data
                   else:
                       if re.search(self.options['data_end_token'],self.data):
                           string_out=self.data
                       else:
                           string_out=self.data+self.options['data_end_token']
            else:
                    if self.options['data_end_token'] is None:
                        if re.match(self.options['data_begin_token'],self.data):
                            string_out=self.data
                        else:
                            string_out=self.options['data_begin_token']+self.data
        elif type(self.data) in [ListType,np.ndarray]:
            try:
                    #If the first row is a string, we should strip all the tokens and add them back in
                    if type(self.data[0]) is StringType:
                        if self.options['data_begin_token'] is None:
                            string_out=string_list_collapse(self.data)
                        else:
                            if re.match(self.options['data_begin_token'],self.data[0]):
                                if self.options['data_end_token'] is None:
                                    string_out=string_list_collapse(self.data)
                                else:
                                    if re.search(self.options['data_end_token'],self.data[-1]):
                                        string_out=string_list_collapse(self.data)
                                    else:
                                        string_out=string_list_collapse(self.data)+self.options['data_end_token']
                            else:
                                if self.options['data_end_token'] is None:
                                    string_out=self.options['data_begin_token']+string_list_collapse(self.data)
                                else:
                                    if re.search(self.options['data_end_token'],self.data[-1]):
                                        string_out=self.options['data_begin_token']+string_list_collapse(self.data)
                                    else:
                                        string_out=self.options['data_begin_token']+\
                                                   string_list_collapse(self.data)+\
                                                   self.options['data_end_token']
                    elif type(self.data[0]) in [ListType,np.ndarray]:
                        prefix=""
                        if self.options['data_begin_token'] is None:
                            if self.options['data_end_token'] is None:
                                string_out=list_list_to_string(self.data,data_delimiter=self.options['data_delimiter'],
                                                               row_formatter_string=self.options['row_formatter_string'],
                                                               line_begin=self.options["row_begin_token"],
                                                               line_end=self.options["row_end_token"])
                        else:
                            if self.options['data_end_token'] is None:
                                string_out=self.options['data_begin_token']+\
                                           list_list_to_string(self.data,
                                                               data_delimiter=self.options['data_delimiter'],
                                                               row_formatter_string=self.options['row_formatter_string'],
                                                               line_begin=self.options["row_begin_token"],
                                                               line_end=self.options["row_end_token"])
                            else:
                                string_out=self.options['data_begin_token']+\
                                           list_list_to_string(self.data,
                                                               data_delimiter=self.options['data_delimiter'],
                                                               row_formatter_string=\
                                                               self.options['row_formatter_string'],
                                                               line_begin=self.options["row_begin_token"],
                                                               line_end=self.options["row_end_token"])+\
                                                                self.options['data_end_token']
                    else:
                        string_out=list_to_string(self.data,
                                                  data_delimiter=self.options['data_delimiter'],
                                                  row_formatter_string=self.options['row_formatter_string'],
                                                  begin=self.options["row_begin_token"],
                                                  end=self.options["row_end_token"])
            except IndexError:
                pass
        else:
            string_out=ensure_string(self.data)
    return string_out

Returns the footer using options in self.options. If block comment is specified, and the footer is a list it will block comment out the footer. If comment_begin and comment_end are specified it will use those to represent each line of the footer. If footer_begin_token and/or footer_end_token are specified it will wrap the footer in those.

def get_frequency_units(

self)

Returns the frequency units by looking at the 0 index element of column names

def get_frequency_units(self):
    """Returns the frequency units by looking at the 0 index element of column names"""
    pattern='freq\((?P<Frequency_Units>\w+)\)'
    match=re.match(pattern,self.column_names[0])
    return match.groupdict()['Frequency_Units']

def get_header_string(

self)

Returns the header using options in self.options. If block comment is specified, and the header is a list it will block comment out the header. If comment_begin and comment_end are specified it will use those to represent each line of the header. If header_begin_token and/or header_end_token are specified it will wrap the header in those.

def get_header_string(self):
    """Returns the header using options in self.options. If block comment is specified, and the header is a
    list it will block comment out the header. If comment_begin and comment_end are specified it will use
    those to represent each line of the header. If header_begin_token and/or header_end_token are specified it
     will wrap the header in those.
    """
    string_out=""
    header_begin=""
    header_end=""
    if self.options["header_begin_token"] is None:
        header_begin=""
    else:
        header_begin=self.options["header_begin_token"]
    if self.options["header_end_token"] is None:
        header_end=""
    else:
        header_end=self.options["header_end_token"]
    # This writes the header
    if self.header is None:
        string_out= ""
    elif self.options["header_line_types"] is not None:
        for index,line in enumerate(self.options["header_line_types"]):
            if index == len(self.options["header_line_types"])-1:
                end=''
            else:
                end='\n'
            if line in ['header','header_line','normal']:
                string_out=string_out+self.header[index]+end
            elif line in ['line_comment','comment']:
                string_out=string_out+line_comment_string(self.header[index],
                                           comment_begin=self.options["comment_begin"],
                                           comment_end=self.options["comment_end"])+end
            elif line in ['block_comment','block']:
                if index-1<0:
                    block_comment_begin=index
                    block_comment_end=index+2
                    continue
                elif self.options["header_line_types"][index-1] not in ['block_comment','block']:
                    block_comment_begin=index
                    block_comment_end=index+2
                    continue
                else:
                    if index+1>len(self.options["header_line_types"])-1:
                        string_out=string_out+line_list_comment_string(self.header[block_comment_begin:],
                                                                       comment_begin=self.options['block_comment_begin'],
                                                                         comment_end=self.options['block_comment_end'],
                                                                       block=True)+end
                    elif self.options["header_line_types"][index+1] in ['block_comment','block']:
                        block_comment_end+=1
                    else:
                        string_out=string_out+\
                                   line_list_comment_string(self.header[block_comment_begin:block_comment_end],
                                                            comment_begin=self.options['block_comment_begin'],
                                                            comment_end=self.options['block_comment_end'],
                                                            block=True)+end
            else:
                string_out=string_out+line
    elif self.options['treat_header_as_comment'] in [None,True] and self.options["header_line_types"] in [None]:
        # Just happens if the user has set self.header manually
        if type(self.header) is StringType:
            string_out=line_comment_string(self.header,
                                           comment_begin=self.options["comment_begin"],
                                           comment_end=self.options["comment_end"])
            #string_out=re.sub('\n','',string_out,count=1)
        elif type(self.header) is ListType:
            if self.options['block_comment_begin'] is None:
                if self.options['comment_begin'] is None:
                    string_out=string_list_collapse(self.header)
                else:
                    string_out=line_list_comment_string(self.header,comment_begin=self.options['comment_begin'],
                                                    comment_end=self.options['comment_end'])
                    lines_out=string_out.splitlines()
                    # if re.search('\n',self.options['comment_end']):
                    #     string_out=re.sub('\n','',string_out,count=1)
                    #self.options["header_line_types"]=["line_comment" for line in self.header]
            else:
                string_out=line_list_comment_string(self.header,comment_begin=self.options['block_comment_begin'],
                                                    comment_end=self.options['block_comment_end'],block=True)
                #self.options["header_line_types"]=["block_comment" for line in self.header]
    else:
        string_out=ensure_string(self.header,list_delimiter="\n",end_if_list="")
    return header_begin+string_out+header_end

def get_options(

self)

Prints the option list

def get_options(self):
    "Prints the option list"
    for key,value in self.options.iteritems():
        print("{0} = {1}".format(key,value))

def get_options_by_element(

self, element_name)

returns a dictionary of all the options that have to do with element. Element must be header,column_names,data, or footer

def get_options_by_element(self,element_name):
    """ returns a dictionary
     of all the options that have to do with element. Element must be header,column_names,data, or footer"""
    keys_regarding_element=filter(lambda x: re.search(element_name,str(x),re.IGNORECASE),self.options.keys())
    out_dictionary={key:self.options[key] for key in keys_regarding_element}
    #print out_dictionary
    return out_dictionary

def get_row(

self, row_index=None)

Returns the row as a list specified by row_index

def get_row(self,row_index=None):
    """Returns the row as a list specified by row_index"""
    if row_index is None:
        return
    else:
        return self.data[row_index]

def is_valid(

self)

Returns True if ascii table conforms to its specification given by its own options

def is_valid(self):
    """Returns True if ascii table conforms to its specification given by its own options"""
    options={}
    for key,value in self.options.iteritems():
        options[key]=value
        # print("self.options[{0}] is {1} ".format(key,value))
    for element in self.elements:
        if self.__dict__[element] is None:
            options[element]=None
        else:
            options[element]=[]
    options["validate"]=True
    newtable=AsciiDataTable(None,**options)
    lines=self.build_string().splitlines()
    for index,line in enumerate(lines):
        lines[index]=line+"\n"
    newtable.lines=lines
    newtable.__parse__()
    # print newtable.data
    # print newtable.column_names
    # print newtable
    #print_comparison(newtable.footer,None)
    newtable.update_model()
    # The new table rows are not being coerced into the right format
    #print newtable
    #newtable.update_model()
    #print newtable.options
    #print self.options
    #print newtable.data
    # print newtable.options==self.options
    # for option_key,option_value in newtable.options.iteritems():
    #     print("New Table Option {0} is {1} ".format(option_key,option_value))
    #     print("self.options[{0}] is {1} ".format(option_key,self.options[option_key]))
    #     print_comparison(option_value,self.options[option_key])
    # #print self
    return self==newtable

def lines_defined(

self)

If begin_line and end_line for all elements that are None are defined returns True

def lines_defined(self):
    """If begin_line and end_line for all elements that are None are defined returns True"""
    truth_table=[]
    last_element=""
    output=False
    for index,element in enumerate(self.elements):
        if element not in ['inline_comments','metadata'] and self.__dict__[element] is not None:
            try:
                last_element=element
                if not None in [self.options['%s_begin_line'%element],self.options['%s_end_line'%element]]:
                    truth_table.append(True)
                else:
                     truth_table.append(False)
            except:
                return False
    #print truth_table
    # The last_line of the last element is fine to be none
    if truth_table[-1] is False:
        if self.options['%s_begin_line'%last_element] is not None:
            truth_table[-1]=True
    if False in truth_table:
        output=False
    else:
        output=True
    #print output
    return output

Moves the DataTable's footer to the header and updates the model

def remove_column(

self, column_name=None, column_index=None)

Removes the column specified by column_name or column_index and updates the model. The column is removed from column_names, data and if present column_types, column_descriptions and row formatter

def remove_column(self,column_name=None,column_index=None):
    """Removes the column specified by column_name or column_index and updates the model. The column is removed from
    column_names, data and if present column_types, column_descriptions and row formatter"""
    pass

def remove_row(

self, row_index)

Removes the row specified by row_index and updates the model. Note index is relative to the data attribute so to remove the first row use row_index=0 and the last data row is row_index=-1

def remove_row(self,row_index):
    """Removes the row specified by row_index and updates the model. Note index is relative to the
    data attribute so to remove the first row use row_index=0 and the last data row is row_index=-1"""
    self.data.pop(row_index)
    self.update_model()

def save(

self, path=None, **temp_options)

" Saves the file, to save in another ascii format specify elements in temp_options, the options specified do not permanently change the object's options. If path is supplied it saves the file to that path otherwise uses the object's attribute path to define the saving location

def save(self,path=None,**temp_options):
    """" Saves the file, to save in another ascii format specify elements in temp_options, the options
    specified do not permanently change the object's options. If path is supplied it saves the file to that path
    otherwise uses the object's attribute path to define the saving location """
    original_options=self.options
    for key,value in temp_options.iteritems():
        self.options[key]=value
    out_string=self.build_string(**temp_options)
    if path is None:
        path=self.path
    file_out=open(path,'w')
    file_out.write(out_string)
    file_out.close()
    self.options=original_options

def save_schema(

self, path=None, format=None)

Saves the tables options as a text file or pickled dictionary (default). If no name is supplied, autonames it and saves

def save_schema(self,path=None,format=None):
    """Saves the tables options as a text file or pickled dictionary (default).
    If no name is supplied, autonames it and saves"""
    if path is None:
        path=auto_name(self.name.replace('.'+self.options["extension"],""),'Schema',self.options["directory"],'txt')
    if format in [None,'python','pickle']:
        pickle.dump(self.options,open(path,'wb'))
    elif format in ['txt','text','.txt']:
        file_out=open(path,'w')
        keys=self.options.keys()
        keys.sort()
        for key in keys:
            out_key=str(key).replace("\n","\\n")
            out_value=str(self.options[key]).replace("\n","\\n")
            file_out.write("{0} : {1} \n".format(out_key,out_value))
        file_out.close()

def update_column_names(

self)

Update column names adds the value x# for any column that exists in self.data that is not named

def update_column_names(self):
    """Update column names adds the value x# for any column that exists in self.data that is not named"""
    if self.data is None:
        return
    elif type(self.column_names) is StringType:
        self.column_names=split_row(self.column_names,self.options["column_names_delimiter"])
    elif self.column_names is None:
        column_names=[]
        for index,column in enumerate(self.data[0]):
            column_names.append("x"+str(index))
        self.column_names=column_names
        return
    elif len(self.column_names)==len(self.data[0]):
        return
    elif len(self.column_names) < len(self.data[0]):
        for index in range(len(self.column_names),len(self.data[0])):
            self.column_names.append("x"+str(index))
        return

def update_import_options(

self, import_table)

Updates the options in the import table

def update_import_options(self,import_table):
    """Updates the options in the import table"""
    for index,element in enumerate(['header','column_names','data','footer']):
        if self.__dict__[element] is not None:
            print("The {0} variable is {1}".format('index',index))
            print("The {0} variable is {1}".format('element',element))
            print("The {0} variable is {1}".format('import_table',import_table))
            [self.options['%s_begin_line'%element],
                            self.options['%s_end_line'%element],
                            self.options['%s_begin_token'%element],
                            self.options['%s_end_token'%element]]=import_table[index][:]

def update_index(

self)

Updates the index column if it exits, otherwise exits quietly

def update_index(self):
    """ Updates the index column if it exits, otherwise exits quietly
    """
    if 'index' not in self.column_names:
        return
    else:
        try:
            #This should be 0 but just in case
            index_column_number=self.column_names.index('index')
            for i in range(len(self.data)):
                self.data[i][index_column_number]=i
        except:
            pass

def update_model(

self)

Updates the model after a change has been made. If you add anything to the attributes of the model, or change this updates the values. If the model has an index column it will make sure the numbers are correct. In addition, it will update the options dictionary to reflect added rows, changes in deliminators etc.

def update_model(self):
    """Updates the model after a change has been made. If you add anything to the attributes of the model,
    or change this updates the values. If the model has an index column it will make sure the numbers are correct.
    In addition, it will update the options dictionary to reflect added rows, changes in deliminators etc.  """
    if self.column_names is not None and 'index' in self.column_names:
       self.update_index()
    #make sure there are no "\n" characters in the element lists (if so replace them with "") for data this is
    # done on import
    list_types=["header","column_names","footer"]
    for element in list_types:
        if self.__dict__[element] is not None:
            for index,item in enumerate(self.__dict__[element]):
                self.__dict__[element][index]=item.replace("\n","")
    self.update_column_names()
    if self.data is not None:
        self.data=convert_all_rows(self.data,self.options["column_types"])
    self.string=self.build_string()
    self.lines=self.string.splitlines()

class NoiseCalRaw

class NoiseCalRaw():
    pass

Ancestors (in MRO)

class OnePortCalrepModel

class OnePortCalrepModel(AsciiDataTable):
    def __init__(self,file_path,**options):
        "Intializes the OnePortCalrepModel Class, it is assumed that the file is of the .asc or table type"
        # This is a general pattern for adding a lot of options
        defaults= {"data_delimiter": ",", "column_names_delimiter": ",", "specific_descriptor": 'One_Port',
                   "general_descriptor": 'Sparameter', "extension": 'txt', "comment_begin": "#", "comment_end": "\n",
                   "column_types": ['float' for i in range(11)],
                   "column_descriptions": {"Frequency": "Frequency in GHz", "Magnitude": "Linear magnitude",
                                           "uMb": "Uncertainty in magnitude due to standards",
                                           "uMa": "Uncertainty in magnitude due to electronics",
                                           "uMd": "Uncertainty in magnitude for repeated connects",
                                           "uMg": "Total uncertainty in magnitude",
                                           "Phase": "Phase in degrees",
                                           "uPhb": "Uncertainty in phase due to standards",
                                           "uPha": "Uncertainty in phase due to electronics",
                                           "uPhd": "Uncertainty in phase for repeated connects",
                                           "uPhg": "Total uncertainty in phase"}, "header": None,
                   "column_names": ONE_PORT_COLUMN_NAMES, "column_names_end_token": "\n", "data": None,
                   "row_formatter_string": None, "data_table_element_separator": None,"row_begin_token":None,
                   "row_end_token":None,"escape_character":None,
                   "data_begin_token":None,"data_end_token":None}
        self.options={}
        for key,value in defaults.iteritems():
            self.options[key]=value
        for key,value in options.iteritems():
            self.options[key]=value
        # Define Method Aliases if they are available
        if METHOD_ALIASES:
            for command in alias(self):
                exec(command)
        if file_path is not None:
            self.path=file_path
            self.__read_and_fix__()

        #build the row_formatting string, the original files have 4 decimals of precision for freq/gamma and 2 for Phase
        row_formatter=""
        for i in range(11):
            if i<6:
                row_formatter=row_formatter+"{"+str(i)+":.4f}{delimiter}"
            elif i==10:
                row_formatter=row_formatter+"{"+str(i)+":.2f}"
            else:
                row_formatter=row_formatter+"{"+str(i)+":.2f}{delimiter}"
        self.options["row_formatter_string"]=row_formatter
        AsciiDataTable.__init__(self,None,**self.options)
        if file_path is not None:
            self.path=file_path

    def __read_and_fix__(self):
        """Reads in a 1 port ascii file and fixes any issues with inconsistent delimiters, etc"""
        lines=[]
        table_type=self.path.split(".")[-1]
        in_file=open(self.path,'r')
        for line in in_file:
            #if not re.match('[\s]+(?!\w+)',line):
                #print line
            lines.append(line)
        in_file.close()
        # Handle the cases in which it is the comma delimited table
        if re.match('txt',table_type,re.IGNORECASE):
            lines=strip_tokens(lines,*[self.options['data_begin_token'],
                                                    self.options['data_end_token']])
            self.options["data"]=strip_all_line_tokens(lines,begin_token=self.options["row_begin_token"],
                                            end_token=self.options["row_end_token"])
            self.options["data"]=split_all_rows(self.options["data"],delimiter=self.options["data_delimiter"],
                                     escape_character=self.options["escape_character"])
            self.options["data"]=convert_all_rows(self.options["data"],self.options["column_types"])
            #print self.options["data"]
            root_name_pattern=re.compile('(?P<root_name>\w+)[abc].txt',re.IGNORECASE)
            root_name_match=re.search(root_name_pattern,self.path)
            if root_name_match:
                root_name=root_name_match.groupdict()["root_name"]
            else:
                root_name=self.path.split('.')[0]
            self.options["header"]=["Device_Id = {0}".format(root_name)]

        elif re.match("asc",table_type,re.IGNORECASE):
            self.lines=lines
            data_begin_line=self.find_line("TABLE")+2
            # TODO: Replace with parse lines, it ignores blank lines
            data=np.loadtxt(self.path,skiprows=data_begin_line)
            self.options["data"]=data.tolist()
            self.options["header"]=lines[:self.find_line("TABLE")]
            #print("The {0} variable is {1}".format('data.tolist()',data.tolist()))

    def show(self):
        fig, (ax0, ax1) = plt.subplots(nrows=2, sharex=True)
        ax0.errorbar(self.get_column('Frequency'),self.get_column('mag'),
             yerr=self.get_column('uMg'),fmt='k--')
        ax0.set_title('Magnitude S11')
        ax1.errorbar(self.get_column('Frequency'),self.get_column('arg'),
             yerr=self.get_column('uAg'),fmt='ro')
        ax1.set_title('Phase S11')
        plt.show()

Ancestors (in MRO)

Instance variables

var options

Methods

def __init__(

self, file_path, **options)

Intializes the OnePortCalrepModel Class, it is assumed that the file is of the .asc or table type

def __init__(self,file_path,**options):
    "Intializes the OnePortCalrepModel Class, it is assumed that the file is of the .asc or table type"
    # This is a general pattern for adding a lot of options
    defaults= {"data_delimiter": ",", "column_names_delimiter": ",", "specific_descriptor": 'One_Port',
               "general_descriptor": 'Sparameter', "extension": 'txt', "comment_begin": "#", "comment_end": "\n",
               "column_types": ['float' for i in range(11)],
               "column_descriptions": {"Frequency": "Frequency in GHz", "Magnitude": "Linear magnitude",
                                       "uMb": "Uncertainty in magnitude due to standards",
                                       "uMa": "Uncertainty in magnitude due to electronics",
                                       "uMd": "Uncertainty in magnitude for repeated connects",
                                       "uMg": "Total uncertainty in magnitude",
                                       "Phase": "Phase in degrees",
                                       "uPhb": "Uncertainty in phase due to standards",
                                       "uPha": "Uncertainty in phase due to electronics",
                                       "uPhd": "Uncertainty in phase for repeated connects",
                                       "uPhg": "Total uncertainty in phase"}, "header": None,
               "column_names": ONE_PORT_COLUMN_NAMES, "column_names_end_token": "\n", "data": None,
               "row_formatter_string": None, "data_table_element_separator": None,"row_begin_token":None,
               "row_end_token":None,"escape_character":None,
               "data_begin_token":None,"data_end_token":None}
    self.options={}
    for key,value in defaults.iteritems():
        self.options[key]=value
    for key,value in options.iteritems():
        self.options[key]=value
    # Define Method Aliases if they are available
    if METHOD_ALIASES:
        for command in alias(self):
            exec(command)
    if file_path is not None:
        self.path=file_path
        self.__read_and_fix__()
    #build the row_formatting string, the original files have 4 decimals of precision for freq/gamma and 2 for Phase
    row_formatter=""
    for i in range(11):
        if i<6:
            row_formatter=row_formatter+"{"+str(i)+":.4f}{delimiter}"
        elif i==10:
            row_formatter=row_formatter+"{"+str(i)+":.2f}"
        else:
            row_formatter=row_formatter+"{"+str(i)+":.2f}{delimiter}"
    self.options["row_formatter_string"]=row_formatter
    AsciiDataTable.__init__(self,None,**self.options)
    if file_path is not None:
        self.path=file_path

def add_column(

self, column_name=None, column_type=None, column_data=None, format_string=None)

Adds a column with column_name, and column_type. If column data is supplied and it's length is the same as data(same number of rows) then it is added, else self.options['empty_character'] is added in each spot in the preceding rows

def add_column(self,column_name=None,column_type=None,column_data=None,format_string=None):
    """Adds a column with column_name, and column_type. If column data is supplied and it's length is the
    same as data(same number of rows) then it is added, else self.options['empty_character'] is added in each
    spot in the preceding rows"""
    original_column_names=self.column_names[:]
    try:
        self.column_names=original_column_names+[column_name]
        if self.options["column_types"]:
            old_column_types=self.options["column_types"][:]
            self.options["column_types"]=old_column_types+[column_type]
        if len(column_data) == len(self.data):
            for index,row in enumerate(self.data[:]):
                #print("{0} is {1}".format('self.data[index]',self.data[index]))
                #print("{0} is {1}".format('row',row))
                new_row=row[:]
                new_row.append(column_data[index])
                self.data[index]=new_row
        else:
            for index,row in enumerate(self.data[:]):
                self.data[index]=row.append(self.options['empty_value'])
                if column_data is not None:
                    for item in column_data:
                        empty_row=[self.options['empty_value'] for column in original_column_names]
                        empty_row.append(item)
                        self.add_row(empty_row)
        if self.options["row_formatter_string"] is None:
            pass
        else:
            if format_string is None:
                self.options["row_formatter_string"]=self.options["row_formatter_string"]+\
                                                             '{delimiter}'+"{"+str(len(self.column_names)-1)+"}"
            else:
                self.options["row_formatter_string"]=self.options["row_formatter_string"]+format_string
        #self.update_model()
    except:
        self.column_names=original_column_names
        print("Could not add columns")
        raise

def add_index(

self)

Adds a column with name index and values that are 0 referenced indices, does nothing if there is already a column with name index, always inserts it at the 0 position

def add_index(self):
    """Adds a column with name index and values that are 0 referenced indices, does nothing if there is
    already a column with name index, always inserts it at the 0 position"""
    if 'index' in self.column_names:
        print("Add Index passed")
        pass
    else:
        self.column_names.insert(0,'index')
        for index,row in enumerate(self.data):
            self.data[index].insert(0,index)
        if self.options['column_types']:
            self.options['column_types'].insert(0,'int')
        if self.options['row_formatter_string']:
            temp_formatter_list=self.options['row_formatter_string'].split("{delimiter}")
            iterated_row_formatter_list=[temp_formatter_list[i].replace(str(i),str(i+1))
                                         for i in range(len(temp_formatter_list))]
            new_formatter=string_list_collapse(iterated_row_formatter_list,string_delimiter="{delimiter}")
            self.options['row_formatter_string']='{0}{delimiter}'+new_formatter

def add_inline_comment(

self, comment='', line_number=None, string_position=None)

Adds an inline in the specified location

def add_inline_comment(self,comment="",line_number=None,string_position=None):
    "Adds an inline in the specified location"
    try:
        self.inline_comments.append([comment,line_number,string_position])
    except:pass

def add_row(

self, row_data)

Adds a single row given row_data which can be an ordered list/tuple or a dictionary with column names as keys

def add_row(self,row_data):
    """Adds a single row given row_data which can be an ordered list/tuple or a dictionary with
    column names as keys"""
    if len(row_data) not in [len(self.column_names),len(self.column_names)]:
        print(" could not add the row, dimensions do not match")
        return
    if type(row_data) in [ListType,np.ndarray]:
        self.data.append(row_data)
    elif type(row_data) in [DictionaryType]:
        data_list=[row_data[column_name] for column_name in self.column_names]
        self.data.append(data_list)

def build_string(

self, **temp_options)

Builds a string representation of the data table based on self.options, or temp_options. Passing temp_options does not permanently change the model

def build_string(self,**temp_options):
    """Builds a string representation of the data table based on self.options, or temp_options.
    Passing temp_options does not permanently change the model"""
    # store the original options to be put back after the string is made
    original_options=self.options
    for key,value in temp_options.iteritems():
        self.options[key]=value
    section_end=0
    next_section_begin=0
    if self.options['data_table_element_separator'] is None:
        inner_element_spacing=0
    else:
        inner_element_spacing=self.options['data_table_element_separator'].count('\n')-1
    string_out=""
    between_section=""
    if self.options['data_table_element_separator'] is not None:
        between_section=self.options['data_table_element_separator']
    if self.header is None:
        self.options['header_begin_line']=self.options['header_end_line']=None
        pass
    else:
        self.options["header_begin_line"]=0
        if self.data is None and self.column_names is None and self.footer is None:
            string_out=self.get_header_string()
            self.options["header_end_line"]=None
        else:
            string_out=self.get_header_string()+between_section
            last_header_line=self.get_header_string().count('\n')+1
            self.options["header_end_line"]=last_header_line
            next_section_begin=last_header_line+inner_element_spacing
    if self.column_names is None:
        self.options['column_names_begin_line']=self.options['column_names_end_line']=None
        pass
    else:
        self.options["column_names_begin_line"]=next_section_begin
        if self.data is None and self.footer is None:
            self.options["column_names_end_line"]=None
            string_out=string_out+self.get_column_names_string()
        else:
            string_out=string_out+self.get_column_names_string()+between_section
            last_column_names_line=self.get_column_names_string().count('\n')+\
                                   self.options["column_names_begin_line"]+1
            self.options["column_names_end_line"]=last_column_names_line
            next_section_begin=last_column_names_line+inner_element_spacing
    if self.data is None:
        self.options['data_begin_line']=self.options['data_end_line']=None
        pass
    else:
        self.options["data_begin_line"]=next_section_begin
        if self.footer is None:
            self.options["data_end_line"]=None
            string_out=string_out+self.get_data_string()
        else:
            string_out=string_out+self.get_data_string()+between_section
            last_data_line=self.get_data_string().count("\n")+\
                            self.options["data_begin_line"]+1
            self.options["data_end_line"]=last_data_line
            next_section_begin=last_data_line+inner_element_spacing
    if self.footer is None:
        self.options['footer_begin_line']=self.options['footer_end_line']=None
        pass
    else:
        self.options["footer_begin_line"]=next_section_begin
        string_out=string_out+self.get_footer_string()
        self.options['footer_end_line']=None
    # set the options back after the string has been made
    if self.inline_comments is None:
        pass
    else:
        lines=string_out.splitlines()
        for comment in self.inline_comments:
            lines=insert_inline_comment(lines,comment=comment[0],line_number=comment[1],
                                        string_position=comment[2],
                                        begin_token=self.options['inline_comment_begin'],
                                        end_token=self.options['inline_comment_end'])
        string_out=string_list_collapse(lines,string_delimiter='\n')
    self.options=original_options
    return string_out

def change_unit_prefix(

self, column_selector=None, old_prefix=None, new_prefix=None, unit='Hz')

Changes the prefix of the units of the column specified by column_selector (column name or index) example usage is self.change_unit_prefix(column_selector='Frequency',old_prefix=None,new_prefix='G',unit='Hz') to change a column from Hz to GHz. It updates the data values, column_descriptions, and column_units if they exist, see http://www.nist.gov/pml/wmd/metric/prefixes.cfm for possible prefixes

def change_unit_prefix(self,column_selector=None,old_prefix=None,new_prefix=None,unit='Hz'):
    """Changes the prefix of the units of the column specified by column_selector (column name or index)
    example usage is self.change_unit_prefix(column_selector='Frequency',old_prefix=None,new_prefix='G',unit='Hz')
    to change a column from Hz to GHz. It updates the data values, column_descriptions, and column_units if they
    exist, see http://www.nist.gov/pml/wmd/metric/prefixes.cfm for possible prefixes"""
    multipliers={"yotta":10.**24,"Y":10.**24,"zetta":10.**21,"Z":10.**21,"exa":10.**18,"E":10.**18,"peta":10.**15,
                 "P":10.**15,"tera":10.**12,"T":10.**12,"giga":10.**9,"G":10.**9,"mega":10.**6,"M":10.**6,
                 "kilo":10.**3,"k":10.**3,"hecto":10.**2,"h":10.**2,"deka":10.,"da":10.,None:1.,"":1.,
                 "deci":10.**-1,"d":10.**-1,"centi":10.**-2,"c":10.**-2,"milli":10.**-3,"m":10.**-3,
                 "micro":10.**-6,"mu":10.**-6,u"\u00B5":10.**-6,"nano":10.**-9,
                 "n":10.**-9,"pico":10.**-12,"p":10.**-12,"femto":10.**-15,
                 "f":10.**-15,"atto":10.**-18,"a":10.**-18,"zepto":10.**-21,"z":10.**-21,
                 "yocto":10.**-24,"y":10.**-24}
    # change column name into column index
    try:
        if old_prefix is None:
            old_prefix=""
        if new_prefix is None:
            new_prefix=""
        old_unit=old_prefix+unit
        new_unit=new_prefix+unit
        if column_selector in self.column_names:
            column_selector=self.column_names.index(column_selector)
        for index,row in enumerate(self.data):
            if type(self.data[index][column_selector]) in [FloatType,LongType]:
                #print "{0:e}".format(multipliers[old_prefix]/multipliers[new_prefix])
                self.data[index][column_selector]=\
                (multipliers[old_prefix]/multipliers[new_prefix])*self.data[index][column_selector]
            elif type(self.data[index][column_selector]) in [StringType,IntType]:
                self.data[index][column_selector]=\
                str((multipliers[old_prefix]/multipliers[new_prefix])*float(self.data[index][column_selector]))
            else:
                print type(self.data[index][column_selector])
                raise
        if self.options["column_descriptions"] is not None:
            old=self.options["column_descriptions"][column_selector]
            self.options["column_descriptions"][column_selector]=old.replace(old_unit,new_unit)
        if self.options["column_units"] is not None:
            old=self.options["column_units"][column_selector]
            self.options["column_units"][column_selector]=old.replace(old_unit,new_unit)
        if re.search(old_unit,self.column_names[column_selector]):
            old=self.column_names[column_selector]
            self.column_names[column_selector]=old.replace(old_unit,new_unit)
    except:
        print("Could not change the unit prefix of column {0}".format(column_selector))
        raise

def find_line(

self, begin_token)

Finds the first line that has begin token in it

def find_line(self,begin_token):
    """Finds the first line that has begin token in it"""
    for index,line in enumerate(self.lines):
        if re.search(begin_token,line,re.IGNORECASE):
            return index

def get_column(

self, column_name=None, column_index=None)

Returns a column as a list given a column name or column index

def get_column(self,column_name=None,column_index=None):
    """Returns a column as a list given a column name or column index"""
    if column_name is None:
        if column_index is None:
            return
        else:
            column_selector=column_index
    else:
        column_selector=self.column_names.index(column_name)
    out_list=[self.data[i][column_selector] for i in range(len(self.data))]
    return out_list

def get_column_names_string(

self)

Returns the column names as a string using options

def get_column_names_string(self):
    "Returns the column names as a string using options"
    string_out=""
    # This writes the column_names
    column_name_begin=""
    column_name_end=""
    if self.options["column_names_begin_token"] is None:
        column_name_begin=""
    else:
        column_name_begin=self.options["column_names_begin_token"]
    if self.options["column_names_end_token"] is None:
        column_name_end=""
    else:
        column_name_end=self.options["column_names_end_token"]
    if self.column_names is None:
        string_out=""
    else:
        if type(self.column_names) is StringType:
            string_out=self.column_names
        elif type(self.column_names) is ListType:
            string_out=list_to_string(self.column_names,
                                      data_delimiter=self.options["column_names_delimiter"],end="")
            #print("{0} is {1}".format('string_out',string_out))
        else:
            string_out=ensure_string(self.column_names)
    #print column_name_begin,string_out,column_name_end
    return column_name_begin+string_out+column_name_end

def get_data_dictionary_list(

self, use_row_formatter_string=True)

Returns a python list with a row dictionary of form {column_name:data_column}

def get_data_dictionary_list(self,use_row_formatter_string=True):
    """Returns a python list with a row dictionary of form {column_name:data_column}"""
    try:
        if self.options["row_formatter_string"] is None:
            use_row_formatter_string=False
        if use_row_formatter_string:
            list_formatter=[item.replace("{"+str(index),"{0")
                            for index,item in enumerate(self.options["row_formatter_string"].split("{delimiter}"))]
        else:
            list_formatter=["{0}" for i in self.column_names]
        #print self.column_names
        #print self.data
        #print list_formatter
        #print len(self.column_names)==len(self.data[0])
        #print len(list_formatter)==len(self.data[0])
        #print type(self.data[0])
        out_list=[{self.column_names[i]:list_formatter[i].format(value) for i,value in enumerate(line)}
                  for line in self.data]
        return out_list
    except:
        print("Could not form a data_dictionary_list, check that row_formatter_string is properly defined")
        #print(out_list)
        raise

def get_data_string(

self)

Returns the data as a string

def get_data_string(self):
    "Returns the data as a string"
    #Todo:refactor to cut out unused lines
    string_out=""
    if self.data is None:
        string_out= ""
    else:
        if type(self.data) is StringType:
            if self.options['data_begin_token'] is None:
                   if self.options['data_end_token'] is None:
                       string_out=self.data
                   else:
                       if re.search(self.options['data_end_token'],self.data):
                           string_out=self.data
                       else:
                           string_out=self.data+self.options['data_end_token']
            else:
                    if self.options['data_end_token'] is None:
                        if re.match(self.options['data_begin_token'],self.data):
                            string_out=self.data
                        else:
                            string_out=self.options['data_begin_token']+self.data
        elif type(self.data) in [ListType,np.ndarray]:
            try:
                    #If the first row is a string, we should strip all the tokens and add them back in
                    if type(self.data[0]) is StringType:
                        if self.options['data_begin_token'] is None:
                            string_out=string_list_collapse(self.data)
                        else:
                            if re.match(self.options['data_begin_token'],self.data[0]):
                                if self.options['data_end_token'] is None:
                                    string_out=string_list_collapse(self.data)
                                else:
                                    if re.search(self.options['data_end_token'],self.data[-1]):
                                        string_out=string_list_collapse(self.data)
                                    else:
                                        string_out=string_list_collapse(self.data)+self.options['data_end_token']
                            else:
                                if self.options['data_end_token'] is None:
                                    string_out=self.options['data_begin_token']+string_list_collapse(self.data)
                                else:
                                    if re.search(self.options['data_end_token'],self.data[-1]):
                                        string_out=self.options['data_begin_token']+string_list_collapse(self.data)
                                    else:
                                        string_out=self.options['data_begin_token']+\
                                                   string_list_collapse(self.data)+\
                                                   self.options['data_end_token']
                    elif type(self.data[0]) in [ListType,np.ndarray]:
                        prefix=""
                        if self.options['data_begin_token'] is None:
                            if self.options['data_end_token'] is None:
                                string_out=list_list_to_string(self.data,data_delimiter=self.options['data_delimiter'],
                                                               row_formatter_string=self.options['row_formatter_string'],
                                                               line_begin=self.options["row_begin_token"],
                                                               line_end=self.options["row_end_token"])
                        else:
                            if self.options['data_end_token'] is None:
                                string_out=self.options['data_begin_token']+\
                                           list_list_to_string(self.data,
                                                               data_delimiter=self.options['data_delimiter'],
                                                               row_formatter_string=self.options['row_formatter_string'],
                                                               line_begin=self.options["row_begin_token"],
                                                               line_end=self.options["row_end_token"])
                            else:
                                string_out=self.options['data_begin_token']+\
                                           list_list_to_string(self.data,
                                                               data_delimiter=self.options['data_delimiter'],
                                                               row_formatter_string=\
                                                               self.options['row_formatter_string'],
                                                               line_begin=self.options["row_begin_token"],
                                                               line_end=self.options["row_end_token"])+\
                                                                self.options['data_end_token']
                    else:
                        string_out=list_to_string(self.data,
                                                  data_delimiter=self.options['data_delimiter'],
                                                  row_formatter_string=self.options['row_formatter_string'],
                                                  begin=self.options["row_begin_token"],
                                                  end=self.options["row_end_token"])
            except IndexError:
                pass
        else:
            string_out=ensure_string(self.data)
    return string_out

Returns the footer using options in self.options. If block comment is specified, and the footer is a list it will block comment out the footer. If comment_begin and comment_end are specified it will use those to represent each line of the footer. If footer_begin_token and/or footer_end_token are specified it will wrap the footer in those.

def get_header_string(

self)

Returns the header using options in self.options. If block comment is specified, and the header is a list it will block comment out the header. If comment_begin and comment_end are specified it will use those to represent each line of the header. If header_begin_token and/or header_end_token are specified it will wrap the header in those.

def get_header_string(self):
    """Returns the header using options in self.options. If block comment is specified, and the header is a
    list it will block comment out the header. If comment_begin and comment_end are specified it will use
    those to represent each line of the header. If header_begin_token and/or header_end_token are specified it
     will wrap the header in those.
    """
    string_out=""
    header_begin=""
    header_end=""
    if self.options["header_begin_token"] is None:
        header_begin=""
    else:
        header_begin=self.options["header_begin_token"]
    if self.options["header_end_token"] is None:
        header_end=""
    else:
        header_end=self.options["header_end_token"]
    # This writes the header
    if self.header is None:
        string_out= ""
    elif self.options["header_line_types"] is not None:
        for index,line in enumerate(self.options["header_line_types"]):
            if index == len(self.options["header_line_types"])-1:
                end=''
            else:
                end='\n'
            if line in ['header','header_line','normal']:
                string_out=string_out+self.header[index]+end
            elif line in ['line_comment','comment']:
                string_out=string_out+line_comment_string(self.header[index],
                                           comment_begin=self.options["comment_begin"],
                                           comment_end=self.options["comment_end"])+end
            elif line in ['block_comment','block']:
                if index-1<0:
                    block_comment_begin=index
                    block_comment_end=index+2
                    continue
                elif self.options["header_line_types"][index-1] not in ['block_comment','block']:
                    block_comment_begin=index
                    block_comment_end=index+2
                    continue
                else:
                    if index+1>len(self.options["header_line_types"])-1:
                        string_out=string_out+line_list_comment_string(self.header[block_comment_begin:],
                                                                       comment_begin=self.options['block_comment_begin'],
                                                                         comment_end=self.options['block_comment_end'],
                                                                       block=True)+end
                    elif self.options["header_line_types"][index+1] in ['block_comment','block']:
                        block_comment_end+=1
                    else:
                        string_out=string_out+\
                                   line_list_comment_string(self.header[block_comment_begin:block_comment_end],
                                                            comment_begin=self.options['block_comment_begin'],
                                                            comment_end=self.options['block_comment_end'],
                                                            block=True)+end
            else:
                string_out=string_out+line
    elif self.options['treat_header_as_comment'] in [None,True] and self.options["header_line_types"] in [None]:
        # Just happens if the user has set self.header manually
        if type(self.header) is StringType:
            string_out=line_comment_string(self.header,
                                           comment_begin=self.options["comment_begin"],
                                           comment_end=self.options["comment_end"])
            #string_out=re.sub('\n','',string_out,count=1)
        elif type(self.header) is ListType:
            if self.options['block_comment_begin'] is None:
                if self.options['comment_begin'] is None:
                    string_out=string_list_collapse(self.header)
                else:
                    string_out=line_list_comment_string(self.header,comment_begin=self.options['comment_begin'],
                                                    comment_end=self.options['comment_end'])
                    lines_out=string_out.splitlines()
                    # if re.search('\n',self.options['comment_end']):
                    #     string_out=re.sub('\n','',string_out,count=1)
                    #self.options["header_line_types"]=["line_comment" for line in self.header]
            else:
                string_out=line_list_comment_string(self.header,comment_begin=self.options['block_comment_begin'],
                                                    comment_end=self.options['block_comment_end'],block=True)
                #self.options["header_line_types"]=["block_comment" for line in self.header]
    else:
        string_out=ensure_string(self.header,list_delimiter="\n",end_if_list="")
    return header_begin+string_out+header_end

def get_options(

self)

Prints the option list

def get_options(self):
    "Prints the option list"
    for key,value in self.options.iteritems():
        print("{0} = {1}".format(key,value))

def get_options_by_element(

self, element_name)

returns a dictionary of all the options that have to do with element. Element must be header,column_names,data, or footer

def get_options_by_element(self,element_name):
    """ returns a dictionary
     of all the options that have to do with element. Element must be header,column_names,data, or footer"""
    keys_regarding_element=filter(lambda x: re.search(element_name,str(x),re.IGNORECASE),self.options.keys())
    out_dictionary={key:self.options[key] for key in keys_regarding_element}
    #print out_dictionary
    return out_dictionary

def get_row(

self, row_index=None)

Returns the row as a list specified by row_index

def get_row(self,row_index=None):
    """Returns the row as a list specified by row_index"""
    if row_index is None:
        return
    else:
        return self.data[row_index]

def is_valid(

self)

Returns True if ascii table conforms to its specification given by its own options

def is_valid(self):
    """Returns True if ascii table conforms to its specification given by its own options"""
    options={}
    for key,value in self.options.iteritems():
        options[key]=value
        # print("self.options[{0}] is {1} ".format(key,value))
    for element in self.elements:
        if self.__dict__[element] is None:
            options[element]=None
        else:
            options[element]=[]
    options["validate"]=True
    newtable=AsciiDataTable(None,**options)
    lines=self.build_string().splitlines()
    for index,line in enumerate(lines):
        lines[index]=line+"\n"
    newtable.lines=lines
    newtable.__parse__()
    # print newtable.data
    # print newtable.column_names
    # print newtable
    #print_comparison(newtable.footer,None)
    newtable.update_model()
    # The new table rows are not being coerced into the right format
    #print newtable
    #newtable.update_model()
    #print newtable.options
    #print self.options
    #print newtable.data
    # print newtable.options==self.options
    # for option_key,option_value in newtable.options.iteritems():
    #     print("New Table Option {0} is {1} ".format(option_key,option_value))
    #     print("self.options[{0}] is {1} ".format(option_key,self.options[option_key]))
    #     print_comparison(option_value,self.options[option_key])
    # #print self
    return self==newtable

def lines_defined(

self)

If begin_line and end_line for all elements that are None are defined returns True

def lines_defined(self):
    """If begin_line and end_line for all elements that are None are defined returns True"""
    truth_table=[]
    last_element=""
    output=False
    for index,element in enumerate(self.elements):
        if element not in ['inline_comments','metadata'] and self.__dict__[element] is not None:
            try:
                last_element=element
                if not None in [self.options['%s_begin_line'%element],self.options['%s_end_line'%element]]:
                    truth_table.append(True)
                else:
                     truth_table.append(False)
            except:
                return False
    #print truth_table
    # The last_line of the last element is fine to be none
    if truth_table[-1] is False:
        if self.options['%s_begin_line'%last_element] is not None:
            truth_table[-1]=True
    if False in truth_table:
        output=False
    else:
        output=True
    #print output
    return output

Moves the DataTable's footer to the header and updates the model

def remove_column(

self, column_name=None, column_index=None)

Removes the column specified by column_name or column_index and updates the model. The column is removed from column_names, data and if present column_types, column_descriptions and row formatter

def remove_column(self,column_name=None,column_index=None):
    """Removes the column specified by column_name or column_index and updates the model. The column is removed from
    column_names, data and if present column_types, column_descriptions and row formatter"""
    pass

def remove_row(

self, row_index)

Removes the row specified by row_index and updates the model. Note index is relative to the data attribute so to remove the first row use row_index=0 and the last data row is row_index=-1

def remove_row(self,row_index):
    """Removes the row specified by row_index and updates the model. Note index is relative to the
    data attribute so to remove the first row use row_index=0 and the last data row is row_index=-1"""
    self.data.pop(row_index)
    self.update_model()

def save(

self, path=None, **temp_options)

" Saves the file, to save in another ascii format specify elements in temp_options, the options specified do not permanently change the object's options. If path is supplied it saves the file to that path otherwise uses the object's attribute path to define the saving location

def save(self,path=None,**temp_options):
    """" Saves the file, to save in another ascii format specify elements in temp_options, the options
    specified do not permanently change the object's options. If path is supplied it saves the file to that path
    otherwise uses the object's attribute path to define the saving location """
    original_options=self.options
    for key,value in temp_options.iteritems():
        self.options[key]=value
    out_string=self.build_string(**temp_options)
    if path is None:
        path=self.path
    file_out=open(path,'w')
    file_out.write(out_string)
    file_out.close()
    self.options=original_options

def save_schema(

self, path=None, format=None)

Saves the tables options as a text file or pickled dictionary (default). If no name is supplied, autonames it and saves

def save_schema(self,path=None,format=None):
    """Saves the tables options as a text file or pickled dictionary (default).
    If no name is supplied, autonames it and saves"""
    if path is None:
        path=auto_name(self.name.replace('.'+self.options["extension"],""),'Schema',self.options["directory"],'txt')
    if format in [None,'python','pickle']:
        pickle.dump(self.options,open(path,'wb'))
    elif format in ['txt','text','.txt']:
        file_out=open(path,'w')
        keys=self.options.keys()
        keys.sort()
        for key in keys:
            out_key=str(key).replace("\n","\\n")
            out_value=str(self.options[key]).replace("\n","\\n")
            file_out.write("{0} : {1} \n".format(out_key,out_value))
        file_out.close()

def show(

self)

def show(self):
    fig, (ax0, ax1) = plt.subplots(nrows=2, sharex=True)
    ax0.errorbar(self.get_column('Frequency'),self.get_column('mag'),
         yerr=self.get_column('uMg'),fmt='k--')
    ax0.set_title('Magnitude S11')
    ax1.errorbar(self.get_column('Frequency'),self.get_column('arg'),
         yerr=self.get_column('uAg'),fmt='ro')
    ax1.set_title('Phase S11')
    plt.show()

def update_column_names(

self)

Update column names adds the value x# for any column that exists in self.data that is not named

def update_column_names(self):
    """Update column names adds the value x# for any column that exists in self.data that is not named"""
    if self.data is None:
        return
    elif type(self.column_names) is StringType:
        self.column_names=split_row(self.column_names,self.options["column_names_delimiter"])
    elif self.column_names is None:
        column_names=[]
        for index,column in enumerate(self.data[0]):
            column_names.append("x"+str(index))
        self.column_names=column_names
        return
    elif len(self.column_names)==len(self.data[0]):
        return
    elif len(self.column_names) < len(self.data[0]):
        for index in range(len(self.column_names),len(self.data[0])):
            self.column_names.append("x"+str(index))
        return

def update_import_options(

self, import_table)

Updates the options in the import table

def update_import_options(self,import_table):
    """Updates the options in the import table"""
    for index,element in enumerate(['header','column_names','data','footer']):
        if self.__dict__[element] is not None:
            print("The {0} variable is {1}".format('index',index))
            print("The {0} variable is {1}".format('element',element))
            print("The {0} variable is {1}".format('import_table',import_table))
            [self.options['%s_begin_line'%element],
                            self.options['%s_end_line'%element],
                            self.options['%s_begin_token'%element],
                            self.options['%s_end_token'%element]]=import_table[index][:]

def update_index(

self)

Updates the index column if it exits, otherwise exits quietly

def update_index(self):
    """ Updates the index column if it exits, otherwise exits quietly
    """
    if 'index' not in self.column_names:
        return
    else:
        try:
            #This should be 0 but just in case
            index_column_number=self.column_names.index('index')
            for i in range(len(self.data)):
                self.data[i][index_column_number]=i
        except:
            pass

def update_model(

self)

Updates the model after a change has been made. If you add anything to the attributes of the model, or change this updates the values. If the model has an index column it will make sure the numbers are correct. In addition, it will update the options dictionary to reflect added rows, changes in deliminators etc.

def update_model(self):
    """Updates the model after a change has been made. If you add anything to the attributes of the model,
    or change this updates the values. If the model has an index column it will make sure the numbers are correct.
    In addition, it will update the options dictionary to reflect added rows, changes in deliminators etc.  """
    if self.column_names is not None and 'index' in self.column_names:
       self.update_index()
    #make sure there are no "\n" characters in the element lists (if so replace them with "") for data this is
    # done on import
    list_types=["header","column_names","footer"]
    for element in list_types:
        if self.__dict__[element] is not None:
            for index,item in enumerate(self.__dict__[element]):
                self.__dict__[element][index]=item.replace("\n","")
    self.update_column_names()
    if self.data is not None:
        self.data=convert_all_rows(self.data,self.options["column_types"])
    self.string=self.build_string()
    self.lines=self.string.splitlines()

class OnePortRawModel

Class that deals with the OnePort Raw Files after conversion to Ascii using Ron Ginley's converter. These files typically have header information seperated from data by !! Header format is: Line 1: Spid$ - identification of type of system used Line 2: Systemletter$ - letter name indicating which system was used Line 3: Conncal$ - connector type from the system calibration Line 4: Connectors$ - connector type used for the measurement Line 5: Meastype$ - type of measurement (basically 1-port, 2-port or power) Line 6: Datea$ - date of measurement Line 7: Timea$ - time of measurement Line 8: Programm$ - name of program used Line 9: Rev$ - program revision Line 10: Opr$ - operator Line 11: Cfile$ - calibration name Line 12: Cdate$ - calibration date Line 13: Sport - identification of which port or direction was used for measurement Line 14: Numconnects ? number of disconnect/reconnect cycles Line 15: Numrepeats ? number of repeat measurements for each connect (usually 1) Line 16: Nbs ? not sure Line 17: Nfreq ? number of frequencies Line 18: Startfreq ? data row pointer for bdat files Line 19: Devicedescript$ - description of device being measured or of test being done Line 20: Devicenum$ - Identifying number for device ? used for file names

class OnePortRawModel(AsciiDataTable):
    """ Class that deals with the OnePort Raw Files after conversion to Ascii using Ron Ginley's converter.
    These files typically have header information seperated from data by !!
    Header format is:
    Line 1:		Spid$ - identification of type of system used
    Line 2:		Systemletter$ - letter name indicating which system was used
    Line 3:		Conncal$ - connector type from the system calibration
    Line 4:		Connectors$ - connector type used for the measurement
    Line 5:		Meastype$ - type of measurement (basically 1-port, 2-port or power)
    Line 6:		Datea$ - date of measurement
    Line 7:		Timea$ - time of measurement
    Line 8:		Programm$ - name of program used
    Line 9:		Rev$ - program revision
    Line 10:	Opr$ - operator
    Line 11:	Cfile$ - calibration name
    Line 12:	Cdate$ - calibration date
    Line 13:	Sport - identification of which port or direction was used for measurement
    Line 14:	Numconnects ? number of disconnect/reconnect cycles
    Line 15:	Numrepeats ? number of repeat measurements for each connect (usually 1)
    Line 16:	Nbs ? not sure
    Line 17:	Nfreq ? number of frequencies
    Line 18:	Startfreq ? data row pointer for bdat files
    Line 19:	Devicedescript$ - description of device being measured or of test being done
    Line 20:	Devicenum$ - Identifying number for device ? used for file names
    """
    def __init__(self,file_path=None,**options):
        """Initializes the OnePortRaw class, if a file_path is specified opens an existing file, else creates an
        empty container"""
        defaults= {"data_delimiter": ",", "column_names_delimiter": ",", "specific_descriptor": 'One_Port_Raw',
                   "general_descriptor": 'Sparameter', "extension": 'txt', "comment_begin": "#", "comment_end": "\n",
                   "column_types": ['float','int','int','float','float','float','float'],
                   "column_descriptions": {"Frequency":"Frequency in GHz",
                                           "Direction":"Direction of connects, may be unused",
                                           "Connect":"Connect number", "magS11":"Linear magnitude for port 1",
                                           "argS11":"Phase in degrees for port 1",
                                           "magS22":"Linear magnitude for port 2",
                                           "argS22":"Phase in degrees for port 2"}, "header": None,
                   "column_names": ["Frequency","Direction","Connect", "magS11",
                                    "argS11","magS22",  "argS22"],
                   "column_names_end_token": "\n", "data": None,
                   'row_formatter_string': "{0:.5f}{delimiter}{1}{delimiter}{2}{delimiter}"
                                           "{3:.4f}{delimiter}{4:.2f}{delimiter}{5:.4f}{delimiter}{6:.2f}",
                   "data_table_element_separator": None}
        self.options={}
        for key,value in defaults.iteritems():
            self.options[key]=value
        for key,value in options.iteritems():
            self.options[key]=value

        # Define Method Aliases if they are available
        if METHOD_ALIASES:
            for command in alias(self):
                exec(command)
        if file_path is not None:
            self.__read_and_fix__(file_path)
        if COMBINE_S11_S22:
            self.options['row_formatter_string']= "{0:.5f}{delimiter}{1}{delimiter}{2}{delimiter}{3:.4f}{delimiter}{4:.2f}"
            self.options["column_types"]= ['float','int','int','float','float']
            self.options["column_names"]=["Frequency","Direction","Connect", "mag","arg"]
            self.options["column_descriptions"]= {"Frequency":"Frequency in GHz",
                                           "Direction":"Direction of connects, may be unused",
                                           "Connect":"Connect number", "mag":"Linear magnitude",
                                           "arg":"Phase in degrees"}
        AsciiDataTable.__init__(self,None,**self.options)
        self.path=file_path
        self.structure_metadata()


    def __read_and_fix__(self,file_path=None):
        """Inputs in the raw OnePortRaw file and fixes any problems with delimiters,etc."""
        lines=[]
        in_file=open(file_path,'r')
        for index,line in enumerate(in_file):
            lines.append(line)
            if re.match("!!",line):
                data_begin_line=index+1
        self.lines=lines
        in_file.close()
        parse_options={"row_end_token":'\n',
                       "row_pattern":make_row_match_string(self.options["column_names"]),
                       "column_names":self.options["column_names"],"column_types":self.options["column_types"]}
        data=parse_lines(lines[data_begin_line:],**parse_options)
        self.options["data"]=data
        self.options["header"]=lines[:data_begin_line-1]
        if COMBINE_S11_S22:
            new_data=[]
            for index,row in enumerate(self.options["data"][:]):
                new_row=[row[0],row[1],row[2],row[3]+row[5],row[4]+row[6]]
                new_data.append(new_row)
            self.options["data"]=new_data



    def structure_metadata(self):
        """Returns a dictionary of key,value pairs extracted from the header"""
        keys=["System_Id","System_Letter","Connector_Type_Calibration","Connector_Type_Measurement",
              "Measurement_Type","Measurement_Date","Measurement_Time","Program_Used","Program_Revision","Operator",
              "Calibration_Name","Calibration_Date","Port_Used","Number_Connects","Number_Repeats","Nbs",
              "Number_Frequencies","Start_Frequency",
              "Device_Description","Device_Id"]
        self.metadata={}
        if self.header is None:
            pass
        else:
            for index,key in enumerate(keys):
                self.metadata[key]=self.header[index].rstrip().lstrip()
    def show(self):
        fig, (ax0, ax1) = plt.subplots(nrows=2, sharex=True)
        if COMBINE_S11_S22:
            ax0.plot(self.get_column('Frequency'),self.get_column('mag'),'k--')
            ax1.plot(self.get_column('Frequency'),self.get_column('arg'),'ro')
        else:
            ax0.plot(self.get_column('Frequency'),self.get_column('magS11'),'k--')
            ax0.plot(self.get_column('Frequency'),self.get_column('magS22'),'k--')
            ax1.plot(self.get_column('Frequency'),self.get_column('argS11'),'ro')
            ax1.plot(self.get_column('Frequency'),self.get_column('argS22'),'ro')
        ax0.set_title('Magnitude S11')
        ax1.set_title('Phase S11')
        plt.show()

Ancestors (in MRO)

Instance variables

var options

var path

Methods

def __init__(

self, file_path=None, **options)

Initializes the OnePortRaw class, if a file_path is specified opens an existing file, else creates an empty container

def __init__(self,file_path=None,**options):
    """Initializes the OnePortRaw class, if a file_path is specified opens an existing file, else creates an
    empty container"""
    defaults= {"data_delimiter": ",", "column_names_delimiter": ",", "specific_descriptor": 'One_Port_Raw',
               "general_descriptor": 'Sparameter', "extension": 'txt', "comment_begin": "#", "comment_end": "\n",
               "column_types": ['float','int','int','float','float','float','float'],
               "column_descriptions": {"Frequency":"Frequency in GHz",
                                       "Direction":"Direction of connects, may be unused",
                                       "Connect":"Connect number", "magS11":"Linear magnitude for port 1",
                                       "argS11":"Phase in degrees for port 1",
                                       "magS22":"Linear magnitude for port 2",
                                       "argS22":"Phase in degrees for port 2"}, "header": None,
               "column_names": ["Frequency","Direction","Connect", "magS11",
                                "argS11","magS22",  "argS22"],
               "column_names_end_token": "\n", "data": None,
               'row_formatter_string': "{0:.5f}{delimiter}{1}{delimiter}{2}{delimiter}"
                                       "{3:.4f}{delimiter}{4:.2f}{delimiter}{5:.4f}{delimiter}{6:.2f}",
               "data_table_element_separator": None}
    self.options={}
    for key,value in defaults.iteritems():
        self.options[key]=value
    for key,value in options.iteritems():
        self.options[key]=value
    # Define Method Aliases if they are available
    if METHOD_ALIASES:
        for command in alias(self):
            exec(command)
    if file_path is not None:
        self.__read_and_fix__(file_path)
    if COMBINE_S11_S22:
        self.options['row_formatter_string']= "{0:.5f}{delimiter}{1}{delimiter}{2}{delimiter}{3:.4f}{delimiter}{4:.2f}"
        self.options["column_types"]= ['float','int','int','float','float']
        self.options["column_names"]=["Frequency","Direction","Connect", "mag","arg"]
        self.options["column_descriptions"]= {"Frequency":"Frequency in GHz",
                                       "Direction":"Direction of connects, may be unused",
                                       "Connect":"Connect number", "mag":"Linear magnitude",
                                       "arg":"Phase in degrees"}
    AsciiDataTable.__init__(self,None,**self.options)
    self.path=file_path
    self.structure_metadata()

def add_column(

self, column_name=None, column_type=None, column_data=None, format_string=None)

Adds a column with column_name, and column_type. If column data is supplied and it's length is the same as data(same number of rows) then it is added, else self.options['empty_character'] is added in each spot in the preceding rows

def add_column(self,column_name=None,column_type=None,column_data=None,format_string=None):
    """Adds a column with column_name, and column_type. If column data is supplied and it's length is the
    same as data(same number of rows) then it is added, else self.options['empty_character'] is added in each
    spot in the preceding rows"""
    original_column_names=self.column_names[:]
    try:
        self.column_names=original_column_names+[column_name]
        if self.options["column_types"]:
            old_column_types=self.options["column_types"][:]
            self.options["column_types"]=old_column_types+[column_type]
        if len(column_data) == len(self.data):
            for index,row in enumerate(self.data[:]):
                #print("{0} is {1}".format('self.data[index]',self.data[index]))
                #print("{0} is {1}".format('row',row))
                new_row=row[:]
                new_row.append(column_data[index])
                self.data[index]=new_row
        else:
            for index,row in enumerate(self.data[:]):
                self.data[index]=row.append(self.options['empty_value'])
                if column_data is not None:
                    for item in column_data:
                        empty_row=[self.options['empty_value'] for column in original_column_names]
                        empty_row.append(item)
                        self.add_row(empty_row)
        if self.options["row_formatter_string"] is None:
            pass
        else:
            if format_string is None:
                self.options["row_formatter_string"]=self.options["row_formatter_string"]+\
                                                             '{delimiter}'+"{"+str(len(self.column_names)-1)+"}"
            else:
                self.options["row_formatter_string"]=self.options["row_formatter_string"]+format_string
        #self.update_model()
    except:
        self.column_names=original_column_names
        print("Could not add columns")
        raise

def add_index(

self)

Adds a column with name index and values that are 0 referenced indices, does nothing if there is already a column with name index, always inserts it at the 0 position

def add_index(self):
    """Adds a column with name index and values that are 0 referenced indices, does nothing if there is
    already a column with name index, always inserts it at the 0 position"""
    if 'index' in self.column_names:
        print("Add Index passed")
        pass
    else:
        self.column_names.insert(0,'index')
        for index,row in enumerate(self.data):
            self.data[index].insert(0,index)
        if self.options['column_types']:
            self.options['column_types'].insert(0,'int')
        if self.options['row_formatter_string']:
            temp_formatter_list=self.options['row_formatter_string'].split("{delimiter}")
            iterated_row_formatter_list=[temp_formatter_list[i].replace(str(i),str(i+1))
                                         for i in range(len(temp_formatter_list))]
            new_formatter=string_list_collapse(iterated_row_formatter_list,string_delimiter="{delimiter}")
            self.options['row_formatter_string']='{0}{delimiter}'+new_formatter

def add_inline_comment(

self, comment='', line_number=None, string_position=None)

Adds an inline in the specified location

def add_inline_comment(self,comment="",line_number=None,string_position=None):
    "Adds an inline in the specified location"
    try:
        self.inline_comments.append([comment,line_number,string_position])
    except:pass

def add_row(

self, row_data)

Adds a single row given row_data which can be an ordered list/tuple or a dictionary with column names as keys

def add_row(self,row_data):
    """Adds a single row given row_data which can be an ordered list/tuple or a dictionary with
    column names as keys"""
    if len(row_data) not in [len(self.column_names),len(self.column_names)]:
        print(" could not add the row, dimensions do not match")
        return
    if type(row_data) in [ListType,np.ndarray]:
        self.data.append(row_data)
    elif type(row_data) in [DictionaryType]:
        data_list=[row_data[column_name] for column_name in self.column_names]
        self.data.append(data_list)

def build_string(

self, **temp_options)

Builds a string representation of the data table based on self.options, or temp_options. Passing temp_options does not permanently change the model

def build_string(self,**temp_options):
    """Builds a string representation of the data table based on self.options, or temp_options.
    Passing temp_options does not permanently change the model"""
    # store the original options to be put back after the string is made
    original_options=self.options
    for key,value in temp_options.iteritems():
        self.options[key]=value
    section_end=0
    next_section_begin=0
    if self.options['data_table_element_separator'] is None:
        inner_element_spacing=0
    else:
        inner_element_spacing=self.options['data_table_element_separator'].count('\n')-1
    string_out=""
    between_section=""
    if self.options['data_table_element_separator'] is not None:
        between_section=self.options['data_table_element_separator']
    if self.header is None:
        self.options['header_begin_line']=self.options['header_end_line']=None
        pass
    else:
        self.options["header_begin_line"]=0
        if self.data is None and self.column_names is None and self.footer is None:
            string_out=self.get_header_string()
            self.options["header_end_line"]=None
        else:
            string_out=self.get_header_string()+between_section
            last_header_line=self.get_header_string().count('\n')+1
            self.options["header_end_line"]=last_header_line
            next_section_begin=last_header_line+inner_element_spacing
    if self.column_names is None:
        self.options['column_names_begin_line']=self.options['column_names_end_line']=None
        pass
    else:
        self.options["column_names_begin_line"]=next_section_begin
        if self.data is None and self.footer is None:
            self.options["column_names_end_line"]=None
            string_out=string_out+self.get_column_names_string()
        else:
            string_out=string_out+self.get_column_names_string()+between_section
            last_column_names_line=self.get_column_names_string().count('\n')+\
                                   self.options["column_names_begin_line"]+1
            self.options["column_names_end_line"]=last_column_names_line
            next_section_begin=last_column_names_line+inner_element_spacing
    if self.data is None:
        self.options['data_begin_line']=self.options['data_end_line']=None
        pass
    else:
        self.options["data_begin_line"]=next_section_begin
        if self.footer is None:
            self.options["data_end_line"]=None
            string_out=string_out+self.get_data_string()
        else:
            string_out=string_out+self.get_data_string()+between_section
            last_data_line=self.get_data_string().count("\n")+\
                            self.options["data_begin_line"]+1
            self.options["data_end_line"]=last_data_line
            next_section_begin=last_data_line+inner_element_spacing
    if self.footer is None:
        self.options['footer_begin_line']=self.options['footer_end_line']=None
        pass
    else:
        self.options["footer_begin_line"]=next_section_begin
        string_out=string_out+self.get_footer_string()
        self.options['footer_end_line']=None
    # set the options back after the string has been made
    if self.inline_comments is None:
        pass
    else:
        lines=string_out.splitlines()
        for comment in self.inline_comments:
            lines=insert_inline_comment(lines,comment=comment[0],line_number=comment[1],
                                        string_position=comment[2],
                                        begin_token=self.options['inline_comment_begin'],
                                        end_token=self.options['inline_comment_end'])
        string_out=string_list_collapse(lines,string_delimiter='\n')
    self.options=original_options
    return string_out

def change_unit_prefix(

self, column_selector=None, old_prefix=None, new_prefix=None, unit='Hz')

Changes the prefix of the units of the column specified by column_selector (column name or index) example usage is self.change_unit_prefix(column_selector='Frequency',old_prefix=None,new_prefix='G',unit='Hz') to change a column from Hz to GHz. It updates the data values, column_descriptions, and column_units if they exist, see http://www.nist.gov/pml/wmd/metric/prefixes.cfm for possible prefixes

def change_unit_prefix(self,column_selector=None,old_prefix=None,new_prefix=None,unit='Hz'):
    """Changes the prefix of the units of the column specified by column_selector (column name or index)
    example usage is self.change_unit_prefix(column_selector='Frequency',old_prefix=None,new_prefix='G',unit='Hz')
    to change a column from Hz to GHz. It updates the data values, column_descriptions, and column_units if they
    exist, see http://www.nist.gov/pml/wmd/metric/prefixes.cfm for possible prefixes"""
    multipliers={"yotta":10.**24,"Y":10.**24,"zetta":10.**21,"Z":10.**21,"exa":10.**18,"E":10.**18,"peta":10.**15,
                 "P":10.**15,"tera":10.**12,"T":10.**12,"giga":10.**9,"G":10.**9,"mega":10.**6,"M":10.**6,
                 "kilo":10.**3,"k":10.**3,"hecto":10.**2,"h":10.**2,"deka":10.,"da":10.,None:1.,"":1.,
                 "deci":10.**-1,"d":10.**-1,"centi":10.**-2,"c":10.**-2,"milli":10.**-3,"m":10.**-3,
                 "micro":10.**-6,"mu":10.**-6,u"\u00B5":10.**-6,"nano":10.**-9,
                 "n":10.**-9,"pico":10.**-12,"p":10.**-12,"femto":10.**-15,
                 "f":10.**-15,"atto":10.**-18,"a":10.**-18,"zepto":10.**-21,"z":10.**-21,
                 "yocto":10.**-24,"y":10.**-24}
    # change column name into column index
    try:
        if old_prefix is None:
            old_prefix=""
        if new_prefix is None:
            new_prefix=""
        old_unit=old_prefix+unit
        new_unit=new_prefix+unit
        if column_selector in self.column_names:
            column_selector=self.column_names.index(column_selector)
        for index,row in enumerate(self.data):
            if type(self.data[index][column_selector]) in [FloatType,LongType]:
                #print "{0:e}".format(multipliers[old_prefix]/multipliers[new_prefix])
                self.data[index][column_selector]=\
                (multipliers[old_prefix]/multipliers[new_prefix])*self.data[index][column_selector]
            elif type(self.data[index][column_selector]) in [StringType,IntType]:
                self.data[index][column_selector]=\
                str((multipliers[old_prefix]/multipliers[new_prefix])*float(self.data[index][column_selector]))
            else:
                print type(self.data[index][column_selector])
                raise
        if self.options["column_descriptions"] is not None:
            old=self.options["column_descriptions"][column_selector]
            self.options["column_descriptions"][column_selector]=old.replace(old_unit,new_unit)
        if self.options["column_units"] is not None:
            old=self.options["column_units"][column_selector]
            self.options["column_units"][column_selector]=old.replace(old_unit,new_unit)
        if re.search(old_unit,self.column_names[column_selector]):
            old=self.column_names[column_selector]
            self.column_names[column_selector]=old.replace(old_unit,new_unit)
    except:
        print("Could not change the unit prefix of column {0}".format(column_selector))
        raise

def find_line(

self, begin_token)

Finds the first line that has begin token in it

def find_line(self,begin_token):
    """Finds the first line that has begin token in it"""
    for index,line in enumerate(self.lines):
        if re.search(begin_token,line,re.IGNORECASE):
            return index

def get_column(

self, column_name=None, column_index=None)

Returns a column as a list given a column name or column index

def get_column(self,column_name=None,column_index=None):
    """Returns a column as a list given a column name or column index"""
    if column_name is None:
        if column_index is None:
            return
        else:
            column_selector=column_index
    else:
        column_selector=self.column_names.index(column_name)
    out_list=[self.data[i][column_selector] for i in range(len(self.data))]
    return out_list

def get_column_names_string(

self)

Returns the column names as a string using options

def get_column_names_string(self):
    "Returns the column names as a string using options"
    string_out=""
    # This writes the column_names
    column_name_begin=""
    column_name_end=""
    if self.options["column_names_begin_token"] is None:
        column_name_begin=""
    else:
        column_name_begin=self.options["column_names_begin_token"]
    if self.options["column_names_end_token"] is None:
        column_name_end=""
    else:
        column_name_end=self.options["column_names_end_token"]
    if self.column_names is None:
        string_out=""
    else:
        if type(self.column_names) is StringType:
            string_out=self.column_names
        elif type(self.column_names) is ListType:
            string_out=list_to_string(self.column_names,
                                      data_delimiter=self.options["column_names_delimiter"],end="")
            #print("{0} is {1}".format('string_out',string_out))
        else:
            string_out=ensure_string(self.column_names)
    #print column_name_begin,string_out,column_name_end
    return column_name_begin+string_out+column_name_end

def get_data_dictionary_list(

self, use_row_formatter_string=True)

Returns a python list with a row dictionary of form {column_name:data_column}

def get_data_dictionary_list(self,use_row_formatter_string=True):
    """Returns a python list with a row dictionary of form {column_name:data_column}"""
    try:
        if self.options["row_formatter_string"] is None:
            use_row_formatter_string=False
        if use_row_formatter_string:
            list_formatter=[item.replace("{"+str(index),"{0")
                            for index,item in enumerate(self.options["row_formatter_string"].split("{delimiter}"))]
        else:
            list_formatter=["{0}" for i in self.column_names]
        #print self.column_names
        #print self.data
        #print list_formatter
        #print len(self.column_names)==len(self.data[0])
        #print len(list_formatter)==len(self.data[0])
        #print type(self.data[0])
        out_list=[{self.column_names[i]:list_formatter[i].format(value) for i,value in enumerate(line)}
                  for line in self.data]
        return out_list
    except:
        print("Could not form a data_dictionary_list, check that row_formatter_string is properly defined")
        #print(out_list)
        raise

def get_data_string(

self)

Returns the data as a string

def get_data_string(self):
    "Returns the data as a string"
    #Todo:refactor to cut out unused lines
    string_out=""
    if self.data is None:
        string_out= ""
    else:
        if type(self.data) is StringType:
            if self.options['data_begin_token'] is None:
                   if self.options['data_end_token'] is None:
                       string_out=self.data
                   else:
                       if re.search(self.options['data_end_token'],self.data):
                           string_out=self.data
                       else:
                           string_out=self.data+self.options['data_end_token']
            else:
                    if self.options['data_end_token'] is None:
                        if re.match(self.options['data_begin_token'],self.data):
                            string_out=self.data
                        else:
                            string_out=self.options['data_begin_token']+self.data
        elif type(self.data) in [ListType,np.ndarray]:
            try:
                    #If the first row is a string, we should strip all the tokens and add them back in
                    if type(self.data[0]) is StringType:
                        if self.options['data_begin_token'] is None:
                            string_out=string_list_collapse(self.data)
                        else:
                            if re.match(self.options['data_begin_token'],self.data[0]):
                                if self.options['data_end_token'] is None:
                                    string_out=string_list_collapse(self.data)
                                else:
                                    if re.search(self.options['data_end_token'],self.data[-1]):
                                        string_out=string_list_collapse(self.data)
                                    else:
                                        string_out=string_list_collapse(self.data)+self.options['data_end_token']
                            else:
                                if self.options['data_end_token'] is None:
                                    string_out=self.options['data_begin_token']+string_list_collapse(self.data)
                                else:
                                    if re.search(self.options['data_end_token'],self.data[-1]):
                                        string_out=self.options['data_begin_token']+string_list_collapse(self.data)
                                    else:
                                        string_out=self.options['data_begin_token']+\
                                                   string_list_collapse(self.data)+\
                                                   self.options['data_end_token']
                    elif type(self.data[0]) in [ListType,np.ndarray]:
                        prefix=""
                        if self.options['data_begin_token'] is None:
                            if self.options['data_end_token'] is None:
                                string_out=list_list_to_string(self.data,data_delimiter=self.options['data_delimiter'],
                                                               row_formatter_string=self.options['row_formatter_string'],
                                                               line_begin=self.options["row_begin_token"],
                                                               line_end=self.options["row_end_token"])
                        else:
                            if self.options['data_end_token'] is None:
                                string_out=self.options['data_begin_token']+\
                                           list_list_to_string(self.data,
                                                               data_delimiter=self.options['data_delimiter'],
                                                               row_formatter_string=self.options['row_formatter_string'],
                                                               line_begin=self.options["row_begin_token"],
                                                               line_end=self.options["row_end_token"])
                            else:
                                string_out=self.options['data_begin_token']+\
                                           list_list_to_string(self.data,
                                                               data_delimiter=self.options['data_delimiter'],
                                                               row_formatter_string=\
                                                               self.options['row_formatter_string'],
                                                               line_begin=self.options["row_begin_token"],
                                                               line_end=self.options["row_end_token"])+\
                                                                self.options['data_end_token']
                    else:
                        string_out=list_to_string(self.data,
                                                  data_delimiter=self.options['data_delimiter'],
                                                  row_formatter_string=self.options['row_formatter_string'],
                                                  begin=self.options["row_begin_token"],
                                                  end=self.options["row_end_token"])
            except IndexError:
                pass
        else:
            string_out=ensure_string(self.data)
    return string_out

Returns the footer using options in self.options. If block comment is specified, and the footer is a list it will block comment out the footer. If comment_begin and comment_end are specified it will use those to represent each line of the footer. If footer_begin_token and/or footer_end_token are specified it will wrap the footer in those.

def get_header_string(

self)

Returns the header using options in self.options. If block comment is specified, and the header is a list it will block comment out the header. If comment_begin and comment_end are specified it will use those to represent each line of the header. If header_begin_token and/or header_end_token are specified it will wrap the header in those.

def get_header_string(self):
    """Returns the header using options in self.options. If block comment is specified, and the header is a
    list it will block comment out the header. If comment_begin and comment_end are specified it will use
    those to represent each line of the header. If header_begin_token and/or header_end_token are specified it
     will wrap the header in those.
    """
    string_out=""
    header_begin=""
    header_end=""
    if self.options["header_begin_token"] is None:
        header_begin=""
    else:
        header_begin=self.options["header_begin_token"]
    if self.options["header_end_token"] is None:
        header_end=""
    else:
        header_end=self.options["header_end_token"]
    # This writes the header
    if self.header is None:
        string_out= ""
    elif self.options["header_line_types"] is not None:
        for index,line in enumerate(self.options["header_line_types"]):
            if index == len(self.options["header_line_types"])-1:
                end=''
            else:
                end='\n'
            if line in ['header','header_line','normal']:
                string_out=string_out+self.header[index]+end
            elif line in ['line_comment','comment']:
                string_out=string_out+line_comment_string(self.header[index],
                                           comment_begin=self.options["comment_begin"],
                                           comment_end=self.options["comment_end"])+end
            elif line in ['block_comment','block']:
                if index-1<0:
                    block_comment_begin=index
                    block_comment_end=index+2
                    continue
                elif self.options["header_line_types"][index-1] not in ['block_comment','block']:
                    block_comment_begin=index
                    block_comment_end=index+2
                    continue
                else:
                    if index+1>len(self.options["header_line_types"])-1:
                        string_out=string_out+line_list_comment_string(self.header[block_comment_begin:],
                                                                       comment_begin=self.options['block_comment_begin'],
                                                                         comment_end=self.options['block_comment_end'],
                                                                       block=True)+end
                    elif self.options["header_line_types"][index+1] in ['block_comment','block']:
                        block_comment_end+=1
                    else:
                        string_out=string_out+\
                                   line_list_comment_string(self.header[block_comment_begin:block_comment_end],
                                                            comment_begin=self.options['block_comment_begin'],
                                                            comment_end=self.options['block_comment_end'],
                                                            block=True)+end
            else:
                string_out=string_out+line
    elif self.options['treat_header_as_comment'] in [None,True] and self.options["header_line_types"] in [None]:
        # Just happens if the user has set self.header manually
        if type(self.header) is StringType:
            string_out=line_comment_string(self.header,
                                           comment_begin=self.options["comment_begin"],
                                           comment_end=self.options["comment_end"])
            #string_out=re.sub('\n','',string_out,count=1)
        elif type(self.header) is ListType:
            if self.options['block_comment_begin'] is None:
                if self.options['comment_begin'] is None:
                    string_out=string_list_collapse(self.header)
                else:
                    string_out=line_list_comment_string(self.header,comment_begin=self.options['comment_begin'],
                                                    comment_end=self.options['comment_end'])
                    lines_out=string_out.splitlines()
                    # if re.search('\n',self.options['comment_end']):
                    #     string_out=re.sub('\n','',string_out,count=1)
                    #self.options["header_line_types"]=["line_comment" for line in self.header]
            else:
                string_out=line_list_comment_string(self.header,comment_begin=self.options['block_comment_begin'],
                                                    comment_end=self.options['block_comment_end'],block=True)
                #self.options["header_line_types"]=["block_comment" for line in self.header]
    else:
        string_out=ensure_string(self.header,list_delimiter="\n",end_if_list="")
    return header_begin+string_out+header_end

def get_options(

self)

Prints the option list

def get_options(self):
    "Prints the option list"
    for key,value in self.options.iteritems():
        print("{0} = {1}".format(key,value))

def get_options_by_element(

self, element_name)

returns a dictionary of all the options that have to do with element. Element must be header,column_names,data, or footer

def get_options_by_element(self,element_name):
    """ returns a dictionary
     of all the options that have to do with element. Element must be header,column_names,data, or footer"""
    keys_regarding_element=filter(lambda x: re.search(element_name,str(x),re.IGNORECASE),self.options.keys())
    out_dictionary={key:self.options[key] for key in keys_regarding_element}
    #print out_dictionary
    return out_dictionary

def get_row(

self, row_index=None)

Returns the row as a list specified by row_index

def get_row(self,row_index=None):
    """Returns the row as a list specified by row_index"""
    if row_index is None:
        return
    else:
        return self.data[row_index]

def is_valid(

self)

Returns True if ascii table conforms to its specification given by its own options

def is_valid(self):
    """Returns True if ascii table conforms to its specification given by its own options"""
    options={}
    for key,value in self.options.iteritems():
        options[key]=value
        # print("self.options[{0}] is {1} ".format(key,value))
    for element in self.elements:
        if self.__dict__[element] is None:
            options[element]=None
        else:
            options[element]=[]
    options["validate"]=True
    newtable=AsciiDataTable(None,**options)
    lines=self.build_string().splitlines()
    for index,line in enumerate(lines):
        lines[index]=line+"\n"
    newtable.lines=lines
    newtable.__parse__()
    # print newtable.data
    # print newtable.column_names
    # print newtable
    #print_comparison(newtable.footer,None)
    newtable.update_model()
    # The new table rows are not being coerced into the right format
    #print newtable
    #newtable.update_model()
    #print newtable.options
    #print self.options
    #print newtable.data
    # print newtable.options==self.options
    # for option_key,option_value in newtable.options.iteritems():
    #     print("New Table Option {0} is {1} ".format(option_key,option_value))
    #     print("self.options[{0}] is {1} ".format(option_key,self.options[option_key]))
    #     print_comparison(option_value,self.options[option_key])
    # #print self
    return self==newtable

def lines_defined(

self)

If begin_line and end_line for all elements that are None are defined returns True

def lines_defined(self):
    """If begin_line and end_line for all elements that are None are defined returns True"""
    truth_table=[]
    last_element=""
    output=False
    for index,element in enumerate(self.elements):
        if element not in ['inline_comments','metadata'] and self.__dict__[element] is not None:
            try:
                last_element=element
                if not None in [self.options['%s_begin_line'%element],self.options['%s_end_line'%element]]:
                    truth_table.append(True)
                else:
                     truth_table.append(False)
            except:
                return False
    #print truth_table
    # The last_line of the last element is fine to be none
    if truth_table[-1] is False:
        if self.options['%s_begin_line'%last_element] is not None:
            truth_table[-1]=True
    if False in truth_table:
        output=False
    else:
        output=True
    #print output
    return output

Moves the DataTable's footer to the header and updates the model

def remove_column(

self, column_name=None, column_index=None)

Removes the column specified by column_name or column_index and updates the model. The column is removed from column_names, data and if present column_types, column_descriptions and row formatter

def remove_column(self,column_name=None,column_index=None):
    """Removes the column specified by column_name or column_index and updates the model. The column is removed from
    column_names, data and if present column_types, column_descriptions and row formatter"""
    pass

def remove_row(

self, row_index)

Removes the row specified by row_index and updates the model. Note index is relative to the data attribute so to remove the first row use row_index=0 and the last data row is row_index=-1

def remove_row(self,row_index):
    """Removes the row specified by row_index and updates the model. Note index is relative to the
    data attribute so to remove the first row use row_index=0 and the last data row is row_index=-1"""
    self.data.pop(row_index)
    self.update_model()

def save(

self, path=None, **temp_options)

" Saves the file, to save in another ascii format specify elements in temp_options, the options specified do not permanently change the object's options. If path is supplied it saves the file to that path otherwise uses the object's attribute path to define the saving location

def save(self,path=None,**temp_options):
    """" Saves the file, to save in another ascii format specify elements in temp_options, the options
    specified do not permanently change the object's options. If path is supplied it saves the file to that path
    otherwise uses the object's attribute path to define the saving location """
    original_options=self.options
    for key,value in temp_options.iteritems():
        self.options[key]=value
    out_string=self.build_string(**temp_options)
    if path is None:
        path=self.path
    file_out=open(path,'w')
    file_out.write(out_string)
    file_out.close()
    self.options=original_options

def save_schema(

self, path=None, format=None)

Saves the tables options as a text file or pickled dictionary (default). If no name is supplied, autonames it and saves

def save_schema(self,path=None,format=None):
    """Saves the tables options as a text file or pickled dictionary (default).
    If no name is supplied, autonames it and saves"""
    if path is None:
        path=auto_name(self.name.replace('.'+self.options["extension"],""),'Schema',self.options["directory"],'txt')
    if format in [None,'python','pickle']:
        pickle.dump(self.options,open(path,'wb'))
    elif format in ['txt','text','.txt']:
        file_out=open(path,'w')
        keys=self.options.keys()
        keys.sort()
        for key in keys:
            out_key=str(key).replace("\n","\\n")
            out_value=str(self.options[key]).replace("\n","\\n")
            file_out.write("{0} : {1} \n".format(out_key,out_value))
        file_out.close()

def show(

self)

def show(self):
    fig, (ax0, ax1) = plt.subplots(nrows=2, sharex=True)
    if COMBINE_S11_S22:
        ax0.plot(self.get_column('Frequency'),self.get_column('mag'),'k--')
        ax1.plot(self.get_column('Frequency'),self.get_column('arg'),'ro')
    else:
        ax0.plot(self.get_column('Frequency'),self.get_column('magS11'),'k--')
        ax0.plot(self.get_column('Frequency'),self.get_column('magS22'),'k--')
        ax1.plot(self.get_column('Frequency'),self.get_column('argS11'),'ro')
        ax1.plot(self.get_column('Frequency'),self.get_column('argS22'),'ro')
    ax0.set_title('Magnitude S11')
    ax1.set_title('Phase S11')
    plt.show()

def structure_metadata(

self)

Returns a dictionary of key,value pairs extracted from the header

def structure_metadata(self):
    """Returns a dictionary of key,value pairs extracted from the header"""
    keys=["System_Id","System_Letter","Connector_Type_Calibration","Connector_Type_Measurement",
          "Measurement_Type","Measurement_Date","Measurement_Time","Program_Used","Program_Revision","Operator",
          "Calibration_Name","Calibration_Date","Port_Used","Number_Connects","Number_Repeats","Nbs",
          "Number_Frequencies","Start_Frequency",
          "Device_Description","Device_Id"]
    self.metadata={}
    if self.header is None:
        pass
    else:
        for index,key in enumerate(keys):
            self.metadata[key]=self.header[index].rstrip().lstrip()

def update_column_names(

self)

Update column names adds the value x# for any column that exists in self.data that is not named

def update_column_names(self):
    """Update column names adds the value x# for any column that exists in self.data that is not named"""
    if self.data is None:
        return
    elif type(self.column_names) is StringType:
        self.column_names=split_row(self.column_names,self.options["column_names_delimiter"])
    elif self.column_names is None:
        column_names=[]
        for index,column in enumerate(self.data[0]):
            column_names.append("x"+str(index))
        self.column_names=column_names
        return
    elif len(self.column_names)==len(self.data[0]):
        return
    elif len(self.column_names) < len(self.data[0]):
        for index in range(len(self.column_names),len(self.data[0])):
            self.column_names.append("x"+str(index))
        return

def update_import_options(

self, import_table)

Updates the options in the import table

def update_import_options(self,import_table):
    """Updates the options in the import table"""
    for index,element in enumerate(['header','column_names','data','footer']):
        if self.__dict__[element] is not None:
            print("The {0} variable is {1}".format('index',index))
            print("The {0} variable is {1}".format('element',element))
            print("The {0} variable is {1}".format('import_table',import_table))
            [self.options['%s_begin_line'%element],
                            self.options['%s_end_line'%element],
                            self.options['%s_begin_token'%element],
                            self.options['%s_end_token'%element]]=import_table[index][:]

def update_index(

self)

Updates the index column if it exits, otherwise exits quietly

def update_index(self):
    """ Updates the index column if it exits, otherwise exits quietly
    """
    if 'index' not in self.column_names:
        return
    else:
        try:
            #This should be 0 but just in case
            index_column_number=self.column_names.index('index')
            for i in range(len(self.data)):
                self.data[i][index_column_number]=i
        except:
            pass

def update_model(

self)

Updates the model after a change has been made. If you add anything to the attributes of the model, or change this updates the values. If the model has an index column it will make sure the numbers are correct. In addition, it will update the options dictionary to reflect added rows, changes in deliminators etc.

def update_model(self):
    """Updates the model after a change has been made. If you add anything to the attributes of the model,
    or change this updates the values. If the model has an index column it will make sure the numbers are correct.
    In addition, it will update the options dictionary to reflect added rows, changes in deliminators etc.  """
    if self.column_names is not None and 'index' in self.column_names:
       self.update_index()
    #make sure there are no "\n" characters in the element lists (if so replace them with "") for data this is
    # done on import
    list_types=["header","column_names","footer"]
    for element in list_types:
        if self.__dict__[element] is not None:
            for index,item in enumerate(self.__dict__[element]):
                self.__dict__[element][index]=item.replace("\n","")
    self.update_column_names()
    if self.data is not None:
        self.data=convert_all_rows(self.data,self.options["column_types"])
    self.string=self.build_string()
    self.lines=self.string.splitlines()

class PowerCalrepModel

PowerCalrep is a model that holds data output by analyzing several datafiles using the HPBasic program Calrep. The data is stored in 2 tables: a S11 table, and a power table. The data is in linear magnitude and angle in degrees. There are 2 types of files, one is a single file with .asc extension and 2 files with .txt extension

class PowerCalrepModel():
    """PowerCalrep is a model that holds data output by analyzing several datafiles using the HPBasic program
    Calrep. The data is stored in 2 tables: a S11 table, and a power table. The data is in linear
    magnitude and angle in degrees. There are 2 types of files, one is a single file with .asc extension
    and 2 files with .txt extension"""

    def __init__(self,file_path=None,**options):
        """Intializes the PowerCalrep class, if a file path is specified it opens and reads the file"""
        defaults= {}
        self.options={}
        for key,value in defaults.iteritems():
            self.options[key]=value
        for key,value in options.iteritems():
            self.options[key]=value
        if file_path is None:
            pass
        elif re.match('asc',file_path.split(".")[-1],re.IGNORECASE):
            self.table_names=['header','S11','Efficiency']
            self.row_pattern=make_row_match_string(ONE_PORT_COLUMN_NAMES)
            self.power_4term_row_pattern=make_row_match_string(POWER_4TERM_COLUMN_NAMES)
            self.power_3term_row_pattern=make_row_match_string(POWER_3TERM_COLUMN_NAMES)
            self.path=file_path
            self.__read_and_fix__()

        elif re.match('txt',file_path.split(".")[-1],re.IGNORECASE) or type(file_path) is ListType:
            self.table_names=['S11','Efficiency']
            if type(file_path) is ListType:
                self.file_names=file_path
                self.tables=[]
                for index,table in enumerate(self.table_names):
                    if index==0:
                        self.tables.append(PowerModel(self.file_names[index]))
                    elif index==1:
                        self.tables.append(OnePortCalrepModel(self.file_names[index]))
            else:
                try:
                    root_name_pattern=re.compile('(?P<root_name>\w+)[abc].txt',re.IGNORECASE)
                    root_name_match=re.search(root_name_pattern,file_path)
                    root_name=root_name_match.groupdict()["root_name"]
                    directory=os.path.dirname(os.path.realpath(file_path))
                    self.file_names=[os.path.join(directory,root_name+end) for end in ['a.txt','b.txt']]
                    self.tables=[]
                    for index,table in enumerate(self.table_names):
                        if index==0:
                            self.tables.append(OnePortCalrepModel(self.file_names[index]))
                        elif index==1:
                            self.tables.append(PowerModel(self.file_names[index]))
                except:
                    print("Could not import {0} please check that the a,b "
                          "tables are all in the same directory".format(file_path))
                    raise

            # for index,table in enumerate(self.tables):
            #     for column_number,column in enumerate(table.column_names):
            #         if column is not "Frequency":
            #             table.column_names[column_number]=self.table_names[index]+"_"+column

            self.joined_table=ascii_data_table_join("Frequency",self.tables[0],self.tables[1])
            #print self.joined_table

    def __read_and_fix__(self):
        in_file=open(self.path,'r')
        self.lines=[]
        table_locators=["Table 1","Table 2"]
        begin_lines=[]
        for index,line in enumerate(in_file):
            self.lines.append(line)
            for table in table_locators:
                if re.search(table,line,re.IGNORECASE):
                    begin_lines.append(index)
        in_file.close()
        self.table_line_numbers=[]
        for index,begin_line in enumerate(begin_lines):
            if index == 0:
                header_begin_line=0
                header_end_line=begin_line-1
                table_1_begin_line=begin_line+1
                table_1_end_line=begin_lines[index+1]
                self.table_line_numbers.append([header_begin_line,header_end_line])
                self.table_line_numbers.append([table_1_begin_line,table_1_end_line])
            elif index>0 and index<(len(begin_lines)-1):
                table_begin_line=begin_line+2
                print("{0} is {1}".format('begin_line',begin_line))
                table_end_line=begin_lines[index+1]
                self.table_line_numbers.append([table_begin_line,table_end_line])
            elif index==(len(begin_lines)-1):
                table_begin_line=begin_line+1
                table_end_line=None
                self.table_line_numbers.append([table_begin_line,table_end_line])
        self.tables=[]
        for index,name in enumerate(self.table_names):
            self.table_lines=self.lines[self.table_line_numbers[index][0]:self.table_line_numbers[index][1]]
            self.tables.append(self.table_lines)
        for index,table in enumerate(self.table_names):
            if index==0:
                # by using parse_lines we get a list_list of strings instead of list_string
                # we can just remove end lines
                self.tables[index]=strip_all_line_tokens(self.tables[index],begin_token=None,end_token='\n')
            elif index==1:
                column_types=['float' for i in range(len(ONE_PORT_COLUMN_NAMES))]
                options={"row_pattern":self.row_pattern,"column_names":ONE_PORT_COLUMN_NAMES,"output":"list_list"}
                options["column_types"]=column_types
                self.tables[index]=parse_lines(self.tables[index],**options)
                table_options={"data":self.tables[index]}
                self.tables[index]=OnePortCalrepModel(None,**table_options)
            elif index==2:
                # Here we need to test for the type of power model (how many columns)
                test_row=self.tables[index][2]
                if re.match(self.power_3term_row_pattern,test_row) and re.match(self.power_4term_row_pattern,test_row):
                    self.options["column_names"]=POWER_4TERM_COLUMN_NAMES
                    self.power_row_pattern=self.power_4term_row_pattern
                elif re.match(self.power_3term_row_pattern,test_row):
                    self.options["column_names"]=POWER_3TERM_COLUMN_NAMES
                    self.power_row_pattern=self.power_3term_row_pattern
                else:
                    raise ValueError("Power Table Does Not Conform")
                column_types=['float' for i in range(len(self.options["column_names"]))]
                table_options={"row_pattern":self.power_row_pattern,"column_names":self.options["column_names"],
                         "output":"list_list"}
                table_options["column_types"]=column_types
                self.tables[index]=parse_lines(self.tables[index],**table_options)
                table_options["data"]=self.tables[index]
                self.tables[index]=PowerModel(None,**table_options)

        # for table in self.tables:
        #     print table
        #print("Length of table 1 is {0}, Length of table 2 is {1}".format(len(self.tables[1].data),len(self.tables[2].data)))
        self.tables[1].header=self.tables[0]
        self.joined_table=ascii_data_table_join("Frequency",self.tables[1],self.tables[2])

    def __str__(self):
        return self.joined_table.build_string()

    def show(self):
        fig, axes = plt.subplots(nrows=2, ncols=2)
        ax0, ax1, ax2, ax3 = axes.flat
        ax0.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('mag'),
                     yerr=self.joined_table.get_column('uMg'),fmt='k--')
        ax0.set_title('Magnitude S11')
        ax1.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('arg'),
                     yerr=self.joined_table.get_column('uAg'),fmt='ro')
        ax1.set_title('Phase S11')
        ax2.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('Efficiency'),
                     yerr=self.joined_table.get_column('uEe'),fmt='k--')
        ax2.set_title('Effective Efficiency')
        ax3.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('Calibration_Factor'),
                     yerr=self.joined_table.get_column('uCe'),fmt='ro')
        ax3.set_title('Calibration Factor')
        plt.tight_layout()
        plt.show()

Ancestors (in MRO)

Instance variables

var options

Methods

def __init__(

self, file_path=None, **options)

Intializes the PowerCalrep class, if a file path is specified it opens and reads the file

def __init__(self,file_path=None,**options):
    """Intializes the PowerCalrep class, if a file path is specified it opens and reads the file"""
    defaults= {}
    self.options={}
    for key,value in defaults.iteritems():
        self.options[key]=value
    for key,value in options.iteritems():
        self.options[key]=value
    if file_path is None:
        pass
    elif re.match('asc',file_path.split(".")[-1],re.IGNORECASE):
        self.table_names=['header','S11','Efficiency']
        self.row_pattern=make_row_match_string(ONE_PORT_COLUMN_NAMES)
        self.power_4term_row_pattern=make_row_match_string(POWER_4TERM_COLUMN_NAMES)
        self.power_3term_row_pattern=make_row_match_string(POWER_3TERM_COLUMN_NAMES)
        self.path=file_path
        self.__read_and_fix__()
    elif re.match('txt',file_path.split(".")[-1],re.IGNORECASE) or type(file_path) is ListType:
        self.table_names=['S11','Efficiency']
        if type(file_path) is ListType:
            self.file_names=file_path
            self.tables=[]
            for index,table in enumerate(self.table_names):
                if index==0:
                    self.tables.append(PowerModel(self.file_names[index]))
                elif index==1:
                    self.tables.append(OnePortCalrepModel(self.file_names[index]))
        else:
            try:
                root_name_pattern=re.compile('(?P<root_name>\w+)[abc].txt',re.IGNORECASE)
                root_name_match=re.search(root_name_pattern,file_path)
                root_name=root_name_match.groupdict()["root_name"]
                directory=os.path.dirname(os.path.realpath(file_path))
                self.file_names=[os.path.join(directory,root_name+end) for end in ['a.txt','b.txt']]
                self.tables=[]
                for index,table in enumerate(self.table_names):
                    if index==0:
                        self.tables.append(OnePortCalrepModel(self.file_names[index]))
                    elif index==1:
                        self.tables.append(PowerModel(self.file_names[index]))
            except:
                print("Could not import {0} please check that the a,b "
                      "tables are all in the same directory".format(file_path))
                raise
        # for index,table in enumerate(self.tables):
        #     for column_number,column in enumerate(table.column_names):
        #         if column is not "Frequency":
        #             table.column_names[column_number]=self.table_names[index]+"_"+column
        self.joined_table=ascii_data_table_join("Frequency",self.tables[0],self.tables[1])

def show(

self)

def show(self):
    fig, axes = plt.subplots(nrows=2, ncols=2)
    ax0, ax1, ax2, ax3 = axes.flat
    ax0.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('mag'),
                 yerr=self.joined_table.get_column('uMg'),fmt='k--')
    ax0.set_title('Magnitude S11')
    ax1.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('arg'),
                 yerr=self.joined_table.get_column('uAg'),fmt='ro')
    ax1.set_title('Phase S11')
    ax2.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('Efficiency'),
                 yerr=self.joined_table.get_column('uEe'),fmt='k--')
    ax2.set_title('Effective Efficiency')
    ax3.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('Calibration_Factor'),
                 yerr=self.joined_table.get_column('uCe'),fmt='ro')
    ax3.set_title('Calibration Factor')
    plt.tight_layout()
    plt.show()

class PowerModel

class PowerModel(AsciiDataTable):
    def __init__(self,file_path,**options):
        "Intializes the PowerModel Class, it is assumed that the file is of  table type"
        # This is a general pattern for adding a lot of options
        defaults= {"data_delimiter": ",", "column_names_delimiter": ",", "specific_descriptor": 'One_Port',
                   "general_descriptor": 'Power', "extension": 'txt', "comment_begin": "#", "comment_end": "\n",
                   "header": None,
                   "column_names":None, "column_names_end_token": "\n", "data": None,
                   "row_formatter_string": None, "data_table_element_separator": None,"row_begin_token":None,
                   "row_end_token":None,"escape_character":None,
                   "data_begin_token":None,"data_end_token":None}
        self.options={}
        for key,value in defaults.iteritems():
            self.options[key]=value
        for key,value in options.iteritems():
            self.options[key]=value
        # Define Method Aliases if they are available
        if METHOD_ALIASES:
            for command in alias(self):
                exec(command)
        if file_path is not None:
            self.power_4term_row_pattern=make_row_match_string(POWER_4TERM_COLUMN_NAMES)
            self.power_3term_row_pattern=make_row_match_string(POWER_3TERM_COLUMN_NAMES)
            self.path=file_path
            self.__read_and_fix__()
        #build the row_formatting string, the original files have 4 decimals of precision for freq/gamma and 2 for Phase
        row_formatter=""
        for i in range(len(self.options["column_names"])):
            if i<len(self.options["column_names"])-1:
                row_formatter=row_formatter+"{"+str(i)+":.4f}{delimiter}"
            elif i==len(self.options["column_names"])-1:
                row_formatter=row_formatter+"{"+str(i)+":.4f}"
        self.options["row_formatter_string"]=row_formatter
        AsciiDataTable.__init__(self,None,**self.options)
        if file_path is not None:
            self.path=file_path

    def __read_and_fix__(self):
        """Reads in a power ascii file and fixes any issues with inconsistent delimiters, etc"""
        lines=[]
        table_type=self.path.split(".")[-1]
        in_file=open(self.path,'r')
        for line in in_file:
            if not re.match('[\s]+(?!\w+)',line):
                #print line
                lines.append(line)
        # Handle the cases in which it is the comma delimited table
        # Does this need to be parse lines or numpy.loadtxt?
        if re.match('txt',table_type,re.IGNORECASE):
            lines=strip_tokens(lines,*[self.options['data_begin_token'],
                                                    self.options['data_end_token']])
            self.options["data"]=strip_all_line_tokens(lines,begin_token=self.options["row_begin_token"],
                                            end_token=self.options["row_end_token"])
            self.options["data"]=split_all_rows(self.options["data"],delimiter=self.options["data_delimiter"],
                                     escape_character=self.options["escape_character"])
            print("{0} is {1}".format("len(self.options['data'][0])",len(self.options['data'][0])))
            if len(self.options['data'][0])==9:
                self.power_pattern=self.power_3term_row_pattern
                self.options["column_names"]=POWER_3TERM_COLUMN_NAMES
                self.options["column_descriptions"]=POWER_3TERM_COLUMN_DESCRIPTIONS
            elif len(self.options['data'][0])==11:
                self.power_pattern=self.power_4term_row_pattern
                self.options["column_names"]=POWER_4TERM_COLUMN_NAMES
                self.options["column_descriptions"]=POWER_4TERM_COLUMN_DESCRIPTIONS
            self.options["column_types"]= ['float' for i in range(len(self.options["column_names"]))]
            self.options["data"]=convert_all_rows(self.options["data"],self.options["column_types"])
            #print self.options["data"]
            root_name_pattern=re.compile('(?P<root_name>\w+)[abc].txt',re.IGNORECASE)
            root_name_match=re.search(root_name_pattern,self.path)
            root_name=root_name_match.groupdict()["root_name"]
            self.options["header"]=["Device_Id = {0}".format(root_name)]

Ancestors (in MRO)

  • PowerModel
  • pyMez.Code.DataHandlers.GeneralModels.AsciiDataTable

Instance variables

var options

Methods

def __init__(

self, file_path, **options)

Intializes the PowerModel Class, it is assumed that the file is of table type

def __init__(self,file_path,**options):
    "Intializes the PowerModel Class, it is assumed that the file is of  table type"
    # This is a general pattern for adding a lot of options
    defaults= {"data_delimiter": ",", "column_names_delimiter": ",", "specific_descriptor": 'One_Port',
               "general_descriptor": 'Power', "extension": 'txt', "comment_begin": "#", "comment_end": "\n",
               "header": None,
               "column_names":None, "column_names_end_token": "\n", "data": None,
               "row_formatter_string": None, "data_table_element_separator": None,"row_begin_token":None,
               "row_end_token":None,"escape_character":None,
               "data_begin_token":None,"data_end_token":None}
    self.options={}
    for key,value in defaults.iteritems():
        self.options[key]=value
    for key,value in options.iteritems():
        self.options[key]=value
    # Define Method Aliases if they are available
    if METHOD_ALIASES:
        for command in alias(self):
            exec(command)
    if file_path is not None:
        self.power_4term_row_pattern=make_row_match_string(POWER_4TERM_COLUMN_NAMES)
        self.power_3term_row_pattern=make_row_match_string(POWER_3TERM_COLUMN_NAMES)
        self.path=file_path
        self.__read_and_fix__()
    #build the row_formatting string, the original files have 4 decimals of precision for freq/gamma and 2 for Phase
    row_formatter=""
    for i in range(len(self.options["column_names"])):
        if i<len(self.options["column_names"])-1:
            row_formatter=row_formatter+"{"+str(i)+":.4f}{delimiter}"
        elif i==len(self.options["column_names"])-1:
            row_formatter=row_formatter+"{"+str(i)+":.4f}"
    self.options["row_formatter_string"]=row_formatter
    AsciiDataTable.__init__(self,None,**self.options)
    if file_path is not None:
        self.path=file_path

def add_column(

self, column_name=None, column_type=None, column_data=None, format_string=None)

Adds a column with column_name, and column_type. If column data is supplied and it's length is the same as data(same number of rows) then it is added, else self.options['empty_character'] is added in each spot in the preceding rows

def add_column(self,column_name=None,column_type=None,column_data=None,format_string=None):
    """Adds a column with column_name, and column_type. If column data is supplied and it's length is the
    same as data(same number of rows) then it is added, else self.options['empty_character'] is added in each
    spot in the preceding rows"""
    original_column_names=self.column_names[:]
    try:
        self.column_names=original_column_names+[column_name]
        if self.options["column_types"]:
            old_column_types=self.options["column_types"][:]
            self.options["column_types"]=old_column_types+[column_type]
        if len(column_data) == len(self.data):
            for index,row in enumerate(self.data[:]):
                #print("{0} is {1}".format('self.data[index]',self.data[index]))
                #print("{0} is {1}".format('row',row))
                new_row=row[:]
                new_row.append(column_data[index])
                self.data[index]=new_row
        else:
            for index,row in enumerate(self.data[:]):
                self.data[index]=row.append(self.options['empty_value'])
                if column_data is not None:
                    for item in column_data:
                        empty_row=[self.options['empty_value'] for column in original_column_names]
                        empty_row.append(item)
                        self.add_row(empty_row)
        if self.options["row_formatter_string"] is None:
            pass
        else:
            if format_string is None:
                self.options["row_formatter_string"]=self.options["row_formatter_string"]+\
                                                             '{delimiter}'+"{"+str(len(self.column_names)-1)+"}"
            else:
                self.options["row_formatter_string"]=self.options["row_formatter_string"]+format_string
        #self.update_model()
    except:
        self.column_names=original_column_names
        print("Could not add columns")
        raise

def add_index(

self)

Adds a column with name index and values that are 0 referenced indices, does nothing if there is already a column with name index, always inserts it at the 0 position

def add_index(self):
    """Adds a column with name index and values that are 0 referenced indices, does nothing if there is
    already a column with name index, always inserts it at the 0 position"""
    if 'index' in self.column_names:
        print("Add Index passed")
        pass
    else:
        self.column_names.insert(0,'index')
        for index,row in enumerate(self.data):
            self.data[index].insert(0,index)
        if self.options['column_types']:
            self.options['column_types'].insert(0,'int')
        if self.options['row_formatter_string']:
            temp_formatter_list=self.options['row_formatter_string'].split("{delimiter}")
            iterated_row_formatter_list=[temp_formatter_list[i].replace(str(i),str(i+1))
                                         for i in range(len(temp_formatter_list))]
            new_formatter=string_list_collapse(iterated_row_formatter_list,string_delimiter="{delimiter}")
            self.options['row_formatter_string']='{0}{delimiter}'+new_formatter

def add_inline_comment(

self, comment='', line_number=None, string_position=None)

Adds an inline in the specified location

def add_inline_comment(self,comment="",line_number=None,string_position=None):
    "Adds an inline in the specified location"
    try:
        self.inline_comments.append([comment,line_number,string_position])
    except:pass

def add_row(

self, row_data)

Adds a single row given row_data which can be an ordered list/tuple or a dictionary with column names as keys

def add_row(self,row_data):
    """Adds a single row given row_data which can be an ordered list/tuple or a dictionary with
    column names as keys"""
    if len(row_data) not in [len(self.column_names),len(self.column_names)]:
        print(" could not add the row, dimensions do not match")
        return
    if type(row_data) in [ListType,np.ndarray]:
        self.data.append(row_data)
    elif type(row_data) in [DictionaryType]:
        data_list=[row_data[column_name] for column_name in self.column_names]
        self.data.append(data_list)

def build_string(

self, **temp_options)

Builds a string representation of the data table based on self.options, or temp_options. Passing temp_options does not permanently change the model

def build_string(self,**temp_options):
    """Builds a string representation of the data table based on self.options, or temp_options.
    Passing temp_options does not permanently change the model"""
    # store the original options to be put back after the string is made
    original_options=self.options
    for key,value in temp_options.iteritems():
        self.options[key]=value
    section_end=0
    next_section_begin=0
    if self.options['data_table_element_separator'] is None:
        inner_element_spacing=0
    else:
        inner_element_spacing=self.options['data_table_element_separator'].count('\n')-1
    string_out=""
    between_section=""
    if self.options['data_table_element_separator'] is not None:
        between_section=self.options['data_table_element_separator']
    if self.header is None:
        self.options['header_begin_line']=self.options['header_end_line']=None
        pass
    else:
        self.options["header_begin_line"]=0
        if self.data is None and self.column_names is None and self.footer is None:
            string_out=self.get_header_string()
            self.options["header_end_line"]=None
        else:
            string_out=self.get_header_string()+between_section
            last_header_line=self.get_header_string().count('\n')+1
            self.options["header_end_line"]=last_header_line
            next_section_begin=last_header_line+inner_element_spacing
    if self.column_names is None:
        self.options['column_names_begin_line']=self.options['column_names_end_line']=None
        pass
    else:
        self.options["column_names_begin_line"]=next_section_begin
        if self.data is None and self.footer is None:
            self.options["column_names_end_line"]=None
            string_out=string_out+self.get_column_names_string()
        else:
            string_out=string_out+self.get_column_names_string()+between_section
            last_column_names_line=self.get_column_names_string().count('\n')+\
                                   self.options["column_names_begin_line"]+1
            self.options["column_names_end_line"]=last_column_names_line
            next_section_begin=last_column_names_line+inner_element_spacing
    if self.data is None:
        self.options['data_begin_line']=self.options['data_end_line']=None
        pass
    else:
        self.options["data_begin_line"]=next_section_begin
        if self.footer is None:
            self.options["data_end_line"]=None
            string_out=string_out+self.get_data_string()
        else:
            string_out=string_out+self.get_data_string()+between_section
            last_data_line=self.get_data_string().count("\n")+\
                            self.options["data_begin_line"]+1
            self.options["data_end_line"]=last_data_line
            next_section_begin=last_data_line+inner_element_spacing
    if self.footer is None:
        self.options['footer_begin_line']=self.options['footer_end_line']=None
        pass
    else:
        self.options["footer_begin_line"]=next_section_begin
        string_out=string_out+self.get_footer_string()
        self.options['footer_end_line']=None
    # set the options back after the string has been made
    if self.inline_comments is None:
        pass
    else:
        lines=string_out.splitlines()
        for comment in self.inline_comments:
            lines=insert_inline_comment(lines,comment=comment[0],line_number=comment[1],
                                        string_position=comment[2],
                                        begin_token=self.options['inline_comment_begin'],
                                        end_token=self.options['inline_comment_end'])
        string_out=string_list_collapse(lines,string_delimiter='\n')
    self.options=original_options
    return string_out

def change_unit_prefix(

self, column_selector=None, old_prefix=None, new_prefix=None, unit='Hz')

Changes the prefix of the units of the column specified by column_selector (column name or index) example usage is self.change_unit_prefix(column_selector='Frequency',old_prefix=None,new_prefix='G',unit='Hz') to change a column from Hz to GHz. It updates the data values, column_descriptions, and column_units if they exist, see http://www.nist.gov/pml/wmd/metric/prefixes.cfm for possible prefixes

def change_unit_prefix(self,column_selector=None,old_prefix=None,new_prefix=None,unit='Hz'):
    """Changes the prefix of the units of the column specified by column_selector (column name or index)
    example usage is self.change_unit_prefix(column_selector='Frequency',old_prefix=None,new_prefix='G',unit='Hz')
    to change a column from Hz to GHz. It updates the data values, column_descriptions, and column_units if they
    exist, see http://www.nist.gov/pml/wmd/metric/prefixes.cfm for possible prefixes"""
    multipliers={"yotta":10.**24,"Y":10.**24,"zetta":10.**21,"Z":10.**21,"exa":10.**18,"E":10.**18,"peta":10.**15,
                 "P":10.**15,"tera":10.**12,"T":10.**12,"giga":10.**9,"G":10.**9,"mega":10.**6,"M":10.**6,
                 "kilo":10.**3,"k":10.**3,"hecto":10.**2,"h":10.**2,"deka":10.,"da":10.,None:1.,"":1.,
                 "deci":10.**-1,"d":10.**-1,"centi":10.**-2,"c":10.**-2,"milli":10.**-3,"m":10.**-3,
                 "micro":10.**-6,"mu":10.**-6,u"\u00B5":10.**-6,"nano":10.**-9,
                 "n":10.**-9,"pico":10.**-12,"p":10.**-12,"femto":10.**-15,
                 "f":10.**-15,"atto":10.**-18,"a":10.**-18,"zepto":10.**-21,"z":10.**-21,
                 "yocto":10.**-24,"y":10.**-24}
    # change column name into column index
    try:
        if old_prefix is None:
            old_prefix=""
        if new_prefix is None:
            new_prefix=""
        old_unit=old_prefix+unit
        new_unit=new_prefix+unit
        if column_selector in self.column_names:
            column_selector=self.column_names.index(column_selector)
        for index,row in enumerate(self.data):
            if type(self.data[index][column_selector]) in [FloatType,LongType]:
                #print "{0:e}".format(multipliers[old_prefix]/multipliers[new_prefix])
                self.data[index][column_selector]=\
                (multipliers[old_prefix]/multipliers[new_prefix])*self.data[index][column_selector]
            elif type(self.data[index][column_selector]) in [StringType,IntType]:
                self.data[index][column_selector]=\
                str((multipliers[old_prefix]/multipliers[new_prefix])*float(self.data[index][column_selector]))
            else:
                print type(self.data[index][column_selector])
                raise
        if self.options["column_descriptions"] is not None:
            old=self.options["column_descriptions"][column_selector]
            self.options["column_descriptions"][column_selector]=old.replace(old_unit,new_unit)
        if self.options["column_units"] is not None:
            old=self.options["column_units"][column_selector]
            self.options["column_units"][column_selector]=old.replace(old_unit,new_unit)
        if re.search(old_unit,self.column_names[column_selector]):
            old=self.column_names[column_selector]
            self.column_names[column_selector]=old.replace(old_unit,new_unit)
    except:
        print("Could not change the unit prefix of column {0}".format(column_selector))
        raise

def find_line(

self, begin_token)

Finds the first line that has begin token in it

def find_line(self,begin_token):
    """Finds the first line that has begin token in it"""
    for index,line in enumerate(self.lines):
        if re.search(begin_token,line,re.IGNORECASE):
            return index

def get_column(

self, column_name=None, column_index=None)

Returns a column as a list given a column name or column index

def get_column(self,column_name=None,column_index=None):
    """Returns a column as a list given a column name or column index"""
    if column_name is None:
        if column_index is None:
            return
        else:
            column_selector=column_index
    else:
        column_selector=self.column_names.index(column_name)
    out_list=[self.data[i][column_selector] for i in range(len(self.data))]
    return out_list

def get_column_names_string(

self)

Returns the column names as a string using options

def get_column_names_string(self):
    "Returns the column names as a string using options"
    string_out=""
    # This writes the column_names
    column_name_begin=""
    column_name_end=""
    if self.options["column_names_begin_token"] is None:
        column_name_begin=""
    else:
        column_name_begin=self.options["column_names_begin_token"]
    if self.options["column_names_end_token"] is None:
        column_name_end=""
    else:
        column_name_end=self.options["column_names_end_token"]
    if self.column_names is None:
        string_out=""
    else:
        if type(self.column_names) is StringType:
            string_out=self.column_names
        elif type(self.column_names) is ListType:
            string_out=list_to_string(self.column_names,
                                      data_delimiter=self.options["column_names_delimiter"],end="")
            #print("{0} is {1}".format('string_out',string_out))
        else:
            string_out=ensure_string(self.column_names)
    #print column_name_begin,string_out,column_name_end
    return column_name_begin+string_out+column_name_end

def get_data_dictionary_list(

self, use_row_formatter_string=True)

Returns a python list with a row dictionary of form {column_name:data_column}

def get_data_dictionary_list(self,use_row_formatter_string=True):
    """Returns a python list with a row dictionary of form {column_name:data_column}"""
    try:
        if self.options["row_formatter_string"] is None:
            use_row_formatter_string=False
        if use_row_formatter_string:
            list_formatter=[item.replace("{"+str(index),"{0")
                            for index,item in enumerate(self.options["row_formatter_string"].split("{delimiter}"))]
        else:
            list_formatter=["{0}" for i in self.column_names]
        #print self.column_names
        #print self.data
        #print list_formatter
        #print len(self.column_names)==len(self.data[0])
        #print len(list_formatter)==len(self.data[0])
        #print type(self.data[0])
        out_list=[{self.column_names[i]:list_formatter[i].format(value) for i,value in enumerate(line)}
                  for line in self.data]
        return out_list
    except:
        print("Could not form a data_dictionary_list, check that row_formatter_string is properly defined")
        #print(out_list)
        raise

def get_data_string(

self)

Returns the data as a string

def get_data_string(self):
    "Returns the data as a string"
    #Todo:refactor to cut out unused lines
    string_out=""
    if self.data is None:
        string_out= ""
    else:
        if type(self.data) is StringType:
            if self.options['data_begin_token'] is None:
                   if self.options['data_end_token'] is None:
                       string_out=self.data
                   else:
                       if re.search(self.options['data_end_token'],self.data):
                           string_out=self.data
                       else:
                           string_out=self.data+self.options['data_end_token']
            else:
                    if self.options['data_end_token'] is None:
                        if re.match(self.options['data_begin_token'],self.data):
                            string_out=self.data
                        else:
                            string_out=self.options['data_begin_token']+self.data
        elif type(self.data) in [ListType,np.ndarray]:
            try:
                    #If the first row is a string, we should strip all the tokens and add them back in
                    if type(self.data[0]) is StringType:
                        if self.options['data_begin_token'] is None:
                            string_out=string_list_collapse(self.data)
                        else:
                            if re.match(self.options['data_begin_token'],self.data[0]):
                                if self.options['data_end_token'] is None:
                                    string_out=string_list_collapse(self.data)
                                else:
                                    if re.search(self.options['data_end_token'],self.data[-1]):
                                        string_out=string_list_collapse(self.data)
                                    else:
                                        string_out=string_list_collapse(self.data)+self.options['data_end_token']
                            else:
                                if self.options['data_end_token'] is None:
                                    string_out=self.options['data_begin_token']+string_list_collapse(self.data)
                                else:
                                    if re.search(self.options['data_end_token'],self.data[-1]):
                                        string_out=self.options['data_begin_token']+string_list_collapse(self.data)
                                    else:
                                        string_out=self.options['data_begin_token']+\
                                                   string_list_collapse(self.data)+\
                                                   self.options['data_end_token']
                    elif type(self.data[0]) in [ListType,np.ndarray]:
                        prefix=""
                        if self.options['data_begin_token'] is None:
                            if self.options['data_end_token'] is None:
                                string_out=list_list_to_string(self.data,data_delimiter=self.options['data_delimiter'],
                                                               row_formatter_string=self.options['row_formatter_string'],
                                                               line_begin=self.options["row_begin_token"],
                                                               line_end=self.options["row_end_token"])
                        else:
                            if self.options['data_end_token'] is None:
                                string_out=self.options['data_begin_token']+\
                                           list_list_to_string(self.data,
                                                               data_delimiter=self.options['data_delimiter'],
                                                               row_formatter_string=self.options['row_formatter_string'],
                                                               line_begin=self.options["row_begin_token"],
                                                               line_end=self.options["row_end_token"])
                            else:
                                string_out=self.options['data_begin_token']+\
                                           list_list_to_string(self.data,
                                                               data_delimiter=self.options['data_delimiter'],
                                                               row_formatter_string=\
                                                               self.options['row_formatter_string'],
                                                               line_begin=self.options["row_begin_token"],
                                                               line_end=self.options["row_end_token"])+\
                                                                self.options['data_end_token']
                    else:
                        string_out=list_to_string(self.data,
                                                  data_delimiter=self.options['data_delimiter'],
                                                  row_formatter_string=self.options['row_formatter_string'],
                                                  begin=self.options["row_begin_token"],
                                                  end=self.options["row_end_token"])
            except IndexError:
                pass
        else:
            string_out=ensure_string(self.data)
    return string_out

Returns the footer using options in self.options. If block comment is specified, and the footer is a list it will block comment out the footer. If comment_begin and comment_end are specified it will use those to represent each line of the footer. If footer_begin_token and/or footer_end_token are specified it will wrap the footer in those.

def get_header_string(

self)

Returns the header using options in self.options. If block comment is specified, and the header is a list it will block comment out the header. If comment_begin and comment_end are specified it will use those to represent each line of the header. If header_begin_token and/or header_end_token are specified it will wrap the header in those.

def get_header_string(self):
    """Returns the header using options in self.options. If block comment is specified, and the header is a
    list it will block comment out the header. If comment_begin and comment_end are specified it will use
    those to represent each line of the header. If header_begin_token and/or header_end_token are specified it
     will wrap the header in those.
    """
    string_out=""
    header_begin=""
    header_end=""
    if self.options["header_begin_token"] is None:
        header_begin=""
    else:
        header_begin=self.options["header_begin_token"]
    if self.options["header_end_token"] is None:
        header_end=""
    else:
        header_end=self.options["header_end_token"]
    # This writes the header
    if self.header is None:
        string_out= ""
    elif self.options["header_line_types"] is not None:
        for index,line in enumerate(self.options["header_line_types"]):
            if index == len(self.options["header_line_types"])-1:
                end=''
            else:
                end='\n'
            if line in ['header','header_line','normal']:
                string_out=string_out+self.header[index]+end
            elif line in ['line_comment','comment']:
                string_out=string_out+line_comment_string(self.header[index],
                                           comment_begin=self.options["comment_begin"],
                                           comment_end=self.options["comment_end"])+end
            elif line in ['block_comment','block']:
                if index-1<0:
                    block_comment_begin=index
                    block_comment_end=index+2
                    continue
                elif self.options["header_line_types"][index-1] not in ['block_comment','block']:
                    block_comment_begin=index
                    block_comment_end=index+2
                    continue
                else:
                    if index+1>len(self.options["header_line_types"])-1:
                        string_out=string_out+line_list_comment_string(self.header[block_comment_begin:],
                                                                       comment_begin=self.options['block_comment_begin'],
                                                                         comment_end=self.options['block_comment_end'],
                                                                       block=True)+end
                    elif self.options["header_line_types"][index+1] in ['block_comment','block']:
                        block_comment_end+=1
                    else:
                        string_out=string_out+\
                                   line_list_comment_string(self.header[block_comment_begin:block_comment_end],
                                                            comment_begin=self.options['block_comment_begin'],
                                                            comment_end=self.options['block_comment_end'],
                                                            block=True)+end
            else:
                string_out=string_out+line
    elif self.options['treat_header_as_comment'] in [None,True] and self.options["header_line_types"] in [None]:
        # Just happens if the user has set self.header manually
        if type(self.header) is StringType:
            string_out=line_comment_string(self.header,
                                           comment_begin=self.options["comment_begin"],
                                           comment_end=self.options["comment_end"])
            #string_out=re.sub('\n','',string_out,count=1)
        elif type(self.header) is ListType:
            if self.options['block_comment_begin'] is None:
                if self.options['comment_begin'] is None:
                    string_out=string_list_collapse(self.header)
                else:
                    string_out=line_list_comment_string(self.header,comment_begin=self.options['comment_begin'],
                                                    comment_end=self.options['comment_end'])
                    lines_out=string_out.splitlines()
                    # if re.search('\n',self.options['comment_end']):
                    #     string_out=re.sub('\n','',string_out,count=1)
                    #self.options["header_line_types"]=["line_comment" for line in self.header]
            else:
                string_out=line_list_comment_string(self.header,comment_begin=self.options['block_comment_begin'],
                                                    comment_end=self.options['block_comment_end'],block=True)
                #self.options["header_line_types"]=["block_comment" for line in self.header]
    else:
        string_out=ensure_string(self.header,list_delimiter="\n",end_if_list="")
    return header_begin+string_out+header_end

def get_options(

self)

Prints the option list

def get_options(self):
    "Prints the option list"
    for key,value in self.options.iteritems():
        print("{0} = {1}".format(key,value))

def get_options_by_element(

self, element_name)

returns a dictionary of all the options that have to do with element. Element must be header,column_names,data, or footer

def get_options_by_element(self,element_name):
    """ returns a dictionary
     of all the options that have to do with element. Element must be header,column_names,data, or footer"""
    keys_regarding_element=filter(lambda x: re.search(element_name,str(x),re.IGNORECASE),self.options.keys())
    out_dictionary={key:self.options[key] for key in keys_regarding_element}
    #print out_dictionary
    return out_dictionary

def get_row(

self, row_index=None)

Returns the row as a list specified by row_index

def get_row(self,row_index=None):
    """Returns the row as a list specified by row_index"""
    if row_index is None:
        return
    else:
        return self.data[row_index]

def is_valid(

self)

Returns True if ascii table conforms to its specification given by its own options

def is_valid(self):
    """Returns True if ascii table conforms to its specification given by its own options"""
    options={}
    for key,value in self.options.iteritems():
        options[key]=value
        # print("self.options[{0}] is {1} ".format(key,value))
    for element in self.elements:
        if self.__dict__[element] is None:
            options[element]=None
        else:
            options[element]=[]
    options["validate"]=True
    newtable=AsciiDataTable(None,**options)
    lines=self.build_string().splitlines()
    for index,line in enumerate(lines):
        lines[index]=line+"\n"
    newtable.lines=lines
    newtable.__parse__()
    # print newtable.data
    # print newtable.column_names
    # print newtable
    #print_comparison(newtable.footer,None)
    newtable.update_model()
    # The new table rows are not being coerced into the right format
    #print newtable
    #newtable.update_model()
    #print newtable.options
    #print self.options
    #print newtable.data
    # print newtable.options==self.options
    # for option_key,option_value in newtable.options.iteritems():
    #     print("New Table Option {0} is {1} ".format(option_key,option_value))
    #     print("self.options[{0}] is {1} ".format(option_key,self.options[option_key]))
    #     print_comparison(option_value,self.options[option_key])
    # #print self
    return self==newtable

def lines_defined(

self)

If begin_line and end_line for all elements that are None are defined returns True

def lines_defined(self):
    """If begin_line and end_line for all elements that are None are defined returns True"""
    truth_table=[]
    last_element=""
    output=False
    for index,element in enumerate(self.elements):
        if element not in ['inline_comments','metadata'] and self.__dict__[element] is not None:
            try:
                last_element=element
                if not None in [self.options['%s_begin_line'%element],self.options['%s_end_line'%element]]:
                    truth_table.append(True)
                else:
                     truth_table.append(False)
            except:
                return False
    #print truth_table
    # The last_line of the last element is fine to be none
    if truth_table[-1] is False:
        if self.options['%s_begin_line'%last_element] is not None:
            truth_table[-1]=True
    if False in truth_table:
        output=False
    else:
        output=True
    #print output
    return output

Moves the DataTable's footer to the header and updates the model

def remove_column(

self, column_name=None, column_index=None)

Removes the column specified by column_name or column_index and updates the model. The column is removed from column_names, data and if present column_types, column_descriptions and row formatter

def remove_column(self,column_name=None,column_index=None):
    """Removes the column specified by column_name or column_index and updates the model. The column is removed from
    column_names, data and if present column_types, column_descriptions and row formatter"""
    pass

def remove_row(

self, row_index)

Removes the row specified by row_index and updates the model. Note index is relative to the data attribute so to remove the first row use row_index=0 and the last data row is row_index=-1

def remove_row(self,row_index):
    """Removes the row specified by row_index and updates the model. Note index is relative to the
    data attribute so to remove the first row use row_index=0 and the last data row is row_index=-1"""
    self.data.pop(row_index)
    self.update_model()

def save(

self, path=None, **temp_options)

" Saves the file, to save in another ascii format specify elements in temp_options, the options specified do not permanently change the object's options. If path is supplied it saves the file to that path otherwise uses the object's attribute path to define the saving location

def save(self,path=None,**temp_options):
    """" Saves the file, to save in another ascii format specify elements in temp_options, the options
    specified do not permanently change the object's options. If path is supplied it saves the file to that path
    otherwise uses the object's attribute path to define the saving location """
    original_options=self.options
    for key,value in temp_options.iteritems():
        self.options[key]=value
    out_string=self.build_string(**temp_options)
    if path is None:
        path=self.path
    file_out=open(path,'w')
    file_out.write(out_string)
    file_out.close()
    self.options=original_options

def save_schema(

self, path=None, format=None)

Saves the tables options as a text file or pickled dictionary (default). If no name is supplied, autonames it and saves

def save_schema(self,path=None,format=None):
    """Saves the tables options as a text file or pickled dictionary (default).
    If no name is supplied, autonames it and saves"""
    if path is None:
        path=auto_name(self.name.replace('.'+self.options["extension"],""),'Schema',self.options["directory"],'txt')
    if format in [None,'python','pickle']:
        pickle.dump(self.options,open(path,'wb'))
    elif format in ['txt','text','.txt']:
        file_out=open(path,'w')
        keys=self.options.keys()
        keys.sort()
        for key in keys:
            out_key=str(key).replace("\n","\\n")
            out_value=str(self.options[key]).replace("\n","\\n")
            file_out.write("{0} : {1} \n".format(out_key,out_value))
        file_out.close()

def update_column_names(

self)

Update column names adds the value x# for any column that exists in self.data that is not named

def update_column_names(self):
    """Update column names adds the value x# for any column that exists in self.data that is not named"""
    if self.data is None:
        return
    elif type(self.column_names) is StringType:
        self.column_names=split_row(self.column_names,self.options["column_names_delimiter"])
    elif self.column_names is None:
        column_names=[]
        for index,column in enumerate(self.data[0]):
            column_names.append("x"+str(index))
        self.column_names=column_names
        return
    elif len(self.column_names)==len(self.data[0]):
        return
    elif len(self.column_names) < len(self.data[0]):
        for index in range(len(self.column_names),len(self.data[0])):
            self.column_names.append("x"+str(index))
        return

def update_import_options(

self, import_table)

Updates the options in the import table

def update_import_options(self,import_table):
    """Updates the options in the import table"""
    for index,element in enumerate(['header','column_names','data','footer']):
        if self.__dict__[element] is not None:
            print("The {0} variable is {1}".format('index',index))
            print("The {0} variable is {1}".format('element',element))
            print("The {0} variable is {1}".format('import_table',import_table))
            [self.options['%s_begin_line'%element],
                            self.options['%s_end_line'%element],
                            self.options['%s_begin_token'%element],
                            self.options['%s_end_token'%element]]=import_table[index][:]

def update_index(

self)

Updates the index column if it exits, otherwise exits quietly

def update_index(self):
    """ Updates the index column if it exits, otherwise exits quietly
    """
    if 'index' not in self.column_names:
        return
    else:
        try:
            #This should be 0 but just in case
            index_column_number=self.column_names.index('index')
            for i in range(len(self.data)):
                self.data[i][index_column_number]=i
        except:
            pass

def update_model(

self)

Updates the model after a change has been made. If you add anything to the attributes of the model, or change this updates the values. If the model has an index column it will make sure the numbers are correct. In addition, it will update the options dictionary to reflect added rows, changes in deliminators etc.

def update_model(self):
    """Updates the model after a change has been made. If you add anything to the attributes of the model,
    or change this updates the values. If the model has an index column it will make sure the numbers are correct.
    In addition, it will update the options dictionary to reflect added rows, changes in deliminators etc.  """
    if self.column_names is not None and 'index' in self.column_names:
       self.update_index()
    #make sure there are no "\n" characters in the element lists (if so replace them with "") for data this is
    # done on import
    list_types=["header","column_names","footer"]
    for element in list_types:
        if self.__dict__[element] is not None:
            for index,item in enumerate(self.__dict__[element]):
                self.__dict__[element][index]=item.replace("\n","")
    self.update_column_names()
    if self.data is not None:
        self.data=convert_all_rows(self.data,self.options["column_types"])
    self.string=self.build_string()
    self.lines=self.string.splitlines()

class PowerRawModel

Class that deals with the PowerRaw Files after conversion to Ascii using Ron Ginley's converter. These files typically have header information seperated from data by !! Header format is: Line 1: Spid$ - identification of type of system used Line 2: Systemletter$ - letter name indicating which system was used Line 3: Conncal$ - connector type from the system calibration Line 4: Connectors$ - connector type used for the measurement Line 5: Meastype$ - type of measurement (basically 1-port, 2-port or power) Line 6: Datea$ - date of measurement Line 7: Timea$ - time of measurement Line 8: Programm$ - name of program used Line 9: Rev$ - program revision Line 10: Opr$ - operator Line 11: Cfile$ - calibration name Line 12: Cdate$ - calibration date Line 13: Sport - identification of which port or direction was used for measurement Line 14: Numconnects ? number of disconnect/reconnect cycles Line 15: Numrepeats ? number of repeat measurements for each connect (usually 1) Line 16: Nbs ? not sure Line 17: Nfreq ? number of frequencies Line 18: Startfreq ? data row pointer for bdat files Line 19: Devicedescript$ - description of device being measured or of test being done Line 20: Devicenum$ - Identifying number for device ? used for file names

class PowerRawModel(AsciiDataTable):
    """ Class that deals with the PowerRaw Files after conversion to Ascii using Ron Ginley's converter.
    These files typically have header information seperated from data by !!
    Header format is:
    Line 1:		Spid$ - identification of type of system used
    Line 2:		Systemletter$ - letter name indicating which system was used
    Line 3:		Conncal$ - connector type from the system calibration
    Line 4:		Connectors$ - connector type used for the measurement
    Line 5:		Meastype$ - type of measurement (basically 1-port, 2-port or power)
    Line 6:		Datea$ - date of measurement
    Line 7:		Timea$ - time of measurement
    Line 8:		Programm$ - name of program used
    Line 9:		Rev$ - program revision
    Line 10:	Opr$ - operator
    Line 11:	Cfile$ - calibration name
    Line 12:	Cdate$ - calibration date
    Line 13:	Sport - identification of which port or direction was used for measurement
    Line 14:	Numconnects ? number of disconnect/reconnect cycles
    Line 15:	Numrepeats ? number of repeat measurements for each connect (usually 1)
    Line 16:	Nbs ? not sure
    Line 17:	Nfreq ? number of frequencies
    Line 18:	Startfreq ? data row pointer for bdat files
    Line 19:	Devicedescript$ - description of device being measured or of test being done
    Line 20:	Devicenum$ - Identifying number for device ? used for file names
    """
    def __init__(self,file_path=None,**options):
        """Initializes the PowerRaw class, if a file_path is specified opens an existing file, else creates an
        empty container"""
        defaults= {"data_delimiter": ",", "column_names_delimiter": ",", "specific_descriptor": 'Raw',
                   "general_descriptor": 'Power', "extension": 'txt', "comment_begin": "#", "comment_end": "\n",
                   "column_types": ['float','int','int','float','float','float','float'],
                   "column_descriptions": {"Frequency":"Frequency in GHz",
                                           "Direction":"Direction of connects, may be unused",
                                           "Connect":"Connect number", "magS11":"Linear magnitude for S11",
                                           "argS11":"Phase in degrees for S11",
                                           "Efficiency":"Effective Efficiency",
                                           "Calibration_Factor":"Effective efficiency "
                                                                "modified by reflection coefficient"},
                   "header": None,
                   "column_names": ["Frequency","Direction","Connect", "magS11",
                                    "argS11","Efficiency","Calibration_Factor"],
                   "column_names_end_token": "\n", "data": None,
                   'row_formatter_string': "{0:.5g}{delimiter}{1}{delimiter}{2}"
                                           "{delimiter}{3:.5g}{delimiter}{4:.3f}{delimiter}"
                                           "{5:.5g}{delimiter}{6:.5g}",
                   "data_table_element_separator": None}
        self.options={}
        for key,value in defaults.iteritems():
            self.options[key]=value
        for key,value in options.iteritems():
            self.options[key]=value
        # Define Method Aliases if they are available
        if METHOD_ALIASES:
            for command in alias(self):
                exec(command)
        if file_path is not None:
            self.__read_and_fix__(file_path)

        AsciiDataTable.__init__(self,None,**self.options)
        self.path=file_path
        self.structure_metadata()

    def __read_and_fix__(self,file_path=None):
        """Inputs in the PowerRaw file and fixes any problems with delimiters,etc."""
        lines=[]
        in_file=open(file_path,'r')
        for index,line in enumerate(in_file):
            lines.append(line)
            if re.search("!!",line):
                data_begin_line=index+1
        self.lines=lines
        in_file.close()
        parse_options={"row_end_token":'\n',
                       "row_pattern":make_row_match_string(self.options["column_names"],delimiter_pattern='[\s|(),]+'),
                       "column_names":self.options["column_names"],"column_types":self.options["column_types"]}
        data=parse_lines(lines[data_begin_line:],**parse_options)
        self.options["data"]=data
        self.options["header"]=lines[:data_begin_line-1]
        #print data


    def structure_metadata(self):
        """Returns a dictionary of key,value pairs extracted from the header"""
        keys=["System_Id","System_Letter","Connector_Type_Calibration","Connector_Type_Measurement",
              "Measurement_Type","Measurement_Date","Measurement_Time","Program_Used","Program_Revision","Operator",
              "Calibration_Name","Calibration_Date","Port_Used","Number_Connects","Number_Repeats","Nbs",
              "Number_Frequencies","Start_Frequency",
              "Device_Description","Device_Id"]
        self.metadata={}
        for index,key in enumerate(keys):
            self.metadata[key]=self.header[index].rstrip().lstrip()

Ancestors (in MRO)

  • PowerRawModel
  • pyMez.Code.DataHandlers.GeneralModels.AsciiDataTable

Instance variables

var options

var path

Methods

def __init__(

self, file_path=None, **options)

Initializes the PowerRaw class, if a file_path is specified opens an existing file, else creates an empty container

def __init__(self,file_path=None,**options):
    """Initializes the PowerRaw class, if a file_path is specified opens an existing file, else creates an
    empty container"""
    defaults= {"data_delimiter": ",", "column_names_delimiter": ",", "specific_descriptor": 'Raw',
               "general_descriptor": 'Power', "extension": 'txt', "comment_begin": "#", "comment_end": "\n",
               "column_types": ['float','int','int','float','float','float','float'],
               "column_descriptions": {"Frequency":"Frequency in GHz",
                                       "Direction":"Direction of connects, may be unused",
                                       "Connect":"Connect number", "magS11":"Linear magnitude for S11",
                                       "argS11":"Phase in degrees for S11",
                                       "Efficiency":"Effective Efficiency",
                                       "Calibration_Factor":"Effective efficiency "
                                                            "modified by reflection coefficient"},
               "header": None,
               "column_names": ["Frequency","Direction","Connect", "magS11",
                                "argS11","Efficiency","Calibration_Factor"],
               "column_names_end_token": "\n", "data": None,
               'row_formatter_string': "{0:.5g}{delimiter}{1}{delimiter}{2}"
                                       "{delimiter}{3:.5g}{delimiter}{4:.3f}{delimiter}"
                                       "{5:.5g}{delimiter}{6:.5g}",
               "data_table_element_separator": None}
    self.options={}
    for key,value in defaults.iteritems():
        self.options[key]=value
    for key,value in options.iteritems():
        self.options[key]=value
    # Define Method Aliases if they are available
    if METHOD_ALIASES:
        for command in alias(self):
            exec(command)
    if file_path is not None:
        self.__read_and_fix__(file_path)
    AsciiDataTable.__init__(self,None,**self.options)
    self.path=file_path
    self.structure_metadata()

def add_column(

self, column_name=None, column_type=None, column_data=None, format_string=None)

Adds a column with column_name, and column_type. If column data is supplied and it's length is the same as data(same number of rows) then it is added, else self.options['empty_character'] is added in each spot in the preceding rows

def add_column(self,column_name=None,column_type=None,column_data=None,format_string=None):
    """Adds a column with column_name, and column_type. If column data is supplied and it's length is the
    same as data(same number of rows) then it is added, else self.options['empty_character'] is added in each
    spot in the preceding rows"""
    original_column_names=self.column_names[:]
    try:
        self.column_names=original_column_names+[column_name]
        if self.options["column_types"]:
            old_column_types=self.options["column_types"][:]
            self.options["column_types"]=old_column_types+[column_type]
        if len(column_data) == len(self.data):
            for index,row in enumerate(self.data[:]):
                #print("{0} is {1}".format('self.data[index]',self.data[index]))
                #print("{0} is {1}".format('row',row))
                new_row=row[:]
                new_row.append(column_data[index])
                self.data[index]=new_row
        else:
            for index,row in enumerate(self.data[:]):
                self.data[index]=row.append(self.options['empty_value'])
                if column_data is not None:
                    for item in column_data:
                        empty_row=[self.options['empty_value'] for column in original_column_names]
                        empty_row.append(item)
                        self.add_row(empty_row)
        if self.options["row_formatter_string"] is None:
            pass
        else:
            if format_string is None:
                self.options["row_formatter_string"]=self.options["row_formatter_string"]+\
                                                             '{delimiter}'+"{"+str(len(self.column_names)-1)+"}"
            else:
                self.options["row_formatter_string"]=self.options["row_formatter_string"]+format_string
        #self.update_model()
    except:
        self.column_names=original_column_names
        print("Could not add columns")
        raise

def add_index(

self)

Adds a column with name index and values that are 0 referenced indices, does nothing if there is already a column with name index, always inserts it at the 0 position

def add_index(self):
    """Adds a column with name index and values that are 0 referenced indices, does nothing if there is
    already a column with name index, always inserts it at the 0 position"""
    if 'index' in self.column_names:
        print("Add Index passed")
        pass
    else:
        self.column_names.insert(0,'index')
        for index,row in enumerate(self.data):
            self.data[index].insert(0,index)
        if self.options['column_types']:
            self.options['column_types'].insert(0,'int')
        if self.options['row_formatter_string']:
            temp_formatter_list=self.options['row_formatter_string'].split("{delimiter}")
            iterated_row_formatter_list=[temp_formatter_list[i].replace(str(i),str(i+1))
                                         for i in range(len(temp_formatter_list))]
            new_formatter=string_list_collapse(iterated_row_formatter_list,string_delimiter="{delimiter}")
            self.options['row_formatter_string']='{0}{delimiter}'+new_formatter

def add_inline_comment(

self, comment='', line_number=None, string_position=None)

Adds an inline in the specified location

def add_inline_comment(self,comment="",line_number=None,string_position=None):
    "Adds an inline in the specified location"
    try:
        self.inline_comments.append([comment,line_number,string_position])
    except:pass

def add_row(

self, row_data)

Adds a single row given row_data which can be an ordered list/tuple or a dictionary with column names as keys

def add_row(self,row_data):
    """Adds a single row given row_data which can be an ordered list/tuple or a dictionary with
    column names as keys"""
    if len(row_data) not in [len(self.column_names),len(self.column_names)]:
        print(" could not add the row, dimensions do not match")
        return
    if type(row_data) in [ListType,np.ndarray]:
        self.data.append(row_data)
    elif type(row_data) in [DictionaryType]:
        data_list=[row_data[column_name] for column_name in self.column_names]
        self.data.append(data_list)

def build_string(

self, **temp_options)

Builds a string representation of the data table based on self.options, or temp_options. Passing temp_options does not permanently change the model

def build_string(self,**temp_options):
    """Builds a string representation of the data table based on self.options, or temp_options.
    Passing temp_options does not permanently change the model"""
    # store the original options to be put back after the string is made
    original_options=self.options
    for key,value in temp_options.iteritems():
        self.options[key]=value
    section_end=0
    next_section_begin=0
    if self.options['data_table_element_separator'] is None:
        inner_element_spacing=0
    else:
        inner_element_spacing=self.options['data_table_element_separator'].count('\n')-1
    string_out=""
    between_section=""
    if self.options['data_table_element_separator'] is not None:
        between_section=self.options['data_table_element_separator']
    if self.header is None:
        self.options['header_begin_line']=self.options['header_end_line']=None
        pass
    else:
        self.options["header_begin_line"]=0
        if self.data is None and self.column_names is None and self.footer is None:
            string_out=self.get_header_string()
            self.options["header_end_line"]=None
        else:
            string_out=self.get_header_string()+between_section
            last_header_line=self.get_header_string().count('\n')+1
            self.options["header_end_line"]=last_header_line
            next_section_begin=last_header_line+inner_element_spacing
    if self.column_names is None:
        self.options['column_names_begin_line']=self.options['column_names_end_line']=None
        pass
    else:
        self.options["column_names_begin_line"]=next_section_begin
        if self.data is None and self.footer is None:
            self.options["column_names_end_line"]=None
            string_out=string_out+self.get_column_names_string()
        else:
            string_out=string_out+self.get_column_names_string()+between_section
            last_column_names_line=self.get_column_names_string().count('\n')+\
                                   self.options["column_names_begin_line"]+1
            self.options["column_names_end_line"]=last_column_names_line
            next_section_begin=last_column_names_line+inner_element_spacing
    if self.data is None:
        self.options['data_begin_line']=self.options['data_end_line']=None
        pass
    else:
        self.options["data_begin_line"]=next_section_begin
        if self.footer is None:
            self.options["data_end_line"]=None
            string_out=string_out+self.get_data_string()
        else:
            string_out=string_out+self.get_data_string()+between_section
            last_data_line=self.get_data_string().count("\n")+\
                            self.options["data_begin_line"]+1
            self.options["data_end_line"]=last_data_line
            next_section_begin=last_data_line+inner_element_spacing
    if self.footer is None:
        self.options['footer_begin_line']=self.options['footer_end_line']=None
        pass
    else:
        self.options["footer_begin_line"]=next_section_begin
        string_out=string_out+self.get_footer_string()
        self.options['footer_end_line']=None
    # set the options back after the string has been made
    if self.inline_comments is None:
        pass
    else:
        lines=string_out.splitlines()
        for comment in self.inline_comments:
            lines=insert_inline_comment(lines,comment=comment[0],line_number=comment[1],
                                        string_position=comment[2],
                                        begin_token=self.options['inline_comment_begin'],
                                        end_token=self.options['inline_comment_end'])
        string_out=string_list_collapse(lines,string_delimiter='\n')
    self.options=original_options
    return string_out

def change_unit_prefix(

self, column_selector=None, old_prefix=None, new_prefix=None, unit='Hz')

Changes the prefix of the units of the column specified by column_selector (column name or index) example usage is self.change_unit_prefix(column_selector='Frequency',old_prefix=None,new_prefix='G',unit='Hz') to change a column from Hz to GHz. It updates the data values, column_descriptions, and column_units if they exist, see http://www.nist.gov/pml/wmd/metric/prefixes.cfm for possible prefixes

def change_unit_prefix(self,column_selector=None,old_prefix=None,new_prefix=None,unit='Hz'):
    """Changes the prefix of the units of the column specified by column_selector (column name or index)
    example usage is self.change_unit_prefix(column_selector='Frequency',old_prefix=None,new_prefix='G',unit='Hz')
    to change a column from Hz to GHz. It updates the data values, column_descriptions, and column_units if they
    exist, see http://www.nist.gov/pml/wmd/metric/prefixes.cfm for possible prefixes"""
    multipliers={"yotta":10.**24,"Y":10.**24,"zetta":10.**21,"Z":10.**21,"exa":10.**18,"E":10.**18,"peta":10.**15,
                 "P":10.**15,"tera":10.**12,"T":10.**12,"giga":10.**9,"G":10.**9,"mega":10.**6,"M":10.**6,
                 "kilo":10.**3,"k":10.**3,"hecto":10.**2,"h":10.**2,"deka":10.,"da":10.,None:1.,"":1.,
                 "deci":10.**-1,"d":10.**-1,"centi":10.**-2,"c":10.**-2,"milli":10.**-3,"m":10.**-3,
                 "micro":10.**-6,"mu":10.**-6,u"\u00B5":10.**-6,"nano":10.**-9,
                 "n":10.**-9,"pico":10.**-12,"p":10.**-12,"femto":10.**-15,
                 "f":10.**-15,"atto":10.**-18,"a":10.**-18,"zepto":10.**-21,"z":10.**-21,
                 "yocto":10.**-24,"y":10.**-24}
    # change column name into column index
    try:
        if old_prefix is None:
            old_prefix=""
        if new_prefix is None:
            new_prefix=""
        old_unit=old_prefix+unit
        new_unit=new_prefix+unit
        if column_selector in self.column_names:
            column_selector=self.column_names.index(column_selector)
        for index,row in enumerate(self.data):
            if type(self.data[index][column_selector]) in [FloatType,LongType]:
                #print "{0:e}".format(multipliers[old_prefix]/multipliers[new_prefix])
                self.data[index][column_selector]=\
                (multipliers[old_prefix]/multipliers[new_prefix])*self.data[index][column_selector]
            elif type(self.data[index][column_selector]) in [StringType,IntType]:
                self.data[index][column_selector]=\
                str((multipliers[old_prefix]/multipliers[new_prefix])*float(self.data[index][column_selector]))
            else:
                print type(self.data[index][column_selector])
                raise
        if self.options["column_descriptions"] is not None:
            old=self.options["column_descriptions"][column_selector]
            self.options["column_descriptions"][column_selector]=old.replace(old_unit,new_unit)
        if self.options["column_units"] is not None:
            old=self.options["column_units"][column_selector]
            self.options["column_units"][column_selector]=old.replace(old_unit,new_unit)
        if re.search(old_unit,self.column_names[column_selector]):
            old=self.column_names[column_selector]
            self.column_names[column_selector]=old.replace(old_unit,new_unit)
    except:
        print("Could not change the unit prefix of column {0}".format(column_selector))
        raise

def find_line(

self, begin_token)

Finds the first line that has begin token in it

def find_line(self,begin_token):
    """Finds the first line that has begin token in it"""
    for index,line in enumerate(self.lines):
        if re.search(begin_token,line,re.IGNORECASE):
            return index

def get_column(

self, column_name=None, column_index=None)

Returns a column as a list given a column name or column index

def get_column(self,column_name=None,column_index=None):
    """Returns a column as a list given a column name or column index"""
    if column_name is None:
        if column_index is None:
            return
        else:
            column_selector=column_index
    else:
        column_selector=self.column_names.index(column_name)
    out_list=[self.data[i][column_selector] for i in range(len(self.data))]
    return out_list

def get_column_names_string(

self)

Returns the column names as a string using options

def get_column_names_string(self):
    "Returns the column names as a string using options"
    string_out=""
    # This writes the column_names
    column_name_begin=""
    column_name_end=""
    if self.options["column_names_begin_token"] is None:
        column_name_begin=""
    else:
        column_name_begin=self.options["column_names_begin_token"]
    if self.options["column_names_end_token"] is None:
        column_name_end=""
    else:
        column_name_end=self.options["column_names_end_token"]
    if self.column_names is None:
        string_out=""
    else:
        if type(self.column_names) is StringType:
            string_out=self.column_names
        elif type(self.column_names) is ListType:
            string_out=list_to_string(self.column_names,
                                      data_delimiter=self.options["column_names_delimiter"],end="")
            #print("{0} is {1}".format('string_out',string_out))
        else:
            string_out=ensure_string(self.column_names)
    #print column_name_begin,string_out,column_name_end
    return column_name_begin+string_out+column_name_end

def get_data_dictionary_list(

self, use_row_formatter_string=True)

Returns a python list with a row dictionary of form {column_name:data_column}

def get_data_dictionary_list(self,use_row_formatter_string=True):
    """Returns a python list with a row dictionary of form {column_name:data_column}"""
    try:
        if self.options["row_formatter_string"] is None:
            use_row_formatter_string=False
        if use_row_formatter_string:
            list_formatter=[item.replace("{"+str(index),"{0")
                            for index,item in enumerate(self.options["row_formatter_string"].split("{delimiter}"))]
        else:
            list_formatter=["{0}" for i in self.column_names]
        #print self.column_names
        #print self.data
        #print list_formatter
        #print len(self.column_names)==len(self.data[0])
        #print len(list_formatter)==len(self.data[0])
        #print type(self.data[0])
        out_list=[{self.column_names[i]:list_formatter[i].format(value) for i,value in enumerate(line)}
                  for line in self.data]
        return out_list
    except:
        print("Could not form a data_dictionary_list, check that row_formatter_string is properly defined")
        #print(out_list)
        raise

def get_data_string(

self)

Returns the data as a string

def get_data_string(self):
    "Returns the data as a string"
    #Todo:refactor to cut out unused lines
    string_out=""
    if self.data is None:
        string_out= ""
    else:
        if type(self.data) is StringType:
            if self.options['data_begin_token'] is None:
                   if self.options['data_end_token'] is None:
                       string_out=self.data
                   else:
                       if re.search(self.options['data_end_token'],self.data):
                           string_out=self.data
                       else:
                           string_out=self.data+self.options['data_end_token']
            else:
                    if self.options['data_end_token'] is None:
                        if re.match(self.options['data_begin_token'],self.data):
                            string_out=self.data
                        else:
                            string_out=self.options['data_begin_token']+self.data
        elif type(self.data) in [ListType,np.ndarray]:
            try:
                    #If the first row is a string, we should strip all the tokens and add them back in
                    if type(self.data[0]) is StringType:
                        if self.options['data_begin_token'] is None:
                            string_out=string_list_collapse(self.data)
                        else:
                            if re.match(self.options['data_begin_token'],self.data[0]):
                                if self.options['data_end_token'] is None:
                                    string_out=string_list_collapse(self.data)
                                else:
                                    if re.search(self.options['data_end_token'],self.data[-1]):
                                        string_out=string_list_collapse(self.data)
                                    else:
                                        string_out=string_list_collapse(self.data)+self.options['data_end_token']
                            else:
                                if self.options['data_end_token'] is None:
                                    string_out=self.options['data_begin_token']+string_list_collapse(self.data)
                                else:
                                    if re.search(self.options['data_end_token'],self.data[-1]):
                                        string_out=self.options['data_begin_token']+string_list_collapse(self.data)
                                    else:
                                        string_out=self.options['data_begin_token']+\
                                                   string_list_collapse(self.data)+\
                                                   self.options['data_end_token']
                    elif type(self.data[0]) in [ListType,np.ndarray]:
                        prefix=""
                        if self.options['data_begin_token'] is None:
                            if self.options['data_end_token'] is None:
                                string_out=list_list_to_string(self.data,data_delimiter=self.options['data_delimiter'],
                                                               row_formatter_string=self.options['row_formatter_string'],
                                                               line_begin=self.options["row_begin_token"],
                                                               line_end=self.options["row_end_token"])
                        else:
                            if self.options['data_end_token'] is None:
                                string_out=self.options['data_begin_token']+\
                                           list_list_to_string(self.data,
                                                               data_delimiter=self.options['data_delimiter'],
                                                               row_formatter_string=self.options['row_formatter_string'],
                                                               line_begin=self.options["row_begin_token"],
                                                               line_end=self.options["row_end_token"])
                            else:
                                string_out=self.options['data_begin_token']+\
                                           list_list_to_string(self.data,
                                                               data_delimiter=self.options['data_delimiter'],
                                                               row_formatter_string=\
                                                               self.options['row_formatter_string'],
                                                               line_begin=self.options["row_begin_token"],
                                                               line_end=self.options["row_end_token"])+\
                                                                self.options['data_end_token']
                    else:
                        string_out=list_to_string(self.data,
                                                  data_delimiter=self.options['data_delimiter'],
                                                  row_formatter_string=self.options['row_formatter_string'],
                                                  begin=self.options["row_begin_token"],
                                                  end=self.options["row_end_token"])
            except IndexError:
                pass
        else:
            string_out=ensure_string(self.data)
    return string_out

Returns the footer using options in self.options. If block comment is specified, and the footer is a list it will block comment out the footer. If comment_begin and comment_end are specified it will use those to represent each line of the footer. If footer_begin_token and/or footer_end_token are specified it will wrap the footer in those.

def get_header_string(

self)

Returns the header using options in self.options. If block comment is specified, and the header is a list it will block comment out the header. If comment_begin and comment_end are specified it will use those to represent each line of the header. If header_begin_token and/or header_end_token are specified it will wrap the header in those.

def get_header_string(self):
    """Returns the header using options in self.options. If block comment is specified, and the header is a
    list it will block comment out the header. If comment_begin and comment_end are specified it will use
    those to represent each line of the header. If header_begin_token and/or header_end_token are specified it
     will wrap the header in those.
    """
    string_out=""
    header_begin=""
    header_end=""
    if self.options["header_begin_token"] is None:
        header_begin=""
    else:
        header_begin=self.options["header_begin_token"]
    if self.options["header_end_token"] is None:
        header_end=""
    else:
        header_end=self.options["header_end_token"]
    # This writes the header
    if self.header is None:
        string_out= ""
    elif self.options["header_line_types"] is not None:
        for index,line in enumerate(self.options["header_line_types"]):
            if index == len(self.options["header_line_types"])-1:
                end=''
            else:
                end='\n'
            if line in ['header','header_line','normal']:
                string_out=string_out+self.header[index]+end
            elif line in ['line_comment','comment']:
                string_out=string_out+line_comment_string(self.header[index],
                                           comment_begin=self.options["comment_begin"],
                                           comment_end=self.options["comment_end"])+end
            elif line in ['block_comment','block']:
                if index-1<0:
                    block_comment_begin=index
                    block_comment_end=index+2
                    continue
                elif self.options["header_line_types"][index-1] not in ['block_comment','block']:
                    block_comment_begin=index
                    block_comment_end=index+2
                    continue
                else:
                    if index+1>len(self.options["header_line_types"])-1:
                        string_out=string_out+line_list_comment_string(self.header[block_comment_begin:],
                                                                       comment_begin=self.options['block_comment_begin'],
                                                                         comment_end=self.options['block_comment_end'],
                                                                       block=True)+end
                    elif self.options["header_line_types"][index+1] in ['block_comment','block']:
                        block_comment_end+=1
                    else:
                        string_out=string_out+\
                                   line_list_comment_string(self.header[block_comment_begin:block_comment_end],
                                                            comment_begin=self.options['block_comment_begin'],
                                                            comment_end=self.options['block_comment_end'],
                                                            block=True)+end
            else:
                string_out=string_out+line
    elif self.options['treat_header_as_comment'] in [None,True] and self.options["header_line_types"] in [None]:
        # Just happens if the user has set self.header manually
        if type(self.header) is StringType:
            string_out=line_comment_string(self.header,
                                           comment_begin=self.options["comment_begin"],
                                           comment_end=self.options["comment_end"])
            #string_out=re.sub('\n','',string_out,count=1)
        elif type(self.header) is ListType:
            if self.options['block_comment_begin'] is None:
                if self.options['comment_begin'] is None:
                    string_out=string_list_collapse(self.header)
                else:
                    string_out=line_list_comment_string(self.header,comment_begin=self.options['comment_begin'],
                                                    comment_end=self.options['comment_end'])
                    lines_out=string_out.splitlines()
                    # if re.search('\n',self.options['comment_end']):
                    #     string_out=re.sub('\n','',string_out,count=1)
                    #self.options["header_line_types"]=["line_comment" for line in self.header]
            else:
                string_out=line_list_comment_string(self.header,comment_begin=self.options['block_comment_begin'],
                                                    comment_end=self.options['block_comment_end'],block=True)
                #self.options["header_line_types"]=["block_comment" for line in self.header]
    else:
        string_out=ensure_string(self.header,list_delimiter="\n",end_if_list="")
    return header_begin+string_out+header_end

def get_options(

self)

Prints the option list

def get_options(self):
    "Prints the option list"
    for key,value in self.options.iteritems():
        print("{0} = {1}".format(key,value))

def get_options_by_element(

self, element_name)

returns a dictionary of all the options that have to do with element. Element must be header,column_names,data, or footer

def get_options_by_element(self,element_name):
    """ returns a dictionary
     of all the options that have to do with element. Element must be header,column_names,data, or footer"""
    keys_regarding_element=filter(lambda x: re.search(element_name,str(x),re.IGNORECASE),self.options.keys())
    out_dictionary={key:self.options[key] for key in keys_regarding_element}
    #print out_dictionary
    return out_dictionary

def get_row(

self, row_index=None)

Returns the row as a list specified by row_index

def get_row(self,row_index=None):
    """Returns the row as a list specified by row_index"""
    if row_index is None:
        return
    else:
        return self.data[row_index]

def is_valid(

self)

Returns True if ascii table conforms to its specification given by its own options

def is_valid(self):
    """Returns True if ascii table conforms to its specification given by its own options"""
    options={}
    for key,value in self.options.iteritems():
        options[key]=value
        # print("self.options[{0}] is {1} ".format(key,value))
    for element in self.elements:
        if self.__dict__[element] is None:
            options[element]=None
        else:
            options[element]=[]
    options["validate"]=True
    newtable=AsciiDataTable(None,**options)
    lines=self.build_string().splitlines()
    for index,line in enumerate(lines):
        lines[index]=line+"\n"
    newtable.lines=lines
    newtable.__parse__()
    # print newtable.data
    # print newtable.column_names
    # print newtable
    #print_comparison(newtable.footer,None)
    newtable.update_model()
    # The new table rows are not being coerced into the right format
    #print newtable
    #newtable.update_model()
    #print newtable.options
    #print self.options
    #print newtable.data
    # print newtable.options==self.options
    # for option_key,option_value in newtable.options.iteritems():
    #     print("New Table Option {0} is {1} ".format(option_key,option_value))
    #     print("self.options[{0}] is {1} ".format(option_key,self.options[option_key]))
    #     print_comparison(option_value,self.options[option_key])
    # #print self
    return self==newtable

def lines_defined(

self)

If begin_line and end_line for all elements that are None are defined returns True

def lines_defined(self):
    """If begin_line and end_line for all elements that are None are defined returns True"""
    truth_table=[]
    last_element=""
    output=False
    for index,element in enumerate(self.elements):
        if element not in ['inline_comments','metadata'] and self.__dict__[element] is not None:
            try:
                last_element=element
                if not None in [self.options['%s_begin_line'%element],self.options['%s_end_line'%element]]:
                    truth_table.append(True)
                else:
                     truth_table.append(False)
            except:
                return False
    #print truth_table
    # The last_line of the last element is fine to be none
    if truth_table[-1] is False:
        if self.options['%s_begin_line'%last_element] is not None:
            truth_table[-1]=True
    if False in truth_table:
        output=False
    else:
        output=True
    #print output
    return output

Moves the DataTable's footer to the header and updates the model

def remove_column(

self, column_name=None, column_index=None)

Removes the column specified by column_name or column_index and updates the model. The column is removed from column_names, data and if present column_types, column_descriptions and row formatter

def remove_column(self,column_name=None,column_index=None):
    """Removes the column specified by column_name or column_index and updates the model. The column is removed from
    column_names, data and if present column_types, column_descriptions and row formatter"""
    pass

def remove_row(

self, row_index)

Removes the row specified by row_index and updates the model. Note index is relative to the data attribute so to remove the first row use row_index=0 and the last data row is row_index=-1

def remove_row(self,row_index):
    """Removes the row specified by row_index and updates the model. Note index is relative to the
    data attribute so to remove the first row use row_index=0 and the last data row is row_index=-1"""
    self.data.pop(row_index)
    self.update_model()

def save(

self, path=None, **temp_options)

" Saves the file, to save in another ascii format specify elements in temp_options, the options specified do not permanently change the object's options. If path is supplied it saves the file to that path otherwise uses the object's attribute path to define the saving location

def save(self,path=None,**temp_options):
    """" Saves the file, to save in another ascii format specify elements in temp_options, the options
    specified do not permanently change the object's options. If path is supplied it saves the file to that path
    otherwise uses the object's attribute path to define the saving location """
    original_options=self.options
    for key,value in temp_options.iteritems():
        self.options[key]=value
    out_string=self.build_string(**temp_options)
    if path is None:
        path=self.path
    file_out=open(path,'w')
    file_out.write(out_string)
    file_out.close()
    self.options=original_options

def save_schema(

self, path=None, format=None)

Saves the tables options as a text file or pickled dictionary (default). If no name is supplied, autonames it and saves

def save_schema(self,path=None,format=None):
    """Saves the tables options as a text file or pickled dictionary (default).
    If no name is supplied, autonames it and saves"""
    if path is None:
        path=auto_name(self.name.replace('.'+self.options["extension"],""),'Schema',self.options["directory"],'txt')
    if format in [None,'python','pickle']:
        pickle.dump(self.options,open(path,'wb'))
    elif format in ['txt','text','.txt']:
        file_out=open(path,'w')
        keys=self.options.keys()
        keys.sort()
        for key in keys:
            out_key=str(key).replace("\n","\\n")
            out_value=str(self.options[key]).replace("\n","\\n")
            file_out.write("{0} : {1} \n".format(out_key,out_value))
        file_out.close()

def structure_metadata(

self)

Returns a dictionary of key,value pairs extracted from the header

def structure_metadata(self):
    """Returns a dictionary of key,value pairs extracted from the header"""
    keys=["System_Id","System_Letter","Connector_Type_Calibration","Connector_Type_Measurement",
          "Measurement_Type","Measurement_Date","Measurement_Time","Program_Used","Program_Revision","Operator",
          "Calibration_Name","Calibration_Date","Port_Used","Number_Connects","Number_Repeats","Nbs",
          "Number_Frequencies","Start_Frequency",
          "Device_Description","Device_Id"]
    self.metadata={}
    for index,key in enumerate(keys):
        self.metadata[key]=self.header[index].rstrip().lstrip()

def update_column_names(

self)

Update column names adds the value x# for any column that exists in self.data that is not named

def update_column_names(self):
    """Update column names adds the value x# for any column that exists in self.data that is not named"""
    if self.data is None:
        return
    elif type(self.column_names) is StringType:
        self.column_names=split_row(self.column_names,self.options["column_names_delimiter"])
    elif self.column_names is None:
        column_names=[]
        for index,column in enumerate(self.data[0]):
            column_names.append("x"+str(index))
        self.column_names=column_names
        return
    elif len(self.column_names)==len(self.data[0]):
        return
    elif len(self.column_names) < len(self.data[0]):
        for index in range(len(self.column_names),len(self.data[0])):
            self.column_names.append("x"+str(index))
        return

def update_import_options(

self, import_table)

Updates the options in the import table

def update_import_options(self,import_table):
    """Updates the options in the import table"""
    for index,element in enumerate(['header','column_names','data','footer']):
        if self.__dict__[element] is not None:
            print("The {0} variable is {1}".format('index',index))
            print("The {0} variable is {1}".format('element',element))
            print("The {0} variable is {1}".format('import_table',import_table))
            [self.options['%s_begin_line'%element],
                            self.options['%s_end_line'%element],
                            self.options['%s_begin_token'%element],
                            self.options['%s_end_token'%element]]=import_table[index][:]

def update_index(

self)

Updates the index column if it exits, otherwise exits quietly

def update_index(self):
    """ Updates the index column if it exits, otherwise exits quietly
    """
    if 'index' not in self.column_names:
        return
    else:
        try:
            #This should be 0 but just in case
            index_column_number=self.column_names.index('index')
            for i in range(len(self.data)):
                self.data[i][index_column_number]=i
        except:
            pass

def update_model(

self)

Updates the model after a change has been made. If you add anything to the attributes of the model, or change this updates the values. If the model has an index column it will make sure the numbers are correct. In addition, it will update the options dictionary to reflect added rows, changes in deliminators etc.

def update_model(self):
    """Updates the model after a change has been made. If you add anything to the attributes of the model,
    or change this updates the values. If the model has an index column it will make sure the numbers are correct.
    In addition, it will update the options dictionary to reflect added rows, changes in deliminators etc.  """
    if self.column_names is not None and 'index' in self.column_names:
       self.update_index()
    #make sure there are no "\n" characters in the element lists (if so replace them with "") for data this is
    # done on import
    list_types=["header","column_names","footer"]
    for element in list_types:
        if self.__dict__[element] is not None:
            for index,item in enumerate(self.__dict__[element]):
                self.__dict__[element][index]=item.replace("\n","")
    self.update_column_names()
    if self.data is not None:
        self.data=convert_all_rows(self.data,self.options["column_types"])
    self.string=self.build_string()
    self.lines=self.string.splitlines()

class ReverbChamber

class ReverbChamber():
    pass

Ancestors (in MRO)

class RobotData

class RobotData():
    pass

Ancestors (in MRO)

class SwitchTermsFR

class SwitchTermsFR():
    pass

Ancestors (in MRO)

class SwitchTermsPort

class SwitchTermsPort():
    pass

Ancestors (in MRO)

class TwoPortCalrepModel

TwoPortCalrepModel is a model that holds data output by analyzing several datafiles using the HPBasic program Calrep. The data is stored in 3 tables: a S11 table, a S21 table and a S22 table. The data is in linear magnitude and angle in degrees. There are 2 types of files, one is a single file with .asc extension and 3 files with .txt extension

class TwoPortCalrepModel():
    """TwoPortCalrepModel is a model that holds data output by analyzing several datafiles using the HPBasic program
    Calrep. The data is stored in 3 tables: a S11 table, a S21 table and a S22 table. The data is in linear
    magnitude and angle in degrees. There are 2 types of files, one is a single file with .asc extension
    and 3 files with .txt extension"""

    def __init__(self,file_path=None,**options):
        """Intializes the TwoPortCalrepModel class, if a file path is specified it opens and reads the file"""
        defaults= {"specific_descriptor": 'Two_Port_Calrep'}
        self.options={}
        for key,value in defaults.iteritems():
            self.options[key]=value
        for key,value in options.iteritems():
            self.options[key]=value
        if file_path is None:
            pass
        elif re.match('asc',file_path.split(".")[-1],re.IGNORECASE):
            self.table_names=['header','S11','S22','S21']
            self.row_pattern=make_row_match_string(ONE_PORT_COLUMN_NAMES)
            self.path=file_path
            self.__read_and_fix__()

        elif re.match('txt',file_path.split(".")[-1],re.IGNORECASE) or type(file_path) is ListType:
            self.table_names=['S11','S22','S21']
            if type(file_path) is ListType:
                self.file_names=file_path
                self.tables=[]
                for index,table in enumerate(self.table_names):
                    if index==2:
                        #fixes a problem with the c tables, extra comma at the end
                        options={"row_end_token":',\n'}
                        self.tables.append(OnePortCalrepModel(self.file_names[index],**options))
                        self.tables[2].options["row_end_token"]=None
                    else:
                        self.tables.append(OnePortCalrepModel(self.file_names[index]))
            else:
                try:
                    root_name_pattern=re.compile('(?P<root_name>\w+)[abc].txt',re.IGNORECASE)
                    root_name_match=re.search(root_name_pattern,file_path)
                    root_name=root_name_match.groupdict()["root_name"]
                    directory=os.path.dirname(os.path.realpath(file_path))
                    self.file_names=[os.path.join(directory,root_name+end) for end in ['a.txt','b.txt','c.txt']]
                    self.tables=[]
                    for index,table in enumerate(self.table_names):
                        if index==2:
                            #fixes a problem with the c tables, extra comma at the end
                            options={"row_end_token":',\n'}
                            self.tables.append(OnePortCalrepModel(self.file_names[index],**options))
                            self.tables[2].options["row_end_token"]=None
                        else:
                            self.tables.append(OnePortCalrepModel(self.file_names[index]))

                except:
                    print("Could not import {0} please check that the a,b,c "
                          "tables are all in the same directory".format(file_path))
                    raise
            for index,table in enumerate(self.tables):
                column_names=[]
                for column_number,column in enumerate(table.column_names):
                    if column is not "Frequency":
                        column_names.append(column+self.table_names[index])
                    else:
                        column_names.append(column)
                #print column_names
                table.column_names=column_names
            if CONVERT_S21:
                for row_number,row in enumerate(self.tables[2].data):
                    new_S21=self.tables[2].data[row_number][1]
                    new_S21=10.**(-1*new_S21/20.)
                    new_value=[self.tables[2].data[row_number][i] for i in range(2,6)]
                    new_value=map(lambda x:abs((1/np.log10(np.e))*new_S21*x/20.),new_value)
                    self.tables[2].data[row_number][1]=new_S21
                    for i in range(2,6):
                        self.tables[2].data[row_number][i]=new_value[i-2]
            for key,value in self.options.iteritems():
                self.tables[0].options[key]=value
            self.joined_table=ascii_data_table_join("Frequency",self.tables[0],self.tables[2])
            self.joined_table=ascii_data_table_join("Frequency",self.joined_table,self.tables[1])

    def __read_and_fix__(self):
        in_file=open(self.path,'r')
        self.lines=[]
        table_locators=["Table 1","Table 2","Table 3"]
        begin_lines=[]
        for index,line in enumerate(in_file):
            self.lines.append(line)
            for table in table_locators:
                if re.search(table,line,re.IGNORECASE):
                    begin_lines.append(index)
        in_file.close()
        self.table_line_numbers=[]
        for index,begin_line in enumerate(begin_lines):
            if index == 0:
                header_begin_line=0
                header_end_line=begin_line-2
                table_1_begin_line=begin_line+3
                table_1_end_line=begin_lines[index+1]#-1
                self.table_line_numbers.append([header_begin_line,header_end_line])
                self.table_line_numbers.append([table_1_begin_line,table_1_end_line])

            elif index>0 and index<(len(begin_lines)-1):
                table_begin_line=begin_line+3
                table_end_line=begin_lines[index+1]#-1
                self.table_line_numbers.append([table_begin_line,table_end_line])

            elif index==(len(begin_lines)-1):
                table_begin_line=begin_line+3
                table_end_line=None
                self.table_line_numbers.append([table_begin_line,table_end_line])
        self.tables=[]
        for index,name in enumerate(self.table_names):
            self.table_lines=self.lines[self.table_line_numbers[index][0]:self.table_line_numbers[index][1]]
            self.tables.append(self.table_lines)
        for index,table in enumerate(self.table_names):
            if index==0:
                # by using parse_lines we get a list_list of strings instead of list_string
                # we can just remove end lines
                self.tables[index]=strip_all_line_tokens(self.tables[index],begin_token=None,end_token='\n')
            else:
                column_types=['float' for i in range(len(ONE_PORT_COLUMN_NAMES))]
                options={"row_pattern":self.row_pattern,"column_names":ONE_PORT_COLUMN_NAMES,"output":"list_list"}
                options["column_types"]=column_types
                self.tables[index]=parse_lines(self.tables[index],**options)

        # need to put S21 mag into linear magnitude
        if CONVERT_S21:
            for row_number,row in enumerate(self.tables[3]):
                new_S21=self.tables[3][row_number][1]
                new_S21=10.**(-1*new_S21/20.)
                new_value=[self.tables[3][row_number][i] for i in range(2,6)]
                new_value=map(lambda x:abs((1/np.log10(np.e))*new_S21*x/20),new_value)
                self.tables[3][row_number][1]=new_S21
                for i in range(2,6):
                    self.tables[3][row_number][i]=new_value[i-2]

        for index,table in enumerate(self.tables):
            #print("{0} is {1}".format("index",index))
            if index==0:
                pass
            else:
                table_options={"data":self.tables[index]}
                self.tables[index]=OnePortCalrepModel(None,**table_options)
                #print("{0} is {1}".format("self.tables[index].column_names",self.tables[index].column_names))
                column_names=[]
                for column_number,column in enumerate(self.tables[index].column_names):
                    if column is not "Frequency":
                        #print("{0} is {1}".format("self.table_names[index]",self.table_names[index]))
                        #print("{0} is {1}".format("column",column))
                        column_names.append(column+self.table_names[:][index])
                    else:
                        column_names.append(column)
                self.tables[index].column_names=column_names

        self.tables[1].header=self.tables[0]
        for key,value in self.options.iteritems():
            self.tables[1].options[key]=value
        self.joined_table=ascii_data_table_join("Frequency",self.tables[1],self.tables[3])
        self.joined_table=ascii_data_table_join("Frequency",self.joined_table,self.tables[2])

    def __str__(self):
        return self.joined_table.build_string()

    def show(self):
        fig, axes = plt.subplots(nrows=3, ncols=2)
        ax0, ax1, ax2, ax3, ax4, ax5 = axes.flat
        ax0.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('magS11'),
             yerr=self.joined_table.get_column('uMgS11'),fmt='k-o')
        ax0.set_title('Magnitude S11')
        ax1.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('argS11'),
             yerr=self.joined_table.get_column('uAgS11'),fmt='ro')
        ax1.set_title('Phase S11')
        ax2.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('magS21'),
             yerr=self.joined_table.get_column('uMgS21'),fmt='k-o')
        ax2.set_title('Magnitude S21')
        ax3.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('argS21'),
             yerr=self.joined_table.get_column('uAgS21'),fmt='ro')
        ax3.set_title('Phase S21')
        ax4.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('magS22'),
             yerr=self.joined_table.get_column('uMgS22'),fmt='k-o')
        ax4.set_title('Magnitude S22')
        ax5.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('argS22'),
             yerr=self.joined_table.get_column('uAgS22'),fmt='ro')
        ax5.set_title('Phase S22')
        plt.tight_layout()
        plt.show()

Ancestors (in MRO)

Instance variables

var options

Methods

def __init__(

self, file_path=None, **options)

Intializes the TwoPortCalrepModel class, if a file path is specified it opens and reads the file

def __init__(self,file_path=None,**options):
    """Intializes the TwoPortCalrepModel class, if a file path is specified it opens and reads the file"""
    defaults= {"specific_descriptor": 'Two_Port_Calrep'}
    self.options={}
    for key,value in defaults.iteritems():
        self.options[key]=value
    for key,value in options.iteritems():
        self.options[key]=value
    if file_path is None:
        pass
    elif re.match('asc',file_path.split(".")[-1],re.IGNORECASE):
        self.table_names=['header','S11','S22','S21']
        self.row_pattern=make_row_match_string(ONE_PORT_COLUMN_NAMES)
        self.path=file_path
        self.__read_and_fix__()
    elif re.match('txt',file_path.split(".")[-1],re.IGNORECASE) or type(file_path) is ListType:
        self.table_names=['S11','S22','S21']
        if type(file_path) is ListType:
            self.file_names=file_path
            self.tables=[]
            for index,table in enumerate(self.table_names):
                if index==2:
                    #fixes a problem with the c tables, extra comma at the end
                    options={"row_end_token":',\n'}
                    self.tables.append(OnePortCalrepModel(self.file_names[index],**options))
                    self.tables[2].options["row_end_token"]=None
                else:
                    self.tables.append(OnePortCalrepModel(self.file_names[index]))
        else:
            try:
                root_name_pattern=re.compile('(?P<root_name>\w+)[abc].txt',re.IGNORECASE)
                root_name_match=re.search(root_name_pattern,file_path)
                root_name=root_name_match.groupdict()["root_name"]
                directory=os.path.dirname(os.path.realpath(file_path))
                self.file_names=[os.path.join(directory,root_name+end) for end in ['a.txt','b.txt','c.txt']]
                self.tables=[]
                for index,table in enumerate(self.table_names):
                    if index==2:
                        #fixes a problem with the c tables, extra comma at the end
                        options={"row_end_token":',\n'}
                        self.tables.append(OnePortCalrepModel(self.file_names[index],**options))
                        self.tables[2].options["row_end_token"]=None
                    else:
                        self.tables.append(OnePortCalrepModel(self.file_names[index]))
            except:
                print("Could not import {0} please check that the a,b,c "
                      "tables are all in the same directory".format(file_path))
                raise
        for index,table in enumerate(self.tables):
            column_names=[]
            for column_number,column in enumerate(table.column_names):
                if column is not "Frequency":
                    column_names.append(column+self.table_names[index])
                else:
                    column_names.append(column)
            #print column_names
            table.column_names=column_names
        if CONVERT_S21:
            for row_number,row in enumerate(self.tables[2].data):
                new_S21=self.tables[2].data[row_number][1]
                new_S21=10.**(-1*new_S21/20.)
                new_value=[self.tables[2].data[row_number][i] for i in range(2,6)]
                new_value=map(lambda x:abs((1/np.log10(np.e))*new_S21*x/20.),new_value)
                self.tables[2].data[row_number][1]=new_S21
                for i in range(2,6):
                    self.tables[2].data[row_number][i]=new_value[i-2]
        for key,value in self.options.iteritems():
            self.tables[0].options[key]=value
        self.joined_table=ascii_data_table_join("Frequency",self.tables[0],self.tables[2])
        self.joined_table=ascii_data_table_join("Frequency",self.joined_table,self.tables[1])

def show(

self)

def show(self):
    fig, axes = plt.subplots(nrows=3, ncols=2)
    ax0, ax1, ax2, ax3, ax4, ax5 = axes.flat
    ax0.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('magS11'),
         yerr=self.joined_table.get_column('uMgS11'),fmt='k-o')
    ax0.set_title('Magnitude S11')
    ax1.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('argS11'),
         yerr=self.joined_table.get_column('uAgS11'),fmt='ro')
    ax1.set_title('Phase S11')
    ax2.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('magS21'),
         yerr=self.joined_table.get_column('uMgS21'),fmt='k-o')
    ax2.set_title('Magnitude S21')
    ax3.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('argS21'),
         yerr=self.joined_table.get_column('uAgS21'),fmt='ro')
    ax3.set_title('Phase S21')
    ax4.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('magS22'),
         yerr=self.joined_table.get_column('uMgS22'),fmt='k-o')
    ax4.set_title('Magnitude S22')
    ax5.errorbar(self.joined_table.get_column('Frequency'),self.joined_table.get_column('argS22'),
         yerr=self.joined_table.get_column('uAgS22'),fmt='ro')
    ax5.set_title('Phase S22')
    plt.tight_layout()
    plt.show()

class TwoPortNRRawModel

Class that deals with the TwoPort Raw Files after conversion to Ascii using Ron Ginley's converter. These files typically have header information seperated from data by !! Header format is: Line 1: Spid$ - identification of type of system used Line 2: Systemletter$ - letter name indicating which system was used Line 3: Conncal$ - connector type from the system calibration Line 4: Connectors$ - connector type used for the measurement Line 5: Meastype$ - type of measurement (basically 1-port, 2-port or power) Line 6: Datea$ - date of measurement Line 7: Timea$ - time of measurement Line 8: Programm$ - name of program used Line 9: Rev$ - program revision Line 10: Opr$ - operator Line 11: Cfile$ - calibration name Line 12: Cdate$ - calibration date Line 13: Sport - identification of which port or direction was used for measurement Line 14: Numconnects ? number of disconnect/reconnect cycles Line 15: Numrepeats ? number of repeat measurements for each connect (usually 1) Line 16: Nbs ? not sure Line 17: Nfreq ? number of frequencies Line 18: Startfreq ? data row pointer for bdat files Line 19: Devicedescript$ - description of device being measured or of test being done Line 20: Devicenum$ - Identifying number for device ? used for file names

class TwoPortNRRawModel(AsciiDataTable):
    """ Class that deals with the TwoPort Raw Files after conversion to Ascii using Ron Ginley's converter.
    These files typically have header information seperated from data by !!
    Header format is:
    Line 1:		Spid$ - identification of type of system used
    Line 2:		Systemletter$ - letter name indicating which system was used
    Line 3:		Conncal$ - connector type from the system calibration
    Line 4:		Connectors$ - connector type used for the measurement
    Line 5:		Meastype$ - type of measurement (basically 1-port, 2-port or power)
    Line 6:		Datea$ - date of measurement
    Line 7:		Timea$ - time of measurement
    Line 8:		Programm$ - name of program used
    Line 9:		Rev$ - program revision
    Line 10:	Opr$ - operator
    Line 11:	Cfile$ - calibration name
    Line 12:	Cdate$ - calibration date
    Line 13:	Sport - identification of which port or direction was used for measurement
    Line 14:	Numconnects ? number of disconnect/reconnect cycles
    Line 15:	Numrepeats ? number of repeat measurements for each connect (usually 1)
    Line 16:	Nbs ? not sure
    Line 17:	Nfreq ? number of frequencies
    Line 18:	Startfreq ? data row pointer for bdat files
    Line 19:	Devicedescript$ - description of device being measured or of test being done
    Line 20:	Devicenum$ - Identifying number for device ? used for file names
    """
    def __init__(self,file_path=None,**options):
        """Initializes the TwoPortRaw class, if a file_path is specified opens an existing file, else creates an
        empty container"""
        defaults= {"data_delimiter": ",", "column_names_delimiter": ",", "specific_descriptor": 'Two_Port_NR_Raw',
                   "general_descriptor": 'Sparameter', "extension": 'txt', "comment_begin": "#", "comment_end": "\n",
                   "column_types": ['float','int','int','float','float','float','float',
                                    'float','float','float','float'],
                   "column_descriptions": {"Frequency":"Frequency in GHz",
                                           "Direction":"Direction of connects, may be unused",
                                           "Connect":"Connect number", "magS11":"Linear magnitude for S11",
                                           "argS11":"Phase in degrees for S11",
                                           "magS12":"Linear magnitude for S21",
                                           "argS12":"Phase in degrees for S21",
                                           "magS21":"Linear magnitude for S21",
                                           "argS21":"Phase in degrees for S21",
                                           "magS22":"Linear magnitude for S22",
                                           "argS22":"Phase in degrees for S22"},
                   "header": None,
                   "column_names": ["Frequency","Direction","Connect", "magS11",
                                    "argS11","magS12","argS12","magS21","argS21","magS22","argS22"],
                   "column_names_end_token": "\n", "data": None,
                   'row_formatter_string': "{0:.5f}{delimiter}{1}{delimiter}{2}"
                                           "{delimiter}{3:.4f}{delimiter}{4:.2f}{delimiter}"
                                           "{5:.4f}{delimiter}{6:.2f}{delimiter}"
                                           "{7:.4f}{delimiter}{8:.2f}{delimiter}"
                                           "{9:.4f}{delimiter}{10:.2f}",
                   "data_table_element_separator": None}
        self.options={}
        for key,value in defaults.iteritems():
            self.options[key]=value
        for key,value in options.iteritems():
            self.options[key]=value
        # Define Method Aliases if they are available
        if METHOD_ALIASES:
            for command in alias(self):
                exec(command)
        if file_path is not None:
            self.__read_and_fix__(file_path)

        AsciiDataTable.__init__(self,None,**self.options)
        self.path=file_path
        self.structure_metadata()

    def __read_and_fix__(self,file_path=None):
        """Inputs in the raw OnePortRaw file and fixes any problems with delimiters,etc."""
        lines=[]
        in_file=open(file_path,'r')
        for index,line in enumerate(in_file):
            lines.append(line)
            if re.search("!!",line):
                data_begin_line=index+1
        self.lines=lines
        in_file.close()
        parse_options={"row_end_token":'\n',
                       "row_pattern":make_row_match_string(self.options["column_names"]),
                       "column_names":self.options["column_names"],"column_types":self.options["column_types"]}
        data=parse_lines(lines[data_begin_line:],**parse_options)
        self.options["data"]=data
        if CONVERT_S21:
            for row_index,row in enumerate(self.options["data"]):
                db_value_S21=row[7]
                mag_value_S21=10.**(-1*db_value_S21/20.)
                db_value_S12=row[5]
                mag_value_S12=10.**(-1*db_value_S12/20.)
                self.options["data"][row_index][5]=mag_value_S12
                self.options["data"][row_index][7]=mag_value_S21
        self.options["header"]=lines[:data_begin_line-1]
        #print data


    def structure_metadata(self):
        """Returns a dictionary of key,value pairs extracted from the header"""
        keys=["System_Id","System_Letter","Connector_Type_Calibration","Connector_Type_Measurement",
              "Measurement_Type","Measurement_Date","Measurement_Time","Program_Used","Program_Revision","Operator",
              "Calibration_Name","Calibration_Date","Port_Used","Number_Connects","Number_Repeats","Nbs",
              "Number_Frequencies","Start_Frequency",
              "Device_Description","Device_Id"]
        self.metadata={}
        for index,key in enumerate(keys):
            self.metadata[key]=self.header[index].rstrip().lstrip()
    def show(self):
        fig, axes = plt.subplots(nrows=3, ncols=2)
        ax0, ax1, ax2, ax3, ax4, ax5 = axes.flat
        ax0.plot(self.get_column('Frequency'),self.get_column('magS11'),'k-o')
        ax0.set_title('Magnitude S11')
        ax1.plot(self.get_column('Frequency'),self.get_column('argS11'),'ro')
        ax1.set_title('Phase S11')
        ax2.plot(self.get_column('Frequency'),self.get_column('magS12'),'b-o')
        ax3.plot(self.get_column('Frequency'),self.get_column('argS12'),'bo')
        ax2.plot(self.get_column('Frequency'),self.get_column('magS21'),'k-o')
        ax2.set_title('Magnitude S21')
        ax3.plot(self.get_column('Frequency'),self.get_column('argS21'),'ro')
        ax3.set_title('Phase S21')
        ax4.plot(self.get_column('Frequency'),self.get_column('magS22'),'k-o')
        ax4.set_title('Magnitude S22')
        ax5.plot(self.get_column('Frequency'),self.get_column('argS22'),'ro')
        ax5.set_title('Phase S22')
        plt.tight_layout()
        plt.show()

Ancestors (in MRO)

Instance variables

var options

var path

Methods

def __init__(

self, file_path=None, **options)

Initializes the TwoPortRaw class, if a file_path is specified opens an existing file, else creates an empty container

def __init__(self,file_path=None,**options):
    """Initializes the TwoPortRaw class, if a file_path is specified opens an existing file, else creates an
    empty container"""
    defaults= {"data_delimiter": ",", "column_names_delimiter": ",", "specific_descriptor": 'Two_Port_NR_Raw',
               "general_descriptor": 'Sparameter', "extension": 'txt', "comment_begin": "#", "comment_end": "\n",
               "column_types": ['float','int','int','float','float','float','float',
                                'float','float','float','float'],
               "column_descriptions": {"Frequency":"Frequency in GHz",
                                       "Direction":"Direction of connects, may be unused",
                                       "Connect":"Connect number", "magS11":"Linear magnitude for S11",
                                       "argS11":"Phase in degrees for S11",
                                       "magS12":"Linear magnitude for S21",
                                       "argS12":"Phase in degrees for S21",
                                       "magS21":"Linear magnitude for S21",
                                       "argS21":"Phase in degrees for S21",
                                       "magS22":"Linear magnitude for S22",
                                       "argS22":"Phase in degrees for S22"},
               "header": None,
               "column_names": ["Frequency","Direction","Connect", "magS11",
                                "argS11","magS12","argS12","magS21","argS21","magS22","argS22"],
               "column_names_end_token": "\n", "data": None,
               'row_formatter_string': "{0:.5f}{delimiter}{1}{delimiter}{2}"
                                       "{delimiter}{3:.4f}{delimiter}{4:.2f}{delimiter}"
                                       "{5:.4f}{delimiter}{6:.2f}{delimiter}"
                                       "{7:.4f}{delimiter}{8:.2f}{delimiter}"
                                       "{9:.4f}{delimiter}{10:.2f}",
               "data_table_element_separator": None}
    self.options={}
    for key,value in defaults.iteritems():
        self.options[key]=value
    for key,value in options.iteritems():
        self.options[key]=value
    # Define Method Aliases if they are available
    if METHOD_ALIASES:
        for command in alias(self):
            exec(command)
    if file_path is not None:
        self.__read_and_fix__(file_path)
    AsciiDataTable.__init__(self,None,**self.options)
    self.path=file_path
    self.structure_metadata()

def add_column(

self, column_name=None, column_type=None, column_data=None, format_string=None)

Adds a column with column_name, and column_type. If column data is supplied and it's length is the same as data(same number of rows) then it is added, else self.options['empty_character'] is added in each spot in the preceding rows

def add_column(self,column_name=None,column_type=None,column_data=None,format_string=None):
    """Adds a column with column_name, and column_type. If column data is supplied and it's length is the
    same as data(same number of rows) then it is added, else self.options['empty_character'] is added in each
    spot in the preceding rows"""
    original_column_names=self.column_names[:]
    try:
        self.column_names=original_column_names+[column_name]
        if self.options["column_types"]:
            old_column_types=self.options["column_types"][:]
            self.options["column_types"]=old_column_types+[column_type]
        if len(column_data) == len(self.data):
            for index,row in enumerate(self.data[:]):
                #print("{0} is {1}".format('self.data[index]',self.data[index]))
                #print("{0} is {1}".format('row',row))
                new_row=row[:]
                new_row.append(column_data[index])
                self.data[index]=new_row
        else:
            for index,row in enumerate(self.data[:]):
                self.data[index]=row.append(self.options['empty_value'])
                if column_data is not None:
                    for item in column_data:
                        empty_row=[self.options['empty_value'] for column in original_column_names]
                        empty_row.append(item)
                        self.add_row(empty_row)
        if self.options["row_formatter_string"] is None:
            pass
        else:
            if format_string is None:
                self.options["row_formatter_string"]=self.options["row_formatter_string"]+\
                                                             '{delimiter}'+"{"+str(len(self.column_names)-1)+"}"
            else:
                self.options["row_formatter_string"]=self.options["row_formatter_string"]+format_string
        #self.update_model()
    except:
        self.column_names=original_column_names
        print("Could not add columns")
        raise

def add_index(

self)

Adds a column with name index and values that are 0 referenced indices, does nothing if there is already a column with name index, always inserts it at the 0 position

def add_index(self):
    """Adds a column with name index and values that are 0 referenced indices, does nothing if there is
    already a column with name index, always inserts it at the 0 position"""
    if 'index' in self.column_names:
        print("Add Index passed")
        pass
    else:
        self.column_names.insert(0,'index')
        for index,row in enumerate(self.data):
            self.data[index].insert(0,index)
        if self.options['column_types']:
            self.options['column_types'].insert(0,'int')
        if self.options['row_formatter_string']:
            temp_formatter_list=self.options['row_formatter_string'].split("{delimiter}")
            iterated_row_formatter_list=[temp_formatter_list[i].replace(str(i),str(i+1))
                                         for i in range(len(temp_formatter_list))]
            new_formatter=string_list_collapse(iterated_row_formatter_list,string_delimiter="{delimiter}")
            self.options['row_formatter_string']='{0}{delimiter}'+new_formatter

def add_inline_comment(

self, comment='', line_number=None, string_position=None)

Adds an inline in the specified location

def add_inline_comment(self,comment="",line_number=None,string_position=None):
    "Adds an inline in the specified location"
    try:
        self.inline_comments.append([comment,line_number,string_position])
    except:pass

def add_row(

self, row_data)

Adds a single row given row_data which can be an ordered list/tuple or a dictionary with column names as keys

def add_row(self,row_data):
    """Adds a single row given row_data which can be an ordered list/tuple or a dictionary with
    column names as keys"""
    if len(row_data) not in [len(self.column_names),len(self.column_names)]:
        print(" could not add the row, dimensions do not match")
        return
    if type(row_data) in [ListType,np.ndarray]:
        self.data.append(row_data)
    elif type(row_data) in [DictionaryType]:
        data_list=[row_data[column_name] for column_name in self.column_names]
        self.data.append(data_list)

def build_string(

self, **temp_options)

Builds a string representation of the data table based on self.options, or temp_options. Passing temp_options does not permanently change the model

def build_string(self,**temp_options):
    """Builds a string representation of the data table based on self.options, or temp_options.
    Passing temp_options does not permanently change the model"""
    # store the original options to be put back after the string is made
    original_options=self.options
    for key,value in temp_options.iteritems():
        self.options[key]=value
    section_end=0
    next_section_begin=0
    if self.options['data_table_element_separator'] is None:
        inner_element_spacing=0
    else:
        inner_element_spacing=self.options['data_table_element_separator'].count('\n')-1
    string_out=""
    between_section=""
    if self.options['data_table_element_separator'] is not None:
        between_section=self.options['data_table_element_separator']
    if self.header is None:
        self.options['header_begin_line']=self.options['header_end_line']=None
        pass
    else:
        self.options["header_begin_line"]=0
        if self.data is None and self.column_names is None and self.footer is None:
            string_out=self.get_header_string()
            self.options["header_end_line"]=None
        else:
            string_out=self.get_header_string()+between_section
            last_header_line=self.get_header_string().count('\n')+1
            self.options["header_end_line"]=last_header_line
            next_section_begin=last_header_line+inner_element_spacing
    if self.column_names is None:
        self.options['column_names_begin_line']=self.options['column_names_end_line']=None
        pass
    else:
        self.options["column_names_begin_line"]=next_section_begin
        if self.data is None and self.footer is None:
            self.options["column_names_end_line"]=None
            string_out=string_out+self.get_column_names_string()
        else:
            string_out=string_out+self.get_column_names_string()+between_section
            last_column_names_line=self.get_column_names_string().count('\n')+\
                                   self.options["column_names_begin_line"]+1
            self.options["column_names_end_line"]=last_column_names_line
            next_section_begin=last_column_names_line+inner_element_spacing
    if self.data is None:
        self.options['data_begin_line']=self.options['data_end_line']=None
        pass
    else:
        self.options["data_begin_line"]=next_section_begin
        if self.footer is None:
            self.options["data_end_line"]=None
            string_out=string_out+self.get_data_string()
        else:
            string_out=string_out+self.get_data_string()+between_section
            last_data_line=self.get_data_string().count("\n")+\
                            self.options["data_begin_line"]+1
            self.options["data_end_line"]=last_data_line
            next_section_begin=last_data_line+inner_element_spacing
    if self.footer is None:
        self.options['footer_begin_line']=self.options['footer_end_line']=None
        pass
    else:
        self.options["footer_begin_line"]=next_section_begin
        string_out=string_out+self.get_footer_string()
        self.options['footer_end_line']=None
    # set the options back after the string has been made
    if self.inline_comments is None:
        pass
    else:
        lines=string_out.splitlines()
        for comment in self.inline_comments:
            lines=insert_inline_comment(lines,comment=comment[0],line_number=comment[1],
                                        string_position=comment[2],
                                        begin_token=self.options['inline_comment_begin'],
                                        end_token=self.options['inline_comment_end'])
        string_out=string_list_collapse(lines,string_delimiter='\n')
    self.options=original_options
    return string_out

def change_unit_prefix(

self, column_selector=None, old_prefix=None, new_prefix=None, unit='Hz')

Changes the prefix of the units of the column specified by column_selector (column name or index) example usage is self.change_unit_prefix(column_selector='Frequency',old_prefix=None,new_prefix='G',unit='Hz') to change a column from Hz to GHz. It updates the data values, column_descriptions, and column_units if they exist, see http://www.nist.gov/pml/wmd/metric/prefixes.cfm for possible prefixes

def change_unit_prefix(self,column_selector=None,old_prefix=None,new_prefix=None,unit='Hz'):
    """Changes the prefix of the units of the column specified by column_selector (column name or index)
    example usage is self.change_unit_prefix(column_selector='Frequency',old_prefix=None,new_prefix='G',unit='Hz')
    to change a column from Hz to GHz. It updates the data values, column_descriptions, and column_units if they
    exist, see http://www.nist.gov/pml/wmd/metric/prefixes.cfm for possible prefixes"""
    multipliers={"yotta":10.**24,"Y":10.**24,"zetta":10.**21,"Z":10.**21,"exa":10.**18,"E":10.**18,"peta":10.**15,
                 "P":10.**15,"tera":10.**12,"T":10.**12,"giga":10.**9,"G":10.**9,"mega":10.**6,"M":10.**6,
                 "kilo":10.**3,"k":10.**3,"hecto":10.**2,"h":10.**2,"deka":10.,"da":10.,None:1.,"":1.,
                 "deci":10.**-1,"d":10.**-1,"centi":10.**-2,"c":10.**-2,"milli":10.**-3,"m":10.**-3,
                 "micro":10.**-6,"mu":10.**-6,u"\u00B5":10.**-6,"nano":10.**-9,
                 "n":10.**-9,"pico":10.**-12,"p":10.**-12,"femto":10.**-15,
                 "f":10.**-15,"atto":10.**-18,"a":10.**-18,"zepto":10.**-21,"z":10.**-21,
                 "yocto":10.**-24,"y":10.**-24}
    # change column name into column index
    try:
        if old_prefix is None:
            old_prefix=""
        if new_prefix is None:
            new_prefix=""
        old_unit=old_prefix+unit
        new_unit=new_prefix+unit
        if column_selector in self.column_names:
            column_selector=self.column_names.index(column_selector)
        for index,row in enumerate(self.data):
            if type(self.data[index][column_selector]) in [FloatType,LongType]:
                #print "{0:e}".format(multipliers[old_prefix]/multipliers[new_prefix])
                self.data[index][column_selector]=\
                (multipliers[old_prefix]/multipliers[new_prefix])*self.data[index][column_selector]
            elif type(self.data[index][column_selector]) in [StringType,IntType]:
                self.data[index][column_selector]=\
                str((multipliers[old_prefix]/multipliers[new_prefix])*float(self.data[index][column_selector]))
            else:
                print type(self.data[index][column_selector])
                raise
        if self.options["column_descriptions"] is not None:
            old=self.options["column_descriptions"][column_selector]
            self.options["column_descriptions"][column_selector]=old.replace(old_unit,new_unit)
        if self.options["column_units"] is not None:
            old=self.options["column_units"][column_selector]
            self.options["column_units"][column_selector]=old.replace(old_unit,new_unit)
        if re.search(old_unit,self.column_names[column_selector]):
            old=self.column_names[column_selector]
            self.column_names[column_selector]=old.replace(old_unit,new_unit)
    except:
        print("Could not change the unit prefix of column {0}".format(column_selector))
        raise

def find_line(

self, begin_token)

Finds the first line that has begin token in it

def find_line(self,begin_token):
    """Finds the first line that has begin token in it"""
    for index,line in enumerate(self.lines):
        if re.search(begin_token,line,re.IGNORECASE):
            return index

def get_column(

self, column_name=None, column_index=None)

Returns a column as a list given a column name or column index

def get_column(self,column_name=None,column_index=None):
    """Returns a column as a list given a column name or column index"""
    if column_name is None:
        if column_index is None:
            return
        else:
            column_selector=column_index
    else:
        column_selector=self.column_names.index(column_name)
    out_list=[self.data[i][column_selector] for i in range(len(self.data))]
    return out_list

def get_column_names_string(

self)

Returns the column names as a string using options

def get_column_names_string(self):
    "Returns the column names as a string using options"
    string_out=""
    # This writes the column_names
    column_name_begin=""
    column_name_end=""
    if self.options["column_names_begin_token"] is None:
        column_name_begin=""
    else:
        column_name_begin=self.options["column_names_begin_token"]
    if self.options["column_names_end_token"] is None:
        column_name_end=""
    else:
        column_name_end=self.options["column_names_end_token"]
    if self.column_names is None:
        string_out=""
    else:
        if type(self.column_names) is StringType:
            string_out=self.column_names
        elif type(self.column_names) is ListType:
            string_out=list_to_string(self.column_names,
                                      data_delimiter=self.options["column_names_delimiter"],end="")
            #print("{0} is {1}".format('string_out',string_out))
        else:
            string_out=ensure_string(self.column_names)
    #print column_name_begin,string_out,column_name_end
    return column_name_begin+string_out+column_name_end

def get_data_dictionary_list(

self, use_row_formatter_string=True)

Returns a python list with a row dictionary of form {column_name:data_column}

def get_data_dictionary_list(self,use_row_formatter_string=True):
    """Returns a python list with a row dictionary of form {column_name:data_column}"""
    try:
        if self.options["row_formatter_string"] is None:
            use_row_formatter_string=False
        if use_row_formatter_string:
            list_formatter=[item.replace("{"+str(index),"{0")
                            for index,item in enumerate(self.options["row_formatter_string"].split("{delimiter}"))]
        else:
            list_formatter=["{0}" for i in self.column_names]
        #print self.column_names
        #print self.data
        #print list_formatter
        #print len(self.column_names)==len(self.data[0])
        #print len(list_formatter)==len(self.data[0])
        #print type(self.data[0])
        out_list=[{self.column_names[i]:list_formatter[i].format(value) for i,value in enumerate(line)}
                  for line in self.data]
        return out_list
    except:
        print("Could not form a data_dictionary_list, check that row_formatter_string is properly defined")
        #print(out_list)
        raise

def get_data_string(

self)

Returns the data as a string

def get_data_string(self):
    "Returns the data as a string"
    #Todo:refactor to cut out unused lines
    string_out=""
    if self.data is None:
        string_out= ""
    else:
        if type(self.data) is StringType:
            if self.options['data_begin_token'] is None:
                   if self.options['data_end_token'] is None:
                       string_out=self.data
                   else:
                       if re.search(self.options['data_end_token'],self.data):
                           string_out=self.data
                       else:
                           string_out=self.data+self.options['data_end_token']
            else:
                    if self.options['data_end_token'] is None:
                        if re.match(self.options['data_begin_token'],self.data):
                            string_out=self.data
                        else:
                            string_out=self.options['data_begin_token']+self.data
        elif type(self.data) in [ListType,np.ndarray]:
            try:
                    #If the first row is a string, we should strip all the tokens and add them back in
                    if type(self.data[0]) is StringType:
                        if self.options['data_begin_token'] is None:
                            string_out=string_list_collapse(self.data)
                        else:
                            if re.match(self.options['data_begin_token'],self.data[0]):
                                if self.options['data_end_token'] is None:
                                    string_out=string_list_collapse(self.data)
                                else:
                                    if re.search(self.options['data_end_token'],self.data[-1]):
                                        string_out=string_list_collapse(self.data)
                                    else:
                                        string_out=string_list_collapse(self.data)+self.options['data_end_token']
                            else:
                                if self.options['data_end_token'] is None:
                                    string_out=self.options['data_begin_token']+string_list_collapse(self.data)
                                else:
                                    if re.search(self.options['data_end_token'],self.data[-1]):
                                        string_out=self.options['data_begin_token']+string_list_collapse(self.data)
                                    else:
                                        string_out=self.options['data_begin_token']+\
                                                   string_list_collapse(self.data)+\
                                                   self.options['data_end_token']
                    elif type(self.data[0]) in [ListType,np.ndarray]:
                        prefix=""
                        if self.options['data_begin_token'] is None:
                            if self.options['data_end_token'] is None:
                                string_out=list_list_to_string(self.data,data_delimiter=self.options['data_delimiter'],
                                                               row_formatter_string=self.options['row_formatter_string'],
                                                               line_begin=self.options["row_begin_token"],
                                                               line_end=self.options["row_end_token"])
                        else:
                            if self.options['data_end_token'] is None:
                                string_out=self.options['data_begin_token']+\
                                           list_list_to_string(self.data,
                                                               data_delimiter=self.options['data_delimiter'],
                                                               row_formatter_string=self.options['row_formatter_string'],
                                                               line_begin=self.options["row_begin_token"],
                                                               line_end=self.options["row_end_token"])
                            else:
                                string_out=self.options['data_begin_token']+\
                                           list_list_to_string(self.data,
                                                               data_delimiter=self.options['data_delimiter'],
                                                               row_formatter_string=\
                                                               self.options['row_formatter_string'],
                                                               line_begin=self.options["row_begin_token"],
                                                               line_end=self.options["row_end_token"])+\
                                                                self.options['data_end_token']
                    else:
                        string_out=list_to_string(self.data,
                                                  data_delimiter=self.options['data_delimiter'],
                                                  row_formatter_string=self.options['row_formatter_string'],
                                                  begin=self.options["row_begin_token"],
                                                  end=self.options["row_end_token"])
            except IndexError:
                pass
        else:
            string_out=ensure_string(self.data)
    return string_out

Returns the footer using options in self.options. If block comment is specified, and the footer is a list it will block comment out the footer. If comment_begin and comment_end are specified it will use those to represent each line of the footer. If footer_begin_token and/or footer_end_token are specified it will wrap the footer in those.

def get_header_string(

self)

Returns the header using options in self.options. If block comment is specified, and the header is a list it will block comment out the header. If comment_begin and comment_end are specified it will use those to represent each line of the header. If header_begin_token and/or header_end_token are specified it will wrap the header in those.

def get_header_string(self):
    """Returns the header using options in self.options. If block comment is specified, and the header is a
    list it will block comment out the header. If comment_begin and comment_end are specified it will use
    those to represent each line of the header. If header_begin_token and/or header_end_token are specified it
     will wrap the header in those.
    """
    string_out=""
    header_begin=""
    header_end=""
    if self.options["header_begin_token"] is None:
        header_begin=""
    else:
        header_begin=self.options["header_begin_token"]
    if self.options["header_end_token"] is None:
        header_end=""
    else:
        header_end=self.options["header_end_token"]
    # This writes the header
    if self.header is None:
        string_out= ""
    elif self.options["header_line_types"] is not None:
        for index,line in enumerate(self.options["header_line_types"]):
            if index == len(self.options["header_line_types"])-1:
                end=''
            else:
                end='\n'
            if line in ['header','header_line','normal']:
                string_out=string_out+self.header[index]+end
            elif line in ['line_comment','comment']:
                string_out=string_out+line_comment_string(self.header[index],
                                           comment_begin=self.options["comment_begin"],
                                           comment_end=self.options["comment_end"])+end
            elif line in ['block_comment','block']:
                if index-1<0:
                    block_comment_begin=index
                    block_comment_end=index+2
                    continue
                elif self.options["header_line_types"][index-1] not in ['block_comment','block']:
                    block_comment_begin=index
                    block_comment_end=index+2
                    continue
                else:
                    if index+1>len(self.options["header_line_types"])-1:
                        string_out=string_out+line_list_comment_string(self.header[block_comment_begin:],
                                                                       comment_begin=self.options['block_comment_begin'],
                                                                         comment_end=self.options['block_comment_end'],
                                                                       block=True)+end
                    elif self.options["header_line_types"][index+1] in ['block_comment','block']:
                        block_comment_end+=1
                    else:
                        string_out=string_out+\
                                   line_list_comment_string(self.header[block_comment_begin:block_comment_end],
                                                            comment_begin=self.options['block_comment_begin'],
                                                            comment_end=self.options['block_comment_end'],
                                                            block=True)+end
            else:
                string_out=string_out+line
    elif self.options['treat_header_as_comment'] in [None,True] and self.options["header_line_types"] in [None]:
        # Just happens if the user has set self.header manually
        if type(self.header) is StringType:
            string_out=line_comment_string(self.header,
                                           comment_begin=self.options["comment_begin"],
                                           comment_end=self.options["comment_end"])
            #string_out=re.sub('\n','',string_out,count=1)
        elif type(self.header) is ListType:
            if self.options['block_comment_begin'] is None:
                if self.options['comment_begin'] is None:
                    string_out=string_list_collapse(self.header)
                else:
                    string_out=line_list_comment_string(self.header,comment_begin=self.options['comment_begin'],
                                                    comment_end=self.options['comment_end'])
                    lines_out=string_out.splitlines()
                    # if re.search('\n',self.options['comment_end']):
                    #     string_out=re.sub('\n','',string_out,count=1)
                    #self.options["header_line_types"]=["line_comment" for line in self.header]
            else:
                string_out=line_list_comment_string(self.header,comment_begin=self.options['block_comment_begin'],
                                                    comment_end=self.options['block_comment_end'],block=True)
                #self.options["header_line_types"]=["block_comment" for line in self.header]
    else:
        string_out=ensure_string(self.header,list_delimiter="\n",end_if_list="")
    return header_begin+string_out+header_end

def get_options(

self)

Prints the option list

def get_options(self):
    "Prints the option list"
    for key,value in self.options.iteritems():
        print("{0} = {1}".format(key,value))

def get_options_by_element(

self, element_name)

returns a dictionary of all the options that have to do with element. Element must be header,column_names,data, or footer

def get_options_by_element(self,element_name):
    """ returns a dictionary
     of all the options that have to do with element. Element must be header,column_names,data, or footer"""
    keys_regarding_element=filter(lambda x: re.search(element_name,str(x),re.IGNORECASE),self.options.keys())
    out_dictionary={key:self.options[key] for key in keys_regarding_element}
    #print out_dictionary
    return out_dictionary

def get_row(

self, row_index=None)

Returns the row as a list specified by row_index

def get_row(self,row_index=None):
    """Returns the row as a list specified by row_index"""
    if row_index is None:
        return
    else:
        return self.data[row_index]

def is_valid(

self)

Returns True if ascii table conforms to its specification given by its own options

def is_valid(self):
    """Returns True if ascii table conforms to its specification given by its own options"""
    options={}
    for key,value in self.options.iteritems():
        options[key]=value
        # print("self.options[{0}] is {1} ".format(key,value))
    for element in self.elements:
        if self.__dict__[element] is None:
            options[element]=None
        else:
            options[element]=[]
    options["validate"]=True
    newtable=AsciiDataTable(None,**options)
    lines=self.build_string().splitlines()
    for index,line in enumerate(lines):
        lines[index]=line+"\n"
    newtable.lines=lines
    newtable.__parse__()
    # print newtable.data
    # print newtable.column_names
    # print newtable
    #print_comparison(newtable.footer,None)
    newtable.update_model()
    # The new table rows are not being coerced into the right format
    #print newtable
    #newtable.update_model()
    #print newtable.options
    #print self.options
    #print newtable.data
    # print newtable.options==self.options
    # for option_key,option_value in newtable.options.iteritems():
    #     print("New Table Option {0} is {1} ".format(option_key,option_value))
    #     print("self.options[{0}] is {1} ".format(option_key,self.options[option_key]))
    #     print_comparison(option_value,self.options[option_key])
    # #print self
    return self==newtable

def lines_defined(

self)

If begin_line and end_line for all elements that are None are defined returns True

def lines_defined(self):
    """If begin_line and end_line for all elements that are None are defined returns True"""
    truth_table=[]
    last_element=""
    output=False
    for index,element in enumerate(self.elements):
        if element not in ['inline_comments','metadata'] and self.__dict__[element] is not None:
            try:
                last_element=element
                if not None in [self.options['%s_begin_line'%element],self.options['%s_end_line'%element]]:
                    truth_table.append(True)
                else:
                     truth_table.append(False)
            except:
                return False
    #print truth_table
    # The last_line of the last element is fine to be none
    if truth_table[-1] is False:
        if self.options['%s_begin_line'%last_element] is not None:
            truth_table[-1]=True
    if False in truth_table:
        output=False
    else:
        output=True
    #print output
    return output

Moves the DataTable's footer to the header and updates the model

def remove_column(

self, column_name=None, column_index=None)

Removes the column specified by column_name or column_index and updates the model. The column is removed from column_names, data and if present column_types, column_descriptions and row formatter

def remove_column(self,column_name=None,column_index=None):
    """Removes the column specified by column_name or column_index and updates the model. The column is removed from
    column_names, data and if present column_types, column_descriptions and row formatter"""
    pass

def remove_row(

self, row_index)

Removes the row specified by row_index and updates the model. Note index is relative to the data attribute so to remove the first row use row_index=0 and the last data row is row_index=-1

def remove_row(self,row_index):
    """Removes the row specified by row_index and updates the model. Note index is relative to the
    data attribute so to remove the first row use row_index=0 and the last data row is row_index=-1"""
    self.data.pop(row_index)
    self.update_model()

def save(

self, path=None, **temp_options)

" Saves the file, to save in another ascii format specify elements in temp_options, the options specified do not permanently change the object's options. If path is supplied it saves the file to that path otherwise uses the object's attribute path to define the saving location

def save(self,path=None,**temp_options):
    """" Saves the file, to save in another ascii format specify elements in temp_options, the options
    specified do not permanently change the object's options. If path is supplied it saves the file to that path
    otherwise uses the object's attribute path to define the saving location """
    original_options=self.options
    for key,value in temp_options.iteritems():
        self.options[key]=value
    out_string=self.build_string(**temp_options)
    if path is None:
        path=self.path
    file_out=open(path,'w')
    file_out.write(out_string)
    file_out.close()
    self.options=original_options

def save_schema(

self, path=None, format=None)

Saves the tables options as a text file or pickled dictionary (default). If no name is supplied, autonames it and saves

def save_schema(self,path=None,format=None):
    """Saves the tables options as a text file or pickled dictionary (default).
    If no name is supplied, autonames it and saves"""
    if path is None:
        path=auto_name(self.name.replace('.'+self.options["extension"],""),'Schema',self.options["directory"],'txt')
    if format in [None,'python','pickle']:
        pickle.dump(self.options,open(path,'wb'))
    elif format in ['txt','text','.txt']:
        file_out=open(path,'w')
        keys=self.options.keys()
        keys.sort()
        for key in keys:
            out_key=str(key).replace("\n","\\n")
            out_value=str(self.options[key]).replace("\n","\\n")
            file_out.write("{0} : {1} \n".format(out_key,out_value))
        file_out.close()

def show(

self)

def show(self):
    fig, axes = plt.subplots(nrows=3, ncols=2)
    ax0, ax1, ax2, ax3, ax4, ax5 = axes.flat
    ax0.plot(self.get_column('Frequency'),self.get_column('magS11'),'k-o')
    ax0.set_title('Magnitude S11')
    ax1.plot(self.get_column('Frequency'),self.get_column('argS11'),'ro')
    ax1.set_title('Phase S11')
    ax2.plot(self.get_column('Frequency'),self.get_column('magS12'),'b-o')
    ax3.plot(self.get_column('Frequency'),self.get_column('argS12'),'bo')
    ax2.plot(self.get_column('Frequency'),self.get_column('magS21'),'k-o')
    ax2.set_title('Magnitude S21')
    ax3.plot(self.get_column('Frequency'),self.get_column('argS21'),'ro')
    ax3.set_title('Phase S21')
    ax4.plot(self.get_column('Frequency'),self.get_column('magS22'),'k-o')
    ax4.set_title('Magnitude S22')
    ax5.plot(self.get_column('Frequency'),self.get_column('argS22'),'ro')
    ax5.set_title('Phase S22')
    plt.tight_layout()
    plt.show()

def structure_metadata(

self)

Returns a dictionary of key,value pairs extracted from the header

def structure_metadata(self):
    """Returns a dictionary of key,value pairs extracted from the header"""
    keys=["System_Id","System_Letter","Connector_Type_Calibration","Connector_Type_Measurement",
          "Measurement_Type","Measurement_Date","Measurement_Time","Program_Used","Program_Revision","Operator",
          "Calibration_Name","Calibration_Date","Port_Used","Number_Connects","Number_Repeats","Nbs",
          "Number_Frequencies","Start_Frequency",
          "Device_Description","Device_Id"]
    self.metadata={}
    for index,key in enumerate(keys):
        self.metadata[key]=self.header[index].rstrip().lstrip()

def update_column_names(

self)

Update column names adds the value x# for any column that exists in self.data that is not named

def update_column_names(self):
    """Update column names adds the value x# for any column that exists in self.data that is not named"""
    if self.data is None:
        return
    elif type(self.column_names) is StringType:
        self.column_names=split_row(self.column_names,self.options["column_names_delimiter"])
    elif self.column_names is None:
        column_names=[]
        for index,column in enumerate(self.data[0]):
            column_names.append("x"+str(index))
        self.column_names=column_names
        return
    elif len(self.column_names)==len(self.data[0]):
        return
    elif len(self.column_names) < len(self.data[0]):
        for index in range(len(self.column_names),len(self.data[0])):
            self.column_names.append("x"+str(index))
        return

def update_import_options(

self, import_table)

Updates the options in the import table

def update_import_options(self,import_table):
    """Updates the options in the import table"""
    for index,element in enumerate(['header','column_names','data','footer']):
        if self.__dict__[element] is not None:
            print("The {0} variable is {1}".format('index',index))
            print("The {0} variable is {1}".format('element',element))
            print("The {0} variable is {1}".format('import_table',import_table))
            [self.options['%s_begin_line'%element],
                            self.options['%s_end_line'%element],
                            self.options['%s_begin_token'%element],
                            self.options['%s_end_token'%element]]=import_table[index][:]

def update_index(

self)

Updates the index column if it exits, otherwise exits quietly

def update_index(self):
    """ Updates the index column if it exits, otherwise exits quietly
    """
    if 'index' not in self.column_names:
        return
    else:
        try:
            #This should be 0 but just in case
            index_column_number=self.column_names.index('index')
            for i in range(len(self.data)):
                self.data[i][index_column_number]=i
        except:
            pass

def update_model(

self)

Updates the model after a change has been made. If you add anything to the attributes of the model, or change this updates the values. If the model has an index column it will make sure the numbers are correct. In addition, it will update the options dictionary to reflect added rows, changes in deliminators etc.

def update_model(self):
    """Updates the model after a change has been made. If you add anything to the attributes of the model,
    or change this updates the values. If the model has an index column it will make sure the numbers are correct.
    In addition, it will update the options dictionary to reflect added rows, changes in deliminators etc.  """
    if self.column_names is not None and 'index' in self.column_names:
       self.update_index()
    #make sure there are no "\n" characters in the element lists (if so replace them with "") for data this is
    # done on import
    list_types=["header","column_names","footer"]
    for element in list_types:
        if self.__dict__[element] is not None:
            for index,item in enumerate(self.__dict__[element]):
                self.__dict__[element][index]=item.replace("\n","")
    self.update_column_names()
    if self.data is not None:
        self.data=convert_all_rows(self.data,self.options["column_types"])
    self.string=self.build_string()
    self.lines=self.string.splitlines()

class TwoPortRawModel

Class that deals with the TwoPort Raw Files after conversion to Ascii using Ron Ginley's converter. These files typically have header information seperated from data by !! Header format is: Line 1: Spid$ - identification of type of system used Line 2: Systemletter$ - letter name indicating which system was used Line 3: Conncal$ - connector type from the system calibration Line 4: Connectors$ - connector type used for the measurement Line 5: Meastype$ - type of measurement (basically 1-port, 2-port or power) Line 6: Datea$ - date of measurement Line 7: Timea$ - time of measurement Line 8: Programm$ - name of program used Line 9: Rev$ - program revision Line 10: Opr$ - operator Line 11: Cfile$ - calibration name Line 12: Cdate$ - calibration date Line 13: Sport - identification of which port or direction was used for measurement Line 14: Numconnects ? number of disconnect/reconnect cycles Line 15: Numrepeats ? number of repeat measurements for each connect (usually 1) Line 16: Nbs ? not sure Line 17: Nfreq ? number of frequencies Line 18: Startfreq ? data row pointer for bdat files Line 19: Devicedescript$ - description of device being measured or of test being done Line 20: Devicenum$ - Identifying number for device ? used for file names

class TwoPortRawModel(AsciiDataTable):
    """ Class that deals with the TwoPort Raw Files after conversion to Ascii using Ron Ginley's converter.
    These files typically have header information seperated from data by !!
    Header format is:
    Line 1:		Spid$ - identification of type of system used
    Line 2:		Systemletter$ - letter name indicating which system was used
    Line 3:		Conncal$ - connector type from the system calibration
    Line 4:		Connectors$ - connector type used for the measurement
    Line 5:		Meastype$ - type of measurement (basically 1-port, 2-port or power)
    Line 6:		Datea$ - date of measurement
    Line 7:		Timea$ - time of measurement
    Line 8:		Programm$ - name of program used
    Line 9:		Rev$ - program revision
    Line 10:	Opr$ - operator
    Line 11:	Cfile$ - calibration name
    Line 12:	Cdate$ - calibration date
    Line 13:	Sport - identification of which port or direction was used for measurement
    Line 14:	Numconnects ? number of disconnect/reconnect cycles
    Line 15:	Numrepeats ? number of repeat measurements for each connect (usually 1)
    Line 16:	Nbs ? not sure
    Line 17:	Nfreq ? number of frequencies
    Line 18:	Startfreq ? data row pointer for bdat files
    Line 19:	Devicedescript$ - description of device being measured or of test being done
    Line 20:	Devicenum$ - Identifying number for device ? used for file names
    """
    def __init__(self,file_path=None,**options):
        """Initializes the TwoPortRaw class, if a file_path is specified opens an existing file, else creates an
        empty container"""
        defaults= {"data_delimiter": ",", "column_names_delimiter": ",", "specific_descriptor": 'Two_Port_Raw',
                   "general_descriptor": 'Sparameter', "extension": 'txt', "comment_begin": "#", "comment_end": "\n",
                   "column_types": ['float','int','int','float','float','float','float','float','float'],
                   "column_descriptions": {"Frequency":"Frequency in GHz",
                                           "Direction":"Direction of connects, may be unused",
                                           "Connect":"Connect number", "magS11":"Linear magnitude for S11",
                                           "argS11":"Phase in degrees for S11",
                                           "magS21":"Linear magnitude for S21",
                                           "argS21":"Phase in degrees for S21",
                                           "magS22":"Linear magnitude for S22",
                                           "argS22":"Phase in degrees for S22"},
                   "header": None,
                   "column_names": ["Frequency","Direction","Connect", "magS11",
                                    "argS11","magS21","argS21","magS22","argS22"],
                   "column_names_end_token": "\n", "data": None,
                   'row_formatter_string': "{0:.5f}{delimiter}{1}{delimiter}{2}"
                                           "{delimiter}{3:.4f}{delimiter}{4:.2f}{delimiter}"
                                           "{5:.4f}{delimiter}{6:.2f}{delimiter}"
                                           "{7:.4f}{delimiter}{8:.2f}",
                   "data_table_element_separator": None}
        self.options={}
        for key,value in defaults.iteritems():
            self.options[key]=value
        for key,value in options.iteritems():
            self.options[key]=value
        # Define Method Aliases if they are available
        if METHOD_ALIASES:
            for command in alias(self):
                exec(command)
        if file_path is not None:
            self.__read_and_fix__(file_path)

        AsciiDataTable.__init__(self,None,**self.options)
        self.path=file_path
        self.structure_metadata()

    def __read_and_fix__(self,file_path=None):
        """Inputs in the raw OnePortRaw file and fixes any problems with delimiters,etc."""
        lines=[]
        in_file=open(file_path,'r')
        for index,line in enumerate(in_file):
            lines.append(line)
            if re.search("!!",line):
                data_begin_line=index+1
        self.lines=lines
        in_file.close()
        parse_options={"row_end_token":'\n',
                       "row_pattern":make_row_match_string(self.options["column_names"]),
                       "column_names":self.options["column_names"],"column_types":self.options["column_types"]}
        data=parse_lines(lines[data_begin_line:],**parse_options)
        self.options["data"]=data
        if CONVERT_S21:
            for row_index,row in enumerate(self.options["data"]):
                db_value=row[5]
                mag_value=10.**(-1*db_value/20.)
                self.options["data"][row_index][5]=mag_value

        self.options["header"]=lines[:data_begin_line-1]
        #print data


    def structure_metadata(self):
        """Returns a dictionary of key,value pairs extracted from the header"""
        keys=["System_Id","System_Letter","Connector_Type_Calibration","Connector_Type_Measurement",
              "Measurement_Type","Measurement_Date","Measurement_Time","Program_Used","Program_Revision","Operator",
              "Calibration_Name","Calibration_Date","Port_Used","Number_Connects","Number_Repeats","Nbs",
              "Number_Frequencies","Start_Frequency",
              "Device_Description","Device_Id"]
        self.metadata={}
        for index,key in enumerate(keys):
            self.metadata[key]=self.header[index].rstrip().lstrip()
    def show(self):
        fig, axes = plt.subplots(nrows=3, ncols=2)
        ax0, ax1, ax2, ax3, ax4, ax5 = axes.flat
        ax0.plot(self.get_column('Frequency'),self.get_column('magS11'),'k-o')
        ax0.set_title('Magnitude S11')
        ax1.plot(self.get_column('Frequency'),self.get_column('argS11'),'ro')
        ax1.set_title('Phase S11')
        ax2.plot(self.get_column('Frequency'),self.get_column('magS21'),'k-o')
        ax2.set_title('Magnitude S21')
        ax3.plot(self.get_column('Frequency'),self.get_column('argS21'),'ro')
        ax3.set_title('Phase S21')
        ax4.plot(self.get_column('Frequency'),self.get_column('magS22'),'k-o')
        ax4.set_title('Magnitude S22')
        ax5.plot(self.get_column('Frequency'),self.get_column('argS22'),'ro')
        ax5.set_title('Phase S22')
        plt.tight_layout()
        plt.show()

Ancestors (in MRO)

Instance variables

var options

var path

Methods

def __init__(

self, file_path=None, **options)

Initializes the TwoPortRaw class, if a file_path is specified opens an existing file, else creates an empty container

def __init__(self,file_path=None,**options):
    """Initializes the TwoPortRaw class, if a file_path is specified opens an existing file, else creates an
    empty container"""
    defaults= {"data_delimiter": ",", "column_names_delimiter": ",", "specific_descriptor": 'Two_Port_Raw',
               "general_descriptor": 'Sparameter', "extension": 'txt', "comment_begin": "#", "comment_end": "\n",
               "column_types": ['float','int','int','float','float','float','float','float','float'],
               "column_descriptions": {"Frequency":"Frequency in GHz",
                                       "Direction":"Direction of connects, may be unused",
                                       "Connect":"Connect number", "magS11":"Linear magnitude for S11",
                                       "argS11":"Phase in degrees for S11",
                                       "magS21":"Linear magnitude for S21",
                                       "argS21":"Phase in degrees for S21",
                                       "magS22":"Linear magnitude for S22",
                                       "argS22":"Phase in degrees for S22"},
               "header": None,
               "column_names": ["Frequency","Direction","Connect", "magS11",
                                "argS11","magS21","argS21","magS22","argS22"],
               "column_names_end_token": "\n", "data": None,
               'row_formatter_string': "{0:.5f}{delimiter}{1}{delimiter}{2}"
                                       "{delimiter}{3:.4f}{delimiter}{4:.2f}{delimiter}"
                                       "{5:.4f}{delimiter}{6:.2f}{delimiter}"
                                       "{7:.4f}{delimiter}{8:.2f}",
               "data_table_element_separator": None}
    self.options={}
    for key,value in defaults.iteritems():
        self.options[key]=value
    for key,value in options.iteritems():
        self.options[key]=value
    # Define Method Aliases if they are available
    if METHOD_ALIASES:
        for command in alias(self):
            exec(command)
    if file_path is not None:
        self.__read_and_fix__(file_path)
    AsciiDataTable.__init__(self,None,**self.options)
    self.path=file_path
    self.structure_metadata()

def add_column(

self, column_name=None, column_type=None, column_data=None, format_string=None)

Adds a column with column_name, and column_type. If column data is supplied and it's length is the same as data(same number of rows) then it is added, else self.options['empty_character'] is added in each spot in the preceding rows

def add_column(self,column_name=None,column_type=None,column_data=None,format_string=None):
    """Adds a column with column_name, and column_type. If column data is supplied and it's length is the
    same as data(same number of rows) then it is added, else self.options['empty_character'] is added in each
    spot in the preceding rows"""
    original_column_names=self.column_names[:]
    try:
        self.column_names=original_column_names+[column_name]
        if self.options["column_types"]:
            old_column_types=self.options["column_types"][:]
            self.options["column_types"]=old_column_types+[column_type]
        if len(column_data) == len(self.data):
            for index,row in enumerate(self.data[:]):
                #print("{0} is {1}".format('self.data[index]',self.data[index]))
                #print("{0} is {1}".format('row',row))
                new_row=row[:]
                new_row.append(column_data[index])
                self.data[index]=new_row
        else:
            for index,row in enumerate(self.data[:]):
                self.data[index]=row.append(self.options['empty_value'])
                if column_data is not None:
                    for item in column_data:
                        empty_row=[self.options['empty_value'] for column in original_column_names]
                        empty_row.append(item)
                        self.add_row(empty_row)
        if self.options["row_formatter_string"] is None:
            pass
        else:
            if format_string is None:
                self.options["row_formatter_string"]=self.options["row_formatter_string"]+\
                                                             '{delimiter}'+"{"+str(len(self.column_names)-1)+"}"
            else:
                self.options["row_formatter_string"]=self.options["row_formatter_string"]+format_string
        #self.update_model()
    except:
        self.column_names=original_column_names
        print("Could not add columns")
        raise

def add_index(

self)

Adds a column with name index and values that are 0 referenced indices, does nothing if there is already a column with name index, always inserts it at the 0 position

def add_index(self):
    """Adds a column with name index and values that are 0 referenced indices, does nothing if there is
    already a column with name index, always inserts it at the 0 position"""
    if 'index' in self.column_names:
        print("Add Index passed")
        pass
    else:
        self.column_names.insert(0,'index')
        for index,row in enumerate(self.data):
            self.data[index].insert(0,index)
        if self.options['column_types']:
            self.options['column_types'].insert(0,'int')
        if self.options['row_formatter_string']:
            temp_formatter_list=self.options['row_formatter_string'].split("{delimiter}")
            iterated_row_formatter_list=[temp_formatter_list[i].replace(str(i),str(i+1))
                                         for i in range(len(temp_formatter_list))]
            new_formatter=string_list_collapse(iterated_row_formatter_list,string_delimiter="{delimiter}")
            self.options['row_formatter_string']='{0}{delimiter}'+new_formatter

def add_inline_comment(

self, comment='', line_number=None, string_position=None)

Adds an inline in the specified location

def add_inline_comment(self,comment="",line_number=None,string_position=None):
    "Adds an inline in the specified location"
    try:
        self.inline_comments.append([comment,line_number,string_position])
    except:pass

def add_row(

self, row_data)

Adds a single row given row_data which can be an ordered list/tuple or a dictionary with column names as keys

def add_row(self,row_data):
    """Adds a single row given row_data which can be an ordered list/tuple or a dictionary with
    column names as keys"""
    if len(row_data) not in [len(self.column_names),len(self.column_names)]:
        print(" could not add the row, dimensions do not match")
        return
    if type(row_data) in [ListType,np.ndarray]:
        self.data.append(row_data)
    elif type(row_data) in [DictionaryType]:
        data_list=[row_data[column_name] for column_name in self.column_names]
        self.data.append(data_list)

def build_string(

self, **temp_options)

Builds a string representation of the data table based on self.options, or temp_options. Passing temp_options does not permanently change the model

def build_string(self,**temp_options):
    """Builds a string representation of the data table based on self.options, or temp_options.
    Passing temp_options does not permanently change the model"""
    # store the original options to be put back after the string is made
    original_options=self.options
    for key,value in temp_options.iteritems():
        self.options[key]=value
    section_end=0
    next_section_begin=0
    if self.options['data_table_element_separator'] is None:
        inner_element_spacing=0
    else:
        inner_element_spacing=self.options['data_table_element_separator'].count('\n')-1
    string_out=""
    between_section=""
    if self.options['data_table_element_separator'] is not None:
        between_section=self.options['data_table_element_separator']
    if self.header is None:
        self.options['header_begin_line']=self.options['header_end_line']=None
        pass
    else:
        self.options["header_begin_line"]=0
        if self.data is None and self.column_names is None and self.footer is None:
            string_out=self.get_header_string()
            self.options["header_end_line"]=None
        else:
            string_out=self.get_header_string()+between_section
            last_header_line=self.get_header_string().count('\n')+1
            self.options["header_end_line"]=last_header_line
            next_section_begin=last_header_line+inner_element_spacing
    if self.column_names is None:
        self.options['column_names_begin_line']=self.options['column_names_end_line']=None
        pass
    else:
        self.options["column_names_begin_line"]=next_section_begin
        if self.data is None and self.footer is None:
            self.options["column_names_end_line"]=None
            string_out=string_out+self.get_column_names_string()
        else:
            string_out=string_out+self.get_column_names_string()+between_section
            last_column_names_line=self.get_column_names_string().count('\n')+\
                                   self.options["column_names_begin_line"]+1
            self.options["column_names_end_line"]=last_column_names_line
            next_section_begin=last_column_names_line+inner_element_spacing
    if self.data is None:
        self.options['data_begin_line']=self.options['data_end_line']=None
        pass
    else:
        self.options["data_begin_line"]=next_section_begin
        if self.footer is None:
            self.options["data_end_line"]=None
            string_out=string_out+self.get_data_string()
        else:
            string_out=string_out+self.get_data_string()+between_section
            last_data_line=self.get_data_string().count("\n")+\
                            self.options["data_begin_line"]+1
            self.options["data_end_line"]=last_data_line
            next_section_begin=last_data_line+inner_element_spacing
    if self.footer is None:
        self.options['footer_begin_line']=self.options['footer_end_line']=None
        pass
    else:
        self.options["footer_begin_line"]=next_section_begin
        string_out=string_out+self.get_footer_string()
        self.options['footer_end_line']=None
    # set the options back after the string has been made
    if self.inline_comments is None:
        pass
    else:
        lines=string_out.splitlines()
        for comment in self.inline_comments:
            lines=insert_inline_comment(lines,comment=comment[0],line_number=comment[1],
                                        string_position=comment[2],
                                        begin_token=self.options['inline_comment_begin'],
                                        end_token=self.options['inline_comment_end'])
        string_out=string_list_collapse(lines,string_delimiter='\n')
    self.options=original_options
    return string_out

def change_unit_prefix(

self, column_selector=None, old_prefix=None, new_prefix=None, unit='Hz')

Changes the prefix of the units of the column specified by column_selector (column name or index) example usage is self.change_unit_prefix(column_selector='Frequency',old_prefix=None,new_prefix='G',unit='Hz') to change a column from Hz to GHz. It updates the data values, column_descriptions, and column_units if they exist, see http://www.nist.gov/pml/wmd/metric/prefixes.cfm for possible prefixes

def change_unit_prefix(self,column_selector=None,old_prefix=None,new_prefix=None,unit='Hz'):
    """Changes the prefix of the units of the column specified by column_selector (column name or index)
    example usage is self.change_unit_prefix(column_selector='Frequency',old_prefix=None,new_prefix='G',unit='Hz')
    to change a column from Hz to GHz. It updates the data values, column_descriptions, and column_units if they
    exist, see http://www.nist.gov/pml/wmd/metric/prefixes.cfm for possible prefixes"""
    multipliers={"yotta":10.**24,"Y":10.**24,"zetta":10.**21,"Z":10.**21,"exa":10.**18,"E":10.**18,"peta":10.**15,
                 "P":10.**15,"tera":10.**12,"T":10.**12,"giga":10.**9,"G":10.**9,"mega":10.**6,"M":10.**6,
                 "kilo":10.**3,"k":10.**3,"hecto":10.**2,"h":10.**2,"deka":10.,"da":10.,None:1.,"":1.,
                 "deci":10.**-1,"d":10.**-1,"centi":10.**-2,"c":10.**-2,"milli":10.**-3,"m":10.**-3,
                 "micro":10.**-6,"mu":10.**-6,u"\u00B5":10.**-6,"nano":10.**-9,
                 "n":10.**-9,"pico":10.**-12,"p":10.**-12,"femto":10.**-15,
                 "f":10.**-15,"atto":10.**-18,"a":10.**-18,"zepto":10.**-21,"z":10.**-21,
                 "yocto":10.**-24,"y":10.**-24}
    # change column name into column index
    try:
        if old_prefix is None:
            old_prefix=""
        if new_prefix is None:
            new_prefix=""
        old_unit=old_prefix+unit
        new_unit=new_prefix+unit
        if column_selector in self.column_names:
            column_selector=self.column_names.index(column_selector)
        for index,row in enumerate(self.data):
            if type(self.data[index][column_selector]) in [FloatType,LongType]:
                #print "{0:e}".format(multipliers[old_prefix]/multipliers[new_prefix])
                self.data[index][column_selector]=\
                (multipliers[old_prefix]/multipliers[new_prefix])*self.data[index][column_selector]
            elif type(self.data[index][column_selector]) in [StringType,IntType]:
                self.data[index][column_selector]=\
                str((multipliers[old_prefix]/multipliers[new_prefix])*float(self.data[index][column_selector]))
            else:
                print type(self.data[index][column_selector])
                raise
        if self.options["column_descriptions"] is not None:
            old=self.options["column_descriptions"][column_selector]
            self.options["column_descriptions"][column_selector]=old.replace(old_unit,new_unit)
        if self.options["column_units"] is not None:
            old=self.options["column_units"][column_selector]
            self.options["column_units"][column_selector]=old.replace(old_unit,new_unit)
        if re.search(old_unit,self.column_names[column_selector]):
            old=self.column_names[column_selector]
            self.column_names[column_selector]=old.replace(old_unit,new_unit)
    except:
        print("Could not change the unit prefix of column {0}".format(column_selector))
        raise

def find_line(

self, begin_token)

Finds the first line that has begin token in it

def find_line(self,begin_token):
    """Finds the first line that has begin token in it"""
    for index,line in enumerate(self.lines):
        if re.search(begin_token,line,re.IGNORECASE):
            return index

def get_column(

self, column_name=None, column_index=None)

Returns a column as a list given a column name or column index

def get_column(self,column_name=None,column_index=None):
    """Returns a column as a list given a column name or column index"""
    if column_name is None:
        if column_index is None:
            return
        else:
            column_selector=column_index
    else:
        column_selector=self.column_names.index(column_name)
    out_list=[self.data[i][column_selector] for i in range(len(self.data))]
    return out_list

def get_column_names_string(

self)

Returns the column names as a string using options

def get_column_names_string(self):
    "Returns the column names as a string using options"
    string_out=""
    # This writes the column_names
    column_name_begin=""
    column_name_end=""
    if self.options["column_names_begin_token"] is None:
        column_name_begin=""
    else:
        column_name_begin=self.options["column_names_begin_token"]
    if self.options["column_names_end_token"] is None:
        column_name_end=""
    else:
        column_name_end=self.options["column_names_end_token"]
    if self.column_names is None:
        string_out=""
    else:
        if type(self.column_names) is StringType:
            string_out=self.column_names
        elif type(self.column_names) is ListType:
            string_out=list_to_string(self.column_names,
                                      data_delimiter=self.options["column_names_delimiter"],end="")
            #print("{0} is {1}".format('string_out',string_out))
        else:
            string_out=ensure_string(self.column_names)
    #print column_name_begin,string_out,column_name_end
    return column_name_begin+string_out+column_name_end

def get_data_dictionary_list(

self, use_row_formatter_string=True)

Returns a python list with a row dictionary of form {column_name:data_column}

def get_data_dictionary_list(self,use_row_formatter_string=True):
    """Returns a python list with a row dictionary of form {column_name:data_column}"""
    try:
        if self.options["row_formatter_string"] is None:
            use_row_formatter_string=False
        if use_row_formatter_string:
            list_formatter=[item.replace("{"+str(index),"{0")
                            for index,item in enumerate(self.options["row_formatter_string"].split("{delimiter}"))]
        else:
            list_formatter=["{0}" for i in self.column_names]
        #print self.column_names
        #print self.data
        #print list_formatter
        #print len(self.column_names)==len(self.data[0])
        #print len(list_formatter)==len(self.data[0])
        #print type(self.data[0])
        out_list=[{self.column_names[i]:list_formatter[i].format(value) for i,value in enumerate(line)}
                  for line in self.data]
        return out_list
    except:
        print("Could not form a data_dictionary_list, check that row_formatter_string is properly defined")
        #print(out_list)
        raise

def get_data_string(

self)

Returns the data as a string

def get_data_string(self):
    "Returns the data as a string"
    #Todo:refactor to cut out unused lines
    string_out=""
    if self.data is None:
        string_out= ""
    else:
        if type(self.data) is StringType:
            if self.options['data_begin_token'] is None:
                   if self.options['data_end_token'] is None:
                       string_out=self.data
                   else:
                       if re.search(self.options['data_end_token'],self.data):
                           string_out=self.data
                       else:
                           string_out=self.data+self.options['data_end_token']
            else:
                    if self.options['data_end_token'] is None:
                        if re.match(self.options['data_begin_token'],self.data):
                            string_out=self.data
                        else:
                            string_out=self.options['data_begin_token']+self.data
        elif type(self.data) in [ListType,np.ndarray]:
            try:
                    #If the first row is a string, we should strip all the tokens and add them back in
                    if type(self.data[0]) is StringType:
                        if self.options['data_begin_token'] is None:
                            string_out=string_list_collapse(self.data)
                        else:
                            if re.match(self.options['data_begin_token'],self.data[0]):
                                if self.options['data_end_token'] is None:
                                    string_out=string_list_collapse(self.data)
                                else:
                                    if re.search(self.options['data_end_token'],self.data[-1]):
                                        string_out=string_list_collapse(self.data)
                                    else:
                                        string_out=string_list_collapse(self.data)+self.options['data_end_token']
                            else:
                                if self.options['data_end_token'] is None:
                                    string_out=self.options['data_begin_token']+string_list_collapse(self.data)
                                else:
                                    if re.search(self.options['data_end_token'],self.data[-1]):
                                        string_out=self.options['data_begin_token']+string_list_collapse(self.data)
                                    else:
                                        string_out=self.options['data_begin_token']+\
                                                   string_list_collapse(self.data)+\
                                                   self.options['data_end_token']
                    elif type(self.data[0]) in [ListType,np.ndarray]:
                        prefix=""
                        if self.options['data_begin_token'] is None:
                            if self.options['data_end_token'] is None:
                                string_out=list_list_to_string(self.data,data_delimiter=self.options['data_delimiter'],
                                                               row_formatter_string=self.options['row_formatter_string'],
                                                               line_begin=self.options["row_begin_token"],
                                                               line_end=self.options["row_end_token"])
                        else:
                            if self.options['data_end_token'] is None:
                                string_out=self.options['data_begin_token']+\
                                           list_list_to_string(self.data,
                                                               data_delimiter=self.options['data_delimiter'],
                                                               row_formatter_string=self.options['row_formatter_string'],
                                                               line_begin=self.options["row_begin_token"],
                                                               line_end=self.options["row_end_token"])
                            else:
                                string_out=self.options['data_begin_token']+\
                                           list_list_to_string(self.data,
                                                               data_delimiter=self.options['data_delimiter'],
                                                               row_formatter_string=\
                                                               self.options['row_formatter_string'],
                                                               line_begin=self.options["row_begin_token"],
                                                               line_end=self.options["row_end_token"])+\
                                                                self.options['data_end_token']
                    else:
                        string_out=list_to_string(self.data,
                                                  data_delimiter=self.options['data_delimiter'],
                                                  row_formatter_string=self.options['row_formatter_string'],
                                                  begin=self.options["row_begin_token"],
                                                  end=self.options["row_end_token"])
            except IndexError:
                pass
        else:
            string_out=ensure_string(self.data)
    return string_out

Returns the footer using options in self.options. If block comment is specified, and the footer is a list it will block comment out the footer. If comment_begin and comment_end are specified it will use those to represent each line of the footer. If footer_begin_token and/or footer_end_token are specified it will wrap the footer in those.

def get_header_string(

self)

Returns the header using options in self.options. If block comment is specified, and the header is a list it will block comment out the header. If comment_begin and comment_end are specified it will use those to represent each line of the header. If header_begin_token and/or header_end_token are specified it will wrap the header in those.

def get_header_string(self):
    """Returns the header using options in self.options. If block comment is specified, and the header is a
    list it will block comment out the header. If comment_begin and comment_end are specified it will use
    those to represent each line of the header. If header_begin_token and/or header_end_token are specified it
     will wrap the header in those.
    """
    string_out=""
    header_begin=""
    header_end=""
    if self.options["header_begin_token"] is None:
        header_begin=""
    else:
        header_begin=self.options["header_begin_token"]
    if self.options["header_end_token"] is None:
        header_end=""
    else:
        header_end=self.options["header_end_token"]
    # This writes the header
    if self.header is None:
        string_out= ""
    elif self.options["header_line_types"] is not None:
        for index,line in enumerate(self.options["header_line_types"]):
            if index == len(self.options["header_line_types"])-1:
                end=''
            else:
                end='\n'
            if line in ['header','header_line','normal']:
                string_out=string_out+self.header[index]+end
            elif line in ['line_comment','comment']:
                string_out=string_out+line_comment_string(self.header[index],
                                           comment_begin=self.options["comment_begin"],
                                           comment_end=self.options["comment_end"])+end
            elif line in ['block_comment','block']:
                if index-1<0:
                    block_comment_begin=index
                    block_comment_end=index+2
                    continue
                elif self.options["header_line_types"][index-1] not in ['block_comment','block']:
                    block_comment_begin=index
                    block_comment_end=index+2
                    continue
                else:
                    if index+1>len(self.options["header_line_types"])-1:
                        string_out=string_out+line_list_comment_string(self.header[block_comment_begin:],
                                                                       comment_begin=self.options['block_comment_begin'],
                                                                         comment_end=self.options['block_comment_end'],
                                                                       block=True)+end
                    elif self.options["header_line_types"][index+1] in ['block_comment','block']:
                        block_comment_end+=1
                    else:
                        string_out=string_out+\
                                   line_list_comment_string(self.header[block_comment_begin:block_comment_end],
                                                            comment_begin=self.options['block_comment_begin'],
                                                            comment_end=self.options['block_comment_end'],
                                                            block=True)+end
            else:
                string_out=string_out+line
    elif self.options['treat_header_as_comment'] in [None,True] and self.options["header_line_types"] in [None]:
        # Just happens if the user has set self.header manually
        if type(self.header) is StringType:
            string_out=line_comment_string(self.header,
                                           comment_begin=self.options["comment_begin"],
                                           comment_end=self.options["comment_end"])
            #string_out=re.sub('\n','',string_out,count=1)
        elif type(self.header) is ListType:
            if self.options['block_comment_begin'] is None:
                if self.options['comment_begin'] is None:
                    string_out=string_list_collapse(self.header)
                else:
                    string_out=line_list_comment_string(self.header,comment_begin=self.options['comment_begin'],
                                                    comment_end=self.options['comment_end'])
                    lines_out=string_out.splitlines()
                    # if re.search('\n',self.options['comment_end']):
                    #     string_out=re.sub('\n','',string_out,count=1)
                    #self.options["header_line_types"]=["line_comment" for line in self.header]
            else:
                string_out=line_list_comment_string(self.header,comment_begin=self.options['block_comment_begin'],
                                                    comment_end=self.options['block_comment_end'],block=True)
                #self.options["header_line_types"]=["block_comment" for line in self.header]
    else:
        string_out=ensure_string(self.header,list_delimiter="\n",end_if_list="")
    return header_begin+string_out+header_end

def get_options(

self)

Prints the option list

def get_options(self):
    "Prints the option list"
    for key,value in self.options.iteritems():
        print("{0} = {1}".format(key,value))

def get_options_by_element(

self, element_name)

returns a dictionary of all the options that have to do with element. Element must be header,column_names,data, or footer

def get_options_by_element(self,element_name):
    """ returns a dictionary
     of all the options that have to do with element. Element must be header,column_names,data, or footer"""
    keys_regarding_element=filter(lambda x: re.search(element_name,str(x),re.IGNORECASE),self.options.keys())
    out_dictionary={key:self.options[key] for key in keys_regarding_element}
    #print out_dictionary
    return out_dictionary

def get_row(

self, row_index=None)

Returns the row as a list specified by row_index

def get_row(self,row_index=None):
    """Returns the row as a list specified by row_index"""
    if row_index is None:
        return
    else:
        return self.data[row_index]

def is_valid(

self)

Returns True if ascii table conforms to its specification given by its own options

def is_valid(self):
    """Returns True if ascii table conforms to its specification given by its own options"""
    options={}
    for key,value in self.options.iteritems():
        options[key]=value
        # print("self.options[{0}] is {1} ".format(key,value))
    for element in self.elements:
        if self.__dict__[element] is None:
            options[element]=None
        else:
            options[element]=[]
    options["validate"]=True
    newtable=AsciiDataTable(None,**options)
    lines=self.build_string().splitlines()
    for index,line in enumerate(lines):
        lines[index]=line+"\n"
    newtable.lines=lines
    newtable.__parse__()
    # print newtable.data
    # print newtable.column_names
    # print newtable
    #print_comparison(newtable.footer,None)
    newtable.update_model()
    # The new table rows are not being coerced into the right format
    #print newtable
    #newtable.update_model()
    #print newtable.options
    #print self.options
    #print newtable.data
    # print newtable.options==self.options
    # for option_key,option_value in newtable.options.iteritems():
    #     print("New Table Option {0} is {1} ".format(option_key,option_value))
    #     print("self.options[{0}] is {1} ".format(option_key,self.options[option_key]))
    #     print_comparison(option_value,self.options[option_key])
    # #print self
    return self==newtable

def lines_defined(

self)

If begin_line and end_line for all elements that are None are defined returns True

def lines_defined(self):
    """If begin_line and end_line for all elements that are None are defined returns True"""
    truth_table=[]
    last_element=""
    output=False
    for index,element in enumerate(self.elements):
        if element not in ['inline_comments','metadata'] and self.__dict__[element] is not None:
            try:
                last_element=element
                if not None in [self.options['%s_begin_line'%element],self.options['%s_end_line'%element]]:
                    truth_table.append(True)
                else:
                     truth_table.append(False)
            except:
                return False
    #print truth_table
    # The last_line of the last element is fine to be none
    if truth_table[-1] is False:
        if self.options['%s_begin_line'%last_element] is not None:
            truth_table[-1]=True
    if False in truth_table:
        output=False
    else:
        output=True
    #print output
    return output

Moves the DataTable's footer to the header and updates the model

def remove_column(

self, column_name=None, column_index=None)

Removes the column specified by column_name or column_index and updates the model. The column is removed from column_names, data and if present column_types, column_descriptions and row formatter

def remove_column(self,column_name=None,column_index=None):
    """Removes the column specified by column_name or column_index and updates the model. The column is removed from
    column_names, data and if present column_types, column_descriptions and row formatter"""
    pass

def remove_row(

self, row_index)

Removes the row specified by row_index and updates the model. Note index is relative to the data attribute so to remove the first row use row_index=0 and the last data row is row_index=-1

def remove_row(self,row_index):
    """Removes the row specified by row_index and updates the model. Note index is relative to the
    data attribute so to remove the first row use row_index=0 and the last data row is row_index=-1"""
    self.data.pop(row_index)
    self.update_model()

def save(

self, path=None, **temp_options)

" Saves the file, to save in another ascii format specify elements in temp_options, the options specified do not permanently change the object's options. If path is supplied it saves the file to that path otherwise uses the object's attribute path to define the saving location

def save(self,path=None,**temp_options):
    """" Saves the file, to save in another ascii format specify elements in temp_options, the options
    specified do not permanently change the object's options. If path is supplied it saves the file to that path
    otherwise uses the object's attribute path to define the saving location """
    original_options=self.options
    for key,value in temp_options.iteritems():
        self.options[key]=value
    out_string=self.build_string(**temp_options)
    if path is None:
        path=self.path
    file_out=open(path,'w')
    file_out.write(out_string)
    file_out.close()
    self.options=original_options

def save_schema(

self, path=None, format=None)

Saves the tables options as a text file or pickled dictionary (default). If no name is supplied, autonames it and saves

def save_schema(self,path=None,format=None):
    """Saves the tables options as a text file or pickled dictionary (default).
    If no name is supplied, autonames it and saves"""
    if path is None:
        path=auto_name(self.name.replace('.'+self.options["extension"],""),'Schema',self.options["directory"],'txt')
    if format in [None,'python','pickle']:
        pickle.dump(self.options,open(path,'wb'))
    elif format in ['txt','text','.txt']:
        file_out=open(path,'w')
        keys=self.options.keys()
        keys.sort()
        for key in keys:
            out_key=str(key).replace("\n","\\n")
            out_value=str(self.options[key]).replace("\n","\\n")
            file_out.write("{0} : {1} \n".format(out_key,out_value))
        file_out.close()

def show(

self)

def show(self):
    fig, axes = plt.subplots(nrows=3, ncols=2)
    ax0, ax1, ax2, ax3, ax4, ax5 = axes.flat
    ax0.plot(self.get_column('Frequency'),self.get_column('magS11'),'k-o')
    ax0.set_title('Magnitude S11')
    ax1.plot(self.get_column('Frequency'),self.get_column('argS11'),'ro')
    ax1.set_title('Phase S11')
    ax2.plot(self.get_column('Frequency'),self.get_column('magS21'),'k-o')
    ax2.set_title('Magnitude S21')
    ax3.plot(self.get_column('Frequency'),self.get_column('argS21'),'ro')
    ax3.set_title('Phase S21')
    ax4.plot(self.get_column('Frequency'),self.get_column('magS22'),'k-o')
    ax4.set_title('Magnitude S22')
    ax5.plot(self.get_column('Frequency'),self.get_column('argS22'),'ro')
    ax5.set_title('Phase S22')
    plt.tight_layout()
    plt.show()

def structure_metadata(

self)

Returns a dictionary of key,value pairs extracted from the header

def structure_metadata(self):
    """Returns a dictionary of key,value pairs extracted from the header"""
    keys=["System_Id","System_Letter","Connector_Type_Calibration","Connector_Type_Measurement",
          "Measurement_Type","Measurement_Date","Measurement_Time","Program_Used","Program_Revision","Operator",
          "Calibration_Name","Calibration_Date","Port_Used","Number_Connects","Number_Repeats","Nbs",
          "Number_Frequencies","Start_Frequency",
          "Device_Description","Device_Id"]
    self.metadata={}
    for index,key in enumerate(keys):
        self.metadata[key]=self.header[index].rstrip().lstrip()

def update_column_names(

self)

Update column names adds the value x# for any column that exists in self.data that is not named

def update_column_names(self):
    """Update column names adds the value x# for any column that exists in self.data that is not named"""
    if self.data is None:
        return
    elif type(self.column_names) is StringType:
        self.column_names=split_row(self.column_names,self.options["column_names_delimiter"])
    elif self.column_names is None:
        column_names=[]
        for index,column in enumerate(self.data[0]):
            column_names.append("x"+str(index))
        self.column_names=column_names
        return
    elif len(self.column_names)==len(self.data[0]):
        return
    elif len(self.column_names) < len(self.data[0]):
        for index in range(len(self.column_names),len(self.data[0])):
            self.column_names.append("x"+str(index))
        return

def update_import_options(

self, import_table)

Updates the options in the import table

def update_import_options(self,import_table):
    """Updates the options in the import table"""
    for index,element in enumerate(['header','column_names','data','footer']):
        if self.__dict__[element] is not None:
            print("The {0} variable is {1}".format('index',index))
            print("The {0} variable is {1}".format('element',element))
            print("The {0} variable is {1}".format('import_table',import_table))
            [self.options['%s_begin_line'%element],
                            self.options['%s_end_line'%element],
                            self.options['%s_begin_token'%element],
                            self.options['%s_end_token'%element]]=import_table[index][:]

def update_index(

self)

Updates the index column if it exits, otherwise exits quietly

def update_index(self):
    """ Updates the index column if it exits, otherwise exits quietly
    """
    if 'index' not in self.column_names:
        return
    else:
        try:
            #This should be 0 but just in case
            index_column_number=self.column_names.index('index')
            for i in range(len(self.data)):
                self.data[i][index_column_number]=i
        except:
            pass

def update_model(

self)

Updates the model after a change has been made. If you add anything to the attributes of the model, or change this updates the values. If the model has an index column it will make sure the numbers are correct. In addition, it will update the options dictionary to reflect added rows, changes in deliminators etc.

def update_model(self):
    """Updates the model after a change has been made. If you add anything to the attributes of the model,
    or change this updates the values. If the model has an index column it will make sure the numbers are correct.
    In addition, it will update the options dictionary to reflect added rows, changes in deliminators etc.  """
    if self.column_names is not None and 'index' in self.column_names:
       self.update_index()
    #make sure there are no "\n" characters in the element lists (if so replace them with "") for data this is
    # done on import
    list_types=["header","column_names","footer"]
    for element in list_types:
        if self.__dict__[element] is not None:
            for index,item in enumerate(self.__dict__[element]):
                self.__dict__[element][index]=item.replace("\n","")
    self.update_column_names()
    if self.data is not None:
        self.data=convert_all_rows(self.data,self.options["column_types"])
    self.string=self.build_string()
    self.lines=self.string.splitlines()