cis_interface.dataio package

Subpackages

Submodules

cis_interface.dataio.AsciiFile module

class cis_interface.dataio.AsciiFile.AsciiFile(filepath, io_mode, comment='#', newline='n', open_as_binary=True)

Bases: object

close()

Close the associated file descriptor if it is open.

is_open

bool – Returns True if the file descriptor is open.

open()

Open the associated file descriptor if it is not already open.

open_mode

str – Mode that should be used to open the file.

readline()

Continue reading lines until a valid line (uncommented) is encountered

Returns:

End of file flag and the line that was read

(None if the end of file was encountered).

Return type:tuple (bool, str)

readline_full()

Read a line and return it if it is not a comment.

Returns:

End of file flag and the line that was read (an

empty string if the end of file was encountered). If the line is a comment, None is returned.

Return type:tuple (bool, str)

writeline(line)

Write a line to the file, adding a newline character if it is not present.

Parameters:line (str/bytes) – Line to be written with/without the newline character. Raises:TypeError – If line is not the correct bytes type.

writeline_full(line)

Write a line to the file in its present state. If it is not open, nothing happens.

Parameters:line (str/bytes) – Line to be written. Raises:TypeError – If line is not the correct bytes type.

cis_interface.dataio.AsciiTable module

class cis_interface.dataio.AsciiTable.AsciiTable(filepath, io_mode, format_str=None, dtype=None, column_names=None, use_astropy=False, column='t', **kwargs)

Bases: cis_interface.dataio.AsciiFile.AsciiFile

arr

Numpy array of table contents if opened in read mode.

array_to_bytes(arr=None, order='C')

Convert arr to bytestring.

Parameters:

• arr (np.ndarray, optional) – Array to write to bytestring. If None the array of table data is used. This can also be a list of arrays, one for each field in the table, or a list of lists, one for each element containing the fields for that element.
• order (str, optional) – Order that array should be written to the bytestring. Defaults to ‘C’.

Returns:

Bytestring.

Return type:

str

Raises:

• TypeError – If the provided array is not a numpy array, list, or tuple.
• ValueError – If the array is not the correct type.
• ValueError – If there are not enough arrays in the input list.
• ValueError – If any of the listed arrays doesn’t have enough fields.
• ValueError – If any of the listed arrays doesn’t have enough elements.

bytes_to_array(data, order='C')

Process bytes according to the table format and return it as an array.

Parameters:

• data (bytes) – Byte string of table data.
• order (str, optional) – Order of data for reshaping. Defaults to ‘C’.

Returns:

Numpy array containing data from bytes.

Return type:

np.ndarray

discover_format_str()

Determine the format string by reading it from the file. The format string is assumed to start with a comment and contain C-style format codes (e.g. ‘%f’).

Raises:RuntimeError – If a format string cannot be located within the file.

dtype

fmts

List of formats in format string.

format_line(*args)

Create a line from the provided arguments using the table format.

Parameters:*args – Arguments to create line from. Returns:The line created from the arguments. Return type:str Raises:RuntimeError – If the incorrect number of arguments are passed.

format_str

ncols

process_line(line)

Extract values from the columns in the line using the table format.

Parameters:line (str) – String to extract arguments from. Returns:The arguments extracted from line. Return type:tuple

read_array(names=None)

Read the table in as an array.

Parameters:names (list, optional) – List of column names to label columns. If not provided, existing names are used if they exist. Defaults to None. Returns:Array of table contents. Return type:np.ndarray Raises:ValueError – If names are provided, but not the same number as there are columns.

read_bytes(order='C', **kwargs)

Read the table in as array and encode as bytes.

Parameters:

• order (str, optional) – Order that array should be written to the bytestring. Defaults to ‘C’.
• **kwargs – Additional keyword arguments are passed to read_array.

Returns:

Array as bytes.

Return type:

bytes

readline()

Continue reading lines until a valid line (uncommented) is encountered and return the arguments found there.

Returns:

End of file flag and the arguments that

were read from the line. If the end of file is reached, None is returned.

Return type:tuple (bool, tuple)

readline_full(validate=False)

Read a line and return it if it is not a comment.

Parameters:validate (bool, optional) – If True, the line is checked to see if it matches the expected table format. Defaults to False. Returns:

End of file flag and the line that was read (an

empty string if the end of file was encountered). If the line is a comment, None is returned.

Return type:tuple (bool, str)

update_dtype(new_dtype)

Change the data type and update the format string.

Parameters:new_dtype (str or np.dtype) – New numpy data type.

update_format_str(new_format_str)

Change the format string and update the data type.

Parameters:new_format_str (str) – New format string.

validate_line(line)

Assert that the line matches the format string and produces the expected number of values.

Raises:

• TypeError – If the line is not a bytes/str.
• AssertionError – If the line does not match the format string.

write_array(array, names=None, skip_header=False)

Write a numpy array to the table.

Parameters:

• array (np.ndarray) – Array to be written.
• names (list, optional) – List of column names to write out. If not provided, existing names are used if they exist. Defaults to None.
• skip_header (bool, optional) – If True, no header information is written (it is assumed it was already written. Defaults to False.

Raises:

ValueError – If names are provided, but not the same number as there are columns.

write_bytes(data, order='C', **kwargs)

Write a numpy array to the table.

Parameters:

• data (bytes) – Bytes string to be interpreted as array and written to file.
• order (str, optional) – Order of data for reshaping. Defaults to ‘C’.
• **kwargs – Additional keyword arguments are passed to write_array.

writeformat()

Write the format string to the file.

writeheader(names=None)

Write header including column names and format.

Parameters:names (list, optional) – List of names of columns. Defaults to None and the ones provided at construction are used if they exist. Otherwise, no names are written.

writeline(*args)

Write arguments to a file in the table format.

Parameters:*args – Any number of arguments that should be written to the file.

writeline_full(line, validate=False)

Write a line to the file in its present state.

Parameters:

• line (str) – Line to be written.
• validate (bool, optional) – If True, the line is checked to see if it matches the expected table format. Defaults to False.

writenames(names=None)

Write column names to file.

Parameters:names (list, optional) – List of names of columns. Defaults to None and the ones provided at construction are used if they exist. Otherwise, no names are written. Raises:IndexError – If there are not enough names for all of the columns.

cis_interface.dataio.AsciiTable.cformat2nptype(cfmt)

Convert a c format string to a numpy data type.

Parameters:

cfmt (str) – c format that should be translated.

Returns:

Corresponding numpy data type.

Return type:

str

Raises:

• TypeError – if cfmt is not a string.
• ValueError – If the c format does not begin with ‘%’.
• ValueError – If the c format does not contain type info.
• ValueError – If the c format cannot be translated to a numpy datatype.

cis_interface.dataio.AsciiTable.cformat2pyscanf(cfmt)

Convert a c format specification string to a version that the python scanf module can use.

Parameters:

cfmt (str) – C format specification string.

Returns:

Version of cfmt that can be parsed by scanf.

Return type:

str

Raises:

• TypeError – if cfmt is not a bytes/str.
• ValueError – If the c format does not begin with ‘%’.
• ValueError – If the c format does not contain type info.

cis_interface.dataio.AsciiTable.nptype2cformat(nptype)

Convert a numpy data type to a c format string.

Parameters:

nptype (str or numpy.dtype) – Numpy data type that should be converted.

Returns:

Corresponding c format specification string.

Return type:

str

Raises:

• TypeError – If nptype is not a string or numpy.dtype.
• ValueError – If a matching format string cannot be determined.

Module contents

Routines for standardized I/O.