Source code for ChiantiPy.core.IpyMspectrum

from datetime import datetime
import copy
import warnings

import numpy as np
try:
    from ipyparallel import Client
except ImportError:
    warnings.warn("ipyparallel not found. You won't be able to use the ipymspectrum module")

import ChiantiPy
import ChiantiPy.tools.data as chdata
import ChiantiPy.tools.constants as const
import ChiantiPy.tools.filters as chfilters
import ChiantiPy.tools.util as util
import ChiantiPy.Gui as chgui
from ChiantiPy.base import ionTrails
from ChiantiPy.base import specTrails


[docs]class ipymspectrum(ionTrails, specTrails): ''' this is the multiprocessing version of spectrum for using inside an IPython Qtconsole or notebook. be for creating an instance, it is necessary to type something like the following into a console > ipcluster3 start --n=3 or > ipcluster start --n=3 this is the way to invoke things under the IPython 6 notation Calculate the emission spectrum as a function of temperature and density. temperature and density can be arrays but, unless the size of either is one (1), the two must have the same size the returned spectrum will be convolved with a filter of the specified width on the specified wavelength array the default filter is gaussianR with a resolving power of 100. Other filters, such as gaussian, box and lorentz, are available in ChiantiPy.filters. When using the box filter, the width should equal the wavelength interval to keep the units of the continuum and line spectrum the same. A selection of elements can be make with elementList a list containing the names of elements that are desired to be included, e.g., ['fe','ni'] A selection of ions can be make with ionList containing the names of the desired lines in Chianti notation, i.e. C VI = c_6 Both elementList and ionList can not be specified at the same time a minimum abundance can be specified so that the calculation can be speeded up by excluding elements with a low abundance. With solar photospheric abundances - setting minAbund = 1.e-4 will include H, He, C, O, Ne setting minAbund = 2.e-5 adds N, Mg, Si, S, Fe setting minAbund = 1.e-6 adds Na, Al, Ar, Ca, Ni Setting em will multiply the spectrum at each temperature by the value of em. em [for emission measure], can be a float or an array of the same length as the temperature/density. allLines = 1 will include lines with either theoretical or observed wavelengths. allLines=0 will include only those lines with observed wavelengths proc = the number of processors to use timeout - a small but non-zero value seems to be necessary ''' def __init__(self, temperature, eDensity, wavelength, filter=(chfilters.gaussianR, 1000.), label=None, elementList = None, ionList = None, minAbund=None, keepIons=0, doLines=1, doContinuum=1, allLines = 1, em=None, abundanceName=0, verbose=0, timeout=0.1): # wavelength = np.atleast_1d(wavelength) if wavelength.size < 2: print((' wavelength must have at least two values, current length %3i'%(wavelength.size))) return t1 = datetime.now() # rcAll = Client() # all_engines = rcAll[:] lbvAll = rcAll.load_balanced_view() # # # creates Intensity dict from first ion calculated # setupIntensity = 0 # self.Defaults = chdata.Defaults # self.Temperature = np.asarray(temperature,'float64') self.EDensity = np.asarray(eDensity,'float64') self.NEDens = self.EDensity.size ndens = self.EDensity.size ntemp = self.Temperature.size tst1 = ndens == ntemp tst1a = ndens != ntemp tst2 = ntemp > 1 tst3 = ndens > 1 tst4 = ndens > 1 and ntemp > 1 if tst1 and ntemp == 1: self.NTempDen = 1 elif tst1a and (tst2 or tst3) and not tst4: self.NTempDen = ntemp*ndens if ntemp == self.NTempDen and ndens != self.NTempDen: self.EDensity = np.ones_like(self.Temperature)*self.EDensity elif ndens == self.NTempDen and ntemp != self.NTempDen: self.Temperature = np.ones_like(self.EDensity)*self.Temperature elif tst1 and tst4: self.NTempDen = ntemp if verbose: print(('NTempDen: %5i'%(self.NTempDen))) # # if em == None: em = np.ones(self.NTempDen, 'float64') ylabel = r'erg cm$^{-2}$ s$^{-1}$ sr$^{-1} \AA^{-1}$ ($\int\,$ N$_e\,$N$_H\,$d${\it l}$)$^{-1}$' elif type(em) == float: em = np.ones(self.NTempDen, 'float64')*em ylabel = r'erg cm$^{-2}$ s$^{-1}$ sr$^{-1} \AA^{-1}$ $' elif type(em) == list or type(em) == tuple or type(em) == np.ndarray: em = np.asarray(em, 'float64') ylabel = r'erg cm$^{-2}$ s$^{-1}$ sr$^{-1} \AA^{-1}$ $' self.Em = em if verbose: print(('len of self.Em %5i'%(len(self.Em)))) # # if self.Em.any() > 0.: ylabel = r'erg cm$^{-2}$ s$^{-1}$ sr$^{-1} \AA^{-1}$ $' else: ylabel = r'erg cm$^{-2}$ s$^{-1}$ sr$^{-1} \AA^{-1}$ ($\int\,$ N$_e\,$N$_H\,$d${\it l}$)$^{-1}$' # xlabel = 'Wavelength ('+self.Defaults['wavelength'] +')' # self.AllLines = allLines # if not abundanceName: self.AbundanceName = self.Defaults['abundfile'] else: if abundanceName in chdata.Abundance: self.AbundanceName = abundanceName else: abundChoices = list(chdata.Abundance.keys()) abundChoice = chgui.gui.selectorDialog(abundChoices,label='Select Abundance name') abundChoice_idx = abundChoice.selectedIndex self.AbundanceName = abundChoices[abundChoice_idx[0]] abundanceName = self.AbundanceName print((' Abundance chosen: %s '%(self.AbundanceName))) # # abundAll = chdata.Abundance[self.AbundanceName]['abundance'] self.AbundAll = abundAll self.MinAbund = minAbund # #ionInfo = chio.masterListInfo() wavelength = np.asarray(wavelength) nWvl = wavelength.size self.Wavelength = wavelength # # freeFree = np.zeros((self.NTempDen, nWvl), 'float64').squeeze() freeBound = np.zeros((self.NTempDen, nWvl), 'float64').squeeze() twoPhoton = np.zeros((self.NTempDen, nWvl), 'float64').squeeze() lineSpectrum = np.zeros((self.NTempDen, nWvl), 'float64').squeeze() # # allInpt = [] # if keepIons: self.IonInstances = {} self.FbInstances = {} self.FfInstances = {} # # ionGate creates the self.Todo list # self.ionGate(elementList = elementList, ionList = ionList, minAbund=minAbund, doLines=doLines, doContinuum=doContinuum, verbose = verbose) # for akey in sorted(self.Todo.keys()): zStuff = util.convertName(akey) Z = zStuff['Z'] abundance = chdata.Abundance[self.AbundanceName]['abundance'][Z - 1] if verbose: print((' %5i %5s abundance = %10.2e '%(Z, const.El[Z-1], abundance))) if verbose: print((' doing ion %s for the following processes %s'%(akey, self.Todo[akey]))) if 'ff' in self.Todo[akey]: allInpt.append([akey, 'ff', temperature, wavelength, abundance, em]) if 'fb' in self.Todo[akey]: allInpt.append([akey, 'fb', temperature, wavelength, abundance, em]) if 'line' in self.Todo[akey]: allInpt.append([akey, 'line', temperature, eDensity, wavelength, filter, allLines, abundance, em, doContinuum]) # result = lbvAll.map_sync(doAll, allInpt) if verbose: print(' got all ff, fb, line results') ionsCalculated = [] # for ijk in range(len(result)): out = result[ijk] if type(out) != list: print(' a problem has occured - this can be caused by') print('running Python3 and not using ipcluster3') return ionS = out[0] if verbose: print((' collecting calculation for %s'%(ionS))) ionsCalculated.append(ionS) calcType = out[1] if verbose: print((' processing %s results'%(calcType))) # if calcType == 'ff': thisFf = out[2] if keepIons: self.FfInstances[ionS] = thisFf freeFree += thisFf elif calcType == 'fb': thisFb = out[2] if verbose: print((' fb ion = %s'%(ionS))) if hasattr(thisFb, 'FreeBound'): if 'errorMessage' not in sorted(thisFb.keys()): if keepIons: self.FbInstances[ionS] = thisFb freeBound += thisFb['rate'] else: print((thisFb['errorMessage'])) elif calcType == 'line': thisIon = out[2] if not 'errorMessage' in sorted(thisIon.Intensity.keys()): if keepIons: self.IonInstances[ionS] = thisIon thisIntensity = thisIon.Intensity ## self.IonInstances.append(copy.deepcopy(thisIon)) if setupIntensity: for akey in sorted(self.Intensity.keys()): self.Intensity[akey] = np.hstack((self.Intensity[akey], thisIntensity[akey])) else: setupIntensity = 1 self.Intensity = thisIntensity # lineSpectrum += thisIon.Spectrum['intensity'] # check for two-photon emission if len(out) == 4: tp = out[3] if self.NTempDen == 1: twoPhoton += tp['intensity'] else: for iTempDen in range(self.NTempDen): twoPhoton[iTempDen] += tp['rate'][iTempDen] else: if 'errorMessage' in sorted(thisIon.Intensity.keys()): print((thisIon.Intensity['errorMessage'])) # # self.IonsCalculated = ionsCalculated # # self.FreeFree = {'wavelength':wavelength, 'intensity':freeFree.squeeze()} self.FreeBound = {'wavelength':wavelength, 'intensity':freeBound.squeeze()} self.LineSpectrum = {'wavelength':wavelength, 'intensity':lineSpectrum.squeeze()} self.TwoPhoton = {'wavelength':wavelength, 'intensity':twoPhoton.squeeze()} # total = freeFree + freeBound + lineSpectrum + twoPhoton # t2 = datetime.now() dt=t2-t1 print((' elapsed seconds = %12.3e'%(dt.seconds))) rcAll.purge_results('all') # if self.NTempDen == 1: integrated = total else: integrated = total.sum(axis=0) # if type(label) == type(''): if hasattr(self, 'Spectrum'): print(' hasattr = true') self.Spectrum[label] = {'wavelength':wavelength, 'intensity':total.squeeze(), 'filter':filter[0].__name__, 'width':filter[1], 'integrated':integrated, 'em':em, 'Abundance':self.AbundanceName, 'xlabel':xlabel, 'ylabel':ylabel} else: self.Spectrum = {label:{'wavelength':wavelength, 'intensity':total.squeeze(), 'filter':filter[0].__name__, 'width':filter[1], 'integrated':integrated, 'em':em, 'Abundance':self.AbundanceName, 'xlabel':xlabel, 'ylabel':ylabel}} else: self.Spectrum = {'wavelength':wavelength, 'intensity':total.squeeze(), 'filter':filter[0].__name__, 'width':filter[1], 'integrated':integrated, 'em':em, 'Abundance':self.AbundanceName, 'xlabel':xlabel, 'ylabel':ylabel}
# # ------------------------------------------------------------------------- #
[docs]def doAll(inpt): ''' to process ff, fb and line inputs ''' ionS = inpt[0] calcType = inpt[1] if calcType == 'ff': temperature = inpt[2] wavelength = inpt[3] abund = inpt[4] em = inpt[5] FF = ChiantiPy.core.continuum(ionS, temperature, abundance=abund, em=em) FF.freeFree(wavelength) # can not do a deep copy of # return [ionS, calcType, copy.deepcopy(cont)] return [ionS, calcType, copy.copy(FF.FreeFree)] elif calcType == 'fb': temperature = inpt[2] wavelength = inpt[3] abund = inpt[4] em = inpt[5] cont = ChiantiPy.core.continuum(ionS, temperature, abundance=abund, em=em) try: cont.freeBound(wavelength) return [ionS, calcType, {'rate': cont.FreeBound}] except ValueError: return [ionS, calcType, {'errorMessage': 'No free-bound information available.'}] elif calcType == 'line': temperature = inpt[2] density = inpt[3] wavelength = inpt[4] wvlRange = [wavelength.min(), wavelength.max()] filter = inpt[5] allLines = inpt[6] abund = inpt[7] em = inpt[8] doContinuum = inpt[9] thisIon = ChiantiPy.core.ion(ionS, temperature, density, abundance=abund, em=em) thisIon.intensity(wvlRange = wvlRange, allLines = allLines) if 'errorMessage' not in list(thisIon.Intensity.keys()): thisIon.spectrum(wavelength, filter=filter, allLines=allLines) outList = [ionS, calcType, copy.deepcopy(thisIon)] if not thisIon.Dielectronic and doContinuum: if (thisIon.Z - thisIon.Ion) in [0, 1]: thisIon.twoPhoton(wavelength) outList.append(thisIon.TwoPhoton) return outList