Source code for ChiantiPy.core.Mspectrum

from datetime import datetime
import copy
import multiprocessing as mp

import numpy as np

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
import ChiantiPy.tools.mputil as mputil


[docs]class mspectrum(ionTrails, specTrails): ''' this is the multiprocessing version of spectrum set proc to the desired number of processors, default=3 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 chianti.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=0, elementList = None, ionList = None, minAbund=None, keepIons=0, abundance=None, doLines=1, doContinuum=1, allLines = 1, em=None, proc=3, 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() # creates Intensity dict from first ion calculated setupIntensity = 0 # self.Defaults = chdata.Defaults self.Temperature = np.asarray(temperature, 'float64') nTemp = self.Temperature.size self.EDensity = np.asarray(eDensity, 'float64') nDen = self.EDensity.size nTempDen = max([nTemp, nDen]) self.NTempDen = 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 and em > 0.: 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 self.Defaults['wavelength'] == 'angstrom': xlabel = 'Wavelength ('+self.Defaults['wavelength'].capitalize() +')' else: xlabel = 'Wavelength ('+self.Defaults['wavelength'] +')' # # self.AllLines = allLines self.MinAbund = minAbund # if abundance is not None: if type(abundance) == str: if abundance in chdata.AbundanceList: self.AbundanceName = abundance else: abundChoices = chdata.AbundanceList abundChoice = chGui.gui.selectorDialog(abundChoices,label='Select Abundance name') abundChoice_idx = abundChoice.selectedIndex self.AbundanceName = abundChoices[abundChoice_idx[0]] if verbose: print(('Abundance file chosen: %s'%(self.AbundanceName))) else: print(' keyword abundance must be a string, either a blank (\'\') or the name of an abundance file') return else: self.AbundanceName = self.Defaults['abundfile'] if hasattr(self,'AbundanceName'): self.Abundance = chdata.Abundance[self.AbundanceName]['abundance'] # abundAll = chdata.Abundance[self.AbundanceName]['abundance'] self.AbundAll = abundAll # wavelength = np.asarray(wavelength) nWvl = wavelength.size self.Wavelength = wavelength # proc = min([proc, mp.cpu_count()]) # freeFree = np.zeros((nTempDen, nWvl), 'float64').squeeze() freeBound = np.zeros((nTempDen, nWvl), 'float64').squeeze() twoPhoton = np.zeros((nTempDen, nWvl), 'float64').squeeze() lineSpectrum = np.zeros((nTempDen, nWvl), 'float64').squeeze() # # free-free multiprocessing setup ffWorkerQ = mp.Queue() ffDoneQ = mp.Queue() # # free-bound multiprocessing setup # fbWorkerQ = mp.Queue() fbDoneQ = mp.Queue() # # ion multiprocessing setup ionWorkerQ = mp.Queue() ionDoneQ = mp.Queue() # self.IonsCalculated = [] if keepIons: if doLines: self.IonInstances = {} self.Finished = [] # self.ionGate(elementList = elementList, ionList = ionList, minAbund=minAbund, doLines=doLines, doContinuum=doContinuum, verbose = verbose) for one in list(self.Todo.keys()): print((' %s %s'%(one, self.Todo[one]))) # for akey in sorted(self.Todo.keys()): # zStuff = util.convertName(akey) # Z = zStuff['Z'] # abundance = self.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]: ffWorkerQ.put((akey, temperature, wavelength, abundance, em)) if 'fb' in self.Todo[akey]: fbWorkerQ.put((akey, temperature, wavelength, abundance, em)) if 'line' in self.Todo[akey]: ionWorkerQ.put((akey, temperature, eDensity, wavelength, filter, allLines, abundance, em, doContinuum)) # ffWorkerQSize = ffWorkerQ.qsize() fbWorkerQSize = fbWorkerQ.qsize() ionWorkerQSize = ionWorkerQ.qsize() if doContinuum: ffProcesses = [] for i in range(proc): p = mp.Process(target=mputil.doFfQ, args=(ffWorkerQ, ffDoneQ)) p.start() ffProcesses.append(p) # timeout is not necessary for p in ffProcesses: if p.is_alive(): p.join(timeout=timeout) # for iff in range(ffWorkerQSize): thisFreeFree = ffDoneQ.get() freeFree += thisFreeFree['intensity'] for p in ffProcesses: if not isinstance(p, str): p.terminate() # fbProcesses = [] for i in range(proc): p = mp.Process(target=mputil.doFbQ, args=(fbWorkerQ, fbDoneQ)) p.start() fbProcesses.append(p) # timeout is not necessary for p in fbProcesses: if p.is_alive(): p.join(timeout=timeout) # for ifb in range(fbWorkerQSize): thisFreeBound = fbDoneQ.get() freeBound += thisFreeBound['intensity'].squeeze() for p in fbProcesses: if not isinstance(p, str): p.terminate() # if doLines: ionProcesses = [] if ionWorkerQSize < proc: proc = ionWorkerQSize for i in range(proc): p = mp.Process(target=mputil.doIonQ, args=(ionWorkerQ, ionDoneQ)) p.start() ionProcesses.append(p) # timeout is not necessary for p in ionProcesses: # if p.is_alive(): # p.join() p.join(timeout=timeout) # for ijk in range(ionWorkerQSize): out = ionDoneQ.get() ionS = out[0] if verbose: print((' collecting ion calculation for %s'%(ionS))) thisIon = out[1] thisIntensity = thisIon.Intensity if not 'errorMessage' in sorted(thisIntensity.keys()): self.Finished.append(ionS) if keepIons: self.IonInstances[ionS] = copy.deepcopy(thisIon) if setupIntensity: for akey in sorted(self.Intensity.keys()): self.Intensity[akey] = np.hstack((copy.copy(self.Intensity[akey]), thisIntensity[akey])) else: setupIntensity = 1 self.Intensity = thisIntensity # if not 'errorMessage' in sorted(thisIon.Spectrum.keys()): lineSpectrum += thisIon.Spectrum['intensity'] # check for two-photon emission if len(out) == 3: tp = out[2] twoPhoton += tp['intensity'] else: if 'errorMessage' in sorted(thisIntensity.keys()): print((thisIntensity['errorMessage'])) # for p in ionProcesses: if not isinstance(p, str): p.terminate() # # # 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 = %12.3f'%(dt.seconds))) # if nTempDen == 1: integrated = total else: integrated = total.sum(axis=0) # if type(label) == type(''): if hasattr(self, 'Spectrum'): self.Spectrum[label] = {'wavelength':wavelength, 'intensity':total.squeeze(), 'filter':filter[0].__name__, 'width':filter[1], 'integrated':integrated, 'ions':self.IonsCalculated, 'em':em, 'Abundance':self.AbundanceName, 'xlabel':xlabel, 'ylabel':ylabel, 'minAbund':minAbund} else: self.Spectrum = {label:{'wavelength':wavelength, 'intensity':total.squeeze(), 'filter':filter[0].__name__, 'width':filter[1], 'integrated':integrated, 'ions':self.IonsCalculated, 'em':em, 'Abundance':self.AbundanceName, 'xlabel':xlabel, 'ylabel':ylabel}, 'minAbund':minAbund} else: self.Spectrum ={'wavelength':wavelength, 'intensity':total.squeeze(), 'filter':filter[0].__name__, 'width':filter[1], 'integrated':integrated, 'ions':self.IonsCalculated, 'em':em, 'Abundance':self.AbundanceName, 'xlabel':xlabel, 'ylabel':ylabel, 'minAbund':minAbund}