def __init__(self, ionStr, temperature, abundance=0, abundanceName=0, em=0, verbose=0):
nameDict = util.convertName(ionStr)
self.Z = nameDict['Z']
self.Ion = nameDict['Ion']
self.IonStr = ionStr
self.Dielectronic = 0
self.Defaults = chdata.Defaults
self.AbundanceName = self.Defaults['abundfile']
self.IoneqName = self.Defaults['ioneqfile']
#
# ip in eV, reading Ip of next lower level, needed for freeBound
if self.Ion == 1:
if verbose:
print(' for %s this is the neutral ions an does not produce a continuum'%(ionStr))
return
# the Ip is only relevant to the free-free methods
# self.Ip = ip[self.Z-1, self.Ion-1]
self.Ipr = ip[self.Z-1, self.Ion-2]
#
if type(temperature) == float and temperature > 0.:
self.Temperature = np.asarray(temperature,'float64')
elif type(temperature) == list or type(temperature) == tuple or type(temperature) == np.ndarray:
temperature = np.asarray(temperature, 'float64')
self.Temperature = temperature
#
if abundance:
self.Abundance = abundance
elif abundanceName:
if abundanceName in sorted(chdata.Abundance.keys()):
self.AbundanceName = abundanceName
self.Abundance = chdata.Abundance[self.AbundanceName]['abundance'][self.Z-1]
else:
abundChoices = sorted(chdata.Abundance.keys())
# for one in wvl[topLines]:
# wvlChoices.append('%12.3f'%(one))
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))
self.Abundance = chdata.Abundance[self.AbundanceName]['abundance'][self.Z-1]
else:
self.AbundanceName = self.Defaults['abundfile']
self.Abundance = chdata.Abundance[self.AbundanceName]['abundance'][self.Z-1]
#
self.ioneqOne()
#
if type(em) == int and em == 0:
em = np.ones_like(self.Temperature, 'float64')
self.Em = em
elif type(em) == float and em > 0.:
em = np.ones_like(self.Temperature, 'float64')*em
self.Em = em
elif type(em) == list or type(em) == tuple or type(em) == np.ndarray:
em = np.asarray(em, 'float64')
self.Em = em
def freeBoundLoss(self, **kwargs):
"""
Calculate the free-bound energy loss rate of an ion. The result is returned to the
`free_bound_loss` attribute.
The free-bound loss rate can be calculated by integrating the free-bound emission over the wavelength.
This is difficult using the expression in `calculate_free_bound_emission` so we instead use the
approach of [1]_ and [2]_. Eq. 1a of [2]_ can be integrated over wavelength to get the free-bound loss rate,
.. math::
\\frac{dW}{dtdV} = C_{ff}\\frac{k}{hc}T^{1/2}G_{fb},
in units of erg :math:`\mathrm{cm}^3\,\mathrm{s}^{-1}` where :math:`G_{fb}` is the free-bound Gaunt factor as
given by Eq. 15 of [2]_ (see `mewe_gaunt_factor` for more details) and :math:`C_{ff}` is the numerical constant
as given in Eq. 4 of [1]_ and can be written in terms of the fine structure constant :math:`\\alpha`,
.. math::
C_{ff}\\frac{k}{hc} = \\frac{8}{3}\left(\\frac{\pi}{6}\\right)^{1/2}\\frac{h^2\\alpha^3}{\pi^2}\\frac{k_B}{m_e^{3/2}} \\approx 1.43\\times10^{-27}
References
----------
.. [1] Gronenschild, E.H.B.M. and Mewe, R., 1978, A&AS, `32, 283 <http://adsabs.harvard.edu/abs/1978A%26AS...32..283G>`_
.. [2] Mewe, R. et al., 1986, A&AS, `65, 511 <http://adsabs.harvard.edu/abs/1986A%26AS...65..511M>`_
"""
nameDict = ch_util.convertName(self.ion_string)
lower = nameDict['lower']
self.Recombined_fblvl = ch_io.fblvlRead(lower)
if 'errorMessage' in self.Recombined_fblvl:
errorMessage = 'No free-bound information available for {}'.format(
self.ion_string)
rate = np.zeros_like(self.Temperature)
self.FreeBoundLoss = {'rate': rate, 'errorMessage': errorMessage}
return
# Calculate Gaunt factor according to Mewe
gaunt_factor = self.mewe_gaunt_factor()
# Numerical prefactor
prefactor = (8. / 3. * np.sqrt(np.pi / 6.) * (ch_const.planck**2) *
(ch_const.fine**3) / (np.pi**2) *
(ch_const.boltzmann**(1. / 2.)) /
(ch_const.emass**(3. / 2.)))
self.FreeBoundLoss = {
'rate': gaunt_factor * np.sqrt(self.Temperature) * prefactor,
'temperature': self.Temperature
}
def __init__(self, ion_string, temperature, abundance=None, em=None):
self.ion_string = ion_string
self.nameDict = ch_util.convertName(ion_string)
self.Z = self.nameDict['Z']
self.stage = self.nameDict['Ion']
self.Temperature = np.atleast_1d(temperature)
self.NTemperature = self.Temperature.size
self.Defaults = ch_data.Defaults
if em is None:
self.Em = 1. * np.ones_like(self.Temperature)
elif type(em) is list:
self.Em = np.asarray(em)
elif type(em) is np.ndarray:
self.Em = em
elif type(em) is float:
self.Em = em * np.ones_like(self.Temperature)
self.Ip = ch_data.Ip[self.Z - 1, self.stage - 1]
self.Ipr = ch_data.Ip[self.Z - 1, self.stage - 2]
self.ionization_potential = ch_data.Ip[self.Z - 1, self.stage -
1] * ch_const.ev2Erg
self.IprErg = self.Ipr * ch_const.ev2Erg
# Set abundance
if abundance is not None:
try:
self.Abundance = float(abundance)
except ValueError:
if abundance in ch_data.AbundanceList:
self.AbundanceName = abundance
else:
abundChoices = ch_data.AbundanceList
abundChoice = chGui.gui.selectorDialog(
abundChoices, label='Select Abundance name')
abundChoice_idx = abundChoice.selectedIndex
self.AbundanceName = abundChoices[abundChoice_idx[0]]
else:
self.AbundanceName = ch_data.Defaults['abundfile']
if not hasattr(self, 'Abundance'):
self.Abundance = ch_data.Abundance[
self.AbundanceName]['abundance'][self.Z - 1]
self.ioneqOne()
def freeBoundLoss(self, **kwargs):
"""
Calculate the free-bound energy loss rate of an ion. The result is returned to the
`free_bound_loss` attribute.
The free-bound loss rate can be calculated by integrating the free-bound emission over the wavelength.
This is difficult using the expression in `calculate_free_bound_emission` so we instead use the
approach of [1]_ and [2]_. Eq. 1a of [2]_ can be integrated over wavelength to get the free-bound loss rate,
.. math::
\\frac{dW}{dtdV} = C_{ff}\\frac{k}{hc}T^{1/2}G_{fb},
in units of erg :math:`\mathrm{cm}^3\,\mathrm{s}^{-1}` where :math:`G_{fb}` is the free-bound Gaunt factor as
given by Eq. 15 of [2]_ (see `mewe_gaunt_factor` for more details) and :math:`C_{ff}` is the numerical constant
as given in Eq. 4 of [1]_ and can be written in terms of the fine structure constant :math:`\\alpha`,
.. math::
C_{ff}\\frac{k}{hc} = \\frac{8}{3}\left(\\frac{\pi}{6}\\right)^{1/2}\\frac{h^2\\alpha^3}{\pi^2}\\frac{k_B}{m_e^{3/2}} \\approx 1.43\\times10^{-27}
References
----------
.. [1] Gronenschild, E.H.B.M. and Mewe, R., 1978, A&AS, `32, 283 <http://adsabs.harvard.edu/abs/1978A%26AS...32..283G>`_
.. [2] Mewe, R. et al., 1986, A&AS, `65, 511 <http://adsabs.harvard.edu/abs/1986A%26AS...65..511M>`_
"""
nameDict = ch_util.convertName(self.ion_string)
lower = nameDict['lower']
self.Recombined_fblvl = ch_io.fblvlRead(lower)
if 'errorMessage' in self.Recombined_fblvl:
errorMessage = 'No free-bound information available for {}'.format(self.ion_string)
rate = np.zeros_like(self.Temperature)
self.FreeBoundLoss = {'rate':rate, 'errorMessage':errorMessage}
return
# Calculate Gaunt factor according to Mewe
gaunt_factor = self.mewe_gaunt_factor()
# Numerical prefactor
prefactor = (8./3.*np.sqrt(np.pi/6.)*(ch_const.planck**2)*(ch_const.fine**3)/(np.pi**2)
* (ch_const.boltzmann**(1./2.))/(ch_const.emass**(3./2.)))
self.FreeBoundLoss = {'rate':gaunt_factor*np.sqrt(self.Temperature)*prefactor, 'temperature':self.Temperature}
def __init__(self, ion_string, temperature, abundance=None, em=None):
self.ion_string = ion_string
self.nameDict = ch_util.convertName(ion_string)
self.Z = self.nameDict['Z']
self.stage = self.nameDict['Ion']
self.Temperature = np.atleast_1d(temperature)
self.NTemperature = self.Temperature.size
self.Defaults = ch_data.Defaults
if em is None:
self.Em = 1.*np.ones_like(self.Temperature)
elif type(em) == np.ndarray:
self.Em = em
elif type(em) == type(1.):
self.Em = em*np.ones_like(self.Temperature)
self.Ip = ch_data.Ip[self.Z-1, self.stage-1]
self.Ipr = ch_data.Ip[self.Z-1, self.stage-2]
self.ionization_potential = ch_data.Ip[self.Z-1, self.stage-1]*ch_const.ev2Erg
self.IprErg = self.Ipr*ch_const.ev2Erg
# Set abundance
if abundance is not None:
try:
self.abundance = float(abundance)
except ValueError:
if abundance in ch_data.AbundanceList:
self.abundance_name = abundance
else:
abundChoices = ch_data.AbundanceList
abundChoice = chGui.gui.selectorDialog(abundChoices, label='Select Abundance name')
abundChoice_idx = abundChoice.selectedIndex
self.abundance_name = abundChoices[abundChoice_idx[0]]
else:
self.abundance_name = ch_data.Defaults['abundfile']
if not hasattr(self, 'abundance'):
self.abundance = ch_data.Abundance[self.abundance_name]['abundance'][self.Z-1]
self.ioneqOne()
def __init__(self,
temperature,
eDensity,
wvlRange,
elementList=None,
ionList=None,
minAbund=None,
keepIons=0,
em=None,
abundance=None,
verbose=0,
allLines=1):
#
t1 = datetime.now()
# creates Intensity dict from first ion calculated
setupIntensity = 0
#
self.Defaults = chdata.Defaults
temperature = np.asarray(temperature, 'float64')
self.Temperature = temperature
eDensity = np.asarray(eDensity, 'float64')
self.EDensity = eDensity
#
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 em == None:
em = np.ones(self.NTempDen, 'float64')
elif type(em) == float and em > 0.:
em = np.ones(self.NTempDen, 'float64') * em
elif type(em) == list or type(em) == tuple or type(em) == np.ndarray:
em = np.asarray(em, 'float64')
self.Em = em
#
#
if abundance != None:
if abundance in list(chdata.Abundance.keys()):
self.AbundanceName = abundance
else:
abundChoices = list(chdata.Abundance.keys())
# for one in wvl[topLines]:
# wvlChoices.append('%12.3f'%(one))
abundChoice = chGui.gui.selectorDialog(
abundChoices,
label='Select Abundance name',
multiChoice=False)
abundChoice_idx = abundChoice.selectedIndex
self.AbundanceName = abundChoices[abundChoice_idx[0]]
print((' Abundance chosen: %s ' % (self.AbundanceName)))
else:
self.AbundanceName = self.Defaults['abundfile']
#
abundAll = chdata.Abundance[self.AbundanceName]['abundance']
# needed by ionGate
self.AbundAll = abundAll
#
# nonzed = abundAll > 0.
# minAbundAll = abundAll[nonzed].min()
# # if minAbund is even set
# if minAbund:
# if minAbund < minAbundAll:
# minAbund = minAbundAll
# self.minAbund = minAbund
# ionInfo = chio.masterListInfo()
# #
self.IonsCalculated = []
if keepIons:
self.IonInstances = {}
self.Finished = []
#
# also needed by ionGate
self.WvlRange = np.asarray(wvlRange, 'float64')
#
self.ionGate(elementList=elementList,
ionList=ionList,
minAbund=minAbund,
doLines=1,
doContinuum=0,
verbose=verbose)
#
for ionS in sorted(self.Todo.keys()):
nameStuff = util.convertName(ionS)
Z = nameStuff['Z']
if verbose:
print(' calculating %s' % (ionS))
thisIon = ChiantiPy.core.ion(ionS,
temperature,
eDensity,
abundance=abundAll[Z - 1],
em=em)
thisIon.intensity(allLines=allLines)
self.IonsCalculated.append(ionS)
#
if 'errorMessage' not in list(thisIon.Intensity.keys()):
self.Finished.append(ionS)
# thisIon.spectrum(wavelength, filter=filter)
if keepIons:
self.IonInstances[ionS] = copy.deepcopy(thisIon)
if setupIntensity:
for akey in self.Intensity:
self.Intensity[akey] = np.hstack(
(copy.copy(self.Intensity[akey]),
thisIon.Intensity[akey]))
else:
setupIntensity = 1
# print(' creating Intensity dict from ion %s'%(ionS))
self.Intensity = thisIon.Intensity
else:
if verbose:
print(thisIon.Intensity['errorMessage'])
#
#
t2 = datetime.now()
dt = t2 - t1
print(' elapsed seconds = %12.3f' % (dt.seconds))
return
def __init__(self,
temperature,
eDensity,
elementList=0,
ionList=0,
minAbund=0,
doContinuum=1,
abundance=None,
verbose=0,
allLines=1,
keepIons=0):
t1 = datetime.now()
masterlist = chdata.MasterList
# use the ionList but make sure the ions are in the database
if ionList:
alist = []
for one in ionList:
if masterlist.count(one):
alist.append(one)
else:
if verbose:
pstring = ' %s not in CHIANTI database' % (one)
print(pstring)
masterlist = alist
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])
#
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',
multiChoice=False)
abundChoice_idx = abundChoice.selectedIndex
self.AbundanceName = abundChoices[abundChoice_idx[0]]
if verbose:
print(' %s abundances chosen' % (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']
# # needed by ionGate
self.AbundAll = self.Abundance
#
nonzed = self.Abundance > 0.
minAbundAll = self.Abundance[nonzed].min()
# if minAbund is even set
if minAbund:
if minAbund < minAbundAll:
minAbund = minAbundAll
self.MinAbund = minAbund
# ionInfo = util.masterListInfo()
#
freeFreeLoss = np.zeros((nTempDen), 'float64').squeeze()
freeBoundLoss = np.zeros((nTempDen), 'float64').squeeze()
twoPhotonLoss = np.zeros((nTempDen), 'float64').squeeze()
boundBoundLoss = np.zeros((nTempDen), 'float64').squeeze()
twoPhotonLoss = np.zeros((nTempDen), 'float64').squeeze()
#
self.IonsCalculated = []
if keepIons:
self.IonInstances = {}
self.Finished = []
#
self.WvlRange = [0., 1.e+30]
#
self.ionGate(elementList=elementList,
ionList=ionList,
minAbund=minAbund,
doContinuum=doContinuum,
doWvlTest=0,
verbose=verbose)
#
#
for akey in sorted(self.Todo.keys()):
zStuff = util.convertName(akey)
Z = zStuff['Z']
ionstage = zStuff['Ion']
dielectronic = zStuff['Dielectronic']
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 ionstage != 1:
if verbose:
print(' calculating ff continuum for : %s' % (akey))
if 'ff' in self.Todo[akey]:
# need to skip the neutral
cont = continuum(akey, temperature, abundance=abundance)
cont.freeFreeLoss()
freeFreeLoss += cont.FreeFreeLoss['rate']
if 'fb' in self.Todo[akey]:
if verbose:
print(' calculating fb continuum for : %s' % (akey))
cont = continuum(akey, temperature, abundance=abundance)
cont.freeBoundLoss()
if 'errorMessage' not in cont.FreeBoundLoss.keys():
freeBoundLoss += cont.FreeBoundLoss['rate']
if 'line' in self.Todo[akey]:
if verbose:
print(' calculating spectrum for : %s' % (akey))
thisIon = ion(akey, temperature, eDensity, abundance=abundance)
thisIon.intensity(allLines=allLines)
self.IonsCalculated.append(akey)
if 'errorMessage' not in list(thisIon.Intensity.keys()):
self.Finished.append(akey)
thisIon.boundBoundLoss()
boundBoundLoss += thisIon.BoundBoundLoss['rate']
else:
if verbose:
print(thisIon.Intensity['errorMessage'])
# get 2 photon emission for H and He sequences
if (Z - ionstage) in [0, 1] and not dielectronic:
thisIon.twoPhotonLoss()
twoPhotonLoss += thisIon.TwoPhotonLoss['rate']
self.FreeFreeLoss = freeFreeLoss
self.FreeBoundLoss = freeBoundLoss
self.BoundBoundLoss = boundBoundLoss
self.TwoPhotonLoss = twoPhotonLoss
#
total = freeFreeLoss + freeBoundLoss + boundBoundLoss + twoPhotonLoss
t2 = datetime.now()
dt = t2 - t1
print(' elapsed seconds = %10.2e' % (dt.seconds))
xlabel = 'Temperature (K)'
ylabel = r'erg s$^{-1}$ cm$^{3}$'
self.RadLoss = {
'rate': total,
'temperature': self.Temperature,
'density': self.EDensity,
'minAbund': minAbund,
'abundance': self.AbundanceName,
'ylabel': ylabel,
'xlabel': xlabel
}
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}
def __init__(self, temperature, eDensity, elementList=0, ionList = 0, minAbund=0, doContinuum=1, abundanceName=0, verbose=0, allLines=1, keepIons=0):
t1 = datetime.now()
masterlist = chdata.MasterList
# use the ionList but make sure the ions are in the database
if ionList:
alist=[]
for one in ionList:
if masterlist.count(one):
alist.append(one)
else:
if verbose:
pstring = ' %s not in CHIANTI database'%(one)
print(pstring)
masterlist = alist
self.Defaults=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])
if not abundanceName:
self.AbundanceName = self.Defaults['abundfile']
else:
if abundanceName in sorted(chdata.Abundance.keys()):
self.AbundanceName = abundanceName
else:
abundChoices = sorted(chdata.Abundance.keys())
# for one in wvl[topLines]:
# wvlChoices.append('%12.3f'%(one))
abundChoice = chgui.gui.selectorDialog(abundChoices,label='Select Abundance name')
abundChoice_idx = abundChoice.selectedIndex
self.AbundanceName = abundChoices[abundChoice_idx[0]]
abund = self.AbundanceName
print(' Abundance chosen: %s '%(self.AbundanceName))
#
abundAll = chdata.Abundance[self.AbundanceName]['abundance']
# needed by ionGate
self.AbundAll = abundAll
#
nonzed = abundAll > 0.
minAbundAll = abundAll[nonzed].min()
# if minAbund is even set
if minAbund:
if minAbund < minAbundAll:
minAbund = minAbundAll
# ionInfo = util.masterListInfo()
#
freeFreeLoss = np.zeros((nTempDen), 'float64').squeeze()
freeBoundLoss = np.zeros((nTempDen), 'float64').squeeze()
twoPhotonLoss = np.zeros((nTempDen), 'float64').squeeze()
boundBoundLoss = np.zeros((nTempDen), 'float64').squeeze()
twoPhotonLoss = np.zeros((nTempDen), 'float64').squeeze()
#
self.IonsCalculated = []
if keepIons:
self.IonInstances = {}
self.Finished = []
#
self.WvlRange = [0., 1.e+30]
#
self.ionGate(elementList = elementList, ionList = ionList, minAbund=minAbund, doContinuum=doContinuum, doWvlTest=0, verbose=verbose)
#
#
for akey in sorted(self.Todo.keys()):
zStuff = util.convertName(akey)
Z = zStuff['Z']
ionstage = zStuff['Ion']
dielectronic = zStuff['Dielectronic']
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 ionstage != 1:
if verbose:
print(' calculating ff continuum for : %s'%(akey))
if 'ff' in self.Todo[akey]:
# need to skip the neutral
cont = chianti.core.continuum(akey, temperature, abundanceName=self.AbundanceName)
cont.freeFreeLoss()
freeFreeLoss += cont.FreeFreeLoss['rate']
# if nTempDen == 1:
# freeFree += cont.FreeFreeLoss['rate']
# else:
# for iTempDen in range(nTempDen):
# freeFree[iTempDen] += cont.FreeFree['rate'][iTempDen]*em[iTempDen]
# freeFree += cont.FreeFree['rate']
if 'fb' in self.Todo[akey]:
if verbose:
print(' calculating fb continuum for : %s'%(akey))
# try:
# does cont already exist - i.e did we create it for ff
if hasattr(cont, 'FreeFreeLoss'):
cont.freeBoundLoss()
else:
cont = chianti.core.continuum(akey, temperature, abundanceName=self.AbundanceName)
cont.freeBoundLoss()
if 'errorMessage' not in list(cont.FreeBoundLoss.keys()):
# an fblvl file exists for this ions
freeBoundLoss += cont.FreeBoundLoss['rate']
# except:
# cont = chianti.core.continuum(akey, temperature, abundanceName=self.AbundanceName)
# cont.freeBoundLoss()
# if 'errorMessage' not in list(cont.FreeBound.keys()):
# # an fblvl file exists for this ions
# freeBoundLoss += cont.FreeBoundLoss['rate']
# if nTempDen == 1:
# freeBoundLoss += cont.FreeBoundLoss['rate']
# else:
# for iTempDen in range(nTempDen):
# freeBound[iTempDen] += cont.FreeBound['rate'][iTempDen]*em[iTempDen]
# freeBound += cont.FreeBound['rate']
if 'line' in self.Todo[akey]:
if verbose:
print(' calculating spectrum for : %s'%(akey))
thisIon = chianti.core.ion(akey, temperature, eDensity, abundanceName=self.AbundanceName)
thisIon.intensity(allLines=allLines)
self.IonsCalculated.append(akey)
if 'errorMessage' not in list(thisIon.Intensity.keys()):
self.Finished.append(akey)
thisIon.boundBoundLoss()
# self.IonInstances[akey] = copy.deepcopy(thisIon)
# if setupIntensity:
# for bkey in self.Intensity:
# self.Intensity[bkey] = np.hstack((copy.copy(self.Intensity[bkey]), thisIon.Intensity[bkey]))
# else:
# setupIntensity = 1
# self.Intensity = thisIon.Intensity
boundBoundLoss += thisIon.BoundBoundLoss['rate']
# if nTempDen == 1:
# lineSpectrum += thisIon.Spectrum['intensity']
# else:
# for iTempDen in range(nTempDen):
# lineSpectrum[iTempDen] += thisIon.Spectrum['intensity'][iTempDen]
else:
if verbose:
print(thisIon.Intensity['errorMessage'])
# get 2 photon emission for H and He sequences
if (Z - ionstage) in [0, 1] and not dielectronic:
thisIon.twoPhotonLoss()
twoPhotonLoss += thisIon.TwoPhotonLoss['rate']
# for iz in range(31):
# abundance = chdata.Abundance['abundance'][iz-1]
# if abundance >= minAbund:
# print(' %5i %5s abundance = %10.2e '%(iz, const.El[iz-1], abundance))
# #
# for ionstage in range(1, iz+2):
# ionS = util.zion2name(iz, ionstage)
## print ' ionS = ', ionS
# masterListTest = ionS in masterlist
# masterListInfoTest = ionS in sorted(ionInfo.keys())
# if masterListTest or masterListInfoTest:
# ioneqTest = (self.Temperature.max() >= ionInfo[ionS]['tmin']) and (self.Temperature.min() <= ionInfo[ionS]['tmax'])
# # construct similar test for the dielectronic files
# ionSd = util.zion2name(iz, ionstage, dielectronic=1)
# masterListTestD = ionSd in masterlist
# masterListInfoTestD = ionSd in sorted(ionInfo.keys())
# if masterListTestD or masterListInfoTestD:
# ioneqTestD = (self.Temperature.max() >= ionInfo[ionSd]['tmin']) and (self.Temperature.min() <=ionInfo[ionSd]['tmax'])
# ionstageTest = ionstage > 1
# if ionstageTest and ioneqTest and doContinuum:
# # ionS is the target ion, cannot be the neutral for the continuum
# print(' calculating continuum for %s'%(ionS))
# cont = chianti.core.continuum(ionS, temperature, abund=abund)
# cont.freeFreeLoss()
# # print dir(thisIon)
# # print ' wvl = ', thisIon.FreeFree['wvl']
## if nTempDen ==1:
# freeFreeLoss += cont.FreeFreeLoss['rate']
## else:
## for iTempDen in range(nTempDen):
## freeFreeLoss[iTempDen] += cont.FreeFreeLoss['rate'][iTempDen]
# #
# cont.freeBoundLoss()
# if 'errorMessage' not in sorted(cont.FreeBoundLoss.keys()):
# # an fblvl file exists for this ions
## if nTempDen == 1:
# freeBoundLoss += cont.FreeBoundLoss['rate']
## else:
## freeBound[iTempDen] += cont.FreeBound['rate'][iTempDen]
# if masterListTest and ioneqTest:
# print(' calculating spectrum for %s '%(ionS))
# thisIon = chianti.core.ion(ionS, temperature, density, abund=abund)
## print ' dir = ', dir(thisIon)
## thisIon.emiss(wvlRange = wvlRange, allLines=allLines)
# thisIon.boundBoundLoss( allLines=allLines)
# # check that there are lines in this wavelength range
# if 'errorMessage' not in sorted(thisIon.BoundBoundLoss.keys()):
# thisIon.boundBoundLoss()
## intensity = thisIon.Intensity['intensity']
## if nTempDen == 1:
# boundBoundLoss += thisIon.BoundBoundLoss['rate']
## else:
## for iTempDen in range(nTempDen):
## lineSpectrum[iTempDen] += thisIon.Spectrum['intensity'][iTempDen]
# # get 2 photon emission for H and He sequences
# if (iz - ionstage) in [0, 1]:
# thisIon.twoPhotonLoss()
# twoPhotonLoss += thisIon.TwoPhotonLoss['rate']
# # get dielectronic lines
# if masterListTestD and ioneqTestD:
# print(' calculating spectrum for %s '%(ionSd))
# thisIon = chianti.core.ion(ionSd, temperature, density, abund=abund)
## print ' dir = ', dir(thisIon)
## have to do all lines for the dielectronic satellites
## thisIon.emiss(allLines=1)
# thisIon.intensity(allLines=allLines)
# # check that there are lines in this wavelength range - probably not redundant
# if 'errorMessage' not in sorted(thisIon.Intensity.keys()):
# thisIon.boundBoundLoss()
## if nTempDen == 1:
# boundBoundLoss += thisIon.BoundBoundLoss['rate']
## else:
## for iTempDen in range(nTempDen):
## lineSpectrum[iTempDen] += thisIon.Spectrum['intensity'][iTempDen]
self.FreeFreeLoss = freeFreeLoss
self.FreeBoundLoss = freeBoundLoss
self.BoundBoundLoss = boundBoundLoss
self.TwoPhotonLoss = twoPhotonLoss
#
total = freeFreeLoss + freeBoundLoss + boundBoundLoss + twoPhotonLoss
t2 = datetime.now()
dt=t2-t1
print(' elapsed seconds = %10.2e'%(dt.seconds))
self.RadLoss = {'rate':total, 'temperature':self.Temperature, 'density':self.EDensity, 'minAbund':minAbund, 'abundance':self.AbundanceName}
def __init__(self, temperature, eDensity, elementList=0, ionList = 0, minAbund=0, doContinuum=1, abundanceName=0, verbose=0, allLines=1, keepIons=0):
t1 = datetime.now()
masterlist = chdata.MasterList
# use the ionList but make sure the ions are in the database
if ionList:
alist=[]
for one in ionList:
if masterlist.count(one):
alist.append(one)
else:
if verbose:
pstring = ' %s not in CHIANTI database'%(one)
print(pstring)
masterlist = alist
self.Defaults=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])
if not abundanceName:
self.AbundanceName = self.Defaults['abundfile']
else:
if abundanceName in sorted(chdata.Abundance.keys()):
self.AbundanceName = abundanceName
else:
abundChoices = sorted(chdata.Abundance.keys())
# for one in wvl[topLines]:
# wvlChoices.append('%12.3f'%(one))
abundChoice = chgui.gui.selectorDialog(abundChoices,label='Select Abundance name')
abundChoice_idx = abundChoice.selectedIndex
self.AbundanceName = abundChoices[abundChoice_idx[0]]
# abund = self.AbundanceName
print(' Abundance chosen: %s '%(self.AbundanceName))
#
abundAll = chdata.Abundance[self.AbundanceName]['abundance']
# needed by ionGate
self.AbundAll = abundAll
#
nonzed = abundAll > 0.
minAbundAll = abundAll[nonzed].min()
# if minAbund is even set
if minAbund:
if minAbund < minAbundAll:
minAbund = minAbundAll
# ionInfo = util.masterListInfo()
#
freeFreeLoss = np.zeros((nTempDen), 'float64').squeeze()
freeBoundLoss = np.zeros((nTempDen), 'float64').squeeze()
twoPhotonLoss = np.zeros((nTempDen), 'float64').squeeze()
boundBoundLoss = np.zeros((nTempDen), 'float64').squeeze()
twoPhotonLoss = np.zeros((nTempDen), 'float64').squeeze()
#
self.IonsCalculated = []
if keepIons:
self.IonInstances = {}
self.Finished = []
#
self.WvlRange = [0., 1.e+30]
#
self.ionGate(elementList = elementList, ionList = ionList, minAbund=minAbund, doContinuum=doContinuum, doWvlTest=0, verbose=verbose)
#
#
for akey in sorted(self.Todo.keys()):
zStuff = util.convertName(akey)
Z = zStuff['Z']
ionstage = zStuff['Ion']
dielectronic = zStuff['Dielectronic']
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 ionstage != 1:
if verbose:
print(' calculating ff continuum for : %s'%(akey))
if 'ff' in self.Todo[akey]:
# need to skip the neutral
cont = ChiantiPy.core.continuum(akey, temperature, abundanceName=self.AbundanceName)
cont.freeFreeLoss()
freeFreeLoss += cont.FreeFreeLoss['rate']
if 'fb' in self.Todo[akey]:
if verbose:
print(' calculating fb continuum for : %s'%(akey))
# try:
# does cont already exist - i.e did we create it for ff
if hasattr(cont, 'FreeFreeLoss'):
cont.freeBoundLoss()
else:
cont = ChiantiPy.core.continuum(akey, temperature, abundanceName=self.AbundanceName)
cont.freeBoundLoss()
if 'errorMessage' not in list(cont.FreeBoundLoss.keys()):
# an fblvl file exists for this ions
freeBoundLoss += cont.FreeBoundLoss['rate']
if 'line' in self.Todo[akey]:
if verbose:
print(' calculating spectrum for : %s'%(akey))
thisIon = ChiantiPy.core.ion(akey, temperature, eDensity, abundance=self.AbundanceName)
thisIon.intensity(allLines=allLines)
self.IonsCalculated.append(akey)
if 'errorMessage' not in list(thisIon.Intensity.keys()):
self.Finished.append(akey)
thisIon.boundBoundLoss()
boundBoundLoss += thisIon.BoundBoundLoss['rate']
else:
if verbose:
print(thisIon.Intensity['errorMessage'])
# get 2 photon emission for H and He sequences
if (Z - ionstage) in [0, 1] and not dielectronic:
thisIon.twoPhotonLoss()
twoPhotonLoss += thisIon.TwoPhotonLoss['rate']
self.FreeFreeLoss = freeFreeLoss
self.FreeBoundLoss = freeBoundLoss
self.BoundBoundLoss = boundBoundLoss
self.TwoPhotonLoss = twoPhotonLoss
#
total = freeFreeLoss + freeBoundLoss + boundBoundLoss + twoPhotonLoss
t2 = datetime.now()
dt=t2-t1
print(' elapsed seconds = %10.2e'%(dt.seconds))
xlabel = 'Temperature (K)'
ylabel = r'erg s$^{-1}$ cm$^{3}$'
self.RadLoss = {'rate':total, 'temperature':self.Temperature, 'density':self.EDensity, 'minAbund':minAbund, 'abundance':self.AbundanceName, ylabel:ylabel, xlabel:xlabel}
def ionGate(self,
elementList=None,
ionList=None,
minAbund=None,
doLines=1,
doContinuum=1,
doWvlTest=1,
verbose=0):
'''
creates a list of ions for free-free, free-bound, and line intensity calculations
if doing the radiative losses, accept all wavelength -> doWvlTest=0
the list is a dictionary self.Todo
'''
#
masterlist = chdata.MasterList
abundAll = self.AbundAll
#
nonzed = abundAll > 0.
minAbundAll = abundAll[nonzed].min()
if minAbund:
if minAbund < minAbundAll:
minAbund = minAbundAll
ionInfo = chio.masterListInfo()
#
if hasattr(self, 'Wavelength'):
wvlRange = [self.Wavelength.min(), self.Wavelength.max()]
elif hasattr(self, 'WvlRange'):
wvlRange = self.WvlRange
else:
print(' need a wavelength range in ionGate ')
#
temperature = self.Temperature
#
# use the ionList but make sure the ions are in the database
self.Todo = {}
#
#
if elementList:
for i, element in enumerate(elementList):
elementList[i] = element.lower()
if verbose:
print('el = %s' % (element))
z = const.El.index(element.lower()) + 1
for one in masterlist:
nameDict = util.convertName(one)
if nameDict['Element'].lower() in elementList:
if verbose:
print(' ion = %s' % (one))
if doLines:
self.Todo[one] = 'line'
for stage in range(2, z + 2):
name = util.zion2name(z, stage)
if doContinuum and not nameDict['Dielectronic']:
if name not in self.Todo.keys():
self.Todo[name] = 'ff'
else:
self.Todo[name] += '_ff'
self.Todo[name] += '_fb'
if ionList:
for one in ionList:
nameDict = util.convertName(one)
if masterlist.count(one):
if doLines:
self.Todo[one] = 'line'
else:
if verbose:
pstring = ' %s not in CHIANTI database' % (one)
print(pstring)
if doContinuum and not nameDict['Dielectronic']:
if one not in self.Todo.keys():
self.Todo[one] = 'ff'
else:
self.Todo[one] += '_ff'
self.Todo[one] += '_fb'
#
#
#
if minAbund:
for iz in range(1, 31):
abundance = chdata.Abundance[self.AbundanceName]['abundance'][
iz - 1]
if abundance >= minAbund:
if verbose:
print(' %5i %5s abundance = %10.2e ' %
(iz, const.El[iz - 1], abundance))
#
for ionstage in range(1, iz + 1):
ionS = util.zion2name(iz, ionstage)
masterListTest = ionS in masterlist
masterListInfoTest = ionS in sorted(ionInfo.keys())
if masterListTest or masterListInfoTest:
if masterListTest or masterListInfoTest:
if doWvlTest:
wvlTestMin = wvlRange[0] <= ionInfo[ionS][
'wmax']
wvlTestMax = wvlRange[1] >= ionInfo[ionS][
'wmin']
else:
wvlTestMin = 1
wvlTestMax = 1
ioneqTest = (
temperature.max() >= ionInfo[ionS]['tmin']
) and (temperature.min() <= ionInfo[ionS]['tmax'])
# construct similar test for the dielectronic files
ionSd = util.zion2name(iz, ionstage, dielectronic=1)
masterListTestD = ionSd in masterlist
masterListInfoTestD = ionSd in sorted(ionInfo.keys())
if masterListTestD or masterListInfoTestD:
if doWvlTest:
wvlTestMinD = wvlRange[0] <= ionInfo[ionSd][
'wmax']
wvlTestMaxD = wvlRange[1] >= ionInfo[ionSd][
'wmin']
else:
wvlTestMinD = 1
wvlTestMaxD = 1
ioneqTestD = (
temperature.max() >= ionInfo[ionSd]['tmin']
) and (temperature.min() <= ionInfo[ionSd]['tmax'])
#
if masterListTest and wvlTestMin and wvlTestMax and ioneqTest and doLines:
if ionS in sorted(self.Todo.keys()):
self.Todo[ionS] += '_line'
else:
self.Todo[ionS] = 'line'
# get dielectronic lines
if verbose:
print(' for ion %s do : %s' %
(ionS, self.Todo[ionS]))
if masterListTestD and wvlTestMinD and wvlTestMaxD and ioneqTestD and doLines:
if ionSd in sorted(self.Todo.keys()):
self.Todo[ionSd] += '_line'
else:
self.Todo[ionSd] = 'line'
if verbose:
print(' for ion %s do : %s' %
(ionSd, self.Todo[ionSd]))
#
#
for ionstage in range(2, iz + 2):
ionS = util.zion2name(iz, ionstage)
if ionS in ionInfo.keys():
ioneqTest = (
temperature.max() >= ionInfo[ionS]['tmin']
) and (temperature.min() <= ionInfo[ionS]['tmax'])
else:
ioneqTest = 1
# construct similar test for the dielectronic files
if ioneqTest and doContinuum:
# ionS is the target ion, cannot be the neutral for the continuum
# if verbose:
# print(' setting up continuum calculation for %s '%(ionS))
if ionS in sorted(self.Todo.keys()):
self.Todo[ionS] += '_ff_fb'
else:
self.Todo[ionS] = 'ff_fb'
if verbose:
print(' for ion %s do : %s' %
(ionS, self.Todo[ionS]))
if len(self.Todo.keys()) == 0:
print(' no elements have been selected')
print(
' it is necessary to provide an elementList, an ionList, or set minAbund > 0.'
)
return
def __init__(self, temperature, eDensity, wavelength, filter=(chfilters.gaussianR, 1000.), label=0, elementList = 0, ionList = 0, minAbund=0, doContinuum=1, em=0, keepIons=0, abundance=None, verbose=0, allLines=1):
#
t1 = datetime.now()
# creates Intensity dict from first ion calculated
setupIntensity = 0
#
self.Defaults=defaults
self.Temperature = np.asarray(temperature, 'float64')
nTemp = self.Temperature.size
self.EDensity = np.asarray(eDensity, 'float64')
nDen = self.EDensity.size
self.NTempDen = max([nTemp, nDen])
nTempDen = self.NTempDen
self.Wavelength = wavelength
#
if type(em) == int and em == 0:
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$^{-1} \AA^{-1}$ $'
elif type(em) == list or type(em) == tuple:
em = np.asarray(em, 'float64')
ylabel = r'erg cm$^{-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'] +')'
#
#
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]]
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']
# needed by ionGate
self.AbundAll = abundAll
#
self.MinAbund = minAbund
wavelength = np.asarray(wavelength)
nWvl = wavelength.size
self.Wavelength = wavelength
wvlRange = [wavelength.min(), wavelength.max()]
#
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()
#
self.IonsCalculated = []
if keepIons:
self.IonInstances = {}
self.Finished = []
#
self.ionGate(elementList = elementList, ionList = ionList, minAbund=minAbund, doContinuum=doContinuum, verbose = verbose)
#
for akey in sorted(self.Todo.keys()):
zStuff = util.convertName(akey)
Z = zStuff['Z']
ionstage = zStuff['Ion']
dielectronic = zStuff['Dielectronic']
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]:
if verbose:
print(' calculating ff continuum for : %s'%(akey))
FF = ChiantiPy.core.continuum(akey, temperature, abundance=abundance, em=em)
FF.freeFree(wavelength)
if 'errorMessage' not in list(FF.FreeFree.keys()):
freeFree += FF.FreeFree['rate']
if 'fb' in self.Todo[akey]:
if verbose:
print(' calculating fb continuum for : %s'%(akey))
FB = ChiantiPy.core.continuum(akey, temperature, abundance=abundance, em=em)
FB.freeBound(wavelength)
if 'errorMessage' not in list(FB.FreeBound.keys()):
# an fblvl file exists for this ions
freeBound += FB.FreeBound['rate']
if 'line' in self.Todo[akey]:
if verbose:
print(' calculating spectrum for : %s'%(akey))
thisIon = ChiantiPy.core.ion(akey, temperature, eDensity, abundance=abundance)
thisIon.intensity(wvlRange=wvlRange, allLines=allLines, em=em)
self.IonsCalculated.append(akey)
if 'errorMessage' not in list(thisIon.Intensity.keys()):
self.Finished.append(akey)
thisIon.spectrum(wavelength, filter=filter, allLines=allLines, em=em)
if keepIons:
self.IonInstances[akey] = copy.deepcopy(thisIon)
if setupIntensity:
for bkey in self.Intensity:
self.Intensity[bkey] = np.hstack((copy.copy(self.Intensity[bkey]), thisIon.Intensity[bkey]))
else:
setupIntensity = 1
self.Intensity = thisIon.Intensity
lineSpectrum += thisIon.Spectrum['intensity']
else:
if verbose:
print(thisIon.Intensity['errorMessage'])
# get 2 photon emission for H and He sequences
if (Z - ionstage) in [0, 1] and not dielectronic:
thisIon.twoPhoton(wavelength)
twoPhoton += thisIon.TwoPhoton['rate']
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
self.Total = total
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, 'em':em, 'ions':self.IonsCalculated,
'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, 'em':em, 'ions':self.IonsCalculated,
'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,
'Abundance':self.AbundanceName, 'xlabel':xlabel, 'ylabel':ylabel, 'minAbund':minAbund}
def __init__(self, temperature, eDensity, wvlRange, elementList=0, ionList=0, minAbund=0, keepIons=0, em=0, abundanceName=0, verbose=0, allLines=1):
#
t1 = datetime.now()
# creates Intensity dict from first ion calculated
setupIntensity = 0
#
self.Defaults=defaults
temperature = np.asarray(temperature, 'float64')
self.Temperature = temperature
eDensity = np.asarray(eDensity, 'float64')
self.EDensity = eDensity
#
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 type(em) == int and em == 0:
em = np.ones(self.NTempDen, 'float64')
elif type(em) == float and em > 0.:
em = np.ones(self.NTempDen, 'float64')*em
elif type(em) == list or type(em) == tuple:
em = np.asarray(em, 'float64')
self.Em = em
#
#
if abundanceName:
if abundanceName in list(chdata.Abundance.keys()):
self.AbundanceName = abundanceName
else:
abundChoices = list(chdata.Abundance.keys())
# for one in wvl[topLines]:
# wvlChoices.append('%12.3f'%(one))
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)))
else:
self.AbundanceName = self.Defaults['abundfile']
#
abundAll = chdata.Abundance[self.AbundanceName]['abundance']
# needed by ionGate
self.AbundAll = abundAll
#
# nonzed = abundAll > 0.
# minAbundAll = abundAll[nonzed].min()
# # if minAbund is even set
# if minAbund:
# if minAbund < minAbundAll:
# minAbund = minAbundAll
# self.minAbund = minAbund
# ionInfo = chio.masterListInfo()
# #
self.IonsCalculated = []
if keepIons:
self.IonInstances = {}
self.Finished = []
#
# also needed by ionGate
self.WvlRange = np.asarray(wvlRange, 'float64')
#
self.ionGate(elementList = elementList, ionList = ionList, minAbund=minAbund, doContinuum=0, verbose = verbose)
#
for ionS in sorted(self.Todo.keys()):
nameStuff = util.convertName(ionS)
Z = nameStuff['Z']
if verbose:
print(' calculating %s'%(ionS))
thisIon = ChiantiPy.core.ion(ionS, temperature, eDensity, abundance=abundAll[Z-1])
thisIon.intensity(wvlRange=wvlRange, allLines = allLines, em=em)
self.IonsCalculated.append(ionS)
#
if 'errorMessage' not in list(thisIon.Intensity.keys()):
self.Finished.append(ionS)
# thisIon.spectrum(wavelength, filter=filter)
if keepIons:
self.IonInstances[ionS] = copy.deepcopy(thisIon)
if setupIntensity:
for akey in self.Intensity:
self.Intensity[akey] = np.hstack((copy.copy(self.Intensity[akey]), thisIon.Intensity[akey]))
else:
setupIntensity = 1
# print(' creating Intensity dict from ion %s'%(ionS))
self.Intensity = thisIon.Intensity
else:
if verbose:
print(thisIon.Intensity['errorMessage'])
#
#
t2 = datetime.now()
dt=t2-t1
print(' elapsed seconds = %12.3f'%(dt.seconds))
return
def __init__(self, temperature, eDensity, wavelength, filter=(chfilters.gaussianR, 1000.), label=0, elementList = 0, ionList = 0, minAbund=0, doContinuum=1, em=0, keepIons=0, abundanceName=0, verbose=0, allLines=1):
#
t1 = datetime.now()
# creates Intensity dict from first ion calculated
setupIntensity = 0
#
masterlist = chdata.MasterList
# use the ionList but make sure the ions are in the database
#if elementList:
#for i, one in enumerate(elementList):
#elementList[i] = one.lower()
#alist = []
#for one in masterlist:
#stuff = util.convertName(one)
#if stuff['Element'] in elementList:
#alist.append(one)
#masterlist = alist
#elif ionList:
#alist=[]
#for one in ionList:
#if masterlist.count(one):
#alist.append(one)
#else:
#if verbose:
#pstring = ' %s not in CHIANTI database'%(one)
#print(pstring)
#masterlist = alist
self.Defaults=defaults
self.Temperature = np.asarray(temperature, 'float64')
nTemp = self.Temperature.size
self.EDensity = np.asarray(eDensity, 'float64')
nDen = self.EDensity.size
self.NTempDen = max([nTemp, nDen])
nTempDen = self.NTempDen
self.Wavelength = wavelength
#
if type(em) == int and em == 0:
em = np.ones(self.NTempDen, 'float64')
elif type(em) == float and em > 0.:
em = np.ones(self.NTempDen, 'float64')*em
elif type(em) == list or type(em) == tuple:
em = np.asarray(em, 'float64')
self.Em = 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.AbundanceName = defaults['abundfile']
#self.AbundanceAll = chdata.AbundanceAll
#
if abundanceName:
if abundanceName in list(chdata.Abundance.keys()):
self.AbundanceName = abundanceName
else:
abundChoices = list(chdata.Abundance.keys())
# for one in wvl[topLines]:
# wvlChoices.append('%12.3f'%(one))
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)))
else:
self.AbundanceName = self.Defaults['abundfile']
#
abundAll = chdata.Abundance[self.AbundanceName]['abundance']
# needed by ionGate
self.AbundAll = abundAll
#
nonzed = abundAll > 0.
minAbundAll = abundAll[nonzed].min()
# if minAbund is even set
if minAbund:
if minAbund < minAbundAll:
minAbund = minAbundAll
else:
minAbund = minAbundAll
self.MinAbund = minAbund
# ionInfo = chio.masterListInfo()
wavelength = np.asarray(wavelength)
nWvl = wavelength.size
self.Wavelength = wavelength
wvlRange = [wavelength.min(), wavelength.max()]
#
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()
#
self.IonsCalculated = []
if keepIons:
self.IonInstances = {}
self.Finished = []
#
self.ionGate(elementList = elementList, ionList = ionList, minAbund=minAbund, doContinuum=doContinuum, verbose = verbose)
#
for akey in sorted(self.Todo.keys()):
zStuff = util.convertName(akey)
Z = zStuff['Z']
ionstage = zStuff['Ion']
dielectronic = zStuff['Dielectronic']
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]:
if verbose:
print(' calculating ff continuum for : %s'%(akey))
FF = chianti.core.continuum(akey, temperature, abundanceName=self.AbundanceName, em=em)
FF.freeFree(wavelength)
# if nTempDen == 1:
# freeFree += cont.FreeFree['rate']*em[0]
# else:
# for iTempDen in range(nTempDen):
# freeFree[iTempDen] += cont.FreeFree['rate'][iTempDen]*em[iTempDen]
freeFree += FF.FreeFree['rate']
if 'fb' in self.Todo[akey]:
if verbose:
print(' calculating fb continuum for : %s'%(akey))
try:
FB = chianti.core.continuum(akey, temperature, abundanceName=self.AbundanceName, em=em)
FB.freeBound(wavelength)
if 'errorMessage' not in list(cont.FreeBound.keys()):
# an fblvl file exists for this ions
freeBound += FB.FreeBound['rate']
except:
cont = chianti.core.continuum(akey, temperature, abundanceName=self.AbundanceName)
cont.freeBound(wavelength)
# if 'errorMessage' not in list(cont.FreeBound.keys()):
# # an fblvl file exists for this ions
# if nTempDen == 1:
# freeBound += cont.FreeBound['rate']*em[0]
# else:
# for iTempDen in range(nTempDen):
# freeBound[iTempDen] += cont.FreeBound['rate'][iTempDen]*em[iTempDen]
# freeBound += cont.FreeBound['rate']
if 'line' in self.Todo[akey]:
if verbose:
print(' calculating spectrum for : %s'%(akey))
thisIon = chianti.core.ion(akey, temperature, eDensity, abundanceName=self.AbundanceName)
thisIon.intensity(wvlRange=wvlRange, allLines=allLines, em=em)
self.IonsCalculated.append(akey)
if 'errorMessage' not in list(thisIon.Intensity.keys()):
self.Finished.append(akey)
thisIon.spectrum(wavelength, filter=filter, allLines=allLines, em=em)
if keepIons:
self.IonInstances[akey] = copy.deepcopy(thisIon)
if setupIntensity:
for bkey in self.Intensity:
self.Intensity[bkey] = np.hstack((copy.copy(self.Intensity[bkey]), thisIon.Intensity[bkey]))
else:
setupIntensity = 1
self.Intensity = thisIon.Intensity
lineSpectrum += thisIon.Spectrum['intensity']
# if nTempDen == 1:
# lineSpectrum += thisIon.Spectrum['intensity']
# else:
# for iTempDen in range(nTempDen):
# lineSpectrum[iTempDen] += thisIon.Spectrum['intensity'][iTempDen]
else:
if verbose:
print(thisIon.Intensity['errorMessage'])
# get 2 photon emission for H and He sequences
if (Z - ionstage) in [0, 1] and not dielectronic:
thisIon.twoPhoton(wavelength)
twoPhoton += thisIon.TwoPhoton['rate']
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
self.Total = total
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, 'em':em, 'ions':self.IonsCalculated,
'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, 'ions':self.IonsCalculated,
'Abundance':self.AbundanceName, 'xlabel':xlabel, 'ylabel':ylabel}}
else:
self.Spectrum ={'wavelength':wavelength, 'intensity':total.squeeze(), 'filter':filter[0].__name__, 'width':filter[1], 'integrated':integrated, 'ions':self.IonsCalculated,
'Abundance':self.AbundanceName, 'xlabel':xlabel, 'ylabel':ylabel}
def ionGate(self, elementList = None, ionList = None, minAbund=None, doLines=1, doContinuum=1, doWvlTest=1, verbose=0):
'''
creates a list of ions for free-free, free-bound, and line intensity calculations
if doing the radiative losses, accept all wavelength -> doWvlTest=0
the list is a dictionary self.Todo
'''
#
masterlist = chdata.MasterList
abundAll = self.AbundAll
#
nonzed = abundAll > 0.
minAbundAll = abundAll[nonzed].min()
if minAbund:
if minAbund < minAbundAll:
minAbund = minAbundAll
ionInfo = chio.masterListInfo()
#
if hasattr(self, 'Wavelength'):
wvlRange = [self.Wavelength.min(), self.Wavelength.max()]
elif hasattr(self, 'WvlRange'):
wvlRange = self.WvlRange
else:
print(' need a wavelength range in ionGate ')
#
temperature = self.Temperature
#
# use the ionList but make sure the ions are in the database
self.Todo = {}
#
#
if elementList:
for i, element in enumerate(elementList):
elementList[i] = element.lower()
if verbose:
print('el = %s'%(element))
z = const.El.index(element.lower()) + 1
for one in masterlist:
nameDict = util.convertName(one)
if nameDict['Element'].lower() in elementList:
if verbose:
print(' ion = %s'%(one))
if doLines:
self.Todo[one] = 'line'
for stage in range(2, z+2):
name = util.zion2name(z, stage)
if doContinuum and not nameDict['Dielectronic']:
if name not in self.Todo.keys():
self.Todo[name] = 'ff'
else:
self.Todo[name] += '_ff'
self.Todo[name] += '_fb'
if ionList:
for one in ionList:
nameDict = util.convertName(one)
if masterlist.count(one):
if doLines:
self.Todo[one] = 'line'
else:
if verbose:
pstring = ' %s not in CHIANTI database'%(one)
print(pstring)
if doContinuum and not nameDict['Dielectronic']:
if one not in self.Todo.keys():
self.Todo[one] = 'ff'
else:
self.Todo[one] += '_ff'
self.Todo[one] += '_fb'
#
#
#
if minAbund:
for iz in range(1, 31):
abundance = chdata.Abundance[self.AbundanceName]['abundance'][iz-1]
if abundance >= minAbund:
if verbose:
print(' %5i %5s abundance = %10.2e '%(iz, const.El[iz-1], abundance))
#
for ionstage in range(1, iz+1):
ionS = util.zion2name(iz, ionstage)
masterListTest = ionS in masterlist
masterListInfoTest = ionS in sorted(ionInfo.keys())
if masterListTest or masterListInfoTest:
if masterListTest or masterListInfoTest:
if doWvlTest:
wvlTestMin = wvlRange[0] <= ionInfo[ionS]['wmax']
wvlTestMax = wvlRange[1] >= ionInfo[ionS]['wmin']
else:
wvlTestMin = 1
wvlTestMax = 1
ioneqTest = (temperature.max() >= ionInfo[ionS]['tmin']) and (temperature.min() <= ionInfo[ionS]['tmax'])
# construct similar test for the dielectronic files
ionSd = util.zion2name(iz, ionstage, dielectronic=1)
masterListTestD = ionSd in masterlist
masterListInfoTestD = ionSd in sorted(ionInfo.keys())
if masterListTestD or masterListInfoTestD:
if doWvlTest:
wvlTestMinD = wvlRange[0] <= ionInfo[ionSd]['wmax']
wvlTestMaxD = wvlRange[1] >= ionInfo[ionSd]['wmin']
else:
wvlTestMinD = 1
wvlTestMaxD = 1
ioneqTestD = (temperature.max() >= ionInfo[ionSd]['tmin']) and (temperature.min() <=ionInfo[ionSd]['tmax'])
#
if masterListTest and wvlTestMin and wvlTestMax and ioneqTest and doLines:
if ionS in sorted(self.Todo.keys()):
self.Todo[ionS] += '_line'
else:
self.Todo[ionS] = 'line'
# get dielectronic lines
if verbose:
print(' for ion %s do : %s'%(ionS, self.Todo[ionS]))
if masterListTestD and wvlTestMinD and wvlTestMaxD and ioneqTestD and doLines:
if ionSd in sorted(self.Todo.keys()):
self.Todo[ionSd] += '_line'
else:
self.Todo[ionSd] = 'line'
if verbose:
print(' for ion %s do : %s'%(ionSd, self.Todo[ionSd]))
#
#
for ionstage in range(2, iz+2):
ionS = util.zion2name(iz, ionstage)
if ionS in ionInfo.keys():
ioneqTest = (temperature.max() >= ionInfo[ionS]['tmin']) and (temperature.min() <= ionInfo[ionS]['tmax'])
else:
ioneqTest = 1
# construct similar test for the dielectronic files
if ioneqTest and doContinuum:
# ionS is the target ion, cannot be the neutral for the continuum
# if verbose:
# print(' setting up continuum calculation for %s '%(ionS))
if ionS in sorted(self.Todo.keys()):
self.Todo[ionS] += '_ff_fb'
else:
self.Todo[ionS] = 'ff_fb'
if verbose:
print(' for ion %s do : %s'%(ionS, self.Todo[ionS]))
if len(self.Todo.keys()) == 0:
print(' no elements have been selected')
print(' it is necessary to provide an elementList, an ionList, or set minAbund > 0.')
return
def __init__(self,
temperature,
eDensity,
wvlRange,
elementList=None,
ionList=None,
minAbund=None,
keepIons=0,
em=None,
abundance=None,
verbose=0,
allLines=1):
#
t1 = datetime.now()
# creates Intensity dict from first ion calculated
setupIntensity = 0
#
self.argCheck(temperature=temperature,
eDensity=eDensity,
pDensity=None,
em=em,
verbose=verbose)
self.Defaults = chdata.Defaults
#
#
if abundance is not None:
if abundance in list(chdata.Abundance.keys()):
self.AbundanceName = abundance
else:
abundChoices = list(chdata.Abundance.keys())
abundChoice = chGui.gui.selectorDialog(
abundChoices,
label='Select Abundance name',
multiChoice=False)
abundChoice_idx = abundChoice.selectedIndex
self.AbundanceName = abundChoices[abundChoice_idx[0]]
print((' Abundance chosen: %s ' % (self.AbundanceName)))
else:
self.AbundanceName = self.Defaults['abundfile']
#
abundAll = chdata.Abundance[self.AbundanceName]['abundance']
# needed by ionGate
self.AbundAll = abundAll
#
# nonzed = abundAll > 0.
# minAbundAll = abundAll[nonzed].min()
# # if minAbund is even set
# if minAbund:
# if minAbund < minAbundAll:
# minAbund = minAbundAll
# self.minAbund = minAbund
# ionInfo = chio.masterListInfo()
# #
self.IonsCalculated = []
if keepIons:
self.IonInstances = {}
self.Finished = []
#
# also needed by ionGate
self.WvlRange = np.asarray(wvlRange, 'float64')
#
self.ionGate(elementList=elementList,
ionList=ionList,
minAbund=minAbund,
doLines=1,
doContinuum=0,
verbose=verbose)
#
for ionS in sorted(self.Todo.keys()):
nameStuff = util.convertName(ionS)
Z = nameStuff['Z']
if verbose:
print(' calculating %s' % (ionS))
thisIon = ChiantiPy.core.ion(ionS,
temperature,
eDensity,
abundance=abundAll[Z - 1],
em=em)
thisIon.intensity(allLines=allLines)
self.IonsCalculated.append(ionS)
#
if 'errorMessage' not in list(thisIon.Intensity.keys()):
self.Finished.append(ionS)
# thisIon.spectrum(wavelength, filter=filter)
if keepIons:
self.IonInstances[ionS] = copy.deepcopy(thisIon)
if setupIntensity:
for akey in self.Intensity:
self.Intensity[akey] = np.hstack(
(copy.copy(self.Intensity[akey]),
thisIon.Intensity[akey]))
else:
setupIntensity = 1
# print(' creating Intensity dict from ion %s'%(ionS))
self.Intensity = thisIon.Intensity
else:
if verbose:
print(thisIon.Intensity['errorMessage'])
#
#
t2 = datetime.now()
dt = t2 - t1
print(' elapsed seconds = %12.3f' % (dt.seconds))
return
def __init__(self,
temperature,
eDensity,
wavelength,
filter=(chfilters.gaussianR, 1000.),
label=None,
elementList=None,
ionList=None,
minAbund=None,
doLines=1,
doContinuum=1,
em=None,
keepIons=0,
abundance=None,
verbose=0,
allLines=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.Wavelength = wavelength
#
self.argCheck(temperature=temperature,
eDensity=eDensity,
pDensity=None,
em=em,
verbose=verbose)
nTempDens = self.NTempDens
if self.Em.max() == 1.:
ylabel = r'erg cm$^{-2}$ s$^{-1}$ sr$^{-1} \AA^{-1}$ ($\int\,$ N$_e\,$N$_H\,$d${\it l}$)$^{-1}$'
else:
ylabel = r'erg cm$^{-2}$ s$^{-1}$ sr$^{-1} \AA^{-1}$ $'
#
# print(' em = %12.2e '%(em[0]))
#
if self.Defaults['wavelength'] == 'angstrom':
xlabel = 'Wavelength (' + self.Defaults['wavelength'].capitalize(
) + ')'
else:
xlabel = 'Wavelength (' + self.Defaults['wavelength'] + ')'
#
#
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',
multiChoice=False)
abundChoice_idx = abundChoice.selectedIndex
self.AbundanceName = abundChoices[abundChoice_idx[0]]
print((' Abundance 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']
# needed by ionGate
self.AbundAll = abundAll
#
self.MinAbund = minAbund
wavelength = np.asarray(wavelength)
nWvl = wavelength.size
self.Wavelength = wavelength
#
freeFree = np.zeros((nTempDens, nWvl), np.float64).squeeze()
freeBound = np.zeros((nTempDens, nWvl), np.float64).squeeze()
twoPhoton = np.zeros((nTempDens, nWvl), np.float64).squeeze()
lineSpectrum = np.zeros((nTempDens, nWvl), np.float64).squeeze()
#
self.IonsCalculated = []
if keepIons:
self.IonInstances = {}
self.FfInstances = {}
self.FbInstances = {}
self.Finished = []
#
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']
ionstage = zStuff['Ion']
dielectronic = zStuff['Dielectronic']
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]:
if verbose:
print(' calculating ff continuum for : %s' % (akey))
FF = ChiantiPy.core.continuum(akey,
temperature,
abundance=abundance,
em=em)
FF.freeFree(wavelength)
freeFree += FF.FreeFree['intensity'].squeeze()
if keepIons:
self.FfInstances[akey] = copy.deepcopy(FF)
if 'fb' in self.Todo[akey]:
if verbose:
print(' calculating fb continuum for : %s' % (akey))
FB = ChiantiPy.core.continuum(akey,
temperature,
abundance=abundance,
em=em)
FB.freeBound(wavelength)
if 'errorMessage' not in FB.FreeBound.keys():
freeBound += FB.FreeBound['intensity'].squeeze()
if keepIons:
self.FbInstances[akey] = copy.deepcopy(FB)
else:
if verbose:
print(FB.FreeBound['errorMessage'])
if 'line' in self.Todo[akey]:
if verbose:
print(' calculating spectrum for : %s' % (akey))
thisIon = ChiantiPy.core.ion(akey,
temperature,
eDensity,
pDensity='default',
abundance=abundance,
em=em)
thisIon.intensity(allLines=allLines)
self.IonsCalculated.append(akey)
if 'errorMessage' not in list(thisIon.Intensity.keys()):
self.Finished.append(akey)
thisIon.spectrum(wavelength,
filter=filter,
allLines=allLines)
if keepIons:
self.IonInstances[akey] = copy.deepcopy(thisIon)
if setupIntensity:
for bkey in self.Intensity:
self.Intensity[bkey] = np.hstack(
(copy.copy(self.Intensity[bkey]),
thisIon.Intensity[bkey]))
else:
setupIntensity = 1
self.Intensity = thisIon.Intensity
lineSpectrum += thisIon.Spectrum['intensity'].squeeze()
else:
if verbose:
print(thisIon.Intensity['errorMessage'])
# get 2 photon emission for H and He sequences
if (Z - ionstage) in [0, 1] and not dielectronic:
thisIon.twoPhoton(wavelength)
twoPhoton += thisIon.TwoPhoton['intensity'].squeeze()
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
self.Total = total
t2 = datetime.now()
dt = t2 - t1
print(' elapsed seconds = %12.3f' % (dt.seconds))
if nTempDens == 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,
'em': em,
'ions': self.IonsCalculated,
'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,
'em': em,
'ions': self.IonsCalculated,
'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,
'Abundance': self.AbundanceName,
'xlabel': xlabel,
'ylabel': ylabel,
'minAbund': minAbund
}
def __init__(self, temperature, eDensity, wavelength, filter=(chfilters.gaussianR, 1000.), label=0, elementList = 0, ionList = 0, minAbund=0, keepIons=0, abundanceName=0, doContinuum=1, allLines = 1, em =0, proc=3, verbose = 0, timeout=0.1):
#
t1 = datetime.now()
# creates Intensity dict from first ion calculated
setupIntensity = 0
#
#masterlist = chdata.MasterList
# use the ionList but make sure the ions are in the database
#if elementList:
#for i, one in enumerate(elementList):
#elementList[i] = one.lower()
#alist = []
#for one in masterlist:
#stuff = util.convertName(one)
#if stuff['Element'] in elementList:
#alist.append(one)
#masterlist = alist
#elif ionList:
#alist=[]
#for one in ionList:
#if masterlist.count(one):
#alist.append(one)
#else:
#if verbose:
#pstring = ' %s not in CHIANTI database'%(one)
#print(pstring)
#masterlist = alist
self.Defaults = defaults
#
masterlist = chdata.MasterList
self.Defaults = 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 type(em) == int and em == 0:
em = np.ones(self.NTempDen, 'float64')
elif type(em) == float and em > 0.:
em = np.ones(self.NTempDen, 'float64')*em
elif type(em) == list or type(em) == tuple:
em = np.asarray(em, 'float64')
self.Em = 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())
# for one in wvl[topLines]:
# wvlChoices.append('%12.3f'%(one))
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
#
# nonzed = abundAll > 0.
# minAbundAll = abundAll[nonzed].min()
# # if minAbund is even set
# if minAbund:
# if minAbund < minAbundAll:
# minAbund = minAbundAll
#ionInfo = chio.masterListInfo()
wavelength = np.asarray(wavelength)
nWvl = wavelength.size
self.Wavelength = wavelength
# wvlRange = [wavelength.min(), wavelength.max()]
#
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:
self.IonInstances = {}
self.Finished = []
#
# self.Todo = []
self.ionGate(elementList = elementList, ionList = ionList, minAbund=minAbund, 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]:
# if verbose:
# print(' doing ff')
ffWorkerQ.put((akey, temperature, wavelength, abundance, em))
# allInpt.append([akey, 'ff', temperature, wavelength, abundance])
if 'fb' in self.Todo[akey]:
# if verbose:
# print(' doing fb')
fbWorkerQ.put((akey, temperature, wavelength, abundance, em))
# allInpt.append([akey, 'fb', temperature, wavelength, abundance])
if 'line' in self.Todo[akey]:
# if verbose:
# print(' doing line')
ionWorkerQ.put((akey, temperature, eDensity, wavelength, filter, allLines, abundance, em, doContinuum))
# allInpt.append([akey, 'line', 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 i in range(proc):
# ffProcesses.append('STOP')
#
for iff in range(ffWorkerQSize):
thisFreeFree = ffDoneQ.get()
# freeFree += thisFreeFree['rate']
# if nTempDen ==1:
# freeFree += thisFreeFree['rate']*em[0]
# else:
# for iTempDen in range(nTempDen):
# freeFree[iTempDen] += thisFreeFree['rate'][iTempDen]*em[iTempDen]
freeFree += thisFreeFree['rate']
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 i in range(proc):
# fbProcesses.append('STOP')
#
for ifb in range(fbWorkerQSize):
thisFreeBound = fbDoneQ.get()
if 'rate' in sorted(thisFreeBound.keys()):
# freeBound += thisFreeBound['rate']
# if nTempDen ==1:
# freeBound += thisFreeBound['rate']*em[0]
# else:
# for iTempDen in range(nTempDen):
# freeBound[iTempDen] += thisFreeBound['rate'][iTempDen]*em[iTempDen]
freeBound += thisFreeBound['rate']
for p in fbProcesses:
if not isinstance(p, str):
p.terminate()
#
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)
# ionWorkerQ.put('STOP')
# timeout is not necessary
for p in ionProcesses:
# print' process is alive: ', p.is_alive()
if p.is_alive():
# p.join()
p.join(timeout=timeout)
# for i in range(proc):
# ionProcesses.append('STOP')
#
for ijk in range(ionWorkerQSize):
out = ionDoneQ.get()
ions = out[0]
if verbose:
print(' collecting calculation for %s'%(ions))
thisIon = out[1]
# thisSpectrum = thisIon.Spectrum
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']
# if nTempDen == 1:
# lineSpectrum += thisSpectrum['intensity']
# else:
# for iTempDen in range(nTempDen):
# lineSpectrum[iTempDen] += thisSpectrum['intensity'][iTempDen]
# check for two-photon emission
if len(out) == 3:
tp = out[2]
twoPhoton += tp['rate']
# if nTempDen == 1:
# twoPhoton += tp['rate']*em[0]
# else:
# for iTempDen in range(nTempDen):
# twoPhoton[iTempDen] += tp['rate'][iTempDen]*em[iTempDen]
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,
'ions':self.IonsCalculated, '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, 'ions':self.IonsCalculated, 'em':em,
'ions':self.IonsCalculated, 'Abundance':self.AbundanceName, 'xlabel':xlabel, 'ylabel':ylabel}}
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}
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,
abundance=None,
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 abundance != None:
if abundance in list(chdata.Abundance.keys()):
self.AbundanceName = abundance
else:
abundChoices = list(chdata.Abundance.keys())
abundChoice = chGui.gui.selectorDialog(
abundChoices,
label='Select Abundance name',
multiChoice=False)
abundChoice_idx = abundChoice.selectedIndex
self.AbundanceName = abundChoices[abundChoice_idx[0]]
print((' Abundance chosen: %s ' % (self.AbundanceName)))
else:
self.AbundanceName = self.Defaults['abundfile']
#
#
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['intensity']
elif calcType == 'fb':
thisFb = out[2]
if verbose:
print(' fb ion = %s' % (ionS))
if 'intensity' in thisFb.keys():
if 'errorMessage' not in sorted(thisFb.keys()):
if keepIons:
self.FbInstances[ionS] = thisFb
freeBound += thisFb['intensity']
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
}
def __init__(self, temperature, eDensity, wavelength, filter=(chfilters.gaussianR, 1000.), label=0, elementList = 0, ionList = 0, minAbund=1.e-6, keepIons=0, abundance=None, doContinuum=1, allLines = 1, em =0, proc=3, verbose = 0, timeout=0.1):
#
t1 = datetime.now()
# creates Intensity dict from first ion calculated
setupIntensity = 0
#
self.Defaults = defaults
#
# masterlist = chdata.MasterList
self.Defaults = 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 type(em) == int and em == 0:
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:
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:
self.IonInstances = {}
self.Finished = []
#
# self.Todo = []
self.ionGate(elementList = elementList, ionList = ionList, minAbund=minAbund, doContinuum=doContinuum, verbose = verbose)
#
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()
if 'rate' in sorted(thisFreeFree.keys()):
freeFree += thisFreeFree['rate']
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()
if 'rate' in sorted(thisFreeBound.keys()):
freeBound += thisFreeBound['rate']
for p in fbProcesses:
if not isinstance(p, str):
p.terminate()
#
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 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['rate']
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}
