def intensityRatio(self, wvlRange=None, wvlRanges=None, top=10):
"""
Plot the ratio of 2 lines or sums of lines.
Shown as a function of density and/or temperature.
For a single wavelength range, set wvlRange = [wMin, wMax]
For multiple wavelength ranges, set wvlRanges = [[wMin1,wMax1],[wMin2,wMax2], ...]
A plot of relative emissivities is shown and then a dialog appears for the user to
choose a set of lines.
"""
#
# self.Emiss={"temperature":temperature,"density":density,"wvl":wvl,"emiss":em,
# "plotLabels":plotLabels}
#
#
if not hasattr(self, 'Intensity'):
try:
self.intensity()
except:
print(
' intensities not calculated and emiss() is unable to calculate them'
)
print(' perhaps the temperature and/or eDensity are not set')
return
#
# everything in self.Intensity should be a numpy array
#
intens = copy.copy(self.Intensity)
intensity = intens['intensity']
#
#
fontsize = 14
#
# temperature = self.Temperature
eDensity = self.EDensity
temperature = self.Temperature
intensity = intens['intensity']
#
# temp=np.asarray(temperature,'Float32')
ntemp = temperature.size
if ntemp > 0:
if temperature[0] == temperature[-1]:
ntemp = 1
#
ndens = eDensity.size
if ndens > 0:
if eDensity[0] == eDensity[-1]:
ndens = 1
#
print(' ndens = %5i ntemp = %5i' % (ndens, ntemp))
ionS = intens['ionS']
# see if we are dealing with more than a single ion
ionSet = set(ionS)
ionNum = len(ionSet)
wvl = intens["wvl"]
# plotLabels = intens["plotLabels"]
# xLabel = plotLabels["xLabel"]
# yLabel = plotLabels["yLabel"]
#
# find which lines are in the wavelength range if it is set
#
#
if wvlRange:
igvl = util.between(wvl, wvlRange)
if len(igvl) == 0:
print('no lines in wavelength range %12.2f - %12.2f' %
(wvlRange[0], wvlRange[1]))
return
elif wvlRanges:
igvl = []
for awvlRange in wvlRanges:
igvl.extend(util.between(wvl, awvlRange))
if len(igvl) == 0:
print('no lines in wavelength ranges specified ')
return
else:
igvl = range(len(wvl))
#
nlines = len(igvl)
#
# print ' nlines = ',nlines
# print ' iglv = ',igvl
igvl = np.take(igvl, wvl[igvl].argsort())
# find the top most intense lines
#
if top > nlines:
top = nlines
#
maxIntens = np.zeros(nlines, 'Float64')
for iline in range(nlines):
maxIntens[iline] = intensity[:, igvl[iline]].max()
for iline in range(nlines):
if maxIntens[iline] == maxIntens.max():
maxAll = intensity[:, igvl[iline]]
# line=range(nlines)
igvlsort = np.take(igvl, np.argsort(maxIntens))
# print 'igvlsort = ', igvlsort
topLines = igvlsort[-top:]
# print ' topLines = ', topLines
maxWvl = '%5.3f' % wvl[topLines[-1]]
# maxline=topLines[-1]
#
topLines = topLines[wvl[topLines].argsort()]
#
#
# need to make sure there are no negative values before plotting
good = intensity > 0.
intensMin = intensity[good].min()
bad = intensity <= 0.
intensity[bad] = intensMin
#
#
# ntemp=self.Temperature.size
#
# ndens=self.EDensity.size
#
ylabel = 'Emissivity relative to ' + maxWvl
if ionNum == 1:
title = self.Spectroscopic
else:
title = ''
#
#
if ndens == 1 and ntemp == 1:
print(' only a single temperature and eDensity')
return
elif ndens == 1:
xlabel = 'Temperature (K)'
xvalues = self.Temperature
outTemperature = self.Temperature
# outDensity=np.zeros(ntemp,'Float64')
# outDensity.fill(self.EDensity[0])
outDensity = self.EDensity
desc_str = ' Density = %10.2e (cm)$^{-3}$' % self.EDensity[0]
elif ntemp == 1:
xvalues = self.EDensity
# outTemperature=np.zeros(ndens,'Float64')
# outTemperature.fill(self.Temperature[0])
outTemperature = self.Temperature
outDensity = self.EDensity
xlabel = r'$\rm{Electron Density (cm)^{-3}}$'
desc_str = ' Temp = %10.2e (K)' % self.Temperature[0]
else:
outTemperature = self.Temperature
outDensity = self.EDensity
xlabel = 'Temperature (K)'
xvalues = self.Temperature
desc_str = ' Variable Density'
#
# put all actual plotting here
#
pl.ion()
# if chInteractive:
# pl.ion()
# else:
# pl.ioff()
#
# maxAll is an array
ymax = np.max(intensity[:, topLines[0]] / maxAll)
ymin = ymax
pl.figure()
ax = pl.subplot(111)
nxvalues = len(xvalues)
for iline in range(top):
tline = topLines[iline]
pl.loglog(xvalues, intensity[:, tline] / maxAll)
if np.min(intensity[:, tline] / maxAll) < ymin:
ymin = np.min(intensity[:, tline] / maxAll)
if np.max(intensity[:, tline] / maxAll) > ymax:
ymax = np.max(intensity[:, tline] / maxAll)
skip = 2
start = divmod(iline, nxvalues)[1]
for ixvalue in range(start, nxvalues, nxvalues // skip):
if ionNum == 1:
text = '%10.4f' % (wvl[tline])
else:
text = '%s %10.4f' % (ionS[tline], wvl[tline])
pl.text(xvalues[ixvalue],
intensity[ixvalue, tline] / maxAll[ixvalue], text)
pl.xlim(xvalues.min(), xvalues.max())
# pl.ylim(ymin, ymax)
pl.xlabel(xlabel, fontsize=fontsize)
pl.ylabel(ylabel, fontsize=fontsize)
if ndens == ntemp and ntemp > 1:
pl.text(0.07,
0.5,
title,
horizontalalignment='left',
verticalalignment='center',
fontsize=fontsize,
transform=ax.transAxes)
#
ax2 = pl.twiny()
xlabelDen = r'Electron Density (cm$^{-3}$)'
pl.xlabel(xlabelDen, fontsize=fontsize)
pl.loglog(eDensity,
intensity[:, topLines[top - 1]] / maxAll,
visible=False)
ax2.xaxis.tick_top()
pl.ylim(ymin / 1.2, 1.2 * ymax)
else:
pl.ylim(ymin / 1.2, 1.2 * ymax)
pl.title(title + desc_str, fontsize=fontsize)
pl.draw()
# need time to let matplotlib finish plotting
time.sleep(0.5)
#
# get line selection
#
selectTags = []
for itop in topLines:
if ionNum == 1:
selectTags.append(str(wvl[itop]))
else:
selectTags.append(ionS[itop] + ' ' + str(wvl[itop]))
#
# numden = chGui.gui.choice2Dialog(wvl[topLines])
numden = chGui.gui.choice2Dialog(selectTags)
#
# num_idx and den_idx are tuples
#
num_idx = numden.numIndex
if len(num_idx) == 0:
print(' no numerator lines were selected')
return
#
den_idx = numden.denIndex
if len(den_idx) == 0:
print(' no denominator lines were selected')
return
#
numIntens = np.zeros(len(xvalues), 'Float64')
for aline in num_idx:
numIntens += intensity[:, topLines[aline]]
#
denIntens = np.zeros(len(xvalues), 'Float64')
for aline in den_idx:
denIntens += intensity[:, topLines[aline]]
#
# plot the desired ratio
# maxAll is an array
pl.figure()
ax = pl.subplot(111)
pl.loglog(xvalues, numIntens / denIntens)
pl.xlim(xvalues.min(), xvalues.max())
pl.xlabel(xlabel, fontsize=fontsize)
pl.ylabel('Ratio (' + self.Defaults['flux'] + ')', fontsize=fontsize)
if ionNum == 1:
desc = ionS[0]
else:
desc = ''
for aline in num_idx:
if ionNum == 1:
desc += ' ' + str(wvl[topLines[aline]])
else:
desc += ' ' + ionS[topLines[aline]] + ' ' + str(
wvl[topLines[aline]])
desc += ' / '
for aline in den_idx:
if ionNum == 1:
desc += ' ' + str(wvl[topLines[aline]])
else:
desc += ' ' + ionS[topLines[aline]] + ' ' + str(
wvl[topLines[aline]])
if ndens == ntemp and ntemp > 1:
pl.text(0.07,
0.5,
desc,
horizontalalignment='left',
verticalalignment='center',
fontsize=fontsize,
transform=ax.transAxes)
#
ax2 = pl.twiny()
xlabelDen = r'Electron Density (cm$^{-3}$)'
pl.xlabel(xlabelDen, fontsize=fontsize)
pl.loglog(eDensity, numIntens / denIntens, visible=False)
ax2.xaxis.tick_top()
else:
# pl.ylim(ymin, ymax)
pl.title(desc, fontsize=fontsize)
# desc=title+' '+str(wvl[num_line])+' / '+str(wvl[den_line])+' '+desc_str
# pl.title(desc, fontsize=fontsize)
# pl.title(title+' '+str(wvl[num_line])+' / '+str(wvl[den_line])+' '+desc_str,fontsize=fontsize)
# pl.draw()
# pl.ioff()
# pl.show()
#
# intensityRatioFileName=self.IonStr
# for aline in num_idx:
# intensityRatioFileName+= '_%3i'%(wvl[topLines[aline]])
# intensityRatioFileName+='_2'
# for aline in den_idx:
# intensityRatioFileName+= '_%3i'%(wvl[topLines[aline]])
cnt = desc.count(' ')
intensityRatioFileName = desc.replace(' ', '_', cnt) + '.rat'
intensityRatioFileName = intensityRatioFileName.lstrip('_').replace(
'_/_', '-')
self.IntensityRatio = {
'ratio': numIntens / denIntens,
'desc': desc,
'temperature': outTemperature,
'eDensity': outDensity,
'filename': intensityRatioFileName,
'numIdx': num_idx,
'denIdx': den_idx
}
def intensityList(self,
index=-1,
wvlRange=None,
wvlRanges=None,
top=10,
relative=0,
outFile=0):
'''
List the line intensities
wvlRange, a 2 element tuple, list or array determines the wavelength range
Top specifies to plot only the top strongest lines, default = 10
normalize = 1 specifies whether to normalize to strongest line, default = 0
rewrite of emissList
'''
#
#
if not hasattr(self, 'Intensity'):
try:
self.intensity()
except:
print(
' intensities not calculated and emiss() is unable to calculate them'
)
print(' perhaps the temperature and/or eDensity are not set')
return
#
# everything in self.Intensity should be a numpy array
#
#
#
temperature = self.Temperature
eDensity = self.EDensity
#
ndens = eDensity.size
ntemp = temperature.size
#
#
intens = copy.deepcopy(self.Intensity)
intensity = intens['intensity']
ionS = intens['ionS']
wvl = intens['wvl']
lvl1 = intens['lvl1']
lvl2 = intens['lvl2']
pretty1 = intens['pretty1']
pretty2 = intens['pretty2']
obs = intens['obs']
avalue = intens['avalue']
#
if ndens == 1 and ntemp == 1:
dstr = ' - Density = %10.2e (cm$^{-3}$)' % (eDensity)
tstr = ' - T = %10.2e (K)' % (temperature)
elif ndens == 1 and ntemp > 1:
if index < 0:
index = ntemp / 2
print('using index = %5i specifying temperature = %10.2e' %
(index, temperature[index]))
self.Message = 'using index = %5i specifying temperature = %10.2e' % (
index, temperature[index])
intensity = intensity[index]
elif ndens > 1 and ntemp == 1:
if index < 0:
index = ntemp / 2
print('using index =%5i specifying eDensity = %10.2e' %
(index, eDensity[index]))
self.Message = 'using index =%5i specifying eDensity = %10.2e' % (
index, eDensity[index])
intensity = intensity[index]
elif ndens > 1 and ntemp > 1:
if index < 0:
index = ntemp / 2
print(
'using index = %5i specifying temperature = %10.2e, eDensity = %10.2e'
% (index, temperature[index], eDensity[index]))
self.Message = 'using index = %5i specifying temperature = %10.2e, eDensity = %10.2e' % (
index, temperature[index], eDensity[index])
intensity = intensity[index]
#
# print('shpae of intensity 0 = %5i %5i'%(intensity.shape))
#
if wvlRange:
wvlIndex = util.between(wvl, wvlRange)
elif wvlRanges:
wvlIndex = []
for awvlRange in wvlRanges:
wvlIndex.extend(util.between(wvl, awvlRange))
else:
wvlIndex = range(wvl.size)
#
# get lines in the specified wavelength range
#
# print('shpae of intensity 1 = %5i %5i'%(intensity.shape))
#
intensity = intensity[wvlIndex]
ionS = ionS[wvlIndex]
wvl = wvl[wvlIndex]
lvl1 = lvl1[wvlIndex]
lvl2 = lvl2[wvlIndex]
avalue = avalue[wvlIndex]
pretty1 = pretty1[wvlIndex]
pretty2 = pretty2[wvlIndex]
obs = obs[wvlIndex]
#
self.Error = 0
if wvl.size == 0:
print('No lines in this wavelength interval')
self.Error = 1
self.Message = 'No lines in this wavelength interval'
return
#
elif top == 0:
top = wvl.size
elif top > wvl.size:
top = wvl.size
#
# sort by intensity
#
isrt = np.argsort(intensity)
ionS = ionS[isrt[-top:]]
wvl = wvl[isrt[-top:]]
lvl1 = lvl1[isrt[-top:]]
lvl2 = lvl2[isrt[-top:]]
obs = obs[isrt[-top:]]
intensity = intensity[isrt[-top:]]
avalue = avalue[isrt[-top:]]
pretty1 = pretty1[isrt[-top:]]
pretty2 = pretty2[isrt[-top:]]
#
# print('shpae of intensity 2= %5i %5i'%(intensity.shape))
#
# must follow setting top
#
if relative:
intensity = intensity / intensity[:top].max()
#
#
idx = np.argsort(wvl)
fmt1 = '%5s %5s %5s %25s - %-25s %12s %12s %12s %3s'
fmt = '%5s %5i %5i %25s - %-25s %12.4f %12.3e %12.2e %1s'
print(' ')
print(' ------------------------------------------')
print(' ')
print(fmt1 % ('Ion', 'lvl1', 'lvl2', 'lower', 'upper', 'Wvl(A)',
'Intensity', 'A value', 'Obs'))
for kdx in idx:
print(fmt %
(ionS[kdx], lvl1[kdx], lvl2[kdx], pretty1[kdx], pretty2[kdx],
wvl[kdx], intensity[kdx], avalue[kdx], obs[kdx]))
print(' ')
print(' ------------------------------------------')
print(' ')
#
self.Intensity['wvlTop'] = wvl[idx]
self.Intensity['intensityTop'] = intensity[idx]
if outFile:
fmt1a = '%5s %5s %5s %25s - %-25s %12s %12s %12s %3s \n'
fmt = '%5s %5i %5i %25s - %-25s %12.4f %12.3e %12.2e %1s \n'
outpt = open(outFile, 'w')
outpt.write(fmt1a % ('Ion', 'lvl1', 'lvl2', 'lower', 'upper',
'Wvl(A)', 'Intensity', 'A value', 'Obs'))
for kdx in idx:
outpt.write(fmt % (ionS[kdx], lvl1[kdx], lvl2[kdx],
pretty1[kdx], pretty2[kdx], wvl[kdx],
intensity[kdx], avalue[kdx], obs[kdx]))
outpt.close()
def intensityPlot(self,
index=-1,
wvlRange=None,
top=10,
linLog='lin',
relative=0,
verbose=0,
plotFile=0,
saveFile=0,
em=0):
'''Plot the line intensities.
wvlRange, a 2 element tuple, list or array determines the wavelength range
Top specifies to plot only the top strongest lines, default = 10
linLog specifies a linear or log plot, want either lin or log, default = lin
normalize = 1 specifies whether to normalize to strongest line, default = 0'''
#
title = self.Spectroscopic
#
if hasattr(self, 'Intensity'):
intens = self.Intensity['intensity']
else:
try:
self.intensity(em=em)
intens = self.Intensity['intensity']
except:
print(
' emissivities not calculated and emiss() is unable to calculate them'
)
print(' perhaps the temperature and/or eDensity are not set')
return
wvl = self.Intensity['wvl']
temperature = self.Temperature
eDensity = self.EDensity
#
ndens = eDensity.size
ntemp = temperature.size
#
if ndens == 1 and ntemp == 1:
dstr = ' - Density = %10.2e (cm$^{-3}$)' % (eDensity)
tstr = ' - T = %10.2e (K)' % (temperature)
elif ndens == 1 and ntemp > 1:
if index < 0:
index = ntemp / 2
print('using index = %5i specifying temperature = %10.2e' %
(index, temperature[index]))
self.Message = 'using index = %5i specifying temperature = %10.2e' % (
index, temperature[index])
# if chInteractive:
# print 'using index = %5i specifying temperature = %10.2e'%(index, temperature[index])
# else:
# self.Message = 'using index = %5i specifying temperature = %10.2e'%(index, temperature[index])
intensity = self.Intensity['intensity'][index]
dstr = ' - Density = %10.2e (cm$^{-3}$)' % eDensity
tstr = ' - T = %10.2e (K)' % temperature[index]
elif ndens > 1 and ntemp == 1:
if index < 0:
index = ntemp / 2
print('using index =%5i specifying eDensity = %10.2e' %
(index, eDensity[index]))
self.Message = 'using index =%5i specifying eDensity = %10.2e' % (
index, eDensity[index])
# if chInteractive:
# print 'using index =%5i specifying eDensity = %10.2e'%(index, eDensity[index])
# else:
# self.Message = 'using index =%5i specifying eDensity = %10.2e'%(index, eDensity[index])
intensity = self.Intensity['intensity'][index]
dstr = ' - Density = %10.2e (cm$^{-3}$)' % eDensity[index]
tstr = ' - T = %10.2e (K)' % temperature
elif ndens > 1 and ntemp > 1:
if index < 0:
index = ntemp / 2
print(
'using index = %5i specifying temperature = %10.2e, eDensity = %10.2e'
% (index, temperature[index], eDensity[index]))
self.Message = 'using index = %5i specifying temperature = %10.2e, eDensity = %10.2e' % (
index, temperature[index], eDensity[index])
# if chInteractive:
# print 'using index = %5i specifying temperature = %10.2e, eDensity = %10.2e'%(index, temperature[index], eDensity[index])
# else:
# self.Message = 'using index = %5i specifying temperature = %10.2e, eDensity = %10.2e'%(index, temperature[index], eDensity[index])
intensity = self.Intensity['intensity'][index]
dstr = ' - Density = %10.2e (cm$^{-3}$)' % eDensity[index]
tstr = ' - T = %10.2e (K)' % temperature[index]
if type(wvlRange) != type(None):
wvlIndex = util.between(wvl, wvlRange)
else:
wvlIndex = range(wvl.size)
intensity = intensity[wvlIndex]
wvl = wvl[wvlIndex]
#
self.Error = 0
if wvl.size == 0:
print('No lines in this wavelength interval')
self.Error = 1
self.Message = 'No lines in this wavelength interval'
# if chInteractive:
# print 'No lines in this wavelength interval'
# else:
# self.Error = 1
# self.Message = 'No lines in this wavelength interval'
return
elif top == 0:
top = wvl.size
elif wvl.size > top:
intsrt = np.argsort(intensity)
wvl = wvl[intsrt[-top:]]
intensity = intensity[intsrt[-top:]]
else:
top = wvl.size
# must follow setting top
#
pl.figure()
ylabel = 'intensity'
if relative:
intensity = intensity / intensity[-1]
ylabel += ' (Relative)'
#
xlabel = 'Wavelength (' + self.Defaults['wavelength'] + ')'
#
ymin = 10.**(np.log10(intensity[0].min()).round(0) - 0.5)
#
pl.ion()
# if chInteractive:
# pl.ion()
# else:
# pl.ioff()
#
for idx in range(top):
xx = [wvl[idx], wvl[idx]]
if linLog == 'lin':
yy = [0., intensity[idx]]
pl.plot(xx, yy)
else:
yy = [ymin / 10., intensity[idx]]
pl.semilogy(xx, yy)
pl.xlabel(xlabel)
pl.ylabel(ylabel)
pl.title(title + tstr + dstr)
if wvlRange:
pl.axis([wvlRange[0], wvlRange[1], ymin, intensity.max()])
if plotFile:
pl.savefig(plotFile)
def intensityRatio(self,wvlRange=None, wvlRanges=None,top=10):
"""
Plot the ratio of 2 lines or sums of lines.
Shown as a function of density and/or temperature.
For a single wavelength range, set wvlRange = [wMin, wMax]
For multiple wavelength ranges, set wvlRanges = [[wMin1,wMax1],[wMin2,wMax2], ...]
A plot of relative emissivities is shown and then a dialog appears for the user to
choose a set of lines.
"""
#
# self.Emiss={"temperature":temperature,"density":density,"wvl":wvl,"emiss":em,
# "plotLabels":plotLabels}
#
#
if not hasattr(self, 'Intensity'):
try:
self.intensity()
except:
print(' intensities not calculated and emiss() is unable to calculate them')
print(' perhaps the temperature and/or eDensity are not set')
return
#
# everything in self.Intensity should be a numpy array
#
# intens = copy.copy(self.Intensity)
# intensity = intens['intensity']
#
#
fontsize=14
#
# temperature = self.Temperature
eDensity = self.EDensity
temperature = self.Temperature
# intensity = intens['intensity']
#
# temp=np.asarray(temperature,'Float32')
ntemp = temperature.size
if ntemp > 0:
if temperature[0] == temperature[-1]:
ntemp = 1
#
ndens = eDensity.size
if ndens > 0:
if eDensity[0] == eDensity[-1]:
ndens = 1
#
print(' ndens = %5i ntemp = %5i'%(ndens, ntemp))
ionS = self.Intensity['ionS']
# see if we are dealing with more than a single ion
ionSet = set(ionS)
ionNum = len(ionSet)
wvl = self.Intensity["wvl"]
# plotLabels = intens["plotLabels"]
# xLabel = plotLabels["xLabel"]
# yLabel = plotLabels["yLabel"]
#
# find which lines are in the wavelength range if it is set
#
#
if wvlRange:
igvl=util.between(wvl,wvlRange)
if len(igvl) == 0:
print('no lines in wavelength range %12.2f - %12.2f'%(wvlRange[0], wvlRange[1]))
return
elif wvlRanges:
igvl = []
for awvlRange in wvlRanges:
igvl.extend(util.between(wvl,awvlRange))
if len(igvl) == 0:
print('no lines in wavelength ranges specified ')
return
else:
igvl=range(len(wvl))
#
nlines=len(igvl)
#
# print ' nlines = ',nlines
# print ' iglv = ',igvl
igvl=np.take(igvl,wvl[igvl].argsort())
# find the top most intense lines
#
if top > nlines:
top=nlines
#
intensity = self.Intensity['intensity']
maxIntens = np.zeros(nlines,'Float64')
for iline in range(nlines):
maxIntens[iline] = intensity[:, igvl[iline]].max()
for iline in range(nlines):
if maxIntens[iline]==maxIntens.max():
maxAll=intensity[:, igvl[iline]]
# line=range(nlines)
igvlsort=np.take(igvl,np.argsort(maxIntens))
# print 'igvlsort = ', igvlsort
topLines=igvlsort[-top:]
# print ' topLines = ', topLines
maxWvl='%5.3f' % wvl[topLines[-1]]
# maxline=topLines[-1]
#
topLines=topLines[wvl[topLines].argsort()]
#
#
# need to make sure there are no negative values before plotting
good = intensity > 0.
intensMin = intensity[good].min()
bad = intensity <= 0.
intensity[bad] = intensMin
#
#
# ntemp=self.Temperature.size
#
# ndens=self.EDensity.size
#
ylabel='Intensity relative to '+maxWvl
if ionNum == 1:
title=self.Spectroscopic
else:
title = ''
#
#
if ndens==1 and ntemp==1:
print(' only a single temperature and eDensity')
return
elif ndens == 1:
xlabel='Temperature (K)'
xvalues=self.Temperature
outTemperature=self.Temperature
# outDensity=np.zeros(ntemp,'Float64')
# outDensity.fill(self.EDensity[0])
outDensity = self.EDensity
desc_str=' Density = %10.2e (cm)$^{-3}$' % self.EDensity[0]
elif ntemp == 1:
xvalues=self.EDensity
# outTemperature=np.zeros(ndens,'Float64')
# outTemperature.fill(self.Temperature[0])
outTemperature = self.Temperature
outDensity=self.EDensity
xlabel=r'$\rm{Electron Density (cm)^{-3}}$'
desc_str=' Temp = %10.2e (K)' % self.Temperature[0]
else:
outTemperature=self.Temperature
outDensity=self.EDensity
xlabel='Temperature (K)'
xvalues=self.Temperature
desc_str=' Variable Density'
#
# put all actual plotting here
#
pl.ion()
# if chInteractive:
# pl.ion()
# else:
# pl.ioff()
#
# maxAll is an array
ymax = np.max(intensity[:, topLines[0]]/maxAll)
ymin = ymax
pl.figure()
ax = pl.subplot(111)
nxvalues=len(xvalues)
for iline in range(top):
tline=topLines[iline]
pl.loglog(xvalues,intensity[:, tline]/maxAll)
if np.min(intensity[:, tline]/maxAll) < ymin:
ymin = np.min(intensity[:, tline]/maxAll)
if np.max(intensity[:, tline]/maxAll) > ymax:
ymax = np.max(intensity[:, tline]/maxAll)
skip=2
start=divmod(iline,nxvalues)[1]
for ixvalue in range(start,nxvalues,nxvalues//skip):
if ionNum == 1:
text = '%10.4f'%(wvl[tline])
else:
text = '%s %10.4f'%(ionS[tline], wvl[tline])
pl.text(xvalues[ixvalue], intensity[ixvalue, tline]/maxAll[ixvalue], text)
pl.xlim(xvalues.min(),xvalues.max())
# pl.ylim(ymin, ymax)
pl.xlabel(xlabel,fontsize=fontsize)
pl.ylabel(ylabel,fontsize=fontsize)
if ndens == ntemp and ntemp > 1:
pl.text(0.07, 0.5,title, horizontalalignment='left', verticalalignment='center', fontsize=fontsize, transform = ax.transAxes)
#
ax2 = pl.twiny()
xlabelDen=r'Electron Density (cm$^{-3}$)'
pl.xlabel(xlabelDen, fontsize=fontsize)
pl.loglog(eDensity,intensity[:, topLines[top-1]]/maxAll, visible=False)
ax2.xaxis.tick_top()
pl.ylim(ymin/1.2, 1.2*ymax)
else:
pl.ylim(ymin/1.2, 1.2*ymax)
pl.title(title+desc_str,fontsize=fontsize)
pl.draw()
# need time to let matplotlib finish plotting
time.sleep(0.5)
#
# get line selection
#
selectTags = []
for itop in topLines:
if ionNum == 1:
selectTags.append(str(wvl[itop]))
else:
selectTags.append(ionS[itop]+ ' '+ str(wvl[itop]))
#
# numden = chGui.gui.choice2Dialog(wvl[topLines])
numden = chGui.gui.choice2Dialog(selectTags)
#
# num_idx and den_idx are tuples
#
num_idx=numden.numIndex
if len(num_idx) == 0:
print(' no numerator lines were selected')
return
#
den_idx=numden.denIndex
if len(den_idx) == 0:
print(' no denominator lines were selected')
return
#
numIntens=np.zeros(len(xvalues),'Float64')
for aline in num_idx:
numIntens += intensity[:, topLines[aline]]
#
denIntens = np.zeros(len(xvalues),'Float64')
for aline in den_idx:
denIntens += intensity[:, topLines[aline]]
#
# plot the desired ratio
# maxAll is an array
pl.figure()
ax = pl.subplot(111)
pl.loglog(xvalues,numIntens/denIntens)
pl.xlim(xvalues.min(),xvalues.max())
pl.xlabel(xlabel,fontsize=fontsize)
pl.ylabel('Ratio ('+self.Defaults['flux']+')',fontsize=fontsize)
if ionNum == 1:
desc = ionS[0]
else:
desc = ''
for aline in num_idx:
if ionNum == 1:
desc += ' ' + str(wvl[topLines[aline]])
else:
desc += ' ' + ionS[topLines[aline]] + ' ' + str(wvl[topLines[aline]])
desc += ' / '
for aline in den_idx:
if ionNum == 1:
desc += ' ' + str(wvl[topLines[aline]])
else:
desc += ' ' + ionS[topLines[aline]] + ' ' + str(wvl[topLines[aline]])
if ndens == ntemp and ntemp > 1:
pl.text(0.07, 0.5,desc, horizontalalignment='left', verticalalignment='center', fontsize=fontsize, transform = ax.transAxes)
#
ax2 = pl.twiny()
xlabelDen=r'Electron Density (cm$^{-3}$)'
pl.xlabel(xlabelDen, fontsize=fontsize)
pl.loglog(eDensity,numIntens/denIntens, visible=False)
ax2.xaxis.tick_top()
else:
# pl.ylim(ymin, ymax)
pl.title(desc,fontsize=fontsize)
# desc=title+' '+str(wvl[num_line])+' / '+str(wvl[den_line])+' '+desc_str
# pl.title(desc, fontsize=fontsize)
# pl.title(title+' '+str(wvl[num_line])+' / '+str(wvl[den_line])+' '+desc_str,fontsize=fontsize)
# pl.draw()
# pl.ioff()
# pl.show()
#
# intensityRatioFileName=self.IonStr
# for aline in num_idx:
# intensityRatioFileName+= '_%3i'%(wvl[topLines[aline]])
# intensityRatioFileName+='_2'
# for aline in den_idx:
# intensityRatioFileName+= '_%3i'%(wvl[topLines[aline]])
cnt = desc.count(' ')
intensityRatioFileName = desc.replace(' ', '_', cnt) + '.rat'
intensityRatioFileName = intensityRatioFileName.lstrip('_').replace('_/_','-')
self.IntensityRatio={'ratio':numIntens/denIntens,'desc':desc,
'temperature':outTemperature,'eDensity':outDensity,'filename':intensityRatioFileName, 'numIdx':num_idx, 'denIdx':den_idx}
def intensityPlot(self, index=-1, wvlRange=None, top=10, linLog='lin', relative=0, verbose=0, plotFile = 0, saveFile=0, em=0 ):
'''Plot the line intensities.
wvlRange, a 2 element tuple, list or array determines the wavelength range
Top specifies to plot only the top strongest lines, default = 10
linLog specifies a linear or log plot, want either lin or log, default = lin
normalize = 1 specifies whether to normalize to strongest line, default = 0'''
#
title=self.Spectroscopic
#
if hasattr(self, 'Intensity'):
intens = self.Intensity['intensity']
else:
try:
self.intensity(em=em)
intens = self.Intensity['intensity']
except:
print(' emissivities not calculated and emiss() is unable to calculate them')
print(' perhaps the temperature and/or eDensity are not set')
return
wvl = self.Intensity['wvl']
temperature = self.Temperature
eDensity = self.EDensity
#
ndens = eDensity.size
ntemp = temperature.size
#
if ndens == 1 and ntemp == 1:
dstr = ' - Density = %10.2e (cm$^{-3}$)' %(eDensity)
tstr = ' - T = %10.2e (K)' %(temperature)
elif ndens == 1 and ntemp > 1:
if index < 0:
index = ntemp/2
print('using index = %5i specifying temperature = %10.2e'%(index, temperature[index]))
self.Message = 'using index = %5i specifying temperature = %10.2e'%(index, temperature[index])
# if chInteractive:
# print 'using index = %5i specifying temperature = %10.2e'%(index, temperature[index])
# else:
# self.Message = 'using index = %5i specifying temperature = %10.2e'%(index, temperature[index])
intensity=self.Intensity['intensity'][index]
dstr=' - Density = %10.2e (cm$^{-3}$)' % eDensity
tstr=' - T = %10.2e (K)' % temperature[index]
elif ndens > 1 and ntemp == 1:
if index < 0:
index = ntemp/2
print('using index =%5i specifying eDensity = %10.2e'%(index, eDensity[index]))
self.Message = 'using index =%5i specifying eDensity = %10.2e'%(index, eDensity[index])
# if chInteractive:
# print 'using index =%5i specifying eDensity = %10.2e'%(index, eDensity[index])
# else:
# self.Message = 'using index =%5i specifying eDensity = %10.2e'%(index, eDensity[index])
intensity = self.Intensity['intensity'][index]
dstr=' - Density = %10.2e (cm$^{-3}$)' % eDensity[index]
tstr=' - T = %10.2e (K)' % temperature
elif ndens > 1 and ntemp > 1:
if index < 0:
index = ntemp/2
print('using index = %5i specifying temperature = %10.2e, eDensity = %10.2e'%(index, temperature[index], eDensity[index]))
self.Message = 'using index = %5i specifying temperature = %10.2e, eDensity = %10.2e'%(index, temperature[index], eDensity[index])
# if chInteractive:
# print 'using index = %5i specifying temperature = %10.2e, eDensity = %10.2e'%(index, temperature[index], eDensity[index])
# else:
# self.Message = 'using index = %5i specifying temperature = %10.2e, eDensity = %10.2e'%(index, temperature[index], eDensity[index])
intensity = self.Intensity['intensity'][index]
dstr=' - Density = %10.2e (cm$^{-3}$)' % eDensity[index]
tstr=' - T = %10.2e (K)' % temperature[index]
if type(wvlRange) != type(None):
wvlIndex = util.between(wvl, wvlRange)
else:
wvlIndex = range(wvl.size)
intensity = intensity[wvlIndex]
wvl = wvl[wvlIndex]
#
self.Error = 0
if wvl.size == 0:
print('No lines in this wavelength interval')
self.Error = 1
self.Message = 'No lines in this wavelength interval'
# if chInteractive:
# print 'No lines in this wavelength interval'
# else:
# self.Error = 1
# self.Message = 'No lines in this wavelength interval'
return
elif top == 0:
top = wvl.size
elif wvl.size > top:
intsrt = np.argsort(intensity)
wvl = wvl[intsrt[-top:]]
intensity = intensity[intsrt[-top:]]
else:
top = wvl.size
# must follow setting top
#
pl.figure()
ylabel = 'intensity'
if relative:
intensity = intensity/intensity[-1]
ylabel += ' (Relative)'
#
xlabel = 'Wavelength ('+self.Defaults['wavelength'] +')'
#
ymin = 10.**(np.log10(intensity[0].min()).round(0)-0.5 )
#
pl.ion()
# if chInteractive:
# pl.ion()
# else:
# pl.ioff()
#
for idx in range(top):
xx=[wvl[idx], wvl[idx]]
if linLog == 'lin':
yy=[0., intensity[idx]]
pl.plot(xx, yy)
else:
yy=[ymin/10., intensity[idx]]
pl.semilogy(xx, yy)
pl.xlabel(xlabel)
pl.ylabel(ylabel)
pl.title(title+tstr+dstr)
if wvlRange:
pl.axis([wvlRange[0], wvlRange[1], ymin, intensity.max()])
if plotFile:
pl.savefig(plotFile)
def intensityList(self, index=-1, wvlRange=None, wvlRanges=None, top=10, relative=0, outFile=0 ):
'''
List the line intensities
wvlRange, a 2 element tuple, list or array determines the wavelength range
Top specifies to plot only the top strongest lines, default = 10
normalize = 1 specifies whether to normalize to strongest line, default = 0
rewrite of emissList
'''
#
#
if not hasattr(self, 'Intensity'):
try:
self.intensity()
except:
print(' intensities not calculated and emiss() is unable to calculate them')
print(' perhaps the temperature and/or eDensity are not set')
return
#
# everything in self.Intensity should be a numpy array
#
#
#
temperature = self.Temperature
eDensity = self.EDensity
em = self.Em
#
ndens = eDensity.size
ntemp = temperature.size
#
#
intens = copy.deepcopy(self.Intensity)
intensity = intens['intensity']
ionS = intens['ionS']
wvl = intens['wvl']
lvl1 = intens['lvl1']
lvl2 = intens['lvl2']
pretty1 = intens['pretty1']
pretty2 = intens['pretty2']
obs = intens['obs']
avalue = intens['avalue']
#
if ndens == 1 and ntemp == 1:
dstr = ' - Density = %10.2e (cm$^{-3}$)' %(eDensity)
tstr = ' - T = %10.2e (K)' %(temperature)
elif ndens == 1 and ntemp > 1:
if index < 0:
index = ntemp/2
print('using index = %5i specifying temperature = %10.2e'%(index, temperature[index]))
self.Message = 'using index = %5i specifying temperature = %10.2e'%(index, temperature[index])
intensity=intensity[index]
elif ndens > 1 and ntemp == 1:
if index < 0:
index = ntemp/2
print('using index =%5i specifying eDensity = %10.2e'%(index, eDensity[index]))
self.Message = 'using index =%5i specifying eDensity = %10.2e'%(index, eDensity[index])
intensity=intensity[index]
elif ndens > 1 and ntemp > 1:
if index < 0:
index = ntemp/2
print('using index = %5i specifying temperature = %10.2e, eDensity = %10.2e em = %10.2e'%(index, temperature[index], eDensity[index], em[index]))
self.Message = 'using index = %5i specifying temperature = %10.2e, eDensity = %10.2eem = %10.2e'%(index, temperature[index], eDensity[index], em[index])
intensity=intensity[index]
#
# print('shpae of intensity 0 = %5i %5i'%(intensity.shape))
#
if wvlRange:
wvlIndex=util.between(wvl,wvlRange)
elif wvlRanges:
wvlIndex = []
for awvlRange in wvlRanges:
wvlIndex.extend(util.between(wvl,awvlRange))
else:
wvlIndex = range(wvl.size)
#
# get lines in the specified wavelength range
#
# print('shpae of intensity 1 = %5i %5i'%(intensity.shape))
#
intensity = intensity[wvlIndex]
ionS = ionS[wvlIndex]
wvl = wvl[wvlIndex]
lvl1 = lvl1[wvlIndex]
lvl2 = lvl2[wvlIndex]
avalue = avalue[wvlIndex]
pretty1 = pretty1[wvlIndex]
pretty2 = pretty2[wvlIndex]
obs = obs[wvlIndex]
#
self.Error = 0
if wvl.size == 0:
print('No lines in this wavelength interval')
self.Error = 1
self.Message = 'No lines in this wavelength interval'
return
#
elif top == 0:
top = wvl.size
elif top > wvl.size:
top = wvl.size
#
# sort by intensity
#
isrt = np.argsort(intensity)
ionS = ionS[isrt[-top:]]
wvl = wvl[isrt[-top:]]
lvl1 = lvl1[isrt[-top:]]
lvl2 = lvl2[isrt[-top:]]
obs = obs[isrt[-top:]]
intensity = intensity[isrt[-top:]]
avalue = avalue[isrt[-top:]]
pretty1 = pretty1[isrt[-top:]]
pretty2 = pretty2[isrt[-top:]]
#
# print('shpae of intensity 2= %5i %5i'%(intensity.shape))
#
# must follow setting top
#
if relative:
intensity = intensity/intensity[:top].max()
#
#
idx = np.argsort(wvl)
fmt1 = '%5s %5s %5s %25s - %-25s %12s %12s %12s %3s'
fmt = '%5s %5i %5i %25s - %-25s %12.4f %12.3e %12.2e %1s'
print(' ')
print(' ------------------------------------------')
print(' ')
print(fmt1%('Ion','lvl1','lvl2','lower','upper','Wvl(A)','Intensity','A value','Obs'))
for kdx in idx:
print(fmt%(ionS[kdx], lvl1[kdx], lvl2[kdx], pretty1[kdx], pretty2[kdx], wvl[kdx], intensity[kdx], avalue[kdx], obs[kdx]))
print(' ')
print(' ------------------------------------------')
print(' ')
#
self.Intensity['wvlTop'] = wvl[idx]
self.Intensity['intensityTop'] = intensity[idx]
if outFile:
fmt1a = '%5s %5s %5s %25s - %-25s %12s %12s %12s %3s \n'
fmt = '%5s %5i %5i %25s - %-25s %12.4f %12.3e %12.2e %1s \n'
outpt = open(outFile, 'w')
outpt.write(fmt1a%('Ion','lvl1','lvl2','lower','upper','Wvl(A)','Intensity','A value','Obs'))
for kdx in idx:
outpt.write(fmt%(ionS[kdx], lvl1[kdx], lvl2[kdx], pretty1[kdx], pretty2[kdx], wvl[kdx], intensity[kdx], avalue[kdx], obs[kdx]))
outpt.close()