def intensityRatio(self, wvlRange=None, wvlRanges=None, top=10):
"""
Plot the intensity 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.
Parameters
-----------
wvlRange : array-like
Wavelength range, i.e. min and max
wvlRanges: a tuple, list or array that contains at least 2
2 element tuples, lists or arrays so that multiple
wavelength ranges can be specified
top : `int`
specifies to plot only the top strongest lines, default = 10
"""
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
fontsize = 14
eDensity = self.EDensity
temperature = self.Temperature
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"]
# 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)
igvl = np.take(igvl, wvl[igvl].argsort())
if top > nlines:
top = nlines
intensity = self.Intensity['intensity']
maxIntens = np.zeros(nlines, np.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]]
igvlsort = np.take(igvl, np.argsort(maxIntens))
topLines = igvlsort[-top:]
maxWvl = '%5.3f' % wvl[topLines[-1]]
topLines = topLines[wvl[topLines].argsort()]
print(' maxWvl = %s' % (maxWvl))
# need to make sure there are no negative values before plotting
good = intensity > 0.
intensMin = intensity[good].min()
bad = intensity <= 0.
intensity[bad] = intensMin
ylabel = 'Intensity relative to ' + maxWvl
if ndens == 1 and ntemp == 1:
print(' only a single temperature and eDensity')
return
elif ndens == 1:
xlbl = 'Temperature (K)'
xvalues = self.Temperature
outTemperature = self.Temperature
outDensity = self.EDensity
desc_str = ' Density = %10.2e (cm$^{-3}$)' % self.EDensity[0]
elif ntemp == 1:
xvalues = self.EDensity
outTemperature = self.Temperature
outDensity = self.EDensity
xlbl = 'Electron Density (cm$^{-3}$)'
desc_str = ' Temp = %10.2e (K)' % self.Temperature[0]
else:
outTemperature = self.Temperature
outDensity = self.EDensity
xlbl = 'Temperature (K)'
xvalues = self.Temperature
desc_str = ' Variable Density'
# put all actual plotting here
plt.ion()
# maxAll is an array
ymax = np.max(intensity[:, topLines[0]] / maxAll)
ymin = ymax
plt.figure()
ax = plt.subplot(111)
nxvalues = len(xvalues)
# reversing is necessary - otherwise, get a ymin=ymax and a matplotlib error
for iline in range(top - 1, -1, -1):
tline = topLines[iline]
plt.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])
plt.text(xvalues[ixvalue],
intensity[ixvalue, tline] / maxAll[ixvalue], text)
if ndens == 1:
print('%12.2e %12.2e ' % (xvalues.min(), xvalues.max()))
plt.xlim(xvalues.min(), xvalues.max())
plt.xlabel(xlbl, fontsize=fontsize)
plt.ylabel(ylabel, fontsize=fontsize)
elif ntemp == 1:
ax2 = plt.twiny()
xlblDen = r'Electron Density (cm$^{-3}$)'
plt.xlabel(xlblDen, fontsize=fontsize)
plt.loglog(eDensity,
intensity[:, topLines[top - 1]] / maxAll,
visible=False)
ax2.xaxis.tick_top()
plt.ylim(ymin / 1.2, 1.2 * ymax)
else:
plt.ylim(ymin / 1.2, 1.2 * ymax)
plt.tight_layout()
plt.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(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), np.float64)
for aline in num_idx:
numIntens += intensity[:, topLines[aline]]
denIntens = np.zeros(len(xvalues), np.float64)
for aline in den_idx:
denIntens += intensity[:, topLines[aline]]
# plot the desired ratio
# maxAll is an array
plt.figure()
ax = plt.subplot(111)
plt.loglog(xvalues, numIntens / denIntens)
plt.xlim(xvalues.min(), xvalues.max())
plt.xlabel(xlbl, fontsize=fontsize)
plt.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:
plt.text(0.07,
0.5,
desc,
horizontalalignment='left',
verticalalignment='center',
fontsize=fontsize,
transform=ax.transAxes)
#
ax2 = plt.twiny()
xlblDen = r'Electron Density (cm$^{-3}$)'
plt.xlabel(xlblDen, fontsize=fontsize)
plt.loglog(eDensity, numIntens / denIntens, visible=False)
ax2.xaxis.tick_top()
else:
plt.title(desc, fontsize=fontsize)
plt.tight_layout()
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,
rightDigits=4):
"""
List the line intensities. Checks to see if there is an existing Intensity attribute. If it exists, then those values are used.
Otherwise, the `intensity` method is called.
This method prints an ASCII table with the following columns:
1. Ion: the CHIANTI style notation for the ion, e.g. 'c_4' for C IV
2. lvl1: the lower level of the transition in the CHIANTI .elvlc file
3. lvl2: the upper level of the transition in the CHIANTI .elvlc file
4. lower: the notation, usually in LS coupling, of the lower fine
structure level
5. upper: the notation, usually in LS coupling, of the upper fine
structure level
6. Wvl(A): the wavelength of the transition in units as specified in
the chiantirc file.
7. Intensity
8. A value: the Einstein coefficient for spontaneous emission from
level 'j' to level 'i'
9. Obs: indicates whether the CHIANTI database considers this an
observed line or one obtained from theoretical energy levels
Regarding the intensity column, if 'flux' in the chiantirc file is set
to 'energy', the intensity is given by,
.. math::
I = \Delta E_{ij}n_jA_{ij}\mathrm{Ab}\\frac{1}{N_e}
\\frac{N(X^{+m})}{N(X)}\mathrm{EM},
in units of ergs cm\ :sup:`-2` s\ :sup:`-1` sr\ :sup:`-1`. If 'flux' is set to 'photon',
.. math::
I = n_jA_{ij}\mathrm{Ab}\\frac{1}{N_e}\\frac{N(X^{+m})}{N(X)}
\mathrm{EM},
where,
- :math:`\Delta E_{ij}` is the transition energy (ergs)
- :math:`n_j` is the fractions of ions in level :math:`j`
- :math:`A_{ij}` is the Einstein coefficient for spontaneous emission
from level :math:`j` to level :math:`i` (in s\ :sup:`-1`)
- :math:`\mathrm{Ab}` is the abundance of the specified element
relative to hydrogen
- :math:`N_e` is the electron density (in cm\ :sup:`-3`)
- :math:`N(X^{+m})/N(X)` is the fractional ionization of ion as a
function of temperature
- :math:`\mathrm{EM}` is the emission measure integrated along the
line-of-sight, :math:`\int\mathrm{d}l\,N_eN_H` (cm\ :sup:`-5`) where
:math:`N_H` is the density of hydrogen (neutral + ionized)
(cm\ :sup:`-3`)
Note that if `relative` is set, the line intensity is relative to the
strongest line and so the output will be unitless.
Parameters
-----------
index : `int`,optional
Index the temperature or eDensity array to use.
-1 (default) sets the specified value to the middle of the array
wvlRange : `tuple`
Wavelength range
wvlRanges : a tuple, list or array that contains at least 2
2 element tuples, lists or arrays so that multiple
wavelength ranges can be specified
top : `int`
Number of lines to plot, sorted by descending magnitude.
relative : `int`
specifies whether to normalize to strongest line
default (relative = 0) specified that the intensities should be
their calculated values
outFile : `str`
specifies the file that the intensities should be output to
default(outFile = 0) intensities are output to the terminal
rightDigits: `int`
specifies the format for the wavelengths for the number of digits
to right of the decimal place
"""
if not hasattr(self, 'Intensity'):
try:
self.intensity()
#TODO: specify what exception to catch! or omit the try, catch
except:
print(
' intensities not calculated and emiss() is unable to calculate them'
)
print(' perhaps the temperature and/or eDensity are not set')
return
temperature = self.Temperature
eDensity = self.EDensity
em = self.Em
ndens = eDensity.size
ntemp = temperature.size
intens = copy.deepcopy(self.Intensity)
if 'errorMessage' in intens.keys():
print(' errorMessage: %s' % (intens['errorMessage']))
return
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:
if index < 0:
index = 0
dstr = ' - Density = %10.2e (cm$^{-3}$)' % (eDensity[index])
tstr = ' - T = %10.2e (K)' % (temperature[index])
intensity = intensity[index]
print(' temperature = %10.2e eDensity = %10.2e' %
(temperature[index], eDensity[index]))
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 = %10.2e = %10.2e' % (
index, temperature[index], eDensity[index], em[index])
intensity = intensity[index]
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
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:]]
# 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.' + str(rightDigits) + \
'f %12.2e %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 %12.4' + str(rightDigits) + \
'f %12.2e %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=False,
verbose=False,
plotFile=0,
em=0):
"""
Plot the line intensities. Uses `Intensity` if it already exists. If
not, call the `intensity` method.
Parameters
-----------
index: integer
specified which value of the temperature array or eDensity array to use.
default (index=-1) sets the specified value to the middle of the array
wvlRange: 2 element tuple, list or array determines the wavelength range
top: integer
specifies to plot only the top strongest lines, default = 10
linLog: str
default('lin') produces a plot where the intensity scale is linear
if set to 'log', produces a plot where the intensity scale is logarithmic
normalize: = 1 specifies whether to normalize to strongest line
default (relative = 0) specified that the intensities should be their calculated
values
plotFile:
default=0, the plot is not saved to a file
othewise, the plot is saved to the 'plotFile'
em: emission measure
if an Intensity attribute needs be created, then the emission measure is applied
"""
if hasattr(self, 'Spectroscopic'):
title = self.Spectroscopic
else:
title = ''
if not hasattr(self, 'Intensity'):
try:
self.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:
if index < 0:
index = 0
intensity = self.Intensity['intensity'][index]
dstr = ' - Density = %10.2e (cm$^{-3}$)' % (eDensity[index])
tstr = ' - T = %10.2e (K)' % (temperature[index])
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 = 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])
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])
intensity = self.Intensity['intensity'][index]
dstr = ' - Density = %10.2e (cm$^{-3}$)' % eDensity[index]
tstr = ' - T = %10.2e (K)' % temperature[index]
if wvlRange is not 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'
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
plt.figure()
ylabel = 'intensity'
if relative:
intensity = intensity / intensity[-1]
ylabel += ' (Relative)'
xlbl = 'Wavelength (' + self.Defaults['wavelength'] + ')'
ymin = 10.**(np.log10(intensity[0].min()).round(0) - 0.5)
plt.ion()
for idx in range(top):
xx = [wvl[idx], wvl[idx]]
if linLog == 'lin':
yy = [0., intensity[idx]]
plt.plot(xx, yy)
else:
yy = [ymin / 10., intensity[idx]]
plt.semilogy(xx, yy)
plt.xlabel(xlbl)
plt.ylabel(ylabel)
plt.title(title + tstr + dstr)
plt.tight_layout()
if wvlRange:
plt.axis([wvlRange[0], wvlRange[1], ymin, intensity.max()])
if plotFile:
plt.savefig(plotFile)
def intensityRatio(self, wvlRange=None, wvlRanges=None, top=10):
"""
Plot the intensity 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.
Parameters
-----------
wvlRange : array-like
Wavelength range, i.e. min and max
wvlRanges: a tuple, list or array that contains at least 2
2 element tuples, lists or arrays so that multiple
wavelength ranges can be specified
top : `int`
specifies to plot only the top strongest lines, default = 10
"""
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
fontsize=14
eDensity = self.EDensity
temperature = self.Temperature
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"]
# 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)
igvl=np.take(igvl,wvl[igvl].argsort())
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]]
igvlsort=np.take(igvl,np.argsort(maxIntens))
topLines=igvlsort[-top:]
maxWvl='%5.3f' % wvl[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
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 = self.EDensity
desc_str=' Density = %10.2e (cm)$^{-3}$' % self.EDensity[0]
elif ntemp == 1:
xvalues=self.EDensity
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
plt.ion()
# maxAll is an array
ymax = np.max(intensity[:, topLines[0]]/maxAll)
ymin = ymax
plt.figure()
ax = plt.subplot(111)
nxvalues=len(xvalues)
# reversing is necessary - otherwise, get a ymin=ymax and a matplotlib error
for iline in range(top-1, -1, -1):
tline=topLines[iline]
plt.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])
plt.text(xvalues[ixvalue], intensity[ixvalue, tline]/maxAll[ixvalue], text)
plt.xlim(xvalues.min(),xvalues.max())
plt.xlabel(xlabel,fontsize=fontsize)
plt.ylabel(ylabel,fontsize=fontsize)
if ndens == ntemp and ntemp > 1:
plt.text(0.07, 0.5,title, horizontalalignment='left', verticalalignment='center', fontsize=fontsize, transform = ax.transAxes)
ax2 = plt.twiny()
xlabelDen=r'Electron Density (cm$^{-3}$)'
plt.xlabel(xlabelDen, fontsize=fontsize)
plt.loglog(eDensity,intensity[:, topLines[top-1]]/maxAll, visible=False)
ax2.xaxis.tick_top()
plt.ylim(ymin/1.2, 1.2*ymax)
else:
plt.ylim(ymin/1.2, 1.2*ymax)
plt.title(title+desc_str,fontsize=fontsize)
plt.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(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
plt.figure()
ax = plt.subplot(111)
plt.loglog(xvalues,numIntens/denIntens)
plt.xlim(xvalues.min(),xvalues.max())
plt.xlabel(xlabel,fontsize=fontsize)
plt.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:
plt.text(0.07, 0.5,desc, horizontalalignment='left', verticalalignment='center', fontsize=fontsize, transform = ax.transAxes)
#
ax2 = plt.twiny()
xlabelDen=r'Electron Density (cm$^{-3}$)'
plt.xlabel(xlabelDen, fontsize=fontsize)
plt.loglog(eDensity,numIntens/denIntens, visible=False)
ax2.xaxis.tick_top()
else:
plt.title(desc,fontsize=fontsize)
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=False, verbose=False, plotFile=0, em=0 ):
"""
Plot the line intensities. Uses `Intensity` if it already exists. If
not, call the `intensity` method.
Parameters
-----------
index: integer
specified which value of the temperature array or eDensity array to use.
default (index=-1) sets the specified value to the middle of the array
wvlRange: 2 element tuple, list or array determines the wavelength range
top: integer
specifies to plot only the top strongest lines, default = 10
linLog: str
default('lin') produces a plot where the intensity scale is linear
if set to 'log', produces a plot where the intensity scale is logarithmic
normalize: = 1 specifies whether to normalize to strongest line
default (relative = 0) specified that the intensities should be their calculated
values
plotFile:
default=0, the plot is not saved to a file
othewise, the plot is saved to the 'plotFile'
em: emission measure
if an Intensity attribute needs be created, then the emission measure is applied
"""
if hasattr(self, 'Spectroscopic'):
title = self.Spectroscopic
else:
title = ''
if not hasattr(self, 'Intensity'):
try:
self.intensity(em=em)
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])
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])
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])
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'
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
plt.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 )
plt.ion()
for idx in range(top):
xx=[wvl[idx], wvl[idx]]
if linLog == 'lin':
yy=[0., intensity[idx]]
plt.plot(xx, yy)
else:
yy=[ymin/10., intensity[idx]]
plt.semilogy(xx, yy)
plt.xlabel(xlabel)
plt.ylabel(ylabel)
plt.title(title+tstr+dstr)
if wvlRange:
plt.axis([wvlRange[0], wvlRange[1], ymin, intensity.max()])
if plotFile:
plt.savefig(plotFile)
def intensityList(self, index=-1, wvlRange=None, wvlRanges=None, top=10, relative=0, outFile=0, rightDigits=4 ):
"""
List the line intensities. Checks to see if there is an existing Intensity attribute. If it exists, then those values are used.
Otherwise, the `intensity` method is called.
This method prints an ASCII table with the following columns:
1. Ion: the CHIANTI style notation for the ion, e.g. 'c_4' for C IV
2. lvl1: the lower level of the transition in the CHIANTI .elvlc file
3. lvl2: the upper level of the transition in the CHIANTI .elvlc file
4. lower: the notation, usually in LS coupling, of the lower fine
structure level
5. upper: the notation, usually in LS coupling, of the upper fine
structure level
6. Wvl(A): the wavelength of the transition in units as specified in
the chiantirc file.
7. Intensity
8. A value: the Einstein coefficient for spontaneous emission from
level 'j' to level 'i'
9. Obs: indicates whether the CHIANTI database considers this an
observed line or one obtained from theoretical energy levels
Regarding the intensity column, if 'flux' in the chiantirc file is set
to 'energy', the intensity is given by,
.. math::
I = \Delta E_{ij}n_jA_{ij}\mathrm{Ab}\\frac{1}{N_e}
\\frac{N(X^{+m})}{N(X)}\mathrm{EM},
in units of ergs cm\ :sup:`-2` s\ :sup:`-1` sr\ :sup:`-1`. If 'flux' is set to 'photon',
.. math::
I = n_jA_{ij}\mathrm{Ab}\\frac{1}{N_e}\\frac{N(X^{+m})}{N(X)}
\mathrm{EM},
where,
- :math:`\Delta E_{ij}` is the transition energy (ergs)
- :math:`n_j` is the fractions of ions in level :math:`j`
- :math:`A_{ij}` is the Einstein coefficient for spontaneous emission
from level :math:`j` to level :math:`i` (in s\ :sup:`-1`)
- :math:`\mathrm{Ab}` is the abundance of the specified element
relative to hydrogen
- :math:`N_e` is the electron density (in cm\ :sup:`-3`)
- :math:`N(X^{+m})/N(X)` is the fractional ionization of ion as a
function of temperature
- :math:`\mathrm{EM}` is the emission measure integrated along the
line-of-sight, :math:`\int\mathrm{d}l\,N_eN_H` (cm\ :sup:`-5`) where
:math:`N_H` is the density of hydrogen (neutral + ionized)
(cm\ :sup:`-3`)
Note that if `relative` is set, the line intensity is relative to the
strongest line and so the output will be unitless.
Parameters
-----------
index : `int`,optional
Index the temperature or eDensity array to use.
-1 (default) sets the specified value to the middle of the array
wvlRange : `tuple`
Wavelength range
wvlRanges : a tuple, list or array that contains at least 2
2 element tuples, lists or arrays so that multiple
wavelength ranges can be specified
top : `int`
Number of lines to plot, sorted by descending magnitude.
relative : `int`
specifies whether to normalize to strongest line
default (relative = 0) specified that the intensities should be
their calculated values
outFile : `str`
specifies the file that the intensities should be output to
default(outFile = 0) intensities are output to the terminal
rightDigits: `int`
specifies the format for the wavelengths for the number of digits
to right of the decimal place
"""
if not hasattr(self, 'Intensity'):
try:
self.intensity()
#TODO: specify what exception to catch! or omit the try, catch
except:
print(' intensities not calculated and emiss() is unable to calculate them')
print(' perhaps the temperature and/or eDensity are not set')
return
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 = %10.2e = %10.2e'%(index, temperature[index], eDensity[index], em[index])
intensity=intensity[index]
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
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:]]
# 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.' + str(rightDigits) + \
'f %12.2e %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 %12.4' + str(rightDigits) + \
'f %12.2e %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 intensityList(self, index=-1, wvlRange=None, wvlRanges=None, top=10, relative=0, outFile=0 ):
'''
List the line intensities
First, checks to see if there is an existing Intensity attribute. If it exists, then
'intensityList' uses those values. If it does not exist, then 'intensityList'
invokes the intensity() method to produce the attribute
Arguments.
----------
None
Keyword Arguments.
------------------
index: integer
specified which value of the temperature array or eDensity array to use.
default (index=-1) sets the specified value to the middle of the array
wvlRange: 2 element tuple, list or array determines the wavelength range
wvlRanges: a tuple, list or array that contains at least 2
2 element tuples, lists or arrays so that multiple
wavelength ranges can be specified
top: integer
specifies to plot only the top strongest lines, default = 10
normalize: = 1 specifies whether to normalize to strongest line
default (relative = 0) specified that the intensities should be their calculated
values
outFile: str
specifies the file that the intensities should be output to
default(outFile = 0) intensities are output to the terminal
Output
------
outputs an ascii table with the following columns
Ion: the CHIANTI style notation for the ion, such as, c_4 for C IV
lvl1: the lower level of the transition in the CHIANTI .elvlc file
lvl2: the upper level of the transition in the CHIANTI .elvlc file
lower: the notation, usually in LS coupling, of the lower fine structure level
upper: the notation, usually in LS coupling, of the upper fine structure level
Wvl(A): the wavelength of the transition, usually in Angstroms. However, other
units, such as 'nm' or 'kev' can be specified in the chiantirc file.
Intensity:
if flux set to 'energy' in chiantirc file (default)
intensity = (delta E)_ij * n_j * A_ij * Abund * Ioneq(T) * em
where (delta E)_ij is the transition energy in ergs
n_j: the fractions of ions in level 'j'
A_ij: the Einstein coefficient for spontaneous emission from level 'j' to
level 'i'
Abund: the abundance of the specified element relative to hydrogen 'H'
em: the line-of-sight emission measure -
the integral of n_e * n_H dl along the line-of-sight
n_e: the electron density (cm^-3)
n_H: the density of hydrogen (neutral + ionized) (cm^-3)
dl: the line of sight (cm)
if flux set to 'photon' in chiantirc file
intensity = n_j * A_ij * Abund * Ioneq(T) * em
default(relative = 0): the line intensity in ergs cm^-3 s^-1 str^-1
if relative > : the line intensity relative to the strongest line in the
specified wavelength range(s)
A value: the Einstein coefficient for spontaneous emission from level 'j' to
level 'i'
Obs: indicates whether the CHIANTI database considers this an observed line or one obtained
from theoretical energy levels
'''
#
#
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 = %10.2e = %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()