def load(self, ioneqName=None):
"""
Read temperature and ion fractions from a CHIANTI ".ioneq" file.
"""
if ioneqName is None:
ioneqName = chdata.Defaults['ioneqfile']
ioneqAll = io.ioneqRead(ioneqName)
self.Temperature = ioneqAll['ioneqTemperature']
self.Ioneq = ioneqAll['ioneqAll'][self.Z - 1]
def load(self, ioneqName=None):
"""
Read temperature and ion fractions from a CHIANTI ".ioneq" file.
"""
if ioneqName is None:
ioneqName = chdata.Defaults['ioneqfile']
ioneqAll = io.ioneqRead(ioneqName)
self.Temperature = ioneqAll['ioneqTemperature']
self.Ioneq = ioneqAll['ioneqAll'][self.Z - 1]
def ioneqOne(self):
'''
Provide the ionization equilibrium for the selected ion as a function of temperature.
returned in self.IoneqOne
'''
#
if hasattr(self, 'Temperature'):
temperature = self.Temperature
else:
return
#
if hasattr(self, 'IoneqAll'):
ioneqAll = self.IoneqAll
else:
ioneqAll = io.ioneqRead(ioneqname=self.Defaults['ioneqfile'])
self.ioneqAll = self.IoneqAll
#
ioneqTemperature = ioneqAll['ioneqTemperature']
Z = self.Z
stage = self.Ion
Dielectronic = self.Dielectronic
ioneqOne = np.zeros_like(temperature)
#
thisIoneq = ioneqAll['ioneqAll'][Z - 1,
stage - 1 + Dielectronic].squeeze()
gioneq = thisIoneq > 0.
goodt1 = self.Temperature >= ioneqTemperature[gioneq].min()
goodt2 = self.Temperature <= ioneqTemperature[gioneq].max()
goodt = np.logical_and(goodt1, goodt2)
y2 = splrep(np.log(ioneqTemperature[gioneq]),
np.log(thisIoneq[gioneq]),
s=0)
#
if goodt.sum() > 0:
if self.Temperature.size > 1:
gIoneq = splev(np.log(self.Temperature[goodt]), y2) #,der=0)
ioneqOne[goodt] = np.exp(gIoneq)
else:
gIoneq = splev(np.log(self.Temperature), y2)
ioneqOne = np.exp(gIoneq) * np.ones(self.NTempDen, 'float64')
self.IoneqOne = ioneqOne
else:
self.IoneqOne = np.zeros_like(self.Temperature)
def ioneqOne(self):
'''
Provide the ionization equilibrium for the selected ion as a function of temperature.
Similar to but not identical to ion.ioneqOne()
returned in self.IoneqOne
'''
#
if hasattr(self, 'Temperature'):
temperature = self.Temperature
else:
return
#
if hasattr(self, 'IoneqAll'):
ioneqAll = self.IoneqAll
else:
self.IoneqAll = ch_io.ioneqRead(
ioneqname=self.Defaults['ioneqfile'])
ioneqAll = self.IoneqAll
#
ioneqTemperature = ioneqAll['ioneqTemperature']
Z = self.Z
stage = self.stage
ioneqOne = np.zeros_like(temperature)
#
thisIoneq = ioneqAll['ioneqAll'][Z - 1, stage - 1].squeeze()
gioneq = thisIoneq > 0.
goodt1 = self.Temperature >= ioneqTemperature[gioneq].min()
goodt2 = self.Temperature <= ioneqTemperature[gioneq].max()
goodt = np.logical_and(goodt1, goodt2)
y2 = splrep(np.log(ioneqTemperature[gioneq]),
np.log(thisIoneq[gioneq]),
s=0)
#
if goodt.sum() > 0:
if self.Temperature.size > 1:
gIoneq = splev(np.log(self.Temperature[goodt]), y2) #,der=0)
ioneqOne[goodt] = np.exp(gIoneq)
else:
gIoneq = splev(np.log(self.Temperature), y2)
ioneqOne = np.exp(gIoneq)
ioneqOne = np.atleast_1d(ioneqOne)
self.IoneqOne = ioneqOne
else:
self.IoneqOne = np.zeros_like(self.Temperature)
def ioneqOne(self):
'''
Provide the ionization equilibrium for the selected ion as a function of temperature.
Similar to but not identical to ion.ioneqOne()
returned in self.IoneqOne
'''
#
if hasattr(self, 'Temperature'):
temperature = self.Temperature
else:
return
#
if hasattr(self, 'IoneqAll'):
ioneqAll = self.IoneqAll
else:
self.IoneqAll = ch_io.ioneqRead(ioneqname = self.Defaults['ioneqfile'])
ioneqAll = self.IoneqAll
#
ioneqTemperature = ioneqAll['ioneqTemperature']
Z = self.Z
stage = self.stage
ioneqOne = np.zeros_like(temperature)
#
thisIoneq = ioneqAll['ioneqAll'][Z-1,stage-1].squeeze()
gioneq = thisIoneq > 0.
goodt1 = self.Temperature >= ioneqTemperature[gioneq].min()
goodt2 = self.Temperature <= ioneqTemperature[gioneq].max()
goodt = np.logical_and(goodt1,goodt2)
y2 = splrep(np.log(ioneqTemperature[gioneq]),np.log(thisIoneq[gioneq]),s=0)
#
if goodt.sum() > 0:
if self.Temperature.size > 1:
gIoneq = splev(np.log(self.Temperature[goodt]),y2) #,der=0)
ioneqOne[goodt] = np.exp(gIoneq)
else:
gIoneq = splev(np.log(self.Temperature),y2)
ioneqOne = np.exp(gIoneq)
ioneqOne = np.atleast_1d(ioneqOne)
self.IoneqOne = ioneqOne
else:
self.IoneqOne = np.zeros_like(self.Temperature)
def ioneqOne(self):
'''Provide the ionization equilibrium for the selected ion as a function of temperature.
returned in self.IoneqOne
this is a duplicate of the method ion.ioneqOne '''
#
try:
temperature = self.Temperature
except:
return
#
try:
ioneqAll = self.IoneqAll
except:
self.IoneqAll = chio.ioneqRead(ioneqname = self.Defaults['ioneqfile'])
ioneqAll=self.IoneqAll
#
ioneqTemperature = ioneqAll['ioneqTemperature']
Z=self.Z
Ion=self.Ion
Dielectronic=self.Dielectronic
ioneqOne = np.zeros_like(temperature)
#
thisIoneq=ioneqAll['ioneqAll'][Z-1,Ion-1-Dielectronic].squeeze()
# thisIoneq = self.Ioneq
gioneq=thisIoneq > 0.
goodt1=self.Temperature >= ioneqTemperature[gioneq].min()
goodt2=self.Temperature <= ioneqTemperature[gioneq].max()
goodt=np.logical_and(goodt1,goodt2)
y2=interpolate.splrep(np.log(ioneqTemperature[gioneq]),np.log(thisIoneq[gioneq]),s=0)
#
if goodt.sum() > 0:
if self.Temperature.size > 1:
gIoneq=interpolate.splev(np.log(self.Temperature[goodt]),y2) #,der=0)
ioneqOne[goodt] = np.exp(gIoneq)
else:
gIoneq=interpolate.splev(np.log(self.Temperature),y2)
ioneqOne = np.exp(gIoneq)
else:
ioneqOne = 0.
#
self.IoneqOne = ioneqOne
def plot(self, stages=0, tRange=0, yr=0, oplot=False, label=1, title=1, bw=False, semilogx = 0, verbose=0):
'''
Plots the ionization equilibria.
self.plot(tRange=None, yr=None, oplot=False)
stages = sequence of ions to be plotted, neutral == 1, fully stripped == Z+1
tRange = temperature range, yr = ion fraction range
for overplotting:
oplot="ioneqfilename" such as 'mazzotta'
or if oplot=True or oplot=1 and a widget will come up so that a file can be selected.
bw, if True, the plot is made in black and white
'''
if hasattr(self, 'Ioneq'):
ioneq = getattr(self, 'Ioneq')
else:
print(' must first load or calculate and ionization equilibrium')
return
if bw:
linestyle = ['k-','k--', 'k-.', 'k:']
plt.rcParams['font.size'] = 16.
lw = 2
else:
linestyle = ['b-','r--', 'g-.', 'm:']
plt.rcParams['font.size'] = 14.
lw = 2
#
if not stages:
stages = range(1, self.Z+2)
elif min(stages) < 1 or max(stages) > self.Z+1:
stages = range(1, self.Z+2) # spectroscopic notation
if not tRange:
tRange = [self.Temperature.min(), self.Temperature.max()]
if not yr:
yr = [0.01, 1.1]
xyr = list(tRange)
xyr.extend(list(yr))
#
iz = stages[0]
if semilogx:
plt.semilogx(self.Temperature, ioneq[iz-1], linestyle[0], lw=lw)
else:
plt.loglog(self.Temperature, ioneq[iz-1], linestyle[0], lw=lw)
if label:
idx = self.Ioneq[iz-1] == self.Ioneq[iz-1].max()
if idx.sum() > 1:
jdx = np.arange(len(idx))
idx = int(jdx[idx].max())
ann = const.Ionstage[iz-1]
plt.annotate(ann, [self.Temperature[idx], 0.7*ioneq[iz-1, idx]], ha='center')
for iz in stages[1:]:
if semilogx:
plt.semilogx(self.Temperature, ioneq[iz-1], linestyle[0], lw=lw)
else:
plt.loglog(self.Temperature, ioneq[iz-1], linestyle[0], lw=lw)
if label:
idx = ioneq[iz-1] == ioneq[iz-1].max()
if idx.sum() > 1:
jdx = np.arange(len(idx))
idx = int(jdx[idx].mean())
ann = const.Ionstage[iz-1]
plt.annotate(ann, [self.Temperature[idx], 0.7*ioneq[iz-1, idx]], ha='center')
plt.xlabel('Temperature (K)')
plt.ylabel('Ion Fraction')
atitle = 'Chianti Ionization Equilibrium for '+const.El[self.Z-1].capitalize()
#
if oplot:
if isinstance(oplot,int):
result = io.ioneqRead(ioneqName='')
# print('keys = ', result.keys()
if result != False:
atitle += ' & '+ result['ioneqname'].replace('.ioneq', '')
atitle += ' '+linestyle[0]
for iz in stages:
plt.plot(result['ioneqTemperature'], result['ioneqAll'][self.Z-1, iz-1],linestyle[1], lw=lw)
elif type(oplot) == type('string'):
atitle += ' & ' + oplot
result = io.ioneqRead(ioneqName=oplot)
if result != False:
for iz in stages:
plt.plot(result['ioneqTemperature'], result['ioneqAll'][self.Z-1, iz-1],linestyle[1], lw=lw)
elif type(oplot) == type([]):
for iplot in range(len(oplot)):
result = io.ioneqRead(ioneqName=oplot[iplot])
# print 'keys = ', result.keys()
if result != False:
atitle += ' & '+oplot[iplot]+' '+linestyle[iplot%3]
for iz in stages:
plt.plot(result['ioneqTemperature'], result['ioneqAll'][self.Z-1, iz-1],linestyle[1], lw=lw)
else:
print(' oplot file not understood %s'%(oplot))
if title:
plt.title(atitle)
plt.tight_layout()
plt.axis(xyr)
- `rStar` : distance of the plasma from the source (in units of the source's radius)
- `distance` : distance from the central source
'''
import os
import glob
import traceback
import warnings
import ChiantiPy.tools.io as chio
try:
xuvtop = os.environ['XUVTOP']
Defaults = chio.defaultsRead()
Ip = chio.ipRead()
MasterList = chio.masterListRead()
IoneqAll = chio.ioneqRead(ioneqname=Defaults['ioneqfile'])
ChiantiVersion = chio.versionRead()
keywordArgs = [
'temperature', 'eDensity', 'hDensity', 'pDensity', 'radTemperature',
'rStar', 'distance'
]
AbundanceDefault = chio.abundanceRead(abundancename=Defaults['abundfile'])
AbundanceList = []
for fname in glob.glob(os.path.join(xuvtop, 'abundance', '*.abund')):
AbundanceList.append(os.path.splitext(os.path.basename(fname))[0])
Abundance = {
abundance: chio.abundanceRead(abundancename=abundance)
for abundance in AbundanceList
}
except (KeyError, IOError) as e:
- `rStar` : distance of the plasma from the source (in units of the source's radius)
- `distance` : distance from the central source
'''
import os
import glob
import traceback
import warnings
import ChiantiPy.tools.io as chio
try:
xuvtop = os.environ['XUVTOP']
Defaults = chio.defaultsRead()
Ip = chio.ipRead()
MasterList = chio.masterListRead()
IoneqAll = chio.ioneqRead(ioneqname=Defaults['ioneqfile'])
ChiantiVersion = chio.versionRead()
keywordArgs = ['temperature', 'eDensity', 'hDensity', 'pDensity', 'radTemperature',
'rStar', 'distance']
AbundanceDefault = chio.abundanceRead(abundancename=Defaults['abundfile'])
AbundanceList = []
for fname in glob.glob(os.path.join(xuvtop, 'abundance', '*.abund')):
AbundanceList.append(os.path.splitext(os.path.basename(fname))[0])
Abundance = {abundance: chio.abundanceRead(abundancename=abundance)
for abundance in AbundanceList}
except (KeyError, IOError) as e:
print(traceback.format_exc())
if isinstance(e, KeyError):
warnings.warn(
'XUVTOP environment variable not set. You will not be able to access any data from the CHIANTI database.')
def plot(self, stages=0, xr=0, yr=0, oplot=0, label=1, title=1, bw=0, semilogx = 0):
'''
Plots the ionization equilibria.
self.plot(xr=None, yr=None, oplot=False)
stages = sequence of ions to be plotted, neutral == 1, fully stripped == Z+1
xr = temperature range, yr = ion fraction range
for overplotting:
oplot="ioneqfilename" such as 'mazzotta'
or if oplot=True or oplot=1 and a widget will come up so that a file can be selected.
'''
if hasattr(self, 'Ioneq'):
ioneq = getattr(self, 'Ioneq')
else:
print(' must first load or calculate and ionization equilibrium')
return
if bw:
linestyle = ['k-','k--', 'k-.', 'k:']
plt.rcParams['font.size'] = 16.
lw = 2
else:
linestyle = ['b-','r--', 'g-.', 'm:']
plt.rcParams['font.size'] = 14.
lw = 2
#
if not stages:
stages = range(1, self.Z+2)
elif min(stages) < 1 or max(stages) > self.Z+1:
stages = range(1, self.Z+2) # spectroscopic notation
if not xr:
xr = [self.Temperature.min(), self.Temperature.max()]
if not yr:
yr = [0.01, 1.1]
xyr = list(xr)
xyr.extend(list(yr))
#
iz = stages[0]
if semilogx:
plt.semilogx(self.Temperature, ioneq[iz-1], linestyle[0], lw=lw)
else:
plt.loglog(self.Temperature, ioneq[iz-1], linestyle[0], lw=lw)
if label:
idx = self.Ioneq[iz-1] == self.Ioneq[iz-1].max()
if idx.sum() > 1:
jdx = np.arange(len(idx))
idx = int(jdx[idx].max())
ann = const.Ionstage[iz-1]
plt.annotate(ann, [self.Temperature[idx], 0.7*ioneq[iz-1, idx]], ha='center')
for iz in stages[1:]:
if semilogx:
plt.semilogx(self.Temperature, ioneq[iz-1], linestyle[0], lw=lw)
else:
plt.loglog(self.Temperature, ioneq[iz-1], linestyle[0], lw=lw)
if label:
idx = ioneq[iz-1] == ioneq[iz-1].max()
if idx.sum() > 1:
jdx = np.arange(len(idx))
idx = int(jdx[idx].mean())
ann = const.Ionstage[iz-1]
plt.annotate(ann, [self.Temperature[idx], 0.7*ioneq[iz-1, idx]], ha='center')
plt.xlabel('Temperature (K)')
plt.ylabel('Ion Fraction')
atitle = 'Chianti Ionization Equilibrium for '+const.El[self.Z-1].capitalize()
#
if oplot:
if oplot == 0:
result = io.ioneqRead(ioneqname='')
# print 'keys = ', result.keys()
if result != False:
atitle += ' & '+result['ioneqname'].replace('.ioneq', '')
atitle += ' '+linestyle[0]
for iz in stages:
plt.plot(result['ioneqTemperature'], result['ioneqAll'][self.Z-1, iz-1],linestyle[1], lw=lw)
elif type(oplot) == type('string'):
atitle += ' & ' + oplot
result = io.ioneqRead(ioneqname=oplot)
if result != False:
for iz in stages:
plt.plot(result['ioneqTemperature'], result['ioneqAll'][self.Z-1, iz-1],linestyle[1], lw=lw)
elif type(oplot) == type([]):
for iplot in range(len(oplot)):
result = io.ioneqRead(ioneqname=oplot[iplot])
# print 'keys = ', result.keys()
if result != False:
atitle += ' & '+oplot[iplot]+' '+linestyle[iplot%3]
for iz in stages:
plt.plot(result['ioneqTemperature'], result['ioneqAll'][self.Z-1, iz-1],linestyle[1], lw=lw)
else:
print(' oplot file not understood %s'%(oplot))
if title:
plt.title(atitle)
plt.tight_layout()
plt.axis(xyr)