def testElementCrossSectionsReadout(self):
if DEBUG:
print()
print("Test XCOM Cross Sections Readout")
from PyMca5 import getDataFile
from PyMca5.PyMcaIO import specfile
xcomFile = getDataFile('XCOM_CrossSections.dat')
sf = specfile.Specfile(xcomFile)
for ele in ['Si', 'Fe', 'Pb', 'U']:
if DEBUG:
print("Testing element %s" % ele)
z = self._elements.getz(ele)
scan = sf[z-1]
xcomLabels = scan.alllabels()
self.assertTrue('ENERGY' in xcomLabels[0].upper())
self.assertTrue('COHERENT' in xcomLabels[1].upper())
self.assertTrue('COMPTON' in xcomLabels[2].upper())
self.assertTrue('PHOTO' in xcomLabels[-3].upper())
self.assertTrue('PAIR' in xcomLabels[-2].upper())
self.assertTrue('TOTAL' in xcomLabels[-1].upper())
xcomData = scan.data()
# WARNING: This call is to read XCOM data
# only in case energy is None the data are the same as
# those found later on in the 'xcom' key of the element.
data = self._elements.getelementmassattcoef(ele, energy=None)
# The original data are in the xcom key
data = self._elements.Element[ele]['xcom']
# Energy grid
self.assertTrue(numpy.allclose(data['energy'],
xcomData[0, :]))
# Test the different cross sections
self.assertTrue(numpy.allclose(data['coherent'],
xcomData[1, :]))
self.assertTrue(numpy.allclose(data['compton'],
xcomData[2, :]))
self.assertTrue(numpy.allclose(data['photo'],
xcomData[-3, :]))
self.assertTrue(numpy.allclose(data['pair'],
xcomData[-2, :]))
self.assertTrue(numpy.allclose(data['total'],
xcomData[-1, :]))
total = xcomData[1, :] + xcomData[2, :] +\
xcomData[-3, :] + xcomData[-2, :]
# Check the total is self-consistent
self.assertTrue(numpy.allclose(total, xcomData[-1, :]))
def _initializeBindingEnergies():
#read the specfile data
sf = specfile.Specfile(EADL97_FILE)
scan = sf[0]
labels = scan.alllabels()
data = scan.data()
scan = None
sf = None
i = -1
for element in ElementList:
if element == 'Md':
break
i += 1
EPDL97_DICT[element]['binding'] = {}
for j in range(len(labels)):
if j == 0:
#this is the atomic number
continue
label = labels[j].replace(" ", "").split("(")[0]
EPDL97_DICT[element]['binding'][label] = data[j, i]
from PyMca5 import PyMcaDataDir
dirname = PyMcaDataDir.PYMCA_DATA_DIR
inputfile = os.path.join(dirname, "KShellRates.dat")
if not os.path.exists(inputfile):
dirname = os.path.dirname(dirname)
inputfile = os.path.join(dirname, "KShellRates.dat")
if not os.path.exists(inputfile):
if dirname.lower().endswith(".zip"):
dirname = os.path.dirname(dirname)
inputfile = os.path.join(dirname, "KShellRates.dat")
if not os.path.exists(inputfile):
print("Cannot find inputfile ", inputfile)
raise IOError("Cannot find KShellRates.dat file")
sf = specfile.Specfile(os.path.join(dirname, "KShellRates.dat"))
ElementKShellTransitions = sf[0].alllabels()
ElementKShellRates = numpy.transpose(sf[0].data()).tolist()
ElementKAlphaTransitions = []
ElementKBetaTransitions = []
for transition in ElementKShellTransitions:
if transition[0] == 'K':
if transition[1] == 'L':
ElementKAlphaTransitions.append(transition)
else:
ElementKBetaTransitions.append(transition)
elif transition[0] == 'Z':
ElementKAlphaTransitions.append(transition)
ElementKBetaTransitions.append(transition)
else:
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
#############################################################################*/
__author__ = "V.A. Sole - ESRF Data Analysis"
__contact__ = "*****@*****.**"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import os
import numpy
from PyMca5.PyMcaIO import specfile
from PyMca5 import getDataFile
sf = specfile.Specfile(getDataFile("MShellRates.dat"))
ElementM1ShellTransitions = sf[0].alllabels()
ElementM2ShellTransitions = sf[1].alllabels()
ElementM3ShellTransitions = sf[2].alllabels()
ElementM4ShellTransitions = sf[3].alllabels()
ElementM5ShellTransitions = sf[4].alllabels()
ElementM1ShellRates = numpy.transpose(sf[0].data()).tolist()
ElementM2ShellRates = numpy.transpose(sf[1].data()).tolist()
ElementM3ShellRates = numpy.transpose(sf[2].data()).tolist()
ElementM4ShellRates = numpy.transpose(sf[3].data()).tolist()
ElementM5ShellRates = numpy.transpose(sf[4].data()).tolist()
sf = specfile.Specfile(getDataFile("MShellConstants.dat"))
ElementM1ShellConstants = sf[0].alllabels()
ElementM2ShellConstants = sf[1].alllabels()
ElementM3ShellConstants = sf[2].alllabels()
def Specfile(filename):
if BlissSpecFile.isBlissSpecFile(filename):
return BlissSpecFile.BlissSpecFile(filename)
if sys.version_info < (3, 0):
f = open(filename)
else:
f = open(filename, 'r', errors="ignore")
line0 = f.readline()
if filename.upper().endswith('DTA'):
#TwinMic single column file
line = line0 * 1
line = line.replace('\r', '')
line = line.replace('\n', '')
line = line.replace('\t', ' ')
s = line.split(' ')
if len(s) == 2:
if len(s[-1]) == 0:
try:
float(s[0])
f.close()
output = specfilewrapper(filename, dta=True)
return output
except:
#try to read in other way
pass
# this piece of code checks if we deal with a SPEC file
# Prior to any data, all lines have to be either empty or starting
# by the hash character.
line = line0
while (len(line)):
if len(line) > 1:
if line[0:2] == '#S':
if ('#SIGNALTYPE' in line) or \
('#SPECTRUM' in line):
line = ""
break
elif line[0] not in ['#', ' ', '\r']:
line = ""
break
try:
line = f.readline()
except:
line = ""
break
f.close()
# end of specfile identification
amptek = False
qxas = False
if len(line):
#it is a Specfile
_logger.debug("This looks as a specfile")
output = specfile.Specfile(filename)
elif SPX and ArtaxFileParser.isArtaxFile(filename):
_logger.debug("This looks as an Artax file")
output = ArtaxFileParser.ArtaxFileParser(filename)
else:
_logger.debug("this does not look as a specfile")
if len(line0) > 7:
if line0.startswith('$SPEC_ID') or\
line0.startswith('$DATE_MEA') or\
line0.startswith('$MEAS_TIM') or\
line0.startswith('$Core_ID') or\
line0.startswith('$Section_ID'):
qxas = True
if (not qxas) and line0.startswith('<<'):
amptek = True
if (not qxas) and (
not amptek) and Fit2DChiFileParser.isFit2DChiFile(filename):
return Fit2DChiFileParser.Fit2DChiFileParser(filename)
if (not qxas) and (
not amptek) and APSMEDFileParser.isAPSMEDFile(filename):
return APSMEDFileParser.APSMEDFileParser(filename)
if (not qxas) and (not amptek) and SRSFileParser.isSRSFile(filename):
_logger.debug("SRSFileParser")
return SRSFileParser.SRSFileParser(filename)
if (not qxas) and (
not amptek) and BAXSCSVFileParser.isBAXSCSVFile(filename):
_logger.debug("BAXSCSVFileParser")
return BAXSCSVFileParser.BAXSCSVFileParser(filename)
if (not qxas) and (not amptek) and \
OlympusCSVFileParser.isOlympusCSVFile(filename):
_logger.debug("OlympusCSVFileParser")
return OlympusCSVFileParser.OlympusCSVFileParser(filename)
if (not qxas) and (not amptek) and \
ThermoEMSFileParser.isThermoEMSFile(filename):
_logger.debug("ThermoEMSFileParser")
return ThermoEMSFileParser.ThermoEMSFileParser(filename)
if (not qxas) and (not amptek) and \
JcampFileParser.isJcampFile(filename):
_logger.debug("JcampFileParser")
return JcampFileParser.JcampFileParser(filename)
output = specfilewrapper(filename, amptek=amptek, qxas=qxas)
return output
def _initializeElement(element):
"""
_initializeElement(element)
Supposed to be of internal use.
Reads the file and loads all the relevant element information contained
int the EPDL97 file into the internal dictionary.
"""
#read the specfile data
sf = specfile.Specfile(EPDL97_FILE)
scan_index = ElementList.index(element)
if scan_index > 99:
#just to avoid a crash
#I do not expect any fluorescent analysis of these elements ...
scan_index = 99
scan = sf[scan_index]
labels = scan.alllabels()
data = scan.data()
scan = None
#fill the information into the dictionary
i = -1
for label0 in labels:
i += 1
label = label0.lower()
#translate the label to the PyMca keys
if ('coherent' in label) and ('incoherent' not in label):
EPDL97_DICT[element]['EPDL97']['coherent'] = data[i, :]
EPDL97_DICT[element]['EPDL97']['coherent'].shape = -1
continue
if ('incoherent' in label) and ('plus' not in label):
EPDL97_DICT[element]['EPDL97']['compton'] = data[i, :]
EPDL97_DICT[element]['EPDL97']['compton'].shape = -1
continue
if 'allother' in label:
EPDL97_DICT[element]['EPDL97']['all other'] = data[i, :]
EPDL97_DICT[element]['EPDL97']['all other'].shape = -1
continue
label = label.replace(" ", "").split("(")[0]
if 'energy' in label:
EPDL97_DICT[element]['EPDL97']['energy'] = data[i, :]
EPDL97_DICT[element]['EPDL97']['energy'].shape = -1
continue
if 'photoelectric' in label:
EPDL97_DICT[element]['EPDL97']['photo'] = data[i, :]
EPDL97_DICT[element]['EPDL97']['photo'].shape = -1
#a reference should not be expensive ...
EPDL97_DICT[element]['EPDL97']['photoelectric'] =\
EPDL97_DICT[element]['EPDL97']['photo']
continue
if 'total' in label:
EPDL97_DICT[element]['EPDL97']['total'] = data[i, :]
EPDL97_DICT[element]['EPDL97']['total'].shape = -1
continue
if label[0].upper() in ['K', 'L', 'M']:
#for the time being I do not use the other shells in PyMca
EPDL97_DICT[element]['EPDL97'][label.upper()] = data[i, :]
EPDL97_DICT[element]['EPDL97'][label.upper()].shape = -1
continue
EPDL97_DICT[element]['EPDL97']['pair'] = 0.0 *\
EPDL97_DICT[element]['EPDL97']['energy']
EPDL97_DICT[element]['EPDL97']['photo'] = \
EPDL97_DICT[element]['EPDL97']['total'] -\
EPDL97_DICT[element]['EPDL97']['compton']-\
EPDL97_DICT[element]['EPDL97']['coherent']-\
EPDL97_DICT[element]['EPDL97']['pair']
atomic_shells = ['M5', 'M4', 'M3', 'M2', 'M1', 'L3', 'L2', 'L1', 'K']
# with the new (short) version of the cross-sections file, "all other" contains all
# shells above the M5. Nevertheless, we calculate it
if scan_index > 17:
idx = EPDL97_DICT[element]['EPDL97']['all other'] > 0.0
delta = 0.0
for key in atomic_shells:
delta += EPDL97_DICT[element]['EPDL97'][key]
EPDL97_DICT[element]['EPDL97']['all other'] =\
(EPDL97_DICT[element]['EPDL97']['photo'] - delta) * idx
else:
EPDL97_DICT[element]['EPDL97']['all other'] = 0.0 * \
EPDL97_DICT[element]['EPDL97']['photo']
#take care of rounding problems
idx = EPDL97_DICT[element]['EPDL97']['all other'] < 0.0
EPDL97_DICT[element]['EPDL97']['all other'][idx] = 0.0
def Specfile(filename):
f = open(filename)
line0 = f.readline()
if filename.upper().endswith('DTA'):
#TwinMic single column file
line = line0 * 1
line = line.replace('\r', '')
line = line.replace('\n', '')
line = line.replace('\t', ' ')
s = line.split(' ')
if len(s) == 2:
if len(s[-1]) == 0:
try:
float(s[0])
f.close()
output = specfilewrapper(filename, dta=True)
f.close()
return output
except:
#try to read in other way
pass
line = line0
while (len(line)):
if len(line) > 1:
if line[0:2] == '#S':
if ('#SIGNALTYPE' in line) or \
('#SPECTRUM' in line):
line = ""
break
line = f.readline()
f.close()
amptek = False
qxas = False
if len(line):
#it is a Specfile
_logger.debug("This looks as a specfile")
output = specfile.Specfile(filename)
elif SPX and filename.upper().endswith("SPX"):
_logger.debug("This looks as an SPX file")
output = SPXFileParser.SPXFileParser(filename)
else:
_logger.debug("this does not look as a specfile")
if len(line0) > 7:
if line0.startswith('$SPEC_ID') or\
line0.startswith('$DATE_MEA') or\
line0.startswith('$MEAS_TIM') or\
line0.startswith('$Core_ID') or\
line0.startswith('$Section_ID'):
qxas = True
if (not qxas) and line0.startswith('<<'):
amptek = True
if (not qxas) and (
not amptek) and Fit2DChiFileParser.isFit2DChiFile(filename):
return Fit2DChiFileParser.Fit2DChiFileParser(filename)
if (not qxas) and (
not amptek) and APSMEDFileParser.isAPSMEDFile(filename):
return APSMEDFileParser.APSMEDFileParser(filename)
if (not qxas) and (not amptek) and SRSFileParser.isSRSFile(filename):
_logger.debug("SRSFileParser")
return SRSFileParser.SRSFileParser(filename)
if (not qxas) and (
not amptek) and BAXSCSVFileParser.isBAXSCSVFile(filename):
_logger.debug("BAXSCSVFileParser")
return BAXSCSVFileParser.BAXSCSVFileParser(filename)
if (not qxas) and (not amptek) and \
OlympusCSVFileParser.isOlympusCSVFile(filename):
_logger.debug("OlympusCSVFileParser")
return OlympusCSVFileParser.OlympusCSVFileParser(filename)
if (not qxas) and (not amptek) and \
ThermoEMSFileParser.isThermoEMSFile(filename):
_logger.debug("ThermoEMSFileParser")
return ThermoEMSFileParser.ThermoEMSFileParser(filename)
if (not qxas) and (not amptek) and \
JcampFileParser.isJcampFile(filename):
_logger.debug("JcampFileParser")
return JcampFileParser.JcampFileParser(filename)
output = specfilewrapper(filename, amptek=amptek, qxas=qxas)
return output
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
#############################################################################*/
__author__ = "V.A. Sole - ESRF Data Analysis"
__contact__ = "*****@*****.**"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import os
import numpy
from PyMca5 import getDataFile
from PyMca5.PyMcaIO import specfile
filename = getDataFile("BindingEnergies.dat")
sf = specfile.Specfile(filename)
ElementShells = sf[0].alllabels()
ElementBinding = numpy.transpose(sf[0].data()).tolist()
sf = None
Elements = [
'H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al',
'Si', 'P', 'S', 'Cl', 'Ar', 'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe',
'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb', 'Sr',
'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn',
'Sb', 'Te', 'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm',
'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W',
'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn',
'Fr', 'Ra', 'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf',
'Es', 'Fm', 'Md', 'No', 'Lr', 'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt'
]
filename = "BindingEnergies.dat"
dirname = PyMcaDataDir.PYMCA_DATA_DIR
inputfile = os.path.join(dirname, filename)
if not os.path.exists(inputfile):
dirname = os.path.dirname(dirname)
inputfile = os.path.join(dirname, filename)
if not os.path.exists(inputfile):
if dirname.lower().endswith(".zip"):
dirname = os.path.dirname(dirname)
inputfile = os.path.join(dirname, filename)
if not os.path.exists(inputfile):
print("Cannot find inputfile ", inputfile)
raise IOError("Cannot find BindingEnergies.dat file")
sf = specfile.Specfile(os.path.join(dirname, filename))
ElementShells = sf[0].alllabels()
ElementBinding = numpy.transpose(sf[0].data()).tolist()
sf = None
Elements = ['H', 'He',
'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne',
'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar',
'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe',
'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se',
'Br', 'Kr', 'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo',
'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn',
'Sb', 'Te', 'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce',
'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy',
'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W',
'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb',
import numpy
from PyMca5.PyMcaIO import specfile
from PyMca5 import PyMcaDataDir, getUserDataFile
dirname = PyMcaDataDir.PYMCA_DATA_DIR
inputfile = os.path.join(dirname, "LShellRates.dat")
if not os.path.exists(inputfile):
dirname = os.path.dirname(dirname)
inputfile = os.path.join(dirname, "LShellRates.dat")
if dirname.lower().endswith(".zip"):
dirname = os.path.dirname(dirname)
inputfile = os.path.join(dirname, "LShellRates.dat")
if not os.path.exists(inputfile):
print("Cannot find inputfile ",inputfile)
raise IOError("Cannot find LShellRates.dat file")
sf=specfile.Specfile(getUserDataFile(os.path.join(dirname, "LShellRates.dat")))
ElementL1ShellTransitions = sf[0].alllabels()
ElementL2ShellTransitions = sf[1].alllabels()
ElementL3ShellTransitions = sf[2].alllabels()
ElementL1ShellRates = numpy.transpose(sf[0].data()).tolist()
ElementL2ShellRates = numpy.transpose(sf[1].data()).tolist()
ElementL3ShellRates = numpy.transpose(sf[2].data()).tolist()
sf=specfile.Specfile(getUserDataFile(os.path.join(dirname, "LShellConstants.dat")))
ElementL1ShellConstants = sf[0].alllabels()
ElementL2ShellConstants = sf[1].alllabels()
ElementL3ShellConstants = sf[2].alllabels()
ElementL1ShellValues = numpy.transpose(sf[0].data()).tolist()
ElementL2ShellValues = numpy.transpose(sf[1].data()).tolist()
ElementL3ShellValues = numpy.transpose(sf[2].data()).tolist()
sf=None
filename = "BindingEnergies.dat"
dirname = PyMcaDataDir.PYMCA_DATA_DIR
inputfile = os.path.join(dirname, filename)
if not os.path.exists(inputfile):
dirname = os.path.dirname(dirname)
inputfile = os.path.join(dirname, filename)
if not os.path.exists(inputfile):
if dirname.lower().endswith(".zip"):
dirname = os.path.dirname(dirname)
inputfile = os.path.join(dirname, filename)
if not os.path.exists(inputfile):
print("Cannot find inputfile ", inputfile)
raise IOError("Cannot find BindingEnergies.dat file")
sf = specfile.Specfile(getUserDataFile(os.path.join(dirname, filename)))
ElementShells = sf[0].alllabels()
ElementBinding = numpy.transpose(sf[0].data()).tolist()
sf = None
Elements = [
'H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al',
'Si', 'P', 'S', 'Cl', 'Ar', 'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe',
'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb', 'Sr',
'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn',
'Sb', 'Te', 'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm',
'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W',
'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn',
'Fr', 'Ra', 'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf',
'Es', 'Fm', 'Md', 'No', 'Lr', 'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt'
]
