def getElementsInstance(dataDir=None, bindingEnergies=None, xcomFile=None):
if dataDir is None:
dataDir = DataDir.FISX_DATA_DIR
try:
from PyMca5.PyMcaDataDir import PYMCA_DATA_DIR as pymcaDataDir
from PyMca5 import getDataFile
except:
_logger.info("Using fisx shell constants and ratios")
pymcaDataDir = None
if bindingEnergies is None:
if pymcaDataDir is None:
bindingEnergies = os.path.join(dataDir, "BindingEnergies.dat")
else:
bindingEnergies = getDataFile("BindingEnergies.dat")
if xcomFile is None:
if pymcaDataDir is None:
xcomFile = os.path.join(dataDir, "XCOM_CrossSections.dat")
else:
xcomFile = getDataFile("XCOM_CrossSections.dat")
t0 = time.time()
instance = FisxElements(dataDir, bindingEnergies, xcomFile)
_logger.debug("Shell constants")
# the files should be taken from PyMca to make sure the same data are used
for key in ["K", "L", "M"]:
fname = instance.getShellConstantsFile(key)
if sys.version > '3.0':
# we have to make sure we have got a string
if hasattr(fname, "decode"):
fname = fname.decode("latin-1")
_logger.debug("Before %s", fname)
if pymcaDataDir is not None:
fname = getDataFile(key + "ShellConstants.dat")
else:
fname = os.path.join(os.path.dirname(fname),
key + "ShellConstants.dat")
instance.setShellConstantsFile(key, fname)
_logger.debug("After %s", instance.getShellConstantsFile(key))
_logger.debug("Radiative transitions")
for key in ["K", "L", "M"]:
fname = instance.getShellRadiativeTransitionsFile(key)
if sys.version > '3.0':
# we have to make sure we have got a string ...
if hasattr(fname, "decode"):
fname = fname.decode("latin-1")
_logger.debug("Before %s", fname)
if pymcaDataDir is not None:
fname = getDataFile(key + "ShellRates.dat")
else:
fname = os.path.join(os.path.dirname(fname),
key + "ShellRates.dat")
instance.setShellRadiativeTransitionsFile(key, fname)
_logger.debug("After %s ",
instance.getShellRadiativeTransitionsFile(key))
_logger.debug("Reading Elapsed = %s", time.time() - t0)
return instance
def getElementsInstance(dataDir=None, bindingEnergies=None, xcomFile=None):
if dataDir is None:
dataDir = DataDir.FISX_DATA_DIR
try:
from PyMca5.PyMcaDataDir import PYMCA_DATA_DIR as pymcaDataDir
from PyMca5 import getDataFile
except:
_logger.info("Using fisx shell constants and ratios")
pymcaDataDir = None
if bindingEnergies is None:
if pymcaDataDir is None:
bindingEnergies = os.path.join(dataDir, "BindingEnergies.dat")
else:
bindingEnergies = getDataFile("BindingEnergies.dat")
if xcomFile is None:
if pymcaDataDir is None:
xcomFile = os.path.join(dataDir, "XCOM_CrossSections.dat")
else:
xcomFile = getDataFile("XCOM_CrossSections.dat")
t0 = time.time()
instance = FisxElements(dataDir, bindingEnergies, xcomFile)
_logger.debug("Shell constants")
# the files should be taken from PyMca to make sure the same data are used
for key in ["K", "L", "M"]:
fname = instance.getShellConstantsFile(key)
if sys.version > '3.0':
# we have to make sure we have got a string
if hasattr(fname, "decode"):
fname = fname.decode("latin-1")
_logger.debug("Before %s", fname)
if pymcaDataDir is not None:
fname = getDataFile(key + "ShellConstants.dat")
else:
fname = os.path.join(os.path.dirname(fname),
key + "ShellConstants.dat")
instance.setShellConstantsFile(key, fname)
_logger.debug("After %s", instance.getShellConstantsFile(key))
_logger.debug("Radiative transitions")
for key in ["K", "L", "M"]:
fname = instance.getShellRadiativeTransitionsFile(key)
if sys.version > '3.0':
# we have to make sure we have got a string ...
if hasattr(fname, "decode"):
fname = fname.decode("latin-1")
_logger.debug("Before %s", fname)
if pymcaDataDir is not None:
fname = getDataFile(key + "ShellRates.dat")
else:
fname = os.path.join(os.path.dirname(fname), key + "ShellRates.dat")
instance.setShellRadiativeTransitionsFile(key, fname)
_logger.debug("After %s ", instance.getShellRadiativeTransitionsFile(key))
_logger.debug("Reading Elapsed = %s", time.time() - t0)
return instance
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, :]))
# 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()
# 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 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',
# 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("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(getDataFile("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
import numpy
log = numpy.log
exp = numpy.exp
ElementList = [
'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'
]
EPDL97_FILE = getDataFile("EPDL97_CrossSections.dat")
EADL97_FILE = getDataFile("EADL97_BindingEnergies.dat")
EPDL97_DICT = {}
for element in ElementList:
EPDL97_DICT[element] = {}
#initialize the dictionary, for the time being compatible with PyMca 4.3.0
EPDL97_DICT = {}
for element in ElementList:
EPDL97_DICT[element] = {}
EPDL97_DICT[element]['binding'] = {}
EPDL97_DICT[element]['EPDL97'] = {}
EPDL97_DICT[element]['original'] = True
# 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
sf = specfile.Specfile(getDataFile("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:
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# 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 sys
import os
from PyMca5.PyMcaIO import ConfigDict
from PyMca5 import getDataFile
dict = ConfigDict.ConfigDict()
dictfile = getDataFile("Scofield1973.dict")
dict.read(dictfile)
# 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 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'
'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']
EPDL97_FILE = getDataFile("EPDL97_CrossSections.dat")
EADL97_FILE = getDataFile("EADL97_BindingEnergies.dat")
EPDL97_DICT = {}
for element in ElementList:
EPDL97_DICT[element] = {}
#initialize the dictionnary, for the time being compatible with PyMca 4.3.0
EPDL97_DICT = {}
for element in ElementList:
EPDL97_DICT[element] = {}
EPDL97_DICT[element]['binding'] = {}
EPDL97_DICT[element]['EPDL97'] = {}
EPDL97_DICT[element]['original'] = True
#fill the dictionnary with the binding energies
# 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
sf=specfile.Specfile(getDataFile("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: