class EDPluginControlDiffractionCTv1_0(EDPluginControl):
"""
This is the EDNA control plug-in for diffraction contrast tomography.
It is intented to run 2D integration provided by Fit2D for example and ....
"""
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputDiffractionCT)
self.m_strControlledPluginReadHeader = "EDPluginControlDCTReadHeaderv1_0"
self.m_edPluginReadHeader = None
self.m_strControlledPluginPowderIntegration = "EDPluginControlDCTPowderIntegrationv1_0"
self.m_edPluginPowderIntegration = None
self.m_xsDataDiffractionCTInstrument = None
self.m_xsDataDiffractionCTImage = None
self.m_xsDataFileInputImage = None
self.m_edPluginControlledPluginWriteSinogram = None
self.m_strControlledPluginWriteSinogram = "EDPluginDCTWriteSinogramv1_0"
self.m_xsDataFileInputPowderDiffraction = None
self.m_xsDataResultDiffractionCT = None
self.m_edPluginWriteSinogram = None
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.checkParameters")
self.checkMandatoryParameters(self.getDataInput(),
"Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getImage(),
"No path to input image")
self.checkMandatoryParameters(
self.getDataInput().getDestinationDirectory(),
"No path to destination directory")
self.checkMandatoryParameters(
self.getDataInput().getSinogramFileNamePrefix(),
"No sinogram prefix given")
self.checkMandatoryParameters(
self.getDataInput().getPowderDiffractionSubdirectory(),
"No subdirectory prefix for powder diffraction patterns")
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.preProcess")
# Load the execution plugin
self.m_edPluginReadHeader = self.loadPlugin(
self.m_strControlledPluginReadHeader)
self.m_edPluginPowderIntegration = self.loadPlugin(
self.m_strControlledPluginPowderIntegration)
self.m_edPluginWriteSinogram = self.loadPlugin(
self.m_strControlledPluginWriteSinogram)
# Set the input data for the read header plugin
xsDataInputReadHeader = XSDataInputReadHeader()
xsdataStringPathToImage = self.getDataInput().getImage().getPath()
self.m_xsDataFileInputImage = XSDataFile()
self.m_xsDataFileInputImage.setPath(xsdataStringPathToImage)
xsDataInputReadHeader.setInputFile(self.m_xsDataFileInputImage)
self.m_edPluginReadHeader.setDataInput(xsDataInputReadHeader)
def process(self, _edObject=None):
EDPluginControl.process(self)
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.process")
self.m_edPluginReadHeader.connectSUCCESS(self.doSuccessReadHeader)
self.m_edPluginReadHeader.connectFAILURE(self.doFailureReadHeader)
self.m_edPluginPowderIntegration.connectSUCCESS(
self.doSuccessPowderIntegration)
self.m_edPluginPowderIntegration.connectFAILURE(
self.doFailurePowderIntegration)
self.m_edPluginWriteSinogram.connectSUCCESS(
self.doSuccessWriteSinogram)
self.m_edPluginWriteSinogram.connectFAILURE(
self.doFailureWriteSinogram)
self.m_edPluginReadHeader.executeSynchronous()
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.postProcess")
self.setDataOutput(self.m_xsDataResultDiffractionCT)
def doSuccessReadHeader(self, _edPlugin=None):
EDVerbose.DEBUG(
"*** EDPluginControlDiffractionCTv1_0.doSuccessReadHeader")
self.retrieveSuccessMessages(
_edPlugin, "EDPluginControlDiffractionCTv1_0.doSuccessReadHeader")
# Translate dictionary to image and instrument objects
xsDataInputPowderIntegration = XSDataInputPowderIntegration()
self.m_xsDataDiffractionCTInstrument = XSDataDiffractionCTInstrument()
self.m_xsDataDiffractionCTImage = XSDataDiffractionCTImage()
xsDataDictionaryHeader = self.m_edPluginReadHeader.getDataOutput(
).getDictionary()
for xsDataKeyValuePair in xsDataDictionaryHeader.getKeyValuePair():
strKey = str(xsDataKeyValuePair.getKey().getValue())
strValue = str(xsDataKeyValuePair.getValue().getValue())
if (strKey == "_diffrn_radiation_wavelength"):
self.m_xsDataDiffractionCTInstrument.set_diffrn_radiation_wavelength(
XSDataWavelength(float(strValue)))
elif (strKey == "_pd_instr_dist_spec/detc"):
self.m_xsDataDiffractionCTInstrument.set_pd_instr_dist_spec_detc(
XSDataLength(float(strValue)))
elif (strKey == "_pd_meas_2theta_range_max"):
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_max(
XSDataAngle(float(strValue)))
elif (strKey == "_pd_meas_2theta_range_min"):
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_min(
XSDataAngle(float(strValue)))
elif (strKey == "_pd_meas_2theta_range_inc"):
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_inc(
XSDataAngle(float(strValue)))
elif (strKey == "_synchrotron_photon-flux"):
self.m_xsDataDiffractionCTInstrument.set_synchrotron_photon_flux(
XSDataFlux(float(strValue)))
elif (strKey == "_synchrotron_ring-intensity"):
self.m_xsDataDiffractionCTInstrument.set_synchrotron_ring_intensity(
XSDataDouble(float(strValue)))
elif (strKey == "_tomo_scan_ampl"):
self.m_xsDataDiffractionCTInstrument.set_tomo_scan_ampl(
XSDataAngle(float(strValue)))
elif (strKey == "_tomo_scan_type"):
self.m_xsDataDiffractionCTInstrument.set_tomo_scan_type(
XSDataString(strValue))
elif (strKey == "_tomo_spec_displ_rotation"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation(
XSDataAngle(float(strValue)))
elif (strKey == "_tomo_spec_displ_rotation_inc"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation_inc(
XSDataAngle(float(strValue)))
elif (strKey == "_tomo_spec_displ_x"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_x_inc"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_inc(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_x_max"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_max(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_x_min"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_min(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_z"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_z_inc"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_inc(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_z_max"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_max(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_z_min"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_min(
XSDataLength(float(strValue)))
elif (strKey == "_pd_instr_special_details_tilt_angle"):
self.m_xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_angle(
XSDataAngle(float(strValue)))
elif (strKey == "_pd_instr_special_details_tilt_rotation"):
self.m_xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_rotation(
XSDataAngle(float(strValue)))
elif (strKey == "_array_element_size[1]"):
self.m_xsDataDiffractionCTImage.set_array_element_size_1(
XSDataLength(float(strValue)))
elif (strKey == "_array_element_size[2]"):
self.m_xsDataDiffractionCTImage.set_array_element_size_2(
XSDataLength(float(strValue)))
elif (strKey == "_diffrn_detector_element.center[1]"):
self.m_xsDataDiffractionCTImage.set_diffrn_detector_element_center_1(
XSDataLength(float(strValue)))
elif (strKey == "_diffrn_detector_element.center[2]"):
self.m_xsDataDiffractionCTImage.set_diffrn_detector_element_center_2(
XSDataLength(float(strValue)))
## Here the tricky case of lists ....
# elif strKey.startswith("_pd_sum_2theta_range_max"):
# if strKey.find("[")>0:
# pyintIndex = int(strKey.split("[")[1].split("]")[0]) - 1 #gets the int that is between []
# else:
# pyintIndex = 0
# while len(self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()) < pyintIndex + 1:
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max().append(None)
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()[pyintIndex] = XSDataAngle(float(strValue))
# elif strKey.startswith("_pd_sum_2theta_range_min"):
# if strKey.find("[")>0:
# pyintIndex = int(strKey.split("[")[1].split("]")[0]) - 1 #gets the int that is between []
# else:
# pyintIndex = 0
# while len(self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()) < pyintIndex + 1:
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min().append(None)
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()[pyintIndex] = XSDataAngle(float(strValue))
##end Seems OK 20091023
elif (strKey == "_file_correction_image_dark-current"):
xsDataFileDark = XSDataFile()
xsDataFileDark.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_dark_current(
xsDataFileDark)
elif (strKey == "_file_correction_image_flat-field"):
xsDataFileFlat = XSDataFile()
xsDataFileFlat.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_flat_field(
xsDataFileFlat)
elif (strKey == "_file_correction_image-mask"):
xsDataFileMask = XSDataFile()
xsDataFileMask.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_mask(
xsDataFileMask)
elif (strKey == "_file_correction_spline_spatial-distortion"):
xsDataFileSpatialDist = XSDataFile()
xsDataFileSpatialDist.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_spline_spatial_distortion(
xsDataFileSpatialDist)
xsDataInputPowderIntegration.setImageParameters(
self.m_xsDataDiffractionCTImage)
xsDataInputPowderIntegration.setInstrumentParameters(
self.m_xsDataDiffractionCTInstrument)
xsDataInputPowderIntegration.setImageFile(self.m_xsDataFileInputImage)
self.m_edPluginPowderIntegration.setDataInput(
xsDataInputPowderIntegration)
self.m_edPluginPowderIntegration.executeSynchronous()
def doFailureReadHeader(self, _edPlugin=None):
EDVerbose.DEBUG(
"*** EDPluginControlDiffractionCTv1_0.doFailureReadHeader")
self.retrieveFailureMessages(
_edPlugin, "EDPluginControlDiffractionCTv1_0.doFailureReadHeader")
def doSuccessPowderIntegration(self, _edPlugin=None):
EDVerbose.DEBUG(
"*** EDPluginControlDiffractionCTv1_0.doSuccessPowderIntegration")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlDiffractionCTv1_0.doSuccessPowderIntegration")
self.m_xsDataResultDiffractionCT = XSDataResultDiffractionCT()
# Copy file to final destination and add path to result object
xsDataFileIntegratedIntensities = self.m_edPluginPowderIntegration.getDataOutput(
).getIntegratedIntensities()
EDVerbose.DEBUG("Path to cif: " +
xsDataFileIntegratedIntensities.getPath().getValue())
EDVerbose.DEBUG("%s" % xsDataFileIntegratedIntensities)
if (xsDataFileIntegratedIntensities is not None):
strOutputFilePath = xsDataFileIntegratedIntensities.getPath(
).getValue()
strDestinationDirectory = self.getDataInput(
).getDestinationDirectory().getPath().getValue()
strPowderDiffractionSubdirectory = self.getDataInput(
).getPowderDiffractionSubdirectory().getValue()
if not os.path.isdir(strDestinationDirectory):
os.mkdir(strDestinationDirectory)
if self.m_xsDataDiffractionCTInstrument.get_tomo_scan_type(
).getValue().lower() in ["flat", "spiral"]:
# pyintLineNumber = int( abs( float( self.cif[ "_tomo_spec_displ_rotation" ] ) / float( self.cif[ "_tomo_spec_displ_rotation_inc" ] ) ) )
pyintLineNumber = int(
abs(self.m_xsDataDiffractionCTInstrument.
get_tomo_spec_displ_rotation().getValue()) /
self.m_xsDataDiffractionCTInstrument.
get_tomo_spec_displ_rotation_inc().getValue())
elif self.m_xsDataDiffractionCTInstrument.get_tomo_scan_type(
).getValue().lower(
) == "mapping": #I agree mappings are not sinograms but the really looks like, no ?
# pyintLineNumber = int( abs( ( float( self.cif[ "_tomo_spec_displ_z" ]) - float ( self.cif [ "_tomo_spec_displ_z_min" ] ) ) / float( self.cif["_tomo_spec_displ_z_inc"] ) ) )
pyintLineNumber = int(
abs(self.m_xsDataDiffractionCTInstrument.
get_tomo_spec_displ_z().getValue() -
self.m_xsDataDiffractionCTInstrument.
get_tomo_spec_displ_z_min().getValue()) /
self.m_xsDataDiffractionCTInstrument.
get_tomo_spec_displ_z_inc().getValue())
else:
pyintLineNumber = None
if pyintLineNumber is not None:
pystrDestinationSubDir = "%s%04i" % (
strPowderDiffractionSubdirectory, pyintLineNumber)
strDestinationDirectoryWithSub = os.path.join(
strDestinationDirectory, pystrDestinationSubDir)
strDestinationFilePath = os.path.join(
strDestinationDirectoryWithSub,
os.path.basename(strOutputFilePath))
if not os.path.isdir(
os.path.join(strDestinationDirectoryWithSub)):
os.mkdir(strDestinationDirectoryWithSub)
EDVerbose.DEBUG("Full path should be now: %s" %
strDestinationFilePath)
else:
EDVerbose.DEBUG(
"No modification of the output directory: I was not able to determine on which line of the sinogram I am."
)
strDestinationFilePath = os.path.abspath(
os.path.join(strDestinationDirectory,
EDUtilsFile.getBaseName(strOutputFilePath)))
EDUtilsFile.copyFile(strOutputFilePath, strDestinationFilePath)
xsDataFileDestination = XSDataFile()
xsDataFileDestination.setPath(XSDataString(strDestinationFilePath))
self.m_xsDataResultDiffractionCT.setIntegratedIntensities(
xsDataFileDestination)
xsDataPathSinogramDirectory = XSDataFile()
xsDataPathSinogramDirectory.setPath(
XSDataString(strDestinationDirectory))
xsDataInputWriteSinogram = XSDataInputWriteSinogram()
xsDataInputWriteSinogram.setSinogramDirectory(
xsDataPathSinogramDirectory)
xsDataInputWriteSinogram.setIntegratedIntensities(
xsDataFileDestination)
xsDataInputWriteSinogram.setSinogramFileNamePrefix(
self.getDataInput().getSinogramFileNamePrefix())
self.m_edPluginWriteSinogram.setDataInput(xsDataInputWriteSinogram)
self.m_edPluginWriteSinogram.executeSynchronous()
def doFailurePowderIntegration(self, _edPlugin=None):
EDVerbose.DEBUG(
"*** EDPluginControlDiffractionCTv1_0.doFailurePowderIntegration")
self.retrieveFailureMessages(
_edPlugin,
"EDPluginControlDiffractionCTv1_0.doFailurePowderIntegration")
def doSuccessWriteSinogram(self, _edPlugin=None):
EDVerbose.DEBUG(
"*** EDPluginControlDiffractionCTv1_0.doSuccessWriteSinogram")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlDiffractionCTv1_0.doSuccessWriteSinogram")
xsDataResultWriteSinogram = self.m_edPluginWriteSinogram.getDataOutput(
)
if (xsDataResultWriteSinogram is not None):
self.m_xsDataResultDiffractionCT.setSinogramFile(
xsDataResultWriteSinogram.getSinogramFile())
def doFailureWriteSinogram(self, _edPlugin=None):
EDVerbose.DEBUG(
"*** EDPluginControlDiffractionCTv1_0.doFailureWriteSinogram")
self.retrieveFailureMessages(
_edPlugin,
"EDPluginControlDiffractionCTv1_0.doFailureWriteSinogram")
def setup(self, _listInput=[], _mode="offline"):
"""Configure the various options"""
bOK = False
if _listInput == []:
_listInput = [os.getcwd()]
while not bOK:
strtmp = raw_input(
"What are the input directories (mandatory, space separated) %s: "
% _listInput).strip()
if len(strtmp) > 0:
bAllExists = True
lstTemp = shlex.split(strtmp)
for oneDir in shlex.split(strtmp):
if not os.path.exists(oneDir):
EDVerbose.screen("No such file or directory: %s" %
oneDir)
bAllExists = False
if bAllExists is True:
self.listInput = lstTemp
bOK = True
else:
self.listInput = _listInput
bOK = True
bOK = False
while not bOK:
strtmp = raw_input(
"What is operation mode [offline|online|all] (mandatory: %s): "
% _mode).strip().lower()
if len(strtmp) > 0:
bOK = True
if strtmp == "offline":
self.bNewerOnly = False
self.strMode = "OffLine"
elif strtmp == "online":
self.bNewerOnly = True
self.strMode = "dirwatch"
elif strtmp == "all":
self.bNewerOnly = False
self.strMode = "dirwatch"
else:
bOK = False
bOK = False
while not bOK:
strtmp = raw_input(
"What is the destination directory (mandatory): ").strip()
if os.path.isdir(strtmp):
self.destinationDirectory = XSDataFile()
self.destinationDirectory.setPath(
XSDataString(os.path.abspath(strtmp)))
bOK = True
bOK = False
while not bOK:
strtmp = raw_input(
"What is the sinogram filename prefix (mandatory): ").strip()
if strtmp != "":
self.sinogramFileNamePrefix = XSDataString(strtmp)
bOK = True
bOK = False
while not bOK:
strtmp = raw_input(
"What is the powder diffraction subdirectory (mandatory): "
).strip()
if strtmp != "":
self.powderDiffractionSubdirectory = XSDataString(strtmp)
bOK = True
strtmp = raw_input(
"What is the powder diffraction output format (CHI or CIF, if any ): "
).strip().lower()
if strtmp.find("cif") >= 0:
self.powderDiffractionFormat = XSDataString("cif")
elif strtmp.find("chi") >= 0:
self.powderDiffractionFormat = XSDataString("chi")
strtmp = raw_input("Process all files ending with: ").strip()
if len(strtmp) > 0:
for oneExt in shlex.split(strtmp):
self.listExtensions.append(oneExt)
strtmp = raw_input("Exclude all files starting with: ").strip()
if len(strtmp) > 0:
for oneExt in shlex.split(strtmp):
self.listExcludedPrefix.append(oneExt)
strtmp = raw_input(
"Do you want to over-ride metadata from the headers [y|N]: "
).strip().lower()
if len(strtmp) > 0 and strtmp[0] == "y":
strtmp = raw_input("What is the flat field image: ").strip()
if os.path.isfile(strtmp):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
flatFieldImage = XSDataFile()
flatFieldImage.setPath(XSDataString(os.path.abspath(strtmp)))
self.forceImage.set_file_correction_image_flat_field(
flatFieldImage)
strtmp = raw_input("What is the dark current image: ").strip()
if os.path.isfile(strtmp):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
darkCurrentImage = XSDataFile()
darkCurrentImage.setPath(XSDataString(os.path.abspath(strtmp)))
self.forceImage.set_file_correction_image_dark_current(
darkCurrentImage)
strtmp = raw_input("What is the mask file: ").strip()
if os.path.isfile(strtmp):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
maskFile = XSDataFile()
maskFile.setPath(XSDataString(strtmp))
self.forceImage.set_file_correction_image_mask(maskFile)
strtmp = raw_input("What is the spline file: ").strip()
if os.path.isfile(strtmp):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
splineFile = XSDataFile()
splineFile.setPath(XSDataString(os.path.abspath(strtmp)))
self.forceImage.set_file_correction_spline_spatial_distortion(
splineFile)
strtmp = raw_input(
"What is the wavelength (like 0.7 A): ").replace(
"(", "").replace(")", "").strip()
w = strtmp.split()
if len(w) > 0:
try:
f = float(w[0])
except ValueError:
print("unable to understand what you said, skipping")
else:
wavelength = XSDataWavelength()
wavelength.setValue(f)
if len(w) == 2:
wavelength.setUnit(XSDataString(w[1]))
if self.forceInstrument is None:
self.forceInstrument = XSDataDiffractionCTInstrument()
self.forceInstrument.set_diffrn_radiation_wavelength(
wavelength)
strtmp = raw_input(
"What is the distance between the sample and the detector along the beam: "
).replace("(", "").replace(")", "").strip()
w = strtmp.split()
if len(w) > 0:
try:
f = float(w[0])
except ValueError:
print("unable to understand what you said, skipping")
else:
distance = XSDataLength()
distance.setValue(f)
if len(w) == 2:
distance.setUnit(XSDataString(w[1]))
if self.forceInstrument is None:
self.forceInstrument = XSDataDiffractionCTInstrument()
self.forceInstrument.set_pd_instr_dist_spec_detc(distance)
strtmp = raw_input(
"What is the pixel size (like 52.8 um 53.2 um): ").replace(
"(", "").replace(")", "").strip()
w = strtmp.split()
if len(w) > 0:
xsdata1 = None
xsdata2 = None
if len(w) == 4:
try:
f1 = float(w[0])
f2 = float(w[2])
except ValueError:
print "Unable to convert to float !!! skipping"
else:
xsdata1 = XSDataLength()
xsdata1.setValue(f1)
xsdata1.setUnit(XSDataString(w[1]))
xsdata2 = XSDataLength()
xsdata2.setValue(f2)
xsdata2.setUnit(XSDataString(w[3]))
elif len(w) == 2:
try:
f1 = float(w[0])
f2 = float(w[1])
except ValueError:
print "Unable to convert to float !!! skipping"
else:
xsdata1 = XSDataLength()
xsdata1.setValue(f1)
xsdata2 = XSDataLength()
xsdata2.setValue(f2)
else:
print("unable to understand what you said, skipping")
if (xsdata1 is not None) and (xsdata2 is not None):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
self.forceImage.set_array_element_size_1(xsdata1)
self.forceImage.set_array_element_size_2(xsdata2)
strtmp = raw_input(
"What is the beam center in distance, not pixels (like 53.5 mm 48.2 mm): "
).strip().replace("(", "").replace(")", "").strip()
w = strtmp.split()
if len(w) > 0:
xsdata1 = None
xsdata2 = None
if len(w) == 4:
try:
f1 = float(w[0])
f2 = float(w[2])
except ValueError:
print "Unable to convert to float !!! skipping"
else:
xsdata1 = XSDataLength()
xsdata1.setValue(f1)
xsdata1.setUnit(XSDataString(w[1]))
xsdata2 = XSDataLength()
xsdata2.setValue(f2)
xsdata2.setUnit(XSDataString(w[3]))
elif len(w) == 2:
try:
f1 = float(w[0])
f2 = float(w[1])
except ValueError, IndexError:
print "Unable to convert to float !!! skipping"
else:
xsdata1 = XSDataLength()
xsdata1.setValue(f1)
xsdata2 = XSDataLength()
xsdata2.setValue(f2)
else:
print("unable to understand what you said, skipping")
if (xsdata1 is not None) and (xsdata2 is not None):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
self.forceImage.set_diffrn_detector_element_center_1(
xsdata1)
self.forceImage.set_diffrn_detector_element_center_2(
xsdata2)
strtmp = raw_input("What is the detector tilt angle: ").strip()
tiltAngle = None
try:
tiltAngle = XSDataAngle(float(strtmp))
except ValueError:
print("unable to understand what you said, skipping")
else:
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
self.forceImage.set_pd_instr_special_details_tilt_angle(
tiltAngle)
strtmp = raw_input("What is the tilt plan rotation: ").strip()
tiltRotation = None
try:
tiltRotation = XSDataAngle(float(strtmp))
except ValueError:
print("unable to understand what you said, skipping")
else:
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
self.forceImage.set_pd_instr_special_details_tilt_rotation(
tiltRotation)
strtmp = raw_input(
"What is the number of fast motor steps (you will have n+1 points): "
).strip()
try:
self.fastMotorSteps = int(strtmp)
except ValueError:
fastMotorSteps = None
else:
if self.forceInstrument is None:
self.forceInstrument = XSDataDiffractionCTInstrument()
self.forceInstrument.set_tomo_spec_displ_x_max(
XSDataLength(self.fastMotorSteps))
self.forceInstrument.set_tomo_spec_displ_x_min(XSDataLength(0))
self.forceInstrument.set_tomo_spec_displ_x_inc(XSDataLength(1))
self.forceInstrument.set_tomo_scan_type(XSDataString("flat"))
strtmp = raw_input(
"What is the number of slow motor steps (you will have n+1 points): "
).strip()
try:
self.slowMotorSteps = int(strtmp)
except ValueError:
self.slowMotorSteps = None
else:
if self.forceInstrument is None:
self.forceInstrument = XSDataDiffractionCTInstrument()
self.forceInstrument.set_tomo_scan_ampl(
XSDataLength(self.slowMotorSteps))
self.forceInstrument.set_tomo_spec_displ_rotation_inc(
XSDataLength(1))
self.forceInstrument.set_tomo_scan_type(XSDataString("flat"))
strtmp = raw_input(
"What is the index offset of your images: ").strip()
try:
self.indexOffset = int(strtmp)
except ValueError:
print("unable to understand what you said, skipping")
def doSuccessReadHeader(self, _edPlugin=None):
EDVerbose.DEBUG(
"*** EDPluginControlDiffractionCTv1_0.doSuccessReadHeader")
self.retrieveSuccessMessages(
_edPlugin, "EDPluginControlDiffractionCTv1_0.doSuccessReadHeader")
# Translate dictionary to image and instrument objects
xsDataInputPowderIntegration = XSDataInputPowderIntegration()
self.m_xsDataDiffractionCTInstrument = XSDataDiffractionCTInstrument()
self.m_xsDataDiffractionCTImage = XSDataDiffractionCTImage()
xsDataDictionaryHeader = self.m_edPluginReadHeader.getDataOutput(
).getDictionary()
for xsDataKeyValuePair in xsDataDictionaryHeader.getKeyValuePair():
strKey = str(xsDataKeyValuePair.getKey().getValue())
strValue = str(xsDataKeyValuePair.getValue().getValue())
if (strKey == "_diffrn_radiation_wavelength"):
self.m_xsDataDiffractionCTInstrument.set_diffrn_radiation_wavelength(
XSDataWavelength(float(strValue)))
elif (strKey == "_pd_instr_dist_spec/detc"):
self.m_xsDataDiffractionCTInstrument.set_pd_instr_dist_spec_detc(
XSDataLength(float(strValue)))
elif (strKey == "_pd_meas_2theta_range_max"):
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_max(
XSDataAngle(float(strValue)))
elif (strKey == "_pd_meas_2theta_range_min"):
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_min(
XSDataAngle(float(strValue)))
elif (strKey == "_pd_meas_2theta_range_inc"):
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_inc(
XSDataAngle(float(strValue)))
elif (strKey == "_synchrotron_photon-flux"):
self.m_xsDataDiffractionCTInstrument.set_synchrotron_photon_flux(
XSDataFlux(float(strValue)))
elif (strKey == "_synchrotron_ring-intensity"):
self.m_xsDataDiffractionCTInstrument.set_synchrotron_ring_intensity(
XSDataDouble(float(strValue)))
elif (strKey == "_tomo_scan_ampl"):
self.m_xsDataDiffractionCTInstrument.set_tomo_scan_ampl(
XSDataAngle(float(strValue)))
elif (strKey == "_tomo_scan_type"):
self.m_xsDataDiffractionCTInstrument.set_tomo_scan_type(
XSDataString(strValue))
elif (strKey == "_tomo_spec_displ_rotation"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation(
XSDataAngle(float(strValue)))
elif (strKey == "_tomo_spec_displ_rotation_inc"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation_inc(
XSDataAngle(float(strValue)))
elif (strKey == "_tomo_spec_displ_x"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_x_inc"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_inc(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_x_max"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_max(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_x_min"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_min(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_z"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_z_inc"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_inc(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_z_max"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_max(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_z_min"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_min(
XSDataLength(float(strValue)))
elif (strKey == "_pd_instr_special_details_tilt_angle"):
self.m_xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_angle(
XSDataAngle(float(strValue)))
elif (strKey == "_pd_instr_special_details_tilt_rotation"):
self.m_xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_rotation(
XSDataAngle(float(strValue)))
elif (strKey == "_array_element_size[1]"):
self.m_xsDataDiffractionCTImage.set_array_element_size_1(
XSDataLength(float(strValue)))
elif (strKey == "_array_element_size[2]"):
self.m_xsDataDiffractionCTImage.set_array_element_size_2(
XSDataLength(float(strValue)))
elif (strKey == "_diffrn_detector_element.center[1]"):
self.m_xsDataDiffractionCTImage.set_diffrn_detector_element_center_1(
XSDataLength(float(strValue)))
elif (strKey == "_diffrn_detector_element.center[2]"):
self.m_xsDataDiffractionCTImage.set_diffrn_detector_element_center_2(
XSDataLength(float(strValue)))
## Here the tricky case of lists ....
# elif strKey.startswith("_pd_sum_2theta_range_max"):
# if strKey.find("[")>0:
# pyintIndex = int(strKey.split("[")[1].split("]")[0]) - 1 #gets the int that is between []
# else:
# pyintIndex = 0
# while len(self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()) < pyintIndex + 1:
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max().append(None)
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()[pyintIndex] = XSDataAngle(float(strValue))
# elif strKey.startswith("_pd_sum_2theta_range_min"):
# if strKey.find("[")>0:
# pyintIndex = int(strKey.split("[")[1].split("]")[0]) - 1 #gets the int that is between []
# else:
# pyintIndex = 0
# while len(self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()) < pyintIndex + 1:
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min().append(None)
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()[pyintIndex] = XSDataAngle(float(strValue))
##end Seems OK 20091023
elif (strKey == "_file_correction_image_dark-current"):
xsDataFileDark = XSDataFile()
xsDataFileDark.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_dark_current(
xsDataFileDark)
elif (strKey == "_file_correction_image_flat-field"):
xsDataFileFlat = XSDataFile()
xsDataFileFlat.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_flat_field(
xsDataFileFlat)
elif (strKey == "_file_correction_image-mask"):
xsDataFileMask = XSDataFile()
xsDataFileMask.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_mask(
xsDataFileMask)
elif (strKey == "_file_correction_spline_spatial-distortion"):
xsDataFileSpatialDist = XSDataFile()
xsDataFileSpatialDist.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_spline_spatial_distortion(
xsDataFileSpatialDist)
xsDataInputPowderIntegration.setImageParameters(
self.m_xsDataDiffractionCTImage)
xsDataInputPowderIntegration.setInstrumentParameters(
self.m_xsDataDiffractionCTInstrument)
xsDataInputPowderIntegration.setImageFile(self.m_xsDataFileInputImage)
self.m_edPluginPowderIntegration.setDataInput(
xsDataInputPowderIntegration)
self.m_edPluginPowderIntegration.executeSynchronous()
class EDPluginControlDiffractionCTv1_1(EDPluginControl):
"""
This is the EDNA control plug-in for diffraction contrast tomography.
It is intented to run 2D integration provided by Fit2D for example and ....
"""
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputDiffractionCT)
self.strControlledPluginReadHeader = "EDPluginControlDCTReadHeaderv1_0"
self.edPluginReadHeader = None
self.strControlledPluginPowderIntegration = "EDPluginControlDCTPowderIntegrationv1_1"
self.edPluginPowderIntegration = None
self.xsDataDiffractionCTInstrument = None
self.xsDataDiffractionCTImage = None
self.xsDataFileInputImage = None
self.strControlledPluginHDF5MapSpectra = "EDPluginHDF5MapOfSpectrav10"
self.strControlledPluginExportAsciiPowder = "EDPluginExportAsciiPowderv1_0"
self.xsDataFileInputPowderDiffraction = None
self.xsDataResultDiffractionCT = None
self.edPluginHDF5MapSpectra = None
self.edPluginExportAsciiPowder = None
self.xsdForceImageParam = None
self.xsdForceScanParam = None
self.powderDiffractionFormat = "edf" #default output format
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_1.checkParameters")
self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getImage(), "No path to input image")
self.checkMandatoryParameters(self.getDataInput().getDestinationDirectory(), "No path to destination directory")
self.checkMandatoryParameters(self.getDataInput().getSinogramFileNamePrefix(), "No sinogram prefix given")
self.checkMandatoryParameters(self.getDataInput().getPowderDiffractionSubdirectory(), "No subdirectory prefix for powder diffraction patterns")
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_1.preProcess")
# Load the execution plugin
self.edPluginReadHeader = self.loadPlugin(self.strControlledPluginReadHeader)
self.edPluginPowderIntegration = self.loadPlugin(self.strControlledPluginPowderIntegration)
sdi = self.getDataInput()
self.xsdForceImageParam = sdi.getOverrideImageParam()
self.xsdForceScanParam = sdi.getOverrideScanParam()
if sdi.getPowderDiffractionFormat() is not None:
self.powderDiffractionFormat = sdi.getPowderDiffractionFormat().getValue()
# Set the input data for the read header plugin
xsDataInputReadHeader = XSDataInputReadHeader()
xsdataStringPathToImage = sdi.getImage().getPath()
self.xsDataFileInputImage = XSDataFile()
self.xsDataFileInputImage.setPath(xsdataStringPathToImage)
xsDataInputReadHeader.setInputFile(self.xsDataFileInputImage)
self.edPluginReadHeader.setDataInput(xsDataInputReadHeader)
def process(self, _edObject=None):
EDPluginControl.process(self)
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_1.process")
self.edPluginReadHeader.connectSUCCESS(self.doSuccessReadHeader)
self.edPluginReadHeader.connectFAILURE(self.doFailureReadHeader)
self.edPluginPowderIntegration.connectSUCCESS(self.doSuccessPowderIntegration)
self.edPluginPowderIntegration.connectFAILURE(self.doFailurePowderIntegration)
self.edPluginReadHeader.executeSynchronous()
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_1.postProcess")
self.setDataOutput(self.xsDataResultDiffractionCT)
def doSuccessReadHeader(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_1.doSuccessReadHeader")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlDiffractionCTv1_1.doSuccessReadHeader")
# Translate dictionary to image and instrument objects
xsDataInputPowderIntegration = XSDataInputPowderIntegration()
self.xsDataDiffractionCTInstrument = XSDataDiffractionCTInstrument()
self.xsDataDiffractionCTImage = XSDataDiffractionCTImage()
xsDataDictionaryHeader = self.edPluginReadHeader.getDataOutput().getDictionary()
for xsDataKeyValuePair in xsDataDictionaryHeader.getKeyValuePair():
strKey = str(xsDataKeyValuePair.getKey().getValue())
lstValue = xsDataKeyValuePair.getValue().getValue().split()
if len(lstValue) == 2:
strValue = lstValue[0]
strUnit = lstValue[1]
else:
strValue = xsDataKeyValuePair.getValue().getValue()
strUnit = None
if (strKey == "_diffrn_radiation_wavelength"):
xsd = EDUtilsUnit.toXSD(XSDataWavelength, strValue)
# if strUnit is None: strUnit = "A"
# xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_diffrn_radiation_wavelength(xsd)
elif (strKey == "_pd_instr_dist_spec/detc"):
xsd = EDUtilsUnit.toXSD(XSDataLength, strValue)
# if strUnit is None: strUnit = "mm"
# xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_instr_dist_spec_detc(xsd)
elif (strKey == "_pd_meas_2theta_range_max"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_max(xsd)
elif (strKey == "_pd_meas_2theta_range_min"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_min(xsd)
elif (strKey == "_pd_meas_2theta_range_inc"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_inc(xsd)
elif (strKey == "_synchrotron_photon-flux"):
self.xsDataDiffractionCTInstrument.set_synchrotron_photon_flux(XSDataFlux(float(strValue)))
elif (strKey == "_synchrotron_ring-intensity"):
self.xsDataDiffractionCTInstrument.set_synchrotron_ring_intensity(XSDataDouble(float(strValue)))
elif (strKey == "_tomo_scan_ampl"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_scan_ampl(xsd)
elif (strKey == "_tomo_scan_type"):
self.xsDataDiffractionCTInstrument.set_tomo_scan_type(XSDataString(strValue))
elif (strKey == "_tomo_spec_displ_rotation"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation(xsd)
elif (strKey == "_tomo_spec_displ_rotation_inc"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation_inc(xsd)
elif (strKey == "_tomo_spec_displ_x"):
xsd = EDUtilsUnit.toXSD(XSDataLength, strValue)
# if strUnit is None: strUnit = "mm"
# xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x(xsd)
elif (strKey == "_tomo_spec_displ_x_inc"):
xsd = EDUtilsUnit.toXSD(XSDataLength, strValue)
# if strUnit is None: strUnit = "mm"
# xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_inc(xsd)
elif (strKey == "_tomo_spec_displ_x_max"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_max(xsd)
elif (strKey == "_tomo_spec_displ_x_min"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_min(xsd)
elif (strKey == "_tomo_spec_displ_z"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z(xsd)
elif (strKey == "_tomo_spec_displ_z_inc"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_inc(xsd)
elif (strKey == "_tomo_spec_displ_z_max"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_max(xsd)
elif (strKey == "_tomo_spec_displ_z_min"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_min(xsd)
elif (strKey == "_pd_instr_special_details_tilt_angle"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_angle(xsd)
elif (strKey == "_pd_instr_special_details_tilt_rotation"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_rotation(xsd)
elif (strKey == "_array_element_size[1]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "m"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_array_element_size_1(xsd)
elif (strKey == "_array_element_size[2]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "m"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_array_element_size_2(xsd)
elif (strKey == "_diffrn_detector_element.center[1]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_diffrn_detector_element_center_1(xsd)
elif (strKey == "_diffrn_detector_element.center[2]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_diffrn_detector_element_center_2(xsd)
# elif strKey.startswith("_pd_sum_2theta_range_max"):
# if strKey.find("[") > 0:
# pyintIndex = int(strKey.split("[")[1].split("]")[0]) - 1 #gets the int that is between []
# else:
# pyintIndex = 0
# while len(self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()) < pyintIndex + 1:
# self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max().append(None)
# xsd = XSDataAngle(float(strValue))
# if strUnit is None: strUnit = "deg"
# xsd.setUnit(XSDataString(strUnit))
# self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()[pyintIndex] = xsd
# elif strKey.startswith("_pd_sum_2theta_range_min"):
# if strKey.find("[") > 0:
# pyintIndex = int(strKey.split("[")[1].split("]")[0]) - 1 #gets the int that is between []
# else:
# pyintIndex = 0
# while len(self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()) < pyintIndex + 1:
# self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min().append(None)
# xsd = XSDataAngle(float(strValue))
# if strUnit is None: strUnit = "deg"
# xsd.setUnit(XSDataString(strUnit))
# self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()[pyintIndex] = xsd
elif (strKey == "_file_correction_image_dark-current"):
xsDataFileDark = XSDataFile()
xsDataFileDark.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_image_dark_current(xsDataFileDark)
elif (strKey == "_file_correction_image_flat-field"):
xsDataFileFlat = XSDataFile()
xsDataFileFlat.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_image_flat_field(xsDataFileFlat)
elif (strKey == "_file_correction_image-mask"):
xsDataFileMask = XSDataFile()
xsDataFileMask.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_image_mask(xsDataFileMask)
elif (strKey == "_file_correction_spline_spatial-distortion"):
xsDataFileSpatialDist = XSDataFile()
xsDataFileSpatialDist.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_spline_spatial_distortion(xsDataFileSpatialDist)
if self.xsdForceImageParam is not None:
self.forceImageParam(self.xsdForceImageParam)
if self.xsdForceScanParam is not None:
self.forceScanParam(self.xsdForceScanParam)
xsDataInputPowderIntegration.setImageParameters(self.xsDataDiffractionCTImage)
xsDataInputPowderIntegration.setInstrumentParameters(self.xsDataDiffractionCTInstrument)
xsDataInputPowderIntegration.setImageFile(self.xsDataFileInputImage)
# Set the destination directory for output XRPD file
strDestinationDirectory = os.path.join(self.getDataInput().getDestinationDirectory().getPath().getValue(), \
self.getDataInput().getPowderDiffractionSubdirectory().getValue())
if self.xsDataDiffractionCTInstrument.get_tomo_scan_type().getValue().lower() in ["flat", "spiral"]:
pyintLineNumber = int(abs(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_rotation().getValue()) / self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_rotation_inc().getValue())
elif self.xsDataDiffractionCTInstrument.get_tomo_scan_type().getValue().lower() == "mapping": #I agree mappings are not sinograms but the really looks like, no ?
pyintLineNumber = int(abs(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z().getValue() - self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_min().getValue()) / self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_inc().getValue())
else:
pyintLineNumber = None
try:
strDestinationDirectory = "%s%04i" % (strDestinationDirectory, pyintLineNumber)
except TypeError:
pass #if pyintLineNumber is none: do not add suffix
xsDataInputPowderIntegration.setDestinationDir(XSDataFile(XSDataString(strDestinationDirectory)))
self.edPluginPowderIntegration.setDataInput(xsDataInputPowderIntegration)
self.edPluginPowderIntegration.executeSynchronous()
def doFailureReadHeader(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_1.doFailureReadHeader")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlDiffractionCTv1_1.doFailureReadHeader")
self.setFailure()
def doSuccessPowderIntegration(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_1.doSuccessPowderIntegration")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlDiffractionCTv1_1.doSuccessPowderIntegration")
self.xsDataResultDiffractionCT = XSDataResultDiffractionCT()
xsDataFileIntegratedIntensities = _edPlugin.getDataOutput().getIntegratedIntensities()
if (xsDataFileIntegratedIntensities is not None):
# EDVerbose.DEBUG(self.edPluginPowderIntegration.getDataOutput().mashal())
xsdPathFileIntegratedIntensities = xsDataFileIntegratedIntensities.getPath()
if self.powderDiffractionFormat == "edf":
self.xsDataResultDiffractionCT.setIntegratedIntensities(xsDataFileIntegratedIntensities)
else:
xsdInput1DPowderEDF = XSDataInput1DPowderEDF()
xsdInput1DPowderEDF.setEdfFile(xsDataFileIntegratedIntensities)
xsdOutFile = XSDataFile()
xsdOutFile.setPath(XSDataString(os.path.splitext(xsdPathFileIntegratedIntensities.getValue())[0] + "." + self.powderDiffractionFormat))
xsdInput1DPowderEDF.setOutputFile(xsdOutFile)
xsdInput1DPowderEDF.setOutputFormat(XSDataString(self.powderDiffractionFormat))
self.edPluginExportAsciiPowder = self.loadPlugin(self.strControlledPluginExportAsciiPowder)
self.edPluginExportAsciiPowder.setDataInput(xsdInput1DPowderEDF)
self.edPluginExportAsciiPowder.connectSUCCESS(self.doSuccessExportAsciiPowder)
self.edPluginExportAsciiPowder.connectFAILURE(self.doFailureExportAsciiPowder)
self.edPluginExportAsciiPowder.execute()
xsDataInputHDF5MapSpectra = XSDataInputHDF5MapSpectra()
xsDataMesh = XSDataMeshScan()
xsDataSpectrum = XSDataSpectrum()
xsDataSpectrum.setPath(xsdPathFileIntegratedIntensities)
strDestinationFile = os.path.join(self.getDataInput().getDestinationDirectory().getPath().getValue(), \
self.getDataInput().getSinogramFileNamePrefix().getValue() + ".h5")
xsDataPathSinogram = XSDataFile()
xsDataPathSinogram.setPath(XSDataString(strDestinationFile))
xsDataInputHDF5MapSpectra.setHDF5File(xsDataPathSinogram)
xsDataInputHDF5MapSpectra.setInternalHDF5Path(XSDataString("RawDCT"))
if self.xsDataDiffractionCTInstrument.get_tomo_scan_type().getValue().lower() in ["flat", "spiral"]:
xsDataSpectrum.setFastMotorPosition(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x())
xsDataMesh.setFastMotorStart(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x_min())
xsDataMesh.setFastMotorStop(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x_max())
xsSteps = XSDataInteger(int(round(\
(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x_max().getValue() - \
self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x_min().getValue()) / \
self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x_inc().getValue() \
)))
xsDataMesh.setFastMotorSteps(xsSteps)
xsDataMesh.setSlowMotorStart(XSDataDouble(0.0))
xsDataMesh.setSlowMotorStop(self.xsDataDiffractionCTInstrument.get_tomo_scan_ampl())
xsSteps = XSDataInteger(int(round(\
self.xsDataDiffractionCTInstrument.get_tomo_scan_ampl().getValue() / \
self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_rotation_inc().getValue())))
xsDataMesh.setSlowMotorSteps(xsSteps)
xsDataSpectrum.setSlowMotorPosition(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_rotation())
elif self.xsDataDiffractionCTInstrument.get_tomo_scan_type().getValue().lower() == "mapping": #I agree mappings are not sinograms but the really looks like, no ?
xsDataSpectrum.setFastMotorPosition(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x())
xsDataSpectrum.setSlowMotorPosition(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z())
xsSteps = XSDataInteger(int(round(\
(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x_max().getValue() - \
self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x_min().getValue()) / \
self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x_inc().getValue() \
)))
xsDataMesh.setFastMotorSteps(xsSteps)
xsDataMesh.setFastMotorStop(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x_max())
xsDataMesh.setFastMotorStart(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x_min())
xsSteps = XSDataInteger(int(round(\
(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_max().getValue() - \
self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_min().getValue()) / \
self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_inc().getValue() \
)))
xsDataMesh.setSlowMotorSteps(xsSteps)
xsDataMesh.setSlowMotorStop(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_max())
xsDataMesh.setSlowMotorStart(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_min())
xsDataSpectrum.setMeshScan(xsDataMesh)
xsDataInputHDF5MapSpectra.setInputSpectrumFile([xsDataSpectrum])
self.edPluginHDF5MapSpectra = self.loadPlugin(self.strControlledPluginHDF5MapSpectra)
self.edPluginHDF5MapSpectra.setDataInput(xsDataInputHDF5MapSpectra)
self.edPluginHDF5MapSpectra.connectSUCCESS(self.doSuccessWriteSinogram)
self.edPluginHDF5MapSpectra.connectFAILURE(self.doFailureWriteSinogram)
self.edPluginHDF5MapSpectra.execute()
def doFailurePowderIntegration(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_1.doFailurePowderIntegration")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlDiffractionCTv1_1.doFailurePowderIntegration")
self.setFailure()
def doSuccessWriteSinogram(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_1.doSuccessWriteSinogram")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlDiffractionCTv1_1.doSuccessWriteSinogram")
xsDataResultWriteSinogram = self.edPluginHDF5MapSpectra.getDataOutput()
if (xsDataResultWriteSinogram is not None):
self.xsDataResultDiffractionCT.setSinogramFile([xsDataResultWriteSinogram.getHDF5File()])
def doFailureWriteSinogram(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_1.doFailureWriteSinogram")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlDiffractionCTv1_1.doFailureWriteSinogram")
self.setFailure()
def doSuccessExportAsciiPowder(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_1.doSuccessExportAsciiPowder")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlDiffractionCTv1_1.doSuccessExportAsciiPowder")
xsDataResultExport1DPower = _edPlugin.getDataOutput()
if (xsDataResultExport1DPower is not None):
self.xsDataResultDiffractionCT.setIntegratedIntensities(xsDataResultExport1DPower.getOutputFile())
def doFailureExportAsciiPowder(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_1.doFailureExportAsciiPowder")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlDiffractionCTv1_1.doFailureExportAsciiPowder")
self.setFailure()
def forceImageParam(self, xsdForceImageParam):
"""
Helper function to override self.xsDataDiffractionCTImage with the contents of xsdForceImageParam
@param xsDataDiffractionCTImage: instance of XSDataDiffractionCTImage
@return: None
"""
if xsdForceImageParam.get_array_element_size_1() is not None:
self.xsDataDiffractionCTImage.set_array_element_size_1(xsdForceImageParam.get_array_element_size_1())
if xsdForceImageParam.get_array_element_size_2() is not None:
self.xsDataDiffractionCTImage.set_array_element_size_2(xsdForceImageParam.get_array_element_size_2())
if xsdForceImageParam.get_diffrn_detector_element_center_1() is not None:
self.xsDataDiffractionCTImage.set_diffrn_detector_element_center_1(xsdForceImageParam.get_diffrn_detector_element_center_1())
if xsdForceImageParam.get_diffrn_detector_element_center_2() is not None:
self.xsDataDiffractionCTImage.set_diffrn_detector_element_center_2(xsdForceImageParam.get_diffrn_detector_element_center_2())
if xsdForceImageParam.get_file_correction_image_dark_current() is not None:
self.xsDataDiffractionCTImage.set_file_correction_image_dark_current(xsdForceImageParam.get_file_correction_image_dark_current())
if xsdForceImageParam.get_file_correction_image_flat_field() is not None:
self.xsDataDiffractionCTImage.set_file_correction_image_flat_field(xsdForceImageParam.get_file_correction_image_flat_field())
if xsdForceImageParam.get_file_correction_image_mask() is not None:
self.xsDataDiffractionCTImage.set_file_correction_image_mask(xsdForceImageParam.get_file_correction_image_mask())
if xsdForceImageParam.get_file_correction_spline_spatial_distortion() is not None:
self.xsDataDiffractionCTImage.set_file_correction_spline_spatial_distortion(xsdForceImageParam.get_file_correction_spline_spatial_distortion())
if xsdForceImageParam.get_pd_instr_special_details_tilt_angle() is not None:
self.xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_angle(xsdForceImageParam.get_pd_instr_special_details_tilt_angle())
if xsdForceImageParam.get_pd_instr_special_details_tilt_rotation() is not None:
self.xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_rotation(xsdForceImageParam.get_pd_instr_special_details_tilt_rotation())
def forceScanParam(self, xsdForceScanParam):
"""
Helper function to override self.xsDataDiffractionCTInstrument with the contents of xsdForceScanParam
@param xsdForceScanParam: instance of XSDataDiffractionCTInstrument
@return: None
"""
if xsdForceScanParam.get_diffrn_radiation_wavelength() is not None:
self.xsDataDiffractionCTInstrument.set_diffrn_radiation_wavelength(xsdForceScanParam.get_diffrn_radiation_wavelength())
if xsdForceScanParam.get_pd_instr_dist_spec_detc() is not None:
self.xsDataDiffractionCTInstrument.set_pd_instr_dist_spec_detc(xsdForceScanParam.get_pd_instr_dist_spec_detc())
if xsdForceScanParam.get_pd_meas_2theta_range_inc() is not None:
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_inc(xsdForceScanParam.get_pd_meas_2theta_range_inc())
if xsdForceScanParam.get_pd_meas_2theta_range_max() is not None:
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_max(xsdForceScanParam.get_pd_meas_2theta_range_max())
if xsdForceScanParam.get_pd_meas_2theta_range_min() is not None:
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_min(xsdForceScanParam.get_pd_meas_2theta_range_min())
if xsdForceScanParam.get_synchrotron_photon_flux() is not None:
self.xsDataDiffractionCTInstrument.set_synchrotron_photon_flux(xsdForceScanParam.get_synchrotron_photon_flux())
if xsdForceScanParam.get_synchrotron_ring_intensity() is not None:
self.xsDataDiffractionCTInstrument.set_synchrotron_ring_intensity(xsdForceScanParam.get_synchrotron_ring_intensity())
if xsdForceScanParam.get_tomo_scan_ampl() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_scan_ampl(xsdForceScanParam.get_tomo_scan_ampl())
if xsdForceScanParam.get_tomo_scan_type() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_scan_type(xsdForceScanParam.get_tomo_scan_type())
if xsdForceScanParam.get_tomo_spec_displ_rotation() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation(xsdForceScanParam.get_tomo_spec_displ_rotation())
if xsdForceScanParam.get_tomo_spec_displ_rotation_inc() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation_inc(xsdForceScanParam.get_tomo_spec_displ_rotation_inc())
if xsdForceScanParam.get_tomo_spec_displ_x_min() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_min(xsdForceScanParam.get_tomo_spec_displ_x_min())
if xsdForceScanParam.get_tomo_spec_displ_x_max() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_max(xsdForceScanParam.get_tomo_spec_displ_x_max())
if xsdForceScanParam.get_tomo_spec_displ_x_inc() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_inc(xsdForceScanParam.get_tomo_spec_displ_x_inc())
if xsdForceScanParam.get_tomo_spec_displ_x() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x(xsdForceScanParam.get_tomo_spec_displ_x())
if xsdForceScanParam.get_tomo_spec_displ_z() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z(xsdForceScanParam.get_tomo_spec_displ_z())
if xsdForceScanParam.get_tomo_spec_displ_z_inc() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_inc(xsdForceScanParam.get_tomo_spec_displ_z_inc())
if xsdForceScanParam.get_tomo_spec_displ_z_max() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_max(xsdForceScanParam.get_tomo_spec_displ_z_max())
if xsdForceScanParam.get_tomo_spec_displ_z_min() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_min(xsdForceScanParam.get_tomo_spec_displ_z_min())
def setup(self, _listInput=[], _mode="offline"):
"""Configure the various options"""
bOK = False
if _listInput == []:
_listInput = [os.getcwd()]
while not bOK:
strtmp = raw_input("What are the input directories (mandatory, space separated) %s: " % _listInput).strip()
if len(strtmp) > 0:
bAllExists = True
lstTemp = shlex.split(strtmp)
for oneDir in shlex.split(strtmp):
if not os.path.exists(oneDir):
EDVerbose.screen("No such file or directory: %s" % oneDir)
bAllExists = False
if bAllExists is True:
self.listInput = lstTemp
bOK = True
else:
self.listInput = _listInput
bOK = True
bOK = False
while not bOK:
strtmp = raw_input("What is operation mode [offline|online|all] (mandatory: %s): " % _mode).strip().lower()
if len(strtmp) > 0:
bOK = True
if strtmp == "offline":
self.bNewerOnly = False
self.strMode = "OffLine"
elif strtmp == "online":
self.bNewerOnly = True
self.strMode = "dirwatch"
elif strtmp == "all":
self.bNewerOnly = False
self.strMode = "dirwatch"
else:
bOK = False
bOK = False
while not bOK:
strtmp = raw_input("What is the destination directory (mandatory): ").strip()
if os.path.isdir(strtmp):
self.destinationDirectory = XSDataFile()
self.destinationDirectory.setPath(XSDataString(os.path.abspath(strtmp)))
bOK = True
bOK = False
while not bOK:
strtmp = raw_input("What is the sinogram filename prefix (mandatory): ").strip()
if strtmp != "":
self.sinogramFileNamePrefix = XSDataString(strtmp)
bOK = True
bOK = False
while not bOK:
strtmp = raw_input("What is the powder diffraction subdirectory (mandatory): ").strip()
if strtmp != "":
self.powderDiffractionSubdirectory = XSDataString(strtmp)
bOK = True
strtmp = raw_input("What is the powder diffraction output format (CHI or CIF, if any ): ").strip().lower()
if strtmp.find("cif") >= 0:
self.powderDiffractionFormat = XSDataString("cif")
elif strtmp.find("chi") >= 0:
self.powderDiffractionFormat = XSDataString("chi")
strtmp = raw_input("Process all files ending with: ").strip()
if len(strtmp) > 0:
for oneExt in shlex.split(strtmp):
self.listExtensions.append(oneExt)
strtmp = raw_input("Exclude all files starting with: ").strip()
if len(strtmp) > 0:
for oneExt in shlex.split(strtmp):
self.listExcludedPrefix.append(oneExt)
strtmp = raw_input("Do you want to over-ride metadata from the headers [y|N]: ").strip().lower()
if len(strtmp) > 0 and strtmp[0] == "y":
strtmp = raw_input("What is the flat field image: ").strip()
if os.path.isfile(strtmp):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
flatFieldImage = XSDataFile()
flatFieldImage.setPath(XSDataString(os.path.abspath(strtmp)))
self.forceImage.set_file_correction_image_flat_field(flatFieldImage)
strtmp = raw_input("What is the dark current image: ").strip()
if os.path.isfile(strtmp):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
darkCurrentImage = XSDataFile()
darkCurrentImage.setPath(XSDataString(os.path.abspath(strtmp)))
self.forceImage.set_file_correction_image_dark_current(darkCurrentImage)
strtmp = raw_input("What is the mask file: ").strip()
if os.path.isfile(strtmp):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
maskFile = XSDataFile()
maskFile.setPath(XSDataString(strtmp))
self.forceImage.set_file_correction_image_mask(maskFile)
strtmp = raw_input("What is the spline file: ").strip()
if os.path.isfile(strtmp):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
splineFile = XSDataFile()
splineFile.setPath(XSDataString(os.path.abspath(strtmp)))
self.forceImage.set_file_correction_spline_spatial_distortion(splineFile)
strtmp = raw_input("What is the wavelength (like 0.7 A): ").replace("(", "").replace(")", "").strip()
w = strtmp.split()
if len(w) > 0:
try:
f = float(w[0])
except ValueError:
print("unable to understand what you said, skipping")
else:
wavelength = XSDataWavelength()
wavelength.setValue(f)
if len(w) == 2:
wavelength.setUnit(XSDataString(w[1]))
if self.forceInstrument is None:
self.forceInstrument = XSDataDiffractionCTInstrument()
self.forceInstrument.set_diffrn_radiation_wavelength(wavelength)
strtmp = raw_input("What is the distance between the sample and the detector along the beam: ").replace("(", "").replace(")", "").strip()
w = strtmp.split()
if len(w) > 0:
try:
f = float(w[0])
except ValueError:
print("unable to understand what you said, skipping")
else:
distance = XSDataLength()
distance.setValue(f)
if len(w) == 2:
distance.setUnit(XSDataString(w[1]))
if self.forceInstrument is None:
self.forceInstrument = XSDataDiffractionCTInstrument()
self.forceInstrument.set_pd_instr_dist_spec_detc(distance)
strtmp = raw_input("What is the pixel size (like 52.8 um 53.2 um): ").replace("(", "").replace(")", "").strip()
w = strtmp.split()
if len(w) > 0:
xsdata1 = None
xsdata2 = None
if len(w) == 4:
try:
f1 = float(w[0])
f2 = float(w[2])
except ValueError:
print "Unable to convert to float !!! skipping"
else:
xsdata1 = XSDataLength()
xsdata1.setValue(f1)
xsdata1.setUnit(XSDataString(w[1]))
xsdata2 = XSDataLength()
xsdata2.setValue(f2)
xsdata2.setUnit(XSDataString(w[3]))
elif len(w) == 2:
try:
f1 = float(w[0])
f2 = float(w[1])
except ValueError:
print "Unable to convert to float !!! skipping"
else:
xsdata1 = XSDataLength()
xsdata1.setValue(f1)
xsdata2 = XSDataLength()
xsdata2.setValue(f2)
else:
print("unable to understand what you said, skipping")
if (xsdata1 is not None) and (xsdata2 is not None):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
self.forceImage.set_array_element_size_1(xsdata1)
self.forceImage.set_array_element_size_2(xsdata2)
strtmp = raw_input("What is the beam center in distance, not pixels (like 53.5 mm 48.2 mm): ").strip().replace("(", "").replace(")", "").strip()
w = strtmp.split()
if len(w) > 0:
xsdata1 = None
xsdata2 = None
if len(w) == 4:
try:
f1 = float(w[0])
f2 = float(w[2])
except ValueError:
print "Unable to convert to float !!! skipping"
else:
xsdata1 = XSDataLength()
xsdata1.setValue(f1)
xsdata1.setUnit(XSDataString(w[1]))
xsdata2 = XSDataLength()
xsdata2.setValue(f2)
xsdata2.setUnit(XSDataString(w[3]))
elif len(w) == 2:
try:
f1 = float(w[0])
f2 = float(w[1])
except ValueError, IndexError:
print "Unable to convert to float !!! skipping"
else:
xsdata1 = XSDataLength()
xsdata1.setValue(f1)
xsdata2 = XSDataLength()
xsdata2.setValue(f2)
else:
print("unable to understand what you said, skipping")
if (xsdata1 is not None) and (xsdata2 is not None):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
self.forceImage.set_diffrn_detector_element_center_1(xsdata1)
self.forceImage.set_diffrn_detector_element_center_2(xsdata2)
strtmp = raw_input("What is the detector tilt angle: ").strip()
tiltAngle = None
try:
tiltAngle = XSDataAngle(float(strtmp))
except ValueError:
print("unable to understand what you said, skipping")
else:
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
self.forceImage.set_pd_instr_special_details_tilt_angle(tiltAngle)
strtmp = raw_input("What is the tilt plan rotation: ").strip()
tiltRotation = None
try:
tiltRotation = XSDataAngle(float(strtmp))
except ValueError:
print("unable to understand what you said, skipping")
else:
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
self.forceImage.set_pd_instr_special_details_tilt_rotation(tiltRotation)
strtmp = raw_input("What is the number of fast motor steps (you will have n+1 points): ").strip()
try:
self.fastMotorSteps = int(strtmp)
except ValueError:
fastMotorSteps = None
else:
if self.forceInstrument is None:
self.forceInstrument = XSDataDiffractionCTInstrument()
self.forceInstrument.set_tomo_spec_displ_x_max(XSDataLength(self.fastMotorSteps))
self.forceInstrument.set_tomo_spec_displ_x_min(XSDataLength(0))
self.forceInstrument.set_tomo_spec_displ_x_inc(XSDataLength(1))
self.forceInstrument.set_tomo_scan_type(XSDataString("flat"))
strtmp = raw_input("What is the number of slow motor steps (you will have n+1 points): ").strip()
try:
self.slowMotorSteps = int(strtmp)
except ValueError:
self.slowMotorSteps = None
else:
if self.forceInstrument is None:
self.forceInstrument = XSDataDiffractionCTInstrument()
self.forceInstrument.set_tomo_scan_ampl(XSDataLength(self.slowMotorSteps))
self.forceInstrument.set_tomo_spec_displ_rotation_inc(XSDataLength(1))
self.forceInstrument.set_tomo_scan_type(XSDataString("flat"))
strtmp = raw_input("What is the index offset of your images: ").strip()
try:
self.indexOffset = int(strtmp)
except ValueError:
print("unable to understand what you said, skipping")
def doSuccessReadHeader(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_1.doSuccessReadHeader")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlDiffractionCTv1_1.doSuccessReadHeader")
# Translate dictionary to image and instrument objects
xsDataInputPowderIntegration = XSDataInputPowderIntegration()
self.xsDataDiffractionCTInstrument = XSDataDiffractionCTInstrument()
self.xsDataDiffractionCTImage = XSDataDiffractionCTImage()
xsDataDictionaryHeader = self.edPluginReadHeader.getDataOutput().getDictionary()
for xsDataKeyValuePair in xsDataDictionaryHeader.getKeyValuePair():
strKey = str(xsDataKeyValuePair.getKey().getValue())
lstValue = xsDataKeyValuePair.getValue().getValue().split()
if len(lstValue) == 2:
strValue = lstValue[0]
strUnit = lstValue[1]
else:
strValue = xsDataKeyValuePair.getValue().getValue()
strUnit = None
if (strKey == "_diffrn_radiation_wavelength"):
xsd = EDUtilsUnit.toXSD(XSDataWavelength, strValue)
# if strUnit is None: strUnit = "A"
# xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_diffrn_radiation_wavelength(xsd)
elif (strKey == "_pd_instr_dist_spec/detc"):
xsd = EDUtilsUnit.toXSD(XSDataLength, strValue)
# if strUnit is None: strUnit = "mm"
# xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_instr_dist_spec_detc(xsd)
elif (strKey == "_pd_meas_2theta_range_max"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_max(xsd)
elif (strKey == "_pd_meas_2theta_range_min"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_min(xsd)
elif (strKey == "_pd_meas_2theta_range_inc"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_inc(xsd)
elif (strKey == "_synchrotron_photon-flux"):
self.xsDataDiffractionCTInstrument.set_synchrotron_photon_flux(XSDataFlux(float(strValue)))
elif (strKey == "_synchrotron_ring-intensity"):
self.xsDataDiffractionCTInstrument.set_synchrotron_ring_intensity(XSDataDouble(float(strValue)))
elif (strKey == "_tomo_scan_ampl"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_scan_ampl(xsd)
elif (strKey == "_tomo_scan_type"):
self.xsDataDiffractionCTInstrument.set_tomo_scan_type(XSDataString(strValue))
elif (strKey == "_tomo_spec_displ_rotation"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation(xsd)
elif (strKey == "_tomo_spec_displ_rotation_inc"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation_inc(xsd)
elif (strKey == "_tomo_spec_displ_x"):
xsd = EDUtilsUnit.toXSD(XSDataLength, strValue)
# if strUnit is None: strUnit = "mm"
# xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x(xsd)
elif (strKey == "_tomo_spec_displ_x_inc"):
xsd = EDUtilsUnit.toXSD(XSDataLength, strValue)
# if strUnit is None: strUnit = "mm"
# xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_inc(xsd)
elif (strKey == "_tomo_spec_displ_x_max"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_max(xsd)
elif (strKey == "_tomo_spec_displ_x_min"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_min(xsd)
elif (strKey == "_tomo_spec_displ_z"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z(xsd)
elif (strKey == "_tomo_spec_displ_z_inc"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_inc(xsd)
elif (strKey == "_tomo_spec_displ_z_max"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_max(xsd)
elif (strKey == "_tomo_spec_displ_z_min"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_min(xsd)
elif (strKey == "_pd_instr_special_details_tilt_angle"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_angle(xsd)
elif (strKey == "_pd_instr_special_details_tilt_rotation"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_rotation(xsd)
elif (strKey == "_array_element_size[1]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "m"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_array_element_size_1(xsd)
elif (strKey == "_array_element_size[2]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "m"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_array_element_size_2(xsd)
elif (strKey == "_diffrn_detector_element.center[1]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_diffrn_detector_element_center_1(xsd)
elif (strKey == "_diffrn_detector_element.center[2]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_diffrn_detector_element_center_2(xsd)
# elif strKey.startswith("_pd_sum_2theta_range_max"):
# if strKey.find("[") > 0:
# pyintIndex = int(strKey.split("[")[1].split("]")[0]) - 1 #gets the int that is between []
# else:
# pyintIndex = 0
# while len(self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()) < pyintIndex + 1:
# self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max().append(None)
# xsd = XSDataAngle(float(strValue))
# if strUnit is None: strUnit = "deg"
# xsd.setUnit(XSDataString(strUnit))
# self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()[pyintIndex] = xsd
# elif strKey.startswith("_pd_sum_2theta_range_min"):
# if strKey.find("[") > 0:
# pyintIndex = int(strKey.split("[")[1].split("]")[0]) - 1 #gets the int that is between []
# else:
# pyintIndex = 0
# while len(self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()) < pyintIndex + 1:
# self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min().append(None)
# xsd = XSDataAngle(float(strValue))
# if strUnit is None: strUnit = "deg"
# xsd.setUnit(XSDataString(strUnit))
# self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()[pyintIndex] = xsd
elif (strKey == "_file_correction_image_dark-current"):
xsDataFileDark = XSDataFile()
xsDataFileDark.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_image_dark_current(xsDataFileDark)
elif (strKey == "_file_correction_image_flat-field"):
xsDataFileFlat = XSDataFile()
xsDataFileFlat.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_image_flat_field(xsDataFileFlat)
elif (strKey == "_file_correction_image-mask"):
xsDataFileMask = XSDataFile()
xsDataFileMask.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_image_mask(xsDataFileMask)
elif (strKey == "_file_correction_spline_spatial-distortion"):
xsDataFileSpatialDist = XSDataFile()
xsDataFileSpatialDist.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_spline_spatial_distortion(xsDataFileSpatialDist)
if self.xsdForceImageParam is not None:
self.forceImageParam(self.xsdForceImageParam)
if self.xsdForceScanParam is not None:
self.forceScanParam(self.xsdForceScanParam)
xsDataInputPowderIntegration.setImageParameters(self.xsDataDiffractionCTImage)
xsDataInputPowderIntegration.setInstrumentParameters(self.xsDataDiffractionCTInstrument)
xsDataInputPowderIntegration.setImageFile(self.xsDataFileInputImage)
# Set the destination directory for output XRPD file
strDestinationDirectory = os.path.join(self.getDataInput().getDestinationDirectory().getPath().getValue(), \
self.getDataInput().getPowderDiffractionSubdirectory().getValue())
if self.xsDataDiffractionCTInstrument.get_tomo_scan_type().getValue().lower() in ["flat", "spiral"]:
pyintLineNumber = int(abs(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_rotation().getValue()) / self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_rotation_inc().getValue())
elif self.xsDataDiffractionCTInstrument.get_tomo_scan_type().getValue().lower() == "mapping": #I agree mappings are not sinograms but the really looks like, no ?
pyintLineNumber = int(abs(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z().getValue() - self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_min().getValue()) / self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_inc().getValue())
else:
pyintLineNumber = None
try:
strDestinationDirectory = "%s%04i" % (strDestinationDirectory, pyintLineNumber)
except TypeError:
pass #if pyintLineNumber is none: do not add suffix
xsDataInputPowderIntegration.setDestinationDir(XSDataFile(XSDataString(strDestinationDirectory)))
self.edPluginPowderIntegration.setDataInput(xsDataInputPowderIntegration)
self.edPluginPowderIntegration.executeSynchronous()
class EDPluginControlDiffractionCTv1_2(EDPluginControl):
"""
This is the EDNA control plug-in for diffraction contrast tomography.
It is intented to run 2D integration provided by SPD for example and create a sinogram as a 3D array in HDF5....
"""
CONF_INPUT_IMAGE_SIZE = "inputImageSize"
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputDiffractionCT)
self.strControlledPluginReadHeader = "EDPluginControlDCTReadHeaderv1_0"
self.strControlledPluginPowderIntegration = "EDPluginControlDCTPowderIntegrationv1_1"
self.strControlledPluginHDF5MapSpectra = "EDPluginHDF5MapOfSpectrav10"
self.strControlledPluginExportAsciiPowder = "EDPluginExportAsciiPowderv1_0"
self.strControlledPluginWait = "EDPluginWaitFile"
self.edPluginPowderIntegration = None
self.xsDataDiffractionCTInstrument = None
self.xsDataDiffractionCTImage = None
self.xsDataFileInputImage = None
self.xsDataFileInputPowderDiffraction = None
self.xsDataResultDiffractionCT = None
self.edPluginHDF5MapSpectra = None
self.edPluginExportAsciiPowder = None
self.xsdForceImageParam = None
self.xsdForceScanParam = None
self.powderDiffractionFormat = "edf" #default output format
self.iImageSize = 100 #Default value
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_2.checkParameters")
self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getImage(), "No path to input image")
self.checkMandatoryParameters(self.getDataInput().getDestinationDirectory(), "No path to destination directory")
self.checkMandatoryParameters(self.getDataInput().getSinogramFileNamePrefix(), "No sinogram prefix given")
self.checkMandatoryParameters(self.getDataInput().getPowderDiffractionSubdirectory(), "No subdirectory prefix for powder diffraction patterns")
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_2.preProcess")
# Load the execution plugin
self.edPluginPowderIntegration = self.loadPlugin(self.strControlledPluginPowderIntegration)
self.edPluginHDF5MapSpectra = self.loadPlugin(self.strControlledPluginHDF5MapSpectra)
self.edPluginExportAsciiPowder = self.loadPlugin(self.strControlledPluginExportAsciiPowder)
sdi = self.getDataInput()
self.xsDataFileInputImage = self.getDataInput().getImage()
self.xsdForceImageParam = sdi.getOverrideImageParam()
self.xsdForceScanParam = sdi.getOverrideScanParam()
if sdi.getPowderDiffractionFormat() is not None:
self.powderDiffractionFormat = sdi.getPowderDiffractionFormat().getValue()
def configure(self):
"""
Configures the plugin from the configuration file with the following parameters
- Excpected image size
"""
EDPluginControl.configure(self)
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_2.configure")
xsPluginItem = self.getConfiguration()
if (xsPluginItem == None):
EDVerbose.warning("EDPluginControlDiffractionCTv1_2.configure: No plugin item defined.")
xsPluginItem = XSPluginItem()
strImageSize = EDConfiguration.getStringParamValue(xsPluginItem, EDPluginControlDiffractionCTv1_2.CONF_INPUT_IMAGE_SIZE)
if(strImageSize == None):
EDVerbose.WARNING("EDPluginControlDiffractionCTv1_2.configure: No configuration parameter found for: %s, using default value: %s " % (\
EDPluginControlDiffractionCTv1_2.CONF_INPUT_IMAGE_SIZE, self.iImageSize))
else:
self.iImageSize = int(strImageSize)
def process(self, _edObject=None):
EDPluginControl.process(self)
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_2.process")
#===============================================================================
# Wait File
#===============================================================================
edPluginWaitFile = self.loadPlugin(self.strControlledPluginWait)
xsdin = XSDataInputWaitFile()
xsdin.setExpectedFile(self.xsDataFileInputImage)
xsdin.setExpectedSize(XSDataInteger(self.iImageSize))
edPluginWaitFile.setDataInput(xsdin)
edPluginWaitFile.connectSUCCESS(self.doSuccessWaitFile)
edPluginWaitFile.connectFAILURE(self.doFailureWaitFile)
edPluginWaitFile.executeSynchronous()
#===============================================================================
# #ReadHeader
#===============================================================================
edPluginReadHeader = self.loadPlugin(self.strControlledPluginReadHeader)
# Set the input data for the read header plugin
xsDataInputReadHeader = XSDataInputReadHeader()
xsDataInputReadHeader.setInputFile(self.xsDataFileInputImage)
edPluginReadHeader.setDataInput(xsDataInputReadHeader)
edPluginReadHeader.connectSUCCESS(self.doSuccessReadHeader)
edPluginReadHeader.connectFAILURE(self.doFailureReadHeader)
edPluginReadHeader.executeSynchronous()
################################################################################
# Powder Integration
################################################################################
self.edPluginPowderIntegration.connectSUCCESS(self.doSuccessPowderIntegration)
self.edPluginPowderIntegration.connectFAILURE(self.doFailurePowderIntegration)
self.edPluginPowderIntegration.executeSynchronous()
self.edPluginHDF5MapSpectra.connectSUCCESS(self.doSuccessWriteSinogram)
self.edPluginHDF5MapSpectra.connectFAILURE(self.doFailureWriteSinogram)
self.edPluginHDF5MapSpectra.execute()
self.edPluginExportAsciiPowder.connectSUCCESS(self.doSuccessExportAsciiPowder)
self.edPluginExportAsciiPowder.connectFAILURE(self.doFailureExportAsciiPowder)
self.edPluginExportAsciiPowder.execute()
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_2.postProcess")
self.synchronizePlugins()
self.setDataOutput(self.xsDataResultDiffractionCT)
def doSuccessWaitFile(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_2.doSuccessWaitFile")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlDiffractionCTv1_2.doSuccessWaitFile")
def doFailureWaitFile(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_2.doFailureWaitFile")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlDiffractionCTv1_2.doFailureWaitFile")
EDVerbose.ERROR("Failure in WaitFile of %s " % _edPlugin.getDataInput().marshal())
self.setFailure()
def doSuccessReadHeader(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_2.doSuccessReadHeader")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlDiffractionCTv1_2.doSuccessReadHeader")
# Translate dictionary to image and instrument objects
xsDataInputPowderIntegration = XSDataInputPowderIntegration()
self.xsDataDiffractionCTInstrument = XSDataDiffractionCTInstrument()
self.xsDataDiffractionCTImage = XSDataDiffractionCTImage()
xsdOut = _edPlugin.getDataOutput()
if xsdOut is None:
strErr = "EDPluginControlDiffractionCTv1_2.doSuccessReadHeader: xsdataResult is None"
EDVerbose.ERROR(strErr)
self.setFailure()
raise RuntimeError(strErr)
xsDataDictionaryHeader = xsdOut.getDictionary()
for xsDataKeyValuePair in xsDataDictionaryHeader.getKeyValuePair():
strKey = str(xsDataKeyValuePair.getKey().getValue())
lstValue = xsDataKeyValuePair.getValue().getValue().split()
if len(lstValue) == 2:
strValue = lstValue[0]
strUnit = lstValue[1]
else:
strValue = xsDataKeyValuePair.getValue().getValue()
strUnit = None
if (strKey == "_diffrn_radiation_wavelength"):
xsd = EDUtilsUnit.toXSD(XSDataWavelength, strValue)
self.xsDataDiffractionCTInstrument.set_diffrn_radiation_wavelength(xsd)
elif (strKey == "_pd_instr_dist_spec/detc"):
xsd = EDUtilsUnit.toXSD(XSDataLength, strValue)
self.xsDataDiffractionCTInstrument.set_pd_instr_dist_spec_detc(xsd)
elif (strKey == "_pd_meas_2theta_range_max"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_max(xsd)
elif (strKey == "_pd_meas_2theta_range_min"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_min(xsd)
elif (strKey == "_pd_meas_2theta_range_inc"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_inc(xsd)
elif (strKey == "_synchrotron_photon-flux"):
self.xsDataDiffractionCTInstrument.set_synchrotron_photon_flux(XSDataFlux(float(strValue)))
elif (strKey == "_synchrotron_ring-intensity"):
self.xsDataDiffractionCTInstrument.set_synchrotron_ring_intensity(XSDataDouble(float(strValue)))
elif (strKey == "_tomo_scan_ampl"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_scan_ampl(xsd)
elif (strKey == "_tomo_scan_type"):
self.xsDataDiffractionCTInstrument.set_tomo_scan_type(XSDataString(strValue))
elif (strKey == "_tomo_spec_displ_rotation"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation(xsd)
elif (strKey == "_tomo_spec_displ_rotation_inc"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation_inc(xsd)
elif (strKey == "_tomo_spec_displ_x"):
xsd = EDUtilsUnit.toXSD(XSDataLength, strValue)
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x(xsd)
elif (strKey == "_tomo_spec_displ_x_inc"):
xsd = EDUtilsUnit.toXSD(XSDataLength, strValue)
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_inc(xsd)
elif (strKey == "_tomo_spec_displ_x_max"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_max(xsd)
elif (strKey == "_tomo_spec_displ_x_min"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_min(xsd)
elif (strKey == "_tomo_spec_displ_z"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z(xsd)
elif (strKey == "_tomo_spec_displ_z_inc"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_inc(xsd)
elif (strKey == "_tomo_spec_displ_z_max"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_max(xsd)
elif (strKey == "_tomo_spec_displ_z_min"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_min(xsd)
elif (strKey == "_pd_instr_special_details_tilt_angle"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_angle(xsd)
elif (strKey == "_pd_instr_special_details_tilt_rotation"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_rotation(xsd)
elif (strKey == "_array_element_size[1]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "m"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_array_element_size_1(xsd)
elif (strKey == "_array_element_size[2]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "m"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_array_element_size_2(xsd)
elif (strKey == "_diffrn_detector_element.center[1]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_diffrn_detector_element_center_1(xsd)
elif (strKey == "_diffrn_detector_element.center[2]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_diffrn_detector_element_center_2(xsd)
elif (strKey == "_file_correction_image_dark-current"):
xsDataFileDark = XSDataFile()
xsDataFileDark.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_image_dark_current(xsDataFileDark)
elif (strKey == "_file_correction_image_flat-field"):
xsDataFileFlat = XSDataFile()
xsDataFileFlat.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_image_flat_field(xsDataFileFlat)
elif (strKey == "_file_correction_image-mask"):
xsDataFileMask = XSDataFile()
xsDataFileMask.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_image_mask(xsDataFileMask)
elif (strKey == "_file_correction_spline_spatial-distortion"):
xsDataFileSpatialDist = XSDataFile()
xsDataFileSpatialDist.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_spline_spatial_distortion(xsDataFileSpatialDist)
if self.xsdForceImageParam is not None:
self.forceImageParam(self.xsdForceImageParam)
if self.xsdForceScanParam is not None:
self.forceScanParam(self.xsdForceScanParam)
xsDataInputPowderIntegration.setImageParameters(self.xsDataDiffractionCTImage)
xsDataInputPowderIntegration.setInstrumentParameters(self.xsDataDiffractionCTInstrument)
xsDataInputPowderIntegration.setImageFile(self.xsDataFileInputImage)
# Set the destination directory for output XRPD file
strDestinationDirectory = os.path.join(self.getDataInput().getDestinationDirectory().getPath().getValue(), \
self.getDataInput().getPowderDiffractionSubdirectory().getValue())
if self.xsDataDiffractionCTInstrument.get_tomo_scan_type().getValue().lower() in ["flat", "spiral"]:
pyintLineNumber = int(abs(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_rotation().getValue()) / self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_rotation_inc().getValue())
elif self.xsDataDiffractionCTInstrument.get_tomo_scan_type().getValue().lower() == "mapping": #I agree mappings are not sinograms but the really looks like, no ?
pyintLineNumber = int(abs(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z().getValue() - self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_min().getValue()) / self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_inc().getValue())
else:
pyintLineNumber = None
try:
strDestinationDirectory = "%s%04i" % (strDestinationDirectory, pyintLineNumber)
except TypeError:
pass #if pyintLineNumber is none: do not add suffix
xsDataInputPowderIntegration.setDestinationDir(XSDataFile(XSDataString(strDestinationDirectory)))
self.edPluginPowderIntegration.setDataInput(xsDataInputPowderIntegration)
def doFailureReadHeader(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_2.doFailureReadHeader")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlDiffractionCTv1_2.doFailureReadHeader")
self.setFailure()
def doSuccessPowderIntegration(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_2.doSuccessPowderIntegration")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlDiffractionCTv1_2.doSuccessPowderIntegration")
self.xsDataResultDiffractionCT = XSDataResultDiffractionCT()
xsDataFileIntegratedIntensities = _edPlugin.getDataOutput().getIntegratedIntensities()
if (xsDataFileIntegratedIntensities is not None):
# EDVerbose.DEBUG(self.edPluginPowderIntegration.getDataOutput().mashal())
xsdPathFileIntegratedIntensities = xsDataFileIntegratedIntensities.getPath()
if self.powderDiffractionFormat == "edf":
self.xsDataResultDiffractionCT.setIntegratedIntensities(xsDataFileIntegratedIntensities)
else:
xsdInput1DPowderEDF = XSDataInput1DPowderEDF()
xsdInput1DPowderEDF.setEdfFile(xsDataFileIntegratedIntensities)
xsdOutFile = XSDataFile()
xsdOutFile.setPath(XSDataString(os.path.splitext(xsdPathFileIntegratedIntensities.getValue())[0] + "." + self.powderDiffractionFormat))
xsdInput1DPowderEDF.setOutputFile(xsdOutFile)
xsdInput1DPowderEDF.setOutputFormat(XSDataString(self.powderDiffractionFormat))
self.edPluginExportAsciiPowder.setDataInput(xsdInput1DPowderEDF)
xsDataInputHDF5MapSpectra = XSDataInputHDF5MapSpectra()
xsDataMesh = XSDataMeshScan()
xsDataSpectrum = XSDataSpectrum()
xsDataSpectrum.setPath(xsdPathFileIntegratedIntensities)
strDestinationFile = os.path.join(self.getDataInput().getDestinationDirectory().getPath().getValue(), \
self.getDataInput().getSinogramFileNamePrefix().getValue() + ".h5")
xsDataPathSinogram = XSDataFile()
xsDataPathSinogram.setPath(XSDataString(strDestinationFile))
xsDataInputHDF5MapSpectra.setHDF5File(xsDataPathSinogram)
xsDataInputHDF5MapSpectra.setInternalHDF5Path(XSDataString("RawDCT"))
if self.xsDataDiffractionCTInstrument.get_tomo_scan_type().getValue().lower() in ["flat", "spiral"]:
xsDataSpectrum.setFastMotorPosition(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x())
xsDataMesh.setFastMotorStart(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x_min())
xsDataMesh.setFastMotorStop(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x_max())
xsSteps = XSDataInteger(int(round(\
(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x_max().getValue() - \
self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x_min().getValue()) / \
self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x_inc().getValue() \
)))
xsDataMesh.setFastMotorSteps(xsSteps)
xsDataMesh.setSlowMotorStart(XSDataDouble(0.0))
xsDataMesh.setSlowMotorStop(self.xsDataDiffractionCTInstrument.get_tomo_scan_ampl())
xsSteps = XSDataInteger(int(round(\
self.xsDataDiffractionCTInstrument.get_tomo_scan_ampl().getValue() / \
self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_rotation_inc().getValue())))
xsDataMesh.setSlowMotorSteps(xsSteps)
xsDataSpectrum.setSlowMotorPosition(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_rotation())
elif self.xsDataDiffractionCTInstrument.get_tomo_scan_type().getValue().lower() == "mapping": #I agree mappings are not sinograms but the really looks like, no ?
xsDataSpectrum.setFastMotorPosition(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x())
xsDataSpectrum.setSlowMotorPosition(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z())
xsSteps = XSDataInteger(int(round(\
(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x_max().getValue() - \
self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x_min().getValue()) / \
self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x_inc().getValue() \
)))
xsDataMesh.setFastMotorSteps(xsSteps)
xsDataMesh.setFastMotorStop(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x_max())
xsDataMesh.setFastMotorStart(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_x_min())
xsSteps = XSDataInteger(int(round(\
(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_max().getValue() - \
self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_min().getValue()) / \
self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_inc().getValue() \
)))
xsDataMesh.setSlowMotorSteps(xsSteps)
xsDataMesh.setSlowMotorStop(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_max())
xsDataMesh.setSlowMotorStart(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_min())
xsDataSpectrum.setMeshScan(xsDataMesh)
xsDataInputHDF5MapSpectra.setInputSpectrumFile([xsDataSpectrum])
self.edPluginHDF5MapSpectra.setDataInput(xsDataInputHDF5MapSpectra)
def doFailurePowderIntegration(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_2.doFailurePowderIntegration")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlDiffractionCTv1_2.doFailurePowderIntegration")
self.setFailure()
def doSuccessWriteSinogram(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_2.doSuccessWriteSinogram")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlDiffractionCTv1_2.doSuccessWriteSinogram")
xsDataResultWriteSinogram = self.edPluginHDF5MapSpectra.getDataOutput()
if (xsDataResultWriteSinogram is not None):
self.xsDataResultDiffractionCT.setSinogramFile([xsDataResultWriteSinogram.getHDF5File()])
def doFailureWriteSinogram(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_2.doFailureWriteSinogram")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlDiffractionCTv1_2.doFailureWriteSinogram")
self.setFailure()
def doSuccessExportAsciiPowder(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_2.doSuccessExportAsciiPowder")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlDiffractionCTv1_2.doSuccessExportAsciiPowder")
xsDataResultExport1DPower = _edPlugin.getDataOutput()
if (xsDataResultExport1DPower is not None):
self.xsDataResultDiffractionCT.setIntegratedIntensities(xsDataResultExport1DPower.getOutputFile())
def doFailureExportAsciiPowder(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_2.doFailureExportAsciiPowder")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlDiffractionCTv1_2.doFailureExportAsciiPowder")
self.setFailure()
def forceImageParam(self, xsdForceImageParam):
"""
Helper function to override self.xsDataDiffractionCTImage with the contents of xsdForceImageParam
@param xsDataDiffractionCTImage: instance of XSDataDiffractionCTImage
@return: None
"""
if xsdForceImageParam.get_array_element_size_1() is not None:
self.xsDataDiffractionCTImage.set_array_element_size_1(xsdForceImageParam.get_array_element_size_1())
if xsdForceImageParam.get_array_element_size_2() is not None:
self.xsDataDiffractionCTImage.set_array_element_size_2(xsdForceImageParam.get_array_element_size_2())
if xsdForceImageParam.get_diffrn_detector_element_center_1() is not None:
self.xsDataDiffractionCTImage.set_diffrn_detector_element_center_1(xsdForceImageParam.get_diffrn_detector_element_center_1())
if xsdForceImageParam.get_diffrn_detector_element_center_2() is not None:
self.xsDataDiffractionCTImage.set_diffrn_detector_element_center_2(xsdForceImageParam.get_diffrn_detector_element_center_2())
if xsdForceImageParam.get_file_correction_image_dark_current() is not None:
self.xsDataDiffractionCTImage.set_file_correction_image_dark_current(xsdForceImageParam.get_file_correction_image_dark_current())
if xsdForceImageParam.get_file_correction_image_flat_field() is not None:
self.xsDataDiffractionCTImage.set_file_correction_image_flat_field(xsdForceImageParam.get_file_correction_image_flat_field())
if xsdForceImageParam.get_file_correction_image_mask() is not None:
self.xsDataDiffractionCTImage.set_file_correction_image_mask(xsdForceImageParam.get_file_correction_image_mask())
if xsdForceImageParam.get_file_correction_spline_spatial_distortion() is not None:
self.xsDataDiffractionCTImage.set_file_correction_spline_spatial_distortion(xsdForceImageParam.get_file_correction_spline_spatial_distortion())
if xsdForceImageParam.get_pd_instr_special_details_tilt_angle() is not None:
self.xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_angle(xsdForceImageParam.get_pd_instr_special_details_tilt_angle())
if xsdForceImageParam.get_pd_instr_special_details_tilt_rotation() is not None:
self.xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_rotation(xsdForceImageParam.get_pd_instr_special_details_tilt_rotation())
def forceScanParam(self, xsdForceScanParam):
"""
Helper function to override self.xsDataDiffractionCTInstrument with the contents of xsdForceScanParam
@param xsdForceScanParam: instance of XSDataDiffractionCTInstrument
@return: None
"""
if xsdForceScanParam.get_diffrn_radiation_wavelength() is not None:
self.xsDataDiffractionCTInstrument.set_diffrn_radiation_wavelength(xsdForceScanParam.get_diffrn_radiation_wavelength())
if xsdForceScanParam.get_pd_instr_dist_spec_detc() is not None:
self.xsDataDiffractionCTInstrument.set_pd_instr_dist_spec_detc(xsdForceScanParam.get_pd_instr_dist_spec_detc())
if xsdForceScanParam.get_pd_meas_2theta_range_inc() is not None:
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_inc(xsdForceScanParam.get_pd_meas_2theta_range_inc())
if xsdForceScanParam.get_pd_meas_2theta_range_max() is not None:
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_max(xsdForceScanParam.get_pd_meas_2theta_range_max())
if xsdForceScanParam.get_pd_meas_2theta_range_min() is not None:
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_min(xsdForceScanParam.get_pd_meas_2theta_range_min())
if xsdForceScanParam.get_synchrotron_photon_flux() is not None:
self.xsDataDiffractionCTInstrument.set_synchrotron_photon_flux(xsdForceScanParam.get_synchrotron_photon_flux())
if xsdForceScanParam.get_synchrotron_ring_intensity() is not None:
self.xsDataDiffractionCTInstrument.set_synchrotron_ring_intensity(xsdForceScanParam.get_synchrotron_ring_intensity())
if xsdForceScanParam.get_tomo_scan_ampl() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_scan_ampl(xsdForceScanParam.get_tomo_scan_ampl())
if xsdForceScanParam.get_tomo_scan_type() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_scan_type(xsdForceScanParam.get_tomo_scan_type())
if xsdForceScanParam.get_tomo_spec_displ_rotation() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation(xsdForceScanParam.get_tomo_spec_displ_rotation())
if xsdForceScanParam.get_tomo_spec_displ_rotation_inc() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation_inc(xsdForceScanParam.get_tomo_spec_displ_rotation_inc())
if xsdForceScanParam.get_tomo_spec_displ_x_min() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_min(xsdForceScanParam.get_tomo_spec_displ_x_min())
if xsdForceScanParam.get_tomo_spec_displ_x_max() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_max(xsdForceScanParam.get_tomo_spec_displ_x_max())
if xsdForceScanParam.get_tomo_spec_displ_x_inc() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_inc(xsdForceScanParam.get_tomo_spec_displ_x_inc())
if xsdForceScanParam.get_tomo_spec_displ_x() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x(xsdForceScanParam.get_tomo_spec_displ_x())
if xsdForceScanParam.get_tomo_spec_displ_z() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z(xsdForceScanParam.get_tomo_spec_displ_z())
if xsdForceScanParam.get_tomo_spec_displ_z_inc() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_inc(xsdForceScanParam.get_tomo_spec_displ_z_inc())
if xsdForceScanParam.get_tomo_spec_displ_z_max() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_max(xsdForceScanParam.get_tomo_spec_displ_z_max())
if xsdForceScanParam.get_tomo_spec_displ_z_min() is not None:
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_min(xsdForceScanParam.get_tomo_spec_displ_z_min())
def doSuccessReadHeader(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_2.doSuccessReadHeader")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlDiffractionCTv1_2.doSuccessReadHeader")
# Translate dictionary to image and instrument objects
xsDataInputPowderIntegration = XSDataInputPowderIntegration()
self.xsDataDiffractionCTInstrument = XSDataDiffractionCTInstrument()
self.xsDataDiffractionCTImage = XSDataDiffractionCTImage()
xsdOut = _edPlugin.getDataOutput()
if xsdOut is None:
strErr = "EDPluginControlDiffractionCTv1_2.doSuccessReadHeader: xsdataResult is None"
EDVerbose.ERROR(strErr)
self.setFailure()
raise RuntimeError(strErr)
xsDataDictionaryHeader = xsdOut.getDictionary()
for xsDataKeyValuePair in xsDataDictionaryHeader.getKeyValuePair():
strKey = str(xsDataKeyValuePair.getKey().getValue())
lstValue = xsDataKeyValuePair.getValue().getValue().split()
if len(lstValue) == 2:
strValue = lstValue[0]
strUnit = lstValue[1]
else:
strValue = xsDataKeyValuePair.getValue().getValue()
strUnit = None
if (strKey == "_diffrn_radiation_wavelength"):
xsd = EDUtilsUnit.toXSD(XSDataWavelength, strValue)
self.xsDataDiffractionCTInstrument.set_diffrn_radiation_wavelength(xsd)
elif (strKey == "_pd_instr_dist_spec/detc"):
xsd = EDUtilsUnit.toXSD(XSDataLength, strValue)
self.xsDataDiffractionCTInstrument.set_pd_instr_dist_spec_detc(xsd)
elif (strKey == "_pd_meas_2theta_range_max"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_max(xsd)
elif (strKey == "_pd_meas_2theta_range_min"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_min(xsd)
elif (strKey == "_pd_meas_2theta_range_inc"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_inc(xsd)
elif (strKey == "_synchrotron_photon-flux"):
self.xsDataDiffractionCTInstrument.set_synchrotron_photon_flux(XSDataFlux(float(strValue)))
elif (strKey == "_synchrotron_ring-intensity"):
self.xsDataDiffractionCTInstrument.set_synchrotron_ring_intensity(XSDataDouble(float(strValue)))
elif (strKey == "_tomo_scan_ampl"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_scan_ampl(xsd)
elif (strKey == "_tomo_scan_type"):
self.xsDataDiffractionCTInstrument.set_tomo_scan_type(XSDataString(strValue))
elif (strKey == "_tomo_spec_displ_rotation"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation(xsd)
elif (strKey == "_tomo_spec_displ_rotation_inc"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation_inc(xsd)
elif (strKey == "_tomo_spec_displ_x"):
xsd = EDUtilsUnit.toXSD(XSDataLength, strValue)
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x(xsd)
elif (strKey == "_tomo_spec_displ_x_inc"):
xsd = EDUtilsUnit.toXSD(XSDataLength, strValue)
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_inc(xsd)
elif (strKey == "_tomo_spec_displ_x_max"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_max(xsd)
elif (strKey == "_tomo_spec_displ_x_min"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_min(xsd)
elif (strKey == "_tomo_spec_displ_z"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z(xsd)
elif (strKey == "_tomo_spec_displ_z_inc"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_inc(xsd)
elif (strKey == "_tomo_spec_displ_z_max"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_max(xsd)
elif (strKey == "_tomo_spec_displ_z_min"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_min(xsd)
elif (strKey == "_pd_instr_special_details_tilt_angle"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_angle(xsd)
elif (strKey == "_pd_instr_special_details_tilt_rotation"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_rotation(xsd)
elif (strKey == "_array_element_size[1]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "m"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_array_element_size_1(xsd)
elif (strKey == "_array_element_size[2]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "m"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_array_element_size_2(xsd)
elif (strKey == "_diffrn_detector_element.center[1]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_diffrn_detector_element_center_1(xsd)
elif (strKey == "_diffrn_detector_element.center[2]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_diffrn_detector_element_center_2(xsd)
elif (strKey == "_file_correction_image_dark-current"):
xsDataFileDark = XSDataFile()
xsDataFileDark.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_image_dark_current(xsDataFileDark)
elif (strKey == "_file_correction_image_flat-field"):
xsDataFileFlat = XSDataFile()
xsDataFileFlat.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_image_flat_field(xsDataFileFlat)
elif (strKey == "_file_correction_image-mask"):
xsDataFileMask = XSDataFile()
xsDataFileMask.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_image_mask(xsDataFileMask)
elif (strKey == "_file_correction_spline_spatial-distortion"):
xsDataFileSpatialDist = XSDataFile()
xsDataFileSpatialDist.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_spline_spatial_distortion(xsDataFileSpatialDist)
if self.xsdForceImageParam is not None:
self.forceImageParam(self.xsdForceImageParam)
if self.xsdForceScanParam is not None:
self.forceScanParam(self.xsdForceScanParam)
xsDataInputPowderIntegration.setImageParameters(self.xsDataDiffractionCTImage)
xsDataInputPowderIntegration.setInstrumentParameters(self.xsDataDiffractionCTInstrument)
xsDataInputPowderIntegration.setImageFile(self.xsDataFileInputImage)
# Set the destination directory for output XRPD file
strDestinationDirectory = os.path.join(self.getDataInput().getDestinationDirectory().getPath().getValue(), \
self.getDataInput().getPowderDiffractionSubdirectory().getValue())
if self.xsDataDiffractionCTInstrument.get_tomo_scan_type().getValue().lower() in ["flat", "spiral"]:
pyintLineNumber = int(abs(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_rotation().getValue()) / self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_rotation_inc().getValue())
elif self.xsDataDiffractionCTInstrument.get_tomo_scan_type().getValue().lower() == "mapping": #I agree mappings are not sinograms but the really looks like, no ?
pyintLineNumber = int(abs(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z().getValue() - self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_min().getValue()) / self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_inc().getValue())
else:
pyintLineNumber = None
try:
strDestinationDirectory = "%s%04i" % (strDestinationDirectory, pyintLineNumber)
except TypeError:
pass #if pyintLineNumber is none: do not add suffix
xsDataInputPowderIntegration.setDestinationDir(XSDataFile(XSDataString(strDestinationDirectory)))
self.edPluginPowderIntegration.setDataInput(xsDataInputPowderIntegration)
class EDPluginControlDiffractionCTv1_0(EDPluginControl):
"""
This is the EDNA control plug-in for diffraction contrast tomography.
It is intented to run 2D integration provided by Fit2D for example and ....
"""
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputDiffractionCT)
self.m_strControlledPluginReadHeader = "EDPluginControlDCTReadHeaderv1_0"
self.m_edPluginReadHeader = None
self.m_strControlledPluginPowderIntegration = "EDPluginControlDCTPowderIntegrationv1_0"
self.m_edPluginPowderIntegration = None
self.m_xsDataDiffractionCTInstrument = None
self.m_xsDataDiffractionCTImage = None
self.m_xsDataFileInputImage = None
self.m_edPluginControlledPluginWriteSinogram = None
self.m_strControlledPluginWriteSinogram = "EDPluginDCTWriteSinogramv1_0"
self.m_xsDataFileInputPowderDiffraction = None
self.m_xsDataResultDiffractionCT = None
self.m_edPluginWriteSinogram = None
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.checkParameters")
self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getImage(), "No path to input image")
self.checkMandatoryParameters(self.getDataInput().getDestinationDirectory(), "No path to destination directory")
self.checkMandatoryParameters(self.getDataInput().getSinogramFileNamePrefix(), "No sinogram prefix given")
self.checkMandatoryParameters(
self.getDataInput().getPowderDiffractionSubdirectory(),
"No subdirectory prefix for powder diffraction patterns",
)
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.preProcess")
# Load the execution plugin
self.m_edPluginReadHeader = self.loadPlugin(self.m_strControlledPluginReadHeader)
self.m_edPluginPowderIntegration = self.loadPlugin(self.m_strControlledPluginPowderIntegration)
self.m_edPluginWriteSinogram = self.loadPlugin(self.m_strControlledPluginWriteSinogram)
# Set the input data for the read header plugin
xsDataInputReadHeader = XSDataInputReadHeader()
xsdataStringPathToImage = self.getDataInput().getImage().getPath()
self.m_xsDataFileInputImage = XSDataFile()
self.m_xsDataFileInputImage.setPath(xsdataStringPathToImage)
xsDataInputReadHeader.setInputFile(self.m_xsDataFileInputImage)
self.m_edPluginReadHeader.setDataInput(xsDataInputReadHeader)
def process(self, _edObject=None):
EDPluginControl.process(self)
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.process")
self.m_edPluginReadHeader.connectSUCCESS(self.doSuccessReadHeader)
self.m_edPluginReadHeader.connectFAILURE(self.doFailureReadHeader)
self.m_edPluginPowderIntegration.connectSUCCESS(self.doSuccessPowderIntegration)
self.m_edPluginPowderIntegration.connectFAILURE(self.doFailurePowderIntegration)
self.m_edPluginWriteSinogram.connectSUCCESS(self.doSuccessWriteSinogram)
self.m_edPluginWriteSinogram.connectFAILURE(self.doFailureWriteSinogram)
self.m_edPluginReadHeader.executeSynchronous()
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.postProcess")
self.setDataOutput(self.m_xsDataResultDiffractionCT)
def doSuccessReadHeader(self, _edPlugin=None):
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.doSuccessReadHeader")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlDiffractionCTv1_0.doSuccessReadHeader")
# Translate dictionary to image and instrument objects
xsDataInputPowderIntegration = XSDataInputPowderIntegration()
self.m_xsDataDiffractionCTInstrument = XSDataDiffractionCTInstrument()
self.m_xsDataDiffractionCTImage = XSDataDiffractionCTImage()
xsDataDictionaryHeader = self.m_edPluginReadHeader.getDataOutput().getDictionary()
for xsDataKeyValuePair in xsDataDictionaryHeader.getKeyValuePair():
strKey = str(xsDataKeyValuePair.getKey().getValue())
strValue = str(xsDataKeyValuePair.getValue().getValue())
if strKey == "_diffrn_radiation_wavelength":
self.m_xsDataDiffractionCTInstrument.set_diffrn_radiation_wavelength(XSDataWavelength(float(strValue)))
elif strKey == "_pd_instr_dist_spec/detc":
self.m_xsDataDiffractionCTInstrument.set_pd_instr_dist_spec_detc(XSDataLength(float(strValue)))
elif strKey == "_pd_meas_2theta_range_max":
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_max(XSDataAngle(float(strValue)))
elif strKey == "_pd_meas_2theta_range_min":
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_min(XSDataAngle(float(strValue)))
elif strKey == "_pd_meas_2theta_range_inc":
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_inc(XSDataAngle(float(strValue)))
elif strKey == "_synchrotron_photon-flux":
self.m_xsDataDiffractionCTInstrument.set_synchrotron_photon_flux(XSDataFlux(float(strValue)))
elif strKey == "_synchrotron_ring-intensity":
self.m_xsDataDiffractionCTInstrument.set_synchrotron_ring_intensity(XSDataDouble(float(strValue)))
elif strKey == "_tomo_scan_ampl":
self.m_xsDataDiffractionCTInstrument.set_tomo_scan_ampl(XSDataAngle(float(strValue)))
elif strKey == "_tomo_scan_type":
self.m_xsDataDiffractionCTInstrument.set_tomo_scan_type(XSDataString(strValue))
elif strKey == "_tomo_spec_displ_rotation":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation(XSDataAngle(float(strValue)))
elif strKey == "_tomo_spec_displ_rotation_inc":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation_inc(XSDataAngle(float(strValue)))
elif strKey == "_tomo_spec_displ_x":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_x_inc":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_inc(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_x_max":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_max(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_x_min":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_min(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_z":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_z_inc":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_inc(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_z_max":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_max(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_z_min":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_min(XSDataLength(float(strValue)))
elif strKey == "_pd_instr_special_details_tilt_angle":
self.m_xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_angle(XSDataAngle(float(strValue)))
elif strKey == "_pd_instr_special_details_tilt_rotation":
self.m_xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_rotation(XSDataAngle(float(strValue)))
elif strKey == "_array_element_size[1]":
self.m_xsDataDiffractionCTImage.set_array_element_size_1(XSDataLength(float(strValue)))
elif strKey == "_array_element_size[2]":
self.m_xsDataDiffractionCTImage.set_array_element_size_2(XSDataLength(float(strValue)))
elif strKey == "_diffrn_detector_element.center[1]":
self.m_xsDataDiffractionCTImage.set_diffrn_detector_element_center_1(XSDataLength(float(strValue)))
elif strKey == "_diffrn_detector_element.center[2]":
self.m_xsDataDiffractionCTImage.set_diffrn_detector_element_center_2(XSDataLength(float(strValue)))
## Here the tricky case of lists ....
# elif strKey.startswith("_pd_sum_2theta_range_max"):
# if strKey.find("[")>0:
# pyintIndex = int(strKey.split("[")[1].split("]")[0]) - 1 #gets the int that is between []
# else:
# pyintIndex = 0
# while len(self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()) < pyintIndex + 1:
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max().append(None)
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()[pyintIndex] = XSDataAngle(float(strValue))
# elif strKey.startswith("_pd_sum_2theta_range_min"):
# if strKey.find("[")>0:
# pyintIndex = int(strKey.split("[")[1].split("]")[0]) - 1 #gets the int that is between []
# else:
# pyintIndex = 0
# while len(self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()) < pyintIndex + 1:
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min().append(None)
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()[pyintIndex] = XSDataAngle(float(strValue))
##end Seems OK 20091023
elif strKey == "_file_correction_image_dark-current":
xsDataFileDark = XSDataFile()
xsDataFileDark.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_dark_current(xsDataFileDark)
elif strKey == "_file_correction_image_flat-field":
xsDataFileFlat = XSDataFile()
xsDataFileFlat.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_flat_field(xsDataFileFlat)
elif strKey == "_file_correction_image-mask":
xsDataFileMask = XSDataFile()
xsDataFileMask.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_mask(xsDataFileMask)
elif strKey == "_file_correction_spline_spatial-distortion":
xsDataFileSpatialDist = XSDataFile()
xsDataFileSpatialDist.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_spline_spatial_distortion(xsDataFileSpatialDist)
xsDataInputPowderIntegration.setImageParameters(self.m_xsDataDiffractionCTImage)
xsDataInputPowderIntegration.setInstrumentParameters(self.m_xsDataDiffractionCTInstrument)
xsDataInputPowderIntegration.setImageFile(self.m_xsDataFileInputImage)
self.m_edPluginPowderIntegration.setDataInput(xsDataInputPowderIntegration)
self.m_edPluginPowderIntegration.executeSynchronous()
def doFailureReadHeader(self, _edPlugin=None):
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.doFailureReadHeader")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlDiffractionCTv1_0.doFailureReadHeader")
def doSuccessPowderIntegration(self, _edPlugin=None):
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.doSuccessPowderIntegration")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlDiffractionCTv1_0.doSuccessPowderIntegration")
self.m_xsDataResultDiffractionCT = XSDataResultDiffractionCT()
# Copy file to final destination and add path to result object
xsDataFileIntegratedIntensities = self.m_edPluginPowderIntegration.getDataOutput().getIntegratedIntensities()
EDVerbose.DEBUG("Path to cif: " + xsDataFileIntegratedIntensities.getPath().getValue())
EDVerbose.DEBUG("%s" % xsDataFileIntegratedIntensities)
if xsDataFileIntegratedIntensities is not None:
strOutputFilePath = xsDataFileIntegratedIntensities.getPath().getValue()
strDestinationDirectory = self.getDataInput().getDestinationDirectory().getPath().getValue()
strPowderDiffractionSubdirectory = self.getDataInput().getPowderDiffractionSubdirectory().getValue()
if not os.path.isdir(strDestinationDirectory):
os.mkdir(strDestinationDirectory)
if self.m_xsDataDiffractionCTInstrument.get_tomo_scan_type().getValue().lower() in ["flat", "spiral"]:
# pyintLineNumber = int( abs( float( self.cif[ "_tomo_spec_displ_rotation" ] ) / float( self.cif[ "_tomo_spec_displ_rotation_inc" ] ) ) )
pyintLineNumber = int(
abs(self.m_xsDataDiffractionCTInstrument.get_tomo_spec_displ_rotation().getValue())
/ self.m_xsDataDiffractionCTInstrument.get_tomo_spec_displ_rotation_inc().getValue()
)
elif (
self.m_xsDataDiffractionCTInstrument.get_tomo_scan_type().getValue().lower() == "mapping"
): # I agree mappings are not sinograms but the really looks like, no ?
# pyintLineNumber = int( abs( ( float( self.cif[ "_tomo_spec_displ_z" ]) - float ( self.cif [ "_tomo_spec_displ_z_min" ] ) ) / float( self.cif["_tomo_spec_displ_z_inc"] ) ) )
pyintLineNumber = int(
abs(
self.m_xsDataDiffractionCTInstrument.get_tomo_spec_displ_z().getValue()
- self.m_xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_min().getValue()
)
/ self.m_xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_inc().getValue()
)
else:
pyintLineNumber = None
if pyintLineNumber is not None:
pystrDestinationSubDir = "%s%04i" % (strPowderDiffractionSubdirectory, pyintLineNumber)
strDestinationDirectoryWithSub = os.path.join(strDestinationDirectory, pystrDestinationSubDir)
strDestinationFilePath = os.path.join(
strDestinationDirectoryWithSub, os.path.basename(strOutputFilePath)
)
if not os.path.isdir(os.path.join(strDestinationDirectoryWithSub)):
os.mkdir(strDestinationDirectoryWithSub)
EDVerbose.DEBUG("Full path should be now: %s" % strDestinationFilePath)
else:
EDVerbose.DEBUG(
"No modification of the output directory: I was not able to determine on which line of the sinogram I am."
)
strDestinationFilePath = os.path.abspath(
os.path.join(strDestinationDirectory, EDUtilsFile.getBaseName(strOutputFilePath))
)
EDUtilsFile.copyFile(strOutputFilePath, strDestinationFilePath)
xsDataFileDestination = XSDataFile()
xsDataFileDestination.setPath(XSDataString(strDestinationFilePath))
self.m_xsDataResultDiffractionCT.setIntegratedIntensities(xsDataFileDestination)
xsDataPathSinogramDirectory = XSDataFile()
xsDataPathSinogramDirectory.setPath(XSDataString(strDestinationDirectory))
xsDataInputWriteSinogram = XSDataInputWriteSinogram()
xsDataInputWriteSinogram.setSinogramDirectory(xsDataPathSinogramDirectory)
xsDataInputWriteSinogram.setIntegratedIntensities(xsDataFileDestination)
xsDataInputWriteSinogram.setSinogramFileNamePrefix(self.getDataInput().getSinogramFileNamePrefix())
self.m_edPluginWriteSinogram.setDataInput(xsDataInputWriteSinogram)
self.m_edPluginWriteSinogram.executeSynchronous()
def doFailurePowderIntegration(self, _edPlugin=None):
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.doFailurePowderIntegration")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlDiffractionCTv1_0.doFailurePowderIntegration")
def doSuccessWriteSinogram(self, _edPlugin=None):
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.doSuccessWriteSinogram")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlDiffractionCTv1_0.doSuccessWriteSinogram")
xsDataResultWriteSinogram = self.m_edPluginWriteSinogram.getDataOutput()
if xsDataResultWriteSinogram is not None:
self.m_xsDataResultDiffractionCT.setSinogramFile(xsDataResultWriteSinogram.getSinogramFile())
def doFailureWriteSinogram(self, _edPlugin=None):
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.doFailureWriteSinogram")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlDiffractionCTv1_0.doFailureWriteSinogram")
def doSuccessReadHeader(self, _edPlugin=None):
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.doSuccessReadHeader")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlDiffractionCTv1_0.doSuccessReadHeader")
# Translate dictionary to image and instrument objects
xsDataInputPowderIntegration = XSDataInputPowderIntegration()
self.m_xsDataDiffractionCTInstrument = XSDataDiffractionCTInstrument()
self.m_xsDataDiffractionCTImage = XSDataDiffractionCTImage()
xsDataDictionaryHeader = self.m_edPluginReadHeader.getDataOutput().getDictionary()
for xsDataKeyValuePair in xsDataDictionaryHeader.getKeyValuePair():
strKey = str(xsDataKeyValuePair.getKey().getValue())
strValue = str(xsDataKeyValuePair.getValue().getValue())
if strKey == "_diffrn_radiation_wavelength":
self.m_xsDataDiffractionCTInstrument.set_diffrn_radiation_wavelength(XSDataWavelength(float(strValue)))
elif strKey == "_pd_instr_dist_spec/detc":
self.m_xsDataDiffractionCTInstrument.set_pd_instr_dist_spec_detc(XSDataLength(float(strValue)))
elif strKey == "_pd_meas_2theta_range_max":
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_max(XSDataAngle(float(strValue)))
elif strKey == "_pd_meas_2theta_range_min":
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_min(XSDataAngle(float(strValue)))
elif strKey == "_pd_meas_2theta_range_inc":
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_inc(XSDataAngle(float(strValue)))
elif strKey == "_synchrotron_photon-flux":
self.m_xsDataDiffractionCTInstrument.set_synchrotron_photon_flux(XSDataFlux(float(strValue)))
elif strKey == "_synchrotron_ring-intensity":
self.m_xsDataDiffractionCTInstrument.set_synchrotron_ring_intensity(XSDataDouble(float(strValue)))
elif strKey == "_tomo_scan_ampl":
self.m_xsDataDiffractionCTInstrument.set_tomo_scan_ampl(XSDataAngle(float(strValue)))
elif strKey == "_tomo_scan_type":
self.m_xsDataDiffractionCTInstrument.set_tomo_scan_type(XSDataString(strValue))
elif strKey == "_tomo_spec_displ_rotation":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation(XSDataAngle(float(strValue)))
elif strKey == "_tomo_spec_displ_rotation_inc":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation_inc(XSDataAngle(float(strValue)))
elif strKey == "_tomo_spec_displ_x":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_x_inc":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_inc(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_x_max":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_max(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_x_min":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_min(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_z":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_z_inc":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_inc(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_z_max":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_max(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_z_min":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_min(XSDataLength(float(strValue)))
elif strKey == "_pd_instr_special_details_tilt_angle":
self.m_xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_angle(XSDataAngle(float(strValue)))
elif strKey == "_pd_instr_special_details_tilt_rotation":
self.m_xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_rotation(XSDataAngle(float(strValue)))
elif strKey == "_array_element_size[1]":
self.m_xsDataDiffractionCTImage.set_array_element_size_1(XSDataLength(float(strValue)))
elif strKey == "_array_element_size[2]":
self.m_xsDataDiffractionCTImage.set_array_element_size_2(XSDataLength(float(strValue)))
elif strKey == "_diffrn_detector_element.center[1]":
self.m_xsDataDiffractionCTImage.set_diffrn_detector_element_center_1(XSDataLength(float(strValue)))
elif strKey == "_diffrn_detector_element.center[2]":
self.m_xsDataDiffractionCTImage.set_diffrn_detector_element_center_2(XSDataLength(float(strValue)))
## Here the tricky case of lists ....
# elif strKey.startswith("_pd_sum_2theta_range_max"):
# if strKey.find("[")>0:
# pyintIndex = int(strKey.split("[")[1].split("]")[0]) - 1 #gets the int that is between []
# else:
# pyintIndex = 0
# while len(self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()) < pyintIndex + 1:
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max().append(None)
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()[pyintIndex] = XSDataAngle(float(strValue))
# elif strKey.startswith("_pd_sum_2theta_range_min"):
# if strKey.find("[")>0:
# pyintIndex = int(strKey.split("[")[1].split("]")[0]) - 1 #gets the int that is between []
# else:
# pyintIndex = 0
# while len(self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()) < pyintIndex + 1:
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min().append(None)
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()[pyintIndex] = XSDataAngle(float(strValue))
##end Seems OK 20091023
elif strKey == "_file_correction_image_dark-current":
xsDataFileDark = XSDataFile()
xsDataFileDark.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_dark_current(xsDataFileDark)
elif strKey == "_file_correction_image_flat-field":
xsDataFileFlat = XSDataFile()
xsDataFileFlat.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_flat_field(xsDataFileFlat)
elif strKey == "_file_correction_image-mask":
xsDataFileMask = XSDataFile()
xsDataFileMask.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_mask(xsDataFileMask)
elif strKey == "_file_correction_spline_spatial-distortion":
xsDataFileSpatialDist = XSDataFile()
xsDataFileSpatialDist.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_spline_spatial_distortion(xsDataFileSpatialDist)
xsDataInputPowderIntegration.setImageParameters(self.m_xsDataDiffractionCTImage)
xsDataInputPowderIntegration.setInstrumentParameters(self.m_xsDataDiffractionCTInstrument)
xsDataInputPowderIntegration.setImageFile(self.m_xsDataFileInputImage)
self.m_edPluginPowderIntegration.setDataInput(xsDataInputPowderIntegration)
self.m_edPluginPowderIntegration.executeSynchronous()