def preProcess(self):
"""
"""
EDTestCasePluginExecute.preProcess(self)
self.loadTestImage([ "diff6105.edf", "flats0001.edf", "darks0001.edf", "frelon_spline_file_to_correct_SPD.spline" ])
strPathToCifHeaders = (os.path.abspath(os.path.join(self.getPluginTestsDataHome(), "default_headers.cif")))
cifDictDefaultHeaders = CIF()
cifDictDefaultHeaders.loadCIF(strPathToCifHeaders)
strImageDir = self.getTestsDataImagesHome()
strPathToInputImage = os.path.abspath(os.path.join(strImageDir, "diff6105.edf"))
strPathToDarkImage = os.path.abspath(os.path.join(strImageDir, "darks0001.edf"))
strPathToFlatImage = os.path.abspath(os.path.join(strImageDir, "flats0001.edf"))
strPathToSplineFile = os.path.abspath(os.path.join(strImageDir, "frelon_spline_file_to_correct_SPD.spline"))
cifDictDefaultHeaders[ "_file_correction_image_dark-current" ] = strPathToDarkImage
cifDictDefaultHeaders[ "_file_correction_image_flat-field" ] = strPathToFlatImage
cifDictDefaultHeaders[ "_file_correction_spline_spatial-distortion" ] = strPathToSplineFile
strPathToTestImage = os.path.abspath(os.path.join(strImageDir, "test.edf"))
strPathToTestCif = os.path.abspath(os.path.join(strImageDir, "test.cif"))
if os.path.isfile(strPathToTestImage):
os.remove(strPathToTestImage)
EDFfileCompleter.edf_keywords_completion(strPathToInputImage, cifDictDefaultHeaders, strPathToTestImage)
cifDictDefaultHeaders.saveCIF(strPathToTestCif)
for oneLoop in loops:
oneLoopIdx = 0 #this is a index of the loop
for oneLoopdict in oneLoop[1]:
oneLoopIdx += 1
for loopKey in oneLoop[0]:
headers["%s[%i]" %
(loopKey, oneLoopIdx)] = oneLoopdict[loopKey]
else:
headers[key] = keywords[key]
outfile = EDF.EdfFile(edfout)
outfile.WriteImage(headers, data)
if __name__ == '__main__':
EDF_to_process = []
cif = CIF()
if len(sys.argv) == 0:
raise "Please enter the name of a EDF file to be completed"
for i in sys.argv[1:]:
if os.path.isfile(i):
if os.path.splitext(i)[1].lower() == ".edf":
EDF_to_process.append(i)
elif os.path.splitext(i)[1].lower() == ".cif":
print "I agree with you: it would be nice to be allowed to give a CIF input file to feed the system"
cif.loadCIF(i)
else:
print "Sorry I don't know what to do with this %s file" % i
else:
print "Sorry %s is not a readable file" % i
if len(cif) == 0:
for oneLoop in loops:
oneLoopIdx = 0 #this is a index of the loop
for oneLoopdict in oneLoop[1]:
oneLoopIdx += 1
for loopKey in oneLoop[0]:
headers[ "%s[%i]" % (loopKey , oneLoopIdx) ] = oneLoopdict [ loopKey ]
else:
headers[key] = keywords[key]
outfile = EDF.EdfFile(edfout)
outfile.WriteImage(headers, data)
if __name__ == '__main__':
EDF_to_process = []
cif = CIF()
if len(sys.argv) == 0:
raise "Please enter the name of a EDF file to be completed"
for i in sys.argv[1:]:
if os.path.isfile(i):
if os.path.splitext(i)[1].lower() == ".edf" :
EDF_to_process.append(i)
elif os.path.splitext(i)[1].lower() == ".cif" :
print "I agree with you: it would be nice to be allowed to give a CIF input file to feed the system"
cif.loadCIF(i)
else:
print "Sorry I don't know what to do with this %s file" % i
else:
print "Sorry %s is not a readable file" % i
if len(cif) == 0:
def preProcess(self, _edObject=None):
"""
"""
EDPluginExec.preProcess(self)
EDVerbose.DEBUG("*** EDPluginDCTWriteSinogramv1_0.preProcess")
pyStrPathToInputCIFFile = self.getDataInput().getIntegratedIntensities().getPath().getValue()
EDVerbose.DEBUG("This is the file which will be analyzed: %s" % pyStrPathToInputCIFFile)
self.pystrPathToSinogramsDir = self.getDataInput().getSinogramDirectory().getPath().getValue()
if not PyOs.path.isdir(self.pystrPathToSinogramsDir):
PyOs.makedirs(self.pystrPathToSinogramsDir)
self.pystrSinogramPrefix = self.getDataInput().getSinogramFileNamePrefix().getValue()
EDVerbose.DEBUG(
"Now generation of the SinoGrams, Path: %s, Prefix= %s"
% (self.pystrPathToSinogramsDir, self.pystrSinogramPrefix)
)
if not EDUtilsPath.existPath(pyStrPathToInputCIFFile):
pyStrErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (
self.getPluginName() + ".preProcess",
pyStrPathToInputFile,
)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
raise RuntimeError, pyStrErrorMessage
# File exists, try to read it with the CIF library
try:
self.m_cifPowderData = CIF()
self.m_cifPowderData.loadCIF(pyStrPathToInputCIFFile)
EDVerbose.DEBUG("Parsing of the CIF file %s successful" % pyStrPathToInputCIFFile)
except Exception:
pyStrErrorMessage = EDMessage.ERROR_UNEXPECTED_01 % (
"EDPluginDCTWriteSinogramv1_0.preProcess: Error when trying to read CIF file : %s"
% pyStrPathToInputCIFFile
)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
# Just raise the exception in order to not loose the error stack trace
raise
if not self.m_cifPowderData.exists("_tomo_scan_type"):
EDVerbose.DEBUG(
"How do you want to generate a Sinogram if you are lacking essential things like the scan type !!!!"
)
raise
self.pydMetaDataEDF = self.m_cifPowderData.copy() # This is a simple python dictionary
if self.pydMetaDataEDF.has_key("loop_"):
self.pydMetaDataEDF.pop("loop_")
if self.pydMetaDataEDF.has_key("_synchrotron_photon-flux"):
self.pydMetaDataEDF.pop("_synchrotron_photon-flux")
if self.pydMetaDataEDF.has_key("_synchrotron_ring-intensity"):
self.pydMetaDataEDF.pop("_synchrotron_ring-intensity")
if self.pydMetaDataEDF.has_key("_tomo_spec_displ_rotation"):
self.pydMetaDataEDF.pop("_tomo_spec_displ_rotation")
if self.pydMetaDataEDF.has_key("_tomo_spec_displ_x"):
self.pydMetaDataEDF.pop("_tomo_spec_displ_x")
if self.pydMetaDataEDF.has_key("_tomo_spec_displ_z"):
self.pydMetaDataEDF.pop("_tomo_spec_displ_z")
self.powderIntegrator = PowderIntegrator(self.m_cifPowderData)
self.pyintXpos, self.pyintYpos = self.powderIntegrator.getSinogramPosition()
(Xmax, Ymax) = self.powderIntegrator.getSinogramSize()
self.pydProcessSinograms = {}
for pystrSinogramSuffix in ["PhotonFlux", "IntegratedRaw", "IntegratedCor"]:
pystrSinogramFullPath = PyOs.path.join(
self.pystrPathToSinogramsDir, self.pystrSinogramPrefix + "Sinogram" + pystrSinogramSuffix
)
self.pydProcessSinograms[pystrSinogramFullPath] = pystrSinogramSuffix
if self.m_cifPowderData.exists("_pd_sum_2theta_range_min"):
for basename in ["Raw", "Cor"]:
startregion = float(self.m_cifPowderData["_pd_sum_2theta_range_min"])
stopregion = float(self.m_cifPowderData["_pd_sum_2theta_range_max"])
pystrSinogramFilename = "%sSinogramROI%i-%i%s" % (
self.pystrSinogramPrefix,
int(round(startregion)),
int(round(stopregion)),
basename,
)
pystrSinogramFullPath = PyOs.path.join(self.pystrPathToSinogramsDir, pystrSinogramFilename)
self.pydProcessSinograms[pystrSinogramFullPath] = [startregion, stopregion]
else:
for oneloop in self.m_cifPowderData["loop_"]:
if "_pd_sum_2theta_range_min" in oneloop[0]:
for i in oneloop[1]:
startregion = float(i["_pd_sum_2theta_range_min"])
stopregion = float(i["_pd_sum_2theta_range_max"])
for basename in ["Raw", "Cor"]:
pystrSinogramFilename = "%sSinogramROI%i-%i%s" % (
self.pystrSinogramPrefix,
int(round(startregion)),
int(round(stopregion)),
basename,
)
pystrSinogramFullPath = PyOs.path.join(self.pystrPathToSinogramsDir, pystrSinogramFilename)
self.pydProcessSinograms[pystrSinogramFullPath] = [startregion, stopregion]
class EDPluginDCTWriteSinogramv1_0(EDPluginExec):
"""
This plugin is a part of the DiffractionCT project.
It takes as input the path to a CIF file containing integrated
intensities as well as the necessary header information.
The CIF file could for example be the result of a 2D azimuthal
integration performed by the plugin
EDPluginControlDCTPowderIntegration-v1.0.
It also takes as input the path to the directory where the
sinogram images are (or will be if they don't exist) stored,
as well as a sinogram file name prefix.
The EDPluginDCTWriteSinogramv1_0 plugin produces one or several
sinogram images depending on the header information in the CIF file.
The XSDataResultWriteSinogram object contains a list of paths to
these images.
"""
def __init__(self):
"""
Sets the data input class to XSDataInputWriteSinogram
"""
EDPluginExec.__init__(self)
self.setXSDataInputClass(XSDataInputWriteSinogram)
# self.getXSDataOutputClass( XSDataResultWriteSinogram )
self.m_cifPowderData = None
def checkParameters(self):
"""
Checks the mandatory input parameter "integratedIntensities" which is
the file path to the incoming CIF file.
"""
EDVerbose.DEBUG("*** EDPluginDCTWriteSinogramv1_0.checkParameters")
self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getIntegratedIntensities(), "integratedIntensities")
self.checkMandatoryParameters(self.getDataInput().getSinogramDirectory(), "sinogramDirectory")
self.checkMandatoryParameters(self.getDataInput().getSinogramFileNamePrefix(), "sinogramFileNamePrefix")
def preProcess(self, _edObject=None):
"""
"""
EDPluginExec.preProcess(self)
EDVerbose.DEBUG("*** EDPluginDCTWriteSinogramv1_0.preProcess")
pyStrPathToInputCIFFile = self.getDataInput().getIntegratedIntensities().getPath().getValue()
EDVerbose.DEBUG("This is the file which will be analyzed: %s" % pyStrPathToInputCIFFile)
self.pystrPathToSinogramsDir = self.getDataInput().getSinogramDirectory().getPath().getValue()
if not PyOs.path.isdir(self.pystrPathToSinogramsDir):
PyOs.makedirs(self.pystrPathToSinogramsDir)
self.pystrSinogramPrefix = self.getDataInput().getSinogramFileNamePrefix().getValue()
EDVerbose.DEBUG(
"Now generation of the SinoGrams, Path: %s, Prefix= %s"
% (self.pystrPathToSinogramsDir, self.pystrSinogramPrefix)
)
if not EDUtilsPath.existPath(pyStrPathToInputCIFFile):
pyStrErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (
self.getPluginName() + ".preProcess",
pyStrPathToInputFile,
)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
raise RuntimeError, pyStrErrorMessage
# File exists, try to read it with the CIF library
try:
self.m_cifPowderData = CIF()
self.m_cifPowderData.loadCIF(pyStrPathToInputCIFFile)
EDVerbose.DEBUG("Parsing of the CIF file %s successful" % pyStrPathToInputCIFFile)
except Exception:
pyStrErrorMessage = EDMessage.ERROR_UNEXPECTED_01 % (
"EDPluginDCTWriteSinogramv1_0.preProcess: Error when trying to read CIF file : %s"
% pyStrPathToInputCIFFile
)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
# Just raise the exception in order to not loose the error stack trace
raise
if not self.m_cifPowderData.exists("_tomo_scan_type"):
EDVerbose.DEBUG(
"How do you want to generate a Sinogram if you are lacking essential things like the scan type !!!!"
)
raise
self.pydMetaDataEDF = self.m_cifPowderData.copy() # This is a simple python dictionary
if self.pydMetaDataEDF.has_key("loop_"):
self.pydMetaDataEDF.pop("loop_")
if self.pydMetaDataEDF.has_key("_synchrotron_photon-flux"):
self.pydMetaDataEDF.pop("_synchrotron_photon-flux")
if self.pydMetaDataEDF.has_key("_synchrotron_ring-intensity"):
self.pydMetaDataEDF.pop("_synchrotron_ring-intensity")
if self.pydMetaDataEDF.has_key("_tomo_spec_displ_rotation"):
self.pydMetaDataEDF.pop("_tomo_spec_displ_rotation")
if self.pydMetaDataEDF.has_key("_tomo_spec_displ_x"):
self.pydMetaDataEDF.pop("_tomo_spec_displ_x")
if self.pydMetaDataEDF.has_key("_tomo_spec_displ_z"):
self.pydMetaDataEDF.pop("_tomo_spec_displ_z")
self.powderIntegrator = PowderIntegrator(self.m_cifPowderData)
self.pyintXpos, self.pyintYpos = self.powderIntegrator.getSinogramPosition()
(Xmax, Ymax) = self.powderIntegrator.getSinogramSize()
self.pydProcessSinograms = {}
for pystrSinogramSuffix in ["PhotonFlux", "IntegratedRaw", "IntegratedCor"]:
pystrSinogramFullPath = PyOs.path.join(
self.pystrPathToSinogramsDir, self.pystrSinogramPrefix + "Sinogram" + pystrSinogramSuffix
)
self.pydProcessSinograms[pystrSinogramFullPath] = pystrSinogramSuffix
if self.m_cifPowderData.exists("_pd_sum_2theta_range_min"):
for basename in ["Raw", "Cor"]:
startregion = float(self.m_cifPowderData["_pd_sum_2theta_range_min"])
stopregion = float(self.m_cifPowderData["_pd_sum_2theta_range_max"])
pystrSinogramFilename = "%sSinogramROI%i-%i%s" % (
self.pystrSinogramPrefix,
int(round(startregion)),
int(round(stopregion)),
basename,
)
pystrSinogramFullPath = PyOs.path.join(self.pystrPathToSinogramsDir, pystrSinogramFilename)
self.pydProcessSinograms[pystrSinogramFullPath] = [startregion, stopregion]
else:
for oneloop in self.m_cifPowderData["loop_"]:
if "_pd_sum_2theta_range_min" in oneloop[0]:
for i in oneloop[1]:
startregion = float(i["_pd_sum_2theta_range_min"])
stopregion = float(i["_pd_sum_2theta_range_max"])
for basename in ["Raw", "Cor"]:
pystrSinogramFilename = "%sSinogramROI%i-%i%s" % (
self.pystrSinogramPrefix,
int(round(startregion)),
int(round(stopregion)),
basename,
)
pystrSinogramFullPath = PyOs.path.join(self.pystrPathToSinogramsDir, pystrSinogramFilename)
self.pydProcessSinograms[pystrSinogramFullPath] = [startregion, stopregion]
def process(self, _edObject=None):
"""
This method does the calculations and create / modifies the sinograms
Pay attention: the xy coordinate are inverted when calling here to have x first coordinate as horizontal, what is different from the math convention (line/column)
"""
EDPluginExec.process(self)
EDVerbose.DEBUG("*** EDPluginDCTWriteSinogramv1_0.process")
if self.m_cifPowderData is not None:
borg2DImageWriter = Borg2DImageWriter()
EDVerbose.DEBUG(
"Now generation of the Sinograms, Path: %s, pixel position= %i,%i"
% (self.pystrPathToSinogramsDir, self.pyintXpos, self.pyintYpos)
)
for pystrSinogramFullPath in self.pydProcessSinograms:
EDVerbose.DEBUG(
"Writing Sinogram %s pixel (%i,%i)" % (pystrSinogramFullPath, self.pyintXpos, self.pyintYpos)
)
self.xMax, self.yMax = self.powderIntegrator.getSinogramSize()
# Change here if there is a new version of BorgDImageWriter
if not PyOs.path.isfile(pystrSinogramFullPath + "Size%ix%i.edf" % (self.yMax, self.xMax)):
EDVerbose.DEBUG("Creating Sinogram %s size (%i,%i)" % (pystrSinogramFullPath, self.xMax, self.yMax))
borg2DImageWriter.newFile(filename=pystrSinogramFullPath, size=(self.yMax, self.xMax))
if isinstance(self.pydProcessSinograms[pystrSinogramFullPath], str) or isinstance(
self.pydProcessSinograms[pystrSinogramFullPath], unicode
):
# EDVerbose.DEBUG( "Keyword= %s "%self.pydProcessSinograms[ pystrSinogramFullPath ])
if self.pydProcessSinograms[pystrSinogramFullPath] == "PhotonFlux":
EDVerbose.DEBUG("PhotonFlux= %s " % self.powderIntegrator.pyfPhotonFlux)
borg2DImageWriter.set(
filename=pystrSinogramFullPath,
position=(self.pyintYpos, self.pyintXpos),
value=self.powderIntegrator.pyfPhotonFlux,
)
elif self.pydProcessSinograms[pystrSinogramFullPath] == "IntegratedRaw":
EDVerbose.DEBUG("IntegratedRaw= %s " % self.powderIntegrator.integrate())
borg2DImageWriter.set(
filename=pystrSinogramFullPath,
position=(self.pyintYpos, self.pyintXpos),
value=self.powderIntegrator.integrate(),
)
elif self.pydProcessSinograms[pystrSinogramFullPath] == "IntegratedCor":
EDVerbose.DEBUG(
"IntegratedCor= %s "
% (self.powderIntegrator.integrate() / self.powderIntegrator.pyfPhotonFlux)
)
borg2DImageWriter.set(
filename=pystrSinogramFullPath,
position=(self.pyintYpos, self.pyintXpos),
value=(self.powderIntegrator.integrate() / self.powderIntegrator.pyfPhotonFlux),
)
elif isinstance(self.pydProcessSinograms[pystrSinogramFullPath], list):
if pystrSinogramFullPath[-3:] == "Raw":
EDVerbose.DEBUG(
"Raw %s - %s= %s "
% (
self.pydProcessSinograms[pystrSinogramFullPath][0],
self.pydProcessSinograms[pystrSinogramFullPath][1],
self.powderIntegrator.integrate(
*tuple(self.pydProcessSinograms[pystrSinogramFullPath])
),
)
)
borg2DImageWriter.set(
filename=pystrSinogramFullPath,
position=(self.pyintYpos, self.pyintXpos),
value=(
self.powderIntegrator.integrate(*tuple(self.pydProcessSinograms[pystrSinogramFullPath]))
),
)
elif pystrSinogramFullPath[-3:] == "Cor":
EDVerbose.DEBUG(
"Cor %s - %s= %s "
% (
self.pydProcessSinograms[pystrSinogramFullPath][0],
self.pydProcessSinograms[pystrSinogramFullPath][1],
self.powderIntegrator.integrate(*tuple(self.pydProcessSinograms[pystrSinogramFullPath]))
/ self.powderIntegrator.pyfPhotonFlux,
)
)
borg2DImageWriter.set(
filename=pystrSinogramFullPath,
position=(self.pyintYpos, self.pyintXpos),
value=(
self.powderIntegrator.integrate(*tuple(self.pydProcessSinograms[pystrSinogramFullPath]))
/ self.powderIntegrator.pyfPhotonFlux
),
)
def postProcess(self, _edObject=None):
"""
"""
EDPluginExec.postProcess(self)
EDVerbose.DEBUG("*** EDPluginDCTWriteSinogramv1_0.postProcess")
xsDataResultWriteSinogram = XSDataResultWriteSinogram()
for pystrPathToOneSinogram in self.pydProcessSinograms:
oneSinogram = XSDataFile()
oneSinogram.setPath(XSDataString(pystrPathToOneSinogram + "Size%ix%i.edf" % (self.yMax, self.xMax)))
xsDataResultWriteSinogram.addSinogramFile(oneSinogram)
EDVerbose.DEBUG("Adding sinogram: %s" % pystrPathToOneSinogram)
self.setDataOutput(xsDataResultWriteSinogram)
def preProcess(self, _edObject=None):
"""
"""
EDPluginExec.preProcess(self)
EDVerbose.DEBUG("*** EDPluginDCTWriteSinogramv1_0.preProcess")
pyStrPathToInputCIFFile = self.getDataInput().getIntegratedIntensities(
).getPath().getValue()
EDVerbose.DEBUG("This is the file which will be analyzed: %s" %
pyStrPathToInputCIFFile)
self.pystrPathToSinogramsDir = self.getDataInput(
).getSinogramDirectory().getPath().getValue()
if not PyOs.path.isdir(self.pystrPathToSinogramsDir):
PyOs.makedirs(self.pystrPathToSinogramsDir)
self.pystrSinogramPrefix = self.getDataInput(
).getSinogramFileNamePrefix().getValue()
EDVerbose.DEBUG(
"Now generation of the SinoGrams, Path: %s, Prefix= %s" %
(self.pystrPathToSinogramsDir, self.pystrSinogramPrefix))
if (not EDUtilsPath.existPath(pyStrPathToInputCIFFile)):
pyStrErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (
self.getPluginName() + ".preProcess", pyStrPathToInputFile)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
raise RuntimeError, pyStrErrorMessage
# File exists, try to read it with the CIF library
try:
self.m_cifPowderData = CIF()
self.m_cifPowderData.loadCIF(pyStrPathToInputCIFFile)
EDVerbose.DEBUG("Parsing of the CIF file %s successful" %
pyStrPathToInputCIFFile)
except Exception:
pyStrErrorMessage = EDMessage.ERROR_UNEXPECTED_01 % (
"EDPluginDCTWriteSinogramv1_0.preProcess: Error when trying to read CIF file : %s"
% pyStrPathToInputCIFFile)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
# Just raise the exception in order to not loose the error stack trace
raise
if not self.m_cifPowderData.exists("_tomo_scan_type"):
EDVerbose.DEBUG(
"How do you want to generate a Sinogram if you are lacking essential things like the scan type !!!!"
)
raise
self.pydMetaDataEDF = self.m_cifPowderData.copy(
) #This is a simple python dictionary
if self.pydMetaDataEDF.has_key("loop_"):
self.pydMetaDataEDF.pop("loop_")
if self.pydMetaDataEDF.has_key("_synchrotron_photon-flux"):
self.pydMetaDataEDF.pop("_synchrotron_photon-flux")
if self.pydMetaDataEDF.has_key("_synchrotron_ring-intensity"):
self.pydMetaDataEDF.pop("_synchrotron_ring-intensity")
if self.pydMetaDataEDF.has_key("_tomo_spec_displ_rotation"):
self.pydMetaDataEDF.pop("_tomo_spec_displ_rotation")
if self.pydMetaDataEDF.has_key("_tomo_spec_displ_x"):
self.pydMetaDataEDF.pop("_tomo_spec_displ_x")
if self.pydMetaDataEDF.has_key("_tomo_spec_displ_z"):
self.pydMetaDataEDF.pop("_tomo_spec_displ_z")
self.powderIntegrator = PowderIntegrator(self.m_cifPowderData)
self.pyintXpos, self.pyintYpos = self.powderIntegrator.getSinogramPosition(
)
(Xmax, Ymax) = self.powderIntegrator.getSinogramSize()
self.pydProcessSinograms = {}
for pystrSinogramSuffix in [
"PhotonFlux", "IntegratedRaw", "IntegratedCor"
]:
pystrSinogramFullPath = PyOs.path.join(
self.pystrPathToSinogramsDir,
self.pystrSinogramPrefix + "Sinogram" + pystrSinogramSuffix)
self.pydProcessSinograms[
pystrSinogramFullPath] = pystrSinogramSuffix
if self.m_cifPowderData.exists("_pd_sum_2theta_range_min"):
for basename in ["Raw", "Cor"]:
startregion = float(
self.m_cifPowderData["_pd_sum_2theta_range_min"])
stopregion = float(
self.m_cifPowderData["_pd_sum_2theta_range_max"])
pystrSinogramFilename = "%sSinogramROI%i-%i%s" % (
self.pystrSinogramPrefix, int(
round(startregion)), int(round(stopregion)), basename)
pystrSinogramFullPath = PyOs.path.join(
self.pystrPathToSinogramsDir, pystrSinogramFilename)
self.pydProcessSinograms[pystrSinogramFullPath] = [
startregion, stopregion
]
else:
for oneloop in self.m_cifPowderData["loop_"]:
if "_pd_sum_2theta_range_min" in oneloop[0]:
for i in oneloop[1]:
startregion = float(i["_pd_sum_2theta_range_min"])
stopregion = float(i["_pd_sum_2theta_range_max"])
for basename in ["Raw", "Cor"]:
pystrSinogramFilename = "%sSinogramROI%i-%i%s" % (
self.pystrSinogramPrefix,
int(round(startregion)), int(
round(stopregion)), basename)
pystrSinogramFullPath = PyOs.path.join(
self.pystrPathToSinogramsDir,
pystrSinogramFilename)
self.pydProcessSinograms[pystrSinogramFullPath] = [
startregion, stopregion
]
class EDPluginDCTWriteSinogramv1_0(EDPluginExec):
"""
This plugin is a part of the DiffractionCT project.
It takes as input the path to a CIF file containing integrated
intensities as well as the necessary header information.
The CIF file could for example be the result of a 2D azimuthal
integration performed by the plugin
EDPluginControlDCTPowderIntegration-v1.0.
It also takes as input the path to the directory where the
sinogram images are (or will be if they don't exist) stored,
as well as a sinogram file name prefix.
The EDPluginDCTWriteSinogramv1_0 plugin produces one or several
sinogram images depending on the header information in the CIF file.
The XSDataResultWriteSinogram object contains a list of paths to
these images.
"""
def __init__(self):
"""
Sets the data input class to XSDataInputWriteSinogram
"""
EDPluginExec.__init__(self)
self.setXSDataInputClass(XSDataInputWriteSinogram)
# self.getXSDataOutputClass( XSDataResultWriteSinogram )
self.m_cifPowderData = None
def checkParameters(self):
"""
Checks the mandatory input parameter "integratedIntensities" which is
the file path to the incoming CIF file.
"""
EDVerbose.DEBUG("*** EDPluginDCTWriteSinogramv1_0.checkParameters")
self.checkMandatoryParameters(self.getDataInput(),
"Data Input is None")
self.checkMandatoryParameters(
self.getDataInput().getIntegratedIntensities(),
"integratedIntensities")
self.checkMandatoryParameters(
self.getDataInput().getSinogramDirectory(), "sinogramDirectory")
self.checkMandatoryParameters(
self.getDataInput().getSinogramFileNamePrefix(),
"sinogramFileNamePrefix")
def preProcess(self, _edObject=None):
"""
"""
EDPluginExec.preProcess(self)
EDVerbose.DEBUG("*** EDPluginDCTWriteSinogramv1_0.preProcess")
pyStrPathToInputCIFFile = self.getDataInput().getIntegratedIntensities(
).getPath().getValue()
EDVerbose.DEBUG("This is the file which will be analyzed: %s" %
pyStrPathToInputCIFFile)
self.pystrPathToSinogramsDir = self.getDataInput(
).getSinogramDirectory().getPath().getValue()
if not PyOs.path.isdir(self.pystrPathToSinogramsDir):
PyOs.makedirs(self.pystrPathToSinogramsDir)
self.pystrSinogramPrefix = self.getDataInput(
).getSinogramFileNamePrefix().getValue()
EDVerbose.DEBUG(
"Now generation of the SinoGrams, Path: %s, Prefix= %s" %
(self.pystrPathToSinogramsDir, self.pystrSinogramPrefix))
if (not EDUtilsPath.existPath(pyStrPathToInputCIFFile)):
pyStrErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (
self.getPluginName() + ".preProcess", pyStrPathToInputFile)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
raise RuntimeError, pyStrErrorMessage
# File exists, try to read it with the CIF library
try:
self.m_cifPowderData = CIF()
self.m_cifPowderData.loadCIF(pyStrPathToInputCIFFile)
EDVerbose.DEBUG("Parsing of the CIF file %s successful" %
pyStrPathToInputCIFFile)
except Exception:
pyStrErrorMessage = EDMessage.ERROR_UNEXPECTED_01 % (
"EDPluginDCTWriteSinogramv1_0.preProcess: Error when trying to read CIF file : %s"
% pyStrPathToInputCIFFile)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
# Just raise the exception in order to not loose the error stack trace
raise
if not self.m_cifPowderData.exists("_tomo_scan_type"):
EDVerbose.DEBUG(
"How do you want to generate a Sinogram if you are lacking essential things like the scan type !!!!"
)
raise
self.pydMetaDataEDF = self.m_cifPowderData.copy(
) #This is a simple python dictionary
if self.pydMetaDataEDF.has_key("loop_"):
self.pydMetaDataEDF.pop("loop_")
if self.pydMetaDataEDF.has_key("_synchrotron_photon-flux"):
self.pydMetaDataEDF.pop("_synchrotron_photon-flux")
if self.pydMetaDataEDF.has_key("_synchrotron_ring-intensity"):
self.pydMetaDataEDF.pop("_synchrotron_ring-intensity")
if self.pydMetaDataEDF.has_key("_tomo_spec_displ_rotation"):
self.pydMetaDataEDF.pop("_tomo_spec_displ_rotation")
if self.pydMetaDataEDF.has_key("_tomo_spec_displ_x"):
self.pydMetaDataEDF.pop("_tomo_spec_displ_x")
if self.pydMetaDataEDF.has_key("_tomo_spec_displ_z"):
self.pydMetaDataEDF.pop("_tomo_spec_displ_z")
self.powderIntegrator = PowderIntegrator(self.m_cifPowderData)
self.pyintXpos, self.pyintYpos = self.powderIntegrator.getSinogramPosition(
)
(Xmax, Ymax) = self.powderIntegrator.getSinogramSize()
self.pydProcessSinograms = {}
for pystrSinogramSuffix in [
"PhotonFlux", "IntegratedRaw", "IntegratedCor"
]:
pystrSinogramFullPath = PyOs.path.join(
self.pystrPathToSinogramsDir,
self.pystrSinogramPrefix + "Sinogram" + pystrSinogramSuffix)
self.pydProcessSinograms[
pystrSinogramFullPath] = pystrSinogramSuffix
if self.m_cifPowderData.exists("_pd_sum_2theta_range_min"):
for basename in ["Raw", "Cor"]:
startregion = float(
self.m_cifPowderData["_pd_sum_2theta_range_min"])
stopregion = float(
self.m_cifPowderData["_pd_sum_2theta_range_max"])
pystrSinogramFilename = "%sSinogramROI%i-%i%s" % (
self.pystrSinogramPrefix, int(
round(startregion)), int(round(stopregion)), basename)
pystrSinogramFullPath = PyOs.path.join(
self.pystrPathToSinogramsDir, pystrSinogramFilename)
self.pydProcessSinograms[pystrSinogramFullPath] = [
startregion, stopregion
]
else:
for oneloop in self.m_cifPowderData["loop_"]:
if "_pd_sum_2theta_range_min" in oneloop[0]:
for i in oneloop[1]:
startregion = float(i["_pd_sum_2theta_range_min"])
stopregion = float(i["_pd_sum_2theta_range_max"])
for basename in ["Raw", "Cor"]:
pystrSinogramFilename = "%sSinogramROI%i-%i%s" % (
self.pystrSinogramPrefix,
int(round(startregion)), int(
round(stopregion)), basename)
pystrSinogramFullPath = PyOs.path.join(
self.pystrPathToSinogramsDir,
pystrSinogramFilename)
self.pydProcessSinograms[pystrSinogramFullPath] = [
startregion, stopregion
]
def process(self, _edObject=None):
"""
This method does the calculations and create / modifies the sinograms
Pay attention: the xy coordinate are inverted when calling here to have x first coordinate as horizontal, what is different from the math convention (line/column)
"""
EDPluginExec.process(self)
EDVerbose.DEBUG("*** EDPluginDCTWriteSinogramv1_0.process")
if (self.m_cifPowderData is not None):
borg2DImageWriter = Borg2DImageWriter()
EDVerbose.DEBUG(
"Now generation of the Sinograms, Path: %s, pixel position= %i,%i"
%
(self.pystrPathToSinogramsDir, self.pyintXpos, self.pyintYpos))
for pystrSinogramFullPath in self.pydProcessSinograms:
EDVerbose.DEBUG(
"Writing Sinogram %s pixel (%i,%i)" %
(pystrSinogramFullPath, self.pyintXpos, self.pyintYpos))
self.xMax, self.yMax = self.powderIntegrator.getSinogramSize()
#Change here if there is a new version of BorgDImageWriter
if not PyOs.path.isfile(pystrSinogramFullPath +
"Size%ix%i.edf" %
(self.yMax, self.xMax)):
EDVerbose.DEBUG(
"Creating Sinogram %s size (%i,%i)" %
(pystrSinogramFullPath, self.xMax, self.yMax))
borg2DImageWriter.newFile(filename=pystrSinogramFullPath,
size=(self.yMax, self.xMax))
if isinstance(
self.pydProcessSinograms[pystrSinogramFullPath],
str) or isinstance(
self.pydProcessSinograms[pystrSinogramFullPath],
unicode):
# EDVerbose.DEBUG( "Keyword= %s "%self.pydProcessSinograms[ pystrSinogramFullPath ])
if self.pydProcessSinograms[
pystrSinogramFullPath] == "PhotonFlux":
EDVerbose.DEBUG("PhotonFlux= %s " %
self.powderIntegrator.pyfPhotonFlux)
borg2DImageWriter.set(
filename=pystrSinogramFullPath,
position=(self.pyintYpos, self.pyintXpos),
value=self.powderIntegrator.pyfPhotonFlux)
elif self.pydProcessSinograms[
pystrSinogramFullPath] == "IntegratedRaw":
EDVerbose.DEBUG("IntegratedRaw= %s " %
self.powderIntegrator.integrate())
borg2DImageWriter.set(
filename=pystrSinogramFullPath,
position=(self.pyintYpos, self.pyintXpos),
value=self.powderIntegrator.integrate())
elif self.pydProcessSinograms[
pystrSinogramFullPath] == "IntegratedCor":
EDVerbose.DEBUG("IntegratedCor= %s " %
(self.powderIntegrator.integrate() /
self.powderIntegrator.pyfPhotonFlux))
borg2DImageWriter.set(
filename=pystrSinogramFullPath,
position=(self.pyintYpos, self.pyintXpos),
value=(self.powderIntegrator.integrate() /
self.powderIntegrator.pyfPhotonFlux))
elif isinstance(
self.pydProcessSinograms[pystrSinogramFullPath], list):
if pystrSinogramFullPath[-3:] == "Raw":
EDVerbose.DEBUG("Raw %s - %s= %s " % (
self.pydProcessSinograms[pystrSinogramFullPath][0],
self.pydProcessSinograms[pystrSinogramFullPath][1],
self.powderIntegrator.integrate(*tuple(
self.pydProcessSinograms[pystrSinogramFullPath]
))))
borg2DImageWriter.set(
filename=pystrSinogramFullPath,
position=(self.pyintYpos, self.pyintXpos),
value=(self.powderIntegrator.integrate(*tuple(
self.pydProcessSinograms[pystrSinogramFullPath]
))))
elif pystrSinogramFullPath[-3:] == "Cor":
EDVerbose.DEBUG("Cor %s - %s= %s " % (
self.pydProcessSinograms[pystrSinogramFullPath][0],
self.pydProcessSinograms[pystrSinogramFullPath][1],
self.powderIntegrator.integrate(*tuple(
self.pydProcessSinograms[pystrSinogramFullPath]
)) / self.powderIntegrator.pyfPhotonFlux))
borg2DImageWriter.set(
filename=pystrSinogramFullPath,
position=(self.pyintYpos, self.pyintXpos),
value=(self.powderIntegrator.integrate(*tuple(
self.pydProcessSinograms[pystrSinogramFullPath]
)) / self.powderIntegrator.pyfPhotonFlux))
def postProcess(self, _edObject=None):
"""
"""
EDPluginExec.postProcess(self)
EDVerbose.DEBUG("*** EDPluginDCTWriteSinogramv1_0.postProcess")
xsDataResultWriteSinogram = XSDataResultWriteSinogram()
for pystrPathToOneSinogram in self.pydProcessSinograms:
oneSinogram = XSDataFile()
oneSinogram.setPath(
XSDataString(pystrPathToOneSinogram + "Size%ix%i.edf" %
(self.yMax, self.xMax)))
xsDataResultWriteSinogram.addSinogramFile(oneSinogram)
EDVerbose.DEBUG("Adding sinogram: %s" % pystrPathToOneSinogram)
self.setDataOutput(xsDataResultWriteSinogram)
if cif["_tomo_scan_type"].lower() == "mapping": #I agree mappings are not sinograms but the really looks like, no ?
self.pyintXpos = int(abs((float(self.cif[ "_tomo_spec_displ_x" ]) - float (self.cif [ "_tomo_spec_displ_x_min" ])) / float(self.cif["_tomo_spec_displ_x_inc"])))
self.pyintYpos = 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"])))
return self.pyintXpos, self.pyintYpos
############################################################################################
###################### Start of the program ###############################################
############################################################################################
if len(sys.argv) == 2:
strPathToCif = sys.argv[1]
else:
strPathToCif = "test-powder.cif"
pystSinogramFilename = "test-sinogram.edf"
cif = CIF()
cif.loadCIF(strPathToCif)
if not cif.exists("_tomo_scan_type"):
print "How do you want to generate a Sinogram if you are lacking essential things like the scan type"
pydMetaDataEDF = cif.copy()
pydMetaDataEDF.pop("loop_")
pydMetaDataEDF.pop("_synchrotron_photon-flux")
pydMetaDataEDF.pop("_synchrotron_ring-intensity")
pydMetaDataEDF.pop("_tomo_spec_displ_rotation")
pydMetaDataEDF.pop("_tomo_spec_displ_x")
pydMetaDataEDF.pop("_tomo_spec_displ_z")
roi = PowderIntegrator(cif)
pyintXpos, pyintYpos = roi.getSinogramPosition()
strLockFile = lockFile(suffix=os.path.splitext(strPathToCif)[0], path='.', basename="lock")
float(self.cif["_tomo_spec_displ_z_min"])) /
float(self.cif["_tomo_spec_displ_z_inc"])))
return self.pyintXpos, self.pyintYpos
############################################################################################
###################### Start of the program ###############################################
############################################################################################
if len(sys.argv) == 2:
strPathToCif = sys.argv[1]
else:
strPathToCif = "test-powder.cif"
pystSinogramFilename = "test-sinogram.edf"
cif = CIF()
cif.loadCIF(strPathToCif)
if not cif.exists("_tomo_scan_type"):
print "How do you want to generate a Sinogram if you are lacking essential things like the scan type"
pydMetaDataEDF = cif.copy()
pydMetaDataEDF.pop("loop_")
pydMetaDataEDF.pop("_synchrotron_photon-flux")
pydMetaDataEDF.pop("_synchrotron_ring-intensity")
pydMetaDataEDF.pop("_tomo_spec_displ_rotation")
pydMetaDataEDF.pop("_tomo_spec_displ_x")
pydMetaDataEDF.pop("_tomo_spec_displ_z")
roi = PowderIntegrator(cif)
pyintXpos, pyintYpos = roi.getSinogramPosition()
strLockFile = lockFile(suffix=os.path.splitext(strPathToCif)[0],
