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:
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
]
