def preProcess(self, _edObject=None):
"""
Preprocess methods for the EDPluginSPDCakev1_5 :
- tilts the mask if needed
"""
EDPluginSPDCorrectv10.preProcess(self, _edObject)
self.DEBUG("EDPluginSPDCakev1_5.preProcess")
if ("MaskFile" in self.dictGeometry) and (self.dictGeometry["MaskFile"] not in EDPluginSPDCakev1_5.__dictMask):
self.correctMask()
def __init__(self):
"""
Constructor of the plugin: just do some simple initialization
"""
self.bDeleteCorImg = False
EDPluginSPDCorrectv10.__init__(self)
if self.getClassName() == "EDPluginSPDCakev1_5":
self.setXSDataInputClass(XSDataInputSPDCake)
self.bCorrectTiltMask = False
def __init__(self):
"""
Constructor of the plugin: just do some simple initialization
"""
self.bDeleteCorImg = False
EDPluginSPDCorrectv10.__init__(self)
if self.getClassName() == "EDPluginSPDCakev1_5":
self.setXSDataInputClass(XSDataInputSPDCake)
self.bCorrectTiltMask = False
def preProcess(self, _edObject=None):
"""
Preprocess methods for the EDPluginSPDCakev1_5 :
- tilts the mask if needed
"""
EDPluginSPDCorrectv10.preProcess(self, _edObject)
self.DEBUG("EDPluginSPDCakev1_5.preProcess")
if ("MaskFile" in self.dictGeometry) and (
self.dictGeometry["MaskFile"]
not in EDPluginSPDCakev1_5.__dictMask):
self.correctMask()
def getInputParameter(self):
"""
Read all the input parameters and store them in instance variables called self.dictGeometry and self.pathToInputFile
"""
self.DEBUG("EDPluginSPDCakev1_5.getInputParameter")
EDPluginSPDCorrectv10.getInputParameter(self)
if self.xsDataInputSPD.getStartAzimuth() is not None:
if self.xsDataInputSPD.getStartAzimuth().getUnit() is not None:
self.dictGeometry["StartAzimuth"] = EDUtilsUnit.getValue(self.xsDataInputSPD.getStartAzimuth(), "deg")
else:
self.WARNING("You did not specify the StartAzimuth Unit, Falling back to Deg (not Rad)")
self.dictGeometry["StartAzimuth"] = self.xsDataInputSPD.getStartAzimuth().getValue()
if self.xsDataInputSPD.getStopAzimuth() is not None:
if self.xsDataInputSPD.getStopAzimuth().getUnit() is not None:
self.dictGeometry["StopAzimuth"] = EDUtilsUnit.getValue(self.xsDataInputSPD.getStopAzimuth(), "deg")
else:
self.WARNING("You did not specify the StopAzimuth Unit, Falling back to Deg (not Rad)")
self.dictGeometry["StopAzimuth"] = self.xsDataInputSPD.getStopAzimuth().getValue()
if self.xsDataInputSPD.getStepAzimuth() is not None:
if self.xsDataInputSPD.getStepAzimuth().getUnit() is not None:
self.dictGeometry["StepAzimuth"] = EDUtilsUnit.getValue(self.xsDataInputSPD.getStepAzimuth(), "deg")
else:
self.WARNING("You did not specify the StepAzimuth Unit, Falling back to Deg (not Rad)")
self.dictGeometry["StepAzimuth"] = self.xsDataInputSPD.getStepAzimuth().getValue()
if self.xsDataInputSPD.getInnerRadius() is not None:
self.dictGeometry["InnerRadius"] = self.xsDataInputSPD.getInnerRadius().getValue()
if self.xsDataInputSPD.getOuterRadius() is not None:
self.dictGeometry["OuterRadius"] = self.xsDataInputSPD.getOuterRadius().getValue()
if self.xsDataInputSPD.getOutputDirCake() is not None:
self.dictGeometry["OutputDirCake"] = self.xsDataInputSPD.getOutputDirCake().getPath().getValue()
EDUtilsPath.createFolder(self.dictGeometry["OutputDirCake"])
if self.dictGeometry["OutputDirCake"] != self.dictGeometry["OutputDir"]:
self.setFireAndForget(False)
else:
self.dictGeometry["OutputDirCake"] = self.dictGeometry["OutputDir"]
if self.xsDataInputSPD.getMaskFile() is not None:
self.dictGeometry["MaskFile"] = self.xsDataInputSPD.getMaskFile().getPath().getValue()
if not os.path.isfile(self.dictGeometry["MaskFile"]):
self.ERROR("Mask file %s does not exist " % self.dictGeometry["MaskFile"])
self.dictGeometry.pop("MaskFile")
if self.xsDataInputSPD.getIntensityScaleFactor() is not None:
self.dictGeometry["IntensityScaleFactor"] = self.xsDataInputSPD.getIntensityScaleFactor().getValue()
if self.xsDataInputSPD.getDeleteCorImg() is not None:
self.bDeleteCorImg = (self.xsDataInputSPD.getDeleteCorImg().getValue() in ["1", 1, "true", "True", True])
if self.bDeleteCorImg:
self.setFireAndForget(False)
if self.xsDataInputSPD.getCorrectTiltMask() is not None:
self.bCorrectTiltMask = bool(self.xsDataInputSPD.getCorrectTiltMask().getValue())
def generateSPDCommand(self):
"""
This method creates the SPD command line for image correction.
"""
EDPluginSPDCorrectv10.generateSPDCommand(self)
self.DEBUG("EDPluginSPDCackev1_5.generateSPDCommand")
lstCmdLineOption = [self.getSPDConfig()]
lstCmdLineOption.append("cor_ext=.cor azim_int=1 azim_pass=0")
if self.dictGeometry.has_key("OutputFileType") and (self.getClassName() == "EDPluginSPDCakev1_5"):
if self.dictGeometry["OutputFileType"].startswith("."):
lstCmdLineOption.append("azim_ext=%s" % self.dictGeometry["OutputFileType"])
else:
lstCmdLineOption.append("azim_ext=.%s" % self.dictGeometry["OutputFileType"])
pixelSize = min(self.dictGeometry["PixelSizeX"], self.dictGeometry["PixelSizeY"])
if "InnerRadius" in self.dictGeometry:
lstCmdLineOption.append("azim_r0=%s" % (self.dictGeometry["InnerRadius"] * pixelSize))
if "OuterRadius" in self.dictGeometry:
lstCmdLineOption.append("azim_r_num=%s" % ((self.dictGeometry["OuterRadius"] - self.dictGeometry["InnerRadius"])))
else:
if ("BeamCenterX" in self.dictGeometry) and\
("BeamCenterY" in self.dictGeometry) and\
("BufferSizeX" in self.dictGeometry) and\
("BufferSizeY" in self.dictGeometry) and\
("PixelSizeX" in self.dictGeometry) and\
("PixelSizeY" in self.dictGeometry):
maxXdist = max(abs(self.dictGeometry["BeamCenterX"]), abs(self.dictGeometry["BufferSizeX"] - self.dictGeometry["BeamCenterX"])) * self.dictGeometry["PixelSizeX"]
maxYdist = max(abs(self.dictGeometry["BeamCenterY"]), abs(self.dictGeometry["BufferSizeY"] - self.dictGeometry["BeamCenterY"])) * self.dictGeometry["PixelSizeY"]
MaxRadius = int(math.sqrt(maxXdist ** 2 + maxYdist ** 2) / min(self.dictGeometry["PixelSizeX"], self.dictGeometry["PixelSizeY"]))
lstCmdLineOption.append("azim_r_num=%s" % MaxRadius)
if "StartAzimuth" in self.dictGeometry:
lstCmdLineOption.append("azim_a0=%s" % self.dictGeometry["StartAzimuth"])
if "StepAzimuth" in self.dictGeometry:
lstCmdLineOption.append("azim_da=%s" % self.dictGeometry["StepAzimuth"])
if "StopAzimuth" in self.dictGeometry:
lstCmdLineOption.append("azim_a_num=%s" % int(round((self.dictGeometry["StopAzimuth"] - self.dictGeometry["StartAzimuth"]) / self.dictGeometry["StepAzimuth"])))
if "MaskFile" in self.dictGeometry:
if self.dictGeometry["MaskFile"] in EDPluginSPDCakev1_5.__dictMask:
lstCmdLineOption.append('mask_file=%s' % os.path.abspath(EDPluginSPDCakev1_5.__dictMask[self.dictGeometry["MaskFile"]]))
else:
lstCmdLineOption.append('mask_file=%s' % os.path.abspath(self.dictGeometry["MaskFile"]))
if "IntensityScaleFactor" in self.dictGeometry:
lstCmdLineOption.append("ave_scf=%s" % self.dictGeometry["IntensityScaleFactor"])
strCmdLineOption = " ".join(lstCmdLineOption)
self.DEBUG("SPD Command line:\n" + strCmdLineOption)
self.setSPDConfig(strCmdLineOption)
def generateSPDCommand(self):
"""
This method creates the SPD command line for image correction.
"""
EDPluginSPDCorrectv10.generateSPDCommand(self)
self.DEBUG("EDPluginSPDCackev1_5.generateSPDCommand")
lstCmdLineOption = [self.getSPDConfig()]
lstCmdLineOption.append("cor_ext=.cor azim_int=1 azim_pass=0")
if self.dictGeometry.has_key("OutputFileType") and (
self.getClassName() == "EDPluginSPDCakev1_5"):
if self.dictGeometry["OutputFileType"].startswith("."):
lstCmdLineOption.append("azim_ext=%s" %
self.dictGeometry["OutputFileType"])
else:
lstCmdLineOption.append("azim_ext=.%s" %
self.dictGeometry["OutputFileType"])
pixelSize = min(self.dictGeometry["PixelSizeX"],
self.dictGeometry["PixelSizeY"])
if "InnerRadius" in self.dictGeometry:
lstCmdLineOption.append(
"azim_r0=%s" % (self.dictGeometry["InnerRadius"] * pixelSize))
if "OuterRadius" in self.dictGeometry:
lstCmdLineOption.append("azim_r_num=%s" %
((self.dictGeometry["OuterRadius"] -
self.dictGeometry["InnerRadius"])))
else:
if ("BeamCenterX" in self.dictGeometry) and\
("BeamCenterY" in self.dictGeometry) and\
("BufferSizeX" in self.dictGeometry) and\
("BufferSizeY" in self.dictGeometry) and\
("PixelSizeX" in self.dictGeometry) and\
("PixelSizeY" in self.dictGeometry):
maxXdist = max(
abs(self.dictGeometry["BeamCenterX"]),
abs(self.dictGeometry["BufferSizeX"] -
self.dictGeometry["BeamCenterX"])
) * self.dictGeometry["PixelSizeX"]
maxYdist = max(
abs(self.dictGeometry["BeamCenterY"]),
abs(self.dictGeometry["BufferSizeY"] -
self.dictGeometry["BeamCenterY"])
) * self.dictGeometry["PixelSizeY"]
MaxRadius = int(
math.sqrt(maxXdist**2 + maxYdist**2) /
min(self.dictGeometry["PixelSizeX"],
self.dictGeometry["PixelSizeY"]))
lstCmdLineOption.append("azim_r_num=%s" % MaxRadius)
if "StartAzimuth" in self.dictGeometry:
lstCmdLineOption.append("azim_a0=%s" %
self.dictGeometry["StartAzimuth"])
if "StepAzimuth" in self.dictGeometry:
lstCmdLineOption.append("azim_da=%s" %
self.dictGeometry["StepAzimuth"])
if "StopAzimuth" in self.dictGeometry:
lstCmdLineOption.append("azim_a_num=%s" % int(
round((self.dictGeometry["StopAzimuth"] -
self.dictGeometry["StartAzimuth"]) /
self.dictGeometry["StepAzimuth"])))
if "MaskFile" in self.dictGeometry:
if self.dictGeometry["MaskFile"] in EDPluginSPDCakev1_5.__dictMask:
lstCmdLineOption.append(
'mask_file=%s' %
os.path.abspath(EDPluginSPDCakev1_5.__dictMask[
self.dictGeometry["MaskFile"]]))
else:
lstCmdLineOption.append(
'mask_file=%s' %
os.path.abspath(self.dictGeometry["MaskFile"]))
if "IntensityScaleFactor" in self.dictGeometry:
lstCmdLineOption.append("ave_scf=%s" %
self.dictGeometry["IntensityScaleFactor"])
strCmdLineOption = " ".join(lstCmdLineOption)
self.DEBUG("SPD Command line:\n" + strCmdLineOption)
self.setSPDConfig(strCmdLineOption)
def getInputParameter(self):
"""
Read all the input parameters and store them in instance variables called self.dictGeometry and self.pathToInputFile
"""
self.DEBUG("EDPluginSPDCakev1_5.getInputParameter")
EDPluginSPDCorrectv10.getInputParameter(self)
if self.xsDataInputSPD.getStartAzimuth() is not None:
if self.xsDataInputSPD.getStartAzimuth().getUnit() is not None:
self.dictGeometry["StartAzimuth"] = EDUtilsUnit.getValue(
self.xsDataInputSPD.getStartAzimuth(), "deg")
else:
self.WARNING(
"You did not specify the StartAzimuth Unit, Falling back to Deg (not Rad)"
)
self.dictGeometry[
"StartAzimuth"] = self.xsDataInputSPD.getStartAzimuth(
).getValue()
if self.xsDataInputSPD.getStopAzimuth() is not None:
if self.xsDataInputSPD.getStopAzimuth().getUnit() is not None:
self.dictGeometry["StopAzimuth"] = EDUtilsUnit.getValue(
self.xsDataInputSPD.getStopAzimuth(), "deg")
else:
self.WARNING(
"You did not specify the StopAzimuth Unit, Falling back to Deg (not Rad)"
)
self.dictGeometry[
"StopAzimuth"] = self.xsDataInputSPD.getStopAzimuth(
).getValue()
if self.xsDataInputSPD.getStepAzimuth() is not None:
if self.xsDataInputSPD.getStepAzimuth().getUnit() is not None:
self.dictGeometry["StepAzimuth"] = EDUtilsUnit.getValue(
self.xsDataInputSPD.getStepAzimuth(), "deg")
else:
self.WARNING(
"You did not specify the StepAzimuth Unit, Falling back to Deg (not Rad)"
)
self.dictGeometry[
"StepAzimuth"] = self.xsDataInputSPD.getStepAzimuth(
).getValue()
if self.xsDataInputSPD.getInnerRadius() is not None:
self.dictGeometry[
"InnerRadius"] = self.xsDataInputSPD.getInnerRadius().getValue(
)
if self.xsDataInputSPD.getOuterRadius() is not None:
self.dictGeometry[
"OuterRadius"] = self.xsDataInputSPD.getOuterRadius().getValue(
)
if self.xsDataInputSPD.getOutputDirCake() is not None:
self.dictGeometry[
"OutputDirCake"] = self.xsDataInputSPD.getOutputDirCake(
).getPath().getValue()
EDUtilsPath.createFolder(self.dictGeometry["OutputDirCake"])
if self.dictGeometry["OutputDirCake"] != self.dictGeometry[
"OutputDir"]:
self.setFireAndForget(False)
else:
self.dictGeometry["OutputDirCake"] = self.dictGeometry["OutputDir"]
if self.xsDataInputSPD.getMaskFile() is not None:
self.dictGeometry["MaskFile"] = self.xsDataInputSPD.getMaskFile(
).getPath().getValue()
if not os.path.isfile(self.dictGeometry["MaskFile"]):
self.ERROR("Mask file %s does not exist " %
self.dictGeometry["MaskFile"])
self.dictGeometry.pop("MaskFile")
if self.xsDataInputSPD.getIntensityScaleFactor() is not None:
self.dictGeometry[
"IntensityScaleFactor"] = self.xsDataInputSPD.getIntensityScaleFactor(
).getValue()
if self.xsDataInputSPD.getDeleteCorImg() is not None:
self.bDeleteCorImg = (
self.xsDataInputSPD.getDeleteCorImg().getValue()
in ["1", 1, "true", "True", True])
if self.bDeleteCorImg:
self.setFireAndForget(False)
if self.xsDataInputSPD.getCorrectTiltMask() is not None:
self.bCorrectTiltMask = bool(
self.xsDataInputSPD.getCorrectTiltMask().getValue())
def postProcess(self, _edObject=None):
"""
postProcess of the plugin EDPluginSPDCakev1_5.py:
- convert to HDF if needed (to be implemented)
- convert to chiplot or xye or cif if needed
- move images (if needed) or delete .cor image
- set result XML
"""
EDPluginSPDCorrectv10.postProcess(self)
self.DEBUG("EDPluginSPDCakev1_5.postProcess")
if not os.path.isdir(self.dictGeometry["OutputDirCake"]):
os.makedirs(self.dictGeometry["OutputDirCake"])
strInputImagePathNoSfx = os.path.splitext(
os.path.basename(self.pathToInputFile))[0]
strSpdoutCake = strInputImagePathNoSfx + self.dictGeometry[
"OutputFileType"]
strOutputCakeFilePath = os.path.join(
self.dictGeometry["OutputDirCake"], strSpdoutCake)
xsDataResultSPD = XSDataResultSPDCake()
if not self.getFireAndForget():
strTempFilePath = None
if "corrected" in self.dictRes:
strSpdoutCor = self.dictRes["corrected"]
if "regrouped" in self.dictRes:
strTempFilePath = self.dictRes["regrouped"]
if self.dictGeometry["OutputFileType"].lower() in [
".hdf5", ".nexus", ".h5", ".nx"
]:
self.WARNING(
"HDF5/Nexus output is not yet implemented in the SPD plugin."
)
if strTempFilePath is None:
self.WARNING(
"Cannot copy output to %s as there is not input: %s " %
(strOutputCakeFilePath, self.dictRes))
elif os.path.exists(strOutputCakeFilePath):
self.WARNING(
"Destination file exists, I will leave result file in %s."
% strTempFilePath)
strOutputCakeFilePath = strTempFilePath
else:
shutil.move(strTempFilePath, strOutputCakeFilePath)
strOutputCorFilePath = os.path.join(self.dictGeometry["OutputDir"],
os.path.split(strSpdoutCor)[1])
if self.bDeleteCorImg:
if os.path.isfile(strSpdoutCor):
os.remove(strSpdoutCor)
else:
self.WARNING("Corrected file vanished before removal %s" %
strSpdoutCor)
else:
strTempFilePathCor = os.path.join(self.getWorkingDirectory(),
strSpdoutCor)
if self.dictGeometry["OutputFileType"].lower() in [
".hdf5", ".nexus", ".h5", ".nx"
]:
self.WARNING(
"HDF5/Nexus output is not yet implemented in the SPD plugin."
)
elif self.dictGeometry["OutputFileType"].lower() not in [
".edf", ".azim", ".cor"
]:
self.WARNING(
"Output file format %s is not yet implemented in the SPD plugin."
% self.dictGeometry["OutputFileType"])
if os.path.exists(strOutputCorFilePath):
self.WARNING(
"Destination file exists, I will leave result file in %s."
% strTempFilePathCor)
strOutputCorFilePath = os.path.abspath(strTempFilePathCor)
else:
shutil.move(strTempFilePath, strOutputCorFilePath)
xsDataFileCorr = XSDataFile()
xsDataFileCorr.setPath(XSDataString(strOutputCorFilePath))
xsDataResultSPD.setcorrectedFile(xsDataFileCorr)
# # Create the output data
xsDataFileCake = XSDataFile()
xsDataFileCake.setPath(XSDataString(strOutputCakeFilePath))
xsDataResultSPD.setCakedFile(xsDataFileCake)
self.setDataOutput(xsDataResultSPD)
def postProcess(self, _edObject=None):
"""
postProcess of the plugin EDPluginSPDCakev1_5.py:
- convert to HDF if needed (to be implemented)
- convert to chiplot or xye or cif if needed
- move images (if needed) or delete .cor image
- set result XML
"""
EDPluginSPDCorrectv10.postProcess(self)
self.DEBUG("EDPluginSPDCakev1_5.postProcess")
if not os.path.isdir(self.dictGeometry["OutputDirCake"]):
os.makedirs(self.dictGeometry["OutputDirCake"])
strInputImagePathNoSfx = os.path.splitext(os.path.basename(self.pathToInputFile))[0]
strSpdoutCake = strInputImagePathNoSfx + self.dictGeometry["OutputFileType"]
strOutputCakeFilePath = os.path.join(self.dictGeometry["OutputDirCake"], strSpdoutCake)
xsDataResultSPD = XSDataResultSPDCake()
if not self.getFireAndForget():
strTempFilePath = None
if "corrected" in self.dictRes:
strSpdoutCor = self.dictRes["corrected"]
if "regrouped" in self.dictRes:
strTempFilePath = self.dictRes["regrouped"]
if self.dictGeometry["OutputFileType"].lower() in [".hdf5", ".nexus", ".h5", ".nx"]:
self.WARNING("HDF5/Nexus output is not yet implemented in the SPD plugin.")
if strTempFilePath is None:
self.WARNING("Cannot copy output to %s as there is not input: %s " % (strOutputCakeFilePath, self.dictRes))
elif os.path.exists(strOutputCakeFilePath):
self.WARNING("Destination file exists, I will leave result file in %s." % strTempFilePath)
strOutputCakeFilePath = strTempFilePath
else:
shutil.move(strTempFilePath, strOutputCakeFilePath)
strOutputCorFilePath = os.path.join(self.dictGeometry["OutputDir"], os.path.split(strSpdoutCor)[1])
if self.bDeleteCorImg:
if os.path.isfile(strSpdoutCor):
os.remove(strSpdoutCor)
else:
self.WARNING("Corrected file vanished before removal %s" % strSpdoutCor)
else:
strTempFilePathCor = os.path.join(self.getWorkingDirectory(), strSpdoutCor)
if self.dictGeometry["OutputFileType"].lower() in [".hdf5", ".nexus", ".h5", ".nx"]:
self.WARNING("HDF5/Nexus output is not yet implemented in the SPD plugin.")
elif self.dictGeometry["OutputFileType"].lower() not in [".edf", ".azim", ".cor"] :
self.WARNING("Output file format %s is not yet implemented in the SPD plugin." % self.dictGeometry["OutputFileType"])
if os.path.exists(strOutputCorFilePath):
self.WARNING("Destination file exists, I will leave result file in %s." % strTempFilePathCor)
strOutputCorFilePath = os.path.abspath(strTempFilePathCor)
else:
shutil.move(strTempFilePath, strOutputCorFilePath)
xsDataFileCorr = XSDataFile()
xsDataFileCorr.setPath(XSDataString(strOutputCorFilePath))
xsDataResultSPD.setcorrectedFile(xsDataFileCorr)
# # Create the output data
xsDataFileCake = XSDataFile()
xsDataFileCake.setPath(XSDataString(strOutputCakeFilePath))
xsDataResultSPD.setCakedFile(xsDataFileCake)
self.setDataOutput(xsDataResultSPD)
