def process(self, _edObject=None):
EDPluginControl.process(self)
h5Grp = EDPluginHDF5.createStructure(self.HDF5filename.path.value, self.internalHDF5Path.value)
self.DEBUG("EDPluginControlFullFieldXASv1_0.process")
self.makeHDF5OffsetStructure()
if self.energy is not None:
self.makeHDF5EnergyStructure()
edPluginExecNormalize = self.loadPlugin(self.__strControlledNormalize)
edPluginExecNormalize.connectSUCCESS(self.doSuccessExecNormalize)
edPluginExecNormalize.connectFAILURE(self.doFailureExecNormalize)
sdi = self.dataInput
xsdInNorm = XSDataInputNormalize(data=sdi.data,
flat=sdi.flat,
dark=sdi.dark,
dataScaleFactor=sdi.dataScaleFactor,
darkScaleFactor=sdi.darkScaleFactor,
flatScaleFactor=sdi.flatScaleFactor)
if self.xsdNormalizedFilename is not None:
xsdInNorm.output = XSDataImageExt(path=self.xsdNormalizedFilename.path)
else:
xsdInNorm.output = XSDataImageExt(shared=XSDataString("Normalized-%06i" % sdi.index.value))
edPluginExecNormalize.dataInput = xsdInNorm
edPluginExecNormalize.executeSynchronous()
if self.xsdAlignStack is not None:
edPluginAlign = self.loadPlugin(self.__strControlledAlign)
edPluginAlign.dataInput = self.xsdAlignStack
edPluginAlign.connectSUCCESS(self.doSuccessExecAlign)
edPluginAlign.connectFAILURE(self.doFailureExecAlign)
edPluginAlign.executeSynchronous()
def preProcess(self, _edObject=None):
EDPluginHDF5.preProcess(self)
self.DEBUG("EDPluginHDF5StackImagesv10.preProcess")
for onefile in self.dataInput.inputImageFile:
if onefile is None:
self.ERROR("Please investigate why EDPluginHDF5StackImagesv10.dataInput.inputImageFile is a list containing None !!!!")
self.setFailure()
continue
if onefile.path is not None:
self.listImageFilenames.append(onefile.path.value)
if onefile.date is not None:
self.listImageDates.append(onefile.date.value)
if onefile.number is not None:
self.listForcedPositions.append(onefile.number.value)
self.listArray.append(EDUtilsArray.getArray(onefile))
for oneArray in self.dataInput.inputArray:
self.listArray.append(EDUtilsArray.xsDataToArray(oneArray))
if self.dataInput.index != []:
self.listForcedPositions = [i.value for i in self.dataInput.index]
if self.dataInput.getDeleteInputImage() is not None:
self.bDeleteImage = bool(self.dataInput.deleteInputImage.value)
if self.listForcedPositions != []:
EDAssert.equal(len(self.listForcedPositions), max(len(self.listImageFilenames), len(self.listArray)), "Forced position list has a good length")
if self.listImageDates != []:
EDAssert.equal(len(self.listImageDates) , len(self.listImageFilenames), "listImageDates has the same size as listImageFilenames")
self.hdf5group = EDPluginHDF5.createStructure(self.strHDF5Filename, self.strHDF5Path, self.dictExtraAttributes)
def process(self, _edObject=None):
EDPluginControl.process(self)
h5Grp = EDPluginHDF5.createStructure(self.HDF5filename.path.value,
self.internalHDF5Path.value)
self.DEBUG("EDPluginControlFullFieldXASv1_0.process")
self.makeHDF5OffsetStructure()
if self.energy is not None:
self.makeHDF5EnergyStructure()
edPluginExecNormalize = self.loadPlugin(self.__strControlledNormalize)
edPluginExecNormalize.connectSUCCESS(self.doSuccessExecNormalize)
edPluginExecNormalize.connectFAILURE(self.doFailureExecNormalize)
sdi = self.dataInput
xsdInNorm = XSDataInputNormalize(data=sdi.data,
flat=sdi.flat,
dark=sdi.dark,
dataScaleFactor=sdi.dataScaleFactor,
darkScaleFactor=sdi.darkScaleFactor,
flatScaleFactor=sdi.flatScaleFactor)
if self.xsdNormalizedFilename is not None:
xsdInNorm.output = XSDataImageExt(
path=self.xsdNormalizedFilename.path)
else:
xsdInNorm.output = XSDataImageExt(
shared=XSDataString("Normalized-%06i" % sdi.index.value))
edPluginExecNormalize.dataInput = xsdInNorm
edPluginExecNormalize.executeSynchronous()
if self.xsdAlignStack is not None:
edPluginAlign = self.loadPlugin(self.__strControlledAlign)
edPluginAlign.dataInput = self.xsdAlignStack
edPluginAlign.connectSUCCESS(self.doSuccessExecAlign)
edPluginAlign.connectFAILURE(self.doFailureExecAlign)
edPluginAlign.executeSynchronous()
def makeHDF5EnergyStructure(self):
self.DEBUG("EDPluginControlFullFieldXASv1_0.makeHDF5EnergyStructure")
h5Grp = EDPluginHDF5.createStructure(self.HDF5filename.path.value, self.internalHDF5Path.value)
with EDPluginHDF5.getFileLock(self.HDF5filename.path.value):
if self.DSenergy in h5Grp:
dataset = h5Grp[self.DSenergy]
else:
dataset = h5Grp.create_dataset(self.DSenergy, shape=(1 + max(self.index, self.reference),), dtype="float32", maxshape=(None,), chunks=(1,))
for key in EDPluginControlFullFieldXASv1_0.energyAttr:
dataset.attrs.create(key, EDPluginControlFullFieldXASv1_0.energyAttr[key])
if self.index >= dataset.shape[0]:
dataset.resize((self.index + 1,))
dataset[self.index] = self.energy
def makeHDF5MaxIntStructure(self, _fMaxIntensity):
self.DEBUG("EDPluginControlFullFieldXASv1_0.makeHDF5MaxIntStructure")
h5Grp = EDPluginHDF5.createStructure(self.HDF5filename.path.value, self.internalHDF5Path.value)
with EDPluginHDF5.getFileLock(self.HDF5filename.path.value):
#Seems strange to redefine h5Grp but if there is a flush in between: h5Grp could be closed
h5Grp = EDPluginHDF5.getHDF5File(self.HDF5filename.path.value)[self.internalHDF5Path.value]
if "maxInt" in h5Grp:
dataset = h5Grp["maxInt"]
else:
dataset = h5Grp.create_dataset("maxInt", shape=(1 + max(self.index, self.reference),), dtype="float32", maxshape=(None,), chunks=(1,))
for key in EDPluginControlFullFieldXASv1_0.maxIntAttr:
dataset.attrs.create(key, EDPluginControlFullFieldXASv1_0.maxIntAttr[key])
if self.index >= dataset.shape[0]:
dataset.resize((self.index + 1,))
dataset[self.index] = _fMaxIntensity
def makeHDF5EnergyStructure(self):
self.DEBUG("EDPluginControlFullFieldXASv1_0.makeHDF5EnergyStructure")
h5Grp = EDPluginHDF5.createStructure(self.HDF5filename.path.value,
self.internalHDF5Path.value)
with EDPluginHDF5.getFileLock(self.HDF5filename.path.value):
if self.DSenergy in h5Grp:
dataset = h5Grp[self.DSenergy]
else:
dataset = h5Grp.create_dataset(
self.DSenergy,
shape=(1 + max(self.index, self.reference), ),
dtype="float32",
maxshape=(None, ),
chunks=(1, ))
for key in EDPluginControlFullFieldXASv1_0.energyAttr:
dataset.attrs.create(
key, EDPluginControlFullFieldXASv1_0.energyAttr[key])
if self.index >= dataset.shape[0]:
dataset.resize((self.index + 1, ))
dataset[self.index] = self.energy
def makeHDF5MaxIntStructure(self, _fMaxIntensity):
self.DEBUG("EDPluginControlFullFieldXASv1_0.makeHDF5MaxIntStructure")
h5Grp = EDPluginHDF5.createStructure(self.HDF5filename.path.value,
self.internalHDF5Path.value)
with EDPluginHDF5.getFileLock(self.HDF5filename.path.value):
#Seems strange to redefine h5Grp but if there is a flush in between: h5Grp could be closed
h5Grp = EDPluginHDF5.getHDF5File(
self.HDF5filename.path.value)[self.internalHDF5Path.value]
if "maxInt" in h5Grp:
dataset = h5Grp["maxInt"]
else:
dataset = h5Grp.create_dataset(
"maxInt",
shape=(1 + max(self.index, self.reference), ),
dtype="float32",
maxshape=(None, ),
chunks=(1, ))
for key in EDPluginControlFullFieldXASv1_0.maxIntAttr:
dataset.attrs.create(
key, EDPluginControlFullFieldXASv1_0.maxIntAttr[key])
if self.index >= dataset.shape[0]:
dataset.resize((self.index + 1, ))
dataset[self.index] = _fMaxIntensity