def preProcess(self, _edObject=None):
EDPluginHDF5.preProcess(self)
self.DEBUG("EDPluginHDF5StackImagesv10test.preProcess")
for onefile in self.dataInput.inputImageFile:
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.getInputArray():
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")
def process(self, _edObject=None):
EDPluginHDF5.process(self)
self.DEBUG("EDPluginHDF5MapOfSpectrav10.process")
maxSize = (((self.meshScan["SlowMotorSteps"]),
(self.meshScan["FastMotorSteps"])))
for filename in self.listSpectrumFilenames:
self.listArray.append(fabio.open(filename).data)
if self.listForcedPositions == []:
for oneArray in self.listArray:
self.processOneSpectrum(oneArray,
position=maxSize,
maxSize=maxSize)
else:
for i in range(len(self.listForcedPositions)):
fSlowPosition = (self.listForcedPositions[i]["Slow"] - self.meshScan["SlowMotorStart"]) / \
(self.meshScan["SlowMotorStop"] - self.meshScan["SlowMotorStart"]) * \
(self.meshScan["SlowMotorSteps" ])
fFastPosition = (self.listForcedPositions[i]["Fast"] - self.meshScan["FastMotorStart"]) / \
(self.meshScan["FastMotorStop"] - self.meshScan["FastMotorStart"]) * \
(self.meshScan["FastMotorSteps" ])
self.processOneSpectrum(
self.listArray[i],
(int(round(fSlowPosition)), int(round(fFastPosition))),
maxSize=maxSize)
def makeHDF5NeXus(self):
self.DEBUG("EDPluginControlFullFieldXASv1_0.makeHDF5NeXus")
with EDPluginHDF5.getFileLock(self.HDF5filename.path.value):
#Seems strange to redefine h5Grp but if there is a flush in between: h5Grp could be closed
entry = EDPluginHDF5.getHDF5File(self.HDF5filename.path.value)[self.internalHDF5Path.value]
if not "title" in entry:
entry.create_dataset("title", data=self.TITLE)
if not "program" in entry:
entry.create_dataset("program", data="EDNA EDPluginControlFullFieldXASv1_0")
if not "start_time" in entry:
entry.create_dataset("start_time", data=EDPluginHDF5.getIsoTime(self.start_time))
########################################################################
# Huge hack: for scalar modification: use [()] to refer to the data !!!
########################################################################
if "end_time" in entry:
entry["end_time"][()] = EDPluginHDF5.getIsoTime()
else:
entry.create_dataset("end_time", data=EDPluginHDF5.getIsoTime())
if "duration" in entry:
entry["duration"][()] = time.time() - self.start_time
else:
entry.create_dataset("duration", data=time.time() - self.start_time, dtype="float")
if self.NXdata not in entry:
nxdata = entry.create_group(self.NXdata)
for k, v in self.NXdataAttr.items():
nxdata.attrs[k] = v
else:
nxdata = entry[self.NXdata]
for ds in [self.DSstack, self.DSenergy]:
if (ds in entry) and (ds not in nxdata):
nxdata[ds] = entry[ds]
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):
EDPluginHDF5.process(self)
self.DEBUG("EDPluginHDF5StackImagesv10.process")
length = len(self.listForcedPositions)
if length == 0:
for oneFilename in self.listImageFilenames:
header, data = self.readImage(oneFilename)
self.DEBUG("Writing image %s on top of the stack" %
(oneFilename))
self.processOneImage(data,
position=None,
filename=oneFilename,
dictHeaders=header)
for oneArray in self.listArray:
self.DEBUG("Writing image from array on top of the stack")
self.processOneImage(oneArray)
else:
if len(self.listImageFilenames) == length:
for i in xrange(length):
self.DEBUG("Writing image %s at position %i" %
(self.listImageFilenames[i],
self.listForcedPositions[i]))
header, data = self.readImage(self.listImageFilenames[i])
self.processOneImage(data,
position=self.listForcedPositions[i],
filename=self.listImageFilenames[i],
dictHeaders=header)
elif len(self.listArray) == length:
for i in xrange(length):
self.DEBUG("Writing image from array at position %i" %
(self.listForcedPositions[i]))
self.processOneImage(self.listArray[i],
self.listForcedPositions[i])
def hdf5_offset(self, index, offset):
with EDPluginHDF5.getFileLock(self.xsdHDF5File.path.value):
grp = EDPluginHDF5.getHDF5File(self.xsdHDF5File.path.value)[self.xsdHDF5Internal.value]
ds = grp["Offsets"]
if self.MaxOffset:
if "MaxOffset" not in ds.attrs:
ds.attrs["MaxOffset"] = self.MaxOffset
ds[index, :] = offset
def hdf5_offset(self, index, offset):
with EDPluginHDF5.getFileLock(self.xsdHDF5File.path.value):
grp = EDPluginHDF5.getHDF5File(
self.xsdHDF5File.path.value)[self.xsdHDF5Internal.value]
ds = grp["Offsets"]
if self.MaxOffset:
if "MaxOffset" not in ds.attrs:
ds.attrs["MaxOffset"] = self.MaxOffset
ds[index, :] = offset
def makeHDF5OffsetStructure(self):
self.DEBUG("EDPluginControlFullFieldXASv1_0.makeHDF5OffsetStructure")
with EDPluginHDF5.getFileLock(self.HDF5filename.path.value):
h5Grp = EDPluginHDF5.getHDF5File(self.HDF5filename.path.value)[self.internalHDF5Path.value]
if "Offsets" in h5Grp:
dataset = h5Grp["Offsets"]
else:
dataset = h5Grp.create_dataset("Offsets", shape=(1 + max(self.index, self.reference), 2), dtype="float32", maxshape=(None, 2), chunks=(1, 2))
if self.index >= dataset.shape[0]:
dataset.resize((self.index + 1, 2))
def __init__(self):
"""
"""
EDPluginHDF5.__init__(self)
self.setXSDataInputClass(XSDataInputHDF5StackImages)
self.strHDF5Filename = None
self.listImageFilenames = []
self.listForcedPositions = []
self.listImageDates = []
self.listArray = []
self.bDeleteImage = False
self.hdf5group = None #Name of the group(directory) where we will work
def __init__(self):
"""
"""
EDPluginHDF5.__init__(self)
self.setXSDataInputClass(XSDataInputHDF5StackImages)
self.strHDF5Filename = None
self.listImageFilenames = []
self.listForcedPositions = []
self.listImageDates = []
self.listArray = []
self.bDeleteImage = False
self.hdf5group = None #Name of the group(directory) where we will work
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 __init__(self):
"""
"""
EDPluginHDF5.__init__(self)
self.setXSDataInputClass(XSDataInputHDF5MapSpectra)
self.listSpectrumFilenames = []
self.listForcedPositions = []
self.listSpectrumFileType = []
self.listArray = []
self.meshScan = {"FastMotorSteps":0,
"FastMotorStart":0,
"FastMotorStop":0,
"SlowMotorSteps":0,
"SlowMotorStart":0,
"SlowMotorStop":0, }
self.bDeleteSpectrum = False
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 makeHDF5OffsetStructure(self):
self.DEBUG("EDPluginControlFullFieldXASv1_0.makeHDF5OffsetStructure")
with EDPluginHDF5.getFileLock(self.HDF5filename.path.value):
h5Grp = EDPluginHDF5.getHDF5File(
self.HDF5filename.path.value)[self.internalHDF5Path.value]
if "Offsets" in h5Grp:
dataset = h5Grp["Offsets"]
else:
dataset = h5Grp.create_dataset(
"Offsets",
shape=(1 + max(self.index, self.reference), 2),
dtype="float32",
maxshape=(None, 2),
chunks=(1, 2))
if self.index >= dataset.shape[0]:
dataset.resize((self.index + 1, 2))
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 __init__(self):
"""
"""
EDPluginHDF5.__init__(self)
self.setXSDataInputClass(XSDataInputHDF5MapSpectra)
self.listSpectrumFilenames = []
self.listForcedPositions = []
self.listSpectrumFileType = []
self.listArray = []
self.meshScan = {
"FastMotorSteps": 0,
"FastMotorStart": 0,
"FastMotorStop": 0,
"SlowMotorSteps": 0,
"SlowMotorStart": 0,
"SlowMotorStop": 0,
}
self.bDeleteSpectrum = False
def postProcess(self, _edObject=None):
EDPluginHDF5.postProcess(self)
self.DEBUG("EDPluginHDF5MapOfSpectrav10.postProcess")
xsDataResult = XSDataResultHDF5MapSpectra()
if os.path.isfile(self.strHDF5Filename):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.strHDF5Filename))
xsDataResult.setHDF5File(xsDataFile)
xsDataResult.setInternalHDF5Path(XSDataString(self.strHDF5Path))
self.setDataOutput(xsDataResult)
# Delete input images if requested
if self.bDeleteSpectrum:
for oneImage in self.listSpectrumFilenames:
os.remove(oneImage)
# De-Allocate memory
self.listSpectrumFilenames = []
self.listForcedPositions = []
self.listSpectrumFileType = []
self.listArray = []
def postProcess(self, _edObject=None):
EDPluginHDF5.postProcess(self)
self.DEBUG("EDPluginHDF5StackImagesv10.postProcess")
xsDataResult = XSDataResultHDF5StackImages()
if os.path.isfile(self.strHDF5Filename):
xsDataFile = XSDataFile(path=XSDataString(value=self.strHDF5Filename))
xsDataResult.setHDF5File(xsDataFile)
xsDataResult.setInternalHDF5Path(XSDataString(self.strHDF5Path))
self.setDataOutput(xsDataResult)
# Delete input images if requested
if self.bDeleteImage:
for oneImage in self.listImageFilenames:
os.remove(oneImage)
#De-allocate memory no more used.
self.listImageFilenames = []
self.listForcedPositions = []
self.listImageDates = []
self.listArray = []
def postProcess(self, _edObject=None):
EDPluginHDF5.postProcess(self)
self.DEBUG("EDPluginHDF5MapOfSpectrav10.postProcess")
xsDataResult = XSDataResultHDF5MapSpectra()
if os.path.isfile(self.strHDF5Filename):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.strHDF5Filename))
xsDataResult.setHDF5File(xsDataFile)
xsDataResult.setInternalHDF5Path(XSDataString(self.strHDF5Path))
self.setDataOutput(xsDataResult)
# Delete input images if requested
if self.bDeleteSpectrum:
for oneImage in self.listSpectrumFilenames:
os.remove(oneImage)
# De-Allocate memory
self.listSpectrumFilenames = []
self.listForcedPositions = []
self.listSpectrumFileType = []
self.listArray = []
def postProcess(self, _edObject=None):
EDPluginHDF5.postProcess(self)
self.DEBUG("EDPluginHDF5StackImagesv10test.postProcess")
xsDataResult = XSDataResultHDF5StackImages()
if os.path.isfile(self.strHDF5Filename):
xsDataFile = XSDataFile(path=XSDataString(value=self.strHDF5Filename))
xsDataResult.setHDF5File(xsDataFile)
xsDataResult.setInternalHDF5Path(XSDataString(self.strHDF5Path))
self.setDataOutput(xsDataResult)
# Delete input images if requested
if self.bDeleteImage:
for oneImage in self.listImageFilenames:
os.remove(oneImage)
#De-allocate memory no more used.
self.listImageFilenames = []
self.listForcedPositions = []
self.listImageDates = []
self.listArray = []
def process(self, _edObject=None):
EDPluginHDF5.process(self)
self.DEBUG("EDPluginHDF5MapOfSpectrav10.process")
maxSize = (((self.meshScan["SlowMotorSteps" ]), (self.meshScan["FastMotorSteps" ])))
for filename in self.listSpectrumFilenames:
self.listArray.append(fabio.open(filename).data)
if self.listForcedPositions == []:
for oneArray in self.listArray:
self.processOneSpectrum(oneArray, position=maxSize, maxSize=maxSize)
else:
for i in range(len(self.listForcedPositions)):
fSlowPosition = (self.listForcedPositions[i]["Slow"] - self.meshScan["SlowMotorStart"]) / \
(self.meshScan["SlowMotorStop"] - self.meshScan["SlowMotorStart"]) * \
(self.meshScan["SlowMotorSteps" ])
fFastPosition = (self.listForcedPositions[i]["Fast"] - self.meshScan["FastMotorStart"]) / \
(self.meshScan["FastMotorStop"] - self.meshScan["FastMotorStart"]) * \
(self.meshScan["FastMotorSteps" ])
self.processOneSpectrum(self.listArray[i], (int(round(fSlowPosition)), int(round(fFastPosition))), maxSize=maxSize)
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 preProcess(self, _edObject=None):
EDPluginHDF5.preProcess(self)
self.DEBUG("EDPluginHDF5MapOfSpectrav10.preProcess")
for oneSpectrum in self.getDataInput().getInputSpectrumFile():
if oneSpectrum.getPath() is not None:
strFileName = oneSpectrum.getPath().getValue()
self.DEBUG("getInputSpectrumFile: %s" % strFileName)
self.listSpectrumFilenames.append(strFileName)
elif oneSpectrum.getArray() is not None:
self.DEBUG("getInputArray: %s" % strFileName)
self.listArray.append(EDUtilsArray.xsDataToArray())
else:
self.ERROR("A spectrum should either contain an image file or an array.")
self.setFailure()
raise
if (oneSpectrum.getFastMotorPosition() is not None) and (oneSpectrum.getSlowMotorPosition() is not None):
self.listForcedPositions.append({"Slow":oneSpectrum.getSlowMotorPosition().getValue(),
"Fast":oneSpectrum.getFastMotorPosition().getValue()})
if oneSpectrum.getFileType() is not None:
self.listSpectrumFileType.append(oneSpectrum.getFileType.getValue())
if oneSpectrum.getMeshScan() is not None:
XSDMesh = oneSpectrum.getMeshScan()
# self.DEBUG(XSDMesh.marshal())
self.meshScan["FastMotorSteps"] = XSDMesh.getFastMotorSteps().getValue()
self.meshScan["FastMotorStart"] = XSDMesh.getFastMotorStart().getValue()
self.meshScan["FastMotorStop" ] = XSDMesh.getFastMotorStop().getValue()
self.meshScan["SlowMotorSteps"] = XSDMesh.getSlowMotorSteps().getValue()
self.meshScan["SlowMotorStart"] = XSDMesh.getSlowMotorStart().getValue()
self.meshScan["SlowMotorStop" ] = XSDMesh.getSlowMotorStop().getValue()
self.DEBUG("MeshScan= %s" % self.meshScan)
if self.getDataInput().getDeleteInputSpectrum() is not None:
if self.getDataInput().getDeleteInputSpectrum() in [True, "true", "True", 1, "1"]:
self.bDeleteSpectrum = True
if len(self.listForcedPositions) > 0 :
EDAssert.equal(len(self.listForcedPositions), max(len(self.listSpectrumFilenames), len(self.listArray)), _strComment="list of forced position has the right size")
self.hdf5group = self.createStructure(self.strHDF5Filename, self.strHDF5Path, self.dictExtraAttributes)
def process(self, _edObject=None):
EDPluginHDF5.process(self)
self.DEBUG("EDPluginHDF5StackImagesv10test.process")
length = len(self.listForcedPositions)
if length == 0:
for oneFilename in self.listImageFilenames:
header, data = self.readImage(oneFilename)
self.DEBUG("Writing image %s on top of the stack" % (oneFilename))
self.processOneImage(data, position=None, filename=oneFilename, dictHeaders=header)
for oneArray in self.listArray:
self.DEBUG("Writing image from array on top of the stack")
self.processOneImage(oneArray)
else:
if len(self.listImageFilenames) == length :
for i in xrange(length):
self.DEBUG("Writing image %s at position %i" % (self.listImageFilenames[i], self.listForcedPositions[i]))
header, data = self.readImage(self.listImageFilenames[i])
self.processOneImage(data, position=self.listForcedPositions[i], filename=self.listImageFilenames[i], dictHeaders=header)
elif len(self.listArray) == length:
for i in xrange(length):
self.DEBUG("Writing image from array at position %i" % (self.listForcedPositions[i]))
self.processOneImage(self.listArray[i], self.listForcedPositions[i])
def makeHDF5NeXus(self):
self.DEBUG("EDPluginControlFullFieldXASv1_0.makeHDF5NeXus")
with EDPluginHDF5.getFileLock(self.HDF5filename.path.value):
#Seems strange to redefine h5Grp but if there is a flush in between: h5Grp could be closed
entry = EDPluginHDF5.getHDF5File(
self.HDF5filename.path.value)[self.internalHDF5Path.value]
if not "title" in entry:
entry.create_dataset("title", data=self.TITLE)
if not "program" in entry:
entry.create_dataset(
"program", data="EDNA EDPluginControlFullFieldXASv1_0")
if not "start_time" in entry:
entry.create_dataset("start_time",
data=EDPluginHDF5.getIsoTime(
self.start_time))
########################################################################
# Huge hack: for scalar modification: use [()] to refer to the data !!!
########################################################################
if "end_time" in entry:
entry["end_time"][()] = EDPluginHDF5.getIsoTime()
else:
entry.create_dataset("end_time",
data=EDPluginHDF5.getIsoTime())
if "duration" in entry:
entry["duration"][()] = time.time() - self.start_time
else:
entry.create_dataset("duration",
data=time.time() - self.start_time,
dtype="float")
if self.NXdata not in entry:
nxdata = entry.create_group(self.NXdata)
for k, v in self.NXdataAttr.items():
nxdata.attrs[k] = v
else:
nxdata = entry[self.NXdata]
for ds in [self.DSstack, self.DSenergy]:
if (ds in entry) and (ds not in nxdata):
nxdata[ds] = entry[ds]
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 preProcess(self, _edObject=None):
EDPluginHDF5.preProcess(self)
self.DEBUG("EDPluginHDF5MapOfSpectrav10.preProcess")
for oneSpectrum in self.getDataInput().getInputSpectrumFile():
if oneSpectrum.getPath() is not None:
strFileName = oneSpectrum.getPath().getValue()
self.DEBUG("getInputSpectrumFile: %s" % strFileName)
self.listSpectrumFilenames.append(strFileName)
elif oneSpectrum.getArray() is not None:
self.DEBUG("getInputArray: %s" % strFileName)
self.listArray.append(EDUtilsArray.xsDataToArray())
else:
self.ERROR(
"A spectrum should either contain an image file or an array."
)
self.setFailure()
raise
if (oneSpectrum.getFastMotorPosition()
is not None) and (oneSpectrum.getSlowMotorPosition()
is not None):
self.listForcedPositions.append({
"Slow":
oneSpectrum.getSlowMotorPosition().getValue(),
"Fast":
oneSpectrum.getFastMotorPosition().getValue()
})
if oneSpectrum.getFileType() is not None:
self.listSpectrumFileType.append(
oneSpectrum.getFileType.getValue())
if oneSpectrum.getMeshScan() is not None:
XSDMesh = oneSpectrum.getMeshScan()
# self.DEBUG(XSDMesh.marshal())
self.meshScan["FastMotorSteps"] = XSDMesh.getFastMotorSteps(
).getValue()
self.meshScan["FastMotorStart"] = XSDMesh.getFastMotorStart(
).getValue()
self.meshScan["FastMotorStop"] = XSDMesh.getFastMotorStop(
).getValue()
self.meshScan["SlowMotorSteps"] = XSDMesh.getSlowMotorSteps(
).getValue()
self.meshScan["SlowMotorStart"] = XSDMesh.getSlowMotorStart(
).getValue()
self.meshScan["SlowMotorStop"] = XSDMesh.getSlowMotorStop(
).getValue()
self.DEBUG("MeshScan= %s" % self.meshScan)
if self.getDataInput().getDeleteInputSpectrum() is not None:
if self.getDataInput().getDeleteInputSpectrum() in [
True, "true", "True", 1, "1"
]:
self.bDeleteSpectrum = True
if len(self.listForcedPositions) > 0:
EDAssert.equal(
len(self.listForcedPositions),
max(len(self.listSpectrumFilenames), len(self.listArray)),
_strComment="list of forced position has the right size")
self.hdf5group = self.createStructure(self.strHDF5Filename,
self.strHDF5Path,
self.dictExtraAttributes)
