def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'output':
obj_ = XSDataImageExt()
obj_.build(child_)
self.setOutput(obj_)
XSDataResult.buildChildren(self, child_, nodeName_)
def postProcess(self, _edObject=None):
EDPluginExec.postProcess(self)
self.DEBUG("EDPluginExecShiftImagev1_0.postProcess")
# Create some output data
xsDataResult = XSDataResultShiftImage()
if self.strOutputType is None:
xsDataResult.setOutputArray(
EDUtilsArray.arrayToXSData(self.npaImage))
elif self.strOutputType == "file":
image = edfimage(data=self.npaImage,
header={
"Offset_1": self.tOffset[0],
"Offset_2": self.tOffset[1],
"Max_Offset": self.MAX_OFFSET_VALUE
})
image.write(self.strOutputImage, force_type=self.npaImage.dtype)
xsdimg = XSDataImageExt(path=XSDataString(self.strOutputImage))
xsDataResult.outputImage = xsdimg
elif self.strOutputType == "shared":
EDShare[self.strOutputImage] = self.npaImage
xsdimg = XSDataImageExt(shared=XSDataString(self.strOutputImage))
xsDataResult.outputImage = xsdimg
elif self.strOutputType == "array":
xsdimg = XSDataImageExt(
array=EDUtilsArray.arrayToXSData(self.npaImage))
xsDataResult.outputImage = xsdimg
self.setDataOutput(xsDataResult)
self.npaImage = None
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 buildChildren(self, child_, nodeName_): if child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'outputMatrix': obj_ = XSDataImageExt() obj_.build(child_) self.setOutputMatrix(obj_) XSDataResult.buildChildren(self, child_, nodeName_)
def testCheckParameters(self):
xsDataInput = XSDataInputPyFAI(detector=XSDataDetector(),
geometry=XSDataGeometry(),
output=XSDataImageExt(),
input=XSDataImageExt(),
nbPt=XSDataInteger())
edPluginExecPyFAIv1_0 = self.createPlugin()
edPluginExecPyFAIv1_0.setDataInput(xsDataInput)
edPluginExecPyFAIv1_0.checkParameters()
def postProcess(self, _edObject=None):
EDPluginExec.postProcess(self)
self.DEBUG("EDPluginExecPyFAIv1_0.postProcess")
# Create some output data
if self.strOutputFile:
output = XSDataImageExt(path=XSDataString(self.strOutputFile))
elif self.shared:
output = XSDataImageExt(shared=XSDataString(self.shared))
else:
output = XSDataImageExt(array=EDUtilsArray.arrayToXSData(self.npaOut))
xsDataResult = XSDataResultPyFAI(output=output)
self.setDataOutput(xsDataResult)
def getFrameRef(cls, index):
"""
Just retrieves the reference in the EDShare store
@return: reference to the frame in EDShare
@rtype: XSDataImageExt
"""
return XSDataImageExt(shared=XSDataString("Normalized-%06i" %
int(index)))
def postProcess(self, _edObject=None):
EDPluginExec.postProcess(self)
self.DEBUG("EDPluginExecNormalizeImagev1_1.postProcess")
xsDataResult = XSDataResultNormalize()
if self.strOutputFilename is not None:
self.DEBUG("Writing file %s" % self.strOutputFilename)
edf = fabio.edfimage.edfimage(data=self.npaNormalized, header={})
edf.write(self.strOutputFilename)
xsdo = XSDataImageExt(path=XSDataString(self.strOutputFilename))
elif self.strOutputShared is not None:
self.DEBUG("EDShare --> %s" % self.strOutputShared)
EDShare[ self.strOutputShared] = self.npaNormalized
xsdo = XSDataImageExt(shared=XSDataString(self.strOutputShared))
else:
xsdo = XSDataImageExt(array=EDUtilsArray.arrayToXSData(self.npaNormalized))
xsDataResult.output = xsdo
# Create some output data
self.setDataOutput(xsDataResult)
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'inputMatrix':
obj_ = XSDataImageExt()
obj_.build(child_)
self.setInputMatrix(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'outputMatrix':
obj_ = XSDataImageExt()
obj_.build(child_)
self.setOutputMatrix(obj_)
XSDataInput.buildChildren(self, child_, nodeName_)
def getXsdDark(self):
"""
return XSDataDark object
"""
if self._xsDataDark is None:
self._xsDataDark = [XSDataImageExt(path=XSDataString(i["path"]),
exposureTime=XSDataTime(i["exposureTime"]))
for i in self.darks]
return self._xsDataDark
def postProcess(self, _edObject=None):
EDPluginExec.postProcess(self)
EDVerbose.DEBUG("EDPluginExecShiftImagev1_0.postProcess")
# Create some output data
xsDataResult = XSDataResultShiftImage()
if self.strOutputImage is None:
#ArrayOutput
xsDataResult.setOutputArray(
EDUtilsArray.arrayToXSData(self.npaImage))
else:
image = edfimage(data=self.npaImage,
header={
"Offset_1": self.tOffset[0],
"Offset_2": self.tOffset[1]
})
image.write(self.strOutputImage, force_type=self.npaImage.dtype)
xsdimg = XSDataImageExt(path=XSDataString(self.strOutputImage))
xsDataResult.setOutputImage(xsdimg)
self.setDataOutput(xsDataResult)
def doSuccessExecAccumultor(self, _edPlugin=None):
with self.semAccumulator:
self.DEBUG("EDPluginControlAlignStackv1_0.doSuccessExecAccumultor")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlAlignStackv1_0.doSuccessExecAccumultor")
for query in _edPlugin.dataOutput.getQuery():
self.addExtraTime(60)
_edPlugin.addExtraTime(60)
accType = query.getItem()[0].getValue().split()[0]
listInt = [
int(i.getValue().split()[1]) for i in query.getItem()
]
if accType == "raw":
listFrame = [self.getFrameRef(i) for i in listInt]
xsdata = XSDataInputMeasureOffset(image=listFrame)
doSIFT = False
if self.xsdMeasureOffset is not None:
xsdata.setCropBorders(
self.xsdMeasureOffset.getCropBorders())
xsdata.setSmoothBorders(
self.xsdMeasureOffset.getSmoothBorders())
xsdata.setBackgroundSubtraction(
self.xsdMeasureOffset.getRemoveBackground())
if self.xsdMeasureOffset.useSift is not None:
doSIFT = self.xsdMeasureOffset.useSift.value
if max(listInt
) > EDPluginControlAlignStackv1_0.__iRefFrame:
listInt.sort()
else:
listInt.sort(reverse=True)
xsdata.setIndex([XSDataInteger(i) for i in listInt])
if doSIFT:
edPluginExecMeasure = self.loadPlugin(
self.__strControlledPluginMeasureSIFT)
else:
edPluginExecMeasure = self.loadPlugin(
self.__strControlledPluginMeasureFFT)
edPluginExecMeasure.setDataInput(xsdata)
edPluginExecMeasure.connectSUCCESS(
self.doSuccessExecMeasureOffset)
edPluginExecMeasure.connectFAILURE(
self.doFailureExecMeasureOffset)
self.queue.put(edPluginExecMeasure)
elif accType == "shift":
shift_1 = 0.0
shift_2 = 0.0
for frame in listInt:
shift_1 += EDPluginControlAlignStackv1_0.__dictRelShift[
frame][0]
shift_2 += EDPluginControlAlignStackv1_0.__dictRelShift[
frame][1]
if listInt[0] > EDPluginControlAlignStackv1_0.__iRefFrame:
iFrameShift = max(listInt)
else:
iFrameShift = min(listInt)
EDPluginControlAlignStackv1_0.__dictAbsShift[
iFrameShift] = (shift_1, shift_2)
self.screen(
"Frame number %i has absolute offset of %.3f,%.3f" %
(iFrameShift, shift_1, shift_2))
edPluginExecShift = self.loadPlugin(
self.__strControlledPluginShift)
edPluginExecShift.dataInput = XSDataInputShiftImage(
index=XSDataInteger(iFrameShift),
offset=[XSDataDouble(shift_1),
XSDataDouble(shift_2)],
inputImage=self.getFrameRef(iFrameShift),
outputImage=XSDataImageExt(
shared=XSDataString("Shifted-%06i" % iFrameShift)))
edPluginExecShift.connectSUCCESS(
self.doSuccessExecShiftImage)
edPluginExecShift.connectFAILURE(
self.doFailureExecShiftImage)
self.queue.put(edPluginExecShift)
self.DEBUG("Items: %s" % EDPluginAccumulatorv1_0.getItems())
self.DEBUG("Queries: %s" % EDPluginAccumulatorv1_0.getQueries())
def doSuccessExecMeasureOffset(self, _edPlugin=None):
with self.semMeasure:
self.DEBUG(
"EDPluginControlAlignStackv1_0.doSuccessExecMeasureOffset")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlAlignStackv1_0.doSuccessExecMeasureOffset")
listIndex = [i.getValue() for i in _edPlugin.dataInput.index]
listIndex.sort()
dataOutput = _edPlugin.dataOutput
if self.bAlwaysMOvsRef:
if min(listIndex) < EDPluginControlAlignStackv1_0.__iRefFrame:
iToShift, iRef = tuple(listIndex)
EDPluginControlAlignStackv1_0.__dictAbsShift[
iToShift] = tuple(
[-i.getValue() for i in dataOutput.getOffset()])
else:
iRef, iToShift = tuple(listIndex)
EDPluginControlAlignStackv1_0.__dictAbsShift[
iToShift] = tuple(
[i.getValue() for i in dataOutput.getOffset()])
self.screen(
"Frame number %i has absolute offset of %.3f,%.3f" %
(iToShift,
EDPluginControlAlignStackv1_0.__dictAbsShift[iToShift][0],
EDPluginControlAlignStackv1_0.__dictAbsShift[iToShift][1])
)
edPluginExecShift = self.loadPlugin(
self.__strControlledPluginShift)
xsdata = XSDataInputShiftImage(
index=XSDataInteger(iToShift),
offset=[
XSDataDouble(i) for i in
EDPluginControlAlignStackv1_0.__dictAbsShift[iToShift]
],
inputImage=self.getFrameRef(iToShift),
outputImage=XSDataImageExt(
shared=XSDataString("Shifted-%06i" % iToShift)))
edPluginExecShift.setDataInput(xsdata)
edPluginExecShift.connectSUCCESS(self.doSuccessExecShiftImage)
edPluginExecShift.connectFAILURE(self.doFailureExecShiftImage)
self.queue.put(edPluginExecShift)
else:
if min(listIndex) < EDPluginControlAlignStackv1_0.__iRefFrame:
iToShift, iRef = tuple(listIndex)
EDPluginControlAlignStackv1_0.__dictRelShift[
iToShift] = tuple(
[-i.value for i in dataOutput.offset])
else:
iRef, iToShift = tuple(listIndex)
EDPluginControlAlignStackv1_0.__dictRelShift[
iToShift] = tuple([i.value for i in dataOutput.offset])
self.screen(
"Frame number %i has relative offset of %.3f,%.3f" %
(iToShift,
EDPluginControlAlignStackv1_0.__dictRelShift[iToShift][0],
EDPluginControlAlignStackv1_0.__dictRelShift[iToShift][1])
)
xsdata = XSDataInputAccumulator(
item=[XSDataString("shift %04i" % iToShift)])
edPluginExecAccumulator = self.loadPlugin(
self.__strControlledPluginAccumulator)
edPluginExecAccumulator.setDataInput(xsdata)
edPluginExecAccumulator.connectSUCCESS(
self.doSuccessExecAccumultor)
edPluginExecAccumulator.connectFAILURE(
self.doFailureExecAccumulator)
self.queue.put(edPluginExecAccumulator)
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlAlignStackv1_0.process")
for iFrame in self.iFrames:
edPluginExecAccumulator = self.loadPlugin(
self.__strControlledPluginAccumulator)
queryRaw = XSDataQuery()
queryShift = XSDataQuery()
queryRaw.setRemoveItems(XSDataBoolean(False))
queryShift.setRemoveItems(XSDataBoolean(False))
xsdataAcc = XSDataInputAccumulator()
if (EDPluginControlAlignStackv1_0.__iRefFrame
== iFrame) or (self.bDoAlign == False):
EDPluginControlAlignStackv1_0.__dictAbsShift[iFrame] = (0.0,
0.0)
EDPluginControlAlignStackv1_0.__dictRelShift[iFrame] = (0.0,
0.0)
self.hdf5_offset(index=iFrame, offset=[0.0, 0.0])
edPluginExecShift = self.loadPlugin(
self.__strControlledPluginShift)
xsdata = XSDataInputShiftImage(
index=XSDataInteger(iFrame),
offset=[
XSDataDouble(i) for i in
EDPluginControlAlignStackv1_0.__dictAbsShift[iFrame]
],
inputImage=self.getFrameRef(iFrame),
outputImage=XSDataImageExt(
shared=XSDataString("Shifted-%06i" % iFrame)))
edPluginExecShift.setDataInput(xsdata)
edPluginExecShift.connectSUCCESS(self.doSuccessExecShiftImage)
edPluginExecShift.connectFAILURE(self.doFailureExecShiftImage)
self.queue.put(edPluginExecShift)
if (self.bDoAlign == False):
self.executeControlledPlugins()
return
elif EDPluginControlAlignStackv1_0.__iRefFrame < iFrame:
if self.bAlwaysMOvsRef:
queryRaw.setItem([
XSDataString(
"raw %04i" %
(EDPluginControlAlignStackv1_0.__iRefFrame)),
XSDataString("raw %04i" % iFrame)
])
xsdataAcc.setQuery([queryRaw])
else:
queryRaw.setItem([
XSDataString("raw %04i" % (iFrame - 1)),
XSDataString("raw %04i" % iFrame)
])
queryShift.setItem([
XSDataString("shift %04i" % i) for i in range(
EDPluginControlAlignStackv1_0.__iRefFrame +
1, iFrame + 1)
])
xsdataAcc.setQuery([queryRaw, queryShift])
elif EDPluginControlAlignStackv1_0.__iRefFrame > iFrame:
if self.bAlwaysMOvsRef:
queryRaw.setItem([
XSDataString("raw %04i" % iFrame),
XSDataString(
"raw %04i" %
(EDPluginControlAlignStackv1_0.__iRefFrame))
])
xsdataAcc.setQuery([queryRaw])
else:
queryRaw.setItem([
XSDataString("raw %04i" % (iFrame + 1)),
XSDataString("raw %04i" % iFrame)
])
queryShift.setItem([
XSDataString("shift %04i" % i) for i in range(
EDPluginControlAlignStackv1_0.__iRefFrame -
1, iFrame - 1, -1)
])
xsdataAcc.setQuery([queryRaw, queryShift])
if (EDPluginControlAlignStackv1_0.__iRefFrame == iFrame):
self.saveReferenceFrame(iFrame)
xsdataAcc.setItem([XSDataString("raw %04i" % iFrame)])
edPluginExecAccumulator.setDataInput(xsdataAcc)
edPluginExecAccumulator.connectSUCCESS(
self.doSuccessExecAccumultor)
edPluginExecAccumulator.connectFAILURE(
self.doFailureExecAccumulator)
self.queue.put(edPluginExecAccumulator)
self.executeControlledPlugins()
def makeXML(self, filename):
"""Here we create the XML string to be passed to the EDNA plugin from the input filename
This can / should be modified by the final user
@param filename: full path of the input file
@type filename: python string representing the path
@rtype: XML string
@return: python string
"""
self.header = None
dirname, basename = os.path.split(filename)
if not basename.startswith(self.prefix):
return
if self.normalizedSuffix and basename.endswith(self.normalizedSuffix):
return
if basename.startswith(self.flatPrefix):
return
if not basename.endswith(self.suffix):
return
if self.fScaleData:
fScaleData = self.fScaleData
else:
fScaleData = self.getNbFrames(filename)
if not fScaleData:
fScaleData = 1.0
if self.fScaleDark:
fScaleDark = self.fScaleDark
else:
fScaleDark = self.getNbFrames(self.darks[0]["path"])
if not fScaleDark:
fScaleDark = 1.0
if isinstance(self.reference, int):
reference = self.reference
else:
reference = -1
xsd = XSDataInputFullFieldXAS(HDF5File=XSDataFile(path=XSDataString(self.HDF5)),
internalHDF5Path=XSDataString(self.internalHdf5),
measureOffset=self.getXSDMeasureOffset(),
dark=self.getXsdDark(),
reference=XSDataInteger(reference),
data=[XSDataImageExt(path=XSDataString(filename),
exposureTime=XSDataTime(self.getExposureTime(filename)))],
dataScaleFactor=XSDataDouble(fScaleData),
darkScaleFactor=XSDataDouble(fScaleDark),
)
if self.dontAlign:
xsd.dontAlign = XSDataBoolean(self.dontAlign)
extendedPrefix = ""
number = ""
started = False
if self.lstSubscanSize:
subScanDigit = []
for i in basename[len(self.prefix):]:
if started and i == "_":
if len(number) > 0:
subScanDigit.append(number)
number = ""
continue
if started and not i.isdigit():
if number:
subScanDigit.append(number)
number = ""
break
if not started:
if i.isdigit():
started = True
else:
extendedPrefix += i
if started:
number += i
if not subScanDigit:
print("ERROR: no index guessed !!!")
return ""
elif len(subScanDigit) == 1:
index = int(subScanDigit[0])
else:# len(subScanDigit) > 1:
index = 0
for i in range(int(subScanDigit[0])):
index += self.lstSubscanSize[i]
index += int(subScanDigit[1])
extendedPrefix += "_".join(subScanDigit[:2])
else:
for i in basename[len(self.prefix):]:
extendedPrefix += i
if started and not i.isdigit():
break
if not started and i.isdigit():
started = True
if started:
number += i
index = int(number)
xsd.index = XSDataInteger(index)
if self.normalizedSuffix:
pr = os.path.splitext(os.path.abspath(filename))[0]
xsd.saveNormalized = XSDataFile(path=XSDataString(pr + self.normalizedSuffix))
energy = self.getEnergy(filename)
if energy is not None:
xsd.energy = XSDataDouble(energy)
flatprefix = self.flatPrefix + extendedPrefix
listFlats = []
for oneFile in os.listdir(dirname):
if oneFile.startswith(flatprefix) and oneFile.endswith(self.suffix):
oneCompleteFile = os.path.abspath(os.path.join(dirname, oneFile))
xsdFileFlat1 = XSDataImageExt(path=XSDataString(oneCompleteFile),
exposureTime=XSDataTime(self.getExposureTime(oneCompleteFile)))
listFlats.append(xsdFileFlat1)
xsd.flat = listFlats
if len(listFlats) != 2:
EDVerbose.WARNING("Not exactly 2 flats were found:" + " ".join([a.path.value for a in listFlats ]))
EDVerbose.WARNING("Those are the flat prefix ans suffix: %s\t%s" % (flatprefix, self.suffix))
if self.fScaleFlat:
fScaleFlat = self.fScaleFlat
else:
fScaleFlat = self.getNbFrames(oneCompleteFile)
if not fScaleFlat:
fScaleFlat = 1.0
xsd.flatScaleFactor = XSDataDouble(fScaleFlat)
return xsd.marshal()
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'data':
obj_ = XSDataImageExt()
obj_.build(child_)
self.data.append(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'dark':
obj_ = XSDataImageExt()
obj_.build(child_)
self.dark.append(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'flat':
obj_ = XSDataImageExt()
obj_.build(child_)
self.flat.append(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'output':
obj_ = XSDataImageExt()
obj_.build(child_)
self.setOutput(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'dataScaleFactor':
obj_ = XSDataDouble()
obj_.build(child_)
self.setDataScaleFactor(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'darkScaleFactor':
obj_ = XSDataDouble()
obj_.build(child_)
self.setDarkScaleFactor(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'flatScaleFactor':
obj_ = XSDataDouble()
obj_.build(child_)
self.setFlatScaleFactor(obj_)
XSDataInput.buildChildren(self, child_, nodeName_)
def buildChildren(self, child_, nodeName_): if child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'data': obj_ = XSDataImageExt() obj_.build(child_) self.data.append(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'dark': obj_ = XSDataImageExt() obj_.build(child_) self.dark.append(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'flat': obj_ = XSDataImageExt() obj_.build(child_) self.flat.append(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'output': obj_ = XSDataImageExt() obj_.build(child_) self.setOutput(obj_) XSDataInput.buildChildren(self, child_, nodeName_)
