def save(self, filename):
"""
Save configuration to file
"""
if isinstance(self.reference, int):
reference = self.reference
else:
reference = -1
xsdi = XSDataInputFullFieldXAS(HDF5File=XSDataFile(XSDataString(self.HDF5)),
internalHDF5Path=XSDataString(self.internalHdf5),
measureOffset=self.getXSDMeasureOffset(),
reference=XSDataInteger(reference),
dark=self.getXsdDark())
with open(filename, "wb") as xmlFile:
xmlFile.write(xsdi.marshal())
def load(self, filename):
"""
Retrieve information from XML file
"""
xsdi = XSDataInputFullFieldXAS.parseFile(filename)
self.HDF5 = xsdi.HDF5File.path.value
self.internalHdf5 = xsdi.internalHDF5Path.value
self.measureOffset = {}
mo = xsdi.measureOffset
if mo:
if mo.alwaysVersusRef:
self.measureOffset[
"alwaysVersusRef"] = mo.alwaysVersusRef.value
if mo.cropBorders:
self.measureOffset["cropBorders"] = [
i.value for i in mo.cropBorders
]
if mo.smoothBorders:
self.measureOffset["smoothBorders"] = [
i.value for i in mo.smoothBorders
]
if mo.sobelFilter:
self.measureOffset["sobelFilter"] = mo.sobelFilter.value
if mo.useSift:
self.measureOffset["useSift"] = mo.useSift.value
if mo.removeBackground:
self.measureOffset[
"removeBackground"] = mo.removeBackground.value
self.reference = xsdi.reference.value
self.darks = [{
"path": i.path.value,
"exposureTime": i.exposureTime.value
} for i in xsdi.dark]
def testCheckParameters(self):
xsDataInput = XSDataInputFullFieldXAS(index=XSDataInteger(0),
HDF5File=XSDataFile(),
internalHDF5Path=XSDataString())
edPluginExecFullFieldXAS = self.createPlugin()
edPluginExecFullFieldXAS.setDataInput(xsDataInput)
edPluginExecFullFieldXAS.checkParameters()
def error(self, strXMLin):
"""
This is an example of XMLerr function ... it prints only the name of the file created
@param srXMLin: The XML string used to launch the job
@type strXMLin: python string with the input XML
@rtype: None
@return: None
"""
if isinstance(strXMLin, (str, unicode)):
xsd = XSDataInputFullFieldXAS.parseString(strXMLin)
else:
xsd = strXMLin
filenames = [i.path.value for i in xsd.getData()]
EDVerbose.ERROR("Error in the processing of: \n %s" % "\n".join(filenames))
self._lstErrorFile.append(filenames)
def error(self, strXMLin):
"""
This is an example of XMLerr function ... it prints only the name of the file created
@param srXMLin: The XML string used to launch the job
@type strXMLin: python string with the input XML
@rtype: None
@return: None
"""
if isinstance(strXMLin, (str, unicode)):
xsd = XSDataInputFullFieldXAS.parseString(strXMLin)
else:
xsd = strXMLin
filenames = [ i.path.value for i in xsd.getData()]
EDVerbose.ERROR("Error in the processing of: \n %s" % "\n".join(filenames))
self._lstErrorFile.append(filenames)
def load(self, filename):
"""
Retrieve information from XML file
"""
xsdi = XSDataInputFullFieldXAS.parseFile(filename)
self.HDF5 = xsdi.HDF5File.path.value
self.internalHdf5 = xsdi.internalHDF5Path.value
self.measureOffset = {}
mo = xsdi.measureOffset
if mo:
if mo.alwaysVersusRef:
self.measureOffset["alwaysVersusRef"] = mo.alwaysVersusRef.value
if mo.cropBorders:
self.measureOffset["cropBorders"] = [i.value for i in mo.cropBorders]
if mo.smoothBorders:
self.measureOffset["smoothBorders"] = [i.value for i in mo.smoothBorders]
if mo.sobelFilter:
self.measureOffset["sobelFilter"] = mo.sobelFilter.value
if mo.useSift:
self.measureOffset["useSift"] = mo.useSift.value
if mo.removeBackground:
self.measureOffset["removeBackground"] = mo.removeBackground.value
self.reference = xsdi.reference.value
self.darks = [{"path": i.path.value, "exposureTime": i.exposureTime.value} for i in xsdi.dark]
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 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()
