def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
EDVerbose.DEBUG("EDPluginBioSaxsReprocessv1_0.preProcess")
# Load the execution plugin
self.__edPluginExecTemplate = self.loadPlugin(
self.__strControlledPluginName)
self.strDetector = self.xsdInputData.getDetector().value
self.strOperation = self.xsdInputData.getOperation().value
self.strDirectory = self.xsdInputData.getDirectory().value
self.beamCenterX = self.xsdInputData.getBeamCenterX().value
self.pixelSizeX = self.xsdInputData.getPixelSizeX().value
self.beamCenterY = self.xsdInputData.getBeamCenterY().value
self.pixelSizeY = self.xsdInputData.getPixelSizeY().value
self.beamStopDiode = self.xsdInputData.beamStopDiode.value
self.code = self.xsdInputData.getCode().value
self.comments = self.xsdInputData.getComments().value
self.concentration = self.xsdInputData.getConcentration().value
self.keepOriginal = bool(self.xsdInputData.getKeepOriginal().value)
self.machineCurrent = self.xsdInputData.machineCurrent.value
self.wavelength = self.xsdInputData.wavelength.value
self.strPrefix = self.xsDataInputSPD.getPrefix.value
self.normalisation = self.xsdInputData.getNomalisation().value
self.maskFile = self.xsdInputData.maskFile.getPath().value
if self.xsdInputData.getRunNumber() is not None:
self.runNumber = self.xsdInputData.getRunNumber().value
if self.xsdInputData.getSpecVersion() is not None:
self.specVersion = self.xsdInputData.getSpecVersion().value
if self.xsdInputData.getSpecVariableAbort() is not None:
self.specAbort = self.xsdInputData.getSpecVariableAbort().value
if self.xsdInputData.getSpecVariableStatus() is not None:
self.specStatus = self.xsdInputData.getSpecVariableStatus().value
if self.specVersion and self.specAbort and self.specStatus:
EDUtilsBioSaxs.initSpec(self.specVersion, self.specStatus,
self.specAbort)
if not os.path.isfile(self.maskFile):
self.showMessage(4,
"Mask file '%s' not found!" % self.strDirectory)
self.setFailure()
# if self.strOperation not in ("-2", "-1", "0", "1", "2", "3"):
if self.strOperation not in [
"normalisation", "reprocess", "average", "complete"
]:
self.showMessage(4, "Invalid operation '%s'!" % self.strOperation)
self.setFailure()
self.firstFrame = self.xsdInputData.getFirstFrame().value
self.lastFrame = self.xsdInputData.getLastFrame().value
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
EDVerbose.DEBUG("EDPluginBioSaxsReprocessv1_0.preProcess")
# Load the execution plugin
self.__edPluginExecTemplate = self.loadPlugin(self.__strControlledPluginName)
self.strDetector = self.xsdInputData.getDetector().value
self.strOperation = self.xsdInputData.getOperation().value
self.strDirectory = self.xsdInputData.getDirectory().value
self.beamCenterX = self.xsdInputData.getBeamCenterX().value
self.pixelSizeX = self.xsdInputData.getPixelSizeX().value
self.beamCenterY = self.xsdInputData.getBeamCenterY().value
self.pixelSizeY = self.xsdInputData.getPixelSizeY().value
self.beamStopDiode = self.xsdInputData.beamStopDiode.value
self.code = self.xsdInputData.getCode().value
self.comments = self.xsdInputData.getComments().value
self.concentration = self.xsdInputData.getConcentration().value
self.keepOriginal = bool(self.xsdInputData.getKeepOriginal().value)
self.machineCurrent = self.xsdInputData.machineCurrent.value
self.wavelength = self.xsdInputData.wavelength.value
self.strPrefix = self.xsDataInputSPD.getPrefix.value
self.normalisation = self.xsdInputData.getNomalisation().value
self.maskFile = self.xsdInputData.maskFile.getPath().value
if self.xsdInputData.getRunNumber() is not None:
self.runNumber = self.xsdInputData.getRunNumber().value
if self.xsdInputData.getSpecVersion() is not None:
self.specVersion = self.xsdInputData.getSpecVersion().value
if self.xsdInputData.getSpecVariableAbort() is not None:
self.specAbort = self.xsdInputData.getSpecVariableAbort().value
if self.xsdInputData.getSpecVariableStatus() is not None:
self.specStatus = self.xsdInputData.getSpecVariableStatus().value
if self.specVersion and self.specAbort and self.specStatus:
EDUtilsBioSaxs.initSpec(self.specVersion, self.specStatus, self.specAbort)
if not os.path.isfile(self.maskFile):
self.showMessage(4, "Mask file '%s' not found!" % self.strDirectory)
self.setFailure()
# if self.strOperation not in ("-2", "-1", "0", "1", "2", "3"):
if self.strOperation not in ["normalisation", "reprocess", "average", "complete"]:
self.showMessage(4, "Invalid operation '%s'!" % self.strOperation)
self.setFailure()
self.firstFrame = self.xsdInputData.getFirstFrame().value
self.lastFrame = self.xsdInputData.getLastFrame().value
def process(self, _edObject=None):
EDPluginControl.process(self)
EDVerbose.DEBUG("EDPluginBioSaxsReprocessv1_0.process")
if not os.path.isdir(self.strDirectory):
self.showMessage(4,
"Directory '%s' not found!" % self.strDirectory)
self.setFailure()
self.strRawDir = os.path.join(self.strDirectory, "raw")
if not os.path.isdir(self.strRawDir):
self.showMessage(4,
"Directory Raw '%s' not found!" % self.strRawDir)
self.setFailure()
self.str1dDir = os.path.join(self.strDirectory, "1d")
if not os.path.isdir(self.str1dDir):
try:
os.mkdir(self.str1dDir)
except:
self.showMessage(
4, "Could not create directory '1d' in '%s'!" %
self.strDirectory)
self.setFailure()
self.str2dDir = os.path.join(self.strDirectory, "2d")
if not os.path.exists(self.str2dDir):
try:
os.mkdir(self.str2dDir)
except Exception:
self.showMessage(
4, "Could not create directory '2d' in '%s'!" %
self.strDirectory)
self.setFailure()
self.strMiscDir = os.path.join(self.strDirectory, "misc")
if not os.path.exists(self.strMiscDir):
try:
os.mkdir(self.strMiscDir)
except Exception:
self.showMessage(
4, "Could not create directory 'misc' in '%s'!" %
self.strDirectory)
self.setFailure()
# runNumberList = []
iFirstFrame = int(self.firstFrame)
iLastFrame = int(self.lastFrame)
if self.runNumber is None:
for filename in os.listdir(self.strRawDir):
fullPathFilename = os.path.join(self.strRawDir, filename)
if os.path.isfile(fullPathFilename):
prefix, run, frame, extra, extension = EDUtilsBioSaxs.getFilenameDetails(
filename)
try:
iFrame = int(frame)
except ValueError:
iFrame = -1
if (prefix == self.strPrefix) and (run != "") and\
(iFrame >= iFirstFrame) and (iFrame <= iLastFrame) and \
((self.strDetector == "pilatus" and extension == "edf") or \
(self.strDetector == "vantec" and extension == "gfrm")):
if run not in self.dictRunFrame:
self.dictRunFrame[run] = [frame]
else:
self.dictRunFrame[run].append(frame)
else:
if self.bIsOnline: #just treat the last frame of the runs
for run in self.runNumber.split(","):
self.dictRunFrame[run] = ["%02d" % int(self.FrameLast)]
else:
listInRunNr = [int(i) for i in self.runNumber.split(",")]
for filename in os.listdir(self.strRawDir):
fullPathFilename = os.path.join(self.strRawDir, filename)
if os.path.isfile(fullPathFilename):
prefix, run, frame, extra, extension = EDUtilsBioSaxs.getFilenameDetails(
filename)
try:
iRun = int(run)
except ValueError:
iRun = -1
try:
iFrame = int(frame)
except ValueError:
iFrame = -1
if (prefix == self.strPrefix) and (iRun in listInRunNr) and \
(iFrame >= iFirstFrame) and (iFrame <= iLastFrame) and \
((self.strDetector == "pilatus" and extension == "edf") or \
(self.strDetector == "vantec" and extension == "gfrm")):
if run not in self.dictRunFrame:
self.dictRunFrame[run] = [frame]
else:
self.dictRunFrame[run].append(frame)
if len(self.dictRunFrame) == 0:
self.showMessage(
4, "There are no runs for prefix '%s'!" % self.strPrefix)
self.setFailure()
else:
runNumberList = self.dictRunFrame.keys()
runNumberList.sort()
#
# hdfDictionary = HDFDictionary.HDFDictionary()
#
# dictionaryEDF = "EDF_" + self.strDetector.upper()
#
# status, dictionary = hdfDictionary.get(os.path.join(sys.path[0], "Reprocess.xml"), dictionaryEDF)
# if status != 0:
# self.showMessage(3, "Could not get '%s' dictionary!" % dictionaryEDF)
#
# #print dictionary
if not self.keepOriginal:
directory1D_REP = ""
directory2D_REP = ""
directoryMISC_REP = ""
else:
i = 0
while True:
directory1D_REP = os.path.join(self.str1dDir,
"reprocess%i" % i)
if os.path.isdir(directory1D_REP):
i += 1
else:
try:
os.mkdir(directory1D_REP)
except Exception:
self.showMessage(
3, "Could not create reprocess directory '%s'!" %
directory1D_REP)
break
i = 0
while True:
directory2D_REP = os.path.join(self.str2dDir,
"reprocess%i" % i)
if os.path.exists(directory2D_REP):
i += 1
else:
try:
os.mkdir(directory2D_REP)
except Exception:
self.showMessage(
3, "Could not create reprocess directory '%s'!" %
directory2D_REP)
break
i = 0
while True:
directoryMISC_REP = os.path.join(self.strMiscDir,
"reprocess%i" % i)
if os.path.exists(directoryMISC_REP):
i += 1
else:
try:
os.mkdir(directoryMISC_REP)
except Exception:
self.showMessage(
3, "Could not create reprocess directory '%s'!" %
directoryMISC_REP)
break
for runNumber in runNumberList:
doOneRunNumber(runNumber)
self.showMessage(0, "The data reprocessing is done!")
self.__edPluginExecTemplate.connectSUCCESS(self.doSuccessExecTemplate)
self.__edPluginExecTemplate.connectFAILURE(self.doFailureExecTemplate)
self.__edPluginExecTemplate.executeSynchronous()
def process(self, _edObject=None):
EDPluginControl.process(self)
EDVerbose.DEBUG("EDPluginBioSaxsReprocessv1_0.process")
if not os.path.isdir(self.strDirectory):
self.showMessage(4, "Directory '%s' not found!" % self.strDirectory)
self.setFailure()
self.strRawDir = os.path.join(self.strDirectory, "raw")
if not os.path.isdir(self.strRawDir):
self.showMessage(4, "Directory Raw '%s' not found!" % self.strRawDir)
self.setFailure()
self.str1dDir = os.path.join(self.strDirectory, "1d")
if not os.path.isdir(self.str1dDir):
try:
os.mkdir(self.str1dDir)
except :
self.showMessage(4, "Could not create directory '1d' in '%s'!" % self.strDirectory)
self.setFailure()
self.str2dDir = os.path.join(self.strDirectory, "2d")
if not os.path.exists(self.str2dDir):
try:
os.mkdir(self.str2dDir)
except Exception:
self.showMessage(4, "Could not create directory '2d' in '%s'!" % self.strDirectory)
self.setFailure()
self.strMiscDir = os.path.join(self.strDirectory, "misc")
if not os.path.exists(self.strMiscDir):
try:
os.mkdir(self.strMiscDir)
except Exception:
self.showMessage(4, "Could not create directory 'misc' in '%s'!" % self.strDirectory)
self.setFailure()
# runNumberList = []
iFirstFrame = int(self.firstFrame)
iLastFrame = int(self.lastFrame)
if self.runNumber is None:
for filename in os.listdir(self.strRawDir):
fullPathFilename = os.path.join(self.strRawDir, filename)
if os.path.isfile(fullPathFilename):
prefix, run, frame, extra, extension = EDUtilsBioSaxs.getFilenameDetails(filename)
try:
iFrame = int(frame)
except ValueError:
iFrame = -1
if (prefix == self.strPrefix) and (run != "") and\
(iFrame >= iFirstFrame) and (iFrame <= iLastFrame) and \
((self.strDetector == "pilatus" and extension == "edf") or \
(self.strDetector == "vantec" and extension == "gfrm")):
if run not in self.dictRunFrame:
self.dictRunFrame[run] = [frame]
else:
self.dictRunFrame[run].append(frame)
else:
if self.bIsOnline: #just treat the last frame of the runs
for run in self.runNumber.split(","):
self.dictRunFrame[run] = ["%02d" % int(self.FrameLast)]
else:
listInRunNr = [int(i) for i in self.runNumber.split(",")]
for filename in os.listdir(self.strRawDir):
fullPathFilename = os.path.join(self.strRawDir, filename)
if os.path.isfile(fullPathFilename):
prefix, run, frame, extra, extension = EDUtilsBioSaxs.getFilenameDetails(filename)
try:
iRun = int(run)
except ValueError:
iRun = -1
try:
iFrame = int(frame)
except ValueError:
iFrame = -1
if (prefix == self.strPrefix) and (iRun in listInRunNr) and \
(iFrame >= iFirstFrame) and (iFrame <= iLastFrame) and \
((self.strDetector == "pilatus" and extension == "edf") or \
(self.strDetector == "vantec" and extension == "gfrm")):
if run not in self.dictRunFrame:
self.dictRunFrame[run] = [frame]
else:
self.dictRunFrame[run].append(frame)
if len(self.dictRunFrame) == 0:
self.showMessage(4, "There are no runs for prefix '%s'!" % self.strPrefix)
self.setFailure()
else:
runNumberList = self.dictRunFrame.keys()
runNumberList.sort()
#
# hdfDictionary = HDFDictionary.HDFDictionary()
#
# dictionaryEDF = "EDF_" + self.strDetector.upper()
#
# status, dictionary = hdfDictionary.get(os.path.join(sys.path[0], "Reprocess.xml"), dictionaryEDF)
# if status != 0:
# self.showMessage(3, "Could not get '%s' dictionary!" % dictionaryEDF)
#
# #print dictionary
if not self.keepOriginal:
directory1D_REP = ""
directory2D_REP = ""
directoryMISC_REP = ""
else:
i = 0
while True:
directory1D_REP = os.path.join(self.str1dDir, "reprocess%i" % i)
if os.path.isdir(directory1D_REP):
i += 1
else:
try:
os.mkdir(directory1D_REP)
except Exception:
self.showMessage(3, "Could not create reprocess directory '%s'!" % directory1D_REP)
break
i = 0
while True:
directory2D_REP = os.path.join(self.str2dDir, "reprocess%i" % i)
if os.path.exists(directory2D_REP):
i += 1
else:
try:
os.mkdir(directory2D_REP)
except Exception:
self.showMessage(3, "Could not create reprocess directory '%s'!" % directory2D_REP)
break
i = 0
while True:
directoryMISC_REP = os.path.join(self.strMiscDir, "reprocess%i" % i)
if os.path.exists(directoryMISC_REP):
i += 1
else:
try:
os.mkdir(directoryMISC_REP)
except Exception:
self.showMessage(3, "Could not create reprocess directory '%s'!" % directoryMISC_REP)
break
for runNumber in runNumberList:
doOneRunNumber(runNumber)
self.showMessage(0, "The data reprocessing is done!")
self.__edPluginExecTemplate.connectSUCCESS(self.doSuccessExecTemplate)
self.__edPluginExecTemplate.connectFAILURE(self.doFailureExecTemplate)
self.__edPluginExecTemplate.executeSynchronous()
