def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
EDVerbose.DEBUG("EDPluginExecSaxsMacv1_0.preProcess")
xsdIn = self.getDataInput()
if xsdIn.getInputImage() is not None:
self.inputImage = xsdIn.getInputImage().getPath().getValue()
if not os.path.isfile(self.inputImage) and "%" not in self.inputImage:
EDVerbose.WARNING("Input file %s does not exist ... try to go on anyway" % self.inputImage)
self.inputImage = None
if xsdIn.getOutputImage() is not None:
self.outputImage = xsdIn.getOutputImage().getPath().getValue()
if xsdIn.getFirstImage() is not None:
self.firstImage = xsdIn.getFirstImage().getValue()
if xsdIn.getLastImage() is not None:
self.lastImage = xsdIn.getLastImage().getValue()
if xsdIn.getOptions() is not None:
self.options = xsdIn.getOptions().getValue()
if xsdIn.getDummy() is not None:
self.dummy = xsdIn.getDummy().getValue()
if xsdIn.getIncrement() is not None:
self.increment = xsdIn.getIncrement().getValue()
if xsdIn.getAddConst() is not None:
self.addConst = xsdIn.getAddConst().getValue()
if xsdIn.getMultConst() is not None:
self.multConst = xsdIn.getMultConst().getValue()
#Create the command line to run the program
self.generateSaxsMacCommand()
def preProcess(self):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG('Truncate: preprocess')
input_file = self.dataInput.input_file.value
output_file = self.dataInput.output_file.value
options = 'hklin {0} hklout {1}'.format(input_file, output_file)
self.setScriptCommandline(options)
self.DEBUG('command line options set to {0}'.format(options))
nres = self.dataInput.nres.value
anom = self.dataInput.anom.value
res = self.dataInput.res.value
if res is None:
res = 0
self.addListCommandExecution('nres {0}'.format(nres))
self.addListCommandExecution('truncate YES')
self.addListCommandExecution('anomalous {0}'.format(anom))
self.addListCommandExecution('plot OFF')
self.addListCommandExecution('labout F=F_xdsproc SIGF=SIGF_xdsproc')
self.addListCommandExecution('falloff YES')
self.addListCommandExecution('resolution 50 {0}'.format(res))
self.addListCommandExecution('PNAME foo')
self.addListCommandExecution('DNAME foo')
self.addListCommandExecution('end')
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
EDVerbose.DEBUG("EDPluginExecDcrawv1_0.preProcess")
self.__strRawFile = self.getDataInput().getRawImagePath().getPath().getValue()
if self.getDataInput().getOutputPath() is not None:
self.__strOutputFile = self.getDataInput().getOutputPath().getPath().getValue()
if self.getDataInput().getExtractThumbnail() is not None:
self.__bExtracThumbnail = (self.getDataInput().getExtractThumbnail().getValue() in [1, "true", "True", "TRUE", True])
########################################################################
# This option is incompatible with all others
########################################################################
if self.__bExtracThumbnail is True:
self.__bWBCamera = False
self.__strOutputType = None #we cannot know what find of thumbnail is saved, can be jpeg, tiff or nothing !
else:
if self.getDataInput().getExportTiff() is not None:
self.__bExportTiff = (self.getDataInput().getExportTiff().getValue() in [1, "true", "True", "TRUE", True])
if self.__bExportTiff:
self.__strOutputType = "tiff"
if self.getDataInput().getWhiteBalanceAuto() is not None:
self.__bWBAuto = (self.getDataInput().getWhiteBalanceAuto().getValue() in [1, "true", "True", "TRUE", True])
if self.__bWBAuto is True: self.__bWBCamera = False
if self.getDataInput().getWhiteBalanceFromCamera() is not None:
self.__bWBCamera = (self.getDataInput().getWhiteBalanceFromCamera().getValue() in [1, "true", "True", "TRUE", True])
if self.getDataInput().getLevelsFromCamera() is not None:
self.__bLevelCamera = (self.getDataInput().getLevelsFromCamera().getValue() in [1, "true", "True", "TRUE", True])
if self.getDataInput().getInterpolationQuality() is not None:
self.__iInterpolate = self.getDataInput().getInterpolationQuality().getValue()
self.generateDcrawCommand()
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginBestv1_2.preProcess")
self.setScriptLogFileName("best.log")
self.setFileBestDat(os.path.join(self.getWorkingDirectory(), "bestfile.dat"))
self.setFileBestPar(os.path.join(self.getWorkingDirectory(), "bestfile.par"))
EDUtilsFile.writeFile(self.getFileBestDat(), self.getDataInput().getBestFileContentDat().getValue())
EDUtilsFile.writeFile(self.getFileBestPar(), self.getDataInput().getBestFileContentPar().getValue())
listBestFileContentHKL = self.getDataInput().getBestFileContentHKL()
iterator = 0
for bestFileContentHKL in listBestFileContentHKL:
iterator = iterator + 1
bestFileHKL = os.path.join(self.getWorkingDirectory(), "bestfile" + str(iterator) + ".hkl")
self.listFileBestHKL.append(bestFileHKL)
EDUtilsFile.writeFile(bestFileHKL, bestFileContentHKL.getValue())
if(self.getDataInput().getComplexity() is not None):
self.setComplexity(self.getDataInput().getComplexity().getValue())
self.initializeCommands()
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginExecMtz2Variousv1_0.preProcess")
xsDataInputRdfit = self.getDataInput()
self.setScriptCommandline(self.generateCommands(xsDataInputRdfit))
self.addListCommandPostExecution("gle -device png -resolution 100 %s" %
self.strScaleIntensityGleFile)
def preProcess(self):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG('XdsToSca: preprocess')
self.addInputLine('xdsfile {0}'.format(self.dataInput.hkl_file.path.value))
self.addInputLine('scafile {0}'.format(self.dataInput.sca_file.path.value))
self.addInputLine('end')
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginExecDammifv0_2.preProcess")
if self.dataInput.order:
self.name = "dammif-%s" % self.dataInput.order.value #I know I only modify the instance variable, not the class one
self.generateDammifScript()
def preProcess(self, _edObject=None):
"""
"""
EDPluginExecProcessScript.preProcess(self)
self.setFileBestDat(
os.path.join(self.getWorkingDirectory(), "bestfile.dat"))
self.setFileBestPar(
os.path.join(self.getWorkingDirectory(), "bestfile.par"))
EDUtilsFile.writeFile(
self.getFileBestDat(),
self.getDataInput().getBestFileContentDat().getValue())
EDUtilsFile.writeFile(
self.getFileBestPar(),
self.getDataInput().getBestFileContentPar().getValue())
listBestFileContentHKL = self.getDataInput().getBestFileContentHKL()
iterator = 0
for bestFileContentHKL in listBestFileContentHKL:
iterator = iterator + 1
bestFileHKL = os.path.join(self.getWorkingDirectory(),
"bestfile" + str(iterator) + ".hkl")
self.listFileBestHKL.append(bestFileHKL)
EDUtilsFile.writeFile(bestFileHKL, bestFileContentHKL.getValue())
if (self.getDataInput().getComplexity() is not None):
self.setComplexity(self.getDataInput().getComplexity().getValue())
self.initializeCommands()
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginExecDataverv1_0.preProcess")
self.lstInFiles = [i.path.value for i in self.dataInput.inputCurve]
if self.dataInput.outputCurve is not None:
self.strOutFile = self.dataInput.outputCurve.path.value
self.generateCommandLine()
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginExecDatcmpv3_0.preProcess")
self.listFiles = [i.path.value for i in self.getDataInput().inputCurve if os.path.isfile(i.path.value)]
if len(self.listFiles) != 2:
self.WARNING("You did not provide the right number of valid files !!! %s" % " ".join(self.listFiles))
self.generateDatcmpScript()
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginExecJesfv1_0.preProcess")
numpyData = EDUtilsArray.xsDataToArray(self.dataInput.data)
numpy.savetxt(os.path.join(self.getWorkingDirectory(), "spectra.dat"),
numpyData)
self.addListCommandExecution("spectra.dat")
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginExecDatcmpv1_0.preProcess")
self.listFiles = [i.path.value for i in self.getDataInput().inputCurve if os.path.isfile(i.path.value)]
if len(self.listFiles) != 2:
self.WARNING("You did not provide the right number of valid files !!! %s" % " ".join(self.listFiles))
self.generateDatcmpScript()
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginExecMtz2Variousv1_0.preProcess")
xsDataInputRdfit = self.getDataInput()
self.setScriptCommandline(self.generateCommands(xsDataInputRdfit))
self.addListCommandPostExecution("gle -device png -resolution 100 %s" % self.strScaleIntensityGleFile)
self.strScaleIntensityPlotPath = os.path.join(self.getWorkingDirectory(), self.strScaleIntensityPlot)
def preProcess(self, _edObject=None):
"""
Pre-Process: Generate the script
"""
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginExecCommandLinev10.preProcess")
self.generateScript()
def preProcess(self):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG('Truncate: preprocess')
input_file = self.dataInput.input_file.value
output_file = self.dataInput.output_file.value
options = 'hklin {0} hklout {1}'.format(input_file, output_file)
self.setScriptCommandline(options)
self.DEBUG('command line options set to {0}'.format(options))
nres = self.dataInput.nres.value
anom = self.dataInput.anom.value
res = self.dataInput.res.value
if res is None:
res = 0
self.addListCommandExecution('nres {0}'.format(nres))
self.addListCommandExecution('truncate YES')
self.addListCommandExecution('anomalous {0}'.format(anom))
self.addListCommandExecution('plot OFF')
self.addListCommandExecution('labout F=F_xdsproc SIGF=SIGF_xdsproc')
self.addListCommandExecution('falloff YES')
self.addListCommandExecution('resolution 50 {0}'.format(res))
self.addListCommandExecution('PNAME foo')
self.addListCommandExecution('DNAME foo')
self.addListCommandExecution('end')
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
EDVerbose.DEBUG("EDPluginSPDCakev1_0.preProcess")
# Check that the input data and correction images are present
xsDataInputSPDCake = self.getDataInput()
pathToInputFile = xsDataInputSPDCake.getInputFile().getPath().getValue()
if (not os.path.exists(pathToInputFile)):
strErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (self.getPluginName() + ".preProcess", pathToInputFile)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
pathToDarkCurrentImageFile = xsDataInputSPDCake.getDarkCurrentImageFile().getPath().getValue()
if (not os.path.exists(pathToDarkCurrentImageFile)):
strErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (self.getPluginName() + ".preProcess", pathToDarkCurrentImageFile)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
pathToFlatFieldImageFile = xsDataInputSPDCake.getFlatFieldImageFile().getPath().getValue()
if (not os.path.exists(pathToFlatFieldImageFile)):
strErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (self.getPluginName() + ".preProcess", pathToFlatFieldImageFile)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
pathToSpatialDistortionFile = xsDataInputSPDCake.getSpatialDistortionFile().getPath().getValue()
if (not os.path.exists(pathToSpatialDistortionFile)):
strErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (self.getPluginName() + ".preProcess", pathToSpatialDistortionFile)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
if xsDataInputSPDCake.getOutputDir() is not None:
self.outputDir = xsDataInputSPDCake.getOutputDir().getPath().getValue()
if not os.path.isdir(self.outputDir):
os.makedirs(self.outputDir)
self.generateSPDCommand()
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginExecDataverv1_0.preProcess")
self.lstInFiles = [i.path.value for i in self.dataInput.inputCurve]
if self.dataInput.outputCurve is not None:
self.strOutFile = self.dataInput.outputCurve.path.value
self.generateCommandLine()
def preProcess(self, _edObject=None):
"""
Sets up the phenix.xtriage command line, uncompress mtz file if necessary
"""
EDPluginExecProcessScript.preProcess(self, _edObject)
self.DEBUG("EDPluginPhenixXtriagev1_1.preProcess...")
# Check if we have a compressed mtz file...
strPathMtz = self.dataInput.mtzFile.path.value
if strPathMtz.endswith(".gz"):
fIn = gzip.open(strPathMtz, "rb")
fileContent = fIn.read()
fIn.close()
strMtzFileName = os.path.basename(strPathMtz).split(".gz")[0]
self.strPathToLocalMtz = os.path.join(self.getWorkingDirectory(), strMtzFileName)
fOut = open(self.strPathToLocalMtz, "wb")
fOut.write(fileContent)
fOut.close()
strPathMtz = self.strPathToLocalMtz
if self.dataInput.obsLabels is not None:
strObsLabels = self.dataInput.obsLabels.value
else:
strObsLabels = "I,SIGI,merged"
strCommandPhenixXtriage = "{0} obs={1}".format(strPathMtz, strObsLabels)
# Necessary for Python 3 environment:
self.addListCommandPreExecution("unset PYTHONPATH")
self.setScriptCommandline(strCommandPhenixXtriage)
def preProcess(self, _edObject=None):
self.setRequireCCP4(True) # GB: this sets dozor env from execProcessScriptSetupCCP4 config param
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginDozorv1_0.preProcess")
xsDataInputDozor = self.getDataInput()
# Retrieve config (if any)
self.ix_min = self.config.get("ix_min")
self.ix_max = self.config.get("ix_max")
self.iy_min = self.config.get("iy_min")
self.iy_max = self.config.get("iy_max")
if self.ix_min is None or self.ix_max is None or self.iy_min is None or self.iy_max is None:
# One configuration value is missing - use default values
if xsDataInputDozor.detectorType.value == "pilatus2m":
self.ix_min = self.ix_min_pilatus2m
self.ix_max = self.ix_max_pilatus2m
self.iy_min = self.iy_min_pilatus2m
self.iy_max = self.iy_max_pilatus2m
else:
self.ix_min = self.ix_min_pilatus6m
self.ix_max = self.ix_max_pilatus6m
self.iy_min = self.iy_min_pilatus6m
self.iy_max = self.iy_max_pilatus6m
self.setScriptCommandline(" dozor.dat")
strCommands = self.generateCommands(xsDataInputDozor)
#self.createImageLinks(xsDataInputDozor)
EDUtilsFile.writeFile(os.path.join(self.getWorkingDirectory(), "dozor.dat"), strCommands)
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginBestv1_3.preProcess")
self.setScriptLogFileName("best.log")
self.setFileBestDat(
os.path.join(self.getWorkingDirectory(), "bestfile.dat"))
self.setFileBestPar(
os.path.join(self.getWorkingDirectory(), "bestfile.par"))
EDUtilsFile.writeFile(self.getFileBestDat(),
self.dataInput.bestFileContentDat.value)
EDUtilsFile.writeFile(self.getFileBestPar(),
self.dataInput.bestFileContentPar.value)
listBestFileContentHKL = self.dataInput.getBestFileContentHKL()
iterator = 0
for bestFileContentHKL in listBestFileContentHKL:
iterator = iterator + 1
bestFileHKL = os.path.join(self.getWorkingDirectory(),
"bestfile" + str(iterator) + ".hkl")
self.listFileBestHKL.append(bestFileHKL)
EDUtilsFile.writeFile(bestFileHKL, bestFileContentHKL.value)
if self.dataInput.complexity is not None:
self.setComplexity(self.dataInput.complexity.value)
self.initializeCommands()
def preProcess(self, _edObject=None):
"""
Pre-Process: Generate the script
"""
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginExecCommandLinev10.preProcess")
self.generateScript()
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
EDVerbose.DEBUG("EDPluginSTACv10.preProcess")
xsPluginItem = self.getConfiguration()
self.addListCommandPreExecution("export STACDIR=%s" % EDConfiguration.getStringParamValue(xsPluginItem, "STACDIR"))
self.addListCommandPreExecution("export BCMDEF=%s" % EDConfiguration.getStringParamValue(xsPluginItem, "BCMDEF"))
self.addListCommandPreExecution("export RUNDIR=%s" % self.getWorkingDirectory())
self.setScriptCommandline("stac.core.STAC_DNA_listener %s -%s/" % (self.getSTACcommand(), self.getWorkingDirectory()))
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginExecRsync.preProcess")
self.strSource = self.dataInput.source.path.value
self.strDestination = self.dataInput.destination.path.value
if self.dataInput.options is not None:
self.strOption = self.dataInput.options.value
self.generateCommandLine()
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginExecDamaverv0_2.preProcess")
self.checkDamaverPath()
self.checkDamaverAutomaticInput()
self.checkDamaverSymmetryInput()
self.generateDamaverScript()
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginBackground3Dv1_0.preProcess")
xsDataInputBackground3D = self.getDataInput()
self.setScriptCommandline("background.dat")
strCommands = self.generateCommands(xsDataInputBackground3D)
self.createImageLinks(xsDataInputBackground3D)
EDUtilsFile.writeFile(os.path.join(self.getWorkingDirectory(), "background.dat"), strCommands)
def preProcess(self):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG('Uniqueify: preprocess')
input_file = self.dataInput.input_file.value
output_file = self.dataInput.output_file.value
options = '{0} {1}'.format(input_file, output_file)
self.setScriptCommandline(options)
self.DEBUG('command line options set to {0}'.format(options))
def preProcess(self):
EDPluginExecProcessScript.preProcess(self)
data_input = self.getDataInput()
self.high = data_input.high
self.low = data_input.low
self.addInputLine('RESOLUTION_SHELLS= %s %s' % (self.low, self.high))
def preProcess(self):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG('Uniqueify: preprocess')
input_file = self.dataInput.input_file.value
output_file = self.dataInput.output_file.value
options = '{0} {1}'.format(input_file, output_file)
self.setScriptCommandline(options)
self.DEBUG('command line options set to {0}'.format(options))
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginSTACv10.preProcess")
xsPluginItem = self.getConfiguration()
self.addListCommandPreExecution("export STACDIR=%s" % EDConfiguration.getStringParamValue(xsPluginItem, "STACDIR"))
self.addListCommandPreExecution("export BCMDEF=%s" % EDConfiguration.getStringParamValue(xsPluginItem, "BCMDEF"))
self.addListCommandPreExecution("export RUNDIR=%s" % self.getWorkingDirectory())
self.setScriptCommandline("stac.core.STAC_DNA_listener %s -%s/" % (self.getSTACcommand(), self.getWorkingDirectory()))
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginExecRsync.preProcess")
self.strSource = self.dataInput.source.path.value
self.strDestination = self.dataInput.destination.path.value
if self.dataInput.options is not None:
self.strOption = self.dataInput.options.value
self.generateCommandLine()
def preProcess( self, _edObject = None ):
EDPluginExecProcessScript.preProcess( self )
EDVerbose.DEBUG( "*** EDPluginExecDIMPLEMTZDUMPv10.preProcess")
self.generateDIMPLEMTZDUMPCommands()
if self.getDataInput().getOutputLogFile() != None:
self.setScriptLogFileName(self.getDataInput().getOutputLogFile().getPath().getValue())
EDVerbose.DEBUG( "*** EDPluginExecDIMPLEPDBSETv10.preProcess - setting log file to: " \
+ self.getScriptLogFileName())
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginExecDamaverv0_3.preProcess")
self.checkDamaverPath()
self.checkDamaverAutomaticInput()
self.checkDamaverSymmetryInput()
self.generateDamaverScript()
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginBackground3Dv1_0.preProcess")
xsDataInputBackground3D = self.getDataInput()
self.setScriptCommandline("background.dat")
strCommands = self.generateCommands(xsDataInputBackground3D)
self.createImageLinks(xsDataInputBackground3D)
EDUtilsFile.writeFile(os.path.join(self.getWorkingDirectory(), "background.dat"), strCommands)
def preProcess(self, _edObject = None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginExecDimplev1_0.preProcess")
xsDataInputDimple = self.getDataInput()
strMtzFile = xsDataInputDimple.mtz.path.value
strPdbFile = xsDataInputDimple.pdb.path.value
self.strDimpleDir = os.path.join(self.getWorkingDirectory(), "dimple")
self.setScriptCommandline(" " + strMtzFile + " " + strPdbFile + " " + self.strDimpleDir)
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginHTML2PDFv1_0.preProcess")
xsDataInputHTML2PDF = self.getDataInput()
if xsDataInputHTML2PDF.resultDirectory is None:
resultDirectory = self.getWorkingDirectory()
else:
resultDirectory = xsDataInputHTML2PDF.resultDirectory.path.value
self.setScriptCommandline(self.generateCommands(xsDataInputHTML2PDF, resultDirectory))
def preProcess(self):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG('XdsToSca: preprocess')
self.addInputLine('xdsfile {0}'.format(
self.dataInput.hkl_file.path.value))
self.addInputLine('scafile {0}'.format(
self.dataInput.sca_file.path.value))
self.addInputLine('end')
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginExecDammifv0_2.preProcess")
if self.dataInput.order:
self.name = "dammif-%s" % self.dataInput.order.value # I know I only modify the instance variable, not the class one
self.generateDammifScript()
# in order avoid 2 dammif starting at the same milisecond, we sleep for up to 64 ms
time.sleep(1e-3 * (self.getId() % 64))
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginExecDatopv1_0.preProcess")
self.outputFile = self.dataInput.outputCurve.path.value
self.strOperation = self.dataInput.operation.value.replace("+", "ADD").replace("-", "SUB").replace("*", "MUL").replace("/", "DIV")
self.lstInputFiles = [ i.path.value for i in self.dataInput.inputCurve]
if self.dataInput.constant is not None:
self.const = self.dataInput.constant.value
self.generateCommandLineOptions()
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginExecCrystFELPostprocessv1_0.preProcess")
self.mtz_filename = "%s_partialator_%s.mtz" % (
self.dataInput.baseFileName.value, self.dataInput.pointGroup.value)
strCommandLine = self.generateCommandLine(self.dataInput)
self.setScriptCommandline(strCommandLine)
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginExecDammifv0_2.preProcess")
if self.dataInput.order:
self.name = "dammif-%s" % self.dataInput.order.value # I know I only modify the instance variable, not the class one
self.generateDammifScript()
# in order avoid 2 dammif starting at the same milisecond, we sleep for up to 64 ms
time.sleep(1e-3 * (self.getId() % 64))
def preProcess(self):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG('Pointless: preprocess')
if self.output_file is not None and self.input_file is not None:
# TODO: ask Max why he forces the version to 6.2.0
options = 'xdsin {0} hklout {1}'.format(self.input_file,
self.output_file)
self.setScriptCommandline(options)
self.DEBUG('command line options set to {0}'.format(options))
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginExecDimplev1_0.preProcess")
xsDataInputDimple = self.getDataInput()
strMtzFile = xsDataInputDimple.mtz.path.value
strPdbFile = xsDataInputDimple.pdb.path.value
self.strDimpleDir = os.path.join(self.getWorkingDirectory(), "dimple")
self.setScriptCommandline(" " + strMtzFile + " " + strPdbFile + " " +
self.strDimpleDir)
def preProcess(self):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG('Pointless: preprocess')
if self.output_file is not None and self.input_file is not None:
# TODO: ask Max why he forces the version to 6.2.0
options = 'xdsin {0} hklout {1}'.format(self.input_file,
self.output_file)
self.setScriptCommandline(options)
self.DEBUG('command line options set to {0}'.format(options))
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
EDVerbose.DEBUG("*** EDPluginFIT2DCakev1_0.preProcess")
# Check that the input data and correction images are present
xsDataInputFIT2DCake = self.getDataInput()
pyStrPathToInputFile = xsDataInputFIT2DCake.getInputFile().getPath(
).getValue()
if (not os.path.exists(pyStrPathToInputFile)):
strErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (
self.getPluginName() + ".preProcess", pyStrPathToInputFile)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
pyStrPathToDarkCurrentImageFile = xsDataInputFIT2DCake.getDarkCurrentImageFile(
).getPath().getValue()
if (not os.path.exists(pyStrPathToDarkCurrentImageFile)):
strErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (
self.getPluginName() + ".preProcess",
pyStrPathToDarkCurrentImageFile)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
pyStrPathToFlatFieldImageFile = xsDataInputFIT2DCake.getFlatFieldImageFile(
).getPath().getValue()
if (not os.path.exists(pyStrPathToFlatFieldImageFile)):
strErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (
self.getPluginName() + ".preProcess",
pyStrPathToFlatFieldImageFile)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
pyStrPathToSpatialDistortionFile = xsDataInputFIT2DCake.getSpatialDistortionFile(
).getPath().getValue()
if (not os.path.exists(pyStrPathToSpatialDistortionFile)):
strErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (
self.getPluginName() + ".preProcess",
pyStrPathToSpatialDistortionFile)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
# Get path to Xvfb program
pluginConfiguration = self.getConfiguration()
if (pluginConfiguration is not None):
self.m_strPathToXvfb = EDConfiguration.getStringParamValue(
pluginConfiguration, self.m_strCONF_PATH_TO_XVFB)
self.m_strArgumentsForXvfb = EDConfiguration.getStringParamValue(
pluginConfiguration, self.m_strCONF_ARGUMENTS_FOR_XVFB)
if (self.m_strPathToXvfb is None):
strErrorMessage = EDMessage.ERROR_NO_PLUGIN_CONFIGURATION_ITEM_FOUND_02 % (
self.getPluginName() + ".preProcess",
self.m_strCONF_PATH_TO_XVFB)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
self.generateFIT2DCommands()
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginSTACv2_0.preProcess")
self.addListCommandPreExecution("export STACDIR=%s" % self.config.get("STACDIR"))
if (self.__pyStrBCMDEF is None):
self.__pyStrBCMDEF = self.config.get("BCMDEF")
self.DEBUG("EDPluginSTACv2_0.preProcess: BCMDEF set to %s" % self.__pyStrBCMDEF)
self.addListCommandPreExecution("export BCMDEF=%s" % self.__pyStrBCMDEF)
self.addListCommandPreExecution("export RUNDIR=%s" % self.getWorkingDirectory())
self.setScriptCommandline("stac.core.STAC_DNA_listener %s -%s/ %s" % (self.getSTACcommand(), self.getWorkingDirectory(), self.getSTACparams()))
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
EDVerbose.DEBUG("*** EDPluginExecDIMPLEFREERFLAGv10.preProcess")
self._hklin = self.getDataInput().getHKLIN().getPath().getValue()
self._hklout = self.getDataInput().getHKLOUT().getPath().getValue()
self.freer_flag_script()
return
def preProcess(self, _edObject=None):
"""
Sets up the Labelit command line
"""
EDPluginExecProcessScript.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginDistlSignalStrengthv1_1.preProcess...")
self.xsDataImage = self.getDataInput().getReferenceImage()
strCommandLine = self.xsDataImage.getPath().getValue()
self.setScriptCommandline(strCommandLine)
self.addListCommandPreExecution("export PYTHONPATH=\"\" ")
def preProcess(self, _edObject=None):
"""
Sets up the Labelit command line
"""
EDPluginExecProcessScript.preProcess(self, _edObject)
self.DEBUG("EDPluginDistlSignalStrengthv1_1.preProcess...")
self.xsDataImage = self.getDataInput().getReferenceImage()
strCommandLine = self.xsDataImage.getPath().getValue()
self.setScriptCommandline(strCommandLine)
self.addListCommandPreExecution("export PYTHONPATH=\"\" ")
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginExecSiftOffsetv1_0.preProcess")
self.inputFiles = [
i.getPath().getValue()
for i in self.getDataInput().getDescriptorFile()
]
self.outFile = os.path.join(self.getWorkingDirectory(),
EDPluginExecSiftOffsetv1_0.OUTPUT)
self.generateAutopanoCommand()
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginExecSiftDescriptorv1_0.preProcess")
self.strImage = self.getDataInput().getImage().getPath().getValue()
if not os.path.isfile(self.strImage):
strError = "Input image file does not exist: %s" % self.strImage
self.ERROR(strError)
self.setFailure()
raise RuntimeError(strError)
self.strKeys = os.path.join(self.getWorkingDirectory(), os.path.basename(self.strImage + ".keys.gz"))
self.generateKeysCommand()
def preProcess(self, _edObject=None):
"""
Sets up the Labelit command line
"""
EDPluginExecProcessScript.preProcess(self, _edObject)
self.DEBUG("EDPluginDistlSignalStrengthThinClientv1_1.preProcess...")
self.xsDataImage = self.getDataInput().getReferenceImage()
strCommandLine = self.xsDataImage.getPath().getValue()
strCommandLine += " %s" % self.strHostName
strCommandLine += " %d" % self.iPortNumber
self.setScriptCommandline(strCommandLine)
self.addListCommandPreExecution("export PYTHONPATH=\"\" ")
def preProcess(self, _edObject = None):
EDPluginExecProcessScript.preProcess(self)
EDVerbose.DEBUG("*** EDPluginExecDIMPLEFREERFLAGv10.preProcess")
self._hklin = self.getDataInput().getHKLIN().getPath(
).getValue()
self._hklout = self.getDataInput().getHKLOUT().getPath(
).getValue()
self.freer_flag_script()
return
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
EDVerbose.DEBUG("EDPluginRaddosev10.preProcess")
self.setScriptLogFileName("raddose.log")
# Fix for bug 432: if flux is close to zero or negative failure
if (self.getDataInput().getBeamFlux().getValue() < 0.1):
strErrorMessage = "EDPluginRaddosev10.preProcess ERROR: Input flux is negative or close to zero. Execution of characterisation aborted."
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
self.initializeCommandExecution()
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG("EDPluginExecDamminv0_2.preProcess")
if self.dataInput.name:
self.__strProjectDesc = self.dataInput.name.value
if self.dataInput.unit:
unit = self.dataInput.unit.value.lower()
if unit in ["a", "ang", "angstrom", "1", "1/a", "a^-1"]:
self.__strAngleUnit = "1"
if unit in ["nm", "nanom", "nanometer", "2", "1/nm", "nm^-1"]:
self.__strAngleUnit = "2"
self.generateDamminScript()
