def postProcess(self, _edObject=None):
EDPluginExec.postProcess(self)
self.DEBUG("EDPluginExecMeasureOffsetv1_0.postProcess")
# Create some output data
xsDataResult = XSDataResultMeasureOffset()
xsDataResult.setOffset(self.tOffset)
self.setDataOutput(xsDataResult)
def configure(self):
"""
Gets the web servise wdsl parameters from the config file and stores them in class member attributes.
"""
EDPluginExec.configure(self)
self.strUserName = str(self.config.get("userName"))
if self.strUserName is None:
self.ERROR("EDPluginISPyBStoreListOfImageQualityIndicatorsv1_4.configure: No user name found in configuration!")
self.setFailure()
self.strPassWord = str(self.config.get("passWord"))
if self.strPassWord is None:
self.ERROR("EDPluginISPyBStoreListOfImageQualityIndicatorsv1_4.configure: No pass word found in configuration!")
self.setFailure()
self.strToolsForAutoprocessingWebServiceWsdl = self.config.get("toolsForAutoprocessingWebServiceWsdl")
if self.strToolsForAutoprocessingWebServiceWsdl is None:
self.ERROR("EDPluginISPyBStoreListOfImageQualityIndicatorsv1_4.configure: No toolsForAutoprocessingWebServiceWsdl found in configuration!")
self.setFailure()
self.strToolsForCollectionWebServiceWsdl = self.config.get("toolsForCollectionWebServiceWsdl")
if self.strToolsForCollectionWebServiceWsdl is None:
self.ERROR("EDPluginISPyBStoreListOfImageQualityIndicatorsv1_4.configure: No toolsForCollectionWebServiceWsdl found in configuration!")
self.setFailure()
strAutoProcProgramId = self.config.get("autoProcProgramId")
if strAutoProcProgramId is None:
self.ERROR("EDPluginISPyBStoreListOfImageQualityIndicatorsv1_4.configure: No autoProcProgramId found in configuration!")
self.setFailure()
else:
self.iAutoProcProgramId = int(strAutoProcProgramId)
def finallyProcess(self, _edObject=None):
EDPluginExec.finallyProcess(self)
self.DEBUG("EDPluginISPyBStoreListOfImageQualityIndicatorsv1_4.finallyProcess")
xsDataResultStoreListOfImageQualityIndicators = XSDataResultStoreListOfImageQualityIndicators()
for iImageQualityIndicatorsId in self.listImageQualityIndicatorsId:
xsDataResultStoreListOfImageQualityIndicators.addImageQualityIndicatorsId(XSDataInteger(iImageQualityIndicatorsId))
self.setDataOutput(xsDataResultStoreListOfImageQualityIndicators)
def postProcess(self, _edObject=None):
"""
Calls the parent preProcess method
Checks that the installed 3rd party software is in the list of
compatible versions
"""
EDPluginExec.postProcess(self)
EDVerbose.DEBUG("EDPluginExecProcessXIA2CORE.postProcess")
# Tests the compatibles executable versions
listCompatibleVersions = self.getListOfCompatibleVersions()
if(len(listCompatibleVersions) != 0):
bFound = False
for compatibleVersion in listCompatibleVersions:
bFound = self.findStringInLog(compatibleVersion)
if(bFound == True):
break
if(bFound == False):
strErrorMessage = "Plugin not compatible with %s, compatible versions are: %s" % \
(self.getStringVersion(),
self.getCompatibleVersionsStringLine())
EDVerbose.warning(strErrorMessage)
self.addWarningMessage(strErrorMessage)
def postProcess(self, _edObject=None):
"""
"""
EDPluginExec.postProcess(self)
EDVerbose.DEBUG("*** EDPluginISPyBv1_1.postProcess")
if self.m_xsDataResultISPyB is not None:
self.setDataOutput(self.m_xsDataResultISPyB)
def process(self, _edObject=None):
EDPluginExec.process(self)
EDVerbose.DEBUG("EDPluginExecPyHSTv10.process")
xsDataInputPyHST = self.getDataInput()
pyhst = PyHST_c.PyHST(xsDataInputPyHST.getOutputFileName(),
Parameters.OVERSAMPLING_FACTOR,
Parameters.START_VOXEL_1 - 1 + 1,
Parameters.START_VOXEL_2 - 1 + 1,
Parameters.END_VOXEL_1 - Parameters.START_VOXEL_1 + 1,
Parameters.END_VOXEL_2 - Parameters.START_VOXEL_2 + 1,
Parameters.ROTATION_AXIS_POSITION,
Parameters.ANGLE_OFFSET * DEG2RAD,
Parameters.ANGLE_BETWEEN_PROJECTIONS * DEG2RAD,
Parameters.NO_SINOGRAM_FILTERING,
dim_1,
num_projections,
BIG_SINOS ,
axis_corrections ,
Parameters.BICUBIC,
Parameters.SUMRULE ,
(angles),
Parameters.PENTEZONE,
Parameters.ZEROOFFMASK,
Parameters.CUMSUM_INTEGRAL
)
def process(self, _edObject=None):
EDPluginExec.process(self)
self.DEBUG("EDPluginExecPlotGlev1_1.process")
for dictPlot in self.listPlot:
if os.path.dirname(dictPlot["script"]) != self.getWorkingDirectory():
shutil.copy(dictPlot["script"], self.getWorkingDirectory())
listDataFiles = dictPlot["data"]
for strDataFileFullPath in listDataFiles:
strDataFile = os.path.basename(strDataFileFullPath)
if not os.path.exists(os.path.join(self.getWorkingDirectory(), strDataFile)):
shutil.copy(strDataFileFullPath, self.getWorkingDirectory())
if EDUtilsPath.isESRF():
# Force PXSOFT version of gle
strCommand = "/opt/pxsoft/bin/gle -verbosity 0 -r 150 -d jpg %s" % os.path.basename(dictPlot["script"])
else:
strCommand = "gle -verbosity 0 -r 150 -d jpg %s" % os.path.basename(dictPlot["script"])
# Copied from EDPluginExecProcess
self.DEBUG(self.getBaseName() + ": Processing")
timer = threading.Timer(float(self.getTimeOut()), self.kill)
timer.start()
try:
self.__subprocess = EDUtilsPlatform.Popen(shlex.split(str(EDUtilsPlatform.escape(strCommand))),
cwd=self.getWorkingDirectory())
self.__iPID = self.__subprocess.pid
self.__strExecutionStatus = str(self.__subprocess.wait())
except OSError as e:
strErrorMessage = self.getPluginName() + " : required program gle not installed"
self.error(strErrorMessage)
self.setFailure()
finally:
timer.cancel()
def finallyProcess(self, _edObject=None):
EDPluginExec.finallyProcess(self)
self.DEBUG("EDPluginISPyBGroupDataCollectionsv1_4.finallyProcess")
xsDataResultISPyBGroupDataCollections = XSDataResultISPyBGroupDataCollections()
for dataCollectionId in self.listDataCollectionIds:
xsDataResultISPyBGroupDataCollections.addDataCollectionId(XSDataInteger(dataCollectionId))
self.setDataOutput(xsDataResultISPyBGroupDataCollections)
def finallyProcess(self, _edObject=None):
EDPluginExec.finallyProcess(self)
self.DEBUG("EDPluginISPyBStoreImageQualityIndicatorsv1_4.finallyProcess")
xsDataResultStoreImageQualityIndicators = XSDataResultStoreImageQualityIndicators()
if self.iImageQualityIndicatorsId is not None:
xsDataResultStoreImageQualityIndicators.setImageQualityIndicatorsId(XSDataInteger(self.iImageQualityIndicatorsId))
self.setDataOutput(xsDataResultStoreImageQualityIndicators)
def finallyProcess(self, _edObject=None):
EDPluginExec.finallyProcess(self)
self.DEBUG("EDPluginISPyBStoreScreeningv1_4.finallyProcess")
xsDataResultISPyBStoreScreening = XSDataResultISPyBStoreScreening()
if self.iScreeningId is not None:
xsDataResultISPyBStoreScreening.screeningId = XSDataInteger(self.iScreeningId)
self.setDataOutput(xsDataResultISPyBStoreScreening)
def postProcess(self, _edObject=None):
EDPluginExec.postProcess(self)
self.DEBUG("EDPluginSubWedgeMergev1_1.postProcess")
xsDataResultSubWedgeMerge = XSDataResultSubWedgeMerge()
for xsDataSubWedgeMerge in self.__listResultSubWedgeMerge:
xsDataResultSubWedgeMerge.addSubWedge(xsDataSubWedgeMerge)
self.setDataOutput(xsDataResultSubWedgeMerge)
def configure(self):
"""
Gets the web servise wdsl parameters from the config file and stores them in class member attributes.
"""
EDPluginExec.configure(self)
self.strUserName = self.config.get("userName")
if self.strUserName is None:
self.ERROR("EDPluginISPyBStoreScreeningv1_4.configure: No user name found in configuration!")
self.setFailure()
self.strPassWord = self.config.get("passWord")
if self.strPassWord is None:
self.ERROR("EDPluginISPyBStoreScreeningv1_4.configure: No pass word found in configuration!")
self.setFailure()
self.strToolsForBLSampleWebServiceWsdl = self.config.get("toolsForBLSampleWebServiceWsdl")
if self.strToolsForBLSampleWebServiceWsdl is None:
self.ERROR("EDPluginISPyBStoreScreeningv1_4.configure: No toolsForBLSampleWebServiceWsdl found in configuration!")
self.setFailure()
self.strToolsForScreeningEDNAWebServiceWsdl = self.config.get("toolsForScreeningEDNAWebServiceWsdl")
if self.strToolsForScreeningEDNAWebServiceWsdl is None:
self.ERROR("EDPluginISPyBStoreScreeningv1_4.configure: No toolsForScreeningEDNAWebServiceWsdl found in configuration!")
self.setFailure()
self.strToolsForCollectionWebServiceWsdl = self.config.get("toolsForCollectionWebServiceWsdl")
if self.strToolsForCollectionWebServiceWsdl is None:
self.ERROR("EDPluginISPyBStoreScreeningv1_4.configure: No toolsForCollectionWebServiceWsdl found in configuration!")
self.setFailure()
def preProcess(self, _edObject=None):
EDPluginExec.preProcess(self)
self.DEBUG("EDPluginExecShiftImagev1_0.preProcess")
sdi = self.dataInput
if sdi.inputImage is not None:
self.npaImage = numpy.array(EDUtilsArray.getArray(sdi.inputImage))
elif sdi.inputArray is not None:
self.npaImage = EDUtilsArray.xsDataToArray(sdi.getInputArray())
else:
self.ERROR("EDPluginExecShiftImagev1_0.preProcess: You should either provide an images or an arrays, but I got: %s" % sdi.marshal())
self.setFailure()
raise RuntimeError
offset = sdi.offset
if len(offset) == 2:
self.tOffset = (offset[0].value, offset[1].value)
elif len(offset) == 1:
self.tOffset = (offset[0].value, offset[0].value)
if sdi.outputImage is not None:
if sdi.outputImage.path is not None:
self.strOutputType = "file"
self.strOutputImage = sdi.outputImage.path.value
if sdi.outputImage.shared is not None:
self.strOutputType = "shared"
self.strOutputImage = sdi.outputImage.shared.value
if sdi.outputImage.array is not None:
self.strOutputType = "array"
def configure(self):
"""
Configures the plugin with executable from configuration file
"""
EDPluginExec.configure(self)
EDVerbose.DEBUG("EDPluginExecProcess.configure")
strExecutable = self.config.get(self.CONF_EXEC_PROCESS_EXECUTABLE, None)
if strExecutable is None:
EDVerbose.DEBUG("EDPluginExecProcess.configure: No configuration parameter found for: %s , using default value: %s"\
% (self.CONF_EXEC_PROCESS_EXECUTABLE, self.getExecutable()))
else:
self.setExecutable(strExecutable)
# test if we're to use oar and check for additional config
if strExecutable == "oarsub":
oar_options = self.config.get("oarOptions", None)
if oar_options is None:
EDVerbose.DEBUG('EDPluginExecProcess.configure: no additional options were specified for oarsub')
self._oar_options = oar_options
oar_poll = self.config.get("oarPollInterval", None)
if oar_poll is None:
EDVerbose.DEBUG('EDPluginExecProcess.configure: oar polling interval not configured')
EDVerbose.DEBUG('EDPluginExecProcess.configure: using default version of {0}'.format(DEFAULT_OAR_POLL_INTERVAL))
self._oar_poll_interval = DEFAULT_OAR_POLL_INTERVAL
else:
self._oar_poll_interval = oar_poll
# The execProcessTimeOut is deprecated, see bug #563
timeOut = self.config.get(self.CONF_EXEC_PROCESS_TIME_OUT, None)
if timeOut is not None:
EDVerbose.WARNING("Use of %s in plugin configuration is deprecated" % self.CONF_EXEC_PROCESS_TIME_OUT)
EDVerbose.WARNING("Please use %s instead." % EDPlugin.CONF_TIME_OUT)
self.setTimeOut(timeOut)
def process(self):
EDPluginExec.process(self)
l = len(self.lstInFiles)
if l > 0:
q0, I0, s0 = numpy.loadtxt(self.lstInFiles[0], unpack=True)
if l > 1:
q1, I1, s1 = numpy.loadtxt(self.lstInFiles[-1], unpack=True)
if self.strOperation in ("ADD", "SUB") and (l == 2):
q = q1
assert abs(q1 - q0).max() < self.epsilon
if self.strOperation == "SUB":
I = I0 - I1
else:
I = I0 + I1
s = numpy.sqrt(s0 * s0 + s1 * s1)
if self.strOperation in ("MUL", "DIV") and (l >= 1) and self.dataInput.constant:
q = q0
if self.strOperation == "MUL":
I = I0 * self.const
s = s0 * self.const
else:
I = I0 / self.const
s = s0 / self.const
m = numpy.vstack((q, I, s))
# numpy.savetxt(self.outputFile, m.T)
with open(self.outputFile, "w") as outfile:
numpy.savetxt(outfile, m.T)
def postProcess(self, _edObject=None):
EDPluginExec.postProcess(self)
EDVerbose.DEBUG("EDPluginExecOutputHTMLv1_0.postProcess")
if self.__strWorkingDir != None:
xsDataFileHTMLFile = XSDataFile()
xsDataFileHTMLDir = XSDataFile()
if self.strBasename is None:
strHTMLFilePath = os.path.join(self.__strWorkingDir, "edna.html")
strHTMLDirPath = os.path.join(self.__strWorkingDir, "edna_html")
else:
strHTMLFilePath = os.path.join(self.strBasename, "edna.html")
strHTMLDirPath = os.path.join(self.strBasename, "edna_html")
if os.path.exists(strHTMLFilePath):
strFileContent = EDUtilsFile.readFile(strHTMLFilePath)
strFileContent = strFileContent.replace("table,td,th { border-style: none;", "div.edna table,td,th { border-style: none;")
strFileContent = strFileContent.replace("td,th { border-style: solid;", "div.edna td,th { border-style: solid;")
strFileContent = strFileContent.replace("th { background-color: gray;", "div.edna th { background-color: gray;")
strFileContent = strFileContent.replace("<body onload=\"initTable('strategyData',false,false);\">", "<body onload=\"initTable('strategyData',false,false);\"><div class = 'edna'> ")
strFileContent = strFileContent.replace("</body>", "</div></body>")
EDUtilsFile.writeFile(strHTMLFilePath, strFileContent)
xsDataFileHTMLFile.setPath(XSDataString(strHTMLFilePath))
xsDataFileHTMLDir.setPath(XSDataString(strHTMLDirPath))
self.setDataOutput(xsDataFileHTMLFile, "htmlFile")
self.setDataOutput(xsDataFileHTMLDir, "htmlDir")
else:
EDVerbose.ERROR("EDPluginExecOutputHTMLv1_0.postProcess: file doesn't exist: " + strHTMLFilePath)
def finallyProcess(self, _edObject=None):
EDPluginExec.finallyProcess(self)
self.DEBUG("EDPluginISPyBGetPdbFilePathv1_4.finallyProcess")
xsDataResultISPyBGetPdbFilePath = XSDataResultISPyBGetPdbFilePath()
if self.strPathToPdbFile is not None:
xsDataResultISPyBGetPdbFilePath.pdbFilePath = XSDataString(self.strPathToPdbFile)
self.setDataOutput(xsDataResultISPyBGetPdbFilePath)
def configure(self):
"""
Gets the web servise wdsl parameters from the config file and stores them in class member attributes.
"""
EDPluginExec.configure(self)
self.strUserName = self.getStringConfigurationParameterValue("userName")
if self.strUserName is None:
self.ERROR("EDPluginISPyBStoreImageQualityIndicatorsv1_3.configure: No user name found in configuration!")
self.setFailure()
self.strPassWord = self.getStringConfigurationParameterValue("passWord")
if self.strPassWord is None:
self.ERROR("EDPluginISPyBStoreImageQualityIndicatorsv1_3.configure: No pass word found in configuration!")
self.setFailure()
self.strImageServiceWdsl = self.getStringConfigurationParameterValue("imageServiceWdsl")
if self.strImageServiceWdsl is None:
self.ERROR("EDPluginISPyBStoreImageQualityIndicatorsv1_3.configure: No imageServiceWdsl found in configuration!")
self.setFailure()
self.strToolsForMXCubeWebServiceWsdl = self.getStringConfigurationParameterValue("toolsForMXCubeWebServiceWsdl")
if self.strToolsForMXCubeWebServiceWsdl is None:
self.ERROR("EDPluginISPyBStoreImageQualityIndicatorsv1_3.configure: No toolsForMXCubeWebServiceWsdl found in configuration!")
self.setFailure()
self.iAutoProcProgramId = self.getIntegerConfigurationParameterValue("autoProcProgramId")
if self.iAutoProcProgramId is None:
self.ERROR("EDPluginISPyBStoreImageQualityIndicatorsv1_3.configure: No autoProcProgramId found in configuration!")
self.setFailure()
def process(self, _edObject=None):
EDPluginExec.process(self)
self.DEBUG("EDPluginExecNormalizeImagev1_1.process")
#numerator part:
fTotalDataTime = 0.0
self.shape = self.listDataArray[0].shape
npaSummedData = numpy.zeros(self.shape, dtype=self.dtype)
for i in range(len(self.listDataArray)):
fTotalDataTime += self.listDataExposure[i]
npaSummedData += numpy.maximum(self.listDataArray[i] - self.getMeanDark(self.listDataExposure[i]), 0)
npaNormalizedData = (npaSummedData / fTotalDataTime).astype(self.dtype)
#denominator part
fTotalFlatTime = 0.0
npaSummedFlat = numpy.zeros(self.shape, dtype=self.dtype)
for i in range(len(self.listFlatArray)):
fTotalFlatTime += self.listFlatExposure[i]
npaSummedFlat += numpy.maximum(self.listFlatArray[i] - self.getMeanDark(self.listFlatExposure[i]), 0)
npaNormalizedFlat = (npaSummedFlat / fTotalFlatTime).astype(self.dtype)
self.npaNormalized = npaNormalizedData / numpy.maximum(npaNormalizedFlat, numpy.ones_like(npaNormalizedFlat))
if self.npaNormalized.dtype != numpy.dtype(self.dtype):
self.npaNormalized = self.npaNormalized.astype(self.dtype)
def process(self, _edObject=None):
"""
First uses the ImageService to find the imageId.
Then uses ToolsForCollectionWebService for storing the image quality indicators.
"""
EDPluginExec.process(self)
self.DEBUG("EDPluginISPyBStoreListOfImageQualityIndicatorsv1_4.process")
httpAuthenticatedToolsForAutoprocessingWebService = HttpAuthenticated(username=self.strUserName, password=self.strPassWord)
clientToolsForAutoprocessingWebService = Client(self.strToolsForAutoprocessingWebServiceWsdl, transport=httpAuthenticatedToolsForAutoprocessingWebService)
# Loop over all input image quality indicators:
listImageQualityIndicatorsForWS = []
for xsDataImageQualityIndicators in self.dataInput.imageQualityIndicators:
#print xsDataImageQualityIndicators.marshal()
imageQualityIndicatorsWS3VO = clientToolsForAutoprocessingWebService.factory.create('imageQualityIndicatorsWS3VO')
strPathToImage = xsDataImageQualityIndicators.getImage().getPath().getValue()
imageQualityIndicatorsWS3VO.fileName = os.path.basename(strPathToImage)
imageQualityIndicatorsWS3VO.fileLocation = os.path.dirname(strPathToImage)
# imageQualityIndicatorsWS3VO.imageId = 0
imageQualityIndicatorsWS3VO.autoProcProgramId = self.iAutoProcProgramId
imageQualityIndicatorsWS3VO.spotTotal = self.getXSValue(xsDataImageQualityIndicators.spotTotal)
imageQualityIndicatorsWS3VO.inResTotal = self.getXSValue(xsDataImageQualityIndicators.inResTotal)
imageQualityIndicatorsWS3VO.goodBraggCandidates = self.getXSValue(xsDataImageQualityIndicators.goodBraggCandidates)
imageQualityIndicatorsWS3VO.iceRings = self.getXSValue(xsDataImageQualityIndicators.iceRings)
imageQualityIndicatorsWS3VO.method1Res = self.getXSValue(xsDataImageQualityIndicators.method1Res)
imageQualityIndicatorsWS3VO.method2Res = self.getXSValue(xsDataImageQualityIndicators.method2Res)
imageQualityIndicatorsWS3VO.maxUnitCell = self.getXSValue(xsDataImageQualityIndicators.maxUnitCell)
imageQualityIndicatorsWS3VO.pctSaturationTop50Peaks = self.getXSValue(xsDataImageQualityIndicators.pctSaturationTop50Peaks)
imageQualityIndicatorsWS3VO.inResolutionOvrlSpots = self.getXSValue(xsDataImageQualityIndicators.inResolutionOvrlSpots)
imageQualityIndicatorsWS3VO.binPopCutOffMethod2Res = self.getXSValue(xsDataImageQualityIndicators.binPopCutOffMethod2Res)
imageQualityIndicatorsWS3VO.totalIntegratedSignal = self.getXSValue(xsDataImageQualityIndicators.totalIntegratedSignal)
imageQualityIndicatorsWS3VO.recordTimeStamp = DateTime(datetime.datetime.now())
listImageQualityIndicatorsForWS.append(imageQualityIndicatorsWS3VO)
self.listImageQualityIndicatorsId = clientToolsForAutoprocessingWebService.service.storeOrUpdateImageQualityIndicatorsForFileNames(
listImageQualityIndicatorsForWS = listImageQualityIndicatorsForWS)
self.DEBUG("EDPluginISPyBStoreListOfImageQualityIndicatorsv1_4.process: listImageQualityIndicatorsId=%r" % self.listImageQualityIndicatorsId)
def process(self, _edObject=None):
EDPluginExec.process(self)
EDVerbose.DEBUG("EDPluginExecProcess.process starting")
if self.getExecutable() == "oarsub":
self.process_on_oar(_edObject)
else:
self.process_locally(_edObject)
def process(self, _edObject=None):
"""
Uses ToolsForCollectionWebService
"""
EDPluginExec.process(self)
self.DEBUG("EDPluginISPyBSetImagesPositionsv1_4.process")
httpAuthenticatedToolsForCollectionWebService = HttpAuthenticated(
username=self.strUserName, password=self.strPassWord
)
clientToolsForCollectionWebService = Client(
self.strToolsForCollectionWebServiceWsdl, transport=httpAuthenticatedToolsForCollectionWebService
)
# Loop over all positions
listImagePosition = []
for xsDataImagePosition in self.dataInput.imagePosition:
imagePosition = clientToolsForCollectionWebService.factory.create("imagePosition")
# Get the workflow ID and status
imagePosition.fileName = os.path.basename(xsDataImagePosition.fileName.path.value)
imagePosition.fileLocation = os.path.dirname(xsDataImagePosition.fileName.path.value)
if xsDataImagePosition.jpegFileFullPath is not None:
imagePosition.jpegFileFullPath = xsDataImagePosition.jpegFileFullPath.path.value
if xsDataImagePosition.jpegThumbnailFileFullPath is not None:
imagePosition.jpegThumbnailFileFullPath = xsDataImagePosition.jpegThumbnailFileFullPath.path.value
listImagePosition.append(imagePosition)
self.listImageCreation = clientToolsForCollectionWebService.service.setImagesPositions(
listImagePosition=listImagePosition
)
self.DEBUG("EDPluginISPyBSetImagesPositionsv1_4.process: listImageCreation=%r" % self.listImageCreation)
def process(self, _edPlugin=None):
EDPluginExec.process(self, _edPlugin)
self.DEBUG("EDPluginExecSimpleHTMLPagev1_1.process...")
if self.xsDataResultCharacterisation is not None:
# WorkflowStepReport
self.workflowStepReport = WorkflowStepReport("Characterisation")
if self.xsDataResultCharacterisation is not None:
self.workflowStepReport.setTitle("Characterisation Results")
else:
self.workflowStepReport.setTitle("No Characterisation Results!")
# Link to the EDNA log file
if self.dataInput.logFile is None:
strPathToLogFile = self.getLogFileName()
else:
strPathToLogFile = self.dataInput.logFile.path.value
if strPathToLogFile is not None:
self.workflowStepReport.addLogFile("EDNA Log", "EDNA log file", strPathToLogFile)
self.dataCollectionInfo()
self.diffractionPlan()
self.strategyResults()
self.graphs()
self.kappaResults()
self.indexingResults()
self.integrationResults()
self.imageQualityIndicatorResults()
self.createThumbnailRowOfImages()
def __init__(self):
"""
"""
EDPluginExec.__init__(self)
self.setXSDataInputClass(XSDataInputBioSaxsMetadatav1_0)
self.xsdInputData = None
self.detector = None
self.detectorDistance = None
self.pixelSize_1 = None
self.pixelSize_2 = None
self.beamCenter_1 = None
self.beamCenter_2 = None
self.beamStopDiode = None
self.wavelength = None
self.maskFile = None
self.normalizationFactor = None
self.machineCurrent = None
self.storageTemperature = None
self.exposureTemperature = None
self.exposureTime = None
self.frameNumber = None
self.frameMax = None
self.timeOfFrame = None
#
self.code = None
self.comments = None
self.concentration = None
self.strInputImage = None
self.strOutputImage = None
self.fabioedf = fabio.edfimage.edfimage()
def process(self, _edObject=None):
"""
Retrieves the contents of the DataCollectionContainer in ISPyB
"""
EDPluginExec.process(self)
self.DEBUG("EDPluginISPyBRetrieveDataCollectionv1_4.process")
infile = self.getDataInput()
inpath = infile.getImage().getPath().getValue()
indir = os.path.dirname(inpath)
infilename = os.path.basename(inpath)
httpAuthenticatedToolsForCollectionWebService = HttpAuthenticated(username=self.strUserName, password=self.strPassWord)
clientToolsForCollectionWebService = Client(self.strToolsForCollectionWebServiceWsdl, transport=httpAuthenticatedToolsForCollectionWebService)
self.collectParameters = None
# DataCollectionProgram
collect_params = clientToolsForCollectionWebService.service.findDataCollectionFromFileLocationAndFileName(
indir,
infilename)
if collect_params is None:
self.ERROR("Couldn't find collect for file %s in ISPyB!" % inpath)
self.setFailure()
else:
# the result is a suds.sudsobject.Object, we need to convert it
res = XSDataISPyBDataCollection()
try:
for k, v in collect_params:
setattr(res, k, v)
except:
self.ERROR('something went wrong converting the result to a XSDataResultRetrieveDataCollection')
self.setFailure()
else:
self.collectParameters = XSDataResultRetrieveDataCollection()
self.collectParameters.dataCollection = res
def configure(self):
"""
Gets the dbserver parameters from the config file and stores them in class member attributes.
"""
EDPluginExec.configure(self)
pluginConfiguration = self.getConfiguration()
if(pluginConfiguration == None):
EDVerbose.DEBUG("*** EDPluginISPyBv1_2.configure: pluginConfiguration is None, using default settings")
else:
EDVerbose.DEBUG("*** EDPluginISPyBv1_2.configure: pluginConfiguration found, using settings from there")
strDbserverHost = EDConfiguration.getStringParamValue(pluginConfiguration, "dbserverHost")
if(strDbserverHost == None):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2.configure", self.getClassName(), \
"Configuration parameter missing: dbserverHost")
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
else:
self.setDbserverHost(strDbserverHost)
strDbserverPort = EDConfiguration.getStringParamValue(pluginConfiguration, "dbserverPort")
if(strDbserverPort == None):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2.configure", self.getClassName(), \
"Configuration parameter missing: dbserverPort")
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
else:
self.setDbserverPort(int (strDbserverPort))
def configure(self):
"""
Gets the configuration parameters (if any).
"""
EDPluginExec.configure(self)
self.DEBUG("EDPluginExecSimpleHTMLPagev1_1.configure")
self.fMinTransmission = self.config.get("minTransmissionWarning", self.fMinTransmission)
def postProcess(self, _edObject=None):
EDPluginExec.postProcess(self)
self.DEBUG("EDPluginISPyBStoreAutoProcv1_4.postProcess")
xsDataResultStoreAutoProc = XSDataResultStoreAutoProc()
if self.iAutoProcId is not None:
xsDataResultStoreAutoProc.setAutoProcId(XSDataInteger(self.iAutoProcId))
self.setDataOutput(xsDataResultStoreAutoProc)
def __init__(self):
"""
Constructor of the plugin
"""
EDPluginExec.__init__(self)
self.setXSDataInputClass(XSDataInputExecThumbnail)
self.inputFilename = None
self.thumbFormat = None
self.colorize = None
self.keepRatio = None
self.gamma = None
self.invert = None
self.equalize = None
self.autocontrast = None
self.output = None
self.format = None
self.height = None
self.width = None
self.normalize = None
self.npaImage = None
self.cropBorders = None
self.log = None
self.minLevel = None
self.maxLevel = None
self.minLevelUnit = None
self.maxLevelUnit = None
self.gaussianBlur = None
self.dilatation = None
def preProcess(self, _edObject=None):
EDPluginExec.preProcess(self)
# Read in input data (if any)
if self.hasDataInput("indexingResult"):
self.__xsDataIndexingResult = self.getDataInput("indexingResult")[0]
if self.hasDataInput("imageQualityIndicators"):
self.__listXSDataImageQualityIndicator = self.getDataInput("imageQualityIndicators")
def preProcess(self, _edObject=None):
EDPluginExec.preProcess(self)
self.DEBUG("EDPluginExecMeasureOffsetv2_0.preProcess")
sdi = self.dataInput
images = sdi.image
arrays = sdi.array
if len(images) == 2:
self.npaIm1 = numpy.array(EDUtilsArray.getArray(images[0]))
self.npaIm2 = numpy.array(EDUtilsArray.getArray(images[1]))
elif len(arrays) == 2:
self.npaIm1 = EDUtilsArray.xsDataToArray(arrays[0])
self.npaIm2 = EDUtilsArray.xsDataToArray(arrays[1])
else:
strError = "EDPluginExecMeasureOffsetv2_0.preProcess: You should either provide two images or two arrays, but I got: %s" % sdi.marshal()[:1000]
self.ERROR(strError)
self.setFailure()
raise RuntimeError(strError)
crop = sdi.cropBorders
if len(crop) > 1 :
self.tCrop = tuple([ i.value for i in crop ])
elif len(crop) == 1:
self.tCrop = (crop[0].value, crop[0].value)
center = sdi.center
if len(center) > 1:
self.tCenter = tuple([ i.value for i in center ])
elif len(center) == 1:
self.tCenter = (center[0].value, center[0].value)
width = sdi.width
if len(width) > 1 :
self.tWidth = tuple([i.value for i in width])
elif len(width) == 1:
self.tWidth = (width[0].value, width[0].value)
smooth = sdi.smoothBorders
if len(smooth) == 2:
self.tSmooth = (smooth[0].value, smooth[1].value)
elif len(smooth) == 1:
self.tSmooth = (smooth[0].value, smooth[0].value)
if sdi.backgroundSubtraction is not None:
self.bBackgroundsubtraction = (sdi.backgroundSubtraction.value in [1, True, "true"])
if sdi.sobelFilter is not None:
self.sobel = (sdi.sobelFilter in [1, True, "true"])
EDAssert.equal(self.npaIm1.shape , self.npaIm2.shape, "Images have the same size")
def process(self, _edObject=None):
EDPluginExec.process(self)
imageFileName = os.path.basename(self.dataInput.image.path.value)
# Default format
strSuffix = "jpg"
strPILFormat = "JPEG"
# Check if format is provided
if self.dataInput.format is not None:
strFormat = self.dataInput.format.value
if strFormat.lower() == "png":
strSuffix = "png"
strPILFormat = "PNG"
# The following code has been adapted from EDPluginExecThumbnail written by J.Kieffer
fabioImage = fabio.openimage.openimage(self.dataInput.image.path.value)
numpyImage = fabioImage.data
dtype = numpyImage.dtype
sortedArray = numpyImage.flatten()
sortedArray.sort()
numpyImage = numpy.maximum(
numpyImage,
int(self.minLevel) * numpy.ones_like(numpyImage))
maxLevel = sortedArray[int(
round(float(self.maxLevel) * sortedArray.size / 100.0))]
numpyImage = numpy.minimum(numpyImage,
maxLevel * numpy.ones_like(numpyImage))
numpyImage = scipy.ndimage.morphology.grey_dilation(
numpyImage, (self.dilatation, self.dilatation))
mumpyImageFloat = (numpyImage.astype(numpy.float32)) / float(maxLevel)
numpyImageInt = (mumpyImageFloat * 255.0).astype(numpy.uint8)
pilOutputImage = ImageOps.invert(Image.fromarray(numpyImageInt, 'L'))
if self.dataInput.height is not None and self.dataInput.width is not None:
pilOutputImage = pilOutputImage.resize(
(self.dataInput.width.value, self.dataInput.height.value),
Image.ANTIALIAS)
if self.dataInput.outputPath is None:
outputPath = os.path.join(
self.getWorkingDirectory(),
os.path.splitext(imageFileName)[0] + "." + strSuffix)
else:
outputPath = self.dataInput.outputPath.path.value
self.DEBUG("Output thumbnail path: %s" % outputPath)
self.width, self.height = pilOutputImage.size
if self.width * self.height > ImageFile.MAXBLOCK:
ImageFile.MAXBLOCK = self.width * self.height
pilOutputImage.save(outputPath,
strPILFormat,
quality=85,
optimize=True)
self.dataOutput.thumbnail = XSDataFile(XSDataString(outputPath))
def postProcess(self, _edObject=None):
EDPluginExec.postProcess(self)
if self.__xsDataIndexingResult != None:
self.setDataOutput(self.__xsDataIndexingResult, "indexingResult")
else:
self.__bIndexingSuccess = False
self.setDataOutput(XSDataBoolean(self.__bIndexingSuccess),
"indexingSuccess")
if self.__strStatusMessageIndexing != None:
self.setDataOutput(XSDataString(self.__strStatusMessageIndexing),
"statusMessageIndexing")
if self.__strStatusMessageImageQualityIndicators != None:
self.setDataOutput(
XSDataString(self.__strStatusMessageImageQualityIndicators),
"statusMessageImageQualityIndicators")
def postProcess(self, _edObject=None):
EDPluginExec.postProcess(self)
EDVerbose.DEBUG("*** EDPluginEDFReadHeaderv1_0.postProcess")
# Create some output data
xsDataResultEDFReadHeader = XSDataResultEDFReadHeader()
if (self.m_edDictionaryHeader is not None):
xsDataDictionary = XSDataDictionary()
for key in self.m_edDictionaryHeader.keys():
xsDataKeyValuePair = XSDataKeyValuePair()
xsDataKeyValuePair.setKey(XSDataString(key))
xsDataKeyValuePair.setValue(
XSDataString(self.m_edDictionaryHeader[key]))
xsDataDictionary.addKeyValuePair(xsDataKeyValuePair)
xsDataResultEDFReadHeader.setDictionary(xsDataDictionary)
self.setDataOutput(xsDataResultEDFReadHeader)
def __init__(self):
EDPluginExec.__init__(self)
self.setXSDataInputClass(XSDataInputSimpleHTMLPage)
self.strPluginExecOutputHTMLName = "EDPluginExecOutputHTMLv1_0"
self.edPluginExecOutputHTML = None
self.strHTML = None
self.xsDataResultCharacterisation = None
self.xsDataKappa_alignment_response = None
self.page = None
self.strPath = None
self.strTableColourTitle1 = "#F5F5FF"
self.strTableColourTitle2 = "#F0F0FF"
self.strTableColourRows = "#FFFFA0"
self.strPageEDNALog = None
self.xsDataSuggestedStrategy = None
def preProcess(self, _edObject=None):
EDPluginExec.preProcess(self)
self.DEBUG("EDPluginExecMatrixInvertv2_0.preProcess")
self.xsdMatIn = self.dataInput.inputMatrix
if self.xsdMatIn.path is not None:
self.matIn = fabio.open(self.xsdMatIn.path.value).data
elif self.xsdMatIn.shared is not None:
self.matIn = EDShare[self.xsdMatIn.shared.value]
elif self.xsdMatIn.array is not None:
self.matIn = EDUtilsArray.xsDataToArray(self.xsdMatIn.array)
else:
self.ERROR("No valid input array provided")
if self.matIn is None:
self.ERROR("Input array is None")
self.setFailure()
def process(self, _edObject=None):
EDPluginExec.process(self)
self.DEBUG("EDPluginExecPlotGlev1_0.process")
for strPath in self.listPlot:
strCommand = "gle -verbosity 0 -r 150 -d jpg %s.gle" % strPath
# Copied from EDPluginExecProcess
self.DEBUG(self.getBaseName() + ": Processing")
timer = threading.Timer(float(self.getTimeOut()), self.kill)
timer.start()
self.__subprocess = EDUtilsPlatform.Popen(
shlex.split(str(EDUtilsPlatform.escape(strCommand))),
cwd=self.getWorkingDirectory())
self.__iPID = self.__subprocess.pid
self.__strExecutionStatus = str(self.__subprocess.wait())
timer.cancel()
def postProcess(self, _edObject=None):
"""
"""
EDPluginExec.postProcess(self)
EDVerbose.DEBUG("*** EDPluginDCTWriteSinogramv1_0.postProcess")
xsDataResultWriteSinogram = XSDataResultWriteSinogram()
for pystrPathToOneSinogram in self.pydProcessSinograms:
oneSinogram = XSDataFile()
oneSinogram.setPath(
XSDataString(pystrPathToOneSinogram + "Size%ix%i.edf" %
(self.yMax, self.xMax)))
xsDataResultWriteSinogram.addSinogramFile(oneSinogram)
EDVerbose.DEBUG("Adding sinogram: %s" % pystrPathToOneSinogram)
self.setDataOutput(xsDataResultWriteSinogram)
def preProcess(self, _edObject=None):
EDPluginExec.preProcess(self)
self.DEBUG("EDPluginExecPlotGlev1_1.preProcess")
FileGle = None
# Check if we have a plotmtv input file
xsDataInput = self.getDataInput()
for xsDataGlePlot in xsDataInput.glePlot:
dictPlot = {}
dictPlot["script"] = xsDataGlePlot.script.path.value
dictPlot["data"] = [xsDataGlePlot.data.path.value]
self.listPlot.append(dictPlot)
if xsDataInput.filePlotMtv is not None:
strPlotMtvPath = xsDataInput.filePlotMtv.path.value
if os.path.exists(strPlotMtvPath):
strPlotMtv = EDUtilsFile.readFile(strPlotMtvPath)
xsDataPlotSet = self.readPlotMtv(strPlotMtv)
else:
self.ERROR("Path to plt mtv file does not exist: %s" % strPlotMtvPath)
self.setFailure()
return
else:
xsDataPlotSet = xsDataInput.plotSet
# Prepare input script
iIndex = 1
if xsDataPlotSet is not None:
for xsDataPlot in xsDataPlotSet.plot:
if xsDataPlot.xsize is None:
xsDataPlot.xsize = 10
if xsDataPlot.ysize is None:
xsDataPlot.ysize = 10
if iIndex in [1, 5, 8]:
xsDataPlot.keypos = "tl"
elif iIndex in [2, 4, 6]:
xsDataPlot.keypos = "tr"
elif iIndex in [3]:
xsDataPlot.keypos = "br"
elif iIndex in [7]:
xsDataPlot.keypos = "bl"
if iIndex == 4:
xsDataPlot.xmax = 500
strPlotFile = os.path.join(self.getWorkingDirectory(), "plot%d" % iIndex)
(strGle, listDataFiles) = self.prepareGleGraph(xsDataPlot)
EDUtilsFile.writeFile(strPlotFile + ".gle", strGle)
dictPlot = {}
dictPlot["script"] = strPlotFile + ".gle"
dictPlot["data"] = listDataFiles
self.listPlot.append(dictPlot)
iIndex += 1
def preProcess(self, _edObject=None):
EDPluginExec.preProcess(self)
self.DEBUG("EDPluginExecSaxsCurvesv1_1.preProcess")
xsdIn = self.getDataInput()
if xsdIn.getInputImage() is not None:
self.inputImage = xsdIn.getInputImage().getPath().getValue()
if not os.path.isfile(self.inputImage):
self.ERROR("Input file %s does not exist ... try to go on anyway" % self.inputImage)
if xsdIn.getOutputDataFile() is not None:
self.outputDataFile = xsdIn.getOutputDataFile().getPath().getValue()
if xsdIn.getOptions() is not None:
self.options = xsdIn.getOptions().getValue()
for oneHeader in xsdIn.getExtraHeaders():
self.extraHeader.append(oneHeader.getValue())
if xsdIn.getHeaderMarker() is not None:
self.headerMarker = xsdIn.getHeaderMarker().getValue()
def preProcess(self, _edPlugin=None):
EDPluginExec.preProcess(self, _edPlugin)
self.DEBUG("EDPluginExecSimpleHTMLPagev2_1.preProcess...")
self.xsDataResultCharacterisation = self.getDataInput(
).getCharacterisationResult()
if self.xsDataResultCharacterisation is None:
if not self.getDataInput().getCharacterisationResultv2_0() is None:
self.xsDataResultCharacterisation = self.getDataInput(
).getCharacterisationResultv2_0(
).getMxv1ResultCharacterisation()
self.xsDataKappa_alignment_response = self.getDataInput(
).getCharacterisationResultv2_0().getPossibleOrientations()
self.xsDataSuggestedOrientation = self.dataInput.characterisationResultv2_0.suggestedOrientation
self.strHtmlFileName = "index.html"
self.strPath = os.path.join(self.getWorkingDirectory(),
self.strHtmlFileName)
def __init__(self):
"""
Constructor of the plugin
"""
EDPluginExec.__init__(self)
self.setXSDataInputClass(XSDataInputNormalize)
self.listDataArray = []
self.listDataExposure = []
self.listDarkArray = []
self.listDarkExposure = []
self.listFlatArray = []
self.listFlatExposure = []
self.npaNormalized = None
self.strOutputFilename = None
self.strOutputShared = None
self.shape = None
def __init__(self):
EDPluginExec.__init__(self)
self.setXSDataInputClass(XSDataInputSimpleHTMLPage)
self.strPluginExecOutputHTMLName = "EDPluginExecOutputHTMLv1_0"
self.edPluginExecOutputHTML = None
self.strHTML = None
self.xsDataResultCharacterisation = None
self.strPath = None
self.strTableColourTitle1 = "#F5F5FF"
self.strTableColourTitle2 = "#F0F0FF"
self.strTableColourRows = "#FFFFA0"
self.strPageEDNALog = None
self.fMinTransmission = 10 # %
self.bIsHelical = False
self.bIsMultiPositional = False
self.workflowStepReport = None
def postProcess(self, _edObject=None):
EDPluginExec.postProcess(self)
EDVerbose.DEBUG("EDPluginExportAsciiPowderv1_0.postProcess")
# Create some output data
xsDataResult = XSDataResult1DPowderEDF()
if self.outputFilename is None:
xsDataResult.setTwoTheta(EDUtilsArray.arrayToXSData(self.npaTwoTheta))
xsDataResult.setIntensity(EDUtilsArray.arrayToXSData(self.npaIntensities))
else:
xsdFile = XSDataFile()
xsdFile.setPath(XSDataString(self.outputFilename))
xsDataResult.setOutputFile(xsdFile)
self.setDataOutput(xsDataResult)
self.npaTwoTheta = None
self.npaIntensities = None
self.inputArray = None
def configure(self,
_bRequireToolsForCollectionWebServiceWsdl=False,
_bRequireToolsForAutoprocessingWebServiceWsdl=False,
_bRequireToolsForBLSampleWebServiceWsdl=False,
_bRequireToolsForScreeningEDNAWebServiceWsdl=False):
"""
Gets the web servise wdsl parameters from the config file and stores them in class member attributes.
"""
EDPluginExec.configure(self)
self.strUserName = str(self.config.get("userName"))
if self.strUserName is None:
self.ERROR(
"{0}.configure: No user name found in configuration!".format(
self.getName()))
self.setFailure()
self.strPassWord = str(self.config.get("passWord"))
if self.strPassWord is None:
self.ERROR("{0}.configure: No pass word found in configuration!")
self.setFailure()
self.strToolsForCollectionWebServiceWsdl = self.config.get(
"toolsForCollectionWebServiceWsdl")
if _bRequireToolsForCollectionWebServiceWsdl and self.strToolsForCollectionWebServiceWsdl is None:
self.ERROR(
"{0}.configure: No toolsForCollectionWebServiceWsdl found in configuration!"
)
self.setFailure()
self.strToolsForAutoprocessingWebServiceWsdl = self.config.get(
"toolsForAutoprocessingWebServiceWsdl")
if _bRequireToolsForAutoprocessingWebServiceWsdl and self.strToolsForAutoprocessingWebServiceWsdl is None:
self.ERROR(
"EDPluginISPyBStoreImageQualityIndicatorsv1_4.configure: No toolsForAutoprocessingWebServiceWsdl found in configuration!"
)
self.setFailure()
self.strToolsForBLSampleWebServiceWsdl = self.config.get(
"toolsForBLSampleWebServiceWsdl")
if _bRequireToolsForBLSampleWebServiceWsdl and self.strToolsForBLSampleWebServiceWsdl is None:
self.ERROR(
"EDPluginISPyBGetSampleInformationv1_4.configure: No toolsForBLSampleWebServiceWsdl found in configuration!"
)
self.setFailure()
self.strToolsForScreeningEDNAWebServiceWsdl = self.config.get(
"toolsForScreeningEDNAWebServiceWsdl")
if _bRequireToolsForScreeningEDNAWebServiceWsdl and self.strToolsForScreeningEDNAWebServiceWsdl is None:
self.ERROR(
"EDPluginISPyBStoreScreeningv1_4.configure: No toolsForScreeningEDNAWebServiceWsdl found in configuration!"
)
self.setFailure()
def postProcess(self, _edObject=None):
"""
Postprocess of the plugin:
* set output of the plugin
* free some memory from large arrays
"""
EDPluginExec.postProcess(self)
EDVerbose.DEBUG("EDPluginPyarchThumbnailv10.postProcess")
# Create some output data
if self.strOutputPath:
xsDataResult = XSDataResultPyarchThumbnail()
if os.path.isfile(self.strOutputPath):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.strOutputPath))
xsDataResult.setThumbnailPath(xsDataFile)
self.setDataOutput(xsDataResult)
def __init__(self):
"""
Initializes process related attributes described above
"""
EDPluginExec.__init__(self)
self.setRequiredToHaveConfiguration()
self.__strConfigExecutable = "cat"
self.__strConfigCommandline = ""
self.__subprocess = None
self.__iPID = None
self.__strCWD = None
self.__strExecutionStatus = ""
self._start_time = None
self._oar_job_id = None
self._timer = None
self._oar_options = None
self._oar_poll_interval = None
def preProcess(self, _edObject=None):
"""
Preprocess of the plugin:
check parameters and extract from EDNA format into something more simple & pythonic
"""
EDPluginExec.preProcess(self)
EDVerbose.DEBUG("EDPluginPyarchThumbnailv10.preProcess")
sdi = self.getDataInput()
if sdi.getInputImagePath() is not None:
self.inputFilename = sdi.getInputImagePath().getPath().getValue()
if not os.path.isfile(self.inputFilename):
EDVerbose.ERROR(
"The input file provided is not a valid file: " +
self.inputFilename)
raise "Not a valid file " + self.inputFilename
# Output path
strImageNameWithoutExt = os.path.basename(
os.path.splitext(self.inputFilename)[0])
strImageDirname = os.path.dirname(self.inputFilename)
strOutputDirname = self.createPyarchFilePath(strImageDirname)
# Check that output pyarch path exists and is writeable:
bIsOk = False
if strOutputDirname:
if not os.path.exists(strOutputDirname):
# Try to create the directory
try:
os.makedirs(strOutputDirname)
bIsOk = True
except BaseException, e:
EDVerbose.WARNING("Couldn't create the directory %s" %
strOutputDirname)
elif os.access(strOutputDirname, os.W_OK):
bIsOk = True
if not bIsOk:
EDVerbose.warning("Cannot write to pyarch directory: %s" %
strOutputDirname)
strOutputDirname = tempfile.mkdtemp(
"", "EDPluginPyarchThumbnailv10_", "/tmp")
EDVerbose.warning("Writing thumbnail images to: %s" %
strOutputDirname)
self.strOutputPath = os.path.join(strOutputDirname,
strImageNameWithoutExt + ".jpeg")
self.strOutputPathThumb = os.path.join(
strOutputDirname, strImageNameWithoutExt + ".thumb.jpeg")
def configure(self):
"""
Gets the web servise wdsl parameters from the config file and stores them in class member attributes.
"""
EDPluginExec.configure(self)
self.strUserName = self.config.get("userName")
if self.strUserName is None:
self.ERROR("EDPluginISPyBGetSampleInformationv1_4.configure: No user name found in configuration!")
self.setFailure()
self.strPassWord = self.config.get("passWord")
if self.strPassWord is None:
self.ERROR("EDPluginISPyBGetSampleInformationv1_4.configure: No pass word found in configuration!")
self.setFailure()
self.strToolsForBLSampleWebServiceWsdl = self.config.get("toolsForBLSampleWebServiceWsdl")
if self.strToolsForBLSampleWebServiceWsdl is None:
self.ERROR("EDPluginISPyBGetSampleInformationv1_4.configure: No toolsForBLSampleWebServiceWsdl found in configuration!")
self.setFailure()
def __init__(self):
EDPluginExec.__init__(self)
self.strWorkingDirectory = None
self.strWorkingDir = None
self.strEDNA2html = None
self.strTitle = None
self.strBasename = None
self.strPath = None
# if not os.environ.has_key("EDNA2html"):
# self.setRequiredToHaveConfiguration(True)
if os.environ.has_key("PATH"):
self.strPath = os.environ["PATH"]
self.setXSDataInputClass(XSDataString, "title")
self.setXSDataInputClass(XSDataString, "basename")
self.setXSDataInputClass(XSDataString, "workingDir")
self.setXSDataInputClass(XSDataFile, "dnaFileDirectory")
def postProcess(self, _edObject=None):
EDPluginExec.postProcess(self)
self.DEBUG("EDPluginExecMatrixInvertv2_0.postProcess")
# Create some output data
xsDataResult = XSDataResultMatrixInvertv2()
xsd = XSDataImageExt()
if self.dataInput.outputMatrix is not None:
if self.dataInput.outputMatrix.path is not None:
fabio.edfimage.edfimage(data=self.matOut).write(self.dataInput.outputMatrix.path.value)
xsd.path = self.dataInput.outputMatrix.path
elif self.dataInput.outputMatrix.shared is not None:
EDShare[self.dataInput.outputMatrix.shared.value] = self.matOut
xsd.shared = self.dataInput.outputMatrix.shared
else:
xsd.array = EDUtilsArray.arrayToXSData(self.matOut, _bIncludeMd5sum=False)
xsDataResult.setOutputMatrix(xsd)
self.setDataOutput(xsDataResult)
def process(self, _edObject=None):
EDPluginExec.process(self)
EDVerbose.DEBUG("EDPluginExecMedianFilterv1_0.process")
ndArray3D = None
for strImgName in self.images:
if not os.path.isfile(strImgName) :
EDVerbose.ERROR("Unable to read file %s" % strImgName)
else:
if not strImgName in self.__dictImages:
data = fabio.open(strImgName).data
shape = data.shape
self.__dictImages[strImgName] = data.reshape(1, shape[0], shape[1])
if ndArray3D is None:
ndArray3D = self.__dictImages[strImgName]
else:
ndArray3D = numpy.concatenate((ndArray3D, self.__dictImages[strImgName]), axis=0)
self.outputArray = scipy.median(ndArray3D, axis=0)
def postProcess(self, _edObject=None):
EDPluginExec.postProcess(self)
EDVerbose.DEBUG("EDPluginExecMedianFilterv1_0.postProcess")
# Create some output data
xsDataResult = XSDataResultMedianFilter()
if self.outputImage is None:
xsDataResult.setOutputArray(
EDUtilsArray.arrayToXSData(self.outputArray))
else:
edf = fabio.edfimage.edfimage(
data=self.outputArray.astype("float32"))
edf.write(self.outputImage)
xsDataResult.setOutputImage(
XSDataImage(XSDataString(self.outputImage)))
self.setDataOutput(xsDataResult)
self.outputArray = None
def preProcess(self, _edObject=None):
EDPluginExec.preProcess(self)
EDVerbose.DEBUG("EDPluginBioSaxsMetadatav1_1.preProcess")
self.strInputImage = self.xsdInputData.getInputImage().getPath().value
if self.xsdInputData.getDetector() is not None:
self.detector = self.xsdInputData.getDetector().value
if self.xsdInputData.detectorDistance is not None:
self.detectorDistance = self.xsdInputData.detectorDistance.value
if self.xsdInputData.beamCenter_1 is not None:
self.beamCenter_1 = self.xsdInputData.beamCenter_1.value
if self.xsdInputData.pixelSize_1 is not None:
self.pixelSize_1 = self.xsdInputData.pixelSize_1.value
if self.xsdInputData.beamCenter_2 is not None:
self.beamCenter_2 = self.xsdInputData.beamCenter_2.value
if self.xsdInputData.pixelSize_2 is not None:
self.pixelSize_2 = self.xsdInputData.pixelSize_2.value
if self.xsdInputData.beamStopDiode is not None:
self.beamStopDiode = self.xsdInputData.beamStopDiode.value
if self.xsdInputData.storageTemperature is not None:
self.storageTemperature = self.xsdInputData.storageTemperature.value
if self.xsdInputData.exposureTemperature is not None:
self.exposureTemperature = self.xsdInputData.exposureTemperature.value
if self.xsdInputData.exposureTime is not None:
self.exposureTime = self.xsdInputData.exposureTemperature.value
if self.xsdInputData.frameNumber is not None:
self.frameNumber = self.xsdInputData.exposureTemperature.value
if self.xsdInputData.frameMax is not None:
self.frameMax = self.xsdInputData.exposureTemperature.value
if self.xsdInputData.code is not None:
self.code = self.xsdInputData.code.value
if self.xsdInputData.comments is not None:
self.comments = self.xsdInputData.comments.value
if self.xsdInputData.concentration is not None:
self.concentration = self.xsdInputData.concentration.value
if self.xsdInputData.machineCurrent is not None:
self.machineCurrent = self.xsdInputData.machineCurrent.value
if self.xsdInputData.wavelength is not None:
self.wavelength = self.xsdInputData.wavelength.value
if self.xsdInputData.normalizationFactor is not None:
self.normalizationFactor = self.xsdInputData.normalizationFactor.value
if self.xsdInputData.maskFile is not None:
self.maskFile = self.xsdInputData.maskFile.getPath().value
if self.xsdInputData.getOutputImage() is not None:
self.strOutputImage = self.xsdInputData.getOutputImage().getPath(
).value
def finallyProcess(self, _edObject=None):
EDPluginExec.finallyProcess(self)
self.DEBUG("EDPluginISPyBSetImagesPositionsv1_4.finallyProcess")
xsDataResultISPyBSetImagesPositions = XSDataResultISPyBSetImagesPositions(
)
for imageCreation in self.listImageCreation:
xsDataISPyBImageCreation = XSDataISPyBImageCreation()
xsDataISPyBImageCreation.fileLocation = XSDataString(
imageCreation.fileLocation)
xsDataISPyBImageCreation.fileName = XSDataString(
imageCreation.fileName)
xsDataISPyBImageCreation.imageId = XSDataInteger(
imageCreation.imageId)
xsDataISPyBImageCreation.isCreated = XSDataBoolean(
imageCreation.isCreated)
xsDataResultISPyBSetImagesPositions.addImageCreation(
xsDataISPyBImageCreation)
self.setDataOutput(xsDataResultISPyBSetImagesPositions)
def __init__(self):
"""
"""
EDPluginExec.__init__(self)
self.setXSDataInputClass(XSDataInputStitchOffsetedImage)
self._lImages = [] #list of ndarrays
self._fDummy = 0
self._lDummies = [
] #list of 2-tuples of floats containing the dummy value and the delta-dummy
self._lOffsets = [
] #list of 2-tuples of floats containing the offset values
self._strOutFile = None
self._strBlending = "max" #can be min or mean or naive
self._bAutoscale = False
self._ndaResult = None
self.tCenter = None
self.tWidth = None
self._strMask = None
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 finallyProcess(self, _edPlugin=None):
EDPluginExec.finallyProcess(self, _edPlugin)
self.DEBUG("EDPluginExecSimpleHTMLPagev1_0.finallyProcess...")
# Render the page
strHTML = str(self.page)
EDUtilsFile.writeFile(self.strPath, strHTML)
xsDataResultSimpleHTMLPage = XSDataResultSimpleHTMLPage()
xsDataResultSimpleHTMLPage.setPathToHTMLFile(XSDataFile(XSDataString(self.strPath)))
xsDataResultSimpleHTMLPage.setPathToHTMLDirectory(XSDataFile(XSDataString(os.path.dirname(self.strPath))))
self.setDataOutput(xsDataResultSimpleHTMLPage)
# Store in Pyarch
strPyarchPath = None
if self.xsDataResultCharacterisation is not None:
strPyarchPath = EDHandlerESRFPyarchv1_0.createPyarchHtmlDirectoryPath(self.xsDataResultCharacterisation.getDataCollection())
if strPyarchPath is None:
# For debugging purposes
strPyarchPath = EDUtilsPath.getEdnaUserTempFolder()
EDHandlerESRFPyarchv1_0.copyHTMLDir(_strPathToHTMLDir=os.path.dirname(self.strPath), _strPathToPyarchDirectory=strPyarchPath)
def process(self, _edObject=None):
EDPluginExec.process(self)
self.DEBUG("EDPluginExecReadDataID24v1_0.process")
self.checkMandatoryParameters(self.dataInput, "Data Input is None")
self.checkMandatoryParameters(self.dataInput.inputFile,
"Data Input 'inputFile' is None")
self.checkMandatoryParameters(
self.dataInput.energyCalibration,
"Data Input 'energyuCalibration' is None")
self.checkMandatoryParameters(
self.dataInput.energyCalibration.a,
"Data Input 'energyCalibration a' is None")
self.checkMandatoryParameters(
self.dataInput.energyCalibration.b,
"Data Input 'energyCalibration b' is None")
# Load input data
listNumpyArray = []
iNumberOfSPectra = 0
iNumberOfEnergies = 0
for xsDataFile in self.dataInput.inputFile:
numpyDataArray = self.loadInputData(xsDataFile.path.value)
# print numpyDataArray.shape
listNumpyArray.append(numpyDataArray)
iNumberOfEnergies = numpyDataArray.shape[0]
iNumberOfSPectra += numpyDataArray.shape[1]
numpyTotalDataArray = numpy.zeros(
(iNumberOfEnergies, iNumberOfSPectra))
# print numpyTotalDataArray.shape
iIndex = 0
for numpyDataArray in listNumpyArray:
iSpectra = numpyDataArray.shape[1]
numpyTotalDataArray[:, iIndex:iIndex + iSpectra] = numpyDataArray
iIndex += iSpectra
# Create energy calibration array
numpyEnergyCalibrationArray = self.createEnergyCalibrationArray(
numpyTotalDataArray.shape[0], self.dataInput.energyCalibration)
# Create some output data
xsDataResultReadDataID24 = XSDataResultReadDataID24()
xsDataResultReadDataID24.energy = EDUtilsArray.arrayToXSData(
numpyEnergyCalibrationArray)
xsDataResultReadDataID24.dataArray = EDUtilsArray.arrayToXSData(
numpyTotalDataArray)
self.setDataOutput(xsDataResultReadDataID24)
def process(self, _edObject=None):
"""
Uses ToolsForCollectionWebService
"""
EDPluginExec.process(self)
self.DEBUG("EDPluginISPyBStoreMotorPositionv1_4.process")
httpAuthenticatedToolsForCollectionWebService = HttpAuthenticated(
username=self.strUserName, password=self.strPassWord)
clientToolsForCollectionWebService = Client(
self.strToolsForCollectionWebServiceWsdl,
transport=httpAuthenticatedToolsForCollectionWebService)
# Loop over all positions
motorPosition = self.createMotorPosition3VO(
clientToolsForCollectionWebService, self.dataInput.motorPosition)
self.motorPositionId = clientToolsForCollectionWebService.service.storeOrUpdateMotorPosition(
motorPosition=motorPosition)
self.DEBUG(
"EDPluginISPyBStoreMotorPositionv1_4.process: motorPositionId=%r" %
self.motorPositionId)