def unitTestArraytoXsdNoNumpy(self):
"""
test the execution of detectNumberOfCPUs
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsArray.unitTestArraytoXsdNoNumpy")
EDAssert.strAlmostEqual(XSDataArray.parseString(self.strXSDataArrayNoNumpy).marshal(),
EDUtilsArray.arrayToXSData(self.arrayNumpy, _bForceNoNumpy=True).marshal(),
_strComment="XSDataArray from (numpyArray) are the same (forced No Numpy)")
EDAssert.strAlmostEqual(XSDataArray.parseString(self.strXSDataArrayNoNumpy).marshal(),
EDUtilsArray.arrayToXSData(self.arrayNoNumpy, _bForceNoNumpy=True).marshal(),
_strComment="XSDataArray from (list of lists) are the same (forced No Numpy)")
def unitTestArraytoXsd(self):
"""
test the execution of xsDataToArray static method
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsArray.unitTestArraytoXsd")
if numpy is not None:
EDAssert.strAlmostEqual(XSDataArray.parseString(self.strXSDataArrayNumpy).marshal(),
EDUtilsArray.arrayToXSData(self.arrayNumpy).marshal(),
_strComment="XSDataArray from (numpyArray) are the same")
else:
EDAssert.strAlmostEqual(XSDataArray.parseString(self.strXSDataArrayNoNumpy).marshal(),
EDUtilsArray.arrayToXSData(self.arrayNumpy).marshal(),
_strComment="XSDataArray from (Non numpy Array) are the same")
def __init__(self, _strTestName=None):
EDTestCase.__init__(self, "EDUtilsArray")
self.strXSDataArrayNumpy = """<?xml version="1.0" ?>
<XSDataArray>
<shape>10</shape>
<shape>10</shape>
<size>100</size>
<dtype>uint8</dtype>
<data>AAECAwQFBgcICQoLDA0ODxAREhMUFRYXGBkaGxwdHh8gISIjJCUmJygpKissLS4vMDEyMzQ1Njc4OTo7PD0+P0BBQkNERUZHSElKS0xNTk9QUVJTVFVWV1hZWltcXV5fYGFiYw==</data>
<coding><value>base64</value></coding>
<md5sum><value>7acedd1a84a4cfcb6e7a16003242945e</value></md5sum>
</XSDataArray>"""
self.xsDataArrayNumpy = XSDataArray.parseString(
self.strXSDataArrayNumpy)
self.strXSDataArrayNoNumpy = """<?xml version="1.0" ?>
<XSDataArray>
<shape>10</shape>
<shape>10</shape>
<size>100</size>
<dtype>int64</dtype>
<data>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</data>
<coding><value>base64</value></coding>
<md5sum><value>13e5d157161f66d98fe0b75ce51c982b</value></md5sum>
</XSDataArray>"""
self.arrayNoNumpy = [[0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
[10, 11, 12, 13, 14, 15, 16, 17, 18, 19],
[20, 21, 22, 23, 24, 25, 26, 27, 28, 29],
[30, 31, 32, 33, 34, 35, 36, 37, 38, 39],
[40, 41, 42, 43, 44, 45, 46, 47, 48, 49],
[50, 51, 52, 53, 54, 55, 56, 57, 58, 59],
[60, 61, 62, 63, 64, 65, 66, 67, 68, 69],
[70, 71, 72, 73, 74, 75, 76, 77, 78, 79],
[80, 81, 82, 83, 84, 85, 86, 87, 88, 89],
[90, 91, 92, 93, 94, 95, 96, 97, 98, 99]]
if numpy is not None:
self.arrayNumpy = numpy.arange(100, dtype="uint8").reshape(
(10, 10))
else:
self.arrayNumpy = self.arrayNoNumpy
def __init__(self, _strTestName=None):
EDTestCase.__init__(self, "EDUtilsArray")
self.strXSDataArrayNumpy = """<?xml version="1.0" ?>
<XSDataArray>
<shape>10</shape>
<shape>10</shape>
<size>100</size>
<dtype>uint8</dtype>
<data>AAECAwQFBgcICQoLDA0ODxAREhMUFRYXGBkaGxwdHh8gISIjJCUmJygpKissLS4vMDEyMzQ1Njc4OTo7PD0+P0BBQkNERUZHSElKS0xNTk9QUVJTVFVWV1hZWltcXV5fYGFiYw==</data>
<coding><value>base64</value></coding>
<md5sum><value>7acedd1a84a4cfcb6e7a16003242945e</value></md5sum>
</XSDataArray>"""
self.xsDataArrayNumpy = XSDataArray.parseString(self.strXSDataArrayNumpy)
self.strXSDataArrayNoNumpy = """<?xml version="1.0" ?>
<XSDataArray>
<shape>10</shape>
<shape>10</shape>
<size>100</size>
<dtype>int64</dtype>
<data>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</data>
<coding><value>base64</value></coding>
<md5sum><value>13e5d157161f66d98fe0b75ce51c982b</value></md5sum>
</XSDataArray>"""
self.arrayNoNumpy = [[0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
[10, 11, 12, 13, 14, 15, 16, 17, 18, 19],
[20, 21, 22, 23, 24, 25, 26, 27, 28, 29],
[30, 31, 32, 33, 34, 35, 36, 37, 38, 39],
[40, 41, 42, 43, 44, 45, 46, 47, 48, 49],
[50, 51, 52, 53, 54, 55, 56, 57, 58, 59],
[60, 61, 62, 63, 64, 65, 66, 67, 68, 69],
[70, 71, 72, 73, 74, 75, 76, 77, 78, 79],
[80, 81, 82, 83, 84, 85, 86, 87, 88, 89],
[90, 91, 92, 93, 94, 95, 96, 97, 98, 99]]
if numpy is not None:
self.arrayNumpy = numpy.arange(100, dtype="uint8").reshape((10, 10))
else:
self.arrayNumpy = self.arrayNoNumpy
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlTRExafsv1_0.process")
self.checkMandatoryParameters(self.dataInput, "Data Input is None")
# Load from disk if necessary
if self.dataInput.energy is None:
if self.dataInput.pathToEnergyArray is None:
strErrorMessage = "Data Input 'energy' is None"
self.addErrorMessage(strErrorMessage)
self.setFailure()
return
else:
strXmlArray = EDUtilsFile.readFile(
self.dataInput.pathToEnergyArray.path.value)
self.dataInput.energy = XSDataArray.parseString(strXmlArray)
if self.dataInput.dataArray is None:
if self.dataInput.pathToDataArray is None:
strErrorMessage = "Data Input 'dataArray' is None"
self.addErrorMessage(strErrorMessage)
self.setFailure()
return
else:
strXmlArray = EDUtilsFile.readFile(
self.dataInput.pathToDataArray.path.value)
self.dataInput.dataArray = XSDataArray.parseString(strXmlArray)
self.checkMandatoryParameters(self.dataInput.dataArray,
"Data Input 'dataArray' is None")
#
numpyDataArray = EDUtilsArray.xsDataToArray(self.dataInput.dataArray)
numpyEnergyCalibrationArray = EDUtilsArray.xsDataToArray(
self.dataInput.energy)
numpySpectraArray = numpy.arange((numpyDataArray.shape[1]))
# Launch Jesf
listEdPluginExecJesf = self.launchJesfPlugins(
numpyDataArray, numpyEnergyCalibrationArray)
# Create nexus file
xsDataInputWriteNexusFile = XSDataInputWriteNexusFile()
xsDataInputWriteNexusFile.instrument = self.dataInput.instrument
xsDataInputWriteNexusFile.outputFileName = self.dataInput.nexusFileName
# Raw data
xsDataNexusArrayGroupRawData = self.createNexusGroup(
_numpyDataArray=numpyDataArray,
_groupTitle="Raw data",
_groupLongName="Raw data",
_numpyXAxisDataArray=numpyEnergyCalibrationArray,
_xAxisTitle="e",
_xAxisLongName="Energy",
_xAxisUnit="kev",
_numpyYAxisDataArray=numpySpectraArray,
_yAxisTitle="n",
_yAxisLongName="Spectra",
_yAxisUnit="")
xsDataInputWriteNexusFile.addNexusGroup(xsDataNexusArrayGroupRawData)
# Create result data arrays
dictResultArrays = self.createResultArrays(listEdPluginExecJesf)
# Add results arrays to nexus file
self.addResultArraysToNexusFile(dictResultArrays,
xsDataInputWriteNexusFile)
#
edPluginExecWriteNexusData = self.loadPlugin(
self.strWriteNexusFilePluginName)
edPluginExecWriteNexusData.dataInput = xsDataInputWriteNexusFile
edPluginExecWriteNexusData.executeSynchronous()
xsDataResultTRExafs = XSDataResultTRExafs()
if not edPluginExecWriteNexusData.isFailure():
xsDataNexusFile = edPluginExecWriteNexusData.dataOutput.outputFilePath
xsDataResultTRExafs.nexusFile = xsDataNexusFile
#
self.dataOutput = xsDataResultTRExafs
def process(self, _edObject = None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlTRExafsv1_0.process")
self.checkMandatoryParameters(self.dataInput, "Data Input is None")
# Load from disk if necessary
if self.dataInput.energy is None:
if self.dataInput.pathToEnergyArray is None:
strErrorMessage = "Data Input 'energy' is None"
self.addErrorMessage(strErrorMessage)
self.setFailure()
return
else:
strXmlArray = EDUtilsFile.readFile(self.dataInput.pathToEnergyArray.path.value)
self.dataInput.energy = XSDataArray.parseString(strXmlArray)
if self.dataInput.dataArray is None:
if self.dataInput.pathToDataArray is None:
strErrorMessage = "Data Input 'dataArray' is None"
self.addErrorMessage(strErrorMessage)
self.setFailure()
return
else:
strXmlArray = EDUtilsFile.readFile(self.dataInput.pathToDataArray.path.value)
self.dataInput.dataArray = XSDataArray.parseString(strXmlArray)
self.checkMandatoryParameters(self.dataInput.dataArray, "Data Input 'dataArray' is None")
#
numpyDataArray = EDUtilsArray.xsDataToArray(self.dataInput.dataArray)
numpyEnergyCalibrationArray = EDUtilsArray.xsDataToArray(self.dataInput.energy)
numpySpectraArray = numpy.arange((numpyDataArray.shape[0]))
# Launch Jesf
listEdPluginExecJesf = self.launchJesfPlugins(numpyDataArray, numpyEnergyCalibrationArray)
# Create nexus file
xsDataInputWriteNexusFile = XSDataInputWriteNexusFile()
xsDataInputWriteNexusFile.instrument = self.dataInput.instrument
xsDataInputWriteNexusFile.outputFileName = self.dataInput.nexusFileName
# Raw data
xsDataNexusArrayGroupRawData = self.createNexusGroup(
_numpyDataArray = numpyDataArray,
_groupTitle = "Raw data",
_groupLongName = "Raw data",
_numpyXAxisDataArray = numpyEnergyCalibrationArray,
_xAxisTitle = "e",
_xAxisLongName = "Energy",
_xAxisUnit = "kev",
_numpyYAxisDataArray = numpySpectraArray,
_yAxisTitle = "n",
_yAxisLongName = "Spectra",
_yAxisUnit = "")
xsDataInputWriteNexusFile.addNexusGroup(xsDataNexusArrayGroupRawData)
# Create result data arrays
dictResultArrays = self.createResultArrays(listEdPluginExecJesf)
# Add results arrays to nexus file
self.addResultArraysToNexusFile(dictResultArrays, xsDataInputWriteNexusFile)
#
edPluginExecWriteNexusData = self.loadPlugin(self.strWriteNexusFilePluginName)
edPluginExecWriteNexusData.dataInput = xsDataInputWriteNexusFile
edPluginExecWriteNexusData.executeSynchronous()
xsDataResultTRExafs = XSDataResultTRExafs()
if not edPluginExecWriteNexusData.isFailure():
xsDataNexusFile = edPluginExecWriteNexusData.dataOutput.outputFilePath
xsDataResultTRExafs.nexusFile = xsDataNexusFile
#
self.dataOutput = xsDataResultTRExafs