def buildChildren(self, child_, nodeName_): if child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'nexusFileName': obj_ = XSDataString() obj_.build(child_) self.setNexusFileName(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'instrument': obj_ = XSDataString() obj_.build(child_) self.setInstrument(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'energy': obj_ = XSDataArray() obj_.build(child_) self.setEnergy(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'dataArray': obj_ = XSDataArray() obj_.build(child_) self.setDataArray(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'pathToEnergyArray': obj_ = XSDataFile() obj_.build(child_) self.setPathToEnergyArray(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'pathToDataArray': obj_ = XSDataFile() obj_.build(child_) self.setPathToDataArray(obj_) XSDataInput.buildChildren(self, child_, nodeName_)
def buildChildren(self, child_, nodeName_): if child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'outputMatrix': obj_ = XSDataArray() obj_.build(child_) self.setOutputMatrix(obj_) XSDataResult.buildChildren(self, child_, nodeName_)
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'outputMatrix':
obj_ = XSDataArray()
obj_.build(child_)
self.setOutputMatrix(obj_)
XSDataResult.buildChildren(self, child_, nodeName_)
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'data':
obj_ = XSDataArray()
obj_.build(child_)
self.setData(obj_)
XSDataInput.buildChildren(self, child_, nodeName_)
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 buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'lineStyle':
value_ = ''
for text__content_ in child_.childNodes:
if text__content_.nodeValue is not None:
value_ += text__content_.nodeValue
self.__lineStyle = value_
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'lineWidth':
if child_.firstChild:
sval_ = child_.firstChild.nodeValue
try:
fval_ = float(sval_)
except ValueError:
raise ValueError('requires float (or double) -- %s' % child_.toxml())
self.__lineWidth = fval_
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'lineColor':
value_ = ''
for text__content_ in child_.childNodes:
if text__content_.nodeValue is not None:
value_ += text__content_.nodeValue
self.__lineColor = value_
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'label':
value_ = ''
for text__content_ in child_.childNodes:
if text__content_.nodeValue is not None:
value_ += text__content_.nodeValue
self.__label = value_
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'markerType':
value_ = ''
for text__content_ in child_.childNodes:
if text__content_.nodeValue is not None:
value_ += text__content_.nodeValue
self.__markerType = value_
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'markerColor':
value_ = ''
for text__content_ in child_.childNodes:
if text__content_.nodeValue is not None:
value_ += text__content_.nodeValue
self.__markerColor = value_
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'data':
obj_ = XSDataArray()
obj_.build(child_)
self.setData(obj_)
XSData.buildChildren(self, child_, nodeName_)
def testCheckParameters(self):
xsDataInput = XSDataInputWriteMatrix()
xsDataInput.setInputMatrix(XSDataArray())
xsDataInput.setOutputMatrixFile(XSDataFile())
edPluginExecMatrixWrite = self.createPlugin()
edPluginExecMatrixWrite.setDataInput(xsDataInput)
edPluginExecMatrixWrite.checkParameters()
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'title':
obj_ = XSDataString()
obj_.build(child_)
self.setTitle(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'long_name':
obj_ = XSDataString()
obj_.build(child_)
self.setLong_name(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'axis':
obj_ = XSDataNexusAxis()
obj_.build(child_)
self.axis.append(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'data':
obj_ = XSDataArray()
obj_.build(child_)
self.setData(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'signal':
obj_ = XSDataInteger()
obj_.build(child_)
self.setSignal(obj_)
XSData.buildChildren(self, child_, nodeName_)
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'title':
obj_ = XSDataString()
obj_.build(child_)
self.setTitle(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'axis':
obj_ = XSDataInteger()
obj_.build(child_)
self.setAxis(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'primary':
obj_ = XSDataInteger()
obj_.build(child_)
self.setPrimary(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'units':
obj_ = XSDataString()
obj_.build(child_)
self.setUnits(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'long_name':
obj_ = XSDataString()
obj_.build(child_)
self.setLong_name(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'axisData':
obj_ = XSDataArray()
obj_.build(child_)
self.setAxisData(obj_)
XSData.buildChildren(self, child_, nodeName_)
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'energy':
obj_ = XSDataArray()
obj_.build(child_)
self.setEnergy(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'dataArray':
obj_ = XSDataArray()
obj_.build(child_)
self.setDataArray(obj_)
XSDataResult.buildChildren(self, child_, nodeName_)
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'edge':
obj_ = XSDataDouble()
obj_.build(child_)
self.setEdge(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'slope':
obj_ = XSDataDouble()
obj_.build(child_)
self.setSlope(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'jump':
obj_ = XSDataDouble()
obj_.build(child_)
self.setJump(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'hwl':
obj_ = XSDataDouble()
obj_.build(child_)
self.setHwl(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'ewl':
obj_ = XSDataDouble()
obj_.build(child_)
self.setEwl(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'fort92':
obj_ = XSDataArray()
obj_.build(child_)
self.setFort92(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'fort95':
obj_ = XSDataArray()
obj_.build(child_)
self.setFort95(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'fort96':
obj_ = XSDataArray()
obj_.build(child_)
self.setFort96(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'fort97':
obj_ = XSDataArray()
obj_.build(child_)
self.setFort97(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'fort98':
obj_ = XSDataArray()
obj_.build(child_)
self.setFort98(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'fort99':
obj_ = XSDataArray()
obj_.build(child_)
self.setFort99(obj_)
XSDataResult.buildChildren(self, child_, nodeName_)
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'energy':
obj_ = XSDataArray()
obj_.build(child_)
self.setEnergy(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'dataArray':
obj_ = XSDataArray()
obj_.build(child_)
self.setDataArray(obj_)
XSDataResult.buildChildren(self, child_, nodeName_)
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 arrayToXSData(cls, _array, _bIncludeMd5sum=True, _bForceNoNumpy=False):
"""
convert a numpy array or a list of list into an XSDataArray object
@param _array: numpy array or array-like list
@param _bIncludeMd5sum: should the md5sum be added to the XSDataArray instance.
It is useful when sending object through the network
It is a problem for testing
@param _bForceNoNumpy: enables tests without numpy
@type includeMd5sum: boolean
@return: XSDataArray instance
"""
if True:
# with cls.semArrayToXSData:
xsdArray = XSDataArray()
stringArray = ""
shape = None
dtype = None
sizeDtype = None
if bHaveNumpy is True and _bForceNoNumpy is False:
EDVerbose.DEBUG("EDUtilsArray.arrayToXSData with numpy")
# Enforce little Endianness
if sys.byteorder == "big":
_array.byteswap(True)
stringArray = _array.tostring()
shape = _array.shape
dtype = str(_array.dtype)
sizeDtype = len(numpy.zeros(1, dtype=_array.dtype).tostring())
else:
EDVerbose.DEBUG("EDUtilsArray.arrayToXSData without numpy")
sizeDtype = 8 # We enforce either double (float64) or int64
shape = []
subarray = _array
while True:
try:
l = len(subarray)
except TypeError:
break
shape.append(l)
if l > 0:
subarray = subarray[0]
else:
break
if len(shape) == 1:
if isinstance(_array[0], floatType):
dtype = "float64"
stringArray = struct.pack("<" + "d" * shape[0], *_array)
else:
dtype = "int64"
stringArray = struct.pack("<" + "l" * shape[0], *_array)
elif len(shape) == 2:
if isinstance(_array[0][0], floatType):
dtype = "float64"
lineshape = "<" + "d" * shape[-1]
else:
dtype = "int64"
lineshape = "<" + "q" * shape[-1]
for subarray in _array:
stringArray += struct.pack(lineshape, *subarray)
elif len(shape) == 3:
if isinstance(_array[0][0][0], floatType):
dtype = "float64"
lineshape = "<" + "d" * shape[-1]
else:
dtype = "int64"
lineshape = "<" + "q" * shape[-1]
for subarray in _array:
for subsubarray in subarray:
stringArray += struct.pack(lineshape, *subsubarray)
else:
EDVerbose.WARNING("EDUtilsArray.arrayToXSDataArray: Array too large %s " % (shape))
xsdArray.setData(base64.b64encode(stringArray))
xsdArray.setCoding(XSDataString("base64"))
xsdArray.setShape(list(shape))
xsdArray.setDtype(dtype)
size = 1
for i in shape:
size *= i
xsdArray.setSize(size)
EDAssert.equal(size * sizeDtype, len(stringArray), "string representing the array has the right size")
if _bIncludeMd5sum is True:
xsdArray.setMd5sum(XSDataString(hashlib.md5(stringArray).hexdigest()))
return xsdArray
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
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'title':
obj_ = XSDataString()
obj_.build(child_)
self.setTitle(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'experimentalDataQ':
obj_ = XSDataDouble()
obj_.build(child_)
self.experimentalDataQ.append(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'experimentalDataQArray':
obj_ = XSDataArray()
obj_.build(child_)
self.setExperimentalDataQArray(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'experimentalDataValues':
obj_ = XSDataDouble()
obj_.build(child_)
self.experimentalDataValues.append(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'experimentalDataIArray':
obj_ = XSDataArray()
obj_.build(child_)
self.setExperimentalDataIArray(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'experimentalDataStdDev':
obj_ = XSDataDouble()
obj_.build(child_)
self.experimentalDataStdDev.append(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'experimentalDataStdArray':
obj_ = XSDataArray()
obj_.build(child_)
self.setExperimentalDataStdArray(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'experimentalDataFile':
obj_ = XSDataFile()
obj_.build(child_)
self.setExperimentalDataFile(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'rMaxSearchSettings':
obj_ = XSDataSolutionScatteringSettings()
obj_.build(child_)
self.setRMaxSearchSettings(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'angularUnits':
obj_ = XSDataInteger()
obj_.build(child_)
self.setAngularUnits(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'symmetry':
obj_ = XSDataString()
obj_.build(child_)
self.setSymmetry(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'mode':
obj_ = XSDataString()
obj_.build(child_)
self.setMode(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'iNbThreads':
obj_ = XSDataInteger()
obj_.build(child_)
self.setINbThreads(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'onlyGnom':
obj_ = XSDataBoolean()
obj_.build(child_)
self.setOnlyGnom(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'plotFit':
obj_ = XSDataBoolean()
obj_.build(child_)
self.setPlotFit(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'qMin':
obj_ = XSDataDouble()
obj_.build(child_)
self.setQMin(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'qMax':
obj_ = XSDataDouble()
obj_.build(child_)
self.setQMax(obj_)
XSDataInput.buildChildren(self, child_, nodeName_)
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'corelationFitValues':
obj_ = XSDataDouble()
obj_.build(child_)
self.corelationFitValues.append(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'fitFile':
obj_ = XSDataFile()
obj_.build(child_)
self.setFitFile(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'lineProfileFitQuality':
obj_ = XSDataDouble()
obj_.build(child_)
self.setLineProfileFitQuality(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'logFile':
obj_ = XSDataFile()
obj_.build(child_)
self.setLogFile(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'pdbMoleculeFile':
obj_ = XSDataFile()
obj_.build(child_)
self.setPdbMoleculeFile(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'pdbSolventFile':
obj_ = XSDataFile()
obj_.build(child_)
self.setPdbSolventFile(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'scatteringFitQ':
obj_ = XSDataDouble()
obj_.build(child_)
self.scatteringFitQ.append(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'scatteringFitValues':
obj_ = XSDataDouble()
obj_.build(child_)
self.scatteringFitValues.append(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'scatteringFitQArray':
obj_ = XSDataArray()
obj_.build(child_)
self.setScatteringFitQArray(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'scatteringFitIarray':
obj_ = XSDataArray()
obj_.build(child_)
self.setScatteringFitIarray(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'meanNSD':
obj_ = XSDataDouble()
obj_.build(child_)
self.setMeanNSD(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'variationNSD':
obj_ = XSDataDouble()
obj_.build(child_)
self.setVariationNSD(obj_)
XSDataResult.buildChildren(self, child_, nodeName_)
def arrayToXSData(cls,
_array,
_bIncludeMd5sum=True,
_bForceNoNumpy=False,
_bUseAsserts=False):
"""
convert a numpy array or a list of list into an XSDataArray object
@param _array: numpy array or array-like list
@param _bIncludeMd5sum: should the md5sum be added to the XSDataArray instance.
It is useful when sending object through the network
It is a problem for testing
@param _bForceNoNumpy: enables tests without numpy
@type includeMd5sum: boolean
@return: XSDataArray instance
"""
stringArray = ""
shape = None
dtype = None
sizeDtype = None
if bHaveNumpy is True and _bForceNoNumpy is False:
EDVerbose.DEBUG("EDUtilsArray.arrayToXSData with numpy")
# Enforce little Endianness
if sys.byteorder == "big":
_array.byteswap(True)
stringArray = _array.tostring()
shape = _array.shape
dtype = str(_array.dtype)
sizeDtype = len(numpy.zeros(1, dtype=_array.dtype).tostring())
else:
EDVerbose.DEBUG("EDUtilsArray.arrayToXSData without numpy")
sizeDtype = 8 # We enforce either double (float64) or int64
shape = []
subarray = _array
while True:
try:
l = len(subarray)
except TypeError:
break
shape.append(l)
if l > 0:
subarray = subarray[0]
else:
break
if len(shape) == 1:
if isinstance(_array[0], floatType):
dtype = "float64"
stringArray = struct.pack("<" + "d" * shape[0], *_array)
else:
dtype = "int64"
stringArray = struct.pack("<" + "l" * shape[0], *_array)
elif len(shape) == 2:
if isinstance(_array[0][0], floatType):
dtype = "float64"
lineshape = "<" + "d" * shape[-1]
else:
dtype = "int64"
lineshape = "<" + "q" * shape[-1]
for subarray in _array:
stringArray += struct.pack(lineshape, *subarray)
elif len(shape) == 3:
if isinstance(_array[0][0][0], floatType):
dtype = "float64"
lineshape = "<" + "d" * shape[-1]
else:
dtype = "int64"
lineshape = "<" + "q" * shape[-1]
for subarray in _array:
for subsubarray in subarray:
stringArray += struct.pack(lineshape, *subsubarray)
else:
EDVerbose.WARNING(
"EDUtilsArray.arrayToXSDataArray: Array too large %s " %
(shape))
size = 1
for i in shape:
size *= i
xsdArray = XSDataArray(data=base64.b64encode(stringArray),
coding=XSDataString("base64"),
shape=list(shape),
dtype=dtype,
size=size)
if _bUseAsserts:
EDAssert.equal(size * sizeDtype, len(stringArray),
"string representing the array has the right size")
if _bIncludeMd5sum is True:
xsdArray.setMd5sum(
XSDataString(hashlib.md5(stringArray).hexdigest()))
return xsdArray
def testCheckParameters(self):
xsDataInput = XSDataInputMatrixInvert()
xsDataInput.setInputMatrix(XSDataArray())
edPluginExecMatrixInvert = self.createPlugin()
edPluginExecMatrixInvert.setDataInput(xsDataInput)
edPluginExecMatrixInvert.checkParameters()