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_ == '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 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_ == '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 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_ == '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 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 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()
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 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_)
