def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecProcessScriptAutoRgv1_0.postProcess")
# Create some output data
# 2.83326 0.011646 2.04258e+07 18565.3 47 81 0.783626 1 bioSaxsMerged.dat
strOutput = self.readProcessLogFile()
xsDataResult = XSDataResultAutoRg()
listXSDOut = []
for line in strOutput.split(os.linesep):
words = line.split(None, 8)
if len(words) < 8:
break
try:
xsData = XSDataAutoRg()
xsData.filename = XSDataFile(XSDataString(words[-1]))
xsData.rg = XSDataLength(float(words[0]))
xsData.rgStdev = XSDataLength(float(words[1]))
xsData.i0 = XSDataDouble(float(words[2]))
xsData.i0Stdev = XSDataDouble(float(words[3]))
xsData.firstPointUsed = XSDataInteger(int(words[4]))
xsData.lastPointUsed = XSDataInteger(int(words[5]))
xsData.quality = XSDataDouble(float(words[6]))
xsData.isagregated = XSDataBoolean(bool(int(words[7])))
except Exception:
strError = "Error in parsing output:" + line
self.error(strError)
self.setFailure()
listXSDOut.append(xsData)
xsDataResult.autoRgOut = listXSDOut
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecProcessScriptAutoRgv1_0.postProcess")
# Create some output data
# 2.83326 0.011646 2.04258e+07 18565.3 47 81 0.783626 1 bioSaxsMerged.dat
strOutput = self.readProcessLogFile()
xsDataResult = XSDataResultAutoRg()
listXSDOut = []
for line in strOutput.split(os.linesep):
words = line.split(None, 8)
if len(words) < 8:
break
try:
xsData = XSDataAutoRg()
xsData.filename = XSDataFile(XSDataString(words[-1]))
xsData.rg = XSDataLength(float(words[0]))
xsData.rgStdev = XSDataLength(float(words[1]))
xsData.i0 = XSDataDouble(float(words[2]))
xsData.i0Stdev = XSDataDouble(float(words[3]))
xsData.firstPointUsed = XSDataInteger(int(words[4]))
xsData.lastPointUsed = XSDataInteger(int(words[5]))
xsData.quality = XSDataDouble(float(words[6]))
xsData.isagregated = XSDataBoolean(bool(int(words[7])))
except Exception:
strError = "Error in parsing output:" + line
self.error(strError)
self.setFailure()
listXSDOut.append(xsData)
xsDataResult.autoRgOut = listXSDOut
self.setDataOutput(xsDataResult)
def testExecute(self):
"""
"""
self.run()
plugin = self.getPlugin()
################################################################################
# Compare XSDataResults
################################################################################
strExpectedOutput = self.readAndParseFile (self.getReferenceDataOutputFile())
EDVerbose.DEBUG("Checking obtained result...")
xsDataResultReference = XSDataResult.parseString(strExpectedOutput)
xsDataResultObtained = plugin.getDataOutput()
EDAssert.strAlmostEqual(xsDataResultReference.marshal(), xsDataResultObtained.marshal(), "XSDataResult output are the same", _strExcluded="bioSaxs")
def process(self):
EDPluginExecProcessScript.process(self)
self.DEBUG("EDPluginExecProcessScriptAutoRgv1_0.process")
# Create some output data
# 2.83326 0.011646 2.04258e+07 18565.3 47 81 0.783626 1 bioSaxsMerged.dat
strOutput = self.readProcessLogFile()
xsDataResult = XSDataResultAutoRg()
dic_Rg = {} #key: filename, value: XSDataAutoRg
listXSDOut = []
for line in strOutput.split(os.linesep):
words = line.split(None, 8)
if len(words) < 8:
break
try:
xsData = XSDataAutoRg()
filename = words[-1]
xsData.rg = XSDataLength(float(words[0]))
xsData.rgStdev = XSDataLength(float(words[1]))
xsData.i0 = XSDataDouble(float(words[2]))
xsData.i0Stdev = XSDataDouble(float(words[3]))
xsData.firstPointUsed = XSDataInteger(int(words[4]))
xsData.lastPointUsed = XSDataInteger(int(words[5]))
xsData.quality = XSDataDouble(float(words[6]))
xsData.isagregated = XSDataDouble(float(words[7]))
except Exception:
strError = "Error in parsing output:" + line
self.error(strError)
self.setFailure()
else:
xsData.filename = XSDataFile(XSDataString(filename))
dic_Rg[filename] = xsData
# listXSDOut.append(xsData)
if self.isFailure():
# Change failure output for ATSAS version >= 2.5 to micmic old version
strErrOutput = self.readProcessErrorLogFile()
for line in strErrOutput.split(os.linesep):
if 'Not enough valid data' in line:
words = line.split()
try:
xsData = XSDataAutoRg()
filename = words[-1].strip("'.")
xsData.rg = XSDataLength(0.0)
xsData.rgStdev = XSDataLength(0.0)
xsData.i0 = XSDataDouble(0.0)
xsData.i0Stdev = XSDataDouble(0.0)
xsData.firstPointUsed = XSDataInteger(0)
xsData.lastPointUsed = XSDataInteger(0)
xsData.quality = XSDataDouble(0.0)
xsData.isagregated = XSDataDouble(0.0)
except Exception:
strError = "Error in parsing output:" + line
self.error(strError)
self.setFailure()
else:
xsData.filename = XSDataFile(XSDataString(filename))
dic_Rg[filename] = xsData
if self.isFailure() and dic_Rg:
# we have some data ... unset the failure flag
self.setFailure(False)
xsData_zero = XSDataAutoRg(isagregated=XSDataDouble(1.0),
quality=XSDataDouble(0.0),
lastPointUsed=XSDataInteger(0),
firstPointUsed=XSDataInteger(0),
i0Stdev=XSDataDouble(0.0),
i0=XSDataDouble(0.0),
rgStdev=XSDataLength(0.0),
rg=XSDataLength(0.0))
for filename in self.inputCurve:
if filename in dic_Rg:
listXSDOut.append(dic_Rg[filename])
else:
xsData_zero.filename = XSDataFile(XSDataString(filename))
listXSDOut.append(xsData_zero)
xsDataResult.autoRgOut = listXSDOut
self.setDataOutput(xsDataResult)
def process(self):
EDPluginExecProcessScript.process(self)
self.DEBUG("EDPluginExecProcessScriptAutoRgv1_0.process")
# Create some output data
# 2.83326 0.011646 2.04258e+07 18565.3 47 81 0.783626 1 bioSaxsMerged.dat
strOutput = self.readProcessLogFile()
xsDataResult = XSDataResultAutoRg()
dic_Rg = {} #key: filename, value: XSDataAutoRg
listXSDOut = []
for line in strOutput.split(os.linesep):
words = line.split(None, 8)
if len(words) < 8:
break
try:
xsData = XSDataAutoRg()
filename = words[-1]
xsData.rg = XSDataLength(float(words[0]))
xsData.rgStdev = XSDataLength(float(words[1]))
xsData.i0 = XSDataDouble(float(words[2]))
xsData.i0Stdev = XSDataDouble(float(words[3]))
xsData.firstPointUsed = XSDataInteger(int(words[4]))
xsData.lastPointUsed = XSDataInteger(int(words[5]))
xsData.quality = XSDataDouble(float(words[6]))
xsData.isagregated = XSDataDouble(float(words[7]))
except Exception:
strError = "Error in parsing output:" + line
self.error(strError)
self.setFailure()
else:
xsData.filename = XSDataFile(XSDataString(filename))
dic_Rg[filename] = xsData
# listXSDOut.append(xsData)
if self.isFailure():
# Change failure output for ATSAS version >= 2.5 to micmic old version
strErrOutput = self.readProcessErrorLogFile()
for line in strErrOutput.split(os.linesep):
if 'Not enough valid data' in line:
words = line.split()
try:
xsData = XSDataAutoRg()
filename = words[-1].strip("'.")
xsData.rg = XSDataLength(0.0)
xsData.rgStdev = XSDataLength(0.0)
xsData.i0 = XSDataDouble(0.0)
xsData.i0Stdev = XSDataDouble(0.0)
xsData.firstPointUsed = XSDataInteger(0)
xsData.lastPointUsed = XSDataInteger(0)
xsData.quality = XSDataDouble(0.0)
xsData.isagregated = XSDataDouble(0.0)
except Exception:
strError = "Error in parsing output:" + line
self.error(strError)
self.setFailure()
else:
xsData.filename = XSDataFile(XSDataString(filename))
dic_Rg[filename] = xsData
if self.isFailure() and dic_Rg:
# we have some data ... unset the failure flag
self.setFailure(False)
xsData_zero = XSDataAutoRg(isagregated=XSDataDouble(1.0),
quality=XSDataDouble(0.0),
lastPointUsed=XSDataInteger(0),
firstPointUsed=XSDataInteger(0),
i0Stdev=XSDataDouble(0.0),
i0=XSDataDouble(0.0),
rgStdev=XSDataLength(0.0),
rg=XSDataLength(0.0))
for filename in self.inputCurve:
if filename in dic_Rg:
listXSDOut.append(dic_Rg[filename])
else:
xsData_zero.filename = XSDataFile(XSDataString(filename))
listXSDOut.append(xsData_zero)
xsDataResult.autoRgOut = listXSDOut
self.setDataOutput(xsDataResult)
