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 doFailureExecAutoRg(self, _edPlugin=None):
self.DEBUG("EDPluginAutoSubv1_1.doFailureExecAutoRg")
self.retrieveFailureMessages(_edPlugin, "EDPluginAutoSubv1_1.doFailureExecAutoRg")
self.lstProcessLog.append("Failure in AutoRg")
if len(_edPlugin.dataInput.inputCurve) == 2:
# we were comparing 2 buffers but were analyzed by AutoRg
for fn in self.buffers:
self.dictRg[fn] = (0, numpy.loadtxt(fn, unpack=True)[1].sum())
elif os.path.exists(self.subtractedCurve):
#we don't want to fail the subtraction plugin because the result has no Rg - default to 0
res = XSDataAutoRg()
res.rg = XSDataLength(0.0)
res.rgStdev = XSDataLength(0.0)
res.i0 = XSDataDouble(0.0)
res.i0Stdev = XSDataDouble(0.0)
res.firstPointUsed = XSDataInteger(0)
res.lastPointUsed = XSDataInteger(0)
res.quality = XSDataDouble(0.0)
res.isagregated = XSDataDouble(bool(0))
res.filename = XSDataFile(XSDataString(self.subtractedCurve))
self.xsDataResult.autoRg = res
else:
self.setFailure()
def doFailureExecAutoRg(self, _edPlugin=None):
self.DEBUG("EDPluginAutoSubv1_0.doFailureExecAutoRg")
self.retrieveFailureMessages(
_edPlugin, "EDPluginAutoSubv1_0.doFailureExecAutoRg")
self.lstProcessLog.append("Failure in AutoRg")
if len(_edPlugin.dataInput.inputCurve) == 2:
# we were comparing 2 buffers but were analyzed by AutoRg
for fn in self.buffers:
self.dictRg[fn] = (0, numpy.loadtxt(fn, unpack=True)[1].sum())
elif os.path.exists(self.subtractedCurve):
#we don't want to fail the subtraction plugin because the result has no Rg - default to 0
res = XSDataAutoRg()
res.rg = XSDataLength(0.0)
res.rgStdev = XSDataLength(0.0)
res.i0 = XSDataDouble(0.0)
res.i0Stdev = XSDataDouble(0.0)
res.firstPointUsed = XSDataInteger(0)
res.lastPointUsed = XSDataInteger(0)
res.quality = XSDataDouble(0.0)
res.isagregated = XSDataBoolean(bool(0))
res.filename = XSDataFile(XSDataString(self.subtractedCurve))
self.xsDataResult.autoRg = res
else:
self.setFailure()
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)