def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlSaxsAnalysisModelingv1_0.process")
if (self.autoRg is None) or (self.gnomFile is None):
self.edPluginAnalysis = self.loadPlugin(self.cpAnalysis)
self.edPluginAnalysis.dataInput = XSDataInputSaxsAnalysis(
scatterCurve=self.dataInput.scatterCurve,
autoRg=self.dataInput.autoRg,
gnomFile=self.dataInput.gnomFile,
graphFormat=self.dataInput.graphFormat)
self.edPluginAnalysis.connectSUCCESS(self.doSuccessAnalysis)
self.edPluginAnalysis.connectFAILURE(self.doFailureAnalysis)
self.edPluginAnalysis.executeSynchronous()
strLog = ""
if self.isFailure():
return
else:
strLog = """Rg = %.2f +/- %2f
I(0) = %.2e +/- %.2e
Points %i to %i
Quality: %4.2f%% Aggregated: %s""" % (
self.autoRg.rg.value, self.autoRg.rgStdev.value,
self.autoRg.i0.value, self.autoRg.i0Stdev.value,
self.autoRg.firstPointUsed.value,
self.autoRg.lastPointUsed.value, self.autoRg.quality.value *
100., self.autoRg.isagregated.value)
if self.gnom is None:
strLog += """
datGnom failed"""
self.addExecutiveSummaryLine(strLog)
self.setFailure()
return
else:
strLog += """
Dmax = %12.2f Total = %12.2f
Guinier = %12.2f Gnom = %12.2f""" % (
self.gnom.dmax.value, self.gnom.total.value,
self.gnom.rgGuinier.value, self.gnom.rgGnom.value)
if self.xVolume is None:
strLog += """
datPorod failed"""
else:
strLog += """
Volume = %12.2f""" % (self.xVolume.value)
self.addExecutiveSummaryLine(strLog)
self.edPluginModeling = self.loadPlugin(self.cpModeling)
self.edPluginModeling.dataInput = XSDataInputSaxsModeling(
gnomFile=self.gnom.gnomFile,
graphFormat=self.dataInput.graphFormat)
self.edPluginModeling.connectSUCCESS(self.doSuccessModeling)
self.edPluginModeling.connectFAILURE(self.doFailureModeling)
self.edPluginModeling.executeSynchronous()
def processMerges(self, run):
# run analysis of merges
for merge in run.merge_curves:
if os.path.exists(merge):
xsdSubtractedCurve = XSDataFile(XSDataString(merge))
self.__edPluginSaxsAnalysis = self.loadPlugin(
self.__strControlledPluginSaxsAnalysis)
self.__edPluginSaxsAnalysis.dataInput = XSDataInputSaxsAnalysis(
scatterCurve=xsdSubtractedCurve,
autoRg=run.merge_Rg[merge],
graphFormat=XSDataString("png"))
self.__edPluginSaxsAnalysis.connectSUCCESS(
self.doSuccessSaxsAnalysis)
self.__edPluginSaxsAnalysis.connectFAILURE(
self.doFailureSaxsAnalysis)
self.__edPluginSaxsAnalysis.executeSynchronous()
xsdBuffer = XSDataFile(XSDataString(run.buffer))
xsdStartFrame = XSDataString(run.merge_framesDIC[merge][0])
xsdEndFrame = XSDataString(run.merge_framesDIC[merge][-1])
self.__edPluginISPyBAnalysis = self.loadPlugin(
self.__strControlledPluginISPyBAnalysis)
try:
inputBioSaxsISPyB = XSDataInputBioSaxsISPyBv1_0(
sample=self.dataOutputBioSaxsISPyB_HPLC.getSample(),
autoRg=run.merge_analysis[merge].autoRg,
gnom=run.merge_analysis[merge].gnom,
volume=run.merge_analysis[merge].volume,
bestBuffer=xsdBuffer,
scatterPlot=run.merge_analysis[merge].scatterPlot,
guinierPlot=run.merge_analysis[merge].guinierPlot,
kratkyPlot=run.merge_analysis[merge].kratkyPlot,
densityPlot=run.merge_analysis[merge].densityPlot)
xsdISPyBin = XSDataInputBioSaxsISPyBHPLCv1_0(
experimentId=self.dataOutputBioSaxsISPyB_HPLC.
getExperimentId(),
startFrame=xsdStartFrame,
endFrame=xsdEndFrame,
dataInputBioSaxs=inputBioSaxsISPyB)
self.__edPluginISPyBAnalysis.dataInput = xsdISPyBin
self.__edPluginISPyBAnalysis.connectSUCCESS(
self.doSuccessISPyBAnalysis)
self.__edPluginISPyBAnalysis.connectFAILURE(
self.doFailureISPyBAnalysis)
self.__edPluginISPyBAnalysis.executeSynchronous()
except Exception as error:
traceback.print_stack()
self.ERROR(
"EDPluginBioSaxsFlushHPLCv1_3 calling to EDPluginHPLCPrimayDataISPyBv1_0: %s"
% error)
# There were some recurring issues with dammin slowing down slavia, therefore I commented this out for the time being
# Martha, 11.7.2014
# mergeNumber = 1
# for merge in run.merge_curves:
# try:
# xsdSubtractedCurve = XSDataFile(XSDataString(merge))
# xsdGnomFile = XSDataFile(XSDataString(run.merge_analysis[merge].gnom.gnomFile.path.value))
# destination = XSDataFile(XSDataString(os.path.join(os.path.dirname(os.path.dirname(merge)), "ednaSAS")))
# self.__edPluginSaxsToSAS = self.loadPlugin(self.__strControlledPluginSaxsModeling)
# print "Changing measurentID by runMerge"
# #In order to keep dammin models in different folder a measurementId should be given
# self.__edPluginISPyBAnalysis.xsDataResult.dataInputBioSaxs.sample.measurementID.value = mergeNumber
# print "------------> MeasurementId changed " + str(self.__edPluginISPyBAnalysis.xsDataResult.dataInputBioSaxs.sample.measurementID.value)
# self.__edPluginSaxsToSAS.dataInput = XSDataInputBioSaxsToSASv1_0(
# sample=self.__edPluginISPyBAnalysis.xsDataResult.dataInputBioSaxs.sample,
# subtractedCurve=xsdSubtractedCurve,
# gnomFile=xsdGnomFile,
# destinationDirectory=destination)
# self.__edPluginSaxsToSAS.connectSUCCESS(self.doSuccessSaxsToSAS)
# self.__edPluginSaxsToSAS.connectFAILURE(self.doFailureSaxsToSAS)
# mergeNumber = mergeNumber + 1;
# self.__edPluginSaxsToSAS.executeSynchronous()
# except Exception as error:
# traceback.print_stack()
# self.ERROR("EDPluginBioSaxsFlushHPLCv1_3 calling to EDPluginBioSaxsToSASv1_1: %s" % error)
self.synchronizePlugins()
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginBioSaxsHPLCv1_0.process")
xsdIn = XSDataInputBioSaxsProcessOneFilev1_0(
rawImage=self.dataInput.rawImage,
sample=self.dataInput.sample,
experimentSetup=self.dataInput.experimentSetup,
rawImageSize=self.dataInput.rawImageSize,
normalizedImage=self.dataInput.normalizedImage,
integratedCurve=self.dataInput.integratedCurve,
runId=self.dataInput.runId,
frameId=self.dataInput.frameId)
self.__edPluginProcessOneFile = self.loadPlugin(
self.strControlledPluginProcessOneFile)
self.__edPluginProcessOneFile.dataInput = xsdIn
self.__edPluginProcessOneFile.connectSUCCESS(
self.doSuccessProcessOneFile)
self.__edPluginProcessOneFile.connectFAILURE(
self.doFailureProcessOneFile)
self.__edPluginProcessOneFile.executeSynchronous()
if self.isFailure():
return
xsdIn = XSDataInputDatcmp(inputCurve=[
XSDataFile(XSDataString(self.hplc_run.first_curve)),
XSDataFile(XSDataString(self.curve))
])
self.__edPluginDatCmp = self.loadPlugin(self.strControlledPluginDatCmp)
self.__edPluginDatCmp.dataInput = xsdIn
self.__edPluginDatCmp.connectSUCCESS(self.doSuccessDatCmp)
self.__edPluginDatCmp.connectFAILURE(self.doFailureDatCmp)
self.__edPluginDatCmp.executeSynchronous()
if self.isFailure() or self.isBuffer:
return
if self.dataInput.subtractedCurve is not None:
subtracted = self.dataInput.subtractedCurve.path.value
else:
subtracted = os.path.splitext(self.curve)[0] + "_sub.dat"
xsdIn = XSDataInputDatop(inputCurve=[
XSDataFile(XSDataString(self.curve)),
XSDataFile(XSDataString(self.hplc_run.first_curve))
],
outputCurve=XSDataFile(
XSDataString(subtracted)),
operation=XSDataString("sub"))
self.__edPluginDatop = self.loadPlugin(self.strControlledPluginDatop)
self.__edPluginDatop.dataInput = xsdIn
self.__edPluginDatop.connectSUCCESS(self.doSuccessDatop)
self.__edPluginDatop.connectFAILURE(self.doFailureDatop)
self.__edPluginDatop.executeSynchronous()
if self.subtracted and os.path.exists(self.subtracted):
xsdIn = XSDataInputSaxsAnalysis(
scatterCurve=XSDataFile(XSDataString(self.subtracted)),
gnomFile=XSDataFile(
XSDataString(
os.path.splitext(self.subtracted)[0] + ".out")))
self.__edPluginSaxsAnalysis = self.loadPlugin(
self.strControlledPluginSaxsAnalysis)
self.__edPluginSaxsAnalysis.dataInput = xsdIn
self.__edPluginSaxsAnalysis.connectSUCCESS(
self.doSuccessSaxsAnalysis)
self.__edPluginSaxsAnalysis.connectFAILURE(
self.doFailureSaxsAnalysis)
self.__edPluginSaxsAnalysis.executeSynchronous()
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginBioSaxsSmartMergev1_7.process")
xsdwf = XSDataInputWaitMultiFile(
timeOut=XSDataTime(30),
expectedSize=XSDataInteger(self.minimumCurveFileSize),
expectedFile=[XSDataFile(i.path) for i in self.lstInput])
self.__edPluginExecWaitFile.setDataInput(xsdwf)
self.__edPluginExecWaitFile.connectFAILURE(self.doFailureExecWait)
self.__edPluginExecWaitFile.connectSUCCESS(self.doSuccessExecWait)
self.__edPluginExecWaitFile.executeSynchronous()
if self.isFailure():
return
if len(self.lstInput) == 1:
inp = self.lstInput[0].path.value
dst = self.dataInput.mergedCurve.path.value
if not os.path.isdir(os.path.dirname(dst)):
self.error("Output directory for %s does not exist" % dst)
os.makedirs(os.path.dirname(dst))
if not os.path.exists(inp):
self.warning("Input %s does not (yet?) exist" % inp)
time.sleep(1.0)
shutil.copyfile(inp, dst)
self.addExecutiveSummaryLine(
"Got only one frame ... nothing to merge !!!")
else:
self.lstMerged = []
if (self.absoluteFidelity is not None) or (self.relativeFidelity
is not None):
if self.absoluteFidelity is not None:
for idx, oneFile in enumerate(self.lstInput[1:]):
self.DEBUG("Calculating similarity of 0 and %s" % idx)
self.datcmp(self.lstInput[0], oneFile)
# edPluginExecAbsoluteFidelity = self.loadPlugin(self.__strControlledPluginDatcmp)
# xsd = XSDataInputDatcmp(inputCurve=[self.lstInput[0], oneFile])
# edPluginExecAbsoluteFidelity.setDataInput(xsd)
# edPluginExecAbsoluteFidelity.connectFAILURE(self.doFailureExecDatcmp)
# edPluginExecAbsoluteFidelity.connectSUCCESS(self.doSuccessExecDatcmp)
# edPluginExecAbsoluteFidelity.execute()
if (self.relativeFidelity is not None):
if (self.absoluteFidelity is None):
self.DEBUG("Calculating similarity of 0 and 1")
self.datcmp(self.lstInput[0], self.lstInput[1])
# edPluginExecAbsoluteFidelity = self.loadPlugin(self.__strControlledPluginDatcmp)
# xsd = XSDataInputDatcmp(inputCurve=[self.lstInput[0], self.lstInput[1] ])
# edPluginExecAbsoluteFidelity.setDataInput(xsd)
# edPluginExecAbsoluteFidelity.connectFAILURE(self.doFailureExecDatcmp)
# edPluginExecAbsoluteFidelity.connectSUCCESS(self.doSuccessExecDatcmp)
# edPluginExecAbsoluteFidelity.execute()
if (len(self.lstInput) > 2):
for idx, oneFile in enumerate(self.lstInput[2:]):
self.DEBUG("Calculating similarity of %s and %s" %
(idx, idx + 1))
self.datcmp(self.lstInput[idx + 1], oneFile)
# edPluginExecRelativeFidelity = self.loadPlugin(self.__strControlledPluginDatcmp)
# xsd = XSDataInputDatcmp(inputCurve=[self.lstInput[idx + 1], oneFile])
# edPluginExecRelativeFidelity.setDataInput(xsd)
# edPluginExecRelativeFidelity.connectFAILURE(self.doFailureExecDatcmp)
# edPluginExecRelativeFidelity.connectSUCCESS(self.doSuccessExecDatcmp)
# edPluginExecRelativeFidelity.execute()
self.synchronizePlugins()
for idx, oneFile in enumerate(self.lstInput):
if idx == 0:
self.lstMerged.append(oneFile)
elif (self.absoluteFidelity
is not None) and (self.relativeFidelity is not None):
if (idx - 1, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (idx - 1, idx) +
"\n".join([
"%s: %s" %
(key, self.dictSimilarities[key])
for key in self.dictSimilarities
]))
self.resynchronize()
if (0, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (0, idx) +
"\n".join([
"%s: %s" %
(key, self.dictSimilarities[key])
for key in self.dictSimilarities
]))
self.resynchronize()
if (self.dictSimilarities[(0, idx)] >=
self.absoluteFidelity) and (self.dictSimilarities[
(idx - 1, idx)] >= self.relativeFidelity):
self.lstMerged.append(oneFile)
elif (self.absoluteFidelity is not None):
if (0, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (0, idx) +
"\n".join([
"%s: %s" %
(key, self.dictSimilarities[key])
for key in self.dictSimilarities
]))
self.resynchronize()
if (self.dictSimilarities[(0, idx)] >=
self.absoluteFidelity):
self.lstMerged.append(oneFile)
elif (self.relativeFidelity is not None):
if (idx - 1, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (idx - 1, idx) +
"\n".join([
"%s: %s" %
(key, self.dictSimilarities[key])
for key in self.dictSimilarities
]))
self.resynchronize()
if (self.dictSimilarities[(idx - 1, idx)] >=
self.relativeFidelity):
self.lstMerged.append(oneFile)
else:
self.lstMerged.append(oneFile)
self.lstMerged.sort(cmp)
if len(self.lstMerged) != len(self.lstInput):
self.strRadiationDamage = "Radiation damage detected, merged %i curves" % len(
self.lstMerged)
self.WARNING(self.strRadiationDamage)
self.addExecutiveSummaryLine("WARNING: " +
self.strRadiationDamage)
self.addExecutiveSummaryLine("Merging files: " + " ".join(
[os.path.basename(i.path.value) for i in self.lstMerged]))
if len(self.lstMerged) == 1:
self.rewriteHeader(self.lstMerged[0].path.value,
self.strMergedFile)
else:
self.__edPluginExecDataver = self.loadPlugin(
self.__strControlledPluginDataver)
xsd = XSDataInputDataver(inputCurve=self.lstMerged)
# outputCurve=self.dataInput.mergedCurve,
self.__edPluginExecDataver.setDataInput(xsd)
self.__edPluginExecDataver.connectSUCCESS(
self.doSuccessExecDataver)
self.__edPluginExecDataver.connectFAILURE(
self.doFailureExecDataver)
self.__edPluginExecDataver.executeSynchronous()
if (self.fConcentration == 0) and (self.strSubFile is not None):
if (self.__class__.lastBuffer
is not None) and (self.__class__.lastSample is not None):
self.__edPluginExecAutoSub = self.loadPlugin(
self.__strControlledPluginAutoSub)
base = "_".join(
os.path.basename(
self.__class__.lastSample.path.value).split("_")[:-1])
suff = os.path.basename(self.strSubFile).split("_")[-1]
sub = os.path.join(os.path.dirname(self.strSubFile),
base + "_" + suff)
self.xsdSubtractedCurve = XSDataFile(XSDataString(sub))
#self.curves.append(xsdSubtractedCurve)
self.__edPluginExecAutoSub.dataInput = XSDataInputAutoSub(
sampleCurve=self.__class__.lastSample,
buffers=[
self.__class__.lastBuffer, self.dataInput.mergedCurve
],
subtractedCurve=self.xsdSubtractedCurve)
self.__edPluginExecAutoSub.connectSUCCESS(
self.doSuccessExecAutoSub)
self.__edPluginExecAutoSub.connectFAILURE(
self.doFailureExecAutoSub)
self.__edPluginExecAutoSub.executeSynchronous()
if self.isFailure():
return
self.__edPluginSaxsAnalysis = self.loadPlugin(
self.__strControlledPluginSaxsAnalysis)
self.__edPluginSaxsAnalysis.dataInput = XSDataInputSaxsAnalysis(
scatterCurve=self.xsdSubtractedCurve,
autoRg=self.autoRg,
graphFormat=XSDataString("png"))
self.__edPluginSaxsAnalysis.connectSUCCESS(
self.doSuccessSaxsAnalysis)
self.__edPluginSaxsAnalysis.connectFAILURE(
self.doFailureSaxsAnalysis)
self.__edPluginSaxsAnalysis.executeSynchronous()
self.__class__.lastBuffer = self.dataInput.mergedCurve
#self.__class__.lastSample = None #Information neededfor transfer to ISPyB
self.forgetLastSample = True
else:
self.__class__.lastSample = self.dataInput.mergedCurve
if self.dataInput.sample and self.dataInput.sample.login and self.dataInput.sample.passwd and self.dataInput.sample.measurementID:
self.addExecutiveSummaryLine("Registering to ISPyB")
self.lstDiscarded = list(set(self.lstInput) - set(self.lstMerged))
self.__class__.dictFrames[self.dataInput.mergedCurve] = {
'averaged': self.lstMerged,
'discarded': self.lstDiscarded
}
self.__edPluginSaxsISPyB = self.loadPlugin(
self.__strControlledPluginSaxsISPyB)
if len(self.lstInput) > 1:
frameAverage = XSDataInteger(len(self.lstInput))
frameMerged = XSDataInteger(len(self.lstMerged))
else:
frameMerged = frameAverage = XSDataInteger(1)
self.curves = [XSDataFile(i.path) for i in self.lstInput]
self.discardedCurves = [
XSDataFile(i.path) for i in self.lstDiscarded
]
self.mergedCurves = [XSDataFile(i.path) for i in self.lstMerged]
averageFilePath = None
if self.strMergedFile is not None:
averageFilePath = XSDataFile(XSDataString(self.strMergedFile))
self.sampleFrames = self.getAveragedFrameByFilename(
self.__class__.lastSample)
lastSample = None
if self.__class__.lastSample is not None:
lastSample = self.__class__.lastSample
subtractedCurve = None
if self.xsdSubtractedCurve is not None:
subtractedCurve = self.xsdSubtractedCurve
else:
subtractedCurve = None
xsdin = XSDataInputBioSaxsISPyBv1_0(
sample=self.dataInput.sample,
autoRg=self.autoRg,
gnom=self.gnom,
volume=self.volume,
frameAverage=frameAverage,
frameMerged=frameMerged,
curves=self.curves,
discardedFrames=self.discardedCurves,
averagedFrames=self.mergedCurves,
averageFilePath=averageFilePath,
bufferFrames=self.bufferFrames,
sampleFrames=self.sampleFrames,
bestBuffer=self.xsBestBuffer,
averageSample=lastSample,
scatterPlot=self.xsScatterPlot,
guinierPlot=self.xsGuinierPlot,
kratkyPlot=self.xsKratkyPlot,
densityPlot=self.xsDensityPlot,
subtractedFilePath=subtractedCurve
# destination=self.dataInput.sample.ispybDestination #duplicate, already in sample
)
self.__edPluginSaxsISPyB.dataInput = xsdin
self.__edPluginSaxsISPyB.connectSUCCESS(self.doSuccessISPyB)
self.__edPluginSaxsISPyB.connectFAILURE(self.doFailureISPyB)
self.__edPluginSaxsISPyB.execute()
# transfer analysis data to correct location on nice
if self.gnom is not None:
self.outdir = os.path.join(
os.path.dirname(os.path.dirname(self.lstStrInput[0])),
"ednaAnalysis")
basename = os.path.basename(
os.path.splitext(self.gnom.gnomFile.path.value)[0])
self.outdir = os.path.join(self.outdir, basename)
if not os.path.isdir(self.outdir):
os.makedirs(self.outdir)
#self.outFile = os.path.join(outdir, "NoResults.html")
workingdir = os.path.dirname(self.gnom.gnomFile.path.value)
self.pluginRsync = self.loadPlugin(self.cpRsync)
self.pluginRsync.dataInput = XSDataInputRsync(
source=XSDataFile(XSDataString(workingdir)),
destination=XSDataFile(XSDataString(self.outdir)),
options=XSDataString("-avx"))
self.pluginRsync.connectSUCCESS(self.doSuccessExecRsync)
self.pluginRsync.connectFAILURE(self.doFailureExecRsync)
self.pluginRsync.executeSynchronous()
if self.forgetLastSample:
#Also redefine dictionary to contain the buffer just processed?
self.__class__.lastSample = None
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginBioSaxsSmartMergev1_5.process")
xsdwf = XSDataInputWaitMultiFile(timeOut=XSDataTime(30),
expectedSize=XSDataInteger(10000),
expectedFile=[XSDataFile(i.path) for i in self.lstInput])
self.__edPluginExecWaitFile.setDataInput(xsdwf)
self.__edPluginExecWaitFile.connectFAILURE(self.doFailureExecWait)
self.__edPluginExecWaitFile.connectSUCCESS(self.doSuccessExecWait)
self.__edPluginExecWaitFile.executeSynchronous()
if self.isFailure():
return
if len(self.lstInput) == 1:
inp = self.lstInput[0].path.value
dst = self.dataInput.mergedCurve.path.value
if not os.path.isdir(os.path.dirname(dst)):
self.error("Output directory for %s does not exist" % dst)
os.makedirs(os.path.dirname(dst))
if not os.path.exists(inp):
self.warning("Input %s does not (yet?) exist" % inp)
time.sleep(1.0)
shutil.copyfile(inp, dst)
self.lstSummary.append("Got only one frame ... nothing to merge !!!")
else:
self.lstMerged = []
if (self.absoluteFidelity is not None) or (self.relativeFidelity is not None):
if self.absoluteFidelity is not None :
for idx, oneFile in enumerate(self.lstInput[1:]):
self.DEBUG("Calculating similarity of 0 and %s" % idx)
edPluginExecAbsoluteFidelity = self.loadPlugin(self.__strControlledPluginDatcmp)
xsd = XSDataInputDatcmp(inputCurve=[self.lstInput[0], oneFile])
edPluginExecAbsoluteFidelity.setDataInput(xsd)
edPluginExecAbsoluteFidelity.connectFAILURE(self.doFailureExecDatcmp)
edPluginExecAbsoluteFidelity.connectSUCCESS(self.doSuccessExecDatcmp)
edPluginExecAbsoluteFidelity.execute()
if (self.relativeFidelity is not None):
if (self.absoluteFidelity is None):
self.DEBUG("Calculating similarity of 0 and 1")
edPluginExecAbsoluteFidelity = self.loadPlugin(self.__strControlledPluginDatcmp)
xsd = XSDataInputDatcmp(inputCurve=[self.lstInput[0], self.lstInput[1] ])
edPluginExecAbsoluteFidelity.setDataInput(xsd)
edPluginExecAbsoluteFidelity.connectFAILURE(self.doFailureExecDatcmp)
edPluginExecAbsoluteFidelity.connectSUCCESS(self.doSuccessExecDatcmp)
edPluginExecAbsoluteFidelity.execute()
if (len(self.lstInput) > 2):
for idx, oneFile in enumerate(self.lstInput[2:]):
self.DEBUG("Calculating similarity of %s and %s" % (idx, idx + 1))
edPluginExecRelativeFidelity = self.loadPlugin(self.__strControlledPluginDatcmp)
xsd = XSDataInputDatcmp(inputCurve=[self.lstInput[idx + 1], oneFile])
edPluginExecRelativeFidelity.setDataInput(xsd)
edPluginExecRelativeFidelity.connectFAILURE(self.doFailureExecDatcmp)
edPluginExecRelativeFidelity.connectSUCCESS(self.doSuccessExecDatcmp)
edPluginExecRelativeFidelity.execute()
self.synchronizePlugins()
for idx, oneFile in enumerate(self.lstInput):
if idx == 0:
self.lstMerged.append(oneFile)
elif (self.absoluteFidelity is not None) and (self.relativeFidelity is not None):
if (idx - 1, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (idx - 1, idx) + "\n".join([ "%s: %s" % (key, self.dictSimilarities[key]) for key in self.dictSimilarities]))
self.resynchronize()
if (0, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (0, idx) + "\n".join([ "%s: %s" % (key, self.dictSimilarities[key]) for key in self.dictSimilarities]))
self.resynchronize()
if (self.dictSimilarities[(0, idx)] >= self.absoluteFidelity) and (self.dictSimilarities[(idx - 1, idx)] >= self.relativeFidelity):
self.lstMerged.append(oneFile)
else:
break
elif (self.absoluteFidelity is not None) :
if (0, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (0, idx) + "\n".join([ "%s: %s" % (key, self.dictSimilarities[key]) for key in self.dictSimilarities]))
self.resynchronize()
if (self.dictSimilarities[(0, idx)] >= self.absoluteFidelity):
self.lstMerged.append(oneFile)
else:
break
elif (self.relativeFidelity is not None) :
if (idx - 1, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (idx - 1, idx) + "\n".join([ "%s: %s" % (key, self.dictSimilarities[key]) for key in self.dictSimilarities]))
self.resynchronize()
if (self.dictSimilarities[(idx - 1, idx)] >= self.relativeFidelity):
self.lstMerged.append(oneFile)
else:
break
else:
self.lstMerged.append(oneFile)
self.lstMerged.sort(cmp)
if len(self.lstMerged) != len(self.lstInput):
self.strRadiationDamage = "Radiation damage detected, merged %i curves" % len(self.lstMerged)
self.WARNING(self.strRadiationDamage)
self.lstSummary.append("WARNING: " + self.strRadiationDamage)
self.lstSummary.append("Merging files: " + " ".join([os.path.basename(i.path.value) for i in self.lstMerged]))
if len(self.lstMerged) == 1:
self.rewriteHeader(self.lstMerged[0].path.value, self.strMergedFile)
else:
self.__edPluginExecDataver = self.loadPlugin(self.__strControlledPluginDataver)
xsd = XSDataInputDataver(inputCurve=self.lstMerged)
# outputCurve=self.dataInput.mergedCurve,
self.__edPluginExecDataver.setDataInput(xsd)
self.__edPluginExecDataver.connectSUCCESS(self.doSuccessExecDataver)
self.__edPluginExecDataver.connectFAILURE(self.doFailureExecDataver)
self.__edPluginExecDataver.executeSynchronous()
if (self.fConcentration == 0) and (self.strSubFile is not None):
if (self.__class__.lastBuffer is not None) and (self.__class__.lastSample is not None):
self.__edPluginExecAutoSub = self.loadPlugin(self.__strControlledPluginAutoSub)
base = "_".join(os.path.basename(self.__class__.lastSample.path.value).split("_")[:-1])
suff = os.path.basename(self.strSubFile).split("_")[-1]
sub = os.path.join(os.path.dirname(self.strSubFile), base + "_" + suff)
xsdSubtractedCurve = XSDataFile(XSDataString(sub))
self.curves.append(xsdSubtractedCurve)
self.__edPluginExecAutoSub.dataInput = XSDataInputAutoSub(sampleCurve=self.__class__.lastSample,
buffers=[self.__class__.lastBuffer, self.dataInput.mergedCurve],
subtractedCurve=xsdSubtractedCurve)
self.__edPluginExecAutoSub.connectSUCCESS(self.doSuccessExecAutoSub)
self.__edPluginExecAutoSub.connectFAILURE(self.doFailureExecAutoSub)
self.__edPluginExecAutoSub.executeSynchronous()
if self.isFailure():
return
self.__edPluginSaxsAnalysis = self.loadPlugin(self.__strControlledPluginSaxsAnalysis)
self.__edPluginSaxsAnalysis.dataInput = XSDataInputSaxsAnalysis(scatterCurve=xsdSubtractedCurve,
autoRg=self.autoRg)
self.__edPluginSaxsAnalysis.connectSUCCESS(self.doSuccessSaxsAnalysis)
self.__edPluginSaxsAnalysis.connectFAILURE(self.doFailureSaxsAnalysis)
self.__edPluginSaxsAnalysis.executeSynchronous()
self.__class__.lastBuffer = self.dataInput.mergedCurve
self.__class__.lastSample = None
else:
self.__class__.lastSample = self.dataInput.mergedCurve
if self.dataInput.sample.login and self.dataInput.sample.passwd and self.dataInput.sample.measurementID:
self.lstSummary.append("Registering to ISPyB")
self.__edPluginSaxsISPyB = self.loadPlugin(self.__strControlledPluginSaxsISPyB)
if len(self.lstInput) > 1:
frameAverage = XSDataInteger(len(self.lstInput))
frameMerged = XSDataInteger(len(self.lstMerged))
else:
frameMerged = frameAverage = XSDataInteger(1)
self.curves = [XSDataFile(i.path) for i in self.lstInput]
if self.strMergedFile is not None:
self.curves.append(XSDataFile(XSDataString(self.strMergedFile)))
xsdin = XSDataInputBioSaxsISPyBv1_0(sample=self.dataInput.sample,
autoRg=self.autoRg,
gnom=self.gnom,
volume=self.volume,
frameAverage=frameAverage,
frameMerged=frameMerged,
curves=self.curves,
bestBuffer=self.xsBestBuffer
# destination=self.dataInput.sample.ispybDestination #duplicate, already in sample
)
self.__edPluginSaxsISPyB.dataInput = xsdin
self.__edPluginSaxsISPyB.connectSUCCESS(self.doSuccessISPyB)
self.__edPluginSaxsISPyB.connectFAILURE(self.doFailureISPyB)
self.__edPluginSaxsISPyB.execute()
