def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginBioSaxsReduceFileSeriev1_0.process")
if self.bSkipProcess:
return
for oneRaw, oneCor, oneInt, oneCrv, oneLog in zip(self.lstRawImg, self.lstCorImg, self.lstIntImg, self.lstIntCrv, self.lstLogFil):
pluginProcessOneFile = self.loadPlugin(self.__strControlledPluginProcessOneFile)
xsd = XSDataInputBioSaxsProcessOneFilev1_0(integratedCurve=oneCrv,
integratedImage=oneInt,
normalizedImage=oneCor,
rawImageSize=self.rawImageSize,
experimentSetup=self.experimentSetup,
sample=self.sample,
rawImage=oneRaw,
logFile=oneLog)
pluginProcessOneFile.dataInput = xsd
pluginProcessOneFile.connectSUCCESS(self.doSuccessExecProcessOneFile)
pluginProcessOneFile.connectFAILURE(self.doFailureExecProcessOneFile)
pluginProcessOneFile.execute()
self.synchronizePlugins()
self.lstCurves.sort()
xsdMerge = XSDataInputBioSaxsSmartMergev1_0()
xsdMerge.absoluteFidelity = self.dataInput.absoluteFidelity
xsdMerge.relativeFidelity = self.dataInput.relativeFidelity
xsdMerge.inputCurves = [XSDataFile(XSDataString(i)) for i in self.lstCurves]
xsdMerge.mergedCurve = XSDataFile(XSDataString(self.strMergedCurve))
edPluginExecSmartMerge = self.loadPlugin(self.__strControlledPluginSmartMerge)
edPluginExecSmartMerge.dataInput = xsdMerge
edPluginExecSmartMerge.connectSUCCESS(self.doSuccessExecSmartMerge)
edPluginExecSmartMerge.connectFAILURE(self.doFailureExecSmartMerge)
edPluginExecSmartMerge.executeSynchronous()
def testCheckParameters(self):
"""
complex type XSDataInputBioSaxsSmartMergev1_0 extends XSDataInput {
inputFile: XSDataFile []
absoluteFidelity: XSDataDouble optional
relativeFidelity: XSDataDouble optional
mergedCurve: XSDataFile
"""
xsDataInput = XSDataInputBioSaxsSmartMergev1_0()
xsDataInput.inputCurves = [XSDataFile()]
xsDataInput.absoluteFidelity = XSDataDouble()
xsDataInput.relativeFidelity = XSDataDouble()
xsDataInput.mergedCurve = XSDataFile()
edPluginExecBioSaxsSmartMerge = self.createPlugin()
edPluginExecBioSaxsSmartMerge.setDataInput(xsDataInput)
edPluginExecBioSaxsSmartMerge.checkParameters()
keys = runs.keys()
keys.sort()
working_dir = "smart_merge-%s" % time.strftime("%Y%m%d-%H%M%S")
base_dir = os.getcwd()
os.makedirs(working_dir)
os.chdir(working_dir)
for run in keys:
dico = runs[run][0]
common_base = os.sep.join((dico["dirname"], "_".join(dico["basename"].split("_")[:-1]))) + "_"
outFile = common_base + "ave.dat"
subdir = os.path.join(os.path.dirname(dico["dirname"]), "ednaSub")
if not subdir:
os.makedirs(subdir)
subFile = os.path.join(subdir, os.path.basename(common_base) + "sub.dat")
xsd = XSDataInputBioSaxsSmartMergev1_0(mergedCurve=XSDataFile(XSDataString(outFile)),
subtractedCurve = XSDataFile(XSDataString(subFile)),
absoluteFidelity=rdabs,
relativeFidelity=rdrel)
if filerange:
xsd.inputCurves = [XSDataFile(XSDataString(os.sep.join((dico["dirname"], dico["basename"]))))
for dico in runs[run]
if dico["frame"] in filerange ]
else:
xsd.inputCurves = [XSDataFile(XSDataString(os.sep.join((dico["dirname"], dico["basename"]))))
for dico in runs[run]
]
reprocess.startJob(xsd)
print("All %i jobs queued after %.3fs" % (len(args), time.time() - reprocess.startTime))
reprocess.join()
if yappi: yappi.stop()
print("All %i jobs processed after %.3fs" % (len(args), time.time() - reprocess.startTime))
if (idx is not None) and (idx in filerange):
listInFiles.append(os.path.abspath(fn))
else:
listInFiles.append(os.path.abspath(fn))
if not outFile:
outFile = os.path.join(os.path.dirname(filenames[0]),
common_base + "ave.dat")
if not subFile:
subdir = os.path.join(
os.path.dirname(os.path.dirname(filenames[0])), "ednaSub")
if not subdir:
os.makedirs(subdir)
subFile = os.path.join(subdir, common_base + "sub.dat")
xsd = XSDataInputBioSaxsSmartMergev1_0(
mergedCurve=XSDataFile(XSDataString(outFile)))
xsd.subtractedCurve = XSDataFile(XSDataString(subFile))
if rdabs:
xsd.absoluteFidelity = XSDataDouble(rdabs)
if rdrel:
xsd.relativeFidelity = XSDataDouble(rdrel)
xsd.inputCurves = [XSDataFile(XSDataString(i)) for i in listInFiles]
myXML = xsd.marshal()
t1 = time.time()
pid = edna.startJob([plugin, myXML])
deltat = time.time() - t1
totaltime += deltat
listjobs.append(pid)
print("%s | Total Time:\t%.3fs /Tango %.3fs\tLast Tango:\t%.3f" %
(pid, time.time() - t0, totaltime, deltat))
else: