def createOutputStep(self):
imgSet = self._getInputParticles()
vol = Volume()
vol.setFileName(self._getExtraPath('relion_class001.mrc'))
vol.setSamplingRate(imgSet.getSamplingRate())
half1 = self._getFileName("final_half1_volume", ref3d=1)
half2 = self._getFileName("final_half2_volume", ref3d=1)
vol.setHalfMaps([half1, half2])
outImgSet = self._createSetOfParticles()
outImgSet.copyInfo(imgSet)
self._fillDataFromIter(outImgSet, self._lastIter())
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(self.inputParticles, vol)
self._defineOutputs(outputParticles=outImgSet)
self._defineTransformRelation(self.inputParticles, outImgSet)
fsc = FSC(objLabel=self.getRunName())
fn = self._getExtraPath("relion_model.star")
table = Table(fileName=fn, tableName='model_class_1')
resolution_inv = table.getColumnValues('rlnResolution')
frc = table.getColumnValues('rlnGoldStandardFsc')
fsc.setData(resolution_inv, frc)
self._defineOutputs(outputFSC=fsc)
self._defineSourceRelation(vol, fsc)
def createOutputStep(self):
imgSet = self.inputParticles.get()
vol = Volume()
lastIter = self._getLastIterNumber()
if self.protType == GOLD_STD:
vol.setFileName(
self._getExtraPath('Refinement/final/vol_%02d.stk' % lastIter))
half1 = self._getExtraPath('Refinement/final/vol_%02d_s1.stk' %
lastIter)
half2 = self._getExtraPath('Refinement/final/vol_%02d_s2.stk' %
lastIter)
else:
vol.setFileName(
self._getExtraPath('Refinement/final/bpr%02d.stk' % lastIter))
half1 = self._getExtraPath('Refinement/final/bpr%02d_sub1.stk' %
lastIter)
half2 = self._getExtraPath('Refinement/final/bpr%02d_sub2.stk' %
lastIter)
vol.setSamplingRate(imgSet.getSamplingRate())
vol.setHalfMaps([half1, half2])
outImgSet = self._createSetOfParticles()
outImgSet.copyInfo(imgSet)
self._fillDataFromDoc(outImgSet)
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(self.inputParticles, vol)
self._defineOutputs(outputParticles=outImgSet)
self._defineTransformRelation(self.inputParticles, outImgSet)
fsc = FSC(objLabel=self.getRunName())
resolution, fscData = self._getFscData(it=lastIter)
fsc.setData(resolution, fscData)
self._defineOutputs(outputFSC=fsc)
self._defineSourceRelation(vol, fsc)
def runCreateOutputStep(self):
''' Create standard output results_images, result_classes'''
#creating results files
imgSet = self.inputParticles.get()
lastIter = self.numberOfIterations.get()
Ts = imgSet.getSamplingRate()
if self.numberOfReferences != 1:
inDocfile = self._getFileName('docfileInputAnglesIters', iter=lastIter)
ClassFnTemplate = '%(rootDir)s/reconstruction_Ref3D_%(ref)03d.vol'
allExpImagesinDocfile = emlib.FileName()
all_exp_images = "all_exp_images"
allExpImagesinDocfile.compose(all_exp_images, inDocfile)
dataClasses = self._getFileName('sqliteClasses')
createClassesFromImages(imgSet, str(allExpImagesinDocfile),
dataClasses, SetOfClasses3D, emlib.MDL_REF3D,
ClassFnTemplate, lastIter)
classes = self._createSetOfClasses3D(imgSet)
clsSet = SetOfClasses3D(dataClasses)
classes.appendFromClasses(clsSet)
volumes = self._createSetOfVolumes()
volumes.setSamplingRate(Ts)
for refN in self.allRefs():
volFn = self._getFileName('reconstructedFileNamesIters',
iter=lastIter,
ref=refN)
volFn = convertToMrc(self, volFn, Ts, True)
vol = Volume()
vol.setFileName(volFn)
volumes.append(vol)
self._defineOutputs(outputVolumes=volumes)
self._defineOutputs(outputClasses=classes)
self._defineSourceRelation(self.inputParticles, volumes)
self._defineSourceRelation(self.inputParticles, classes)
self._defineSourceRelation(self.input3DReferences, volumes)
self._defineSourceRelation(self.input3DReferences, classes)
else:
volFn = self._getFileName('reconstructedFileNamesIters',
iter=lastIter,
ref=1)
halfMap1 = self._getFileName('reconstructedFileNamesItersSplit1',
iter=lastIter,
ref=1)
halfMap2 = self._getFileName('reconstructedFileNamesItersSplit2',
iter=lastIter,
ref=1)
volFn = convertToMrc(self, volFn, Ts, True)
halfMap1 = convertToMrc(self, halfMap1, Ts, True)
halfMap2 = convertToMrc(self, halfMap2, Ts, True)
vol = Volume()
vol.setFileName(volFn)
vol.setSamplingRate(Ts)
vol.setHalfMaps([halfMap1, halfMap2])
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(self.inputParticles, vol)
self._defineSourceRelation(self.input3DReferences, vol)
#create set of images
imgSetOut = self._createSetOfParticles("_iter_%03d" % lastIter)
self._fillParticlesFromIter(imgSetOut, lastIter)
self._defineOutputs(outputParticles=imgSetOut)
self._defineSourceRelation(self.inputParticles, imgSetOut)
self._defineSourceRelation(self.input3DReferences, imgSetOut)
