def createOutput(self): import glob levelFiles = glob.glob(self._getExtraPath("results_classes_level*.xmd")) if levelFiles: levelFiles.sort() lastLevelFile = levelFiles[-1] setOfClasses = self._createSetOfClassesVol() setOfClasses.setImages(self.inputVolumes.get()) readSetOfClassesVol(setOfClasses, lastLevelFile) self._defineOutputs(outputClasses=setOfClasses) self._defineSourceRelation(self.inputVolumes, self.outputClasses) if self.generateAligned.get(): setOfVolumes = self._createSetOfVolumes() fnAligned = self._getExtraPath("results_aligned.xmd") self.runJob( "xmipp_metadata_selfile_create", "-p %s -o %s -s" % (self._getExtraPath("results_aligned.stk"), fnAligned), ) md = MetaData(fnAligned) md.addItemId() md.write(fnAligned) readSetOfVolumes(fnAligned, setOfVolumes) volumeList = self.inputVolumes.get() setOfVolumes.setSamplingRate(volumeList.getSamplingRate()) self._defineOutputs(alignedVolumes=setOfVolumes) self._defineTransformRelation(self.inputVolumes, self.alignedVolumes)
def createOutput(self): import glob levelFiles=glob.glob(self._getExtraPath("results_classes_level*.xmd")) if levelFiles: levelFiles.sort() lastLevelFile=levelFiles[-1] setOfClasses = self._createSetOfClassesVol() setOfClasses.setImages(self.inputVolumes.get()) readSetOfClassesVol(setOfClasses,lastLevelFile) self._defineOutputs(outputClasses=setOfClasses) self._defineSourceRelation(self.inputVolumes, self.outputClasses) if self.generateAligned: setOfVolumes = self._createSetOfVolumes() fnAligned = self._getExtraPath('results_aligned.xmd') readSetOfVolumes(fnAligned,setOfVolumes) volumeList = self.inputVolumes.get() setOfVolumes.setSamplingRate(volumeList.getSamplingRate()) self._defineOutputs(alignedVolumes=setOfVolumes) self._defineTransformRelation(self.inputVolumes, self.alignedVolumes)
def createOutputStep(self): inputSet = self.inputSet.get() fn = self._getPath('proposedVolumes.xmd') # md = xmipp.MetaData(fn) # md.addItemId() # md.write(fn) volumesSet = self._createSetOfVolumes() volumesSet.setSamplingRate(inputSet.getSamplingRate()) self._counter = 0 readSetOfVolumes(fn, volumesSet, postprocessImageRow=self._postprocessVolume) # Set a meanful comment # for vol in volumesSet: # vol.setObjComment('ransac volume %02d' % vol.getObjId()) # volumesSet.update(vol) self._defineOutputs(outputVolumes=volumesSet) self._defineSourceRelation(self.inputSet, volumesSet) self._storeSummaryInfo(self.numVolumes.get())
def createOutput(self): import glob levelFiles = glob.glob( self._getExtraPath("results_classes_level*.xmd")) if levelFiles: levelFiles.sort() lastLevelFile = levelFiles[-1] setOfClasses = self._createSetOfClassesVol() setOfClasses.setImages(self.inputVolumes.get()) readSetOfClassesVol(setOfClasses, lastLevelFile) self._defineOutputs(outputClasses=setOfClasses) self._defineSourceRelation(self.inputVolumes, self.outputClasses) if self.generateAligned: setOfVolumes = self._createSetOfVolumes() fnAligned = self._getExtraPath('results_aligned.xmd') readSetOfVolumes(fnAligned, setOfVolumes) volumeList = self.inputVolumes.get() setOfVolumes.setSamplingRate(volumeList.getSamplingRate()) self._defineOutputs(alignedVolumes=setOfVolumes) self._defineTransformRelation(self.inputVolumes, self.alignedVolumes)
def createOutputStep(self): volume_path = self._getExtraPath(OUTPUT_RESOLUTION_FILE) self.volumesSet = self._createSetOfVolumes('resolutionVol') if (self.halfVolumes): self.volumesSet.setSamplingRate(self.inputVolume.get().getSamplingRate()) else: self.volumesSet.setSamplingRate(self.inputVolumes.get().getSamplingRate()) readSetOfVolumes(volume_path, self.volumesSet) self._defineOutputs(outputVolume=self.volumesSet) if (self.halfVolumes): self._defineSourceRelation(self.inputVolume, self.volumesSet) else: self._defineSourceRelation(self.inputVolumes, self.volumesSet) #Setting the min max for the summary imageFile = self._getExtraPath(OUTPUT_RESOLUTION_FILE_CHIMERA) min_, max_ = self.getMinMax(imageFile) self.min_res_init.set(round(min_*100)/100) self.max_res_init.set(round(max_*100)/100) self._store(self.min_res_init) self._store(self.max_res_init) if self.filterInput.get(): print 'Saving filtered map' volume_filtered_path = self._getExtraPath(FN_FILTERED_MAP) self.volumesSet2 = self._createSetOfVolumes('filteredVol') if (self.halfVolumes): self.volumesSet2.setSamplingRate(self.inputVolume.get().getSamplingRate()) else: self.volumesSet2.setSamplingRate(self.inputVolumes.get().getSamplingRate()) readSetOfVolumes(volume_filtered_path, self.volumesSet2) self._defineOutputs(outputVolume_Filtered=self.volumesSet2) if (self.halfVolumes): self._defineSourceRelation(self.inputVolume, self.volumesSet2) else: self._defineSourceRelation(self.inputVolumes, self.volumesSet2)