Python Volume.setSamplingRate方法代码示例

# 需要导入模块: from pyworkflow.em.data import Volume [as 别名]
# 或者: from pyworkflow.em.data.Volume import setSamplingRate [as 别名]
def runCreateOutputStep(self):
    ''' Create standard output results_images, result_classes'''
    #creating results files
    imgSet = self.inputParticles.get()
    lastIter = self.numberOfIterations.get()
    if self.numberOfReferences != 1:
        inDocfile = self._getFileName('docfileInputAnglesIters', iter=lastIter)
        ClassFnTemplate = '%(rootDir)s/reconstruction_Ref3D_%(ref)03d.vol'
        
        allExpImagesinDocfile = xmipp.FileName()
        all_exp_images="all_exp_images"
        allExpImagesinDocfile.compose(all_exp_images, inDocfile)
        
        dataClasses = self._getFileName('sqliteClasses')
        
        createClassesFromImages(imgSet, str(allExpImagesinDocfile), dataClasses, 
                                SetOfClasses3D, xmipp.MDL_REF3D, ClassFnTemplate, lastIter)
        
        classes = self._createSetOfClasses3D(imgSet)
        clsSet = SetOfClasses3D(dataClasses)
        classes.appendFromClasses(clsSet)
        
        volumes = self._createSetOfVolumes()
        volumes.setSamplingRate(imgSet.getSamplingRate())
        
        for refN in self.allRefs():
            volFn = self._getFileName('reconstructedFileNamesIters', iter=lastIter, ref=refN)
            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)

        vol = Volume()
        vol.setFileName(volFn)
        vol.setSamplingRate(imgSet.getSamplingRate())
        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)

# 需要导入模块: from pyworkflow.em.data import Volume [as 别名]
# 或者: from pyworkflow.em.data.Volume import setSamplingRate [as 别名]
    def importVolumesStep(self, pattern, samplingRate):
        """ Copy images matching the filename pattern
        Register other parameters.
        """
        self.info("Using pattern: '%s'" % pattern)

        # Create a Volume template object
        vol = Volume()
        vol.setSamplingRate(self.samplingRate.get())
        copyOrLink = self.getCopyOrLink()
        imgh = ImageHandler()

        volSet = self._createSetOfVolumes()
        volSet.setSamplingRate(self.samplingRate.get())

        for fileName, fileId in self.iterFiles():
            dst = self._getExtraPath(basename(fileName))
            copyOrLink(fileName, dst)
            x, y, z, n = imgh.getDimensions(dst)
            # First case considers when reading mrc without volume flag
            # Second one considers single volumes (not in stack)
            if (z == 1 and n != 1) or (z !=1 and n == 1):
                vol.setObjId(fileId)
                vol.setLocation(dst)
                volSet.append(vol)
            else:
                for index in range(1, n+1):
                    vol.cleanObjId()
                    vol.setLocation(index, dst)
                    volSet.append(vol)

        if volSet.getSize() > 1:
            self._defineOutputs(outputVolumes=volSet)
        else:
            self._defineOutputs(outputVolume=vol)

# 需要导入模块: from pyworkflow.em.data import Volume [as 别名]
# 或者: from pyworkflow.em.data.Volume import setSamplingRate [as 别名]
    def createOutputStep(self):
        volume=Volume()
        volume.setFileName(self._getExtraPath('sharpenedMap_last.mrc'))
        volume.setSamplingRate(self.inputVolume.get().getSamplingRate())

        self._defineOutputs(sharpened_map=volume)
        self._defineSourceRelation(self.inputVolume, volume)          

# 需要导入模块: from pyworkflow.em.data import Volume [as 别名]
# 或者: from pyworkflow.em.data.Volume import setSamplingRate [as 别名]
 def createOutputStep(self):
     """ Create the output volume 
     """
     outputVolume = Volume()
     outputVolume.setSamplingRate(self.getSampling())
     outputVolume.setFileName(self.getOutputFn())
     self._defineOutputs(outputVolume=outputVolume)
     self._defineTransformRelation(self.inputVolume, outputVolume)

# 需要导入模块: from pyworkflow.em.data import Volume [as 别名]
# 或者: from pyworkflow.em.data.Volume import setSamplingRate [as 别名]
 def createOutputStep(self):
     imgSet = self.inputParticles.get()
     volume = Volume()
     volume.setFileName(self._getFileName('output_volume'))
     volume.setSamplingRate(imgSet.getSamplingRate())
     
     self._defineOutputs(outputVolume=volume)
     self._defineSourceRelation(self.inputParticles, volume)

# 需要导入模块: from pyworkflow.em.data import Volume [as 别名]
# 或者: from pyworkflow.em.data.Volume import setSamplingRate [as 别名]
 def createOutputStep(self):
     volume = Volume()
     volume.setFileName(self._getFileName("finalMap"))
     vol = self.protRefine.get().outputVolume
     pxSize = vol.getSamplingRate()
     volume.setSamplingRate(pxSize)
     self._defineOutputs(outputVolume=volume)
     self._defineSourceRelation(vol, volume)

# 需要导入模块: from pyworkflow.em.data import Volume [as 别名]
# 或者: from pyworkflow.em.data.Volume import setSamplingRate [as 别名]
    def createOutputStep(self):
        
        if not self.realignMovieFrames:
            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())
            blockName = 'model_class_%[email protected]' % 1
            fn = blockName + self._getExtraPath("relion_model.star")
            mData = md.MetaData(fn)
            fsc.loadFromMd(mData,
                           md.RLN_RESOLUTION,
                           md.RLN_MLMODEL_FSC_HALVES_REF)
            self._defineOutputs(outputFSC=fsc)
            self._defineSourceRelation(vol, fsc)

        else:
            movieSet = self.inputMovieParticles.get()
            if self.movieIncludeRotSearch:
                vol = Volume()
                vol.setFileName(self._getExtraPath('relion_class001.mrc'))
                vol.setSamplingRate(movieSet.getSamplingRate())
                half1 = self._getFileName("final_half1_volume", ref3d=1)
                half2 = self._getFileName("final_half2_volume", ref3d=1)
                vol.setHalfMaps([half1, half2])

                self._defineOutputs(outputVolume=vol)
                self._defineSourceRelation(self.inputParticles, vol)
                self._defineSourceRelation(self.inputMovieParticles, vol)

            fnOut = self._getFileName('dataFinal')
            outMovieSet = self._createSetOfMovieParticles()
            outMovieSet.copyInfo(movieSet)
            outMovieSet.setAlignmentProj()
            # not using copyItems since input movie particle
            # set is missing a lot of metadata (CTF, micName etc.)
            # that was created in convertInputStep
            readSetOfParticles(fnOut, outMovieSet, alignType=ALIGN_PROJ,
                               extraLabels=MOVIE_EXTRA_LABELS,
                               postprocessImageRow=self._updateParticle)

            self._defineOutputs(outputParticles=outMovieSet)
            self._defineTransformRelation(self.inputParticles, outMovieSet)
            self._defineTransformRelation(self.inputMovieParticles, outMovieSet)

# 需要导入模块: from pyworkflow.em.data import Volume [as 别名]
# 或者: from pyworkflow.em.data.Volume import setSamplingRate [as 别名]
    def createOutputStep(self):
        imgSet = self.inputParticles.get()
        vol = Volume()
        # FIXME: return two half-volumes as well
        vol.setFileName(self._getPath('volume.stk'))
        vol.setSamplingRate(imgSet.getSamplingRate())

        self._defineOutputs(outputVolume=vol)
        self._defineSourceRelation(self.inputParticles, vol)

# 需要导入模块: from pyworkflow.em.data import Volume [as 别名]
# 或者: from pyworkflow.em.data.Volume import setSamplingRate [as 别名]
    def createOutputStep(self):
        imgSet = self.inputParticles.get()
        vol = Volume()
        #FIXME: return the last completed iteration
        vol.setFileName(self._getExtraPath('Refinement/final/bpr%02d.stk' % (self.numberOfIterations.get() + 1)))
        vol.setSamplingRate(imgSet.getSamplingRate())

        self._defineOutputs(outputVolume=vol)
        self._defineSourceRelation(self.inputParticles, vol)

# 需要导入模块: from pyworkflow.em.data import Volume [as 别名]
# 或者: from pyworkflow.em.data.Volume import setSamplingRate [as 别名]
def runCreateOutputStep(self):
    import pyworkflow.em.metadata as md
    ''' Create standard output results_images, result_classes'''
    #creating results files
    imgSet = self.inputParticles.get()
    lastIter = self.numberOfIterations.get()
    if self.numberOfReferences != 1:
        inDocfile = self._getFileName('docfileInputAnglesIters', iter=lastIter)
        ClassFnTemplate = '%(rootDir)s/reconstruction_Ref3D_%(ref)03d.vol'
        
        allExpImagesinDocfile = xmipp.FileName()
        all_exp_images="all_exp_images"
        allExpImagesinDocfile.compose(all_exp_images, inDocfile)
        
        dataClasses = self._getFileName('sqliteClasses')
        
        createClassesFromImages(imgSet, str(allExpImagesinDocfile), dataClasses, 
                                SetOfClasses3D, xmipp.MDL_REF3D, ClassFnTemplate, lastIter)
        
        classes = self._createSetOfClasses3D(imgSet)
        clsSet = SetOfClasses3D(dataClasses)
        classes.appendFromClasses(clsSet)
        
        volumes = self._createSetOfVolumes()
        volumes.setSamplingRate(imgSet.getSamplingRate())
        
        for refN in self.allRefs():
            volFn = self._getFileName('reconstructedFileNamesIters', iter=lastIter, ref=refN)
            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)
    else:
        volFn = self._getFileName('reconstructedFileNamesIters', iter=lastIter, ref=1)
        vol = Volume()
        vol.setFileName(volFn)
        vol.setSamplingRate(imgSet.getSamplingRate())
        self._defineOutputs(outputVolume=vol)
        self._defineSourceRelation(self.inputParticles, vol)
        
        #create set of images
        imgSetOut = self._createSetOfParticles()
        imgFn = "[email protected]" + self._getFileName('docfileInputAnglesIters', iter=lastIter, ref=1)
        
        imgSetOut.copyInfo(imgSet)
        imgSetOut.setAlignmentProj()
        imgSetOut.copyItems(imgSet,
                            updateItemCallback=self._createItemMatrix,
                            itemDataIterator=md.iterRows(imgFn))
        self._defineOutputs(outputParticles=imgSetOut)
        self._defineSourceRelation(self.inputParticles, imgSetOut)

# 需要导入模块: from pyworkflow.em.data import Volume [as 别名]
# 或者: from pyworkflow.em.data.Volume import setSamplingRate [as 别名]
    def _appendOutputVolume(self, volumeOut):
        vol = Volume()
        vol.setFileName(volumeOut)
        vol.setSamplingRate(self.sampling)
        self.volumesSet.append(vol)

        if self.doFilter.get():
            volumeFilterOut = volumeOut.replace('.vol', '_filtered.vol')
            volf = Volume()
            volf.setFileName(volumeFilterOut)
            volf.setSamplingRate(self.sampling)
            self.volumesFilterSet.append(volf)

# 需要导入模块: from pyworkflow.em.data import Volume [as 别名]
# 或者: from pyworkflow.em.data.Volume import setSamplingRate [as 别名]
    def createOutputStep(self):
        inputVol = self.inputStructure.get()
        pdb = PdbFile(self._getPath('pseudoatoms.pdb'), pseudoatoms=True)
        self.createChimeraScript(inputVol, pdb)
        self._defineOutputs(outputPdb=pdb)
        self._defineSourceRelation(self.inputStructure, pdb)

        volume=Volume()
        volume.setFileName(self._getExtraPath("pseudoatoms_approximation.vol"))
        volume.setSamplingRate(inputVol.getSamplingRate())
        self._defineOutputs(outputVolume=volume)
        self._defineSourceRelation(self.inputStructure.get(),volume)

# 需要导入模块: from pyworkflow.em.data import Volume [as 别名]
# 或者: from pyworkflow.em.data.Volume import setSamplingRate [as 别名]
 def _appendOutputVolume(self, volumeOut):  
                               
     vol = Volume()
     vol.setFileName(volumeOut)
     vol.setSamplingRate(self.inputParticlesTiltPair.get().getUntilted().getSamplingRate())
     self.volumesSet.append(vol)
     
     if self.doFilter.get():
         volumeFilterOut = volumeOut.replace('.vol','_filtered.vol')  
         volf = Volume()
         volf.setFileName(volumeFilterOut)
         volf.setSamplingRate(self.inputParticlesTiltPair.get().getUntilted().getSamplingRate())
         self.volumesFilterSet.append(volf)

# 需要导入模块: from pyworkflow.em.data import Volume [as 别名]
# 或者: from pyworkflow.em.data.Volume import setSamplingRate [as 别名]
    def createOutputStep(self):
        volume = Volume()
        volume.setFileName(self._getExtraPath('postprocess.mrc'))
        volume.setSamplingRate(self.samplingRate)
        vol = self.protRelionRefine.get().outputVolume
        mask = VolumeMask()
        mask.setFileName(self._getExtraPath('postprocess_automask.mrc'))
        mask.setSamplingRate(self.samplingRate)

        self._defineOutputs(outputVolume=volume)
        self._defineOutputs(outputMask=mask)
        self._defineSourceRelation(vol, volume)
        self._defineSourceRelation(vol, mask)

# 需要导入模块: from pyworkflow.em.data import Volume [as 别名]
# 或者: from pyworkflow.em.data.Volume import setSamplingRate [as 别名]
    def createOutputStep(self):
        volume=Volume()
        volume.setFileName(self._getFileName(OUTPUT_RESOLUTION_FILE))
        if (self.halfVolumes):
            volume.setSamplingRate(self.inputVolume.get().getSamplingRate())
            self._defineOutputs(resolution_Volume=volume)
            self._defineSourceRelation(self.inputVolume, volume)
        else:
            volume.setSamplingRate(self.inputVolumes.get().getSamplingRate())
            self._defineOutputs(resolution_Volume=volume)
            self._defineSourceRelation(self.inputVolumes, volume)
            
            
        #Setting the min max for the summary
        imageFile = self._getFileName(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.setFileName(self._getFileName(FN_FILTERED_MAP))
            if (self.halfVolumes):
                volume.setSamplingRate(self.inputVolume.get().getSamplingRate())
                self._defineOutputs(outputVolume_Filtered=volume)
                self._defineSourceRelation(self.inputVolume, volume)
            else:
                volume.setSamplingRate(self.inputVolumes.get().getSamplingRate())
                self._defineOutputs(outputVolume_Filtered=volume)
                self._defineSourceRelation(self.inputVolumes, volume)