本文整理汇总了Python中pyworkflow.em.data.Volume类的典型用法代码示例。如果您正苦于以下问题：Python Volume类的具体用法？Python Volume怎么用？Python Volume使用的例子？那么, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了Volume类的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: createOutputStep
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) 示例2: runCreateOutputStep
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)示例3: createOutputStep
def createOutputStep(self):
volInput = self.inputVolumes.get()
if self._isSingleInput():
# Create the output with the same class as
# the input, that should be Volume or a subclass
# of Volume like VolumeMask
volClass = volInput.getClass()
vol = volClass() # Create an instance with the same class of input
vol.copyInfo(volInput)
vol.setLocation(1, self.outputStk)
self._postprocessOutput(vol)
self._defineOutputs(outputVol=vol)
else:
# ToDo: createSetOfVolumes not work properly when the protocol is resumed.
volumes = self._createSetOfVolumes()
volumes.copyInfo(volInput)
self._preprocessOutput(volumes)
numberOfVols = self.inputVolumes.get().getSize()
for i in range(1, numberOfVols + 1):
vol = Volume()
vol.setLocation(i, self.outputStk)
volumes.append(vol)
self._postprocessOutput(volumes)
self._defineOutputs(outputVol=volumes)
self._defineTransformRelation(volInput, self.outputVol)示例4: createOutputStep
def createOutputStep(self):
numberOfClasses = self.numberOfRef
imgSet = self._getInputParticles()
volumes = self._createSetOfVolumes()
volumes.setSamplingRate(imgSet.getSamplingRate())
for ref in range(1, numberOfClasses + 1):
vol = Volume()
volFn = self._getFileName('iter_vol_class', iter=self._getLastIter(), ref=ref)
vol.setFileName(volFn)
volumes.append(vol)
clsSet = self._createSetOfClasses3D(imgSet)
self._fill3DClasses(clsSet, numberOfClasses)
# Define the outputs and relations
self._defineOutputs(outputClasses=clsSet)
self._defineOutputs(outputVolumes=volumes)
#TODO: save alignment
self._defineSourceRelation(self._getInputParticlesPointer(), clsSet)
self._defineSourceRelation(self._getInputParticlesPointer(), volumes)
if not self.doContinue:
self._defineSourceRelation(self.input3DReference, clsSet)
self._defineSourceRelation(self.input3DReference, volumes)示例5: createOutputStep
def createOutputStep(self):
partSet = self.inputParticles.get()
vol = Volume()
vol.setFileName(self._getFileName("volume"))
vol.copyInfo(partSet)
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(self.inputParticles, vol)示例6: createOutputStep
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)示例7: createOutputStep
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)示例8: createOutputStep
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)示例9: createOutputStep
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)示例10: createOutputStep
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)示例11: createOutput
def createOutput(self):
inputParticles = self.directionalClasses.get()
volumesSet = self._createSetOfVolumes()
volumesSet.setSamplingRate(inputParticles.getSamplingRate())
for i in range(2):
vol = Volume()
vol.setLocation(1, self._getExtraPath("split_v%d.vol"%(i+1)))
volumesSet.append(vol)
self._defineOutputs(outputVolumes=volumesSet)
self._defineSourceRelation(inputParticles, volumesSet)示例12: createOutputStep
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)示例13: _appendOutputVolume
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)示例14: createOutput
def createOutput(self):
volumesSet = self._createSetOfVolumes()
volumesSet.setSamplingRate(self.inputParticles.get().getSamplingRate())
Nvols = len(self.splitPercentiles.get().split())
fnStack = self._getPath("splittedVolumes.stk")
for i in range(Nvols):
vol = Volume()
vol.setLocation(i+1, fnStack)
volumesSet.append(vol)
self._defineOutputs(outputVolumes=volumesSet)
self._defineSourceRelation(self.inputParticles.get(), volumesSet)示例15: createOutputStep
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)