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)
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(self.inputVolumes, self.outputVol)
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)
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)
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)
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)
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)
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)
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)
vol = Volume()
vol.setFileName(volFn)
vol.setSamplingRate(imgSet.getSamplingRate())
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)
def createOutputStep(self):
inputParticles = self.inputParticles.get()
if not self._useSeveralClasses():
newTs = inputParticles.getSamplingRate()
else:
newTs = self.readInfoField(self._getExtraPath(),"sampling",xmippLib.MDL_SAMPLINGRATE)
self.mdClasses = xmippLib.MetaData(self._getDirectionalClassesFn())
self.mdImages = xmippLib.MetaData(self._getDirectionalImagesFn())
classes2D = self._createSetOfClasses2D(inputParticles)
classes2D.getImages().setSamplingRate(newTs)
self.averageSet = self._createSetOfAverages()
self.averageSet.copyInfo(inputParticles)
self.averageSet.setAlignmentProj()
self.averageSet.setSamplingRate(newTs)
# Let's use a SetMdIterator because it should be less particles
# in the metadata produced than in the input set
iterator = md.SetMdIterator(self.mdImages, sortByLabel=md.MDL_ITEM_ID,
updateItemCallback=self._updateParticle,
skipDisabled=True)
fnHomogeneous = self._getExtraPath("images_homogeneous.xmd")
if exists(fnHomogeneous):
homogeneousSet = self._createSetOfParticles()
homogeneousSet.copyInfo(inputParticles)
homogeneousSet.setSamplingRate(newTs)
homogeneousSet.setAlignmentProj()
self.iterMd = md.iterRows(fnHomogeneous, md.MDL_PARTICLE_ID)
self.lastRow = next(self.iterMd)
homogeneousSet.copyItems(inputParticles,
updateItemCallback=self._updateHomogeneousItem)
self._defineOutputs(outputHomogeneous=homogeneousSet)
self._defineSourceRelation(self.inputParticles, homogeneousSet)
classes2D.classifyItems(updateItemCallback=iterator.updateItem,
updateClassCallback=self._updateClass)
self._defineOutputs(outputClasses=classes2D)
self._defineOutputs(outputAverages=self.averageSet)
self._defineSourceRelation(self.inputParticles, classes2D)
self._defineSourceRelation(self.inputParticles, self.averageSet)
if self.splitVolume and self.directionalClasses.get()>1:
volumesSet = self._createSetOfVolumes()
volumesSet.setSamplingRate(newTs)
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)
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)
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)
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)
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)
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)
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)
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)
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_%d@' % 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:
pass
def createOutputStep(self):
imgSet = self._getInputParticles()
vol = Volume()
fnVol = self._getExtraPath('relion_it%03d_class001.mrc') % self._lastIter()
vol.setFileName(fnVol)
vol.setSamplingRate(imgSet.getSamplingRate())
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)
def createOutputStep(self):
imgSet = self._getInputParticles()
vol = Volume()
vol.setFileName(self._getFileName('volume_shiny'))
vol.setSamplingRate(imgSet.getSamplingRate())
shinyPartSet = self._createSetOfParticles()
shinyPartSet.copyInfo(imgSet)
shinyPartSet.setAlignmentProj()
readSetOfParticles(self._getFileName('shiny'), shinyPartSet,
alignType=ALIGN_PROJ)
self._defineOutputs(outputParticles=shinyPartSet)
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(imgSet, shinyPartSet)
self._defineSourceRelation(imgSet, vol)
def createOutputStep(self):
from pyworkflow.em import ALIGN_PROJ
from pyworkflow.em.packages.relion.convert import readSetOfParticles
imgSet = self.refineRun.get()._getInputParticles()
vol = Volume()
vol.setFileName(self._getFileName('volume_shiny', iter=self.refineRun._lastIter()))
vol.setSamplingRate(imgSet.getSamplingRate())
shinyPartSet = self._createSetOfParticles()
shinyPartSet.copyInfo(imgSet)
readSetOfParticles(self._getFileName('shiny'), shinyPartSet, alignType=ALIGN_PROJ)
self._defineOutputs(outputParticles=shinyPartSet)
self._defineSourceRelation(imgSet, shinyPartSet)
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(imgSet, vol)
def createOutputStep(self):
iterN = self.numberOfIterations.get()
partSet = self._getInputParticles()
numRun = self._getRun()
vol = Volume()
vol.setFileName(self._getFileName("volume",run=numRun, iter=iterN))
vol.copyInfo(partSet)
newPartSet = self._createSetOfParticles()
newPartSet.copyInfo(partSet)
self._fillDataFromIter(newPartSet, iterN)
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(self._getInputParticlesPointer(), vol)
self._defineOutputs(outputParticles=newPartSet)
self._defineTransformRelation(self._getInputParticlesPointer(), newPartSet)
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 = "all_exp_images@" + 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)
def _getVolumes(self):
""" Return the list of volumes generated.
The number of volumes in the list will be equal to
the number of classes requested by the user in the protocol. """
# Provide 1 as default value for making it backward compatible
k = self.getAttributeValue('numberOfClasses', 1)
pixelSize = self._getInputParticles().getSamplingRate()
lastIter = self._lastIter()
volumes = []
for i in range(1, k + 1):
vol = Volume(
self._getExtraPath('relion_it%03d_class%03d.mrc') %
(lastIter, i))
vol.setSamplingRate(pixelSize)
volumes.append(vol)
return volumes
def createOutputStep(self):
if not self.realignMovieFrames:
imgSet = self._getInputParticles()
vol = Volume()
vol.setFileName(self._getExtraPath("relion_class001.mrc"))
vol.setSamplingRate(imgSet.getSamplingRate())
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)
else:
pass
def createOutputStep(self):
from glob import glob
classes2DSet = self.inputSet.get()
#volumes = EmanSetOfVolumes(self._getPath('scipion_volumes.json'))
volumes = self._createSetOfVolumes()
if isinstance(self.inputSet.get(), SetOfClasses2D):
volumes.setSamplingRate(classes2DSet.getImages().getSamplingRate())
else:
volumes.setSamplingRate(self.inputSet.get().getSamplingRate())
outputVols = glob(self._getExtraPath('initial_models/model_??_??.hdf'))
outputVols.sort()
for k, volFn in enumerate(outputVols):
vol = Volume()
vol.setFileName(volFn)
vol.setObjComment('eman initial model %02d' % (k+1))
volumes.append(vol)
self._defineOutputs(outputVolumes=volumes)
self._defineSourceRelation(classes2DSet, volumes)
def createOutputStep(self):
iterN = self.numberOfIterations.get()
partSet = self._getInputParticles()
numRun = self._getRun()
vol = Volume()
vol.setFileName(self._getFileName("volume",run=numRun, iter=iterN))
vol.copyInfo(partSet)
self._execEmanProcess(numRun, iterN)
newPartSet = self._createSetOfParticles()
newPartSet.copyInfo(partSet)
newPartSet.setAlignment(em.ALIGN_PROJ)
newPartSet.copyItems(partSet,
updateItemCallback=self._createItemMatrix,
itemDataIterator=self._iterTextFile(iterN))
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(self._getInputParticlesPointer(), vol)
self._defineOutputs(outputParticles=newPartSet)
self._defineTransformRelation(self._getInputParticlesPointer(), newPartSet)
def createOutputStep(self):
if self.range == self.LOW_RESOL:
sampling_new = 1.0
else:
sampling_new = 0.5
volume = Volume()
volume.setFileName(self._getFileName(OUTPUT_RESOLUTION_FILE))
volume.setSamplingRate(sampling_new)
self._defineOutputs(resolution_Volume=volume)
self._defineTransformRelation(self.inputVolume, volume)
#Setting the min max and median for the summary
imageFile = self._getFileName(OUTPUT_RESOLUTION_FILE)
min_, max_, median_ = self.getMinMax(imageFile)
self.min_res_init.set(round(min_ * 100) / 100)
self.max_res_init.set(round(max_ * 100) / 100)
self.median_res_init.set(round(median_ * 100) / 100)
self._store(self.min_res_init)
self._store(self.max_res_init)
self._store(self.median_res_init)
#create Resolution Map to visialize in Chimera
#vol_chimera=Volume()
vol_chimera = self.createChimeraOutput(
self._getFileName(OUTPUT_RESOLUTION_FILE), self.median_res_init)
# self.createChimeraOutput(self._getFileName(OUTPUT_RESOLUTION_FILE),
# self.median_res_init,
# self._getFileName(OUTPUT_RESOLUTION_FILE_CHIMERA))
vol_chimera.write(self._getFileName(OUTPUT_RESOLUTION_FILE_CHIMERA))
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)
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)
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)
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)
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)
def createOutputStep(self):
if not self.realignMovieFrames:
imgSet = self._getInputParticles()
vol = Volume()
vol.setFileName(self._getExtraPath('relion_class001.mrc'))
vol.setSamplingRate(imgSet.getSamplingRate())
outImgSet = self._createSetOfParticles()
outImgsFn = self._getFileName('data', iter=self._lastIter())
outImgSet.copyInfo(imgSet)
outImgSet.setAlignmentProj()
outImgSet.copyItems(imgSet,
updateItemCallback=self._createItemMatrix,
itemDataIterator=md.iterRows(outImgsFn))
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(imgSet, vol)
self._defineOutputs(outputParticles=outImgSet)
self._defineTransformRelation(imgSet, outImgSet)
else:
pass
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)
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)
def createOutputStep(self):
inputVol = self.inputStructure.get()
samplingRate = inputVol.getSamplingRate()
volume = Volume()
volume.setFileName(self._getExtraPath("pseudoatoms_approximation.vol"))
volume.setSamplingRate(samplingRate)
x, y, z = volume.getDim()
xv, yv, zv = inputVol.getOrigin(force=True).getShifts()
t = Transform()
t.setShifts((x / 2. * samplingRate) - xv, (y / 2. * samplingRate) - yv,
(z / 2. * samplingRate) - zv)
volume.setOrigin(inputVol.getOrigin())
self._defineOutputs(outputVolume=volume)
self._defineSourceRelation(self.inputStructure.get(), volume)
pdb = AtomStruct(self._getPath('pseudoatoms.pdb'), pseudoatoms=True)
pdb.setVolume(volume)
pdb.setOrigin(t)
self.createChimeraScript(inputVol, pdb)
self._defineOutputs(outputPdb=pdb)
self._defineSourceRelation(self.inputStructure, pdb)
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)
def createOutputStep(self):
volume = Volume()
volume.setFileName(self._getFileName(FN_RESOLMAP))
volume.setSamplingRate(self.inputVolume.get().getSamplingRate())
self._defineOutputs(resolution_Volume=volume)
self._defineSourceRelation(self.inputVolume, volume)
imageFile = self._getFileName(FN_RESOLMAP)
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)
def convertInputStep(self):
outputParticles = self._createSetOfParticles()
outputParticles.copyInfo(self.inputParticles.get())
outputParticles.copyItems(self.inputParticles.get())
self._defineOutputs(outputParticlesInit=outputParticles)
self._store(outputParticles)
#outputParticles.close()
outputVolumes = Volume()
outputVolumes.setFileName(self.inputVolume.get().getFileName())
outputVolumes.setSamplingRate(self.inputVolume.get().getSamplingRate())
self._defineOutputs(outputVolumesInit=outputVolumes)
self._store(outputVolumes)
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)
def createOutputStep(self):
iterN = self.numberOfIterations.get()
partSet = self._getInputParticles()
numRun = self._getRun()
vol = Volume()
vol.setFileName(self._getFileName("mapFull", run=numRun, iter=iterN))
halfMap1 = self._getFileName("mapEvenUnmasked", run=numRun)
halfMap2 = self._getFileName("mapOddUnmasked", run=numRun)
vol.setHalfMaps([halfMap1, halfMap2])
vol.copyInfo(partSet)
newPartSet = self._createSetOfParticles()
newPartSet.copyInfo(partSet)
self._fillDataFromIter(newPartSet, iterN)
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(self._getInputParticlesPointer(), vol)
self._defineOutputs(outputParticles=newPartSet)
self._defineTransformRelation(self._getInputParticlesPointer(), newPartSet)
def createOutputStep(self):
volume = Volume()
volume.setFileName(self._getFileName(OUTPUT_RESOLUTION_FILE))
volume.setSamplingRate(self.inputVolume.get().getSamplingRate())
self._defineOutputs(resolution_Volume=volume)
self._defineSourceRelation(self.inputVolume, volume)
#Setting the min max for the summary
imageFile = self._getFileName(OUTPUT_RESOLUTION_FILE)
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)
def createOutputStep(self):
imgSet = self._getInputParticles()
vol = Volume()
fnVol = self._getExtraPath(
'relion_it%03d_class001.mrc') % self._lastIter()
vol.setFileName(fnVol)
vol.setSamplingRate(imgSet.getSamplingRate())
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)
def createOutputStep(self):
imgSet = self._getInputParticles()
vol = Volume()
vol.setFileName(self._getFileName('volume_shiny'))
vol.setSamplingRate(imgSet.getSamplingRate())
shinyPartSet = self._createSetOfParticles()
shinyPartSet.copyInfo(imgSet)
shinyPartSet.setAlignmentProj()
readSetOfParticles(self._getFileName('shiny'),
shinyPartSet,
alignType=ALIGN_PROJ)
self._defineOutputs(outputParticles=shinyPartSet)
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(imgSet, shinyPartSet)
self._defineSourceRelation(imgSet, vol)
def createOutputStep(self):
iterN = self.numberOfIterations.get()
partSet = self._getInputParticles()
numRun = self._getRun()
vol = Volume()
vol.setFileName(self._getFileName("volume", run=numRun, iter=iterN))
vol.copyInfo(partSet)
newPartSet = self._createSetOfParticles()
newPartSet.copyInfo(partSet)
self._fillDataFromIter(newPartSet, iterN)
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(self._getInputParticlesPointer(), vol)
self._defineOutputs(outputParticles=newPartSet)
self._defineTransformRelation(self._getInputParticlesPointer(),
newPartSet)
def createOutputStep(self):
iterN = self.numberOfIterations.get()
partSet = self._getInputParticles()
numRun = self._getRun()
vol = Volume()
vol.setFileName(self._getFileName("mapFull",run=numRun, iter=iterN))
halfMap1 = self._getFileName("mapEvenUnmasked", run=numRun)
halfMap2 = self._getFileName("mapOddUnmasked", run=numRun)
vol.setHalfMaps([halfMap1, halfMap2])
vol.copyInfo(partSet)
newPartSet = self._createSetOfParticles()
newPartSet.copyInfo(partSet)
self._fillDataFromIter(newPartSet, iterN)
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(self._getInputParticlesPointer(), vol)
self._defineOutputs(outputParticles=newPartSet)
self._defineTransformRelation(self._getInputParticlesPointer(), newPartSet)
def createOutputStep(self):
classes2DSet = self.inputSet.get()
volumes = self._createSetOfVolumes()
shrink = self.shrink.get()
if isinstance(self.inputSet.get(), SetOfClasses2D):
volumes.setSamplingRate(
classes2DSet.getImages().getSamplingRate() * shrink)
else:
volumes.setSamplingRate(self.inputSet.get().getSamplingRate() *
shrink)
outputVols = self._getVolumes()
for k, volFn in enumerate(outputVols):
vol = Volume()
vol.setFileName(volFn)
vol.setObjComment('eman initial model %02d' % (k + 1))
volumes.append(vol)
self._defineOutputs(outputVolumes=volumes)
self._defineSourceRelation(self.inputSet, volumes)
def createOutputStep(self):
id = self.idx.get()
# inputSetOfVolumes=self.inputSetOfVolumes.get()
inputSetOfClasses3D = self.inputSetOfClasses3D.get()
newVolume = Volume()
#newVolume.setFileName(inputSetOfVolumes[id].getFileName())
#newVolume.setSamplingRate(inputSetOfVolumes[id].getSamplingRate())
newVolume.setFileName(
inputSetOfClasses3D[id].getRepresentative().getFileName())
newVolume.setSamplingRate(inputSetOfClasses3D[id].getSamplingRate())
newParticles = self._createSetOfParticles()
newParticles.setSamplingRate(inputSetOfClasses3D[id].getSamplingRate())
if inputSetOfClasses3D[id].hasAlignmentProj():
newParticles.setAlignmentProj()
newParticles.copyItems(inputSetOfClasses3D[id])
self._defineOutputs(**{'outputAuxVolumes': newVolume})
self._store(newVolume)
self._defineOutputs(**{'outputAuxParticles': newParticles})
self._store(newParticles)
def createOutputStep(self):
from pyworkflow.em import ALIGN_PROJ
from pyworkflow.em.packages.relion.convert import readSetOfParticles
refineRun = self.refineRun.get()
imgSet = refineRun._getInputParticles()
vol = Volume()
vol.setFileName(
self._getFileName('volume_shiny', iter=refineRun._lastIter()))
vol.setSamplingRate(imgSet.getSamplingRate())
shinyPartSet = self._createSetOfParticles()
shinyPartSet.copyInfo(imgSet)
readSetOfParticles(self._getFileName('shiny'),
shinyPartSet,
alignType=ALIGN_PROJ)
self._defineOutputs(outputParticles=shinyPartSet)
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(refineRun.inputParticles, shinyPartSet)
self._defineSourceRelation(refineRun.inputMovieParticles, shinyPartSet)
self._defineSourceRelation(refineRun.inputParticles, vol)
self._defineSourceRelation(refineRun.inputMovieParticles, vol)
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)
def createOutputStep(self):
volSet = self.inputVolumes.get()
if self._isSingleInput():
vol = Volume()
vol.copyInfo(volSet)
if self.doResize:
vol.setSamplingRate(self.samplingRate)
vol.setFileName(self.outputStk)
self._defineOutputs(outputVol=vol)
else:
volumes = self._createSetOfVolumes()
volumes.copyInfo(volSet)
if self.doResize:
volumes.setSamplingRate(self.samplingRate)
for i, vol in enumerate(volSet):
j = i + 1
vol.setSamplingRate(self.samplingRate)
vol.setLocation(j, self.outputStk)
volumes.append(vol)
self._defineOutputs(outputVol=volumes)
self._defineTransformRelation(volSet, self.outputVol)
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)
def createOutputStep(self):
classListProtocols = []
classListIds = []
classListSizes = []
fnOutFile = self.inputMetaProt.get()._getExtraPath('auxOutputFile.txt')
outFile = open(fnOutFile, 'r')
nameRead = outFile.readline()
while nameRead != '':
nameRead = nameRead[:-1]
for i, item in enumerate(self.inputSignifProts):
if nameRead == self.inputSignifProts[i].get()._objLabel:
classListProtocols.append(self.inputSignifProts[i].get())
idRead = outFile.readline()
classListIds.append(int(idRead))
sizeRead = outFile.readline()
classListSizes.append(int(sizeRead))
break
nameRead = outFile.readline()
# print(classListProtocols)
# print(classListIds)
# print(classListSizes)
inputVolume = self.inputMetaProt.get().inputVolume
myVolList = []
# outputVolumes = self._createSetOfVolumes('Def')
# outputVolumes.setDim(inputVolume.get().getDim())
# outputVolumes.setSamplingRate(inputVolume.get().getSamplingRate())
origDim = inputVolume.get().getDim()[0]
for i, prot in enumerate(classListProtocols):
# print("createOutputStep ", i)
classItem = prot.outputClasses[classListIds[i]]
volFn = str(classItem._representative._filename)
volFnOut = self._getExtraPath('outVol%d.vol' % (i + 1))
volDim = classItem._representative.getDim()[0]
if volDim != origDim:
self.runJob("xmipp_image_resize",
"-i %s -o %s --fourier %d" %
(volFn, volFnOut, origDim),
numberOfMpi=self.numberOfMpi.get() *
self.numberOfThreads.get())
else:
copy(volFn, volFnOut)
vol = Volume()
vol.setLocation(volFnOut)
vol.setSamplingRate(inputVolume.get().getSamplingRate())
myVolList.append(vol)
# outputVolumes.append(vol)
# self._defineOutputs(** {'outputVolumesDef': outputVolumes})
# self._store(outputVolumes)
inputParticles = self.inputMetaProt.get().inputParticles
outputDefClasses = self._createSetOfClasses3D(inputParticles.get(),
'Def')
for i, prot in enumerate(classListProtocols):
classItem = prot.outputClasses[classListIds[i]]
signifInputParts = inputParticles.get()
partIds = classItem.getIdSet()
newClass = Class3D()
newClass.copyInfo(signifInputParts)
newClass.setAcquisition(signifInputParts.getAcquisition())
newClass.setRepresentative(myVolList[i])
outputDefClasses.append(newClass)
enabledClass = outputDefClasses[newClass.getObjId()]
enabledClass.enableAppend()
for itemId in partIds:
enabledClass.append(signifInputParts[itemId])
outputDefClasses.update(enabledClass)
self._defineOutputs(**{'outputClasses3DDef': outputDefClasses})
self._store(outputDefClasses)
def createOutputStep(self, outputVol):
vol = Volume()
vol.setFileName(outputVol)
vol.setSamplingRate(self.outputParticles.getSamplingRate())
self._defineOutputs(outputVol=vol)
