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):
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._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 createOutput(self):
fnDir = self._getExtraPath()
Ts=self.readInfoField(fnDir,"sampling",xmippLib.MDL_SAMPLINGRATE)
# Final average
TsOrig=self.inputParticles.get().getSamplingRate()
XdimOrig=self.inputParticles.get().getDimensions()[0]
fnAvg = self._getExtraPath("volumeAvg.vol")
self.runJob("xmipp_image_resize","-i %s --dim %d"%(fnAvg,XdimOrig),numberOfMpi=1)
volume=Volume()
volume.setFileName(fnAvg)
volume.setSamplingRate(TsOrig)
self._defineOutputs(outputVolume=volume)
self._defineSourceRelation(self.inputParticles.get(),volume)
self._defineSourceRelation(self.inputVolumes.get(),volume)
# Swarm of volumes
volSet = self._createSetOfVolumes()
volSet.setSamplingRate(Ts)
for i in range(self.inputVolumes.get().getSize()):
fnVol = self._getExtraPath("volume%03d_best.vol"%i)
vol=Volume()
vol.setFileName(fnVol)
vol.setSamplingRate(Ts)
volSet.append(vol)
self._defineOutputs(outputVolumes=volSet)
self._defineSourceRelation(self.inputParticles.get(),volSet)
self._defineSourceRelation(self.inputVolumes.get(),volSet)
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):
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:
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)
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):
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):
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._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):
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):
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 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):
""" 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):
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):
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):
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):
""" 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):
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:
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)
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):
volume = Volume()
volume.setFileName(self._getFileName(OUTPUT_RESOLUTION_FILE))
if (self.halfVolumes):
volume.setSamplingRate(self.inputVolume.get().getSamplingRate())
volume.setOrigin(self.inputVolume.get().getOrigin(True))
self._defineOutputs(resolution_Volume=volume)
self._defineSourceRelation(self.inputVolume, volume)
inputVolumeFileName = self.inputVolume.get().getFileName()
else:
volume.setSamplingRate(self.inputVolumes.get().getSamplingRate())
volume.setOrigin(self.inputVolumes.get().getOrigin(True))
self._defineOutputs(resolution_Volume=volume)
self._defineSourceRelation(self.inputVolumes, volume)
inputVolumeFileName = self.inputVolumes.get().getFileName()
#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)
# fill ccp4 header so we can transfer the origin to the
# viewer (otherwise since imageFile is not a Scipion object
# no sampling/origin information can be transfered
Ccp4Header(imageFile).copyCCP4Header(inputVolumeFileName,
volume.getShiftsFromOrigin(),
volume.getSamplingRate(),
originField=Ccp4Header.START)
# also update the output volume header. This is not needed
# since sampling and origin is in the database but
# it may be usefull if other programs -outside scipion-
# require these data.
Ccp4Header(volume.getFileName()).copyCCP4Header(
inputVolumeFileName,
volume.getShiftsFromOrigin(),
volume.getSamplingRate(),
originField=Ccp4Header.START)
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 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 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 _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 _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 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):
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 _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):
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):
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 _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):
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):
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):
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):
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):
volume = Volume()
volume.setFileName(self._getExtraPath('sharpenedMap_last.mrc'))
volume.setSamplingRate(self.inputVolume.get().getSamplingRate())
volume.setOrigin(self.inputVolume.get().getOrigin(True))
volumesSet = self._createSetOfVolumes()
volumesSet.setSamplingRate(self.inputVolume.get().getSamplingRate())
for i in range(self.iteration):
vol = Volume()
vol.setLocation(
i, self._getExtraPath('sharpenedMap_%d.mrc' % (i + 1)))
vol.setObjComment("Sharpened Map, \n Epoch %d" % (i + 1))
volumesSet.append(vol)
self._defineOutputs(outputVolumes=volumesSet)
self._defineSourceRelation(self.inputVolume, volumesSet)
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):
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("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):
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):
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):
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 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):
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):
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, outputVol):
vol = Volume()
vol.setFileName(outputVol)
vol.setSamplingRate(self.outputParticles.getSamplingRate())
self._defineOutputs(outputVol=vol)
