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