def createSetStep(self):
setObj = self.createSetObject()
inputObj = self.inputObject.get()
other = self.other.get()
if other and ',Volume' in other:
volId = int(other.split(',')[0])
if isinstance(setObj, emobj.SetOfVolumes):
volSet = emobj.SetOfVolumes(filename=self._dbName)
output = volSet[volId]
else:
classSet = emobj.SetOfClasses3D(filename=self._dbName)
output = classSet[volId].getRepresentative()
self._defineOutputs(outputVolume=output)
elif isinstance(inputObj, emobj.SetOfImages):
self._createSubSetFromImages(inputObj)
elif isinstance(inputObj, emobj.SetOfClasses):
self._createSubSetFromClasses(inputObj)
elif isinstance(inputObj, emobj.SetOfCTF):
outputClassName = self.outputClassName.get()
if outputClassName.startswith('SetOfMicrographs'):
self._createMicsSubSetFromCTF(inputObj)
elif isinstance(inputObj, emobj.SetOfAtomStructs):
self._createSubSetFromAtomStructs(inputObj)
elif isinstance(inputObj, MicrographsTiltPair):
self._createSubSetFromMicrographsTiltPair(inputObj)
elif isinstance(inputObj, ParticlesTiltPair):
self._createSubSetFromParticlesTiltPair(inputObj)
elif isinstance(inputObj, EMProtocol):
if self.other.hasValue():
otherid = self.other.get()
otherObj = self.getProject().mapper.selectById(int(otherid))
if isinstance(setObj, emobj.SetOfClasses):
setObj.setImages(otherObj)
self._createSubSetFromClasses(setObj)
elif isinstance(setObj, emobj.SetOfImages):
setObj.copyInfo(otherObj) # copy info from original images
self._createSubSetFromImages(setObj)
elif isinstance(setObj, emobj.SetOfNormalModes):
self._createSimpleSubset(otherObj)
else:
if isinstance(setObj, emobj.SetOfVolumes):
volSet = emobj.SetOfVolumes(filename=self._dbName)
volSet.loadAllProperties()
self._createSimpleSubset(volSet)
else:
self._createSimpleSubset(inputObj)
def createVolumesSqlite(self,
files,
path,
samplingRate,
updateItemCallback=None):
pwutils.cleanPath(path)
volSet = emobj.SetOfVolumes(filename=path)
volSet.setSamplingRate(samplingRate)
for volFn in files:
vol = emobj.Volume()
vol.setFileName(volFn)
if updateItemCallback:
updateItemCallback(vol)
volSet.append(vol)
volSet.write()
volSet.close()
return volSet
def createSetStep(self):
sourceSet = self.inputObject.get()
markedSet = self.createSetObject(
) # Set equal to sourceSet but marked with disabled
other = self.other.get()
print("Source: %s" % sourceSet)
print("Output type: %s" % self.outputClassName)
print("Subset (sqlite) file: %s" % self.sqliteFile)
if other:
print("Other: %s" % other)
# New recommended way to create subsets: making the set responsible for his own subset process
# Once all Sets implement appendFromSet and the if bellow is gone we can remove this "if"
if getattr(markedSet, "USE_CREATE_COPY_FOR_SUBSET", False):
markedSet.loadAllProperties()
newSet = markedSet.createCopy(self._getPath(),
copyInfo=True,
copyItems=True)
# Define outputs, may be use something more specific than "subset"
self._defineOutputs(subset=newSet)
return
if other and ',Volume' in other:
volId = int(other.split(',')[0])
if isinstance(markedSet, emobj.SetOfVolumes):
volSet = emobj.SetOfVolumes(filename=self._dbName)
output = volSet[volId]
else:
classSet = emobj.SetOfClasses3D(filename=self._dbName)
output = classSet[volId].getRepresentative()
self._defineOutputs(outputVolume=output)
elif isinstance(sourceSet, emobj.SetOfImages):
self._createSubSetFromImages(sourceSet)
elif isinstance(sourceSet, emobj.SetOfClasses):
self._createSubSetFromClasses(sourceSet)
elif isinstance(sourceSet, emobj.SetOfCTF):
outputClassName = self.outputClassName.get()
if outputClassName.startswith('SetOfMicrographs'):
self._createMicsSubSetFromCTF(sourceSet)
elif isinstance(sourceSet, emobj.SetOfAtomStructs):
self._createSubSetFromAtomStructs(sourceSet)
elif isinstance(sourceSet, MicrographsTiltPair):
self._createSubSetFromMicrographsTiltPair(sourceSet)
elif isinstance(sourceSet, ParticlesTiltPair):
self._createSubSetFromParticlesTiltPair(sourceSet)
elif isinstance(sourceSet, EMProtocol):
if self.other.hasValue():
otherid = self.other.get()
otherObj = self.getProject().mapper.selectById(int(otherid))
if isinstance(markedSet, emobj.SetOfClasses):
markedSet.setImages(otherObj)
self._createSubSetFromClasses(markedSet)
elif isinstance(markedSet, emobj.SetOfImages):
markedSet.copyInfo(
otherObj) # copy info from original images
self._createSubSetFromImages(markedSet)
elif isinstance(markedSet, emobj.SetOfNormalModes):
self._createSimpleSubset(otherObj)
else:
if isinstance(markedSet, emobj.SetOfVolumes):
volSet = emobj.SetOfVolumes(filename=self._dbName)
volSet.loadAllProperties()
self._createSimpleSubset(volSet)
# Go for a generic way of creating the set the the
# input set is not registered (typically from viewers)
else:
# We might want to do this before, inside the createSetObject
markedSet.loadAllProperties()
self._createSimpleSubset(markedSet)
else:
self._createSimpleSubset(sourceSet)