def _fillClasses(self, outputClasses):
""" Create the SetOfClasses2D """
inputSet = self.inputClasses.get().getImages()
myRep = md.MetaData('classes@' + self._getExtraPath(
'final_classes.xmd'))
for row in md.iterRows(myRep):
fn = row.getValue(md.MDL_IMAGE)
rep = Particle()
rep.setLocation(xmippToLocation(fn))
repId = row.getObjId()
newClass = Class2D(objId=repId)
newClass.setAlignment2D()
newClass.copyInfo(inputSet)
newClass.setAcquisition(inputSet.getAcquisition())
newClass.setRepresentative(rep)
outputClasses.append(newClass)
i=1
mdBlocks = md.getBlocksInMetaDataFile(self._getExtraPath(
'final_classes.xmd'))
for block in mdBlocks:
if block.startswith('class00'):
mdClass = md.MetaData(block + "@" + self._getExtraPath(
'final_classes.xmd'))
imgClassId = i
newClass = outputClasses[imgClassId]
newClass.enableAppend()
for row in md.iterRows(mdClass):
part = rowToParticle(row)
newClass.append(part)
i+=1
newClass.setAlignment2D()
outputClasses.update(newClass)
def _fillAverages(self, avgSet):
""" Create the SetOfAverages from a given metadata """
myFileClasses = "classes@" + self._getExtraPath('last_classes.xmd')
repSet = md.MetaData(myFileClasses)
for rep in md.iterRows(repSet):
particle = rowToParticle(rep)
repId = rep.getValue(md.MDL_REF) #rep.getObjId()
particle.setObjId(repId)
avgSet.append(particle)
def _fillParticles(self, outputParticles, outputCoords, inputParticles):
""" Create the SetOfParticles and SetOfCoordinates"""
myParticles = md.MetaData(self._getExtraPath('final_images.xmd'))
outputParticles.enableAppend()
outputCoords.enableAppend()
#Calculating the scale that relates the coordinates with the actual
# position in the mic
scale = inputParticles.getSamplingRate() / \
self.inputMics.get().getSamplingRate()
#Dictionary with the name and id of the inpt mics
micDictname = {}
micDictId = {}
for mic in self.inputMics.get():
micKey = mic.getMicName()
micDictname[micKey] = mic.clone()
micKey2 = mic.getObjId()
micDictId[micKey2] = mic.clone()
for row in md.iterRows(myParticles):
#To create the new particle
p = rowToParticle(row)
#To create the new coordinate
newCoord = Coordinate()
coord = p.getCoordinate()
if coord.getMicName() is not None:
micKey = coord.getMicName()
micDict = micDictname
else:
micKey = coord.getMicId()
micDict = micDictId
mic = micDict.get(micKey, None)
if mic is None:
print("Skipping particle, key %s not found" % micKey)
else:
newCoord.copyObjId(p)
x, y = coord.getPosition()
newCoord.setPosition(x * scale, y * scale)
newCoord.setMicrograph(mic)
outputCoords.append(newCoord)
p.setCoordinate(newCoord)
#Storing the new particle
outputParticles.append(p)
boxSize = inputParticles.getXDim() * scale
outputCoords.setBoxSize(boxSize)