def _fillClassesFromNodes(self, classes, nodeList):
""" Create the SetOfClasses2D from the images of each node
in the dendogram.
"""
img = Particle()
sampling = classes.getSamplingRate()
for node in nodeList:
if node.path:
#print "node.path: ", node.path
class2D = Class2D()
avg = Particle()
#avg.copyObjId(class2D)
avg.setLocation(node.avgCount, self.dendroAverages)
avg.setSamplingRate(sampling)
class2D.setRepresentative(avg)
class2D.setSamplingRate(sampling)
classes.append(class2D)
#print "class2D.id: ", class2D.getObjId()
for i in node.imageList:
#img.setObjId(i) # FIXME: this is wrong if the id is different from index
img.cleanObjId()
img.setLocation(int(i), self.dendroImages)
class2D.append(img)
classes.update(class2D)
def createOutputStep(self):
""" Create the SetOfClass from the docfiles with the images-class
assigment, the averages for each class.
"""
particles = self.inputParticles.get()
sampling = particles.getSamplingRate()
classes2D = self._createSetOfClasses2D(particles)
for classId in range(1, self.numberOfClasses.get()+1):
class2D = Class2D()
class2D.setObjId(classId)
avgImg = Particle()
avgImg.setSamplingRate(sampling)
avgFn = self._getPath(self.getClassDir(), 'classavg%03d.stk' % classId)
avgImg.setLocation(1, avgFn)
class2D.setRepresentative(avgImg)
classes2D.append(class2D)
docClass = self._getPath(self.getClassDir(),
'docclass%03d.stk' % classId)
doc = SpiderDocFile(docClass)
for values in doc.iterValues():
imgId = int(values[0])
img = particles[imgId]
class2D.append(img)
self._defineOutputs(outputClasses=classes2D)
self._defineSourceRelation(self.inputParticles, classes2D)
def visualizeClasses(self, e=None):
prot = self.protocol
classDir = prot.getClassDir()
classAvg = 'classavg'
classVar = 'classvar'
classDoc = 'docclass'
ext = prot.getExt()
params = {'[class_dir]': classDir,
'[desired-classes]': self.numberOfClasses.get(),
'[particles]': prot._params['particles'] + '@******',
'[class_doc]': join(classDir, classDoc + '***'),
'[class_avg]': join(classDir, classAvg + '***'),
'[class_var]': join(classDir, classVar + '***'),
}
prot.runTemplate('mda/classavg.msa', prot.getExt(), params)
particles = prot.inputParticles.get()
particles.load()
sampling = particles.getSamplingRate()
setFn = self._getPath('classes2D.sqlite')
cleanPath(setFn)
classes2D = SetOfClasses2D(filename=setFn)
classes2D.setImages(particles)
for classId in range(1, self.numberOfClasses.get()+1):
class2D = Class2D()
class2D.setObjId(classId)
avgImg = Particle()
avgImg.setSamplingRate(sampling)
avgFn = prot._getPath(classDir, classAvg + '%03d.stk' % classId)
avgImg.setLocation(1, avgFn)
#avgImg.setLocation(classId, 'classavg.stk')
class2D.setRepresentative(avgImg)
classes2D.append(class2D)
docClass = prot._getPath(classDir, classDoc + '%03d.stk' % classId)
doc = SpiderDocFile(docClass)
for values in doc.iterValues():
imgId = int(values[0])
img = particles[imgId]
class2D.append(img)
classes2D.update(class2D)
classes2D.write()
classes2D.close()
return [ClassesView(self.getProject(),
prot.strId(), classes2D.getFileName(),
prot.inputParticles.get().strId())]
def _fillParticlesFromNodes(self, particles, nodeList):
""" Create the SetOfClasses2D from the images of each node
in the dendogram.
"""
img = Particle()
for node in nodeList:
if node.path:
for i in node.imageList:
#img.setObjId(i) # FIXME: this is wrong if the id is different from index
img.cleanObjId()
img.setLocation(int(i), self.dendroImages)
particles.append(img)
def createOutputStep(self):
""" Register the output (the alignment and the aligned particles.)
"""
particles = self.inputParticles.get()
# Create the output average image
avg = Particle()
avg.copyInfo(self.inputParticles.get())
avg.setLocation(NO_INDEX, self.getAverage())
self._defineOutputs(outputAverage=avg)
self._defineSourceRelation(particles, avg)
imgSet = self._createSetOfParticles()
imgSet.copyInfo(particles)
imgSet.setAlignment2D()
outputStk = self._getFileName('particlesAligned')
imgSet.readStack(outputStk,
postprocessImage=lambda img: img.setTransform(Transform()))
self._defineOutputs(outputParticles=imgSet)
self._defineTransformRelation(particles, imgSet)
def createOutputStep(self):
""" Register the output (the alignment and the aligned particles.)
"""
outputStk = self._getFileName('particlesAligned')
if not exists(outputStk):
raise Exception('Ouptput stack %s not produced. ' % outputStk)
particles = self.inputParticles.get()
# Create the output average image
avg = Particle()
avg.copyInfo(self.inputParticles.get())
avg.setLocation(NO_INDEX, self.getAverage())
self._defineOutputs(outputAverage=avg)
self._defineSourceRelation(self.inputParticles, avg)
imgSet = self._createSetOfParticles()
imgSet.copyInfo(particles)
imgSet.setAlignment2D()
imgSet.copyItems(particles,
updateItemCallback=self._updateItem,
itemDataIterator=iter(
range(1,
particles.getSize() + 1)))
self._defineOutputs(outputParticles=imgSet)
self._defineTransformRelation(self.inputParticles, imgSet)
def createOutputStep(self):
""" Register the output (the alignment and the aligned particles.)
"""
outputStk = self._getFileName('particlesAligned')
if not exists(outputStk):
raise Exception('Ouptput stack %s not produced. ' % outputStk)
particles = self.inputParticles.get()
# Create the output average image
avg = Particle()
avg.copyInfo(self.inputParticles.get())
avg.setLocation(NO_INDEX, self.getAverage())
self._defineOutputs(outputAverage=avg)
self._defineSourceRelation(self.inputParticles, avg)
imgSet = self._createSetOfParticles()
imgSet.copyInfo(particles)
imgSet.setAlignment2D()
imgSet.copyItems(particles,
updateItemCallback=self._updateItem,
itemDataIterator=iter(range(1, particles.getSize()+1)))
self._defineOutputs(outputParticles=imgSet)
self._defineTransformRelation(self.inputParticles, imgSet)