def createOutputStep(self):
imgSet = self.inputParticles.get()
classes2DSet = self._createSetOfClasses2D(imgSet)
readSetOfClasses2D(classes2DSet, self._getFileName('output_classes'))
self._defineOutputs(outputClasses=classes2DSet)
self._defineSourceRelation(self.inputParticles, classes2DSet)
if not self.doGenerateReferences:
self._defineSourceRelation(self.inputReferences, classes2DSet)
def createOutputStep(self):
imgSet = self.inputParticles.get()
classes2DSet = self._createSetOfClasses2D(imgSet)
readSetOfClasses2D(classes2DSet, self._getFileName('output_classes'))
self._defineOutputs(outputClasses=classes2DSet)
self._defineSourceRelation(imgSet, classes2DSet)
if not self.doGenerateReferences:
self._defineSourceRelation(self.inputReferences.get(), classes2DSet)
def createOutputStep(self):
""" Store the kenserdom object
as result of the protocol.
"""
imgSet = self.inputParticles.get()
classes2DSet = self._createSetOfClasses2D(imgSet)
readSetOfClasses2D(classes2DSet, self._params['kclasses'],
preprocessClass=self._preprocessClass)
self._defineOutputs(outputClasses=classes2DSet)
self._defineSourceRelation(self.inputParticles, classes2DSet)
def createOutputStep(self):
""" Store the kenserdom object
as result of the protocol.
"""
imgSet = self.inputParticles.get()
classes2DSet = self._createSetOfClasses2D(imgSet)
readSetOfClasses2D(classes2DSet,
self._params['kclasses'],
preprocessClass=self._preprocessClass)
self._defineOutputs(outputClasses=classes2DSet)
self._defineSourceRelation(self.inputParticles, classes2DSet)
def createOutputStep(self, subset=''):
""" Store the SetOfClasses2D object
resulting from the protocol execution.
"""
levelMdFiles = self._getLevelMdFiles(subset)
lastMdFn = levelMdFiles[-1]
inputParticles = self.inputParticles.get()
classes2DSet = self._createSetOfClasses2D(inputParticles, subset)
readSetOfClasses2D(classes2DSet, lastMdFn, 'classes')
result = {'outputClasses' + subset: classes2DSet}
self._defineOutputs(**result)
self._defineSourceRelation(self.inputParticles, classes2DSet)
def _getClassesSqlite(self, fnXmd, it):
""" Return the sqlite file given the xmd of classes. """
fnSqlite = join(dirname(fnXmd), 'classes_it%03d.sqlite' % it)
if not exists(fnSqlite): # Create the sqlite if not exists
classes2DSet = SetOfClasses2D(filename=fnSqlite)
classes2DSet.setImages(self.protocol.inputParticles.get())
readSetOfClasses2D(classes2DSet, fnXmd)
classes2DSet.write()
return fnSqlite
def createOutputStep(self, subset=''):
""" Store the SetOfClasses2D object
resulting from the protocol execution.
"""
levelMdFiles = self._getLevelMdFiles(subset)
lastMdFn = levelMdFiles[-1]
inputParticles = self.inputParticles.get()
classes2DSet = self._createSetOfClasses2D(inputParticles, subset)
readSetOfClasses2D(classes2DSet, lastMdFn, 'classes')
result = {'outputClasses' + subset: classes2DSet}
self._defineOutputs(**result)
self._defineSourceRelation(self.inputParticles, classes2DSet)
def createOutputStep(self):
self.plotsDir = self._getExtraPath('plots')
makePath(self.plotsDir)
fnClassVectors = self._params['kvectors'].replace('xmd', 'vec')
f = open(fnClassVectors)
self.classArray = np.fromfile(f, dtype=np.float32)
f.close()
fnImgVectors = self._params['vectors'].replace('xmd', 'vec')
f = open(fnImgVectors)
self.imgArray = np.fromfile(f, dtype=np.float32)
f.close()
self.imgCount = 0
imgSet = self.inputParticles.get()
classes2DSet = self._createSetOfClasses2D(imgSet)
readSetOfClasses2D(classes2DSet, self._params['kclasses'],
preprocessClass=self._preprocessClass,
postprocessImageRow=self._postprocessImageRow)
self._defineOutputs(outputClasses=classes2DSet)
self._defineSourceRelation(self.inputParticles, classes2DSet)
def createOutputStep(self):
self.plotsDir = self._getExtraPath('plots')
makePath(self.plotsDir)
fnClassVectors = self._params['kvectors'].replace('xmd', 'vec')
f = open(fnClassVectors)
self.classArray = np.fromfile(f, dtype=np.float32)
f.close()
fnImgVectors = self._params['vectors'].replace('xmd', 'vec')
f = open(fnImgVectors)
self.imgArray = np.fromfile(f, dtype=np.float32)
f.close()
self.imgCount = 0
imgSet = self.inputParticles.get()
classes2DSet = self._createSetOfClasses2D(imgSet)
readSetOfClasses2D(classes2DSet, self._params['kclasses'],
preprocessClass=self._preprocessClass,
postprocessImageRow=self._postprocessImageRow)
self._defineOutputs(outputClasses=classes2DSet)
self._defineSourceRelation(self.inputParticles, classes2DSet)
