Source code for deepfinder.objects

# -*- coding: utf-8 -*-
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# *
# * Authors: Emmanuel Moebel (
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# * Inria - Centre de Rennes Bretagne Atlantique, France
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from tomo.objects import Coordinate3D, SetOfCoordinates3D
import pyworkflow.object as pwobj
from import EMObject, Volume, SetOfVolumes

[docs]class DeepFinderSegmentation(Volume): """Class for storing tomogram segmentation maps. A segmentation should always be linked to its origin tomogram.""" def __init__(self, **kwargs): Volume.__init__(self, **kwargs) self._acquisition = None self._tsId = pwobj.String(kwargs.get('tsId', None)) self._tomoPointer = pwobj.Pointer(objDoStore=False) self._tomoId = pwobj.Integer() self._tomoName = pwobj.String()
[docs] def getTomogram(self): # does not work, similar problem to Coordinate3D.getVolume # FIXME: Update method __getitem__ and iterItems (already avalailbe in SetOfCoordinates3D and SetOfMeshes) return self._tomoPointer.get()
[docs] def setTomogram(self, tomo): self._tomoPointer.set(tomo) self._tomoId.set(tomo.getObjId()) self._tomoName.set(tomo.getFileName()) self.setSamplingRate(tomo.getSamplingRate())
[docs] def setTomoName(self, tomoName): self._tomoName.set(tomoName)
[docs] def getTomoName(self): return self._tomoName.get()
[docs]class SetOfDeepFinderSegmentations(SetOfVolumes): ITEM_TYPE = DeepFinderSegmentation EXPOSE_ITEMS = True def __init__(self, *args, **kwargs): SetOfVolumes.__init__(self, **kwargs)
[docs]class DeepFinderNet(EMObject): """ Simple class to store the neural network model for DeepFinder. """ def __init__(self, path=None, **kwargs): EMObject.__init__(self, **kwargs) self._path = pwobj.String(path) self._nbOfClasses = pwobj.Integer() # nb of classes corresponding to this model (background included)
[docs] def getPath(self): return self._path.get()
[docs] def setPath(self, path): self._path.set(path)
[docs] def getNbOfClasses(self): return self._nbOfClasses
[docs] def setNbOfClasses(self, nclass): self._nbOfClasses.set(nclass)
def __str__(self): return "DeepFinderModel(path=%s)" % self.getPath()
[docs]class Coordinate3DWithScore(Coordinate3D): """Extension of Coordinate3D adding a score attribute. Useful for automatic particle picking, where algorithms may attribute scores to hits.""" def __init__(self, **kwargs): Coordinate3D.__init__(self, **kwargs) self._score = pwobj.Scalar(kwargs.get('score', None))
[docs] def getScore(self): return self._score.get()
[docs] def setScore(self, x): self._score.set(x)
[docs]class SetOfCoordinates3DWithScore(SetOfCoordinates3D): """ Encapsulate the logic of a set of Coordinate3DWithScore. """ ITEM_TYPE = Coordinate3DWithScore def __init__(self, **kwargs): SetOfCoordinates3D.__init__(self, **kwargs)