Пример #1
0
        def coordsFactory(iteration):
            # newCoord =  Coordinate(x=i, y=i)
            # To avoid dict get
            newCoord = Coordinate()
            newCoord.setX(iteration)
            newCoord.setY(iteration)
            newCoord.extra1 = Integer(1)
            newCoord.extra2 = Integer(1)
            newCoord.extra3 = Integer(1)
            newCoord.extra4 = Integer(1)
            newCoord.extra5 = Integer(1)
            newCoord.extra6 = Integer(1)
            newCoord.extra7 = Integer(1)
            newCoord.extra8 = Integer(1)
            newCoord.extra9 = Integer(1)
            newCoord.extra10 = Integer(1)

            newCoord.extra11 = Integer(1)
            newCoord.extra12 = Integer(1)
            newCoord.extra13 = Integer(1)
            newCoord.extra14 = Integer(1)
            newCoord.extra15 = Integer(1)
            newCoord.extra16 = Integer(1)
            newCoord.extra17 = Integer(1)
            newCoord.extra18 = Integer(1)
            newCoord.extra19 = Integer(1)
            newCoord.extra20 = Integer(1)

            return newCoord
Пример #2
0
 def basiccoordsFactory(self, iteration):
     # newCoord =  Coordinate(x=i, y=i)
     # To avoid dict get
     newCoord = Coordinate()
     newCoord.setX(iteration)
     newCoord.setY(iteration)
     return newCoord
Пример #3
0
    def createOutputStep(self):
        input = self.input.get()
        imgSetOut = self._createSetOfParticles()
        imgSetOut.setSamplingRate(input.getSamplingRate())
        imgSetOut.setAlignmentProj()
        for i, subtomo in enumerate(input.iterItems()):
            idx = subtomo.getObjId()
            p = Particle()
            p.setLocation(ih._convertToLocation((i+1, self._getExtraPath("projections.mrcs"))))
            p._subtomogramID = String(idx)
            if type(subtomo) == SubTomogram:
                if subtomo.hasCoordinate3D():
                    coord = Coordinate()
                    coord.setX(subtomo.getCoordinate3D().getX(const.BOTTOM_LEFT_CORNER))
                    coord.setY(subtomo.getCoordinate3D().getY(const.BOTTOM_LEFT_CORNER))
                    p.setCoordinate(coord)
                p.setClassId(subtomo.getClassId())
            if subtomo.hasTransform():
                transform = Transform()
                transform.setMatrix(subtomo.getTransform().getMatrix())
                p.setTransform(transform)
            imgSetOut.append(p)

        imgSetOut.setObjComment(self.getSummary(imgSetOut))
        self._defineOutputs(outputParticles=imgSetOut)
        self._defineSourceRelation(self.input, imgSetOut)

        if self.radAvg.get():
            avgFile = self._getExtraPath("average.xmp")
            imgh = ih()
            avgImage = imgh.computeAverage(imgSetOut)
            avgImage.write(avgFile)
            avg = Particle()
            avg.setLocation(1, avgFile)
            avg.copyInfo(imgSetOut)
            self._defineOutputs(outputAverage=avg)
            self._defineSourceRelation(self.input, avg)