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
def basiccoordsFactory(self, iteration):
# newCoord = Coordinate(x=i, y=i)
# To avoid dict get
newCoord = Coordinate()
newCoord.setX(iteration)
newCoord.setY(iteration)
return newCoord
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)