def createOutputStep(self):
outVolFn = self._getExtraPath("inputVolumeAligned.mrc")
Ts = self.inputVolume.get().getSamplingRate()
self.runJob("xmipp_image_header",
"-i %s --sampling_rate %f" % (outVolFn, Ts))
outVol = Volume()
outVol.setLocation(outVolFn)
#set transformation matrix
fhInputTranMat = self._getExtraPath('transformation-matrix.txt')
transMatFromFile = np.loadtxt(fhInputTranMat)
transformationMat = np.reshape(transMatFromFile, (4, 4))
transform = Transform()
transform.setMatrix(transformationMat)
outVol.setTransform(transform)
outVol.setSamplingRate(Ts)
outputArgs = {'outputVolume': outVol}
self._defineOutputs(**outputArgs)
self._defineSourceRelation(self.inputVolume, outVol)
#particles....
outParticlesFn = self._getExtraPath('outputParticles.xmd')
outputParticles = self._createSetOfParticles()
outputParticles.copyInfo(self.inputParticles.get())
outputParticles.setAlignmentProj()
readSetOfParticles(outParticlesFn, outputParticles)
outputArgs = {'outputParticles': outputParticles}
self._defineOutputs(**outputArgs)
self._defineSourceRelation(self.inputParticles, outputParticles)
def createOutputStep(self):
Ts = self.inputReference.get().getSamplingRate()
vols = []
idx = 1
for vol in self._iterInputVolumes():
outVol = Volume()
fnOutVol = self._getExtraPath("vol%02d.mrc" % idx)
outVol.setLocation(fnOutVol)
outVol.setObjComment(vol.getObjComment())
#set transformation matrix
fhInputTranMat = self._getExtraPath(
'transformation-matrix_vol%06d.txt' % idx)
transMatFromFile = np.loadtxt(fhInputTranMat)
transformationMat = np.reshape(transMatFromFile, (4, 4))
transform = Transform()
transform.setMatrix(transformationMat)
outVol.setTransform(transform)
vols.append(outVol)
# Set the sampling rate in the mrc header
self.runJob("xmipp_image_header",
"-i %s --sampling_rate %f" % (fnOutVol, Ts))
idx += 1
if len(vols) > 1:
volSet = self._createSetOfVolumes()
volSet.setSamplingRate(Ts)
for vol in vols:
volSet.append(vol)
outputArgs = {'outputVolumes': volSet}
else:
vols[0].setSamplingRate(Ts)
outputArgs = {'outputVolume': vols[0]}
self._defineOutputs(**outputArgs)
if len(vols) > 1:
for pointer in self.inputVolumes:
self._defineSourceRelation(pointer,
outputArgs['outputVolumes'])
else:
for pointer in self.inputVolumes:
self._defineSourceRelation(pointer, outputArgs['outputVolume'])
