def createOutputStep(self):
lastIter = self.getLastIteration(1)
Ts = self.inputSet.get().getSamplingRate()
# To recover the original size of the volume if it was changed
fnVol = self.getIterVolume(lastIter)
Xdim = self.inputSet.get().getDimensions()[0]
if self.useMaxRes and self.newXdim != Xdim:
self.runJob('xmipp_image_resize',
"-i %s --fourier %d" % (fnVol, Xdim),
numberOfMpi=1)
fnMrc = fnVol.replace(".vol", ".mrc")
self.runJob("xmipp_image_convert",
"-i %s -o %s -t vol" % (fnVol, fnMrc),
numberOfMpi=1)
cleanPath(fnVol)
self.runJob("xmipp_image_header",
"-i %s --sampling_rate %f" % (fnMrc, Ts),
numberOfMpi=1)
vol = Volume()
vol.setObjComment('significant volume 1')
vol.setLocation(fnMrc)
vol.setSamplingRate(Ts)
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(self.inputSet, vol)
def createOutputStep(self):
volumesSet = self._createSetOfVolumes()
volumesSet.setSamplingRate(self.inputVolume.get().getSamplingRate())
for i in range(self.iteration):
vol = Volume()
vol.setOrigin(self.inputVolume.get().getOrigin(True))
if (self.iteration > (i + 1)):
vol.setLocation(
i, self._getExtraPath('sharpenedMap_%d.mrc' % (i + 1)))
vol.setObjComment("Sharpened Map, \n Epoch %d" % (i + 1))
else:
vol.setLocation(i, self._getExtraPath('sharpenedMap_last.mrc'))
vol.setObjComment("Sharpened Map, \n Epoch last")
volumesSet.append(vol)
self._defineOutputs(outputVolumes=volumesSet)
self._defineSourceRelation(self.inputVolume, volumesSet)
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'])
