def createOutputStep(self):
lastIter = self.getLastIteration()
if lastIter <= 1:
return
if self.Nvolumes == 1:
vol = em.Volume()
vol.setLocation(
self._getExtraPath('recvol_state1_iter%d.spi' % lastIter))
vol.setSamplingRate(self.inputClasses.get().getSamplingRate())
self._defineOutputs(outputVol=vol)
else:
vol = self._createSetOfVolumes()
vol.setSamplingRate(self.inputClasses.get().getSamplingRate())
fnVolumes = glob(
self._getExtraPath('recvol_state*_iter%d.spi') % lastIter)
fnVolumes.sort()
for fnVolume in fnVolumes:
aux = em.Volume()
aux.setLocation(fnVolume)
vol.append(aux)
self._defineOutputs(outputVolumes=vol)
self._defineSourceRelation(self.inputClasses, vol)
def createOutputStep(self):
lastIter = self._getLastIter()
inputSet = self._getInputParticles()
# Register output volume
volFn = self._getFileName('iter_vol', iter=lastIter)
vol = em.Volume()
vol.setFileName(volFn)
vol.setSamplingRate(inputSet.getSamplingRate())
mapHalf1 = self._getFileName('iter_vol1', iter=lastIter)
mapHalf2 = self._getFileName('iter_vol2', iter=lastIter)
vol.setHalfMaps([mapHalf1, mapHalf2])
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(self._getInputParticlesPointer(), vol)
# Register output Particles with their 3D alignment
partSet = self._createSetOfParticles()
partSet.copyInfo(inputSet)
self._fillDataFromIter(partSet, lastIter)
self._defineOutputs(outputParticles=partSet)
self._defineTransformRelation(self._getInputParticlesPointer(),
partSet)
if not self.doContinue:
self._defineSourceRelation(self.input3DReference, vol)
self._defineSourceRelation(self.input3DReference, partSet)
def createOutputStep(self):
vols = []
for vol in self._iterInputVolumes():
outVol = em.Volume()
outVol.setLocation(vol.outputName)
outVol.setObjLabel(vol.getObjLabel())
outVol.setObjComment(vol.getObjComment())
#set transformation matrix
volId = vol.getObjId()
fhInputTranMat = self._getExtraPath('transformation-matrix_vol%06d.txt'%volId)
transMatFromFile = np.loadtxt(fhInputTranMat)
transformationMat = np.reshape(transMatFromFile,(4,4))
transform = em.Transform()
transform.setMatrix(transformationMat)
outVol.setTransform(transform)
vols.append(outVol)
if len(vols) > 1:
volSet = self._createSetOfVolumes()
volSet.setSamplingRate(self.inputReference.get().getSamplingRate())
for vol in vols:
volSet.append(vol)
outputArgs = {'outputVolumes': volSet}
else:
vols[0].setSamplingRate(self.inputReference.get().getSamplingRate())
outputArgs = {'outputVolume': vols[0]}
self._defineOutputs(**outputArgs)
for pointer in self.inputVolumes:
self._defineSourceRelation(pointer, outputArgs.values()[0])
def createOutput(self):
volume = em.Volume()
volume.setSamplingRate(self.sampling.get())
volume.setFileName(self._getVolName())
self._defineOutputs(outputVolume=volume)
if self.inputPdbData == self.IMPORT_OBJ:
self._defineSourceRelation(self.pdbObj, volume)
def createOutputStep(self):
outVolFn = self._getExtraPath("inputVolumeAligned.vol")
outVol = em.Volume()
outVol.setLocation(outVolFn)
#set transformation matrix
fhInputTranMat = self._getExtraPath('transformation-matrix.txt')
transMatFromFile = np.loadtxt(fhInputTranMat)
transformationMat = np.reshape(transMatFromFile, (4, 4))
transform = em.Transform()
transform.setMatrix(transformationMat)
outVol.setTransform(transform)
outVol.setSamplingRate(self.inputVolume.get().getSamplingRate())
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):
inputAverages = self.inputAverages.get()
imgxdim = inputAverages.getXDim()
fnVol = self._getExtraPath("refine.mrc")
volxdim, _, _, _ = em.ImageHandler().getDimensions(fnVol)
if imgxdim != volxdim:
fnVolOut = self._getPath("volume.vol")
args3 = "-i %s --dim %d -o %s" % (fnVol, imgxdim, fnVolOut)
#TODO maybe change later using Python binding to resize images
import pyworkflow.em.packages.xmipp3 as xmipp3
self.runJob("xmipp_image_resize", args3, env=xmipp3.getEnviron())
else:
fnVolOut = fnVol
vol = em.Volume()
vol.setLocation(fnVolOut)
vol.setSamplingRate(inputAverages.getSamplingRate())
self._defineOutputs(outputVol=vol)
self._defineSourceRelation(self.inputAverages, vol)
def createOutputStep(self):
vols = []
for vol in self._iterInputVolumes():
outVol = em.Volume()
outVol.setLocation(vol.outputName)
outVol.setObjLabel(vol.getObjLabel())
outVol.setObjComment(vol.getObjComment())
vols.append(outVol)
if len(vols) > 1:
volSet = self._createSetOfVolumes()
volSet.setSamplingRate(self.inputReference.get().getSamplingRate())
for vol in vols:
volSet.append(vol)
outputArgs = {'outputVolumes': volSet}
else:
vols[0].setSamplingRate(self.inputReference.get().getSamplingRate())
outputArgs = {'outputVolume': vols[0]}
self._defineOutputs(**outputArgs)
for pointer in self.inputVolumes:
self._defineSourceRelation(pointer, outputArgs.values()[0])
def _defineOutputVol(name, fn):
vol = em.Volume()
vol.copyInfo(self.inputVolume.get())
vol.setLocation(fn)
self._defineOutputs(**{name: vol})
self._defineTransformRelation(self.inputVolume, vol)
def createOutputStep(self):
vol = em.Volume()
vol.setLocation(self._getExtraPath('particles_rec_final.mrc'))
vol.setSamplingRate(self.inputClasses.get().getSamplingRate())
self._defineOutputs(outputVol=vol)
self._defineSourceRelation(self.inputClasses, vol)