def createOutputStep(self):
volume = Volume()
volume.setFileName(self._getFileName(OUTPUT_RESOLUTION_FILE))
if (self.halfVolumes):
volume.setSamplingRate(self.inputVolume.get().getSamplingRate())
volume.setOrigin(self.inputVolume.get().getOrigin(True))
self._defineOutputs(resolution_Volume=volume)
self._defineSourceRelation(self.inputVolume, volume)
inputVolumeFileName = self.inputVolume.get().getFileName()
else:
volume.setSamplingRate(self.inputVolumes.get().getSamplingRate())
volume.setOrigin(self.inputVolumes.get().getOrigin(True))
self._defineOutputs(resolution_Volume=volume)
self._defineSourceRelation(self.inputVolumes, volume)
inputVolumeFileName = self.inputVolumes.get().getFileName()
#Setting the min max for the summary
imageFile = self._getFileName(OUTPUT_RESOLUTION_FILE_CHIMERA)
min_, max_ = self.getMinMax(imageFile)
self.min_res_init.set(round(min_ * 100) / 100)
self.max_res_init.set(round(max_ * 100) / 100)
self._store(self.min_res_init)
self._store(self.max_res_init)
if self.filterInput.get():
print 'Saving filtered map'
volume.setFileName(self._getFileName(FN_FILTERED_MAP))
if (self.halfVolumes):
volume.setSamplingRate(
self.inputVolume.get().getSamplingRate())
self._defineOutputs(outputVolume_Filtered=volume)
self._defineSourceRelation(self.inputVolume, volume)
else:
volume.setSamplingRate(
self.inputVolumes.get().getSamplingRate())
self._defineOutputs(outputVolume_Filtered=volume)
self._defineSourceRelation(self.inputVolumes, volume)
# fill ccp4 header so we can transfer the origin to the
# viewer (otherwise since imageFile is not a Scipion object
# no sampling/origin information can be transfered
Ccp4Header(imageFile).copyCCP4Header(inputVolumeFileName,
volume.getShiftsFromOrigin(),
volume.getSamplingRate(),
originField=Ccp4Header.START)
# also update the output volume header. This is not needed
# since sampling and origin is in the database but
# it may be usefull if other programs -outside scipion-
# require these data.
Ccp4Header(volume.getFileName()).copyCCP4Header(
inputVolumeFileName,
volume.getShiftsFromOrigin(),
volume.getSamplingRate(),
originField=Ccp4Header.START)
def createOutputStep(self):
volume = Volume()
volume.setFileName(self._getExtraPath('sharpenedMap_last.mrc'))
volume.setSamplingRate(self.inputVolume.get().getSamplingRate())
volume.setOrigin(self.inputVolume.get().getOrigin(True))
volumesSet = self._createSetOfVolumes()
volumesSet.setSamplingRate(self.inputVolume.get().getSamplingRate())
for i in range(self.iteration):
vol = Volume()
vol.setLocation(
i, self._getExtraPath('sharpenedMap_%d.mrc' % (i + 1)))
vol.setObjComment("Sharpened Map, \n Epoch %d" % (i + 1))
volumesSet.append(vol)
self._defineOutputs(outputVolumes=volumesSet)
self._defineSourceRelation(self.inputVolume, volumesSet)
def createOutputStep(self):
inputVol = self.inputStructure.get()
samplingRate = inputVol.getSamplingRate()
volume = Volume()
volume.setFileName(self._getExtraPath("pseudoatoms_approximation.vol"))
volume.setSamplingRate(samplingRate)
x, y, z = volume.getDim()
xv, yv, zv = inputVol.getOrigin(force=True).getShifts()
t = Transform()
t.setShifts((x / 2. * samplingRate) - xv, (y / 2. * samplingRate) - yv,
(z / 2. * samplingRate) - zv)
volume.setOrigin(inputVol.getOrigin())
self._defineOutputs(outputVolume=volume)
self._defineSourceRelation(self.inputStructure.get(), volume)
pdb = AtomStruct(self._getPath('pseudoatoms.pdb'), pseudoatoms=True)
pdb.setVolume(volume)
pdb.setOrigin(t)
self.createChimeraScript(inputVol, pdb)
self._defineOutputs(outputPdb=pdb)
self._defineSourceRelation(self.inputStructure, pdb)
