def convertInputStep(self):
""" convert to Xmipp image model"""
if not self._isSingleInput():
writeSetOfVolumes(self.inputVolumes.get(), self.inputFn)
if self.inputVolumes2.get() is not None:
writeSetOfVolumes(self.inputVolumes2.get(),
self._getSecondSetFn())
def convertInputStep(self, outputFn):
inputSet = self.inputSubtomograms.get()
if inputSet.getFirstItem().getFileName().endswith('.mrc') or \
inputSet.getFirstItem().getFileName().endswith('.map'):
S = self._createSetOfSubTomograms()
S.setSamplingRate(inputSet.getSamplingRate())
for subtomo in self.inputSubtomograms.get():
s = subtomo.clone()
s.setFileName(subtomo.getFileName() + ':mrc')
S.append(s)
writeSetOfVolumes(S, outputFn, alignType=pwem.ALIGN_3D)
else:
writeSetOfVolumes(inputSet, outputFn, alignType=pwem.ALIGN_3D)
return [outputFn]
def createInputMd(self, vols):
fnVols = self._getExtraPath('input_volumes.xmd')
if self.copyAlignment:
alignType = vols.getAlignment()
else:
alignType = ALIGN_NONE
writeSetOfVolumes(vols, fnVols,
postprocessImageRow=self._postprocessVolumeRow,
alignType=alignType)
if not vols.hasAlignment() or not self.copyAlignment:
mdFn = md.MetaData(fnVols)
mdFn.fillConstant(md.MDL_ANGLE_ROT, 0.)
mdFn.fillConstant(md.MDL_ANGLE_TILT, 0.)
mdFn.fillConstant(md.MDL_ANGLE_PSI, 0.)
mdFn.fillConstant(md.MDL_SHIFT_X, 0.)
mdFn.fillConstant(md.MDL_SHIFT_Y, 0.)
mdFn.fillConstant(md.MDL_SHIFT_Z, 0.)
mdFn.write(fnVols, md.MD_OVERWRITE)
# set missing angles
missType = ['wedge_y', 'wedge_x', 'pyramid', 'cone']
missNum = self.missingDataType.get()
missAng = self.missingAng.get()
missDataFn = self._getExtraPath('wedges.xmd')
missAngValues = str(missAng).strip().split()
thetaY0, thetaYF, thetaX0, thetaXF = 0, 0, 0, 0
mdFn = md.MetaData()
if missNum == MISSING_WEDGE_X:
thetaX0, thetaXF = missAngValues
elif missNum == MISSING_WEDGE_Y:
thetaY0, thetaYF = missAngValues
elif missNum == MISSING_PYRAMID:
thetaY0, thetaYF, thetaX0, thetaXF = missAngValues
else: # MISSING_CONE
thetaY0 = missAngValues[0]
for i in range(1, vols.getSize() + 1):
row = md.Row()
row.setValue(md.MDL_MISSINGREGION_NR, missNum + 1)
row.setValue(md.MDL_MISSINGREGION_TYPE, missType[missNum])
row.setValue(md.MDL_MISSINGREGION_THX0, float(thetaX0))
row.setValue(md.MDL_MISSINGREGION_THXF, float(thetaXF))
row.setValue(md.MDL_MISSINGREGION_THY0, float(thetaY0))
row.setValue(md.MDL_MISSINGREGION_THYF, float(thetaYF))
row.addToMd(mdFn)
mdFn.write(missDataFn, md.MD_APPEND)
def runCLTomo(self):
fnVols = self._getPath('input_volumes.xmd')
writeSetOfVolumes(self.inputVolumes.get(), fnVols)
params= ' -i ' + fnVols + \
' --oroot ' + self._getExtraPath("results") + \
' --iter ' + str(self.numberOfIterations.get()) + \
' --nref ' + str(self.numberOfReferences.get()) + \
' --sym ' + self.symmetry.get() + \
' --maxFreq ' + str(self.maximumResolution.get()) + \
' --sparsity ' + str(self.sparsity.get()/100.0) + \
' --DWTsparsity ' + str(self.dwtSparsity.get()/100.0) + \
' --maxShiftX ' + str(self.maxShiftX.get()) + \
' --maxShiftY ' + str(self.maxShiftY.get()) + \
' --maxShiftZ ' + str(self.maxShiftZ.get()) + \
' --maxRot ' + str(self.maxRot.get()) + \
' --maxTilt ' + str(self.maxTilt.get()) + \
' --maxPsi ' + str(self.maxPsi.get())
if self.doGenerateInitial.get():
params += ' --nref0 ' + str(self.numberOfReferences0.get())
if self.randomizeOrientation.get():
params += ' --randomizeStartingOrientation'
else:
fnInitialVols = self._getExtraPath('intial_volumes.xmd')
writeSetOfVolumes(self.referenceList.get(), fnInitialVols)
params += ' --ref0 ' + fnInitialVols
if self.inputMask.hasValue():
params += ' --mask binary_file ' + self.inputMask.get(
).getLocation()
if self.generateAligned.get():
params += " --generateAlignedVolumes"
if not self.align:
params += " --dontAlign"
self.runJob('xmipp_mpi_classify_CLTomo',
'%d %s' % (self.numberOfMpi.get(), params),
env=self.getCLTomoEnviron(),
numberOfMpi=1)
def applyAlignStep(self):
"""Align subtomograms to be in the same orientation as the reference"""
inputSet = self.inputSubtomos.get()
outputFn = self._getExtraPath('input_subtomos.xmd')
if inputSet.getFirstItem().getFileName().endswith('.mrc') or \
inputSet.getFirstItem().getFileName().endswith('.map'):
S = self._createSetOfSubTomograms()
S.setSamplingRate(inputSet.getSamplingRate())
for subtomo in inputSet:
s = subtomo.clone()
s.setFileName(subtomo.getFileName() + ':mrc')
S.append(s)
writeSetOfVolumes(S, outputFn, alignType=ALIGN_3D)
else:
writeSetOfVolumes(inputSet, outputFn, alignType=ALIGN_3D)
# Window subtomograms twice their size
windowedStk = self._getExtraPath('windowed_subtomograms.stk')
self.runJob(
'xmipp_transform_window',
'-i %s -o %s --size %d --save_metadata_stack' %
(outputFn, windowedStk, 2 * inputSet.getFirstItem().getDim()[0]),
numberOfMpi=1)
# Add input transform matrix to md generated by xmipp_transform_window
mdWindow = md.MetaData(self._getExtraPath('windowed_subtomograms.xmd'))
mdWindowTransform = md.MetaData()
idList = list(inputSet.getIdSet())
for row in md.iterRows(mdWindow):
rowOut = md.Row()
rowOut.copyFromRow(row)
id = row.getValue(MDL_IMAGE)
id = id.split('@')[0]
id = id.strip('0')
alignmentToRow(inputSet[(idList[int(id) - 1])].getTransform(),
rowOut, ALIGN_3D)
rowOut.addToMd(mdWindowTransform)
mdWindowTransform.write(
self._getExtraPath("window_with_original_geometry.xmd"))
# Align subtomograms
self.runJob(
'xmipp_transform_geometry',
'-i %s -o %s --apply_transform --dont_wrap' %
(self._getExtraPath("window_with_original_geometry.xmd"),
self._getExtraPath('aligned_subtomograms.stk')))
# Window subtomograms to their original size
alignStk = self._getExtraPath('aligned_subtomograms.stk')
outputStk = self._getExtraPath('output_subtomograms.stk')
self.runJob('xmipp_transform_window',
'-i %s -o %s --size %d ' %
(alignStk, outputStk, inputSet.getFirstItem().getDim()[0]),
numberOfMpi=1)
self.alignedSet = self._createSetOfSubTomograms()
self.alignedSet.copyInfo(inputSet)
inputMd = self._getExtraPath('output_subtomograms.stk')
self.alignedSet.copyItems(inputSet,
updateItemCallback=self._updateItemAlign,
itemDataIterator=md.iterRows(
inputMd, sortByLabel=md.MDL_ITEM_ID))
def convertInputStep(self):
""" convert if necessary"""
if not self._isSingleInput():
writeSetOfVolumes(self.inputVolumes.get(), self.inputFn)