def alignParticlesStep(self):
fhInputTranMat = self._getExtraPath('transformation-matrix.txt')
outParticlesFn = self._getExtraPath('outputParticles.xmd')
transMatFromFile = np.loadtxt(fhInputTranMat)
transformationMat = np.reshape(transMatFromFile, (4, 4))
transform = Transform()
transform.setMatrix(transformationMat)
resultMat = Transform()
outputParts = md.MetaData()
mdToAlign = md.MetaData(self.imgsInputFn)
for row in md.iterRows(mdToAlign):
inMat = rowToAlignment(row, ALIGN_PROJ)
partTransformMat = inMat.getMatrix()
partTransformMatrix = np.matrix(partTransformMat)
newTransformMatrix = np.matmul(transformationMat,
partTransformMatrix)
resultMat.setMatrix(newTransformMatrix)
rowOut = md.Row()
rowOut.copyFromRow(row)
alignmentToRow(resultMat, rowOut, ALIGN_PROJ)
rowOut.addToMd(outputParts)
outputParts.write(outParticlesFn)
cleanPath(self.imgsInputFn)
def _appendRctImages(self, particles):
blockMd = "class%06d_images@%s" % (particles.getObjId(),
self.rctClassesFn)
classMd = emlib.MetaData()
partPairs = self.inputParticlesTiltPair.get()
uImages = partPairs.getUntilted()
tImages = partPairs.getTilted()
sangles = partPairs.getCoordsPair().getAngles()
micPairs = partPairs.getCoordsPair().getMicsPair()
uMics = micPairs.getUntilted()
tMics = micPairs.getTilted()
scaleFactor = uImages.getSamplingRate() / particles.getSamplingRate()
for img in particles:
imgId = img.getObjId()
uImg = uImages[imgId]
tImg = tImages[imgId]
if uImg is None or tImg is None:
print(">>> Warning, for id %d, tilted or untilted particle "
"was not found. Ignored." % imgId)
else:
objId = classMd.addObject()
pairRow = emlib.metadata.Row()
pairRow.setValue(emlib.MDL_IMAGE, getImageLocation(uImg))
uCoord = uImg.getCoordinate()
micId = uCoord.getMicId()
uMic = uMics[micId]
angles = sangles[micId]
pairRow.setValue(emlib.MDL_MICROGRAPH, uMic.getFileName())
pairRow.setValue(emlib.MDL_XCOOR, uCoord.getX())
pairRow.setValue(emlib.MDL_YCOOR, uCoord.getY())
pairRow.setValue(emlib.MDL_ENABLED, 1)
pairRow.setValue(emlib.MDL_ITEM_ID, int(imgId))
pairRow.setValue(emlib.MDL_REF, 1)
alignment = img.getTransform()
# Scale alignment by scaleFactor
alignment.scale(scaleFactor)
alignmentToRow(alignment, pairRow, alignType=ALIGN_2D)
pairRow.setValue(emlib.MDL_IMAGE_TILTED,
getImageLocation(tImg))
tMic = tMics[micId]
pairRow.setValue(emlib.MDL_MICROGRAPH_TILTED,
tMic.getFileName())
(angleY, angleY2, angleTilt) = angles.getAngles()
pairRow.setValue(emlib.MDL_ANGLE_Y, float(angleY))
pairRow.setValue(emlib.MDL_ANGLE_Y2, float(angleY2))
pairRow.setValue(emlib.MDL_ANGLE_TILT, float(angleTilt))
pairRow.writeToMd(classMd, objId)
classMd.write(blockMd, emlib.MD_APPEND)
def applyAlignmentStep(self, inputFn):
inputSt = self.inputSubtomograms.get()
# 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' %
(inputFn, windowedStk, 2 * inputSt.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(inputSt.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(inputSt[(idList[int(id) - 1])].getTransform(),
rowOut, pwem.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' %
(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._getPath('output_subtomograms.stk')
self.runJob('xmipp_transform_window',
'-i %s -o %s --size %d ' %
(alignStk, outputStk,
self.inputSubtomograms.get().getFirstItem().getDim()[0]),
numberOfMpi=1)
return [outputStk]
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 realignStep(self):
inputMdName = self._getExtraPath('inputClasses.xmd')
writeSetOfClasses2D(self.inputClasses.get(), inputMdName,
writeParticles=True)
centeredStackName = self._getExtraPath('centeredStack.stk')
self._params = {'input': inputMdName,
'output': centeredStackName}
args = ('-i %(input)s -o %(output)s --save_metadata_transform')
self.runJob("xmipp_transform_center_image", args % self._params,
numberOfMpi=1)
centeredMdName = centeredStackName.replace('stk', 'xmd')
centeredMd = md.MetaData(centeredMdName)
centeredStack = md.MetaData(centeredStackName)
listName = []
listTransform=[]
for rowStk in md.iterRows(centeredStack):
listName.append(rowStk.getValue(md.MDL_IMAGE))
for rowMd in md.iterRows(centeredMd):
listTransform.append(rowToAlignment(rowMd, ALIGN_2D))
mdNewClasses = md.MetaData()
for i, row in enumerate(md.iterRows(inputMdName)):
newRow = md.Row()
newRow.setValue(md.MDL_IMAGE, listName[i])
refNum = row.getValue(md.MDL_REF)
newRow.setValue(md.MDL_REF, refNum)
classCount = row.getValue(md.MDL_CLASS_COUNT)
newRow.setValue(md.MDL_CLASS_COUNT, classCount)
newRow.addToMd(mdNewClasses)
mdNewClasses.write('classes@' + self._getExtraPath('final_classes.xmd'),
MD_APPEND)
mdImages = md.MetaData()
i=0
mdBlocks = md.getBlocksInMetaDataFile(inputMdName)
resultMat = Transform()
for block in mdBlocks:
if block.startswith('class00'):
newMat = listTransform[i]
newMatrix = newMat.getMatrix()
mdClass = md.MetaData(block + "@" + inputMdName)
mdNewClass = md.MetaData()
i+=1
for rowIn in md.iterRows(mdClass):
#To create the transformation matrix (and its parameters)
# for the realigned particles
if rowIn.getValue(md.MDL_ANGLE_PSI)!=0:
flag_psi=True
if rowIn.getValue(md.MDL_ANGLE_ROT)!=0:
flag_psi=False
inMat = rowToAlignment(rowIn, ALIGN_2D)
inMatrix = inMat.getMatrix()
resultMatrix = np.dot(newMatrix,inMatrix)
resultMat.setMatrix(resultMatrix)
rowOut=md.Row()
rowOut.copyFromRow(rowIn)
alignmentToRow(resultMat, rowOut, ALIGN_2D)
if flag_psi==False:
newAngle = rowOut.getValue(md.MDL_ANGLE_PSI)
rowOut.setValue(md.MDL_ANGLE_PSI, 0.)
rowOut.setValue(md.MDL_ANGLE_ROT, newAngle)
#To create the new coordinates for the realigned particles
inPoint = np.array([[0.],[0.],[0.],[1.]])
invResultMat = np.linalg.inv(resultMatrix)
centerPoint = np.dot(invResultMat,inPoint)
rowOut.setValue(md.MDL_XCOOR, rowOut.getValue(
md.MDL_XCOOR)+int(centerPoint[0]))
rowOut.setValue(md.MDL_YCOOR, rowOut.getValue(
md.MDL_YCOOR)+int(centerPoint[1]))
rowOut.addToMd(mdNewClass)
mdNewClass.write(block + "@" + self._getExtraPath(
'final_classes.xmd'), MD_APPEND)
mdImages.unionAll(mdNewClass)
mdImages.write(self._getExtraPath('final_images.xmd'))
def runMapBack(self, classId):
for tomo in self.inputTomograms.get().iterItems():
if self.selection == 0:
TsSubtomo = self.inputClasses.get().getSamplingRate()
else:
TsSubtomo = self.inputRef.get().getSamplingRate()
TsTomo = tomo.getSamplingRate()
scaleFactor = TsSubtomo / TsTomo
mdGeometry = lib.MetaData()
if self.selection == 0:
inputSet = self.inputClasses.get().getFirstItem()
ref = self._getExtraPath("reference%d.mrc" % classId)
else:
inputSet = self.inputSubtomos.get()
ref = self.inputRef.get().getFileName()
for subtomo in inputSet.iterItems():
fn = subtomo.getFileName()
if fn.endswith('.mrc'):
fn += ':mrc'
if subtomo.getCoordinate3D().getVolId() == tomo.getObjId() \
or basename(subtomo.getVolName()) == tomo.getBaseName().partition('import_')[0]:
nRow = md.Row()
nRow.setValue(lib.MDL_ITEM_ID, int(subtomo.getObjId()))
coord = subtomo.getCoordinate3D()
coord.setVolume(tomo)
nRow.setValue(
lib.MDL_XCOOR,
int(
coord.getX(const.BOTTOM_LEFT_CORNER) *
scaleFactor))
nRow.setValue(
lib.MDL_YCOOR,
int(
coord.getY(const.BOTTOM_LEFT_CORNER) *
scaleFactor))
nRow.setValue(
lib.MDL_ZCOOR,
int(
coord.getZ(const.BOTTOM_LEFT_CORNER) *
scaleFactor))
# Compute inverse matrix
A = subtomo.getTransform().getMatrix()
subtomo.getTransform().setMatrix(np.linalg.inv(A))
# Convert transform matrix to Euler Angles (rot, tilt, psi)
alignmentToRow(subtomo.getTransform(), nRow, ALIGN_3D)
nRow.addToMd(mdGeometry)
fnGeometry = self._getExtraPath("geometry%d.xmd" % classId)
mdGeometry.write(fnGeometry)
if TsSubtomo != TsTomo:
factor = TsSubtomo / TsTomo
args = "-i %s -o %s --scale %d" % (ref, ref, factor)
self.runJob('xmipp_transform_geometry', args)
if self.paintingType.get() == 0:
painting = 'copy'
elif self.paintingType.get() == 1:
painting = 'avg %d' % self.threshold.get()
elif self.paintingType.get() == 2:
painting = 'highlight %d' % self.constant.get()
elif self.paintingType.get() == 3:
painting = 'copy_binary %f' % self.threshold.get()
tomogram = self._getExtraPath("tomogram_%d.mrc" % tomo.getObjId())
args = " -i %s -o %s --geom %s --ref %s --method %s" % (
tomogram, tomogram,
self._getExtraPath("geometry%d.xmd" % classId), ref, painting)
self.runJob("xmipp_tomo_map_back", args)