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 _updateParticle(self, item, row):
item.setClassId(row.getValue(md.MDL_REF))
item.setTransform(rowToAlignment(row, ALIGN_2D))
if self.flag_relion:
item._rlnLogLikeliContribution = Float(None)
item._rlnMaxValueProbDistribution = Float(None)
item._rlnGroupName = String(None)
item._rlnNormCorrection = Float(None)
def _updateClass(self, item):
classId = item.getObjId()
classRow = findRow(self.mdClasses, xmippLib.MDL_REF2, classId)
representative = item.getRepresentative()
representative.setTransform(rowToAlignment(classRow, ALIGN_PROJ))
representative.setLocation(xmippToLocation(classRow.getValue(xmippLib.MDL_IMAGE)))
setXmippAttributes(representative, classRow, xmippLib.MDL_ANGLE_ROT)
setXmippAttributes(representative, classRow, xmippLib.MDL_ANGLE_TILT)
setXmippAttributes(representative, classRow, xmippLib.MDL_CLASS_COUNT)
self.averageSet.append(representative)
reprojection = Image()
reprojection.setLocation(xmippToLocation(classRow.getValue(xmippLib.MDL_IMAGE1)))
item.reprojection = reprojection
def _updateParticle(self, item, row):
item.setClassId(row.getValue(md.MDL_REF))
item.setTransform(rowToAlignment(row, ALIGN_PROJ))
item._xmippLogLikeliContribution = Float(row.getValue(md.MDL_LL))
def _updateParticle(self, item, row):
item.setClassId(row.getValue(md.MDL_REF))
item.setTransform(rowToAlignment(row, em.ALIGN_2D))
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'))
