def iterMdRows(md):
""" Iterate over the rows of the given metadata. """
# If md is string, take as filename and create the metadata
if isinstance(md, basestring):
md = xmipp.MetaData(md)
row = XmippMdRow()
for objId in md:
row.readFromMd(md, objId)
yield row
def iterMdRows(md):
""" Iterate over the rows of the given metadata. """
# If md is string, take as filename and create the metadata
if isinstance(md, basestring):
md = xmipp.MetaData(md)
row = XmippMdRow()
for objId in md:
row.readFromMd(md, objId)
yield row
def writeCTFModel(ctfModel, ctfFile):
""" Given a CTFModel object write as Xmipp ctfparam
"""
md = xmipp.MetaData()
objId = md.addObject()
ctfRow = XmippMdRow()
ctfModelToRow(ctfModel, ctfRow)
ctfRow.writeToMd(md, objId)
md.setColumnFormat(False)
md.write(ctfFile)
def writeCTFModel(ctfModel, ctfFile):
""" Given a CTFModel object write as Xmipp ctfparam
"""
md = xmipp.MetaData()
objId = md.addObject()
ctfRow = XmippMdRow()
ctfModelToRow(ctfModel, ctfRow)
ctfRow.writeToMd(md, objId)
md.setColumnFormat(False)
md.write(ctfFile)
def writeSetOfCoordinates(posDir, coordSet):
""" Write a pos file on metadata format for each micrograph
on the coordSet.
Params:
posDir: the directory where the .pos files will be written.
coordSet: the SetOfCoordinates that will be read.
"""
posFiles = []
boxSize = coordSet.getBoxSize() or 100
# Write pos metadatas (one per micrograph)
for mic in coordSet.iterMicrographs():
micName = mic.getFileName()
posFn = join(posDir, replaceBaseExt(micName, "pos"))
md = xmipp.MetaData()
for coord in coordSet.iterCoordinates(micrograph=mic):
objId = md.addObject()
coordRow = XmippMdRow()
coordinateToRow(coord, coordRow)
coordRow.writeToMd(md, objId)
if not md.isEmpty():
md2 = xmipp.MetaData()
objId = md2.addObject()
md2.setValue(xmipp.MDL_PICKING_MICROGRAPH_STATE, 'Manual', objId)
# Write header block
md2.write('header@%s' % posFn)
# Write particles block
md.write('particles@%s' % posFn, xmipp.MD_APPEND)
posFiles.append(posFn)
# Write config.xmd metadata
configFn = join(posDir, 'config.xmd')
md = xmipp.MetaData()
# Write properties block
objId = md.addObject()
micName = removeBaseExt(micName)
md.setValue(xmipp.MDL_MICROGRAPH, str(micName), objId)
#md.setValue(xmipp.MDL_COLOR, int(-16776961), objId)
md.setValue(xmipp.MDL_PICKING_PARTICLE_SIZE, int(boxSize), objId)
md.setValue(xmipp.MDL_PICKING_STATE, 'Manual', objId)
md.write('properties@%s' % configFn)
# Write filters block
md = xmipp.MetaData()
objId = md.addObject()
md.setValue(xmipp.MDL_MACRO_CMD, 'Gaussian_Blur...', objId)
md.setValue(xmipp.MDL_MACRO_CMD_ARGS, 'sigma=2', objId)
md.write('filters@%s' % configFn, xmipp.MD_APPEND)
return posFiles
def writeSetOfClassesVol(classesVolSet, filename, classesBlock='classes'):
""" This function will write a SetOfClassesVol as Xmipp metadata.
Params:
classesVolSet: the SetOfClassesVol instance.
filename: the filename where to write the metadata.
"""
classFn = '%s@%s' % (classesBlock, filename)
classMd = xmipp.MetaData()
classMd.write(classFn) # Empty write to ensure the classes is the first block
classRow = XmippMdRow()
for classVol in classesVolSet:
classVolToRow(classVol, classRow)
classRow.writeToMd(classMd, classMd.addObject())
ref = class3D.getObjId()
imagesFn = 'class%06d_images@%s' % (ref, filename)
imagesMd = xmipp.MetaData()
imgRow = XmippMdRow()
for vol in classVol:
volumeToRow(vol, imgRow)
imgRow.writeToMd(imagesMd, imagesMd.addObject())
imagesMd.write(imagesFn, xmipp.MD_APPEND)
classMd.write(classFn, xmipp.MD_APPEND) # Empty write to ensure the classes is the first block
def getMdFirstRow(filename):
""" Create a MetaData but only read the first row.
This method should be used for validations of labels
or metadata size, but the full metadata is not needed.
"""
md = xmipp.MetaData()
md.read(filename, 1)
if md.getParsedLines():
row = XmippMdRow()
row.readFromMd(md, md.firstObject())
else:
row = None
return row
def getMdFirstRow(filename):
""" Create a MetaData but only read the first row.
This method should be used for validations of labels
or metadata size, but the full metadata is not needed.
"""
md = xmipp.MetaData()
md.read(filename, 1)
if md.getParsedLines():
row = XmippMdRow()
row.readFromMd(md, md.firstObject())
else:
row = None
return row
def writeSetOfClasses2D(classes2DSet, filename, classesBlock='classes', writeParticles=True):
""" This function will write a SetOfClasses2D as Xmipp metadata.
Params:
classes2DSet: the SetOfClasses2D instance.
filename: the filename where to write the metadata.
"""
classFn = '%s@%s' % (classesBlock, filename)
classMd = xmipp.MetaData()
classMd.write(classFn) # Empty write to ensure the classes is the first block
classRow = XmippMdRow()
for class2D in classes2DSet:
class2DToRow(class2D, classRow)
classRow.writeToMd(classMd, classMd.addObject())
if writeParticles:
ref = class2D.getObjId()
imagesFn = 'class%06d_images@%s' % (ref, filename)
imagesMd = xmipp.MetaData()
imgRow = XmippMdRow()
if class2D.getSize() > 0:
for img in class2D:
particleToRow(img, imgRow)
imgRow.writeToMd(imagesMd, imagesMd.addObject())
imagesMd.write(imagesFn, xmipp.MD_APPEND)
classMd.write(classFn, xmipp.MD_APPEND) # Empty write to ensure the classes is the first block
def setOfImagesToMd(imgSet, md, imgToFunc, **kwargs):
""" This function will fill Xmipp metadata from a SetOfMicrographs
Params:
imgSet: the set of images to be converted to metadata
md: metadata to be filled
rowFunc: this function can be used to setup the row before
adding to metadata.
"""
if 'alignType' not in kwargs:
kwargs['alignType'] = imgSet.getAlignment()
for img in imgSet:
objId = md.addObject()
imgRow = XmippMdRow()
imgToFunc(img, imgRow, **kwargs)
imgRow.writeToMd(md, objId)
def setOfImagesToMd(imgSet, md, imgToFunc, **kwargs):
""" This function will fill Xmipp metadata from a SetOfMicrographs
Params:
imgSet: the set of images to be converted to metadata
md: metadata to be filled
rowFunc: this function can be used to setup the row before
adding to metadata.
"""
if 'alignType' not in kwargs:
kwargs['alignType'] = imgSet.getAlignment()
for img in imgSet:
objId = md.addObject()
imgRow = XmippMdRow()
imgToFunc(img, imgRow, **kwargs)
imgRow.writeToMd(md, objId)
def writeSetOfMovies(moviesSet, filename, moviesBlock='movies'):
""" This function will write a SetOfMovies as Xmipp metadata.
Params:
moviesSet: the SetOfMovies instance.
filename: the filename where to write the metadata.
"""
for movie in moviesSet:
ref = movie.getObjId()
micrographsFn = 'movie%06d_micrographs@%s' % (ref, filename)
micrographsMd = xmipp.MetaData()
micRow = XmippMdRow()
for mic in movie:
micrographToRow(mic, micRow)
micRow.writeToMd(micrographsMd, micrographsMd.addObject())
micrographsMd.write(micrographsFn, xmipp.MD_APPEND)
def writeSetOfMovies(moviesSet, filename, moviesBlock='movies'):
""" This function will write a SetOfMovies as Xmipp metadata.
Params:
moviesSet: the SetOfMovies instance.
filename: the filename where to write the metadata.
"""
for movie in moviesSet:
ref = movie.getObjId()
micrographsFn = 'movie%06d_micrographs@%s' % (ref, filename)
micrographsMd = xmipp.MetaData()
micRow = XmippMdRow()
for mic in movie:
micrographToRow(mic, micRow)
micRow.writeToMd(micrographsMd, micrographsMd.addObject())
micrographsMd.write(micrographsFn, xmipp.MD_APPEND)
def micrographToCTFParam(mic, ctfparam):
""" This function is used to convert a Micrograph object
to the .ctfparam metadata needed by some Xmipp programs.
If the micrograph already comes from xmipp, the ctfparam
will be returned, if not, the new file.
"""
ctf = mic.getCTF()
if hasattr(ctf, '_xmippMd'):
return ctf._xmippMd.get()
md = xmipp.MetaData()
md.setColumnFormat(False)
row = XmippMdRow()
ctfModelToRow(ctf, row)
acquisitionToRow(mic.getAcquisition(), row)
row.writeToMd(md, md.addObject())
md.write(ctfparam)
return ctfparam
def writeSetOfDefocusGroups(defocusGroupSet, fnDefocusGroup): # also metadata
""" Write a defocuGroupSet on metadata format.
Params:
defocusGroupSet: the SetOfDefocus that will be read.
fnDefocusGroup: The file where defocusGroup should be written.
"""
md = xmipp.MetaData()
for defocusGroup in defocusGroupSet:
objId = md.addObject()
defocusGroupRow = XmippMdRow()
defocusGroupSetToRow(defocusGroup, defocusGroupRow)
defocusGroupRow.setValue(xmipp.MDL_CTF_GROUP, defocusGroup.getObjId())
defocusGroupRow.setValue(xmipp.MDL_MIN, defocusGroup.getDefocusMin())
defocusGroupRow.setValue(xmipp.MDL_MAX, defocusGroup.getDefocusMax())
defocusGroupRow.setValue(xmipp.MDL_AVG, defocusGroup.getDefocusAvg())
defocusGroupRow.writeToMd(md, objId)
md.write(fnDefocusGroup)
defocusGroupSet._xmippMd = String(fnDefocusGroup)
def micrographToCTFParam(mic, ctfparam):
""" This function is used to convert a Micrograph object
to the .ctfparam metadata needed by some Xmipp programs.
If the micrograph already comes from xmipp, the ctfparam
will be returned, if not, the new file.
"""
ctf = mic.getCTF()
if hasattr(ctf, '_xmippMd'):
return ctf._xmippMd.get()
md = xmipp.MetaData()
md.setColumnFormat(False)
row = XmippMdRow()
ctfModelToRow(ctf, row)
acquisitionToRow(mic.getAcquisition(), row)
row.writeToMd(md, md.addObject())
md.write(ctfparam)
return ctfparam
def writeSetOfClasses2D(classes2DSet, filename, classesBlock='classes', writeParticles=True):
""" This function will write a SetOfClasses2D as Xmipp metadata.
Params:
classes2DSet: the SetOfClasses2D instance.
filename: the filename where to write the metadata.
"""
classFn = '%s@%s' % (classesBlock, filename)
classMd = xmipp.MetaData()
classMd.write(classFn) # Empty write to ensure the classes is the first block
classRow = XmippMdRow()
for class2D in classes2DSet:
class2DToRow(class2D, classRow)
classRow.writeToMd(classMd, classMd.addObject())
if writeParticles:
ref = class2D.getObjId()
imagesFn = 'class%06d_images@%s' % (ref, filename)
imagesMd = xmipp.MetaData()
imgRow = XmippMdRow()
if class2D.getSize() > 0:
for img in class2D:
particleToRow(img, imgRow)
imgRow.writeToMd(imagesMd, imagesMd.addObject())
imagesMd.write(imagesFn, xmipp.MD_APPEND)
classMd.write(classFn, xmipp.MD_APPEND) # Empty write to ensure the classes is the first block
def writeSetOfClassesVol(classesVolSet, filename, classesBlock='classes'):
""" This function will write a SetOfClassesVol as Xmipp metadata.
Params:
classesVolSet: the SetOfClassesVol instance.
filename: the filename where to write the metadata.
"""
classFn = '%s@%s' % (classesBlock, filename)
classMd = xmipp.MetaData()
classMd.write(classFn) # Empty write to ensure the classes is the first block
classRow = XmippMdRow()
for classVol in classesVolSet:
classVolToRow(classVol, classRow)
classRow.writeToMd(classMd, classMd.addObject())
ref = class3D.getObjId()
imagesFn = 'class%06d_images@%s' % (ref, filename)
imagesMd = xmipp.MetaData()
imgRow = XmippMdRow()
for vol in classVol:
volumeToRow(vol, imgRow)
imgRow.writeToMd(imagesMd, imagesMd.addObject())
imagesMd.write(imagesFn, xmipp.MD_APPEND)
classMd.write(classFn, xmipp.MD_APPEND) # Empty write to ensure the classes is the first block
def writeSetOfDefocusGroups(defocusGroupSet, fnDefocusGroup): # also metadata
""" Write a defocuGroupSet on metadata format.
Params:
defocusGroupSet: the SetOfDefocus that will be read.
fnDefocusGroup: The file where defocusGroup should be written.
"""
md = xmipp.MetaData()
for defocusGroup in defocusGroupSet:
objId = md.addObject()
defocusGroupRow = XmippMdRow()
defocusGroupSetToRow(defocusGroup, defocusGroupRow)
defocusGroupRow.setValue(xmipp.MDL_CTF_GROUP, defocusGroup.getObjId())
defocusGroupRow.setValue(xmipp.MDL_MIN, defocusGroup.getDefocusMin())
defocusGroupRow.setValue(xmipp.MDL_MAX, defocusGroup.getDefocusMax())
defocusGroupRow.setValue(xmipp.MDL_AVG, defocusGroup.getDefocusAvg())
defocusGroupRow.writeToMd(md, objId)
md.write(fnDefocusGroup)
defocusGroupSet._xmippMd = String(fnDefocusGroup)
def writeSetOfMicrographsPairs(uSet, tSet, filename):
""" This function will write a MicrographsTiltPair as Xmipp metadata.
Params:
uSet: the untilted set of micrographs to be written
tSet: the tilted set of micrographs to be written
filename: the filename where to write the metadata.
"""
md = xmipp.MetaData()
for micU, micT in izip(uSet, tSet):
objId = md.addObject()
pairRow = XmippMdRow()
pairRow.setValue(xmipp.MDL_ITEM_ID, long(micU.getObjId()))
pairRow.setValue(xmipp.MDL_MICROGRAPH, micU.getFileName())
pairRow.setValue(xmipp.MDL_MICROGRAPH_TILTED, micT.getFileName())
pairRow.writeToMd(md, objId)
md.write(filename)
def writeSetOfCTFs(ctfSet, mdCTF):
""" Write a ctfSet on metadata format.
Params:
ctfSet: the SetOfCTF that will be read.
mdCTF: The file where metadata should be written.
"""
md = xmipp.MetaData()
for ctfModel in ctfSet:
objId = md.addObject()
ctfRow = XmippMdRow()
ctfRow.setValue(xmipp.MDL_MICROGRAPH, ctfModel.getMicFile())
if ctfModel.getPsdFile():
ctfRow.setValue(xmipp.MDL_PSD, ctfModel.getPsdFile())
ctfModelToRow(ctfModel, ctfRow)
ctfRow.writeToMd(md, objId)
md.write(mdCTF)
ctfSet._xmippMd = String(mdCTF)
def writeSetOfMicrographsPairs(uSet, tSet, filename):
""" This function will write a MicrographsTiltPair as Xmipp metadata.
Params:
uSet: the untilted set of micrographs to be written
tSet: the tilted set of micrographs to be written
filename: the filename where to write the metadata.
"""
md = xmipp.MetaData()
for micU, micT in izip(uSet, tSet):
objId = md.addObject()
pairRow = XmippMdRow()
pairRow.setValue(xmipp.MDL_ITEM_ID, long(micU.getObjId()))
pairRow.setValue(xmipp.MDL_MICROGRAPH, micU.getFileName())
pairRow.setValue(xmipp.MDL_MICROGRAPH_TILTED, micT.getFileName())
pairRow.writeToMd(md, objId)
md.write(filename)
def writeSetOfCTFs(ctfSet, mdCTF):
""" Write a ctfSet on metadata format.
Params:
ctfSet: the SetOfCTF that will be read.
mdCTF: The file where metadata should be written.
"""
md = xmipp.MetaData()
for ctfModel in ctfSet:
objId = md.addObject()
ctfRow = XmippMdRow()
ctfRow.setValue(xmipp.MDL_MICROGRAPH, ctfModel.getMicFile())
if ctfModel.getPsdFile():
ctfRow.setValue(xmipp.MDL_PSD, ctfModel.getPsdFile())
ctfModelToRow(ctfModel, ctfRow)
ctfRow.writeToMd(md, objId)
md.write(mdCTF)
ctfSet._xmippMd = String(mdCTF)
def _appendRctImages(self, particles):
blockMd = "class%06d_images@%s" % (particles.getObjId(), self.rctClassesFn)
classMd = xmipp.MetaData()
uImages = self.inputParticlesTiltPair.get().getUntilted()
tImages = self.inputParticlesTiltPair.get().getTilted()
sangles = self.inputParticlesTiltPair.get().getCoordsPair().getAngles()
uMics = self.inputParticlesTiltPair.get().getCoordsPair().getMicsPair().getUntilted()
tMics = tImages.getCoordinates().getMicrographs()
scaleFactor = uImages.getSamplingRate()/particles.getSamplingRate()
for img in particles:
imgId = img.getObjId()
uImg = uImages[imgId]
tImg = tImages[imgId]
objId = classMd.addObject()
pairRow = XmippMdRow()
pairRow.setValue(xmipp.MDL_IMAGE, getImageLocation(uImg))
uCoord = uImg.getCoordinate()
micId = uCoord.getMicId()
uMic = uMics[micId]
angles = sangles[micId]
pairRow.setValue(xmipp.MDL_MICROGRAPH, uMic.getFileName())
pairRow.setValue(xmipp.MDL_XCOOR, uCoord.getX())
pairRow.setValue(xmipp.MDL_YCOOR, uCoord.getY())
pairRow.setValue(xmipp.MDL_ENABLED, 1)
pairRow.setValue(xmipp.MDL_ITEM_ID, long(imgId))
pairRow.setValue(xmipp.MDL_REF, 1)
alignment = img.getTransform()
# Scale alignment by scaleFactor
alignment.scale(scaleFactor)
alignmentToRow(alignment, pairRow, alignType=ALIGN_2D)
pairRow.setValue(xmipp.MDL_IMAGE_TILTED, getImageLocation(tImg))
tMic = tMics[micId]
pairRow.setValue(xmipp.MDL_MICROGRAPH_TILTED, tMic.getFileName())
(angleY, angleY2, angleTilt) = angles.getAngles()
pairRow.setValue(xmipp.MDL_ANGLE_Y, float(angleY))
pairRow.setValue(xmipp.MDL_ANGLE_Y2, float(angleY2))
pairRow.setValue(xmipp.MDL_ANGLE_TILT, float(angleTilt))
pairRow.writeToMd(classMd, objId)
classMd.write(blockMd, xmipp.MD_APPEND)
def rowFromMd(md, objId):
row = XmippMdRow()
row.readFromMd(md, objId)
return row
def rowFromMd(md, objId):
row = XmippMdRow()
row.readFromMd(md, objId)
return row
def _appendRctImages(self, particles):
blockMd = "class%06d_images@%s" % (particles.getObjId(),
self.rctClassesFn)
classMd = xmipp.MetaData()
uImages = self.inputParticlesTiltPair.get().getUntilted()
tImages = self.inputParticlesTiltPair.get().getTilted()
sangles = self.inputParticlesTiltPair.get().getCoordsPair().getAngles()
uMics = self.inputParticlesTiltPair.get().getCoordsPair().getMicsPair(
).getUntilted()
tMics = tImages.getCoordinates().getMicrographs()
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 = XmippMdRow()
pairRow.setValue(xmipp.MDL_IMAGE, getImageLocation(uImg))
uCoord = uImg.getCoordinate()
micId = uCoord.getMicId()
uMic = uMics[micId]
angles = sangles[micId]
pairRow.setValue(xmipp.MDL_MICROGRAPH, uMic.getFileName())
pairRow.setValue(xmipp.MDL_XCOOR, uCoord.getX())
pairRow.setValue(xmipp.MDL_YCOOR, uCoord.getY())
pairRow.setValue(xmipp.MDL_ENABLED, 1)
pairRow.setValue(xmipp.MDL_ITEM_ID, long(imgId))
pairRow.setValue(xmipp.MDL_REF, 1)
alignment = img.getTransform()
# Scale alignment by scaleFactor
alignment.scale(scaleFactor)
alignmentToRow(alignment, pairRow, alignType=ALIGN_2D)
pairRow.setValue(xmipp.MDL_IMAGE_TILTED,
getImageLocation(tImg))
tMic = tMics[micId]
pairRow.setValue(xmipp.MDL_MICROGRAPH_TILTED,
tMic.getFileName())
(angleY, angleY2, angleTilt) = angles.getAngles()
pairRow.setValue(xmipp.MDL_ANGLE_Y, float(angleY))
pairRow.setValue(xmipp.MDL_ANGLE_Y2, float(angleY2))
pairRow.setValue(xmipp.MDL_ANGLE_TILT, float(angleTilt))
pairRow.writeToMd(classMd, objId)
classMd.write(blockMd, xmipp.MD_APPEND)