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 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 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 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 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 _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 _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)
