def getFilePreview(self, objFile):
self._imgPreview = None
self._imgInfo = None
filename = objFile.getPath()
ext = pwutils.getExt(filename)
if ext == '.xmd' or ext == '.ctfparam' or ext == '.pos' or ext == '.doc':
msg = "*Metadata File* "
blocks = emlib.getBlocksInMetaDataFile(filename)
nblocks = len(blocks)
if nblocks <= 1:
mdStr = self._getMdString(filename)
msg += " (single block)\n"
if self._imgInfo:
msg += "\nFirst item: \n" + self._imgInfo
msg += '\n' + mdStr
else:
mdStr = self._getMdString(filename, blocks[0])
msg += " (%d blocks) " % nblocks
if self._imgInfo:
msg += "\nFirst item: \n" + self._imgInfo
msg += "\nFirst block: \n" + mdStr
msg += "\nAll blocks:" + ''.join(
["\n - %s" % b for b in blocks])
elif ext == '.star':
msg = "*Relion STAR file* \n"
msg += self._getMdString(filename)
return self._imgPreview, msg
def runInitAngularReferenceFileStep(self):
'''Create Initial angular file. Either fill it with zeros or copy input'''
#NOTE: if using angles, self.selFileName file should contain angles info
md = emlib.MetaData(self.selFileName)
# Ensure this labels are always
md.addLabel(emlib.MDL_ANGLE_ROT)
md.addLabel(emlib.MDL_ANGLE_TILT)
md.addLabel(emlib.MDL_ANGLE_PSI)
expImages = self._getFileName('inputParticlesDoc')
ctfImages = self._getFileName('imageCTFpairs')
md.write(self._getExpImagesFileName(expImages))
blocklist = emlib.getBlocksInMetaDataFile(ctfImages)
mdCtf = emlib.MetaData()
mdAux = emlib.MetaData()
readLabels = [emlib.MDL_ITEM_ID, emlib.MDL_IMAGE]
for block in blocklist:
#read ctf block from ctf file
mdCtf.read(block + '@' + ctfImages, readLabels)
#add ctf columns to images file
mdAux.joinNatural(md, mdCtf)
# write block in images file with ctf info
mdCtf.write(block + '@' + expImages, emlib.MD_APPEND)
return [expImages]
def _pickMicrograph(self, mic, *args):
micPath = mic.getFileName()
# Get particle picking boxsize from the previous run
boxSize = self.particlePickingRun.outputCoordinates.getBoxSize()
modelRoot = self._getExtraPath('model')
micName = removeBaseExt(micPath)
proceed = True
if self.micsToPick == MICS_SAMEASPICKING:
basePos = replaceBaseExt(micPath, "pos")
fnPos = self.particlePickingRun._getExtraPath(basePos)
if exists(fnPos):
blocks = emlib.getBlocksInMetaDataFile(fnPos)
copy = True
if 'header' in blocks:
mdheader = emlib.MetaData("header@" + fnPos)
state = mdheader.getValue(
emlib.MDL_PICKING_MICROGRAPH_STATE,
mdheader.firstObject())
if state == "Available":
copy = False
if copy:
# Copy manual .pos file of this micrograph
copyFile(fnPos, self._getExtraPath(basename(fnPos)))
proceed = False
if proceed:
args = "-i %s " % micPath
args += "--particleSize %d " % boxSize
args += "--model %s " % modelRoot
args += "--outputRoot %s " % self._getExtraPath(micName)
args += "--mode autoselect --thr %d" % self.numberOfThreads
self.runJob("xmipp_micrograph_automatic_picking", args)
def homogeneizeStep(self):
minClass = self.homogeneize.get()
fnNeighbours = self._getExtraPath("neighbours.xmd")
# Look for the block with the minimum number of images
if minClass == 0:
minClass = 1e38
for block in emlib.getBlocksInMetaDataFile(fnNeighbours):
projNumber = int(block.split("_")[1])
fnDir = self._getExtraPath("direction_%d" % projNumber,
"level_00", "class_classes.xmd")
if exists(fnDir):
blockSize = md.getSize("class000001_images@" + fnDir)
if blockSize < minClass:
minClass = blockSize
# Construct the homogeneized metadata
mdAll = emlib.MetaData()
mdSubset = emlib.MetaData()
mdRandom = emlib.MetaData()
for block in emlib.getBlocksInMetaDataFile(fnNeighbours):
projNumber = int(block.split("_")[1])
fnDir = self._getExtraPath("direction_%d" % projNumber, "level_00",
"class_classes.xmd")
if exists(fnDir):
mdDirection = emlib.MetaData("class000001_images@" + fnDir)
mdRandom.randomize(mdDirection)
mdSubset.selectPart(mdRandom, 0, min(mdRandom.size(),
minClass))
mdAll.unionAll(mdSubset)
mdAll.removeDuplicates(md.MDL_ITEM_ID)
mdAll.sort(md.MDL_ITEM_ID)
mdAll.fillConstant(md.MDL_PARTICLE_ID, 1)
fnHomogeneous = self._getExtraPath("images_homogeneous.xmd")
mdAll.write(fnHomogeneous)
self.runJob("xmipp_metadata_utilities",
'-i %s --operate modify_values "particleId=itemId"' %
fnHomogeneous,
numberOfMpi=1)
def classifyGroupsStep(self):
# Create two metadatas, one for classes and another one for images
mdClasses = emlib.MetaData()
mdImages = emlib.MetaData()
fnNeighbours = self._getExtraPath("neighbours.xmd")
fnGallery = self._getExtraPath("gallery.stk")
self.classCount = 0
self.classImages = set()
for block in emlib.getBlocksInMetaDataFile(fnNeighbours):
# Figure out the projection number from the block name
projNumber = int(block.split("_")[1])
self.classifyOneGroup(projNumber,
projMdBlock="%s@%s" % (block, fnNeighbours),
projRef="%06d@%s" % (projNumber, fnGallery),
mdClasses=mdClasses,
mdImages=mdImages)
galleryMd = emlib.MetaData(self._getExtraPath("gallery.doc"))
# Increment the reference number to starts from 1
galleryMd.operate("ref=ref+1")
mdJoined = emlib.MetaData()
# Add extra information from the gallery metadata
mdJoined.join1(mdClasses, galleryMd, emlib.MDL_REF)
# Remove unnecessary columns
md.keepColumns(mdJoined, "ref", "ref2", "image", "image1",
"classCount", "angleRot", "angleTilt")
# Write both classes and images
fnDirectional = self._getDirectionalClassesFn()
self.info("Writting classes info to: %s" % fnDirectional)
mdJoined.write(fnDirectional)
fnDirectionalImages = self._getDirectionalImagesFn()
self.info("Writing images info to: %s" % fnDirectionalImages)
mdImages.write(fnDirectionalImages)