Source code for relion.convert.convert_utils

# **************************************************************************
# *
# * Authors:     J.M. de la Rosa Trevin ( [1]
# *              Grigory Sharov ( [2]
# *
# * [1] SciLifeLab, Stockholm University
# * [2] MRC Laboratory of Molecular Biology, MRC-LMB
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# * the Free Software Foundation; either version 3 of the License, or
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# * You should have received a copy of the GNU General Public License
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# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307  USA
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# *  All comments concerning this program package may be sent to the
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Utility functions for conversions that will be used from both
newer Relion3.1 routines and old ones.

import os
from emtable import Table

import pyworkflow.utils as pwutils
from pwem.constants import NO_INDEX
from pwem.emlib.image import ImageHandler

from relion import Plugin

[docs]def locationToRelion(index, filename): """ Convert an index and filename location to a string with @ as expected in Relion. """ if index != NO_INDEX: return "%06d@%s" % (index, filename) return filename
[docs]def relionToLocation(filename): """ Return a location (index, filename) given a Relion filename with the index@filename structure. """ if '@' in filename: indexStr, fn = filename.split('@') return int(indexStr), str(fn) else: return NO_INDEX, str(filename)
[docs]def convertBinaryFiles(imgSet, outputDir, extension='mrcs', forceConvert=False): """ Convert binary images files to a format read by Relion. Or create links if there is no need to convert the binary files. Params: imgSet: input image set to be converted. outputDir: where to put the converted file(s) extension: extension accepted by the program forceConvert: if True, the files will be converted and no root will be used Return: A dictionary with old-file as key and new-file as value If empty, not conversion was done. """ filesDict = {} ih = ImageHandler() outputRoot = outputDir if forceConvert else os.path.join(outputDir, 'input') # Get the extension without the dot stackFiles = imgSet.getFiles() ext = pwutils.getExt(next(iter(stackFiles)))[1:] rootDir = pwutils.commonPath(list(stackFiles)) def getUniqueFileName(fn, extension): """ Get an unique file for either link or convert files. It is possible that the base name overlap if they come from different runs. (like particles.mrcs after relion preprocess) """ newFn = os.path.join(outputRoot, pwutils.replaceBaseExt(fn, extension)) newRoot = pwutils.removeExt(newFn) values = filesDict.values() counter = 1 while newFn in values: counter += 1 newFn = '%s_%05d.%s' % (newRoot, counter, extension) return newFn def createBinaryLink(fn): """ Just create a link named .mrcs to Relion understand that it is a binary stack file and not a volume. """ newFn = getUniqueFileName(fn, extension) if not os.path.exists(newFn): pwutils.createLink(fn, newFn) print(" %s -> %s" % (newFn, fn)) return newFn def convertStack(fn): """ Convert from a format that is not read by Relion to an spider stack. """ newFn = getUniqueFileName(fn, 'mrcs') ih.convertStack(fn, newFn) print(" %s -> %s" % (newFn, fn)) return newFn def replaceRoot(fn): """ Link create to the root folder, so just replace that in the name, no need to do anything else. """ return fn.replace(rootDir, outputRoot) if forceConvert: print("convertBinaryFiles: forceConvert = True") mapFunc = convertStack elif ext == extension: print("convertBinaryFiles: creating soft links.") print(" Root: %s -> %s" % (outputRoot, rootDir)) mapFunc = replaceRoot pwutils.createAbsLink(os.path.abspath(rootDir), outputRoot) elif ext == 'mrc' and extension == 'mrcs': print("convertBinaryFiles: creating soft links (mrcs -> mrc).") mapFunc = createBinaryLink elif ext.endswith('hdf'): # assume eman .hdf format print("convertBinaryFiles: converting stacks. (%s -> %s)" % (extension, ext)) mapFunc = convertStack else: mapFunc = None if mapFunc is not None: pwutils.makePath(outputRoot) for fn in stackFiles: newFn = mapFunc(fn) # convert or link filesDict[fn] = newFn # map new filename return filesDict
[docs]def convertBinaryVol(vol, outputDir): """ Convert binary volume to a format read by Relion. Params: vol: input volume object to be converted. outputDir: where to put the converted file(s) Return: new file name of the volume (converted or not). """ ih = ImageHandler() fn = vol.getFileName() if not fn.endswith('.mrc'): newFn = os.path.join(outputDir, pwutils.replaceBaseExt(fn, 'mrc')) ih.convert(fn, newFn) return newFn return fn
[docs]def convertMask(img, outputPath, newPix=None, newDim=None, threshold=True, invert=False): """ Convert mask to mrc format read by Relion. Params: img: input image to be converted. outputPath: it can be either a directory or a file path. If it is a directory, the output name will be inferred from input and put into that directory. If it is not a directory, it is assumed is the output filename. newPix: output pixel size (equals input if None) newDim: output box size Return: new file name of the mask. """ index, filename = img.getLocation() imgFn = locationToRelion(index, filename) inPix = img.getSamplingRate() if os.path.isdir(outputPath): outFn = os.path.join(outputPath, pwutils.replaceBaseExt(imgFn, 'mrc')) else: outFn = outputPath if invert: # unfortunately relion does not allow to use # add_constant and multiply_constant together # so let us multiply first params = '--i %s --o %s --angpix %0.5f' % (imgFn, outFn, inPix) params += ' --multiply_constant -1' pwutils.runJob(None, 'relion_image_handler', params, env=Plugin.getEnviron()) imgFn = outFn params = '--i %s --o %s --angpix %0.5f' % (imgFn, outFn, inPix) if newPix is not None: # be careful with this rescale param # because introduce some artefacts even if # the sampling is the same than the input 3D mask params += ' --rescale_angpix %0.5f' % newPix if newDim is not None: params += ' --new_box %d' % newDim if threshold: params += ' --threshold_above 1 --threshold_below 0' if invert: # unfortunately relion does not allow to use # add_constant and multiply_constant together params += ' --add_constant 1' pwutils.runJob(None, 'relion_image_handler', params, env=Plugin.getEnviron()) return outFn
[docs]def relativeFromFileName(imgRow, prefixPath): """ Remove some prefix from filename in row. """ index, imgPath = relionToLocation(imgRow['rlnImageName']) newImgPath = os.path.relpath(imgPath, prefixPath) imgRow['rlnImageName'] = locationToRelion(index, newImgPath)
[docs]def getVolumesFromPostprocess(postStar): """ Return the filenames of half1, half2 and mask from a given file. """ table = Table(fileName=postStar, tableName='general') row = table[0] return (row.rlnUnfilteredMapHalf1, row.rlnUnfilteredMapHalf2, row.rlnMaskName)