Source code for xmipp3.protocols.protocol_cl2d

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# * Authors:     J.M. De la Rosa Trevin (
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# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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from os.path import join, dirname, exists
from glob import glob

import pyworkflow.protocol.params as param
import pyworkflow.protocol.constants as const
from pyworkflow.utils.path import cleanPath, makePath

import pwem.emlib.metadata as md
from pwem.protocols import ProtClassify2D
from pwem.objects import SetOfClasses2D
from pwem.constants import ALIGN_NONE, ALIGN_2D

from xmipp3.convert import (writeSetOfParticles, createItemMatrix,
                            writeSetOfClasses2D, xmippToLocation,

# Comparison methods enum

# Clustering methods enum

# Classes keys
CLASSES_CORE = '_core'
CLASSES_STABLE_CORE = '_stable_core'

# Suggested number of images per class

[docs]class XmippProtCL2D(ProtClassify2D): """ Classifies a set of images using a clustering algorithm to subdivide the original dataset into a given number of classes. """ _label = 'cl2d' def __init__(self, **args): ProtClassify2D.__init__(self, **args) if self.numberOfMpi.get() < 2: self.numberOfMpi.set(2) def _defineFileNames(self): """ Centralize how files are called within the protocol. """ self.levelPath = self._getExtraPath('level_%(level)02d/') myDict = { 'input_particles': self._getTmpPath('input_particles.xmd'), 'input_references': self._getTmpPath('input_references.xmd'), 'final_classes': self._getPath('classes2D%(sub)s.sqlite'), 'output_particles': self._getExtraPath('images.xmd'), 'level_classes' : self.levelPath + 'level_classes%(sub)s.xmd', 'level_images' : self.levelPath + 'level_images%(sub)s.xmd', 'classes_scipion': (self.levelPath + 'classes_scipion_level_' '%(level)02d%(sub)s.sqlite'), 'classes_hierarchy': self._getExtraPath("classes%(sub)s" "_hierarchy.txt") } self._updateFilenamesDict(myDict) #--------------------------- DEFINE param functions ------------------------ def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputParticles', param.PointerParam, label="Input images", important=True, pointerClass='SetOfParticles', help='Select the input images to be classified.') form.addParam('numberOfClasses', param.IntParam, default=64, label='Number of classes:', help='Number of classes (or references) to be generated.') form.addParam('randomInitialization', param.BooleanParam, default=True, expertLevel=const.LEVEL_ADVANCED, label='Random initialization of classes:', help="Initialize randomly the first classes. If you " "don't initialize randomly, you must supply a set " "of initial classes") form.addParam('initialClasses', param.PointerParam, label="Initial classes", condition="not randomInitialization", pointerClass='SetOfClasses2D, SetOfAverages', help='Set of initial classes to start the classification') form.addParam('numberOfInitialClasses', param.IntParam, default=4, expertLevel=const.LEVEL_ADVANCED, label='Number of initial classes:', condition="randomInitialization", help='Initial number of classes used in the first level.') form.addParam('numberOfIterations', param.IntParam, default=10, expertLevel=const.LEVEL_ADVANCED, label='Number of iterations:', help='Maximum number of iterations within each level.') form.addParam('comparisonMethod', param.EnumParam, choices=['correlation', 'correntropy'], label="Comparison method", default=CMP_CORRELATION, expertLevel=const.LEVEL_ADVANCED, display=param.EnumParam.DISPLAY_COMBO, help='Use correlation or correntropy') form.addParam('clusteringMethod', param.EnumParam, choices=['classical', 'robust'], label="Clustering method", default=CL_CLASSICAL, expertLevel=const.LEVEL_ADVANCED, display=param.EnumParam.DISPLAY_COMBO, help='Use the classical clustering criterion or the ' 'robust') form.addParam('extraParams', param.StringParam, expertLevel=const.LEVEL_ADVANCED, label='Additional parameters', help='Additional parameters for classify_CL2D: \n' ' --verbose, --corrSplit, ...') form.addSection(label='Core analysis') form.addParam('doCore', param.BooleanParam, default=True, label='Perform core analysis', help='An image belongs to the core if it is close (see ' 'Junk Zscore and PCA Zscore) to the class center') form.addParam('thZscore', param.FloatParam, default=3, label='Junk Zscore', expertLevel=const.LEVEL_ADVANCED, condition='doCore', help='Which is the average Z-score to be considered as ' 'junk. Typical values go from 1.5 to 3. For the ' 'Gaussian distribution 99.5% of the data is ' 'within a Z-score of 3. Lower Z-scores reject more ' 'images. Higher Z-scores accept more images.') form.addParam('thPCAZscore', param.FloatParam, default=3, condition='doCore', expertLevel=const.LEVEL_ADVANCED, label='PCA Zscore', help='Which is the PCA Z-score to be considered as junk. ' 'Typical values go from 1.5 to 3. For the Gaussian ' 'distribution 99.5% of the data is within a ' 'Z-score of 3. Lower Z-scores reject more images. ' 'Higher Z-scores accept more images.') form.addParam('doStableCore', param.BooleanParam, default=True, condition='doCore', label='Perform stable core analysis', help='Two images belong to the stable core if they have ' 'been essentially together along the classification ' 'process') form.addParam('tolerance', param.IntParam, default=1, label='Tolerance', expertLevel=const.LEVEL_ADVANCED, condition='doCore and doStableCore', help='An image belongs to the stable core if it has been ' 'with other images in the same class in all the ' 'previous levels except possibly a few of them. ' 'Tolerance defines how few is few. Tolerance=0 ' 'means that an image must be in all previous levels ' 'with the rest of images in the core.',) form.addParam("computeHierarchy", param.BooleanParam, default=False, label="Compute class hierarchy", expertLevel=const.LEVEL_ADVANCED) form.addParam("analyzeRejected", param.BooleanParam, default=False, label="Analyze rejected particles", expertLevel=const.LEVEL_ADVANCED, help='To see the analysis you need to browse the ' 'execution directory and go into the different ' 'levels') form.addParallelSection(threads=0, mpi=4) #--------------------------- INSERT steps functions ------------------------ def _insertAllSteps(self): """ Mainly prepare the command line for call cl2d program""" # Convert input images if necessary self._defineFileNames() if self.initialClasses.get(): initialClassesId = self.initialClasses.get().getObjId() else: initialClassesId = None self._insertFunctionStep('convertInputStep', self.inputParticles.get().getObjId(), initialClassesId) self._params = {'imgsFn': self._getFileName('input_particles'), 'extraDir': self._getExtraPath(), 'nref': self.numberOfClasses.get(), 'nref0': self.numberOfInitialClasses.get(), 'iter': self.numberOfIterations.get(), 'extraParams': self.extraParams.get(''), 'thZscore': self.thZscore.get(), 'thPCAZscore': self.thPCAZscore.get(), 'tolerance': self.tolerance.get(), 'initClassesFn': self._getFileName('input_references') } args = self._defArgsClassify() self._insertClassifySteps("xmipp_classify_CL2D", args, subset=CLASSES) #TODO: Added this If. Check with COSS error if makes sense. #Also, if conditions below are enough to validate that classes core # and stable core are not empty if not self.randomInitialization: self.numberOfInitialClasses.set(self.initialClasses.get().getSize()) # Analyze cores and stable cores if self.numberOfClasses > self.numberOfInitialClasses and self.doCore: program = "xmipp_classify_CL2D_core_analysis" # core analysis args = self._defArgsCoreAnalisys() self._insertClassifySteps(program, args, subset=CLASSES_CORE) if self.analyzeRejected: self._insertFunctionStep('analyzeOutOfCores', CLASSES_CORE) if (self.numberOfClasses > (2 * self.numberOfInitialClasses.get()) and self.doStableCore): # Number of levels should be > 2 # stable core analysis args = self._defArgsCoreAnalisys("stable") self._insertClassifySteps(program, args, subset=CLASSES_STABLE_CORE) if self.analyzeRejected: self._insertFunctionStep('analyzeOutOfCores', CLASSES_STABLE_CORE) def _insertClassifySteps(self, program, args, subset=CLASSES): """ Defines four steps for the subset: 1. Run the main program. 2. Evaluate classes 3. Sort the classes. 4. And create output """ self._insertRunJobStep(program, args % self._params) self._insertFunctionStep('evaluateClassesStep', subset) self._insertFunctionStep('sortClassesStep', subset) self._insertFunctionStep('createOutputStep', subset) #--------------------------- STEPS functions -------------------------------
[docs] def convertInputStep(self, particlesId, classesId): writeSetOfParticles(self.inputParticles.get(), self._getFileName('input_particles'), alignType=ALIGN_NONE) if not self.randomInitialization: if isinstance(self.initialClasses.get(), SetOfClasses2D): writeSetOfClasses2D(self.initialClasses.get(), self._getFileName('input_references'), writeParticles=False) else: writeSetOfParticles(self.initialClasses.get(), self._getFileName('input_references'))
[docs] def sortClassesStep(self, subset=''): """ Sort the classes and provided a quality criterion. """ levelMdFiles = self._getAllLevelMdFiles(subset) for mdFn in levelMdFiles: fnRoot = join(dirname(mdFn), "classes%s_sorted" % subset) params = "-i classes@%s --oroot %s" % (mdFn, fnRoot) self.runJob("xmipp_image_sort", params) mdFnOut = fnRoot + ".xmd" mdOut = md.MetaData(mdFnOut) for objId in mdOut: mdOut.setValue(md.MDL_ITEM_ID, int(mdOut.getValue(md.MDL_REF,objId)),objId) mdOut.write("classes_sorted@" + mdFn, md.MD_APPEND)
[docs] def evaluateClassesStep(self, subset=''): """ Calculate the FRC and output the hierarchy for each level of classes. """ levelMdFiles = self._getAllLevelMdFiles(subset) hierarchyFnOut = self._getExtraPath("classes%s_hierarchy.txt" % subset) prevMdFn = None for mdFn in levelMdFiles: self.runJob("xmipp_classify_evaluate_classes", "-i " + mdFn, numberOfMpi=1) if self.computeHierarchy and prevMdFn is not None: args = "--i1 %s --i2 %s -o %s" % (prevMdFn, mdFn, hierarchyFnOut) if exists(hierarchyFnOut): args += " --append" self.runJob("xmipp_classify_compare_classes", args, numberOfMpi=1) prevMdFn = mdFn
[docs] def createOutputStep(self, subset=''): """ Store the SetOfClasses2D object resulting from the protocol execution. """ inputParticles = self.inputParticles.get() level = self._lastLevel() subsetFn = self._getFileName("level_classes", level=level, sub=subset) if exists(subsetFn): classes2DSet = self._createSetOfClasses2D(inputParticles, subset) self._fillClassesFromLevel(classes2DSet, "last", subset) result = {'outputClasses' + subset: classes2DSet} self._defineOutputs(**result) self._defineSourceRelation(self.inputParticles, classes2DSet)
[docs] def analyzeOutOfCores(self,subset): """ Analyze which images are out of cores """ levelMdFiles = self._getAllLevelMdFiles(subset) for fn in levelMdFiles: mdAll=md.MetaData() blocks = md.getBlocksInMetaDataFile(fn) fnDir=dirname(fn) # Gather all images in block for block in blocks: if block.startswith('class0'): mdClass=md.MetaData(block+"@"+fn) mdAll.unionAll(mdClass) if mdAll.size()>0: # Compute difference to images fnSubset=join(fnDir,"images%s.xmd"%subset) mdAll.write(fnSubset) fnOutOfSubset=join(fnDir,"imagesOut.xmd") inputMd = self._getFileName('input_particles') args = "-i %s --set subtraction %s -o %s" % (inputMd, fnSubset, fnOutOfSubset) self.runJob("xmipp_metadata_utilities", args, numberOfMpi=1, numberOfThreads=1) # Remove disabled and intermediate files mdClass=md.MetaData(fnOutOfSubset) mdClass.removeDisabled() fnRejected="images_rejected@"+fn mdClass.write(fnRejected,md.MD_APPEND) cleanPath(fnOutOfSubset) cleanPath(fnSubset) # If enough images, make a small summary if mdClass.size()>100: from math import ceil fnRejectedDir=join(fnDir,"rejected%s"%subset) makePath(fnRejectedDir) Nclasses=int(ceil(mdClass.size()/300)) self.runJob("xmipp_classify_CL2D", "-i %s --nref0 1 --nref %d --iter 5 --distance " "correlation --classicalMultiref " "--classifyAllImages --odir %s" %( fnRejected, Nclasses, fnRejectedDir))
#--------------------------- INFO functions -------------------------------- def _validate(self): validateMsgs = [] if self.numberOfMpi <= 1: validateMsgs.append('Mpi needs to be greater than 1.') if self.numberOfInitialClasses > self.numberOfClasses: validateMsgs.append('The number of final classes cannot be smaller' ' than the number of initial classes') if isinstance(self.initialClasses.get(), SetOfClasses2D): if not self.initialClasses.get().hasRepresentatives(): validateMsgs.append("The input classes should have " "representatives.") return validateMsgs def _warnings(self): validateMsgs = [] if self.inputParticles.get().getSamplingRate() < 3: validateMsgs.append("The sampling rate is smaller than 3 A/pix, " "consider downsampling the input images to " "speed-up the process. Probably you don't want" " such a precise 2D classification.") return validateMsgs def _citations(self): citations=['Sorzano2010a'] if self.doCore: citations.append('Sorzano2014') return citations def _summaryLevelFiles(self, summary, levelFiles, subset): if levelFiles: levels = [i for i in range(self._lastLevel()+1)] summary.append('Computed classes%s, levels: %s' % (subset, levels)) def _summary(self): self._defineFileNames() summary = [] levelFiles = self._getAllLevelMdFiles() if not hasattr(self, 'outputClasses'): summary.append("Output classes not ready yet.") elif levelFiles: self._summaryLevelFiles(summary, levelFiles, CLASSES) self._summaryLevelFiles(summary, self._getAllLevelMdFiles(CLASSES_CORE), CLASSES_CORE) self._summaryLevelFiles(summary, self._getAllLevelMdFiles(CLASSES_STABLE_CORE), CLASSES_STABLE_CORE) else: summary.append("Input Particles: *%d*\nClassified into *%d* classes\n" % (self.inputParticles.get().getSize(), self.numberOfClasses.get())) # summary.append('- Used a _clustering_ algorithm to subdivide the original dataset into the given number of classes') return summary def _methods(self): strline = '' if hasattr(self, 'outputClasses'): strline += 'We classified %d particles from %s ' % (self.inputParticles.get().getSize(), self.getObjectTag('inputParticles')) strline += 'into %d classes %s using CL2D [Sorzano2010a]. ' % (self.numberOfClasses, self.getObjectTag('outputClasses')) strline += '%s method was used to compare images and %s clustering criterion. '%\ (self.getEnumText('comparisonMethod'), self.getEnumText('clusteringMethod')) if self.numberOfClasses > self.numberOfInitialClasses and self.doCore: strline+='We also calculated the class cores %s' % self.getObjectTag('outputClasses_core') if self.numberOfClasses > (2 * self.numberOfInitialClasses.get()) and self.doStableCore: # Number of levels should be > 2 strline += ' and the class stable cores %s' % self.getObjectTag('outputClasses_stable_core') strline+=' [Sorzano2014].' return [strline] #--------------------------- UTILS functions ------------------------------- def _defArgsClassify(self): # Prepare arguments to call program: xmipp_classify_CL2D args = '-i %(imgsFn)s --odir %(extraDir)s --oroot level --nref ' \ '%(nref)d --iter %(iter)d %(extraParams)s' if self.comparisonMethod == CMP_CORRELATION: args += ' --distance correlation' if self.clusteringMethod == CL_CLASSICAL: args += ' --classicalMultiref' if self.randomInitialization: args += ' --nref0 %(nref0)d' else: args += ' --ref0 %(initClassesFn)s' return args def _defArgsCoreAnalisys(self,coreType="core"): args = " --dir %(extraDir)s --root level " if coreType =="core": args += "--computeCore %(thZscore)f %(thPCAZscore)f" else: args += "--computeStableCore %(tolerance)d" return args def _getAllLevelMdFiles(self, subset=''): """ Grab the metadata class files for each level. """ levelMdFiles = [] lastLevel = self._lastLevel() for i in range(lastLevel): classFn = self._getLevelMdClasses(lev=i, block="", subset=subset) if exists(classFn): levelMdFiles.append(classFn) return levelMdFiles def _createItemMatrix(self, item, row): createItemMatrix(item, row, align=ALIGN_2D) def _updateParticle(self, item, row): item.setClassId(row.getValue(md.MDL_REF)) item.setTransform(rowToAlignment(row, ALIGN_2D)) def _updateClass(self, item): classId = item.getObjId() if classId in self._classesInfo: index, fn, _ = self._classesInfo[classId] item.setAlignment2D() rep = item.getRepresentative() rep.setLocation(index, fn) rep.setSamplingRate(self.inputParticles.get().getSamplingRate()) def _loadClassesInfo(self, filename): """ Read some information about the produced 2D classes from the metadata file. """ self._classesInfo = {} # store classes info, indexed by class id mdClasses = md.MetaData(filename) for classNumber, row in enumerate(md.iterRows(mdClasses)): index, fn = xmippToLocation(row.getValue(md.MDL_IMAGE)) # Store info indexed by id, we need to store the row.clone() since # the same reference is used for iteration self._classesInfo[classNumber + 1] = (index, fn, row.clone()) def _fillClassesFromLevel(self, clsSet, level, subset): """ Create the SetOfClasses2D from a given iteration. """ self._loadClassesInfo(self._getLevelMdClasses(lev=level, subset=subset)) if subset == '' and level == "last": xmpMd = self._getFileName('output_particles') if not exists(xmpMd): xmpMd = self._getLevelMdImages(level, subset) else: xmpMd = self._getLevelMdImages(level, subset) iterator = md.SetMdIterator(xmpMd, sortByLabel=md.MDL_ITEM_ID, updateItemCallback=self._updateParticle, skipDisabled=True) # itemDataIterator is not neccesary because, the class SetMdIterator # contain all the information about the metadata clsSet.classifyItems(updateItemCallback=iterator.updateItem, updateClassCallback=self._updateClass) def _getLevelMdClasses(self, lev=0, block="classes", subset=""): """ Return the classes metadata for this iteration. block parameter can be 'info' or 'classes'.""" if lev == "last": lev = self._lastLevel() mdFile = self._getFileName('level_classes', level=lev, sub=subset) if block: mdFile = block + '@' + mdFile return mdFile def _getLevelMdImages(self, level, subset): if level == "last": level = self._lastLevel() xmpMd = self._getFileName('level_images', level=level, sub=subset) if not exists(xmpMd): self._createLevelMdImages(level, subset) return xmpMd def _createLevelMdImages(self, level, sub): if level == "last": level = self._lastLevel() mdClassesFn = self._getLevelMdClasses(lev=level, block="", subset=sub) mdImgs = md.joinBlocks(mdClassesFn, "class0") mdImgs.write(self._getFileName('level_images',level=level, sub=sub)) def _lastLevel(self): """ Find the last Level number """ clsFn = self._getFileName('level_classes', level=0, sub="") levelTemplate = clsFn.replace('level_00','level_??') lev = len(glob(levelTemplate)) - 1 return lev def _getLevelClasses(self, lev, suffix, clean=False): """ Return a classes .sqlite file for this level. If the file doesn't exists, it will be created by converting from this level level_images.xmd file. """ dataClasses = self._getFileName('classes_scipion', level=lev, sub=suffix) if clean: cleanPath(dataClasses) if not exists(dataClasses): clsSet = SetOfClasses2D(filename=dataClasses) clsSet.setImages(self.inputParticles.get()) self._fillClassesFromLevel(clsSet, level=lev, subset=suffix) clsSet.write() clsSet.close() return dataClasses