def _createClasses(self, partSet): self._classesDict = {} # store classes info, indexed by class id pathDict = {} self.protocol.info('Loading classes info from: %s' % self._modelStarFile) modelMd = md.MetaData('model_classes@' + self._modelStarFile) for classNumber, objId in enumerate(modelMd): row = md.Row() row.readFromMd(modelMd, objId) index, fn = relionToLocation(row.getValue('rlnReferenceImage')) if fn in pathDict: newFn = pathDict.get(fn) else: clsPath = findRootFrom(self._modelStarFile, fn) if clsPath is None: newFn = fn else: newFn = self.protocol._getExtraPath(os.path.basename(fn)) self.copyOrLink(os.path.join(clsPath, fn), newFn) pathDict[fn] = newFn self._classesDict[classNumber+1] = (index, newFn, row) clsSet = self._classesFunc(partSet) clsSet.classifyItems(updateClassCallback=self._updateClass) self.protocol._defineOutputs(outputClasses=clsSet) self.protocol._defineSourceRelation(partSet, clsSet)
def _createClasses(self, partSet): self._classesDict = {} # store classes info, indexed by class id pathDict = {} self.protocol.info('Loading classes info from: %s' % self._modelStarFile) modelMd = md.MetaData('model_classes@' + self._modelStarFile) for classNumber, objId in enumerate(modelMd): row = md.Row() row.readFromMd(modelMd, objId) index, fn = relionToLocation(row.getValue('rlnReferenceImage')) if fn in pathDict: newFn = pathDict.get(fn) else: clsPath = findRootFrom(self._modelStarFile, fn) if clsPath is None: newFn = fn else: newFn = self.protocol._getExtraPath(os.path.basename(fn)) self.copyOrLink(os.path.join(clsPath, fn), newFn) pathDict[fn] = newFn self._classesDict[classNumber + 1] = (index, newFn, row) clsSet = self._classesFunc(partSet) clsSet.classifyItems(updateClassCallback=self._updateClass) self.protocol._defineOutputs(outputClasses=clsSet) self.protocol._defineSourceRelation(partSet, clsSet)
def _findImagesPath(self, label, warnings=True): row = md.getFirstRow(self._starFile) if row is None: raise Exception("Can not import from an empty metadata: %s" % self._starFile) if not row.containsLabel(label): raise Exception("Label *%s* is missing in metadata: %s" % (md.label2Str(label), self._starFile)) index, fn = relionToLocation(row.getValue(label)) self._imgPath = findRootFrom(self._starFile, fn) if warnings and self._imgPath is None: self.protocol.warning( "Binary data was not found from metadata: %s" % self._starFile) if (self._starFile.endswith('_data.star') and self._getModelFile(self._starFile)): self._modelStarFile = self._getModelFile(self._starFile) modelRow = md.getFirstRow(self._modelStarFile) classDimensionality = modelRow.getValue( 'rlnReferenceDimensionality') self._optimiserFile = self._starFile.replace( '_data.star', '_optimiser.star') if not exists(self._optimiserFile): raise Exception("Missing required optimiser star file: %s" % self._optimiserFile) optimiserRow = md.getFirstRow(self._optimiserFile) autoRefine = optimiserRow.containsLabel('rlnModelStarFile2') self.alignType = ALIGN_PROJ if not autoRefine: if classDimensionality == 3: self._classesFunc = self.protocol._createSetOfClasses3D else: self._classesFunc = self.protocol._createSetOfClasses2D self.alignType = ALIGN_2D else: self._classesFunc = None else: self.alignType = ALIGN_NONE self._classesFunc = None self._modelStarFile = None modelRow = None # Check if the MetaData contains either MDL_MICROGRAPH_ID # or MDL_MICROGRAPH, this will be used when imported # particles to keep track of the particle's micrograph self._micIdOrName = (row.containsLabel('rlnMicrographName') or row.containsLabel('rlnMicrographId')) #init dictionary. It will be used in the preprocessing self.micDict = {} return row, modelRow
def _findImagesPath(self, label, warnings=True): row = md.getFirstRow(self._starFile) if row is None: raise Exception("Can not import from an empty metadata: %s" % self._starFile) if not row.containsLabel(label): raise Exception("Label *%s* is missing in metadata: %s" % (md.label2Str(label), self._starFile)) index, fn = relionToLocation(row.getValue(label)) self._imgPath = findRootFrom(self._starFile, fn) if warnings and self._imgPath is None: self.protocol.warning("Binary data was not found from metadata: %s" % self._starFile) if (self._starFile.endswith('_data.star') and self._getModelFile(self._starFile)): self._modelStarFile = self._getModelFile(self._starFile) modelRow = md.getFirstRow(self._modelStarFile) classDimensionality = modelRow.getValue('rlnReferenceDimensionality') self._optimiserFile = self._starFile.replace('_data.star', '_optimiser.star') if not exists(self._optimiserFile): raise Exception("Missing required optimiser star file: %s" % self._optimiserFile) optimiserRow = md.getFirstRow(self._optimiserFile) autoRefine = optimiserRow.containsLabel('rlnModelStarFile2') self.alignType = ALIGN_PROJ if not autoRefine: if classDimensionality == 3: self._classesFunc = self.protocol._createSetOfClasses3D else: self._classesFunc = self.protocol._createSetOfClasses2D self.alignType = ALIGN_2D else: self._classesFunc = None else: self.alignType = ALIGN_NONE self._classesFunc = None self._modelStarFile = None modelRow = None # Check if the MetaData contains either MDL_MICROGRAPH_ID # or MDL_MICROGRAPH, this will be used when imported # particles to keep track of the particle's micrograph self._micIdOrName = (row.containsLabel('rlnMicrographName') or row.containsLabel('rlnMicrographId')) #init dictionary. It will be used in the preprocessing self.micDict = {} return row, modelRow
def _setFileName(self, item, row): relionFn = row.getValue(md.RLN_IMAGE_NAME) indx, fn = relionToLocation(relionFn) item.setLocation(indx, self._getPath(fn)) invFactor = 1 / self._getScaleFactor(item) if invFactor != 1.0: if item.hasCoordinate(): item.scaleCoordinate(invFactor) if item.hasTransform(): item.getTransform().scaleShifts(invFactor)
def _loadClassesInfo(self, iteration): """ Read some information about the produced Relion 3D classes from the *model.star file. """ self._classesInfo = {} # store classes info, indexed by class id modelStar = md.MetaData('model_classes@' + self._getFileName('model', iter=iteration)) for classNumber, row in enumerate(md.iterRows(modelStar)): index, fn = relionToLocation(row.getValue('rlnReferenceImage')) # 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 _loadClassesInfo(self, iteration): """ Read some information about the produced Relion 2D classes from the *model.star file. """ self._classesInfo = {} # store classes info, indexed by class id modelStar = md.MetaData('model_classes@' + self._getFileName('model', iter=iteration)) for classNumber, row in enumerate(md.iterRows(modelStar)): index, fn = relionToLocation(row.getValue('rlnReferenceImage')) # 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())