Source code for pwem.protocols.protocol_classes_selector

# **************************************************************************
# *
# * Authors:     Pablo Conesa [1]
# *
# * [1] Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 3 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307  USA
# *
# *  All comments concerning this program package may be sent to the
# *  e-mail address ''
# *
# **************************************************************************

import pyworkflow.utils as pwutils
import pyworkflow.protocol.params as params

import pwem.objects as emobj
from pwem.protocols import EMProtocol
import logging
logger = logging.getLogger(__file__)

OUTPUT_NAME = "output"

[docs]class ProtClassesSelector(EMProtocol): """ Extracts items from a SetOfClasses based on number of items assigned to the class """ _label = "numeric classes extractor" def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputClasses', params.PointerParam, pointerClass='SetOfClasses', label='Input classes', help='Set of classes to extract items from.') form.addParam('extractRepresentative', params.BooleanParam, label='Extract representative?', help='Set to true if you want to extract the image that represents the class otherwise all ' 'items supporting the class will be extracted.', default = False) form.addParam('firstNElements', params.IntParam, label='Biggest N classes', help='Will take the N biggest classes. Those having most element supporting them.', default=5) # -------------------------- INSERT steps functions --------------------------- def _insertAllSteps(self): """ Insert all steps """ self._insertFunctionStep(self.extractElements.__name__)
[docs] def extractElements(self): count= 0 # For each class (order by number of items) for clazz in self.inputClasses.get().iterItems(orderBy="_size", direction="DESC"): # Increment the count count += 1 # If haven't reached the Nelements if count <= self.firstNElements.get(): print(clazz.getSize()) self._extractElementFromClass(clazz) output = self._getOutputSet() output.write() self._store(output)
def _extractElementFromClass(self, clazz): output = self._getOutputSet() # If taking representatives if self.extractRepresentative.get(): rep = clazz.getRepresentative().clone() output.append(rep) else: # Go through all items and append them for image in clazz: newImage = image.clone() output.append(newImage) def _getOutputSet(self): """ Returns the output set creating it if not yet done""" # If output not created yet if not hasattr(self, OUTPUT_NAME): outputSet = None # Create a set ot items or a set of representatives if self.extractRepresentative.get():"Creating set from representatives.") outputSet = createSetFromRepresentative(self.inputClasses.get(), self._getPath()) else:"Creating set from images.") outputSet = createSetFromImages(self.inputClasses.get(), self._getPath()) self._defineOutputs(**{OUTPUT_NAME:outputSet}) return getattr(self, OUTPUT_NAME) def _summary(self): summary = [] summary.append("%s option selected." % "representative/s" if self.extractRepresentative else "items") summary.append("%s biggest classes to be extracted from." % self.firstNElements.get()) return summary def _methods(self): extractedElement = "representative/s" if self.extractRepresentative else "items" methods = ["The %s of the %s biggest classes were selected from %s." % (extractedElement, self.firstNElements.get(), self.getObjectTag(self.inputClasses))] return methods def _validate(self): errors = [] return errors
# Helpers
[docs]def createSetFromRepresentative(classesSet, path): """ Creates a teh corresponding set from the representative of a set of classes""" rep_type = classesSet.REP_TYPE # need to instantiate the right set based on the representative. # Going from the REP_TYPE to the right set is not straight forward. e.g: # SetOfClasses2D --> REP_TYPE = Particle --> Set for the rep type == SetOfAverages # So we need to make do some manual checks. TODO: have factory methods in the SetOfClasses for the representatives? setClass = None logger.debug("Creating representative set from %s: type %s" % (classesSet.__class__, rep_type)) if rep_type.__name__ == emobj.Particle.__name__: setClass = emobj.SetOfAverages else: setClass = pwutils.Config.getDomain().getObjects()["SetOf%ss" % rep_type.__name__] set = setClass.create(outputPath=path) imgs = classesSet.getImages() set.copyInfo(imgs) return set
[docs]def createSetFromImages(classesSet, path): """ Creates a the corresponding set from the images of a set of classes""" images = classesSet.getImages() # need to instantiate the right set based on the Items. setClass = None logger.debug("Creating an image set from %s: type %s" % (classesSet.__class__, images)) setClass = pwutils.Config.getDomain().getObjects()[images.__class__.__name__] set = setClass.create(outputPath=path) set.copyInfo(images) return set