Source code for pwem.protocols.protocol_2d

# **************************************************************************
# *
# * Authors:     Airen Zaldivar Peraza (azaldivar@cnb.csic.es)
# *
# * 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
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# * 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
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# *  All comments concerning this program package may be sent to the
# *  e-mail address 'scipion@cnb.csic.es'
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# **************************************************************************
"""
Protocol base classes related to 2D processing.
"""
import pyworkflow.protocol.params as params
import pyworkflow.utils as pwutils

import pwem.objects as emobj
from .protocol import EMProtocol


class Prot2D(EMProtocol):
    pass


class ProtAlign2D(Prot2D):
    """ This class will serve as a base for all protocols that align a set of 
        2D images.
        All Align protocols receive as input:
        A set of particles
        and will allow the option to generate the aligned particles.
    """
    def _defineParams(self, form):
        form.addSection(label='Input')
        
        form.addParam('inputParticles', params.PointerParam, important=True,
                      label=pwutils.Message.LABEL_INPUT_PART, pointerClass='SetOfParticles')
        # Hook that should be implemented in subclasses
        self._defineAlignParams(form)
        
    def _defineAlignParams(self, form):
        """ This method should be implemented by subclasses
        to add other parameter relatives to the specific align protocol."""
        pass 
    

class ProtCreateMask2D(Prot2D):
    """ For those protocols who create mask as output. """
    pass


class ProtClassify2D(Prot2D):
    pass


class ProtAnalysis2D(Prot2D):
    pass


# ------------ Some testing protocols -----------------------------------------

class ProtEvenClassify2D:  # ProtClassify2D):
    """ This is a simple classification protocol for testing purposes.
    It will iterate over the images and assign each one to a different
    class. 
    """
    def _defineParams(self, form):
        form.addSection(label='Input')
        
        form.addParam('inputParticles', params.PointerParam, important=True,
                      label=pwutils.Message.LABEL_INPUT_PART, pointerClass='SetOfParticles')
        form.addParam('numberOfClasses', params.IntParam, default=8,
                      label="Number of classes", 
                      help="Select into how many classes do you want to classify your images.")

    def _insertAllSteps(self):
        self._insertFunctionStep('createOutputStep')
        
    def createOutputStep(self):
        """ This single step will do the fullish classification
        and create the output classes.
        """
        classes = self._createSetOfClasses2D()
        n = self.numberOfClasses.get()
        
        for classNumber in range(1, n+1):
            classes.append(emobj.Class2D())
        
        for img in self.inputParticles.get():
            classNumber = (img.getObjId() % n) + 1
            classes[classNumber].append(img)
            
        for cls in classes:
            classes.update(cls)
            
        classes.write()
            
        self._defineOutputs(outputClasses=classes)