Source code for xmipp3.protocols.protocol_apply_alignment

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (
# *
# * 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 2 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.protocol.params as params
from import Message

import pwem.emlib.metadata as md
from pwem.emlib.image import ImageHandler
from pwem.objects import Particle
from pwem.protocols import ProtAlign2D
from pwem.constants import ALIGN_NONE

from xmipp3.convert import xmippToLocation, writeSetOfParticles

[docs]class XmippProtApplyAlignment(ProtAlign2D): """ Apply alignment parameters and produce a new set of images. """ _label = 'apply alignment 2d' #--------------------------- DEFINE param functions -------------------------------------------- def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputParticles', params.PointerParam, important=True, pointerCondition='hasAlignment2D', label=Message.LABEL_INPUT_PART, pointerClass='SetOfParticles', help='Select the particles that you want to apply the' 'alignment parameters.') form.addParallelSection(threads=0, mpi=4) #--------------------------- INSERT steps functions -------------------------------------------- def _insertAllSteps(self): """ Mainly prepare the command line for call cl2d align program""" # Create a metadata with the geometrical information # as expected by Xmipp imgsFn = self._getPath('input_particles.xmd') self._insertFunctionStep('convertInputStep', imgsFn) self._insertFunctionStep('applyAlignmentStep', imgsFn) self._insertFunctionStep('createOutputStep') #--------------------------- STEPS functions --------------------------------------------
[docs] def convertInputStep(self, outputFn): """ Create a metadata with the images and geometrical information. """ writeSetOfParticles(self.inputParticles.get(), outputFn) return [outputFn]
[docs] def applyAlignmentStep(self, inputFn): """ Create a metadata with the images and geometrical information. """ outputStk = self._getPath('aligned_particles.stk') args = '-i %(inputFn)s -o %(outputStk)s --apply_transform ' % locals() self.runJob('xmipp_transform_geometry', args) return [outputStk]
[docs] def createOutputStep(self): particles = self.inputParticles.get() # Generate the SetOfAlignmet alignedSet = self._createSetOfParticles() alignedSet.copyInfo(particles) inputMd = self._getPath('aligned_particles.xmd') alignedSet.copyItems(particles, updateItemCallback=self._updateItem, itemDataIterator=md.iterRows(inputMd, sortByLabel=md.MDL_ITEM_ID)) # Remove alignment 2D alignedSet.setAlignment(ALIGN_NONE) # Define the output average avgFile = self._getExtraPath("average.xmp") imgh = ImageHandler() avgImage = imgh.computeAverage(alignedSet) avgImage.write(avgFile) avg = Particle() avg.setLocation(1, avgFile) avg.copyInfo(alignedSet) self._defineOutputs(outputAverage=avg) self._defineSourceRelation(self.inputParticles, avg) self._defineOutputs(outputParticles=alignedSet) self._defineSourceRelation(self.inputParticles, alignedSet)
#--------------------------- INFO functions -------------------------------------------- def _validate(self): errors = [] return errors def _summary(self): summary = [] if not hasattr(self, 'outputParticles'): summary.append("Output particles not ready yet.") else: summary.append("Applied alignment to %s particles." % self.inputParticles.get().getSize()) return summary def _methods(self): if not hasattr(self, 'outputParticles'): return ["Output particles not ready yet."] else: return ["We applied alignment to %s particles from %s and produced %s." % (self.inputParticles.get().getSize(), self.getObjectTag('inputParticles'), self.getObjectTag('outputParticles'))] #--------------------------- UTILS functions -------------------------------------------- def _updateItem(self, item, row): """ Implement this function to do some update actions over each single item that will be stored in the output Set. """ # By default update the item location (index, filename) with the new binary data location newFn = row.getValue(md.MDL_IMAGE) newLoc = xmippToLocation(newFn) item.setLocation(newLoc) # Also remove alignment info item.setTransform(None)