Source code for relion.protocols.protocol_reconstruct

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [1]
# *
# * [1] SciLifeLab, Stockholm University
# *
# * This program is free software; you can redistribute it and/or modify
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# * the Free Software Foundation; either version 3 of the License, or
# * (at your option) any later version.
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# * 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.
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# * 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 'scipion@cnb.csic.es'
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from pyworkflow.protocol.params import (PointerParam, FloatParam,  
                                        StringParam, BooleanParam,
                                        EnumParam, IntParam, LEVEL_ADVANCED)
from pwem.objects import Volume
from pwem.protocols import ProtReconstruct3D
from pwem.constants import ALIGN_PROJ

import relion.convert as convert


[docs]class ProtRelionReconstruct(ProtReconstruct3D): """ This protocol reconstructs a volume using Relion. Reconstruct a volume from a given set of particles. The alignment parameters will be converted to a Relion star file and used as direction projections to reconstruct. """ _label = 'reconstruct' # -------------------------- DEFINE param functions ----------------------- def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputParticles', PointerParam, pointerClass='SetOfParticles', pointerCondition='hasAlignmentProj', label="Input particles", help='Select the input images from the project.') form.addParam('symmetryGroup', StringParam, default='c1', label="Symmetry group", help='See [[Relion Symmetry][http://www2.mrc-lmb.cam.ac.uk/' 'relion/index.php/Conventions_%26_File_formats#Symmetry]] ' 'page for a description of the symmetry format ' 'accepted by Relion') form.addParam('maxRes', FloatParam, default=-1, label="Maximum resolution (A)", help='Maximum resolution (in Angstrom) to consider \n' 'in Fourier space (default Nyquist).') form.addParam('pad', FloatParam, default=2, label="Padding factor") form.addParam('subset', EnumParam, default=0, choices=['all', 'half1', 'half2'], display=EnumParam.DISPLAY_HLIST, label='Subset to reconstruct', help='Subset of images to consider.') form.addParam('classNum', IntParam, default=-1, label='Use only this class', help='Consider only this class (-1: use all classes)') form.addParam('extraParams', StringParam, default='', expertLevel=LEVEL_ADVANCED, label='Extra parameters: ', help='Extra parameters to *relion_reconstruct* program. ' 'Address to Relion to see full list of options.') form.addSection('CTF') form.addParam('doCTF', BooleanParam, default=False, label='Apply CTF correction?') form.addParam('ctfIntactFirstPeak', BooleanParam, default=False, condition='doCTF', label='Leave CTFs intact until first peak?') form.addParallelSection(threads=0, mpi=1) # -------------------------- INSERT steps functions ----------------------- def _insertAllSteps(self): self._createFilenameTemplates() self._insertFunctionStep('convertInputStep') self._insertReconstructStep() self._insertFunctionStep('createOutputStep') def _getProgram(self, program='relion_reconstruct'): """ Get the program name depending on the MPI use or not. """ if self.numberOfMpi > 1: program += '_mpi' return program def _insertReconstructStep(self): imgSet = self.inputParticles.get() params = ' --i %s' % self._getFileName('input_particles') params += ' --o %s' % self._getFileName('output_volume') params += ' --sym %s' % self.symmetryGroup.get() params += ' --angpix %0.5f' % imgSet.getSamplingRate() params += ' --maxres %0.3f' % self.maxRes.get() params += ' --pad %0.3f' % self.pad.get() subset = -1 if self.subset.get() == 0 else self.subset params += ' --subset %d' % subset params += ' --class %d' % self.classNum.get() if self.doCTF: params += ' --ctf' if self.ctfIntactFirstPeak: params += ' --ctf_intact_first_peak' if imgSet.isPhaseFlipped(): params += ' --ctf_phase_flipped' if self.extraParams.hasValue(): params += " " + self.extraParams.get() self._insertFunctionStep('reconstructStep', params) # -------------------------- STEPS functions ------------------------------
[docs] def reconstructStep(self, params): self.runJob(self._getProgram(), params)
def _createFilenameTemplates(self): """ Centralize how files are called for iterations and references. """ myDict = { 'input_particles': self._getTmpPath('input_particles.star'), 'output_volume': self._getExtraPath('output_volume.mrc') } self._updateFilenamesDict(myDict)
[docs] def convertInputStep(self): """ Create the input file in STAR format as expected by Relion. If the input particles comes from Relion, just link the file. """ imgSet = self.inputParticles.get() imgStar = self._getFileName('input_particles') # Pass stack file as None to avoid write the images files convert.writeSetOfParticles(imgSet, imgStar, outputDir=self._getTmpPath(), alignType=ALIGN_PROJ)
[docs] def createOutputStep(self): imgSet = self.inputParticles.get() volume = Volume() volume.setFileName(self._getFileName('output_volume')) volume.setSamplingRate(imgSet.getSamplingRate()) self._defineOutputs(outputVolume=volume) self._defineSourceRelation(self.inputParticles, volume)
# -------------------------- INFO functions ------------------------------- def _validate(self): errors = [] return errors def _summary(self): summary = [] if not hasattr(self, 'outputVolume'): summary.append("Output volume not ready yet.") else: summary.append("Output volume has been reconstructed.") return summary