Source code for relion.protocols.protocol_postprocess

# **************************************************************************
# *
# * Authors:     Josue Gomez Blanco     (josue.gomez-blanco@mcgill.ca) [1]
# *              J.M. de la Rosa Trevin (delarosatrevin@scilifelab.se) [2]
# *
# * [1] Department of Anatomy and Cell Biology, McGill University
# * [2] SciLifeLab, Stockholm University
# *
# * 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
# *
# *  All comments concerning this program package may be sent to the
# *  e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************

import os
from emtable import Table

import pyworkflow.utils as pwutils
import pyworkflow.protocol.params as params
from pyworkflow.constants import PROD
from pwem.protocols import ProtAnalysis3D
from pwem.emlib.image import ImageHandler
from pwem.objects import Volume

import relion.convert as convert
from .protocol_base import ProtRelionBase


[docs]class ProtRelionPostprocess(ProtAnalysis3D, ProtRelionBase): """ Relion post-processing protocol for automated masking, overfitting estimation, MTF-correction and B-factor sharpening. """ _label = 'post-processing' _devStatus = PROD def _getInputPath(self, *paths): return self._getPath('input', *paths) def _createFilenameTemplates(self): """ Centralize how files are called for iterations and references. """ myDict = { 'finalVolume': self._getInputPath("relion_class001.mrc"), 'half1': self._getInputPath("relion_half1_class001_unfil.mrc"), 'half2': self._getInputPath("relion_half2_class001_unfil.mrc"), 'mask': self._getInputPath("input_mask.mrc"), 'outputVolume': self._getExtraPath('postprocess.mrc') } self._updateFilenamesDict(myDict) # -------------------------- DEFINE param functions ----------------------- def _defineParams(self, form): form.addSection(label='Input') form.addParam('protRefine', params.PointerParam, pointerClass="ProtRefine3D", label='Select a previous refinement protocol', help='Select any previous refinement protocol to get the ' '3D half maps. Note that it is recommended that the ' 'refinement protocol uses a gold-standard method.') form.addParam('solventMask', params.PointerParam, pointerClass="VolumeMask", label='Solvent mask', help="Provide a soft mask where the protein is white " "(1) and the solvent is black (0). Often, the " "softer the mask the higher resolution estimates " "you will get. A soft edge of 5-10 pixels is often " "a good edge width.") form.addParam('calibratedPixelSize', params.FloatParam, default=0, label='Calibrated pixel size (A)', help="Provide the final, calibrated pixel size in " "Angstroms. If 0, the input pixel size will be used. " "This value may be different from the pixel-size " "used thus far, e.g. when you have recalibrated " "the pixel size using the fit to a PDB model. " "The X-axis of the output FSC plot will use this " "calibrated value.") form.addSection(label='Sharpening') group = form.addGroup('MTF') group.addParam('mtf', params.FileParam, label='MTF of the detector', help='User-provided STAR-file with the MTF-curve ' 'of the detector. Use the wizard to load one ' 'of the predefined ones provided at:\n' '- [[https://www3.mrc-lmb.cam.ac.uk/relion/index.php/' 'FAQs#Where_can_I_find_MTF_curves_for_typical_detectors.3F]' '[Relion\'s Wiki FAQs]]\n' ' - [[https://www.gatan.com/techniques/cryo-em#MTF][Gatan\'s website]]\n\n' 'Relion param: *--mtf*') group.addParam('origPixelSize', params.FloatParam, default=-1.0, label='Original detector pixel size (A)', help='This is the original pixel size (in Angstroms)' ' in the raw (non-super-resolution!) micrographs') form.addParam('doAutoBfactor', params.BooleanParam, default=True, label='Estimate B-factor automatically?', help='If set to Yes, then the program will use the ' 'automated procedure described by Rosenthal and ' 'Henderson (2003, JMB) to estimate an overall ' 'B-factor for your map, and sharpen it accordingly.') line = form.addLine('B-factor resolution (A): ', condition='doAutoBfactor', help='There are the frequency (in Angstroms), ' 'lowest and highest, that will be included in ' 'the linear fit of the Guinier plot as ' 'described in Rosenthal and Henderson ' '(2003, JMB).') line.addParam('bfactorLowRes', params.FloatParam, default=10.0, label='low') line.addParam('bfactorHighRes', params.FloatParam, default=0.0, label='high') form.addParam('bfactor', params.FloatParam, default=-350, condition='not doAutoBfactor', label='Provide B-factor:', help='User-provided B-factor (in A^2) for map ' 'sharpening, e.g. -400. Use negative values for ' 'sharpening. Be careful: if you over-sharpen\n' 'your map, you may end up interpreting noise for ' 'signal!\n' 'Relion param: *--adhoc_bfac*') form.addSection(label='Filtering') form.addParam('skipFscWeighting', params.BooleanParam, default=False, label='Skip FSC-weighting for sharpening?', help='If set to No (the default), then the output map ' 'will be low-pass filtered according to the ' 'mask-corrected, gold-standard FSC-curve. ' 'Sometimes, it is also useful to provide an ad-hoc ' 'low-pass filter (option below), as due to local ' 'resolution variations some parts of the map may ' 'be better and other parts may be worse than the ' 'overall resolution as measured by the FSC. In ' 'such cases, set this option to Yes and provide ' 'an ad-hoc filter as described below.') form.addParam('lowRes', params.FloatParam, default=5, condition='skipFscWeighting', label='Ad-hoc low-pass filter (A):', help='This option allows one to low-pass filter the map ' 'at a user-provided frequency (in Angstroms). When ' 'using a resolution that is higher than the ' 'gold-standard FSC-reported resolution, take care ' 'not to interpret noise in the map for signal.') form.addParam('filterEdgeWidth', params.IntParam, default=2, expertLevel=params.LEVEL_ADVANCED, label='Low-pass filter edge width:', help='Width of the raised cosine on the low-pass filter ' 'edge (in resolution shells)\n' 'Relion param: *--filter_edge_width*') form.addParam('randomizeAtFsc', params.FloatParam, default=0.8, expertLevel=params.LEVEL_ADVANCED, label='Randomize phases threshold', help='Randomize phases from the resolution where FSC ' 'drops below this value\n' 'Relion param: *--randomize_at_fsc*') form.addParam('forceMask', params.BooleanParam, default=False, expertLevel=params.LEVEL_ADVANCED, label='Force mask?', help='Use the mask even when the masked resolution ' 'is worse than the unmasked resolution.') form.addParallelSection(threads=0, mpi=0) # -------------------------- INSERT steps functions ------------------------ def _insertAllSteps(self): objId = self.protRefine.get().getObjId() self._createFilenameTemplates() self._defineParamDict() self._insertFunctionStep('convertInputStep', objId) self._insertFunctionStep('postProcessStep', self.paramDict) self._insertFunctionStep('createOutputStep') # -------------------------- STEPS functions -------------------------------
[docs] def convertInputStep(self, protId): pwutils.makePath(self._getInputPath()) protRef = self.protRefine.get() outVol = protRef.outputVolume newDim = outVol.getXDim() newPix = outVol.getSamplingRate() vols = outVol.getHalfMaps().split(',') vols.insert(0, outVol.getFileName()) ih = ImageHandler() convert.convertMask(self.solventMask.get(), self._getFileName('mask'), newPix, newDim) for vol, key in zip(vols, ['outputVolume', 'half1', 'half2']): ih.convert(vol, self._getFileName(key))
[docs] def postProcessStep(self, paramDict): params = ' '.join(['%s %s' % (k, str(v)) for k, v in self.paramDict.items()]) self._runProgram('relion_postprocess', params)
[docs] def createOutputStep(self): volume = Volume() volume.setFileName(self._getFileName('outputVolume')) vol = self.protRefine.get().outputVolume volume.setSamplingRate(self._getOutputPixelSize()) self._defineOutputs(outputVolume=volume) self._defineSourceRelation(vol, volume)
# -------------------------- INFO functions -------------------------------- def _validate(self): errors = [] mtfFile = self.mtf.get() if mtfFile and not os.path.exists(mtfFile): errors.append("Missing MTF-file '%s'" % mtfFile) return errors def _citations(self): return ['Chen2013'] def _summary(self): summary = [] postStarFn = self._getExtraPath("postprocess.star") if os.path.exists(postStarFn): table = Table(fileName=postStarFn, tableName='general') row = table[0] summary.append("Final resolution: *%0.2f A*" % float(row.rlnFinalResolution)) summary.append("B-factor: *%0.2f A\u00B2*" % float(row.rlnBfactorUsedForSharpening)) return summary # -------------------------- UTILS functions ------------------------------ def _defineParamDict(self): """ Define all parameters to run relion_postprocess""" # It seems that in Relion3 now the input should be the map # filename and not the prefix as before inputFn = self._getFileName('half1') self.paramDict = {'--i': inputFn, '--o': self._getExtraPath('postprocess'), '--angpix': self._getOutputPixelSize(), # Expert params '--filter_edge_width': self.filterEdgeWidth.get(), '--randomize_at_fsc': self.randomizeAtFsc.get(), '--mask': self._getFileName('mask') } mtfFile = self.mtf.get() if mtfFile: self.paramDict['--mtf'] = mtfFile if self.doAutoBfactor: self.paramDict['--auto_bfac'] = '' self.paramDict['--autob_lowres'] = self.bfactorLowRes.get() self.paramDict['--autob_highres'] = self.bfactorHighRes.get() else: self.paramDict['--adhoc_bfac'] = self.bfactor.get() if self.skipFscWeighting: self.paramDict['--skip_fsc_weighting'] = '' self.paramDict['--low_pass'] = self.lowRes.get() if self.origPixelSize.get() != -1.0: self.paramDict['--mtf_angpix'] = self.origPixelSize.get() if self.forceMask: self.paramDict['--force_mask'] = '' def _getRelionMapFn(self, fn): return fn.split(':')[0] def _getOutputPixelSize(self): """ Return the output pixel size, using the calibrated pixel size if non zero, or the input one. """ volume = self.protRefine.get().outputVolume cps = self.calibratedPixelSize.get() return cps if cps > 0 else volume.getSamplingRate()