Source code for eman2.protocols.protocol_ctf

# **************************************************************************
# *
# *  Authors:     Grigory Sharov (gsharov@mrc-lmb.cam.ac.uk)
# *
# * MRC Laboratory of Molecular Biology (MRC-LMB)
# *
# * 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.
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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.
# *
# * 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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# **************************************************************************

from pyworkflow.protocol.params import (FloatParam, EnumParam,
                                        BooleanParam)
import pyworkflow.utils as pwutils
from pwem.objects.data import CTFModel, SetOfParticles
from pwem.protocols import ProtProcessParticles

from .. import Plugin
from ..constants import *
from ..convert import writeSetOfParticles, iterLstFile, jsonToCtfModel


[docs]class EmanProtCTFAuto(ProtProcessParticles): """ This protocol wraps *e2ctf_auto.py* EMAN2 program. It automates the CTF fitting and structure factor generation process. """ _label = 'ctf auto' def __init__(self, **kwargs): ProtProcessParticles.__init__(self, **kwargs) def _createFilenameTemplates(self): """ Centralize the names of the files. """ myDict = { 'partSet': self._getExtraPath('sets/all.lst'), 'partSetFlipInvar': self._getExtraPath('sets/all__ctf_flip_invar.lst'), 'partSetFlipFullRes': self._getExtraPath('sets/all__ctf_flip_fullres.lst'), 'partSetFlipLp5': self._getExtraPath('sets/all__ctf_flip_lp5.lst'), 'partSetFlipLp7': self._getExtraPath('sets/all__ctf_flip_lp7.lst'), 'partSetFlipLp12': self._getExtraPath('sets/all__ctf_flip_lp12.lst'), 'partSetFlipLp20': self._getExtraPath('sets/all__ctf_flip_lp20.lst'), } self._updateFilenamesDict(myDict) # --------------------------- DEFINE param functions ---------------------- def _defineProcessParams(self, form): form.addParam('type', EnumParam, choices=['hires', 'midres', 'lores'], label='type', default=HIRES, display=EnumParam.DISPLAY_COMBO, help='Performs CTF processing targeting ' 'different resolution:\n' '*hires* - 2-6 Angstrom\n*midres* - 7-15 Angstrom\n' '*lores* - 15-30 Angstrom') line = form.addLine('Defocus search range (microns)', help='Select _minimum_ and _maximum_ values for ' 'defocus search range (in microns). Underfocus' ' is represented by a positive number.') line.addParam('minDefocus', FloatParam, default=0.6, label='Min') line.addParam('maxDefocus', FloatParam, default=4., label='Max') form.addParam('fromScratch', BooleanParam, default=False, label='Fit from scratch', help='Force refitting of CTF from scratch, ignoring any ' 'previous fits.') form.addParam('astig', BooleanParam, default=False, label='Estimate astigmatism', help='Includes astigmatism in automatic fitting.') form.addParam('phaseEst', BooleanParam, default=False, label='Estimate phase shift', help='Include phase/amplitude contrast in CTF ' 'estimation. For use with hole-less phase plates.') form.addSection(label='Advanced') form.addParam('extrapad', BooleanParam, default=False, label='Extra padding', help='If particles were boxed more tightly than EMAN ' 'requires, this will add some extra padding.') form.addParam('invarType', EnumParam, choices=['auto', 'bispec', 'harmonic'], label='Invariant type', default=INVAR_AUTO, display=EnumParam.DISPLAY_COMBO, help='Which type of invariants to generate') form.addParam('highDensity', BooleanParam, default=False, label='High density ', help='If particles are very close together, this will ' 'interfere with SSNR estimation. ' 'If set uses an alternative strategy, ' 'but may over-estimate SSNR.') form.addParam('invert', BooleanParam, default=False, label='Invert contrast', help='Invert the contrast of the particles in output ' 'files (default false)') form.addParam('constBfact', FloatParam, default=-1.0, label='Constant B-factor', help='Set B-factor to a fixed value, negative value ' 'enables autofitting.') form.addParallelSection(threads=1, mpi=0) # --------------------------- INSERT steps functions ---------------------- def _insertAllSteps(self): self._createFilenameTemplates() self._insertFunctionStep('convertImagesStep') args = self._prepareParams() self._insertFunctionStep('runCTFStep', args) self._insertFunctionStep('createOutputStep') # --------------------------- STEPS functions -----------------------------
[docs] def convertImagesStep(self): partSet = self._getInputParticles() partAlign = partSet.getAlignment() storePath = self._getExtraPath("particles") pwutils.makePath(storePath) writeSetOfParticles(partSet, storePath, alignType=partAlign)
[docs] def runCTFStep(self, args): """ Run the EMAN e2ctf_auto.py program. """ program = Plugin.getProgram('e2ctf_auto.py') self.runJob(program, args, cwd=self._getExtraPath(), numberOfThreads=1)
[docs] def createOutputStep(self): inputSet = self._getInputParticles() outputSets = self._getOutputSets() outputs = {} for key, fn in outputSets.items(): outputSet = self._createSetOfParticles(suffix='_%s' % key) outputSet.copyInfo(inputSet) outputSet.setIsPhaseFlipped(True) outputSet.setHasCTF(True) outputSet.copyItems(inputSet, updateItemCallback=self._updateCTF, itemDataIterator=iterLstFile(self._getFileName(fn))) newPix = self._getNewPixSize(outputSet.getDimensions()[0]) outputSet.setSamplingRate(newPix) summary = self.getSummary(key) outputSet.setObjComment(summary) if key == 'FL': outputName = 'outputParticles_flip_fullRes' elif key == 'bispec': outputName = 'outputParticles_flip_invar' else: outputName = 'outputParticles_flip_lp%s' % key outputs[outputName] = outputSet self._defineOutputs(**outputs) for _, out in self.iterOutputAttributes(SetOfParticles): self._defineSourceRelation(inputSet, out)
# --------------------------- INFO functions ------------------------------ def _validate(self): errors = [] partSet = self._getInputParticles() if partSet.isPhaseFlipped(): errors.append('Input particles are already phase-flipped. ' 'Please provide original raw particle images.') if not self.fromScratch and not partSet.hasCTF(): errors.append('Input particles have no CTF information, ' 'please select _Fit from scratch_ option.') if partSet.getAcquisition() is None: errors.append('Acquisition information missing for input ' 'particles, you cannot estimate CTF!') return errors def _summary(self): summary = [] if self.hasAttribute('outputParticles_flip_invar'): summary.append('CTF estimation on particles completed, ' 'produced filtered particles and bispectra.') else: summary.append('Output is not ready yet.') return summary
[docs] def getSummary(self, key): if key == 'FL': return 'Phase flipped, full resolution' elif key == 'bispec': return 'Bispectra footprints computed from high pass filtered normalized particles' else: return "Phase flipped, low-pass filtered to %d A" % int(key)
# --------------------------- UTILS functions ----------------------------- def _prepareParams(self): partSet = self._getInputParticles() acq = partSet.getAcquisition() args = "--%s" % self.getEnumText('type') args += " --voltage %3d" % acq.getVoltage() args += " --cs %0.3f" % acq.getSphericalAberration() args += " --ac %0.2f" % (100 * acq.getAmplitudeContrast()) args += " --apix %0.3f" % partSet.getSamplingRate() if self.fromScratch: args += " --fromscratch" else: args += " --curdefocusfix" if self.astig: args += " --astigmatism" if self.phaseEst: args += " --phaseplate" if self.extrapad: args += " --extrapad" if self.highDensity: args += " --highdensity" if self.invert: args += " --invert" args += " --invartype %s" % self.getEnumText('invarType') args += " --constbfactor %0.2f --defocusmin %0.2f --defocusmax %0.2f" % ( self.constBfact.get(), self.minDefocus.get(), self.maxDefocus.get()) args += " --threads %d" % self.numberOfThreads.get() args += " --minqual 0" return args def _getInputParticles(self): return self.inputParticles.get() def _updateCTF(self, item, row): fileName = self._getExtraPath(row[1]) item.setLocation(row[0], fileName) if not item.hasCTF(): item.setCTF(CTFModel()) jsonToCtfModel(fileName, item.getCTF()) def _getOutputSets(self): protType = self.getEnumText('type') outputs = {} if protType == 'hires': outputs.update({'FL': 'partSetFlipFullRes', '12': 'partSetFlipLp12', '5': 'partSetFlipLp5'}) elif protType == 'midres': outputs.update({'FL': 'partSetFlipFullRes', '20': 'partSetFlipLp20', '7': 'partSetFlipLp7'}) else: # lores outputs.update({'20': 'partSetFlipLp20', '12': 'partSetFlipLp12'}) outputs['bispec'] = 'partSetFlipInvar' return outputs def _getNewPixSize(self, newBox): # calculates new pix size for binned particles inputParts = self.inputParticles.get() oldDimX = inputParts.getDimensions()[0] oldPixSize = inputParts.getSamplingRate() newPixSize = float(oldDimX) / newBox * oldPixSize return newPixSize