Source code for cryosparc2.protocols.protocol_cryosparc_symmetry_expansion

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# * Authors: Yunior C. Fonseca Reyna    (
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# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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import os

import pyworkflow.utils as pwutils
from pyworkflow.object import String
from pyworkflow.protocol.params import (PointerParam, FloatParam,

from .protocol_base import ProtCryosparcBase
from ..convert import (defineArgs, convertCs2Star, readSetOfParticles)
from ..utils import (addComputeSectionParams, cryosparcValidate, gpusValidate,
                     enqueueJob, waitForCryosparc, clearIntermediateResults,
                     addSymmetryParam, getSymmetry, copyFiles,

[docs]class ProtCryoSparcSymmetryExpansion(ProtCryosparcBase): """ Duplicate particles around a point-group symmetry. """ _label = 'symmetry expansion' _className = "sym_expand" def _initialize(self): self._createFilenameTemplates() def _createFilenameTemplates(self): """ Centralize how files are called. """ myDict = { 'input_particles': self._getTmpPath(''), 'out_particles': self._getExtraPath('') } self._updateFilenamesDict(myDict) def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputParticles', PointerParam, pointerClass='SetOfParticles', pointerCondition='hasAlignmentProj', label="Input particles", important=True, help='Select the experimental particles.') addSymmetryParam(form, help="Symmetry String (C, D, I, O, T). E.g. C1," "D7, C4, etc. Particles will be " "symmetry-expanded at this symmetry.") form.addParam('sym_twist_deg', FloatParam, default=None, allowsNull=True, label='Helical twist (degrees)', help='Helical twist for symmetry expansion. This can be ' 'found in the final iteration of the source Helical ' 'Refinement job streamlog.') form.addParam('sym_rise_A', FloatParam, default=None, allowsNull=True, label='Helical rise (A)', help='Helical rise for symmetry expansion. This can be ' 'found in the final iteration of the source ' 'Helical Refinement job streamlog.') form.addParam('sym_num_rises', IntParam, default=None, allowsNull=True, label='Helical symmetry order (integer)', help='Helical symmetry order for symmetry expansion. ' 'This can be found in the final iteration of the ' 'source Helical Refinement job streamlog.') # --------------[Compute settings]--------------------------- form.addSection(label="Compute settings") addComputeSectionParams(form, allowMultipleGPUs=False) # --------------------------- INSERT steps functions ---------------------- def _insertAllSteps(self): self._createFilenameTemplates() self._defineParamsName() self._initializeCryosparcProject() self._insertFunctionStep(self.convertInputStep) self._insertFunctionStep(self.processStep) self._insertFunctionStep(self.createOutputStep) # --------------------------- STEPS functions ------------------------------
[docs] def processStep(self): print(pwutils.yellowStr("Symmetry Expansion started..."), flush=True) self.doSymmetryExpansion()
[docs] def createOutputStep(self): """ Create the protocol output. Convert cryosparc file to Relion file """ self._initializeUtilsVariables() outputStarFn = self._getFileName('out_particles') csFileName = "particles_expanded.cs" # Copy the CS output expanded particles to extra folder copyFiles(os.path.join(self.projectPath, self.projectName.get(), self.runSymExp.get()), self._getExtraPath(), files=[csFileName]) csFile = os.path.join(self._getExtraPath(), csFileName) argsList = [csFile, outputStarFn] parser = defineArgs() args = parser.parse_args(argsList) convertCs2Star(args) imgSet = self._getInputParticles() self.setFilePattern(imgSet.getFirstItem().getFileName()) outImgSet = self._createSetOfParticles() outImgSet.copyInfo(imgSet) outImgSet.setDim(imgSet.getDim()) self._fillDataFromIter(outImgSet) self._defineOutputs(outputParticles=outImgSet) self._defineTransformRelation(imgSet, outImgSet)
def _fillDataFromIter(self, imgSet): outImgsFn = 'particles@' + self._getFileName('out_particles') readSetOfParticles(outImgsFn, imgSet, postprocessImageRow=self.updateParticlePath, alignType=imgSet.getAlignment()) # --------------------------- INFO functions ------------------------------- def _validate(self): """ Should be overwritten in subclasses to return summary message for NORMAL EXECUTION. """ validateMsgs = cryosparcValidate() if not validateMsgs: validateMsgs = gpusValidate(self.getGpuList(), checkSingleGPU=True) return validateMsgs def _summary(self): summary = [] if not hasattr(self, 'outputParticles'): summary.append("Output Particles not ready yet.") else: summary.append("Input Particles: %s" % self.getObjectTag('inputParticles')) summary.append( "--------------------------------------------------") summary.append("Output particles %s" % self.getObjectTag('outputParticles')) return summary # ---------------Utils Functions------------------------------------------- def _defineParamsName(self): """ Define a list with all protocol parameters names""" self._paramsName = ['sym_symmetry', 'sym_twist_deg', 'sym_rise_A', 'sym_num_rises', 'compute_use_ssd'] self.lane = str(self.getAttributeValue('compute_lane'))
[docs] def doSymmetryExpansion(self): """ Launch a symmetry expansion job """ input_group_connect = {"particles": self.particles.get()} params = {} for paramName in self._paramsName: if paramName == 'sym_symmetry': symetryValue = getSymmetry(self.symmetryGroup.get(), self.symmetryOrder.get()) params[str(paramName)] = symetryValue elif paramName == 'sym_num_rises': if self.getAttributeValue(paramName) is not None and int(self.getAttributeValue(paramName)) > 0: params[str(paramName)] = str(self.getAttributeValue(paramName)) elif self.getAttributeValue(paramName) is not None and float(self.getAttributeValue(paramName)) > 0: params[str(paramName)] = str(self.getAttributeValue(paramName)) # Determinate the GPUs to use (in dependence of # the cryosparc version) try: gpusToUse = self.getGpuList() except Exception: gpusToUse = False runSymExpJob = enqueueJob(self._className, self.projectName.get(), self.workSpaceName.get(), str(params).replace('\'', '"'), str(input_group_connect).replace('\'', '"'), self.lane, gpusToUse) self.runSymExp = String(runSymExpJob.get()) self.currenJob.set(self.runSymExp.get()) self._store(self) waitForCryosparc(self.projectName.get(), self.runSymExp.get(), "An error occurred in the particles subtraction process. " "Please, go to cryoSPARC software for more " "details.") clearIntermediateResults(self.projectName.get(), self.runSymExp.get())