Source code for relion.protocols.protocol_export_ctf

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [1]
# *
# * [1] SciLifeLab, Stockholm University
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# * This program is free software; you can redistribute it and/or modify
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# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
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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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import os

from pwem.objects import SetOfMicrographs
from pwem.protocols import EMProtocol
import pyworkflow.utils as pwutils
import pyworkflow.protocol.params as params

import relion.convert as convert


[docs]class ProtRelionExportCtf(EMProtocol): """ Export a SetOfCTF to a Relion STAR file. """ _label = 'export ctf' CTF_STAR_FILE = 'micrographs_ctf_%06d.star' # -------------------------- DEFINE param functions ----------------------- def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputCTF', params.PointerParam, pointerClass="SetOfCTF", label='Input CTF', help='Select set of CTF that you want to export.') form.addParam('micrographSource', params.EnumParam, choices=['used for CTF estimation', 'other'], default=0, important=True, display=params.EnumParam.DISPLAY_HLIST, label='Micrographs source', help='By default the micrograph used to create the' 'exported STAR files are those used for the CTF ' 'estimation. You can selected *other* to use a ' 'different set of micrographs (e.g., dose weighted)') form.addParam('inputMicrographs', params.PointerParam, pointerClass='SetOfMicrographs', condition='micrographSource == 1', important=True, label='Input micrographs', help='Select the SetOfMicrographs from which to extract.') form.addParallelSection(threads=0, mpi=0) # -------------------------- INSERT steps functions ----------------------- def _insertAllSteps(self): self._insertFunctionStep('writeCtfStarStep')
[docs] def writeCtfStarStep(self): pwutils.cleanPath(self._getExportPath()) pwutils.makePath(self._getExportPath()) inputCTF = self.inputCTF.get() if self.micrographSource == 0: # same as CTF estimation ctfMicSet = inputCTF.getMicrographs() else: ctfMicSet = self.inputMicrographs.get() micSet = SetOfMicrographs(filename=':memory:') psd = inputCTF.getFirstItem().getPsdFile() hasPsd = psd and os.path.exists(psd) if hasPsd: psdPath = self._getExportPath('PSD') pwutils.makePath(psdPath) print("Writing PSD files to %s" % psdPath) for ctf in inputCTF: # Get the corresponding micrograph mic = ctfMicSet[ctf.getObjId()] if mic is None: print("Skipping CTF id: %s, it is missing from input " "micrographs. " % ctf.getObjId()) continue micFn = mic.getFileName() if not os.path.exists(micFn): print("Skipping micrograph %s, it does not exists. " % micFn) continue mic2 = mic.clone() mic2.setCTF(ctf) if hasPsd: psdFile = ctf.getPsdFile() newPsdFile = os.path.join(psdPath, '%s_psd.mrc' % pwutils.removeExt(mic.getMicName())) if not os.path.exists(psdFile): print("PSD file %s does not exits" % psdFile) print("Skipping micrograph %s" % micFn) continue pwutils.copyFile(psdFile, newPsdFile) # PSD path is relative to Export dir newPsdFile = os.path.relpath(newPsdFile, self._getExportPath()) ctf.setPsdFile(newPsdFile) else: # remove pointer to non-existing psd file ctf.setPsdFile(None) micSet.append(mic2) print("Writing set: %s to: %s" % (inputCTF, self._getStarFile())) micDir = self._getExportPath('Micrographs') pwutils.makePath(micDir) starWriter = convert.createWriter(rootDir=self._getExportPath(), outputDir=micDir, useBaseName=True) starWriter.writeSetOfMicrographs(micSet, self._getStarFile())
# -------------------------- INFO functions ------------------------------- def _summary(self): summary = [] if os.path.exists(self._getStarFile()): summary.append("Output is written to: \n%s\n" % os.path.abspath(self._getExportPath())) summary.append("Pixel size: *%0.3f*" % self._getPixelSize()) else: summary.append("No output generated yet.") return summary # --------------------------- UTILS functions ----------------------------- def _getExportPath(self, *paths): return os.path.join(self._getPath('Export'), *paths) def _getStarFile(self): return self._getExportPath(self.CTF_STAR_FILE % self.getObjId()) def _getPixelSize(self): if self.micrographSource == 0: # same as CTF estimation ctfMicSet = self.inputCTF.get().getMicrographs() else: ctfMicSet = self.inputMicrographs.get() return ctfMicSet.getSamplingRate()