Source code for pwem.protocols.protocol_import.ctfs

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (
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# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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from pyworkflow.utils import removeBaseExt
from pyworkflow.protocol.params import PointerParam

from pwem import Domain
import pwem.objects as pwobj

from .base import ProtImportFiles

[docs]class ProtImportCTF(ProtImportFiles): """Common protocol to import a set of ctfs into the project""" # This label should be set in subclasses _label = 'import ctf' _outputClassName = "SetOfCTF" IMPORT_FROM_AUTO = 0 IMPORT_FROM_XMIPP3 = 1 IMPORT_FROM_GRIGORIEFF = 2 IMPORT_FROM_GCTF = 3 IMPORT_FROM_EMAN2 = 4 IMPORT_FROM_SCIPION = 5 # --------------------------- DEFINE param functions ---------------------- def _defineImportParams(self, form): """ Just redefine to put some import parameters. """ form.addParam('inputMicrographs', PointerParam, pointerClass='SetOfMicrographs', label='Input micrographs', help='Select the micrographs for which you want to ' 'update the CTF parameters.') def _getImportChoices(self): """ Return a list of possible choices from which the import can be done. (usually packages formats such as: xmipp3, eman2, relion...etc. """ return ['auto', 'xmipp', 'grigorieff', 'gctf', 'eman2', 'scipion'] def _getDefaultChoice(self): return self.IMPORT_FROM_AUTO def _getFilesCondition(self): """ Return an string representing the condition when to display the files path and pattern to grab files. """ return True # --------------------------- INSERT functions ---------------------------- def _insertAllSteps(self): importFrom = self.importFrom.get() self._insertFunctionStep('importCTFStep', importFrom)
[docs] def getImportClass(self): """ Return the class in charge of importing the files. """ filesPath = self.filesPath.get() importFrom = self.importFrom.get() if importFrom == self.IMPORT_FROM_AUTO: importFrom = self.getFormat() if importFrom == self.IMPORT_FROM_XMIPP3: XmippImport = Domain.importFromPlugin('xmipp3.convert', 'XmippImport', doRaise=True) return XmippImport(self, filesPath) elif importFrom == self.IMPORT_FROM_GRIGORIEFF: GrigorieffLabImportCTF = Domain.importFromPlugin('cistem.convert', 'GrigorieffLabImportCTF', doRaise=True) return GrigorieffLabImportCTF(self) elif importFrom == self.IMPORT_FROM_GCTF: GctfImportCTF = Domain.importFromPlugin('gctf.convert', 'GctfImportCTF', doRaise=True) return GctfImportCTF(self) elif importFrom == self.IMPORT_FROM_EMAN2: EmanImport = Domain.importFromPlugin('eman2.convert', 'EmanImport', doRaise=True) return EmanImport(self, None) elif importFrom == self.IMPORT_FROM_SCIPION: from .dataimport import ScipionImport return ScipionImport(self, self.filesPath.get('').strip()) else: return None
# --------------------------- STEPS functions -----------------------------
[docs] def importCTFStep(self, importFrom): """ Copy ctfs matching the filename pattern. """ ci = self.getImportClass() inputMics = self.inputMicrographs.get() ctfSet = self._createSetOfCTF() ctfSet.setMicrographs(inputMics) outputMics = self._createSetOfMicrographs() pwobj.SetOfMicrographs.copyInfo(outputMics, inputMics) createOutputMics = False files = [f for f, _ in self.iterFiles()] n = len(files) if n == 0: raise Exception("No files where found in path: '%s'\n" "matching the pattern: '%s'" % (self.filesPath, self.filesPattern)) print("Matching files: %s" % n) inputMicBases = [removeBaseExt(m.getFileName()) for m in inputMics] if len(files) > len(inputMicBases): self.warning("WARNING: The number of files matched by your pattern (%d) is larger than " "the number of available micrographs (%d). It is advised to carefully " "review the output of this run or to re-run with a more restrictive pattern." % (n, len(inputMicBases))) def _getMicCTF(mic): micName = mic.getMicName() micBase = removeBaseExt(mic.getFileName()) # see if the base name of this mic is contained in other base names micConflicts = [mc for mc in inputMicBases if micBase in mc and micBase != mc] if micConflicts: self.warning('WARNING: Micrograph base name "%s" conflicts with micrograph(s) "%s". ' 'Will try to find a unique match...' % (micBase, '", "'.join(micConflicts))) # check which matching file only matches with this mic and not its conflicts goodFnMatches = [f for f in files if micBase in f and not any(c in f for c in micConflicts)] for goodFnMatch in goodFnMatches: try: micCtf = ci.importCTF(mic, goodFnMatch) self.warning("WARNING: Assigned file %s to micrograph %s." % (goodFnMatch, micBase)) return micCtf except Exception as ex: self.warning("WARNING: Can't import ctf for micrograph %s from file %s" % (micBase, goodFnMatch)) continue else: return None else: for fileName, fileId in self.iterFiles(): if (fileId == mic.getObjId() or micBase in fileName or micName in fileName): return ci.importCTF(mic, fileName) return None # Check if the CTF import class has a method to retrieve the CTF # from a given micrograph. If not, we will try to associated based # on matching the filename or id getMicCTF = getattr(ci, 'getMicCTF', None) or _getMicCTF for mic in inputMics: ctf = getMicCTF(mic) if ctf is not None: ctfSet.append(ctf) outputMics.append(mic) else: # If CTF is not found for a micrograph remove it from output mics self.warning("CTF for micrograph id %d was not found. Removed " "from set of micrographs." % mic.getObjId()) createOutputMics = True self._defineOutputs(outputCTF=ctfSet) # If some of the micrographs had not ctf a subset of micrographs # have been produced if createOutputMics: self._defineOutputs(outputMicrographs=outputMics) self._defineCtfRelation(outputMics, ctfSet) else: self._defineCtfRelation(inputMics, ctfSet)
# --------------------------- INFO functions ------------------------------ def _summary(self): summary = [] if not hasattr(self, 'outputCTF'): summary.append("Output " + self._outputClassName + " not ready yet.") if self.copyFiles: summary.append("*Warning*: You select to copy files into your project.\n" "This will make another copy of your data and may take \n" "more time to import. ") else: summary.append("Imported *%d* CTFs " % self.outputCTF.getSize()) summary.append("from %s" % self.getPattern()) return summary def _methods(self): methods = [] return methods def _validate(self): errors = [] files = [f for f, _ in self.iterFiles()] if not files: errors.append("No files where found in path: '%s'\n" "matching the pattern: '%s'" % (self.filesPath, self.filesPattern)) return errors # --------------------------- UTILS functions -----------------------------
[docs] def getFormat(self): for fileName, _ in self.iterFiles(): if (fileName.endswith('.log') or fileName.endswith('.txt') or fileName.endswith('.out')): return self.IMPORT_FROM_GRIGORIEFF if fileName.endswith('.ctfparam'): return self.IMPORT_FROM_XMIPP3 if fileName.endswith('.json'): return self.IMPORT_FROM_EMAN2 return -1