Source code for tomo.protocols.protocol_import_coordinates

# coding=utf-8
# **************************************************************************
# *
# * Authors:     Adrian Quintana (adrian@eyeseetea.com) [1]
# *
# * [1] EyeSeeTea Ltd, London, UK
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# * 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 2 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.
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# * 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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import os
from os.path import basename

from pyworkflow import BETA
import pyworkflow.utils as pwutils

import pyworkflow.protocol.params as params
from pyworkflow.plugin import Domain

from ..objects import SetOfCoordinates3D
from .protocol_base import ProtTomoImportFiles
from ..convert import TomoImport
from ..utils import existsPlugin

import tomo.constants as const


[docs]class ProtImportCoordinates3D(ProtTomoImportFiles): """Protocol to import a set of tomograms to the project""" _outputClassName = 'SetOfCoordinates3D' _label = 'import set of coordinates 3D' _devStatus = BETA IMPORT_FROM_AUTO = 'auto' IMPORT_FROM_TXT = 'txt' IMPORT_FROM_EMAN = 'eman' IMPORT_FROM_DYNAMO = 'dynamo' 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. """ importChoices = ['auto', 'txt'] if existsPlugin('emantomo'): importChoices.append('eman') if existsPlugin('dynamo'): importChoices.append('dynamo') return importChoices def _getDefaultChoice(self): return 0 def __init__(self, **args): ProtTomoImportFiles.__init__(self, **args) self.OUTPUT_PREFIX = "outputCoordinates" def _defineParams(self, form): ProtTomoImportFiles._defineParams(self, form) form.addParam('boxSize', params.IntParam, label='Box size') form.addParam('importTomograms', params.PointerParam, pointerClass='SetOfTomograms', label='Input tomograms', help='Select the tomograms/tomogram for which you ' 'want to import coordinates. The file names of the tomogram and ' 'coordinate files must be the same.') def _insertAllSteps(self): self._insertFunctionStep('importCoordinatesStep', self.samplingRate.get()) # --------------------------- STEPS functions -----------------------------
[docs] def importCoordinatesStep(self, samplingRate): importTomograms = self.importTomograms.get() suffix = self._getOutputSuffix(SetOfCoordinates3D) coordsSet = self._createSetOfCoordinates3D(importTomograms, suffix) coordsSet.setBoxSize(self.boxSize.get()) coordsSet.setSamplingRate(samplingRate) coordsSet.setPrecedents(importTomograms) ci = self.getImportClass() for tomo in importTomograms.iterItems(): tomoName = basename(os.path.splitext(tomo.getFileName())[0]) for coordFile, fileId in self.iterFiles(): fileName = basename(os.path.splitext(coordFile)[0]) if tomo is not None and tomoName == fileName: # Parse the coordinates in the given format for this micrograph if self.getImportFrom() == self.IMPORT_FROM_EMAN or self.getImportFrom() == self.IMPORT_FROM_TXT: def addCoordinate(coord, x, y, z): coord.setVolume(tomo.clone()) coord.setPosition(x, y, z, const.BOTTOM_LEFT_CORNER) coordsSet.append(coord) ci.importCoordinates3D(coordFile, addCoordinate) elif self.getImportFrom() == self.IMPORT_FROM_DYNAMO: ci(coordFile, coordsSet, tomo.clone()) args = {} args[self.OUTPUT_PREFIX] = coordsSet self._defineOutputs(**args) self._defineSourceRelation(self.importTomograms, coordsSet)
# --------------------------- INFO functions ------------------------------ def _hasOutput(self): return self.hasAttribute('outputCoordinates3D') def _getCoordsMessage(self): return "Coordinates %s" % self.getObjectTag('outputCoordinates3D') def _summary(self): summary = [] if self._hasOutput(): summary.append("%s imported from:\n%s" % (self._getCoordsMessage(), self.getPattern())) summary.append(u"Sampling rate: *%0.2f* (Å/px)" % self.samplingRate.get()) return summary def _methods(self): methods = [] if self._hasOutput(): methods.append(" %s imported with a sampling rate *%0.2f*" % (self._getCoordsMessage(), self.samplingRate.get()),) return methods def _getVolumeFileName(self, fileName, extension=None): if extension is not None: baseFileName = "import_" + str(basename(fileName)).split(".")[0] + ".%s" % extension else: baseFileName = "import_" + str(basename(fileName)).split(":")[0] return self._getExtraPath(baseFileName) def _validate(self): errors = [] try: next(self.iterFiles()) except StopIteration: errors.append('No files matching the pattern %s were found.' % self.getPattern()) else: tomoFiles = [pwutils.removeBaseExt(file) for file in self.importTomograms.get().getFiles()] coordFiles = [pwutils.removeBaseExt(file) for file, _ in self.iterFiles()] numberMatches = len(set(tomoFiles) & set(coordFiles)) if numberMatches == 0: errors.append("Cannot relate tomogram and coordinate files. In order to stablish a " "relation, the filename of the corresponding tomogram and coordinate " "files must be equal.") return errors def _warnings(self): warnings = [] tomoFiles = [pwutils.removeBaseExt(file) for file in self.importTomograms.get().getFiles()] coordFiles = [pwutils.removeBaseExt(file) for file, _ in self.iterFiles()] numberMatches = len(set(tomoFiles) & set(coordFiles)) if not existsPlugin('emantomo'): warnings.append('Plugin *scipion-em-emantomo* has not being installed. Please, install the Plugin to ' 'import Eman related formats (currently supported formats: ".json"). Otherwise, the protocol ' 'may have unexpected outputs if Eman files are attempted to be imported.\n') if not existsPlugin('dynamo'): warnings.append('Plugin *scipion-em-dynamo* has not being installed. Please, install the Plugin to ' 'import Dynamo related formats (currently supported formats: ".tbl"). Otherwise, the protocol ' 'may have unexpected outputs if Dynamo files are attempted to be imported.\n') if numberMatches < max(len(tomoFiles), len(coordFiles)): warnings.append("Couldn't find a correspondence between all cordinate and tomogram files. " "Association is performed in terms of the file name of the Tomograms and the coordinates. " "(without the extension). For example, if a Tomogram file is named Tomo_1.mrc, the coordinate " "file to be associated to it should be named Tomo_1.ext (being 'ext' any valid extension " "- '.txt', '.tbl', '.json').\n") mismatches_coords = set(coordFiles).difference(tomoFiles) if mismatches_coords: warnings.append("The following coordinate files will not be associated to any Tomogram " "(name without extension):") for file in mismatches_coords: warnings.append("\t%s" % file) warnings.append("\n") mismatches_tomos = set(tomoFiles).difference(coordFiles) if mismatches_tomos: warnings.append("The following Tomogram files will not be associated to any coordinates " "(name without extension):") for file in mismatches_tomos: warnings.append("\t%s" % file) warnings.append("\n") return warnings # ------------------ UTILS functions --------------------------------------
[docs] def getImportFrom(self): importFrom = self._getImportChoices()[self.importFrom.get()] if importFrom == self.IMPORT_FROM_AUTO: importFrom = self.getFormat() return importFrom
[docs] def getFormat(self): for coordFile, _ in self.iterFiles(): if coordFile.endswith('.txt'): return self.IMPORT_FROM_TXT if coordFile.endswith('.json') and existsPlugin('emantomo'): return self.IMPORT_FROM_EMAN if coordFile.endswith('.tbl') and existsPlugin('dynamo'): return self.IMPORT_FROM_DYNAMO return -1
[docs] def getImportClass(self): """ Return the class in charge of importing the files. """ importFrom = self.getImportFrom() if importFrom == self.IMPORT_FROM_EMAN: EmanImport = Domain.importFromPlugin('emantomo.convert', 'EmanTomoImport', errorMsg='Eman is needed to import .json or ' '.box files', doRaise=True) return EmanImport(self, None) elif importFrom == self.IMPORT_FROM_DYNAMO: readDynCoord = Domain.importFromPlugin("dynamo.convert.convert", "readDynCoord") return readDynCoord elif importFrom == self.IMPORT_FROM_TXT: return TomoImport(self) else: self.importFilePath = '' return None