Source code for tomo.protocols.protocol_import_subtomograms

# coding=utf-8
# **************************************************************************
# *
# * Authors:     Adrian Quintana (adrian@eyeseetea.com) [1]
# *              Estrella Fernandez Gimenez (me.fernandez@cnb.csic.es) [2]
# *
# * [1] EyeSeeTea Ltd, London, UK
# * [2] BCU, Centro Nacional de Biotecnologia, CSIC
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# * This program is free software; you can redistribute it and/or modify
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# * the Free Software Foundation; either version 2 of the License, or
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# * This program is distributed in the hope that it will be useful,
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# * 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
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# * 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 os.path import abspath, basename

from pwem.emlib.image import ImageHandler
from pwem.objects import Transform
from pyworkflow import BETA
from pyworkflow.utils.path import createAbsLink

from .protocol_base import ProtTomoImportFiles, ProtTomoImportAcquisition
from ..objects import SubTomogram
from ..utils import _getUniqueFileName


[docs]class ProtImportSubTomograms(ProtTomoImportFiles, ProtTomoImportAcquisition): """Protocol to import a set of tomograms to the project""" _outputClassName = 'SetOfSubTomograms' _label = 'import subtomograms' _devStatus = BETA def __init__(self, **args): ProtTomoImportFiles.__init__(self, **args) def _defineParams(self, form): ProtTomoImportFiles._defineParams(self, form) # form.addParam('importCoordinates', PointerParam, # pointerClass='SetOfCoordinates3D', # allowsNull=True, # label='Input coordinates 3D', # help='Select the coordinates for which the ' # 'subtomograms were extracted.') ProtTomoImportAcquisition._defineParams(self, form) def _insertAllSteps(self): self._insertFunctionStep('importSubTomogramsStep', self.getPattern(), self.samplingRate.get()) self._insertFunctionStep('createOutput') # --------------------------- STEPS functions -----------------------------
[docs] def importSubTomogramsStep( self, pattern, samplingRate ): """ Copy images matching the filename pattern Register other parameters. """ self.info("Using pattern: '%s'" % pattern) # Create a Volume template object subtomo = SubTomogram() subtomo.setSamplingRate(samplingRate) imgh = ImageHandler() self.subtomoSet = self._createSetOfSubTomograms() self.subtomoSet.setSamplingRate(samplingRate) # if self.importCoordinates.get(): # self.coords = [] # for coord3D in self.importCoordinates.get().iterCoordinates(): # self.coords.append(coord3D.clone()) # self.subtomoSet.setCoordinates3D(self.importCoordinates) self._parseAcquisitionData() for fileName, fileId in self.iterFiles(): x, y, z, n = imgh.getDimensions(fileName) if fileName.endswith('.map'): fileName += ':mrc' if fileName.endswith('.mrc') or fileName.endswith(':mrc'): if z == 1 and n != 1: zDim = n n = 1 else: zDim = z else: zDim = z origin = Transform() origin.setShifts(x/-2. * samplingRate, y/-2. * samplingRate, zDim/-2. * samplingRate) subtomo.setOrigin(origin) # read origin from form newFileName = _getUniqueFileName(self.getPattern(), fileName) # newFileName = abspath(self._getVolumeFileName(fileName)) if fileName.endswith(':mrc'): fileName = fileName[:-4] createAbsLink(fileName, self._getExtraPath(newFileName)) if n == 1: self._addSubtomogram(subtomo, self._getExtraPath(fileName), self._getExtraPath(newFileName)) else: for index in range(1, n+1): self._addSubtomogram(subtomo, self._getExtraPath(fileName), self._getExtraPath(newFileName), index=index)
def _addSubtomogram(self, subtomo, fileName, newFileName, index=None): """ adds a subtomogram to a set """ subtomo.cleanObjId() if index is None: subtomo.setFileName(newFileName) else: subtomo.setLocation(index, newFileName) subtomo.setAcquisition(self._extractAcquisitionParameters(fileName)) # self._setCoordinates3D(subtomo) self.subtomoSet.append(subtomo)
[docs] def createOutput(self): self._defineOutputs(outputSubTomograms=self.subtomoSet)
# --------------------------- INFO functions ------------------------------ # def _setCoordinates3D(self, subtomo): # if self.importCoordinates.get(): # if len(self.coords) < 1: # raise Exception("Coordinates 3D and subtomograms should have the same size") # else: # subtomo.setCoordinate3D(self.coords.pop(0)) def _hasOutput(self): return self.hasAttribute('outputSubTomograms') def _getSubTomMessage(self): return "SubTomograms %s" % self.getObjectTag('outputSubTomograms') def _summary(self): summary = [] if self._hasOutput(): summary.append("%s imported from:\n%s" % (self._getSubTomMessage(), self.getPattern())) if self.samplingRate.get(): summary.append(u"Sampling rate: *%0.2f* (Å/px)" % self.samplingRate.get()) ProtTomoImportAcquisition._summary(self, summary, getattr(self, 'outputSubTomograms')) return summary def _methods(self): methods = [] if self._hasOutput(): methods.append(" %s imported with a sampling rate *%0.2f*" % (self._getSubTomMessage(), 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()) return errors