# **************************************************************************
# *
# * Authors: J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es)
# *
# * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * 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 3 of the License, or
# * (at your option) any later version.
# *
# * 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.
# *
# * 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
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************
from os.path import join, basename, exists
from collections import OrderedDict
from pyworkflow.utils import findRootFrom
import pwem.objects as emobj
import pwem.constants as emcts
[docs]class ScipionImport:
""" Import
"""
def __init__(self, protocol, sqliteFile):
self.protocol = protocol
self._sqliteFile = sqliteFile
self.copyOrLink = protocol.getCopyOrLink()
[docs] def importMicrographs(self):
""" Import a SetOfMicrographs from a given sqlite file. """
inputSet = emobj.SetOfMicrographs(filename=self._sqliteFile)
self._findImagesPath(inputSet)
micSet = self.protocol._createSetOfMicrographs()
micSet.setObjComment('Micrographs imported from sqlite file:\n%s'
% self._sqliteFile)
# Update both samplingRate and acquisition with parameters
# selected in the protocol form.
# Acquisition should be updated before, just to ensure that
# scannedPixedSize will be computed properly when calling
# setSamplingRate
self.protocol.fillAcquisition(micSet.getAcquisition())
self.protocol.setSamplingRate(micSet)
micSet.setIsPhaseFlipped(self.protocol.haveDataBeenPhaseFlipped.get())
# Read the micrographs from the 'self._sqliteFile' metadata
# but fixing the filenames with new ones (linked or copy to extraDir)
micSet.copyItems(inputSet, updateItemCallback=self._updateParticle)
self.protocol._defineOutputs(outputMicrographs=micSet)
[docs] def importCoordinates(self, inputMics):
""" Import a SetOfCoordinates from a given sqlite file. """
inputSet = emobj.SetOfCoordinates(filename=self._sqliteFile)
# self._findImagesPath(inputSet)
coorSet = self.protocol._createSetOfCoordinates(inputMics)
coorSet.copyInfo(inputSet)
coorSet.setObjComment('Coordinates imported from sqlite file:\n%s'
% self._sqliteFile)
# Update both samplingRate and acquisition with parameters
# selected in the protocol form.
# Acquisition should be updated before, just to ensure that
# scannedPixedSize will be computed properly when calling
# setSamplingRate
coorSet.setBoxSize(self.protocol.boxSize.get())
# Read the micrographs from the 'self._sqliteFile' metadata
# but fixing the filenames with new ones (linked or copy to extraDir)
coorSet.copyItems(inputSet)
self.protocol._defineOutputs(outputCoordinates=coorSet)
self.protocol._defineSourceRelation(inputMics, coorSet)
[docs] def importParticles(self):
""" Import particles from a metadata 'images.xmd' """
inputSet = emobj.SetOfParticles(filename=self._sqliteFile)
inputSet.loadProperty('_alignment', emcts.ALIGN_NONE)
inputSet.loadProperty('_hasCtf', False)
self._findImagesPath(inputSet)
partSet = self.protocol._createSetOfParticles()
partSet.copyInfo(inputSet)
partSet.setObjComment('Particles imported from Scipion sqlite file:\n%s'
% self._sqliteFile)
partSet.copyItems(inputSet, updateItemCallback=self._updateParticle)
# Update both samplingRate and acquisition with parameters
# selected in the protocol form
self.protocol.setSamplingRate(partSet)
self.protocol.fillAcquisition(partSet.getAcquisition())
partSet.setIsPhaseFlipped(self.protocol.haveDataBeenPhaseFlipped.get())
self.protocol._defineOutputs(outputParticles=partSet)
def _findImagesPath(self, inputSet):
""" Find the relative path from which the images exists
revative to the sqlite location.
"""
# Store which images stack have been linked/copied and the new path
self._imgDict = {}
img = inputSet.getFirstItem()
self._imgPath = findRootFrom(self._sqliteFile, img.getFileName())
if self._imgPath is None:
self.protocol.warning("Binary data was not found from sqlite: %s"
% self._sqliteFile)
[docs] def validate(self):
""" Try to find errors on import. """
errors = []
return errors
[docs] def validateMicrographs(self):
return self.validate()
[docs] def validateParticles(self):
return self.validate()
def _updateParticle(self, particle, partRow):
if self._imgPath:
# Create a link or copy files to extraPath
# and update the Row properly
fn = particle.getFileName()
imgBase = basename(fn)
imgDst = self.protocol._getExtraPath(imgBase)
if not exists(imgDst):
self.copyOrLink(join(self._imgPath, fn), imgDst)
particle.setFileName(imgDst)
[docs] def loadAcquisitionInfo(self):
""" Return a dictionary with acquisition values and
the sampling rate information.
In the case of Scipion, these values will be read from the
'Properties' table of the particles.sqlite file.
"""
acq = OrderedDict()
inputSet = emobj.SetOfParticles(filename=self._sqliteFile)
def _get(key):
return inputSet.getProperty(key)
acq['samplingRate'] = _get('_samplingRate')
acq['voltage'] = _get('_acquisition._voltage')
acq['amplitudeContrast'] = _get('_acquisition._amplitudeContrast')
acq['sphericalAberration'] = float(_get('_acquisition._sphericalAberration'))
return acq
[docs] def getMicCTF(self, mic):
""" Retrieve the CTF associated to this micrograph. """
# The first time this function is called, the set of micrographs
# will be loaded from the given sqlite file
if not hasattr(self, 'ctfSet'):
self.ctfSet = emobj.SetOfCTF(filename=self._sqliteFile)
return self.ctfSet[mic.getObjId()]