Source code for bsoft.convert

# **************************************************************************
# *
# * Authors:     Airen Zaldivar Peraza (azaldivar@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'
# *
# **************************************************************************

import pwem.emlib.metadata as md
from pwem.objects import Coordinate
from pyworkflow.object import String, ObjectWrap
from pyworkflow.utils import join, replaceBaseExt, createLink, exists

from bsoft.constants import *


[docs]def readSetOfCoordinates(outputDir, micSet, coordSet): """ Read from Bsoft .star files. Params: outputDir: the directory where the .star files are. micSet: the SetOfMicrographs to associate the .star, which name should be the same of the micrographs. coordSet: the SetOfCoordinates that will be populated. """ boxSize = 100 for mic in micSet: outputFile = join(outputDir, replaceBaseExt(mic.getFileName(), 'star')) if exists(outputFile): posMd = md.MetaData(outputFile) for objId in posMd: coordRow = rowFromMd(posMd, objId) coord = rowToCoordinate(coordRow) boxSize = 2 * float(coordRow.getValue("particle.x_origin", 50)) coord.setMicrograph(mic) coord.setX(coord.getX()) coord.setY(coord.getY()) coordSet.append(coord) # Add an unique ID that will be propagated to particles # posMd.setValue(md.MDL_PARTICLE_ID, long(coord.getObjId()), objId) # reading origin.x value and converting to particle # size, can change, we take last value coordSet.setBoxSize(boxSize)
[docs]def rowToCoordinate(coordRow): """ Create a Coordinate from a row of a metadata. """ # Check that all required labels are present in the row if _containsAll(coordRow, COOR_DICT): coord = Coordinate() rowToObject(coordRow, coord, COOR_DICT) # , extraLabels=COOR_EXTRA_LABELS) # TODO: switch back on extra labels when # sqlite mapper can tolerate dots in label names else: coord = None return coord
[docs]def rowToObject(row, obj, attrDict, extraLabels=[]): """ This function will convert from a md Row to an EMObject. Params: row: the Row instance (input) obj: the EMObject instance (output) attrDict: dictionary with the map between obj attributes(keys) and row MDLabels in Bsoft (values). """ # Bsoft does not have analogous label for MDL_ENABLED obj.setEnabled(True) for attr, label in attrDict.iteritems(): # all Bsoft labels are strings, so convert to float value = float(row.getValue(label)) if not hasattr(obj, attr): setattr(obj, attr, ObjectWrap(value)) else: getattr(obj, attr).set(value) attrLabels = attrDict.values() for label in extraLabels: if label not in attrLabels and row.hasLabel(label): labelStr = md.label2Str(label) setattr(obj, '_' + labelStr, row.getValueAsObject(label))
[docs]def rowFromMd(mdata, objId): row = md.Row() row.readFromMd(mdata, objId) return row
def _containsAll(row, labels): """ Check if the labels (values) in labelsDict are present in the row. """ values = labels.values() if isinstance(labels, dict) else labels return all(row.containsLabel(l) for l in values)
[docs]def writeSetOfParticles(imgSet, starFile, stackFile): """ This function will write a SetOfImages as Bsoft metadata. Params: imgSet: the SetOfImages instance. starFile: the filename where to write the metadata. """ mdata = md.MetaData() mdata.setColumnFormat(False) imgRow = mdata.Row() imgRow.setValue("micrograph.id", int(1)) imgRow.setValue("particle.x_origin", str(stackFile)) imgRow.writeToMd(mdata, mdata.addObject()) imgSet._bsoftStar = String(starFile)
[docs]def createBsoftInputParticles(imgSet, starFile, stackFile): """ Ensure that 'starFile' is a valid STAR files with particles. If the imgSet comes from Bsoft, just create a link. If not, then write the proper file. """ imgsStar = getattr(imgSet, '_bsoftStar', None) if imgsStar is None: writeSetOfParticles(imgSet, starFile, stackFile) else: imgsFn = imgsStar.get() createLink(imgsFn, imgsStar.get())