# **************************************************************************
# *
# * Authors: Laura del Cano (ldelcano@cnb.csic.es)
# * Yunior C. Fonseca Reyna (cfonseca@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'
# *
# **************************************************************************
"""
This module contains converter functions that will serve to:
1. Write from base classes to Appion specific files
2. Read from Appion files to base classes
"""
from pyworkflow.utils import replaceBaseExt, join, exists
from pwem.objects import Coordinate
import pwem.emlib as emlib
[docs]def readSetOfCoordinates(workDir, micSet, coordSet):
""" Read from Appion .txt files.
It is expected a file named: base.txt under the workDir.
Params:
workDir: where the Appion dogpicker output files are located.
micSet: the SetOfMicrographs to associate the .txt, which
name should be the same of the micrographs.
coordSet: the SetOfCoordinates that will be populated.
"""
for mic in micSet:
micCoordFn = join(workDir, replaceBaseExt(mic.getFileName(), 'txt'))
readCoordinates(mic, micCoordFn, coordSet)
[docs]def readCoordinates(mic, fileName, coordsSet):
if exists(fileName):
md = emlib.MetaData()
md.readPlain(fileName, 'xcoor ycoor')
for objId in md:
x = md.getValue(emlib.MDL_XCOOR, objId)
y = md.getValue(emlib.MDL_YCOOR, objId)
coord = Coordinate()
coord.setPosition(x, y)
coord.setMicrograph(mic)
coordsSet.append(coord)
[docs]def writeSetOfCoordinates():
pass