# **************************************************************************
# *
# * Authors: Jose Gutierrez Tabuenca (jose.gutierrez@cnb.csic.es) [1]
# * J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [2]
# *
# * [1] Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# * [2] SciLifeLab, Stockholm University
# *
# * 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 abspath, basename
from pwem.protocols import ProtParticlePicking
from pyworkflow.protocol.params import FloatParam
from pyworkflow.utils.properties import Message
from pyworkflow.gui.dialog import askYesNo
import bsoft
from bsoft.convert import readSetOfCoordinates
[docs]class BsoftProtParticlePicking(ProtParticlePicking):
"""Protocol to pick particles in a set of micrographs using bsoft"""
_label = 'particle picking'
def __init__(self, **args):
ProtParticlePicking.__init__(self, **args)
# The following attribute is only for testing
def _defineParams(self, form):
ProtParticlePicking._defineParams(self, form)
form.addParam('memory', FloatParam, default=2,
label='Memory to use (In Gb)', expertLevel=2)
def _insertAllSteps(self):
"""The Particle Picking process is realized for a set of micrographs"""
# Get pointer to input micrographs
self.inputMics = self.inputMicrographs.get()
# Launch Particle Picking GUI
self._insertFunctionStep('launchParticlePickGUIStep',
interactive=True)
[docs] def launchParticlePickGUIStep(self):
# Launch the particle picking GUI
outputdir = self._getExtraPath()
for mic in self.inputMics:
micfile = abspath(mic.getFileName())
args = "%s %s" % (micfile, outputdir)
self.runJob("ln -sf", args)
self._enterDir(outputdir)
for mic in self.inputMics:
self.runJob(bsoft.Plugin.getProgram('bshow'), basename(mic.getFileName()),
env=bsoft.Plugin.getEnviron())
# Open dialog to request confirmation to create output
if askYesNo(Message.TITLE_SAVE_OUTPUT,
Message.LABEL_SAVE_OUTPUT, None):
self._leaveDir() # going back to project dir
self._createOutput(outputdir)
[docs] def readSetOfCoordinates(self, workingDir, coordSet):
readSetOfCoordinates(workingDir, self.inputMics, coordSet)
def _methods(self):
return ProtParticlePicking._methods(self)
def _summary(self):
return ProtParticlePicking._summary(self)
def __str__(self):
""" String representation of a Supervised Picking run """
if not hasattr(self, 'outputCoordinates'):
picked = 0
else:
picked = self.outputCoordinates.getSize()
return "Particles picked: %d (from %d micrographs)" % (
picked, self.inputMicrographs.get().getSize())