# ******************************************************************************
# *
# * Authors: Jose Gutierrez (jose.gutierrez@cnb.csic.es) [1]
# *
# * [1] 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 pyworkflow.viewer import Viewer
from .viewer_base import *
from ..protocols import ProtRelionSortParticles
# TODO: deprecate this class
[docs]class RelionSortViewer(Viewer):
""" Visualization of Relion sorting results."""
_environments = [DESKTOP_TKINTER, WEB_DJANGO]
_targets = [ProtRelionSortParticles]
def _visualize(self, obj, **kwargs):
views = []
if obj.hasAttribute('outputParticles'): # Protocol finished
particles = obj.outputParticles
labels = ('id enabled _index _filename _rlnSelectParticlesZscore '
'_coordinate._rlnAutopickFigureOfMerit _sampling '
'_ctfModel._defocusU _ctfModel._defocusV '
'_ctfModel._defocusAngle _transform._matrix')
sortBy = '_rlnSelectParticlesZscore asc'
strId = particles.strId()
fn = particles.getFileName()
views.append(ObjectView(self._project, strId, fn,
viewParams={showj.ORDER: labels,
showj.VISIBLE: labels,
showj.SORT_BY: sortBy,
showj.RENDER: '_filename'}))
fn = obj._getExtraPath('input_particles_sorted.star')
mdFn = md.MetaData(fn)
# If Zscore in output images plot Zscore particle sorting
if mdFn.containsLabel(md.RLN_SELECT_PARTICLES_ZSCORE):
# sort output by Z-score
mdFn.sort(md.RLN_SELECT_PARTICLES_ZSCORE)
xplotter = RelionPlotter(windowTitle="Zscore particles sorting")
xplotter.createSubPlot("Particle sorting", "Particle number",
"Zscore")
xplotter.plotMd(mdFn, False,
mdLabelY=md.RLN_SELECT_PARTICLES_ZSCORE)
views.append(xplotter)
return views