# **************************************************************************
# *
# * Authors: Estrella Fernandez Gimenez
# * Carlos Oscar Sanchez Sorzano
# *
# * 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 2 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 implements visualization program
for ml_tomo.
"""
import os
from xmipp2.protocols import Xmipp2ProtMLTomo
from pyworkflow.viewer import DESKTOP_TKINTER, WEB_DJANGO, ProtocolViewer
from pyworkflow.protocol.params import LabelParam
from pwem.viewers.plotter import EmPlotter
from pwem.viewers.views import DataView
[docs]class Xmipp2ProtMlTomoViewer(ProtocolViewer):
""" Wrapper to visualize different type of objects
with the Xmipp program xmipp_showj. """
_label = 'viewer Ml_Tomo'
_targets = [Xmipp2ProtMLTomo]
_environments = [DESKTOP_TKINTER, WEB_DJANGO]
def _defineParams(self, form):
form.addSection(label='Resolution')
form.addParam('doShowFsc', LabelParam,
label="Display Fourier Shell Correlation")
def _getVisualizeDict(self):
return {'doShowFsc': self._viewFsc}
def _viewFsc(self, e=None):
return self._loadPlots("Fourier Shell Correlation", 'FSC', color='r')
def _loadPlots(self, title, plotLabel, **kwargs):
""" Check if the FSC metadata is generated and if so,
read the plots and the metadata.
*args and **kwargs will be passed to self._createPlot function.
"""
fnFsc = self.protocol._getExtraPath("mltomo.fsc")
if not os.path.exists(fnFsc):
return [self.errorMessage('The FSC file was not produced\n',
title='Missing result file')]
# leer archivo FSC
fnFsc = open(self.protocol._getExtraPath("mltomo.fsc"),'r')
lines = fnFsc.readlines()
freq = []
# fnClasses = self.protocol._getExtraPath("Classes") # generated classes
classes = [] # j,i (j num classes, i num lines)
for i in lines:
freq.append(i.split()) # column frecs
# classes.append(i.split()[j]) # j num class
fnFsc.close()
plotter = EmPlotter(self, freq, classes[1], title, **kwargs) # change class index
return [plotter, DataView(plotLabel)]