Source code for pwem.viewers.viewer_fsc

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es)
# *              Roberto Marabini (roberto@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'
# *
# **************************************************************************

from matplotlib.ticker import FuncFormatter
from matplotlib.widgets import Button

import pyworkflow.viewer as pwviewer
import pyworkflow.utils as pwutils

import pwem.objects as emobj
import pwem.protocols as emprot

from .plotter import EmPlotter, plt


[docs]class FscViewer(pwviewer.Viewer): """ Viewer for plot a FSC object. """ _targets = [emobj.FSC, emobj.SetOfFSCs] _environments = [pwviewer.DESKTOP_TKINTER, pwviewer.WEB_DJANGO] def __init__(self, **kwargs): pwviewer.Viewer.__init__(self, **kwargs) self.threshold = kwargs.get('threshold', 0.143) self.legend = "" self.plotter = EmPlotter(x=1, y=1, windowTitle='FSC', figure=kwargs.get('figure', 'active')) self._lastSubPlot = None self._addButton = kwargs.get('addButton', False) def _formatFreq(self, value, pos): """ Format function for Matplotlib formatter. """ inv = 999. if value: inv = 1 / value return "1/%0.2f" % inv
[docs] def show(self, block=True): self.plotter.show(block=block)
def _plotButton(self): if self._addButton: axcreateFSC = plt.axes([0.75, 0.02, 0.2, 0.050]) # Button does not allow to define text color so # I write it directly axcreateFSC.text(0.5, 0.5, 'create FSC', verticalalignment='center', horizontalalignment='center', transform=axcreateFSC.transAxes, color='white') bcreateFSC = Button(axcreateFSC, '', # leave label empty color=pwutils.Color.RED_COLOR, hovercolor='maroon') bcreateFSC.on_clicked(self.createFSCObject) self._addButton = False return bcreateFSC
[docs] def visualize(self, obj, **kwargs): # Keep input object in case we need to launch # a new protocol and set dependencies self.fscList = [] if isinstance(obj, emobj.SetOfFSCs): for i, fsc in enumerate(obj): self.fscList.append(fsc.clone()) fscLabel = fsc.getObjLabel() or 'FSC %d' % (i + 1) self.plotFsc(fsc, label=fscLabel, **kwargs) else: # single FSC self.plotFsc(obj, **kwargs) self.fscList.append(obj.clone()) bcreateFSC = self._plotButton() # if you do not assign the result # to something it will be # delete self.show()
# return [self.plotter]
[docs] def createFSCObject(self, event): self.project = self.getProject() prot = self.getProject().newProtocol(emprot.ProtCreateFSC) prot.setObjLabel('FSC-%s' % self.label) # label) prot.setInputObj(self.protocol) prot.setInputFscList(self.fscList) self.project.launchProtocol(prot)
[docs] def plotFsc(self, obj, **kwargs): x, y = obj.getData() if self._lastSubPlot is None: a = self.plotter.createSubPlot("FSC", "frequency (1/A)", "fsc") a.set_ylim([-0.1, 1.1]) a.plot([0, x[-1]], [self.threshold, self.threshold], 'k--') a.grid(True) a.xaxis.set_major_formatter(FuncFormatter(self._formatFreq)) self._lastSubPlot = a self.label = kwargs.get('label', self.protocol.getRunName()) self.plotter.plotData(x, y, '-', label=self.label) self.plotter.legend()
# if I run this