Source code for xmipptomo.viewers.viewer_resolution_local_monotomo

# -*- coding: utf-8 -*-
# **************************************************************************
# *
# * Authors:     J.L. Vilas (jlvilas@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 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'
# *
# **************************************************************************

import matplotlib.pyplot as plt
from matplotlib import cm
from pwem.wizards import ColorScaleWizardBase

from pyworkflow.protocol.params import (LabelParam, EnumParam,
                                        IntParam, LEVEL_ADVANCED)
from pyworkflow.viewer import ProtocolViewer, DESKTOP_TKINTER
from pwem.viewers import ChimeraView, DataView, EmPlotter
from pwem.emlib.metadata import MetaData, MDL_X, MDL_COUNT
from pwem.viewers import LocalResolutionViewer
from pwem.constants import AX_Z

from xmipp3.viewers.plotter import XmippPlotter
from xmipptomo.protocols.protocol_resolution_local_monotomo import (XmippProtMonoTomo,
                                                           OUTPUT_RESOLUTION_FILE,
                                                           FN_METADATA_HISTOGRAM)

[docs]class XmippMonoTomoViewer(LocalResolutionViewer): """ Visualization tools for MonoRes results. MonoTomo is a Xmipp package for estimating the local resolution of tomograms, primarily by cryo-electrons tomography (cryo-EM). """ _label = 'viewer MonoTomo' _targets = [XmippProtMonoTomo] _environments = [DESKTOP_TKINTER]
[docs] @staticmethod def getColorMapChoices(): return plt.colormaps()
def __init__(self, *args, **kwargs): ProtocolViewer.__init__(self, *args, **kwargs) def _defineParams(self, form): form.addSection(label='Visualization') form.addParam('doShowVolumeSlices', LabelParam, label="Show resolution slices") form.addParam('doShowOriginalVolumeSlices', LabelParam, label="Show original volume slices") form.addParam('doShowResHistogram', LabelParam, label="Show resolution histogram") group = form.addGroup('Colored resolution Slices and Volumes') group.addParam('sliceAxis', EnumParam, default=AX_Z, choices=['x', 'y', 'z'], display=EnumParam.DISPLAY_HLIST, label='Slice axis') group.addParam('doShowVolumeColorSlices', LabelParam, label="Show colored resolution slices") group.addParam('doShowOneColorslice', LabelParam, expertLevel=LEVEL_ADVANCED, label='Show selected slice') group.addParam('sliceNumber', IntParam, default=-1, expertLevel=LEVEL_ADVANCED, label='Show slice number') group.addParam('doShowChimera', LabelParam, label="Show Resolution map in Chimera") ColorScaleWizardBase.defineColorScaleParams(group, defaultHighest=self.protocol.max_res_init.get(), defaultLowest=self.protocol.min_res_init.get()) def _getVisualizeDict(self): self.protocol._createFilenameTemplates() return {'doShowOriginalVolumeSlices': self._showOriginalVolumeSlices, 'doShowVolumeSlices': self._showVolumeSlices, 'doShowVolumeColorSlices': self._showVolumeColorSlicesResolution, 'doShowOneColorslice': self._showOneColorslice, 'doShowResHistogram': self._plotHistogram, 'doShowChimera': self._showChimera, } def _showVolumeSlices(self, param=None): cm = DataView(self.protocol.resolution_Volume.getFileName()) return [cm] def _showOriginalVolumeSlices(self, param=None): # if self.protocol.halfVolumes.get() is True: # Where is halfVolumes? try: cm = DataView(self.protocol.inputVolume.get().getFileName()) cm2 = DataView(self.protocol.inputVolume2.get().getFileName()) return [cm, cm2] except: cm = DataView(self.protocol.inputVolumes.get().getFileName()) return [cm] def _showVolumeColorSlicesResolution(self, param=None): self._showVolumeColorSlices(OUTPUT_RESOLUTION_FILE) def _showVolumeColorSlices(self, mapFile): imageFile = self.protocol._getFileName(mapFile) imgData, _, _, _ = self.getImgData(imageFile) imgData, min_Res, max_Res, voldim__ = self.getImgData(imageFile) xplotter = XmippPlotter(x=2, y=2, mainTitle="Local Resolution Slices " "along %s-axis." % self._getAxis()) # The slices to be shown are close to the center. Volume size is divided in # 9 segments, the fouth central ones are selected i.e. 3,4,5,6 for i in range(3, 7): sliceNumber = self.getSlice(i, imgData) plot = self._createSlicePlot(imgData, sliceNumber, xplotter) xplotter.getColorBar(plot) return [plt.show(xplotter)] def _showOneColorslice(self, param=None): imageFile = self.protocol._getFileName(OUTPUT_RESOLUTION_FILE) imgData, _, _, volDim = self.getImgData(imageFile) xplotter = XmippPlotter(x=1, y=1, mainTitle="Local Resolution Slices " "along %s-axis." % self._getAxis()) sliceNumber = self.sliceNumber.get() if sliceNumber < 0: sliceNumber = int(volDim[0] / 2) else: sliceNumber -= 1 # sliceNumber has no sense to start in zero plot = self._createSlicePlot(imgData, sliceNumber, xplotter) xplotter.getColorBar(plot) return [plt.show(xplotter)] def _createSlicePlot(self, imgData, sliceNumber, xplotter): a = xplotter.createSubPlot("Slice %s" % (sliceNumber + 1), '', '') matrix = self.getSliceImage(imgData, sliceNumber, self._getAxis()) plot = xplotter.plotMatrix(a, matrix, self.lowest.get(), self.highest.get(), cmap=self.getColorMap(), interpolation="nearest") return plot def _plotHistogram(self, param=None): md = MetaData() md.read(self.protocol._getFileName(FN_METADATA_HISTOGRAM)) x_axis = [] y_axis = [] i = 0 for idx in md: x_axis_ = md.getValue(MDL_X, idx) if i == 0: x0 = x_axis_ elif i == 1: x1 = x_axis_ y_axis_ = md.getValue(MDL_COUNT, idx) i += 1 x_axis.append(x_axis_) y_axis.append(y_axis_) plotter = EmPlotter() plotter.createSubPlot("Resolutions Histogram", "Resolution (A)", "# of Counts") barwidth = x1 - x0 plotter.plotDataBar(x_axis, y_axis, barwidth) return [plotter] def _getAxis(self): return self.getEnumText('sliceAxis') def _showChimera(self, param=None): fnResVol = self.protocol._getFileName(OUTPUT_RESOLUTION_FILE) vol = self.protocol.inputVolume.get() fnOrigMap = vol.getFileName() sampRate = vol.getSamplingRate() cmdFile = self.protocol._getExtraPath('chimera_resolution_map.py') self.createChimeraScript(cmdFile, fnResVol, fnOrigMap, sampRate, numColors=self.intervals.get(), lowResLimit=self.highest.get(), highResLimit=self.lowest.get()) view = ChimeraView(cmdFile) return [view]
[docs] def getColorMap(self): cmap = cm.get_cmap(self.colorMap.get()) if cmap is None: cmap = cm.jet return cmap