Source code for xmipp3.viewers.viewer_resolution_monogenic_signal

# -*- 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
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# *  All comments concerning this program package may be sent to the
# *  e-mail address 'scipion@cnb.csic.es'
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# **************************************************************************
import os

import matplotlib.pyplot as plt
from matplotlib import cm
from pwem.wizards import ColorScaleWizardBase
from pyworkflow.utils import replaceExt
from os.path import exists

from pyworkflow.protocol.params import (LabelParam, EnumParam, PointerParam,
                                        IntParam, LEVEL_ADVANCED)
from pyworkflow.viewer import ProtocolViewer, DESKTOP_TKINTER

from xmipp3.viewers.viewer_resolution_directional import AX_Z
from pwem.viewers import (LocalResolutionViewer, EmPlotter, ChimeraView,
                          DataView)
from pwem.emlib.metadata import MetaData, MDL_X, MDL_COUNT

from xmipp3.protocols.protocol_resolution_monogenic_signal import (
    XmippProtMonoRes, OUTPUT_RESOLUTION_FILE, FN_METADATA_HISTOGRAM,
    OUTPUT_RESOLUTION_FILE_CHIMERA)
from .plotter import XmippPlotter
from pyworkflow.gui import plotter


[docs]class XmippMonoResViewer(LocalResolutionViewer): """ Visualization tools for MonoRes results. MonoRes is a Xmipp packagefor computing the local resolution of 3D density maps studied in structural biology, primarily by cryo-electron microscopy (cryo-EM). """ _label = 'viewer MonoRes' _targets = [XmippProtMonoRes] _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 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 ChimeraX") ColorScaleWizardBase.defineColorScaleParams(group, defaultLowest=self.protocol.min_res_init, defaultHighest=self.protocol.max_res_init) group.addParam('sharpenedMap', PointerParam, pointerClass='Volume', label="(Optional) Color a sharpen map by local resolution in ChimeraX", allowsNull=True, help='Local resolution should be estimated with the raw maps instead' ' of sharpen maps. Information about this in (Vilas et al ' 'Current Opinion in Structural Biology 2021). This entry parameter ' 'allows to color the local resolution in' 'a different map') def _getVisualizeDict(self): self.protocol._createFilenameTemplates() return {'doShowOriginalVolumeSlices': self._showOriginalVolumeSlices, 'doShowVolumeSlices': self._showVolumeSlices, 'doShowVolumeColorSlices': self._showVolumeColorSlices, '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.useHalfVolumes.get(): if self.protocol.hasHalfVolumesFile.get(): fn1, fn2 = self.protocol.associatedHalves.get().getHalfMaps().split(',') else: fn1 = self.protocol.halfMap1.get().getFileName() fn2 = self.protocol.halfMap2.get().getFileName() cm = DataView(fn1) cm2 = DataView(fn2) return [cm, cm2] else: cm = DataView(self.protocol.fullMap.get().getFileName()) return [cm] def _showVolumeColorSlices(self, param=None): if (exists(self.protocol._getExtraPath("mgresolution.mrc"))): imageFile = self.protocol._getExtraPath("mgresolution.mrc") else: imageFile = self.protocol._getExtraPath(OUTPUT_RESOLUTION_FILE) if not os.path.exists(imageFile): imageFile = replaceExt(imageFile, 'mrc') 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) 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") xplotter.getColorBar(plot) return [xplotter] def _showOneColorslice(self, param=None): if (exists(self.protocol._getExtraPath("mgresolution.mrc"))): imageFile = self.protocol._getExtraPath("mgresolution.mrc") else: imageFile = self.protocol._getExtraPath(OUTPUT_RESOLUTION_FILE) if not os.path.exists(imageFile): imageFile = replaceExt(imageFile, 'mrc') imgData, min_Res, max_Res, 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 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") xplotter.getColorBar(plot) return [xplotter] def _plotHistogram(self, param=None): md = MetaData() md.read(self.protocol._getExtraPath(FN_METADATA_HISTOGRAM)) x_axis = [] y_axis = [] for idx in md: x_axis_ = md.getValue(MDL_X, idx) y_axis_ = md.getValue(MDL_COUNT, idx) x_axis.append(x_axis_) y_axis.append(y_axis_) _plotter = EmPlotter() _plotter.createSubPlot("Resolutions Histogram", "Resolution (A)", "# of Counts") barwidth = (x_axis[-1] - x_axis[0]) / len(x_axis) _plotter.plotDataBar(x_axis[:-2], y_axis[:-2], barwidth) return [_plotter] def _getAxis(self): return self.getEnumText('sliceAxis') def _showChimera(self, param=None): if (exists(self.protocol._getExtraPath("MG_Chimera_resolution.mrc"))): fnResVol = self.protocol._getExtraPath("MG_Chimera_resolution.mrc") else: fnResVol = self.protocol._getExtraPath(OUTPUT_RESOLUTION_FILE_CHIMERA) if self.sharpenedMap.get(): fnOrigMap = self.sharpenedMap.get().getFileName() sampRate = self.sharpenedMap.get().getSamplingRate() else: if self.protocol.useHalfVolumes.get(): if self.protocol.hasHalfVolumesFile.get(): vol = self.protocol.associatedHalves.get().getHalfMaps() fnOrigMap, _unused = vol.split(',') sampRate = self.protocol.associatedHalves.get().getSamplingRate() else: vol = self.protocol.halfMap1.get() fnOrigMap = vol.getFileName() sampRate = vol.getSamplingRate() else: vol = self.protocol.fullMap.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