Source code for xmipptomo.viewers.viewer_resolution_local_monotomo

# -*- coding: utf-8 -*-
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# *
# * Authors:     J.L. Vilas (
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# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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# * This program is free software; you can redistribute it and/or modify
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import matplotlib.pyplot as plt
from matplotlib import cm
from pwem.wizards import ColorScaleWizardBase
from pyworkflow.gui.dialog import showError

import os

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

from xmipp3.viewers.plotter import XmippPlotter

from xmipptomo.protocols.protocol_resolution_local_monotomo import (XmippProtMonoTomo,
                                                           TOMOGRAM_RESOLUTION_FILE, FULL_TOMOGRAM_FILE,
                                                           HISTOGRAM_RESOLUTION_FILE, TOMOGRAMFOLDER,
                                                            MRCEXT, XMDEXT)

[docs]class XmippMonoTomoViewer(LocalResolutionViewer): """ Visualization tools for MonoTomo 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): self.selectedTomogram = None ProtocolViewer.__init__(self, *args, **kwargs) def _defineParams(self, form): form.addSection(label='Visualization') form.addParam('inputTomogram', StringParam, label="Select a tomogram", important=True) form.addParam('doShowResolutionSlices', 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 Tomogram in Chimera") ColorScaleWizardBase.defineColorScaleParams(group, defaultHighest=self.protocol.max_res_init, defaultLowest=self.protocol.min_res_init) def _getVisualizeDict(self): return {'doShowOriginalVolumeSlices': self._showOriginalVolumeSlices, 'doShowResolutionSlices': self._showResolutionSlices, 'doShowVolumeColorSlices': self._showVolumeColorSlicesResolution, 'doShowOneColorslice': self._showOneColorslice, 'doShowResHistogram': self._plotHistogram, 'doShowChimera': self._showChimera, } def _showResolutionSlices(self, param=None): if self.validateTomogram(): cm = DataView(self.createPath(TOMOGRAM_RESOLUTION_FILE, MRCEXT)) return [cm] def _showOriginalVolumeSlices(self, param=None): if self.validateTomogram(): cm = DataView(self.createPath(FULL_TOMOGRAM_FILE, MRCEXT)) return [cm] def _showVolumeColorSlicesResolution(self, param=None): if self.validateTomogram(): self._showVolumeColorSlices(self.createPath(TOMOGRAM_RESOLUTION_FILE, MRCEXT)) def _showVolumeColorSlices(self, mapFile): imgData, min_Res, max_Res, voldim__ = self.getImgData(mapFile) 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 [] def _showOneColorslice(self, param=None): imageFile = self.createPath(TOMOGRAM_RESOLUTION_FILE, MRCEXT) 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 [] 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): if self.validateTomogram(): fn = self.createPath(HISTOGRAM_RESOLUTION_FILE, XMDEXT) md = MetaData() 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 _getIdFromString(self, tomoDataStr): ''' This function takes the String with the information of the tomogram, like '25 Tomogram (1000x1000x200)' and returns the id = 25 ''' listInfo = str(tomoDataStr).split() return listInfo[0] def _getAxis(self): return self.getEnumText('sliceAxis') def _showChimera(self, param=None): if self.validateTomogram(): fnResVol = self.createPath(TOMOGRAM_RESOLUTION_FILE, MRCEXT) fnOrigMap = self.createPath(FULL_TOMOGRAM_FILE, MRCEXT) sampRate = 1 #sampling is not set in the binary cmdFile = self.protocol._getExtraPath('') 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
[docs] def createPath(self, fn, ext): ''' This function returns the output path corresponding to a tomogram id, tomId, with a filename (fn) and an extension, ext ''' tomId = self._getIdFromString(self.inputTomogram) return self.protocol.createOutputPath(fn, tomId, ext)
[docs] def validateTomogram(self): ''' This function returns true or false if there is a tomogram selected or not. ''' if not self.inputTomogram.empty(): return True else: showError("Tomogram missing", "You need to select one tomogram.", self.getTkRoot()) return False