Source code for tomo3D.viewers.viewer_triangulations

# -*- coding: utf-8 -*-
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# *
# * Authors:     David Herreros Calero (
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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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# * This program is distributed in the hope that it will be useful,
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# * You should have received a copy of the GNU General Public License
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import pyvista as pv
import numpy as np
from scipy.spatial.distance import pdist
from multiprocessing import Process

from PyQt5.QtWidgets import QApplication, QMainWindow, QDockWidget
from pyvistaqt.plotting import QtInteractor
from PyQt5.QtCore import Qt

[docs]class TriangulationPlot(object): ''' Class to visualize triangulation(s) and/or point cloud(s) with their associated normals Input paramters: - meshes (Mandatory): List containing the pyvista triangulations to be shown by the viewer - clouds (Optional): List containing the original point clouds associated to the triangulations. This parameter is useful to compare the coordinates adjusted to the mesh and the original ones -extNormals (Optional): List containing the original normals associated to each vertex in the Delaunay triangulation. In general, this parameter is used to compare the normals computed inside Scipion (Pyvista normals stored in the meshes objects) and those normals obtained with other software (PySeg, Dynamo...) Usage: import TriangulationPlot plt = TriangulationPlot([mesh], clouds=[cloud], extNormals=[extNormal]) plt.initializePlot() ''' def __init__(self, meshes, clouds=None, extNormals_List=None, extNormals_coords=None): self.clouds = clouds self.meshes = meshes self.extNormals_List = extNormals_List self.extNormals_coords = extNormals_coords self.initialize_PyQt() self.actor_meshes = [] self.actor_normals = [] self.actor_extNormals = [] self.actor_points = [] self.actor_ori_points = [] self.buttonMesh = self.p.add_checkbox_button_widget(callback=self.plotMesh, position=(65., 10.), color_on='white') self.p.add_text('Mesh', position=(10.+48, 65.), font_size=12) self.p.add_text('Normals', position=(200.+44, 65.), font_size=12) self.buttonNormals = self.p.add_checkbox_button_widget(callback=self.plotNormals, position=(265., 10.)) self.p.add_text('Cloud', position=(420.+33, 65.), font_size=12) self.buttonPoints = self.p.add_checkbox_button_widget(callback=self.plotPoints, position=(465., 10.), color_on='black') if self.clouds is not None: self.p.add_text('Original Cloud', position=(598., 65.), font_size=12) self.buttonOriPoints = self.p.add_checkbox_button_widget(callback=self.plotOriPoints, position=(665., 10.), color_on='white') if self.extNormals_List is not None: self.p.add_text('External Normals', position=(598.+198, 65.), font_size=12) self.buttonExtNormals = self.p.add_checkbox_button_widget(callback=self.plotExtNormals, position=(865., 10.), color_on='red')
[docs] def initialize_PyQt(self): = QApplication([]) self.mainWindow = QMainWindow() self.mainWindow.default_style_sheet = self.mainWindow.styleSheet() self.mainWindow.save_commands = True # stores commands internally when True self.mainWindow.hold = False self.mainWindow.load_dialog = None = self.mainWindow.resize(1000, 600) self.p = QtInteractor(self.mainWindow) self.p.app_window = self.mainWindow self.mainWindow.dock_vtk = QDockWidget('Mesh Viewer', self.mainWindow) self.mainWindow.dock_vtk.setWidget(self.p.interactor) self.mainWindow.dock_vtk.setMinimumSize(700, 600) self.mainWindow.addDockWidget(Qt.LeftDockWidgetArea, self.mainWindow.dock_vtk) self.p.add_toolbars()
[docs] def plotMesh(self, value): if value: for mesh in self.meshes: self.actor_meshes.append(self.p.add_mesh(mesh, show_edges=True)) self.buttonPoints.GetRepresentation().SetState(False) if self.buttonOriPoints.GetRepresentation().GetState: for actor in self.actor_ori_points: self.p.remove_actor(actor) self.buttonOriPoints.GetRepresentation().SetState(False) else: for actor in self.actor_meshes: self.p.remove_actor(actor)
[docs] def plotNormals(self, value): if value: for mesh in self.meshes: vecLength = np.amax(pdist(mesh.points)) normals = vecLength * mesh.point_normals self.actor_normals.append(self.p.add_arrows(mesh.points, normals, mag=0.1, color='blue')) else: for actor in self.actor_normals: self.p.remove_actor(actor)
[docs] def plotExtNormals(self, value): if value: for idn, normals in enumerate(self.extNormals_List): normals = pv.pyvista_ndarray(normals) vecLength = np.amax(pdist(self.meshes[idn].points)) normals = vecLength * (normals / np.linalg.norm(normals, axis=1)[:, np.newaxis]) if self.extNormals_coords is None: areZero = np.where((self.meshes[idn].point_normals == (0, 0, 0)).all(axis=1)) normals[areZero] = np.array((0, 0, 0)) self.actor_extNormals.append(self.p.add_arrows(self.meshes[idn].points, normals, mag=0.1, color='red')) else: extNormals_coords = pv.pyvista_ndarray(self.extNormals_coords) self.actor_extNormals.append(self.p.add_arrows(extNormals_coords, normals, mag=0.1, color='red')) else: for actor in self.actor_extNormals: self.p.remove_actor(actor)
[docs] def plotPoints(self, value): if value: for mesh in self.meshes: self.actor_points.append(self.p.add_points(mesh, color='black', point_size=10, render_points_as_spheres=True)) self.buttonMesh.GetRepresentation().SetState(False) else: for actor in self.actor_points: self.p.remove_actor(actor)
[docs] def plotOriPoints(self, value): if value: for cloud in self.clouds: self.actor_ori_points.append(self.p.add_points(cloud, color='white', point_size=10, render_points_as_spheres=True)) if self.buttonMesh.GetRepresentation().GetState(): for actor in self.actor_meshes: self.p.remove_actor(actor) self.buttonMesh.GetRepresentation().SetState(False) else: for actor in self.actor_ori_points: self.p.remove_actor(actor)
[docs] def initializePlot(self):
# The following functions are used to create automatically a "gui thread" to avoid the 'exec_' loop # from freezing the main thread
[docs]def guiThread(classObj, methodName, *args, **kwargs): ''' Create a new process to prevent the exec_ loop of the GUI from blocking the main thread. In order to work, the GUI classes must be instantiated withing the process. ''' proc = Process(target=instantiateClass, args=(classObj, methodName, *args,), kwargs=kwargs) proc.start()
[docs]def instantiateClass(classObj, methodName, *args, **kwargs): ''' Create an instance of any class and call a visualization method (or any other method). - classObj (class): Class to be instantiated - methodName (string): Method from the class to be called after the instantiation - *args (list): extra argument needed to call the class method - **kwargs (dict): arguments to be passed to the contructor of the class ''' try: instance = classObj(**kwargs) runMethod(instance, methodName, *args) except: print('Cannot create instance of class')
[docs]def runMethod(instance, methodName, *args): ''' Execute a method from an instantiated class: - instance (obj): object instantiated from a given class - methodName (string): method belonging to instance to be called - *args (list): extra arguments needed by the method ''' try: method = getattr(instance, methodName) method(*args) except AttributeError: print(methodName + ' is not a member the class')