Source code for pygimli.viewer.pv.draw

#!/usr/bin/env python
# -*- coding: utf-8 -*-

import numpy as np
import pygimli as pg
from .utils import pgMesh2pvMesh

pv = pg.optImport('pyvista', requiredFor="properly visualize 3D data")

[docs]def drawMesh(ax, mesh, notebook=False, **kwargs): """Draw a mesh into a given plotter. Parameters ---------- ax: pyvista.Plotter [optional] The plotter to draw everything. If none is given, one will be created. mesh: pg.Mesh The mesh to show. notebook: bool [False] Sets the plotter up for jupyter notebook/lab. cMap: str ['viridis'] The colormap string. bc: pyvista color ['#EEEEEE'] Background color. style: str['surface'] Possible options:"surface","wireframe","points" label: str Data to be plottet. If None the first is taken. Returns ------- ax: pyvista.Plotter [optional] The plotter """ # sort out a few kwargs to not confuse the plotter initialization opacity = kwargs.pop('alpha', kwargs.pop('opacity', 1)) cMap = kwargs.pop('cMap', None) color = kwargs.pop('color', None) style = kwargs.pop('style', 'surface') returnActor = kwargs.pop('returnActor', False) showMesh = kwargs.pop('showMesh', False) grid = kwargs.pop('grid', False) colorBar = kwargs.pop('colorBar', style != 'wireframe') bc = kwargs.pop('bc', '#EEEEEE') # background color lw = kwargs.pop('line_width', 0.1) filt = kwargs.pop('filter', {}) # show_edges = kwargs.pop('show_edges', True) # not used # name = kwargs.pop('name', 'Mesh') # not used if isinstance(mesh, pg.Mesh): mesh = pgMesh2pvMesh(mesh) dataName = kwargs.pop('label', list(mesh.cell_data.keys())[0]) theme = pv.themes.DefaultTheme() theme.background = bc # seems to be broken .. results on pure black screens on some machines # theme.antialiasing = True theme.font.color = 'k' if ax is None: ax = pv.Plotter(notebook=notebook, theme=theme, **kwargs) if grid is True: pass # implementme ax.show_bounds(all_edges=True, minor_ticks=True) ax.add_axes() for k, fi in filt.items(): if k.lower() == 'clip': if isinstance(mesh, pv.core.pointset.UnstructuredGrid): fi.setdefault('crinkle', True) mesh = mesh.clip(**fi) elif k.lower() == 'threshold': mesh = mesh.threshold(**fi) elif k.lower() == 'slice': mesh = mesh.slice(**fi) else: pg.error('filter:', k, 'not yet implemented') _actor = ax.add_mesh(mesh, # type: pv.UnstructuredGrid scalars=dataName, cmap=cMap, color=color, style=style, show_edges=showMesh, line_width=lw, # edge_color='white', show_scalar_bar=colorBar, opacity=opacity, ) if returnActor: return ax, _actor else: return ax
[docs]def drawModel(ax=None, mesh=None, data=None, **kwargs): """Draw a mesh with given data. Parameters ---------- ax: pyvista.Plotter [None] Pyvista's basic Plotter to add the mesh to. mesh: pg.Mesh The Mesh to plot. data: iterable Data that should be displayed with the mesh. Returns ------- ax: pyvista.Plotter [optional] The plotter """ defaultCMap = kwargs.pop('cMap', 'viridis') dataName = kwargs.pop('label', None) if all(v is None for v in [ax, mesh, data]): pg.critical("At least mesh or data should not be None") return None if kwargs.pop('markers', False) is True: # show boundary mesh with markers data = mesh.boundaryMarkers() defaultCMap ="Set3", max(1, len(pg.unique(data)))) dataName = 'Boundary Marker' mesh = pgMesh2pvMesh(mesh, data, dataName, boundaries=True) else: if data is not None or len(mesh.dataMap()) != 0: kwargs.setdefault('style', 'surface') kwargs['color'] = None if dataName is None and data is not None: if len(data) == mesh.cellCount(): dataName = 'Cell data' elif len(data) == mesh.nodeCount(): dataName = 'Node data' mesh = pgMesh2pvMesh(mesh, data, dataName) kwargs['cMap'] = defaultCMap kwargs['label'] = dataName return drawMesh(ax, mesh, **kwargs)
[docs]def drawSensors(ax, sensors, diam=0.01, color='grey', **kwargs): """ Draw the sensor positions to given mesh or the the one in given plotter. Parameters ---------- ax: pyvista.Plotter The plotter to draw everything. If none is given, one will be created. sensors: iterable Array-like object containing tuple-like (x, y, z) positions. diam: float [0.01] Radius of sphere markers. color: str ['grey'] Color of sphere markers. Returns ------- ax: pyvista.Plotter The plotter containing the mesh and drawn electrode positions. """ for pos in sensors: s = pv.Sphere(radius=diam / 2, center=pos) ax.add_mesh(s, color=color, **kwargs) return ax
[docs]def drawSlice(ax, mesh, normal=[1, 0, 0], **kwargs): """ Parameters ---------- ax: pyvista.Plotter The Plotter to draw on. mesh: pg.Mesh The mesh to take the slice out of. normal: list [[1, 0, 0]] Coordinates to orientate the slice. Returns ------- ax: pyvista.Plotter The plotter containing the mesh and drawn electrode positions. Note ---- Possible kwargs are: normal: tuple(float), str origin: tuple(float) generate_triangles: bool, optional contour: bool, optional They can be found at """ label = kwargs.pop('label', None) data = kwargs.pop('data', None) mesh = pgMesh2pvMesh(mesh, data, label) try: single_slice = mesh.slice(normal, **kwargs) except AssertionError as e: # 'contour' kwarg only works with point data and breaks execution pg.error(e) else: # REVIEW: bounds and axes might be confused with the outline..?! outline = mesh.outline() ax.add_mesh(outline, color="k") ax.add_mesh(single_slice) return ax
[docs]def drawStreamLines(ax, mesh, data, label=None, radius=0.01, **kwargs): """ Draw streamlines of given data. PyVista streamline needs a vector field of gradient data per cell. Parameters ---------- ax: pyvista.Plotter [None] The plotter that should be used for visualization. mesh: pyvista.UnstructuredGrid|pg.Mesh [None] Structure to plot the streamlines in to. If pv grid a check is performed if the data set is already contained. data: iterable [None] Values used for streamlining. label: str Label for the data set. Will be searched for within the data. radius: float [0.01] Radius for the streamline tubes. Note ---- All kwargs will be forwarded to pyvistas streamline filter: """ if label is None: label = 'grad' if isinstance(mesh, pg.Mesh): # create gradient of cell data if not provided if np.ndim(data) == 1: grad = pg.solver.grad(mesh, data) else: grad = data # ensure that it's point/node data in the mesh if len(grad) == mesh.cellCount(): grad = pg.meshtools.cellDataToNodeData(mesh, grad) # add data to the mesh and convert to pyvista grid mesh = pgMesh2pvMesh(mesh, grad.T, label) elif isinstance(mesh, pv.UnstructuredGrid): if label not in mesh.point_arrays: # conversion needed mesh.cell_data_to_point_data() if label is None: label = list(mesh.point_arrays.keys())[0] # kwargs['vectors'] = label streams = mesh.streamlines(vectors=label, **kwargs) ax.add_mesh(, show_scalar_bar=False)