# -*- coding: utf-8 -*-
"""
Plot3d Module
=============
Plotting routines for 3d display of data.
Note
----
This module is using vispy.
"""
__author__ = 'Christoph Kirst <ckirst@rockefeller.edu>'
__license__ = 'MIT License <http://www.opensource.org/licenses/mit-license.php>'
__copyright__ = 'Copyright (c) 2017 by Christoph Kirst, The Rockefeller University, New York City'
import numpy as np
import vispy
#try:
# vispy.use(app='PyQt5'); #avoid use of ipynb_webgl
#except:
# print('qt')
# try:
# vispy.use(app='PySide')
# except:
# print('no')
# print(vispy.app.backends.BACKENDMAP)
import vispy.app
import vispy.scene
#vispy.app.run();
import ClearMap.Visualization.Vispy.TurntableCamera as ttc
import ClearMap.Visualization.Vispy.VolumeVisual as vvi
import ClearMap.Visualization.Color as col
import ClearMap.IO.IO as io
###############################################################################
### 3d plotting
###############################################################################
[docs]def list_line_plot_3d(coordinates, view = None, title = None, center_view = True, **kwargs):
"""Plot lines between coordinates in 3d.
Arguments
---------
coordaintes : array
Coordinate nx3 array.
title : str or None
Window title.
view : view or None
Add plot to this view. if given.
Returns
-------
view : view
The view of the plot.
"""
#visual
Plot3D = vispy.scene.visuals.create_visual_node(vispy.visuals.LinePlotVisual)
#view
title = title if title is not None else 'list_line_plot_3d';
view = initialize_view(view, title=title);
# style
style = dict(width=2.0, color='red', symbol='o',
edge_color='w', face_color = 'blue');
style.update(**kwargs);
#plot
p = Plot3D(coordinates, parent=view.scene, **style)
p.set_gl_state('translucent', blend=True, depth_test=True);
#view.camera.set_range();
if center_view:
_center_view(view);
return p;
[docs]def list_plot_3d(coordinates, view = None, title = None, center_view = True, color = None, **kwargs):
"""Scatter plot of points in 3d.
Arguments
---------
coordaintes : array
Coordinatenx3 array.
title : str or None
Window title.
view : view or None
Add plot to this view. if given.
Returns
-------
view : view
The view of the plot.
"""
#visual
Scatter3D = vispy.scene.visuals.create_visual_node(vispy.visuals.MarkersVisual)
#view
title = title if title is not None else 'list_plot_3d';
view = initialize_view(view, title=title);
#style
if color and 'face_color' not in kwargs.keys():
kwargs.update(face_color=color);
if color and 'edge_color' not in kwargs.keys():
kwargs.update(edge_color=color);
style = dict(face_color='blue', symbol='o', size=10,
edge_width=0.5, edge_color='blue')
style.update(**kwargs)
# plot
p = Scatter3D(parent=view.scene);
p.set_gl_state('translucent', blend=True, depth_test=True);
p.set_data(coordinates, **style)
#view.camera.set_range();
if center_view:
_center_view(view);
return p;
[docs]def plot_3d(source, colormap = None, view = None, title = None, center_view = True, **kwargs):
"""Plot 3d volume.
Arguments
---------
source : array
The 3d volume.
title : str or None
Window title.
view : view or None
Add plot to this view. if given.
Returns
-------
view : view
The view of the plot.
"""
#visual
#VolumePlot3D = vispy.scene.visuals.create_visual_node(vispy.visuals.VolumeVisual)
VolumePlot3D = vispy.scene.visuals.create_visual_node(vvi.VolumeVisual)
#view
title = title if title is not None else 'plot_3d';
#center = (np.array(source.shape) // 2);
view = initialize_view(view, title=title, fov=0, depth_value=10**8)#, center=center)
#style
style = dict(cmap = grays_alpha(), method = 'translucent', relative_step_size=0.5)
style.update(**kwargs);
#source
source = io.as_source(source)[:];
if source.dtype==bool:
source = source.view(dtype='uint8');
#orient
source = source.transpose([2,1,0]);
#plot
p = VolumePlot3D(source, parent=view.scene, **style);
#view.camera.set_range();
if center_view:
_center_view(view);
return p;
[docs]def plot_mesh_3d(coordinates, faces, view = None, shading='smooth', color = None, face_colors = None, vertex_colors = None, mode = 'triangles', center_view = True, title = None, **kwargs):
"""Plot a 3d mesh.
Arguments
---------
coordinates : array
Coordinate nx3 array.
faces : array
Indices of triangular faces, nx3 array.
title : str or None
Window title.
view : view or None
Add plot to this view. if given.
Returns
-------
view : view
The view of the plot.
"""
# build visuals
MeshVisual = vispy.scene.visuals.create_visual_node(vispy.visuals.mesh.MeshVisual)
#view
title = title if title is not None else 'plot_mesh_3d';
view = initialize_view(view, title=title);
#print view
if color is None and face_colors is None and vertex_colors is None:
color ='red';
p = MeshVisual(coordinates, faces, parent=view.scene, shading=shading, color=color, face_colors=face_colors, vertex_colors=vertex_colors, mode=mode, **kwargs)
if center_view:
view.camera.center = np.mean(coordinates, axis=0);
return p;
[docs]def plot_regular_polygon(center, sides=4, title=None, view=None, color='red', border_color=None, border_width=1, radius=1.0, **kwargs):
# build visuals
PolyVisual = vispy.scene.visuals.create_visual_node(vispy.visuals.RegularPolygonVisual)
#view
title = title if title is not None else 'plot_cube';
view = initialize_view(view, title=title);
#print view
p = PolyVisual(center,color=color, border_color=border_color, border_width=border_width, radius=radius, sides=sides, parent=view.scene, **kwargs)
if center_view:
view.camera.center = center;
return p;
[docs]def plot_box(lower, upper, face_color=(1,0,0,0.5), line_color=None, line_width=1,
line_padding = 0, shading='smooth', mode = 'triangles',
title=None, view=None, center_view = True, **kwargs):
"""Plots a box in 3d."""
#TODO: return compound visual
#view
title = title if title is not None else 'plot_box';
view = initialize_view(view, title=title);
#corners
corners = [[0,0,0],[1,0,0],[1,1,0],[0,1,0],
[0,0,1],[1,0,1],[1,1,1],[0,1,1]];
corners = [[lower[d] if c[d] == 0 else upper[d] for d in range(3)] for c in corners]
corners = np.array(corners, dtype=float);
visuals = [];
if face_color is not None:
# build visuals
MeshVisual = vispy.scene.visuals.create_visual_node(vispy.visuals.mesh.MeshVisual)
faces = [[0,1,5],[0,5,4],
[1,2,6],[1,6,5],
[4,5,6],[4,6,7],
[3,0,4],[3,4,7],
[2,3,7],[2,7,6],
[3,2,1],[3,1,0]]
faces = np.array(faces);
mv = MeshVisual(corners, faces, parent=view.scene, shading=shading, color=face_color, mode=mode, **kwargs);
visuals.append(mv);
if line_color is not None:
#visual
LineVisual = vispy.scene.visuals.create_visual_node(vispy.visuals.LineVisual)
lines = np.array([[0,1],[1,2],[2,3],[3,0],[4,5],[5,6],[6,7],[7,4],[0,4],[1,5],[2,6],[3,7]]);
if line_padding != 0:
corners = [[0,0,0],[1,0,0],[1,1,0],[0,1,0],
[0,0,1],[1,0,1],[1,1,1],[0,1,1]];
corners = [[lower[d]-line_padding if c[d] == 0 else upper[d]+line_padding for d in range(3)] for c in corners]
corners = np.array(corners, dtype=float);
lv = LineVisual(corners, parent=view.scene, connect=lines, color=line_color, width=line_width);
visuals.append(lv);
if center_view:
view.camera.center = 0.5 * (np.array(lower) + np.array(upper));
return view;
###############################################################################
### Helpers
###############################################################################
#TODO: vispy.color.ColorMap([col1,col2,...]) is much easier!
[docs]def single_color_colormap(color = (1,1,1), alpha = 0.075, inverse_alpha = False):
color = tuple(col.color(color, alpha=alpha));
if inverse_alpha:
opacity = lambda t : 1-t;
else:
opacity = lambda t : t
class SingleColor(vispy.color.colormap.BaseColormap):
glsl_map = """
vec4 grays(float t) {
return vec4(%g * t, %g * t, %g * t, %g * %s);
}
""" % (color + ('(1-t)' if inverse_alpha else 't',))
def map(self, t):
if isinstance(t, np.ndarray):
return np.hstack([color[0] * t, color[1] * t, color[2] * t, color[3] * opacity(t)]).astype(np.float32)
else:
return np.array([color[0] * t, color[1] * t, color[2] * t, color[3] * opacity(t)], dtype=np.float32)
return SingleColor();
[docs]def grays_alpha(alpha = 0.075, inverse=False):
return single_color_colormap(color = (1,1,1), alpha=alpha, inverse_alpha=inverse);
[docs]def get_view(view):
"""Return the view of the argument.
Arguments
---------
view : view
The vispy window.
Returns
-------
view : view
The vispy view of the plot.
"""
while not isinstance(view, vispy.scene.widgets.viewbox.ViewBox) and hasattr(view, 'parent'):
view = view.parent;
return view;
[docs]def add_axes(view):
"""Add axes to a plot.
Arguments
---------
view : view
The vispy window.
Returns
-------
view : view
The vispy view of the plot.
"""
view = initialize_view(view);
axes = vispy.scene.visuals.XYZAxis(parent=view.scene);
return axes;
[docs]def set_light_to_camera(mesh):
"""Set the light direction to the crrent camera position.
Arguments
---------
mesh : mesh
A vispy mesh.
"""
v = get_view(mesh);
a = np.deg2rad(v.camera.azimuth);
e = np.deg2rad(v.camera.elevation);
direction = (np.cos(a) * np.cos(e), np.sin(a) * np.cos(e), np.sin(e));
#direction = (np.sin(a) * np.cos(e), np.cos(a) * np.cos(e), np.sin(e));
direction = tuple(-d for d in direction)
mesh.light_dir = direction;
[docs]def set_background(view, color):
"""Set the background color of the view.
Arguments
---------
view : view
The vispy window.
color : color specification
The color for the background.
Returns
-------
view : view
The vispy view of the plot.
"""
view = get_view(view);
view.canvas.bgcolor = col.color(color, alpha=True, as_int=False);
return view;
[docs]def center_view(view):
"""Center the camera in a plot.
Arguments
---------
view : view
The vispy window.
Returns
-------
view : view
The vispy view of the plot.
"""
view = get_view(view);
bounds = view.get_scene_bounds();
center = [(b[1] - b[0])*0.5 for b in bounds]
view.camera.center = center;
_center_view = center_view;
[docs]def get_view_parameter(view):
view = get_view(view);
return view.camera.get_state();
[docs]def set_view_parameter(view, parameter):
view = get_view(view);
view.camera.set_state(parameter);
[docs]def initialize_view(view=None, title=None, fov=None, distance=None, elevation=None, azimuth=None, center=None, depth_value=None):
"""Return a deafult view."""
if view is None:
# build canvas
canvas = vispy.scene.SceneCanvas(keys='interactive', title=title, show=True, bgcolor='white')
view = canvas.central_widget.add_view(camera = ttc.TurntableCamera())
view.camera = 'turntable'
if fov is not None:
view.camera.fov = fov
if distance is not None:
view.camera.distance = distance
if elevation is not None:
view.camera.elevation = elevation
if azimuth is not None:
view.camera.azimuth = azimuth;
if center is not None:
view.camera.center = center;
if depth_value is not None:
view.camera.depth_value = depth_value;
else:
view = get_view(view);
return view;
[docs]def save(location, view, transparent = None, *args, **kwargs):
"""Save the current view to a file."""
canvas = get_view(view).canvas;
img = canvas.render(*args, **kwargs);
if transparent is not None:
t = np.logical_and(img[:,:,0] >= transparent, img[:,:,1] >= transparent);
t = np.logical_and(img[:,:,2] >= transparent, t)
img[:,:,3][t]=0;
img = img.transpose([0,1,2]);
else:
img = img[:,:,:3].T;
return io.write(location, img);
###############################################################################
### Tests
###############################################################################
def _test():
import numpy as np
import ClearMap.Visualization.Vispy.Plot3d as p3d;
#reload(p3d)
#plot
coordinates = np.random.rand(40,3)
p1 = p3d.list_plot_3d(coordinates, title='test')
#plot something on top
coordinates = np.random.rand(30,3);
p2 = p3d.list_line_plot_3d(coordinates, color = 'white', face_color='red', view = p1) #analysis:ignore
#volumetric plot
import numpy as np
shape = (31,31,31);
binary = np.zeros(shape, dtype = bool);
grid = np.meshgrid(*[range(s) for s in shape], indexing='ij');
center = tuple(s/2 for s in shape);
distance = np.sum([(g-c)**2 for g,c in zip(grid, center)], axis=0);
binary[distance <= 10**2] = True
p3 = p3d.plot_3d(binary) #analysis:ignore
#reload(p3d)
v = p3d.plot_box((0,0,0),(1,2,3), face_color = (1,0,0,0), line_color='white', line_width=2, line_padding=0.015)
print(v)
Source
