def map_property(
prop: np.ndarray,
colormap: Colormap,
contrast_limits: Union[None, Tuple[float, float]] = None,
) -> Tuple[np.ndarray, Tuple[float, float]]:
"""Apply a colormap to a property
Parameters
----------
prop : np.ndarray
The property to be colormapped
colormap : vispy.color.Colormap
The vispy colormap object to apply to the property
contrast_limits: Union[None, Tuple[float, float]]
The contrast limits for applying the colormap to the property.
If a 2-tuple is provided, it should be provided as (lower_bound, upper_bound).
If None is provided, the contrast limits will be set to (property.min(), property.max()).
Default value is None.
"""
if contrast_limits is None:
contrast_limits = (prop.min(), prop.max())
normalized_properties = np.interp(prop, contrast_limits, (0, 1))
mapped_properties = colormap.map(normalized_properties)
return mapped_properties, contrast_limits
def test_colormap(name):
np.random.seed(0)
cmap = AVAILABLE_COLORMAPS[name]
# Test can map random 0-1 values
values = np.random.rand(50)
colors = cmap.map(values)
assert colors.shape == (len(values), 4)
# Create vispy colormap and check current colormaps match vispy
# colormap
vispy_cmap = VispyColormap(*cmap)
vispy_colors = vispy_cmap.map(values)
np.testing.assert_almost_equal(colors, vispy_colors, decimal=6)
class Viewer3D(object):
"""
A class for displaying a 3D model.
"""
#%%
scaling = 10 # VisPy rendering very poor when values < 1, so scale up
__scene = None # Don't import VisPy unless and until actually needed
__geometry = None
__io = None
__gloo = None
#%%
def __init__(self, background='#cfcfef', scaling=20, el_az=None):
if Viewer3D.__scene is None:
from vispy import scene, geometry, io, gloo
Viewer3D.__scene = scene
Viewer3D.__geometry = geometry
Viewer3D.__io = io
Viewer3D.__gloo = gloo
# Available colormaps in Vispy:
# autumn, blues, cool, greens, reds, spring, summer, fire, grays, hot, ice, winter, light_blues,
# orange, viridis, coolwarm, PuGr, GrBu, GrBu_d, RdBu, cubehelix, single_hue, hsl, husl, diverging, RdYeBuCy
from vispy.color import Colormap
self.__cmap = Colormap(['blue', 'cyan', 'green', 'yellow', 'red'])
if el_az is None:
el = 30
az = 45
else:
el, az = el_az
self.__canvas = Viewer3D.__scene.SceneCanvas(keys='interactive',
size=(1200, 900),
show=True)
# Set up a viewbox to display the cube with interactive arcball
self.__view = self.__canvas.central_widget.add_view()
self.__view.bgcolor = background
self.__view.camera = Viewer3D.__scene.cameras.turntable.TurntableCamera(
scale_factor=scaling, elevation=el, azimuth=az)
self.__view.padding = 5
Viewer3D.__scene.visuals.XYZAxis(parent=self.__view.scene)
self.__vertex = None
self.__vcolor = None
#%%
def Run(self, smooth=True, save_as=None):
if self.__vertex is not None:
data = Viewer3D.__geometry.MeshData(vertices=self.__vertex,
vertex_colors=self.__vcolor)
if smooth:
mesh = Viewer3D.__scene.visuals.Mesh(meshdata=data,
shading='smooth',
parent=self.__view.scene)
else:
mesh = Viewer3D.__scene.visuals.Mesh(meshdata=data,
parent=self.__view.scene)
if save_as is None:
self.__canvas.app.run()
else:
image = self.__canvas.render() # sort-of works, but problematic
Viewer3D.__io.write_png(save_as, image)
#%%
def Line(self, vertices, color=None):
"""
Draws a line in 3D
Parameters
----------
vertices : numpy.ndarray
Array of vertices (Nv,3) to draw line through
color : [r,g,b,a] array
Color to use for drawing line; optional [default: black]
"""
if color is None:
color = 'black'
Viewer3D.__scene.visuals.Line(pos=(vertices * Viewer3D.scaling),
color=color,
parent=self.__view.scene)
#%%
def Add(self, triangle, color, uniform=True):
"""
Adds a triangle to the 3D mesh
Parameters
----------
triangle : numpy.ndarray
Array of vertices (3,3) for triangle
color : [[r,g,b,a],] array
Array of one or three colors to use for displaying face
"""
if self.__vertex is None:
self.__vertex = np.asarray([triangle]) * Viewer3D.scaling
if len(color) == 1:
self.__vcolor = np.zeros((1, 3, 4))
self.__vcolor[0, :] = color[0]
else:
self.__vcolor = np.asarray([color])
else:
vcoord = np.asarray([triangle]) * Viewer3D.scaling
if len(color) == 1:
vcolor = np.zeros((1, 3, 4))
vcolor[0, :] = color[0]
else:
vcolor = np.asarray([color])
self.__vertex = np.append(self.__vertex, vcoord, axis=0)
self.__vcolor = np.append(self.__vcolor, vcolor, axis=0)
#%%
def ColorFromValue(self, c):
"""
Converts a value in a range to a color
Parameters
----------
c : numpy.ndarray
Array of values to map to color
Returns
-------
color : [[r,g,b,a],] array
mapped color
"""
return self.__cmap.map(c)
#%%
def ColorBar(self, description, c_min_max_str):
"""
Add a colorbar to the plot
"""
# Overlays a grid to position subviews & widgets:
grid = self.__canvas.central_widget.add_grid(margin=10)
if sys.platform == "darwin":
# On OSX, positioning of text in colorbar is unhelpful; this hackery seems to make it look okay, however
label = '\n\n ' + description
else:
label = description
cbar = Viewer3D.__scene.widgets.ColorBarWidget(self.__cmap,
'left',
clim=c_min_max_str,
label=label,
axis_ratio=0.075,
padding=[0.5, 0.5],
border_width=1)
grid.add_widget(cbar, col=0)
# which centers the colorbar unless we add something else to effectively nudge it to the left:
view = grid.add_view(col=1, col_span=3)
view.visible = False
galaxy_data = load_galaxy_data("../data/vollim_dr7_cbp_102709.fits")
print("Galaxies: ", galaxy_data.shape)
print("Voids: ", voids_tri_x.shape, voids_tri_y.shape, voids_tri_z.shape,
voids_norm.shape, voids_id.shape)
################################################################################
################################################################################
# Void coloring
#-------------------------------------------------------------------------------
num_voids = len(np.unique(voids_id))
cm = Colormap(
['#880000', '#EEEE00', "#008800", '#EE00EE', '#000088', '#EE00EE'])
void_color_vals = cm.map(np.linspace(0, 1.0, num_voids))
print(void_color_vals.shape)
void_colors = np.empty((num_voids, 4), dtype=np.float32)
for idx in range(void_colors.shape[0]):
void_id = idx
#print(hole_group)
void_colors[idx, :] = void_color_vals[void_id]
################################################################################
################################################################################
print("Holes:", holes_xyz.shape, holes_radii.shape, holes_flags.shape)
################################################################################
#
# VOID COLORING
#
################################################################################
hole_IDs = np.unique(holes_flags)
num_hole_groups = len(hole_IDs)
cm = Colormap(
['#880000', '#EEEE00', "#008800", '#EE00EE', '#000088', '#EE00EE'])
hole_color_vals = cm.map(np.linspace(0, 1.0, num_hole_groups))
print(hole_color_vals.shape)
void_hole_colors = np.empty((holes_xyz.shape[0], 4), dtype=np.float32)
for idx in range(void_hole_colors.shape[0]):
hole_group = holes_flags[idx]
#print(hole_group)
void_hole_colors[idx, :] = hole_color_vals[
hole_group - 1] # uhg you used 1-based indexing WHY? :D
################################################################################