# -*- python -*-
#
# Copyright INRIA - CIRAD - INRA
#
# Distributed under the Cecill-C License.
# See accompanying file LICENSE.txt or copy at
# http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html
#
# ==============================================================================
import k3d
import numpy as np
from matplotlib.colors import rgb2hex
from ._order_color_map import order_color_map
# ==============================================================================
[docs]
def plot_voxel(voxels, color=0x00ff00):
# contiguous array and uint8 are required to avoid k3d implicit cast warning
plt_voxels = k3d.voxels(np.ascontiguousarray(voxels, dtype=np.uint8), color_map=color)
return plt_voxels
[docs]
def plot_points(voxels_position, color=0x00ff00, size=2.0):
plt_points = k3d.points(positions=voxels_position.astype(np.float32),
point_size=size, color=color)
return plt_points
[docs]
def show_point_cloud(xyz_positions,
color=0x00ff00,
size=2):
plot = k3d.plot()
plot += k3d.points(positions=xyz_positions.astype(np.float32),
point_size=size, color=color)
plot.display()
[docs]
def show_voxel_grid(voxel_grid,
color=0x00ff00):
plot = k3d.plot()
voxels = voxel_grid.to_image_3d()
plot += plot_voxel(voxels, color)
plot.display()
[docs]
def show_mesh(vertices, faces, color=0x00ff00):
if type(color) == np.ndarray:
colors = []
for c in color:
hex_col = int(rgb2hex(c / 255.0).replace("#",""), 16)
colors.append(hex_col)
mesh = k3d.mesh(vertices.astype(np.float32), indices=faces.astype(np.uint32), colors=colors)
else:
mesh = k3d.mesh(vertices.astype(np.float32), indices=faces.astype(np.uint32), color=color)
plot = k3d.plot()
plot += mesh
return plot
[docs]
def show_skeleton(
voxel_skeleton,
size=2,
with_voxel=True,
voxels_color=0x00ff00,
polyline_color=0xff0000,
):
plot = k3d.plot()
if with_voxel:
voxels_position = voxel_skeleton.voxels_position()
plot += plot_points(voxels_position, size=size / 2, color=voxels_color)
voxels_position = voxel_skeleton.voxels_position_polyline()
plot += plot_points(voxels_position, size=size, color=polyline_color)
for vs in voxel_skeleton.segments:
for color, index in [(0x0000ff, 0), (0xff0000, -1)]:
plot += plot_points(
np.array([vs.polyline[index]]),
size=size * 2,
color=color,
)
plot.display()
[docs]
def show_segmentation(voxel_segmentation, size=2.0):
plot = k3d.plot()
def get_color(label, info):
if label == "stem":
color = (128, 128, 128)
elif label == "unknown":
color = (255, 255, 255)
elif "pm_leaf_number" in info:
color_map = order_color_map()
color = color_map[info["pm_leaf_number"]]
color = tuple([int(255 * x) for x in color])
else:
if label == "growing_leaf":
color = (255, 0, 0)
else:
color = (0, 255, 0)
return color
for vo in voxel_segmentation.voxel_organs:
voxels_position = np.array(list(map(tuple, list(vo.voxels_position()))))
vo_color = int(rgb2hex(np.array(get_color(vo.label, vo.info)) / 255.0).replace("#", ""), 16)
plot += plot_points(voxels_position, size=size * 1, color=vo_color)
if (
(vo.label == "mature_leaf" or vo.label == "growing_leaf")
and len(vo.voxel_segments) > 0
and "pm_position_tip" in vo.info
):
plot += plot_points(
np.array([vo.info["pm_position_tip"]]),
size=size * 2,
color=0xff0000,
)
plot += plot_points(
np.array([vo.info["pm_position_base"]]),
size=size * 2,
color=0x0000ff,
)
plot.display()
[docs]
def show_synthetic_plant(
vertices, faces, meta_data=None, size=0.5, color=0x00ff00):
plot = k3d.plot()
plot += k3d.mesh(vertices.astype(np.float32), indices=faces.astype(np.uint32), color=color)
if meta_data is not None:
ranks = meta_data["leaf_order"]
polylines = {
n: list(map(np.array, list(zip(*meta_data["leaf_polylines"][i]))))
for i, n in enumerate(ranks)
}
voxels = set()
for leaf_order in polylines:
x, y, z, r = polylines[leaf_order]
polyline = np.array(list(zip(x, y, z))) * 10 - np.array([0, 0, 750])
plot+= plot_points(polyline, size=size, color=0xff0000)
voxels = voxels.union(set(map(tuple, list(polyline))))
plot.display()
