# -*- 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 numpy
import ipyvolume.pylab as ipyvolume
from ._order_color_map import order_color_map
# ==============================================================================
[docs]
def plot_voxel(voxels_position, marker="box", color="green", size=2.0):
if len(voxels_position) > 0:
x, y, z = (voxels_position[:, 0].astype(float),
voxels_position[:, 1].astype(float),
voxels_position[:, 2].astype(float))
ipyvolume.scatter(x, y, z, size=size, marker=marker, color=color)
[docs]
def show_point_cloud(xyz_positions,
color='green',
size=2,
width=500,
height=500):
ipyvolume.figure(width=width, height=height, controls=True, lighting=True)
plot_voxel(xyz_positions, size=size, color=color)
x_min = xyz_positions[:, 0].min()
x_max = xyz_positions[:, 0].max()
y_min = xyz_positions[:, 1].min()
y_max = xyz_positions[:, 1].max()
z_min = xyz_positions[:, 2].min()
z_max = xyz_positions[:, 2].max()
xyz_max = max(x_max - x_min, y_max - y_min, z_max - z_min)
ipyvolume.xlim(x_min, x_min + xyz_max)
ipyvolume.ylim(y_min, y_min + xyz_max)
ipyvolume.zlim(z_min, z_min + xyz_max)
ipyvolume.view(0, 90)
ipyvolume.show()
[docs]
def show_voxel_grid(voxel_grid,
color='green',
size=2,
width=500,
height=500):
ipyvolume.figure(width=width, height=height, controls=True, lighting=True)
plot_voxel(voxel_grid.voxels_position, size=size, color=color)
x_min = voxel_grid.voxels_position[:, 0].min()
x_max = voxel_grid.voxels_position[:, 0].max()
y_min = voxel_grid.voxels_position[:, 1].min()
y_max = voxel_grid.voxels_position[:, 1].max()
z_min = voxel_grid.voxels_position[:, 2].min()
z_max = voxel_grid.voxels_position[:, 2].max()
xyz_max = max(x_max - x_min, y_max - y_min, z_max - z_min)
ipyvolume.xlim(x_min, x_min + xyz_max)
ipyvolume.ylim(y_min, y_min + xyz_max)
ipyvolume.zlim(z_min, z_min + xyz_max)
ipyvolume.view(180, 90)
ipyvolume.show()
[docs]
def show_mesh(vertices, faces, color="green", width=500, height=500):
ipyvolume.figure(width=width, height=height)
ipyvolume.view(180, 90)
ipyvolume.plot_trisurf(
vertices[:, 0], vertices[:, 1], vertices[:, 2], triangles=faces, color=color
)
x_min = vertices[:, 0].min()
x_max = vertices[:, 0].max()
y_min = vertices[:, 1].min()
y_max = vertices[:, 1].max()
z_min = vertices[:, 2].min()
z_max = vertices[:, 2].max()
xyz_max = max(x_max - x_min, y_max - y_min, z_max - z_min)
ipyvolume.xlim(x_min, x_min + xyz_max)
ipyvolume.ylim(y_min, y_min + xyz_max)
ipyvolume.zlim(z_min, z_min + xyz_max)
ipyvolume.show()
[docs]
def show_skeleton(
voxel_skeleton,
size=2,
with_voxel=True,
voxels_color="green",
polyline_color="red",
width=500,
height=500,
):
ipyvolume.figure(width=width, height=height)
ipyvolume.view(180, 90)
if with_voxel:
voxels_position = voxel_skeleton.voxels_position()
plot_voxel(voxels_position, size=size / 2, color=voxels_color)
voxels_position = voxel_skeleton.voxels_position_polyline()
plot_voxel(voxels_position, size=size, color=polyline_color)
for vs in voxel_skeleton.segments:
for color, index in [("blue", 0), ("red", -1)]:
plot_voxel(
numpy.array([vs.polyline[index]]),
size=size * 2,
marker="sphere",
color=color,
)
x_min = voxels_position[:, 0].min()
x_max = voxels_position[:, 0].max()
y_min = voxels_position[:, 1].min()
y_max = voxels_position[:, 1].max()
z_min = voxels_position[:, 2].min()
z_max = voxels_position[:, 2].max()
xyz_max = max(x_max - x_min, y_max - y_min, z_max - z_min)
ipyvolume.xlim(x_min, x_min + xyz_max)
ipyvolume.ylim(y_min, y_min + xyz_max)
ipyvolume.zlim(z_min, z_min + xyz_max)
ipyvolume.show()
[docs]
def show_segmentation(voxel_segmentation, size=2.0, width=500, height=500):
ipyvolume.figure(width=width, height=height)
ipyvolume.view(180, 90)
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 "rgb" + str(color)
for vo in voxel_segmentation.voxel_organs:
voxels_position = numpy.array(list(map(tuple, list(vo.voxels_position()))))
plot_voxel(voxels_position, size=size * 1, color=get_color(vo.label, vo.info))
if (
(vo.label == "mature_leaf" or vo.label == "growing_leaf")
and len(vo.voxel_segments) > 0
and "pm_position_tip" in vo.info
):
plot_voxel(
numpy.array([vo.info["pm_position_tip"]]),
size=size * 2,
color="red",
marker="sphere",
)
plot_voxel(
numpy.array([vo.info["pm_position_base"]]),
size=size * 2,
color="blue",
marker="sphere",
)
voxels_position = numpy.array(list(voxel_segmentation.get_voxels_position()))
x_min = voxels_position[:, 0].min()
x_max = voxels_position[:, 0].max()
y_min = voxels_position[:, 1].min()
y_max = voxels_position[:, 1].max()
z_min = voxels_position[:, 2].min()
z_max = voxels_position[:, 2].max()
xyz_max = max(x_max - x_min, y_max - y_min, z_max - z_min)
ipyvolume.xlim(x_min, x_min + xyz_max)
ipyvolume.ylim(y_min, y_min + xyz_max)
ipyvolume.zlim(z_min, z_min + xyz_max)
ipyvolume.show()
[docs]
def show_synthetic_plant(
vertices, faces, meta_data=None, size=0.5, color="green", width=500, height=500
):
ipyvolume.figure(width=width, height=height)
ipyvolume.view(180, 90)
ipyvolume.plot_trisurf(
vertices[:, 0], vertices[:, 1], vertices[:, 2], triangles=faces, color=color
)
voxels_position = vertices
if meta_data is not None:
ranks = meta_data["leaf_order"]
polylines = {
n: list(map(numpy.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 = numpy.array(list(zip(x, y, z))) * 10 - numpy.array([0, 0, 750])
plot_voxel(polyline, size=size, color="red")
voxels = voxels.union(set(map(tuple, list(polyline))))
voxels = voxels.union(set(map(tuple, list(voxels_position))))
voxels_position = numpy.array(list(voxels), dtype=numpy.intp)
x_min = voxels_position[:, 0].min()
x_max = voxels_position[:, 0].max()
y_min = voxels_position[:, 1].min()
y_max = voxels_position[:, 1].max()
z_min = voxels_position[:, 2].min()
z_max = voxels_position[:, 2].max()
xyz_max = max(x_max - x_min, y_max - y_min, z_max - z_min)
ipyvolume.xlim(x_min, x_min + xyz_max)
ipyvolume.ylim(y_min, y_min + xyz_max)
ipyvolume.zlim(z_min, z_min + xyz_max)
ipyvolume.show()
