# -*- 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
from ._order_color_map import order_color_map
from .scene import Scene
# ==============================================================================
def get_color(label, info):
if label == "stem":
return 0.5, 0.5, 0.5
elif label == "unknown":
return 1, 1, 1
elif "pm_leaf_number" in info:
color_map = order_color_map()
return color_map[info["pm_leaf_number"]]
else:
if label == "growing_leaf":
return 1, 0, 0
else:
return None
def get_actors_from_voxel_organ(voxel_organ, voxels_size, plot_number=True):
actors, text_actors = list(), list()
# voxels_position = numpy.array(
# map(tuple, list(voxel_organ.voxels_position())))
actors.append(
Scene.get_actor_from_voxels(
voxel_organ.voxels_position(),
voxels_size,
color=get_color(voxel_organ.label, voxel_organ.info),
)
)
if (
(voxel_organ.label == "mature_leaf" or voxel_organ.label == "growing_leaf")
and len(voxel_organ.voxel_segments) > 0
and "pm_position_tip" in voxel_organ.info
):
pos = voxel_organ.info["pm_position_base"]
actors.append(
Scene.get_actor_from_ball_position(
voxel_organ.info["pm_position_tip"],
radius=voxels_size * 2,
color=(1, 0, 0),
)
)
actors.append(
Scene.get_actor_from_ball_position(
pos, radius=voxels_size * 2, color=(0, 0, 1)
)
)
r, g, b = (0, 0, 1)
pos = voxel_organ.info["pm_position_tip"]
pos = (pos[0] - 10, pos[1] - 10, pos[2])
if plot_number and "pm_leaf_number" in voxel_organ.info:
order = str(voxel_organ.info["pm_leaf_number"])
text_actors.append(
Scene.get_actor_from_text(
order, position=pos, scale=40, color=(r, g, b)
)
)
return actors, text_actors
# ==============================================================================
def get_actors_from_segmentation_classic_mode(vmsi):
actors, text_actors = list(), list()
for voxel_organ in vmsi.get_leafs():
organ_actors, organ_text_actors = get_actors_from_voxel_organ(
voxel_organ, vmsi.voxels_size
)
actors += organ_actors
text_actors += organ_text_actors
organ_actors, organ_text_actors = get_actors_from_voxel_organ(
vmsi.get_stem(), vmsi.voxels_size
)
actors += organ_actors
text_actors += organ_text_actors
return actors, text_actors
def get_actors_from_segmentation_stem_mode(vmsi):
actors, text_actors = list(), list()
for vo in vmsi.voxel_organs:
color = (0.1, 0.8, 0.1)
if vo.label == "stem":
color = (0, 0, 0)
actors.append(
Scene.get_actor_from_voxels(
vo.voxels_position(), vmsi.voxels_size, color=color
)
)
return actors, text_actors
def get_actors_from_segmentation_skeleton_mode(vmsi, order=None):
actors, text_actors = list(), list()
for vo in vmsi.get_leafs():
actors.append(
Scene.get_actor_from_voxels(
vo.voxels_position(), vmsi.voxels_size * 0.25, color=(0, 1, 0)
)
)
polyline = vo.get_longest_segment().polyline
actors.append(
Scene.get_actor_from_voxels(polyline, vmsi.voxels_size * 1, color=(1, 0, 0))
)
actors.append(
Scene.get_actor_from_ball_position(polyline[0], radius=5, color=(0, 0, 1))
)
actors.append(
Scene.get_actor_from_ball_position(polyline[-1], radius=5, color=(1, 0, 0))
)
if order is not None:
for vo in vmsi.get_leafs():
if "order" in vo.info and vo.info["order"] == order:
vs = vo.get_highest_polyline()
actors.append(
Scene.get_actor_from_voxels(
vs.polyline, vmsi.voxels_size * 1.5, color=(0, 0, 1)
)
)
return actors, text_actors
def get_actors_from_segmentation_split_mode(vmsi):
actors, text_actors = list(), list()
vo_stem = vmsi.get_stem()
actors.append(
Scene.get_actor_from_voxels(
vo_stem.voxels_position(),
vmsi.voxels_size,
color=get_color(vo_stem.label, vo_stem.info),
)
)
for vo in vmsi.get_leafs():
voxels_position = numpy.array(list(map(tuple, list(vo.voxels_position()))))
if "pm_position_tip" in vo.info:
vm = numpy.array(vo.info["pm_vector_mean"])
pos = vo.info["pm_position_base"]
# if vo.label == "growing_leaf":
# pos = pos_stem
# vm = vm * 2
#
# closest_nodes = vo.get_longest_segment().closest_nodes
#
# i = vo.get_longest_segment().polyline.index(
# vo.info['pm_position_base'])
#
# v_base = set.union(*[set(nodes) for nodes in
# closest_nodes[:i]])
#
# v_leaf = set.union(*[set(nodes) for nodes in
# closest_nodes[i:]])
#
# v_base = v_base - v_leaf
# if len(v_base) > 0:
# voxels = numpy.array(map(tuple, list(v_base)))
#
# actors.append(Scene.get_actor_from_voxels(
# voxels + vm,
# vmsi.voxels_size * 0.20,
# color=(0, 0, 0)))
#
# voxels_position = numpy.array(map(tuple, list(v_leaf)))
actors.append(
Scene.get_actor_from_voxels(
voxels_position + vm,
vmsi.voxels_size,
color=get_color(vo.label, vo.info),
)
)
actors.append(
Scene.get_actor_from_ball_position(
vo.info["pm_position_tip"] + vm,
radius=vmsi.voxels_size * 2,
color=(1, 0, 0),
)
)
actors.append(
Scene.get_actor_from_ball_position(
pos + vm, radius=vmsi.voxels_size * 2, color=(0, 0, 1)
)
)
xa, ya, za = pos
xb, yb, zb = tuple(vm)
xc, yc, zc = (xa + xb, ya + yb, za + zb)
actors.append(
Scene.get_actor_from_arrow_vector(
(xa, ya, za), (xc, yc, zc), color=(0, 0, 0), line_width=40
)
)
r, g, b = (0, 0, 1)
pos = vo.info["pm_position_tip"] + vm
pos = (pos[0] - 10, pos[1] - 10, pos[2])
if "pm_leaf_number" in vo.info:
order = str(vo.info["pm_leaf_number"])
text_actors.append(
Scene.get_actor_from_text(
order, position=pos, scale=40, color=(r, g, b)
)
)
return actors, text_actors
# ==============================================================================
[docs]
def show_segmentation(
vmsi,
mode="classic",
windows_size=(600, 800),
screenshot_filename=None,
screenshot_magnification=10,
record_filename=None,
record_quality=2,
record_rate=25,
):
actors, text_actors = list(), list()
if mode == "classic":
actors, text_actors = get_actors_from_segmentation_classic_mode(vmsi)
if mode == "only_stem_colored":
actors, text_actors = get_actors_from_segmentation_stem_mode(vmsi)
if mode == "only_skeleton":
actors, text_actors = get_actors_from_segmentation_skeleton_mode(vmsi)
if mode == "separated_leaf":
actors, text_actors = get_actors_from_segmentation_split_mode(vmsi)
scene = Scene()
scene.add_actors(actors)
scene.add_text_actors(text_actors)
scene.show(
windows_size=windows_size,
screenshot_filename=screenshot_filename,
screenshot_magnification=screenshot_magnification,
record_filename=record_filename,
record_quality=record_quality,
record_rate=record_rate,
)
def record_segmentation(vmsis, filename, record_elevation=20):
scene = Scene()
def func(vmsi):
actors, text_actors = get_actors_from_segmentation_classic_mode(vmsi)
scene.add_actors(actors)
scene.add_text_actors(text_actors)
scene.set_camera(elevation=record_elevation)
scene.record_video(filename, vmsis, func)
