def test_full_cell_with_links(full_cell_mesh, full_cell_merge_log, tmp_path,
monkeypatch):
class MyChunkedGraph(object):
def __init__(a, **kwargs):
pass
def get_merge_log(self, atomic_id):
return full_cell_merge_log
monkeypatch.setattr(trimesh_io.trimesh_repair.chunkedgraph,
'ChunkedGraphClient', MyChunkedGraph)
full_cell_mesh.add_link_edges('test', 5)
mesh_actor = trimesh_vtk.mesh_actor(full_cell_mesh)
eval_actor_image([mesh_actor],
'full_cell_with_links.png',
tmp_path,
scale=1)
mesh_actor = trimesh_vtk.mesh_actor(full_cell_mesh,
opacity=1.0,
show_link_edges=True)
m1 = np.array(full_cell_merge_log['merge_edge_coords'][0])
ctr = np.mean(m1, axis=0)
camera = trimesh_vtk.oriented_camera(ctr,
backoff=5,
up_vector=(0, 0, 1),
backoff_vector=(0, 1, 0))
eval_actor_image([mesh_actor],
'full_cell_show_links.png',
tmp_path,
camera=camera)
def test_full_cell_with_links(full_cell_mesh, full_cell_merge_log, tmp_path):
full_cell_mesh.add_link_edges(merge_log=full_cell_merge_log,
base_resolution=[1, 1, 1])
mesh_actor = trimesh_vtk.mesh_actor(full_cell_mesh)
eval_actor_image([mesh_actor],
'full_cell_with_links.png',
tmp_path,
scale=1)
mesh_actor = trimesh_vtk.mesh_actor(full_cell_mesh,
opacity=1.0,
show_link_edges=True)
m1 = np.array(full_cell_merge_log['merge_edge_coords'][0])
ctr = np.mean(m1, axis=0)
camera = trimesh_vtk.oriented_camera(ctr,
backoff=5,
up_vector=(0, 0, 1),
backoff_vector=(0, 1, 0))
eval_actor_image([mesh_actor],
'full_cell_show_links.png',
tmp_path,
camera=camera)
def test_full_cell_movie(full_cell_mesh, full_cell_soma_pt, tmp_path):
mesh_actor = trimesh_vtk.mesh_actor(full_cell_mesh)
camera = trimesh_vtk.oriented_camera(full_cell_soma_pt, backoff=100)
eval_actor_360([mesh_actor],
'full_cell_movie',
tmp_path,
camera=camera,
scale=1)
def test_full_cell_camera(full_cell_mesh, full_cell_soma_pt, tmp_path):
mesh_actor = trimesh_vtk.mesh_actor(full_cell_mesh)
camera = trimesh_vtk.oriented_camera(full_cell_soma_pt, backoff=100)
eval_actor_image([mesh_actor],
'full_cell_orient_camera.png',
tmp_path,
camera=camera,
scale=1)
scale_bar_actor = trimesh_vtk.scale_bar_actor(
full_cell_soma_pt - [15000, 0, 0], camera)
eval_actor_image([mesh_actor, scale_bar_actor],
'full_cell_scale_bar.png',
tmp_path,
camera=camera,
scale=1)
def test_point_cloud(full_cell_mesh, full_cell_synapses, full_cell_soma_pt,
tmp_path):
mesh_actor = trimesh_vtk.mesh_actor(full_cell_mesh)
camera = trimesh_vtk.oriented_camera(full_cell_soma_pt, backoff=300)
sizes = full_cell_synapses['sizes']
# size points by size, fixed color
syn_actor = trimesh_vtk.point_cloud_actor(full_cell_synapses['positions'],
size=sizes,
color=(1, 0, 0))
eval_actor_image([mesh_actor, syn_actor],
'full_cell_with_synapes_size_scaled.png',
tmp_path,
camera=camera)
# color points by size, mapping sizes
syn_actor = trimesh_vtk.point_cloud_actor(full_cell_synapses['positions'],
size=500,
color=np.clip(sizes, 0, 1000))
eval_actor_image([mesh_actor, syn_actor],
'full_cell_synapes_colored_size.png',
tmp_path,
camera=camera)
# color and size points
syn_actor = trimesh_vtk.point_cloud_actor(full_cell_synapses['positions'],
size=sizes,
color=np.clip(sizes, 0, 1000))
eval_actor_image([mesh_actor, syn_actor],
'full_cell_synapes_colored_and_size.png',
tmp_path,
camera=camera)
# random colors
x = np.linspace(0, 1.0, len(sizes))
rand_colors = np.hstack([
x[:, np.newaxis],
np.abs(x - .5)[:, np.newaxis], (1 - x)[:, np.newaxis]
])
syn_actor = trimesh_vtk.point_cloud_actor(full_cell_synapses['positions'],
size=500,
color=rand_colors)
eval_actor_image([mesh_actor, syn_actor],
'full_cell_synapes_random_colors.png',
tmp_path,
camera=camera)
# random colors uint8
rand_colors_uint8 = np.uint8(rand_colors * 255)
syn_actor = trimesh_vtk.point_cloud_actor(full_cell_synapses['positions'],
size=500,
color=rand_colors_uint8)
eval_actor_image([mesh_actor, syn_actor],
'full_cell_synapes_random_colors_uint8.png',
tmp_path,
camera=camera)
# test failure modes
with pytest.raises(ValueError) as e:
syn_actor = trimesh_vtk.point_cloud_actor(
full_cell_synapses['positions'],
size=np.random.rand(10, 10),
color=(1, 0, 0))
with pytest.raises(ValueError) as e:
syn_actor = trimesh_vtk.point_cloud_actor(
full_cell_synapses['positions'],
size=300,
color=np.random.rand(len(x), 2))