def test_set_camera():
s = Scene()
s.render(interactive=False)
cam = s.plotter.camera
set_camera(s, cam)
set_camera(s, "sagittal")
def test_add_from_files():
scene = Scene()
obj = scene.add("tests/files/CC_134_1_ch1inj.obj", color="red")
assert isinstance(obj, Actor)
scene.render(interactive=False)
del scene
def test_points_density():
s = Scene(title="BR")
mos = s.add_brain_region("MOs", alpha=0.0)
coordinates = get_n_random_points_in_region(mos, 2000)
pd = s.add(PointsDensity(coordinates))
assert isinstance(pd, Actor)
del s
def __init__(self, *args, atlas_name=None, axes=None, **kwargs):
"""
Initialise the qtpy app and the brainrender scene.
Arguments:
----------
atlas_name: str/None. Name of the brainglobe atlas to use
axes: bool. If true axes are shown in the brainrender render
"""
logger.debug("Creating brainrender GUI")
# Initialize parent classes
self.scene = Scene(*args, atlas_name=atlas_name, **kwargs)
UI.__init__(self, *args, **kwargs)
CameraControl.__init__(self)
AddFromFile.__init__(self)
RegionsControl.__init__(self)
ActorsControl.__init__(self)
# Setup brainrender plotter
self.axes = axes
self.atuple = namedtuple("actor", "mesh, is_visible, color, alpha")
self.setup_plotter()
self._update()
self.scene.render()
self.scene._get_inset()
# Setup widgets functionality
self.actors_list.itemDoubleClicked.connect(
self.actor_list_double_clicked)
self.actors_list.clicked.connect(self.actor_list_clicked)
buttons_funcs = dict(
add_brain_regions=self.open_regions_dialog,
add_from_file=self.add_from_file_object,
add_cells=self.add_from_file_cells,
show_structures_tree=self.toggle_treeview,
take_screenshot=self.take_screenshot,
reset=self.reset_camera,
top=self.move_camera_top,
side1=self.move_camera_side1,
side2=self.move_camera_side2,
front=self.move_camera_front,
)
for btn, fun in buttons_funcs.items():
self.buttons[btn].clicked.connect(fun)
self.treeView.clicked.connect(self.add_region_from_tree)
self.alpha_textbox.textChanged.connect(self.update_actor_properties)
self.color_textbox.textChanged.connect(self.update_actor_properties)
self.startup = False
def test_get_camera_params():
s = Scene()
s.render(interactive=False)
cam = s.plotter.camera
params = get_camera_params(scene=s)
params2 = get_camera_params(camera=cam)
check_camera_param(params)
check_camera_param(params2)
def test_atlas_plane(pos, plane, norm):
s = Scene()
p1 = s.atlas.get_plane(plane=plane, pos=pos, norm=norm, sx=1, sy=11)
p2 = s.atlas.get_plane(plane=plane, pos=pos, norm=norm)
assert isinstance(p1, Actor)
assert isinstance(p2, Actor)
s.render(interactive=False)
del s
def test_scene_specials():
scene = Scene()
print(scene)
assert (
str(scene)
== f"A `brainrender.scene.Scene` with {len(scene.actors)} actors."
)
scene.content
scene.render(interactive=False)
del scene
def test_ruler_from_surface():
s = Scene(title="BR")
th = s.add_brain_region("TH", hemisphere="left")
s.add(
ruler_from_surface(th.centerOfMass(),
s.root,
unit_scale=0.01,
units="mm"))
# s.render(interactive=False)
del s
def test_get_actors():
s = Scene()
th = s.add_brain_region("TH")
found1 = s.get_actors(name="TH")
assert len(found1) == 1
assert th in found1
found2 = s.get_actors(br_class="brain region")
assert len(found2) == 2
assert th in found2
assert s.root in found2
def test_cylinder():
s = Scene(title="BR")
th = s.add_brain_region("TH")
s.add(Cylinder(th, s.root))
s.add(Cylinder(th.centerOfMass(), s.root))
s.render(interactive=False)
del s
def test_actor():
s = Scene()
s = s.root
assert isinstance(s, Actor)
print(s)
str(s)
rprint(s)
assert isinstance(s.mesh, Mesh)
assert s.alpha() == s.mesh.alpha()
assert s.name == "root"
assert s.br_class == "brain region"
def test_volume():
scene = Scene(inset=False, root=True)
data = np.load("examples/data/volume.npy")
scene.add(Volume(data, voxel_size=200, as_surface=False, c="Reds"))
scene.add(Volume(data, voxel_size=200, as_surface=True, c="Reds", mode=2))
scene.render(interactive=False)
def test_brain_regions():
scene = Scene()
th = scene.add_brain_region("TH")
assert scene.actors[-1] == th
assert isinstance(th, Actor)
regs = scene.add_brain_region("MOs", "CA1")
assert isinstance(regs, list)
assert len(regs) == 2
nan = scene.add_brain_region("MOs", "CA1")
assert nan is None
noone = scene.add_brain_region("what is this")
assert noone is None
scene.add_brain_region("TH", hemisphere="left")
scene.add_brain_region("CA1", hemisphere="right")
scene.add_brain_region("STN", hemisphere="right")
def test_streamlines():
s = Scene(title="BR")
streams = get_streamlines_for_region("TH", force_download=False)
s.add(Streamlines(streams[0]))
s.add(*make_streamlines(*streams[1:3]))
with pytest.raises(TypeError):
Streamlines([1, 2, 3])
s.render(interactive=False)
del s
def test_ruler():
s = Scene(title="BR")
th = s.add_brain_region("TH", hemisphere="left")
mos = s.add_brain_region("MOs", hemisphere="right")
s.add(
ruler(th.centerOfMass(),
mos.centerOfMass(),
unit_scale=0.01,
units="mm"))
s.render(interactive=False)
del s
def test_points_working():
s = Scene(title="BR")
act = Points(np.load("tests/files/random_cells.npy"))
act2 = Points("tests/files/random_cells.npy", colors="k")
act3 = Points("tests/files/random_cells.npy", name="test")
assert act3.name == "test"
s.add(act)
s.add(act2)
point = Point([100, 233, 422])
s.add(point)
assert isinstance(point, Actor)
assert isinstance(act, Actor)
assert isinstance(act2, Actor)
assert isinstance(act3, Actor)
assert point.name == "Point"
s.render(interactive=False)
del s
def test_actor_removal():
s = Scene()
th = s.add_brain_region("TH")
assert len(s.actors) == 2
s.remove(th)
assert len(s.actors) == 1
s.remove("no actor")
assert len(s.actors) == 1
def test_scene_render():
scene = Scene()
scene.add_brain_region("TH")
scene.render(interactive=False, zoom=1.4)
scene.render(
interactive=False,
camera=dict(
pos=(10705.845660949382, 7435.678067378925, -36936.3695486442,),
viewup=(
-0.0050579179155257475,
-0.9965615097647067,
-0.08270172139591858,
),
clippingRange=(30461.81976236306, 58824.38622122339),
),
)
scene.render(interactive=False, camera="sagittal")
del scene
def test_volume():
s = Scene(inset=False, root=True)
data = np.load("examples/data/volume.npy")
s.add(Volume(data, voxel_size=200, as_surface=False, c="Reds"))
s.add(Volume(data, voxel_size=200, as_surface=True, c="Reds", mode=2))
del s
def test_scene_screenshot(name, scale):
s = Scene(screenshots_folder="tests/screenshots")
s.screenshot(name=name, scale=scale)
shutil.rmtree("tests/screenshots")
s.render(interactive=False)
del s
def test_brain_regions():
scene = Scene()
th = scene.add_brain_region("TH")
assert scene.actors[-1] == th
assert isinstance(th, Actor)
regs = scene.add_brain_region("MOs", "CA1")
assert isinstance(regs, list)
assert len(regs) == 2
noone = scene.add_brain_region("what is this")
assert noone is None
a1 = scene.add_brain_region("TH", hemisphere="left")
a2 = scene.add_brain_region("CA1", hemisphere="right")
assert isinstance(a1, Actor)
assert isinstance(a2, Actor)
scene.render(interactive=False)
del scene
def test_export_for_web():
s = Scene(title="BR")
th = s.add_brain_region("TH")
s.add_label(th, "TH")
path = s.export("test.html")
assert path == "test.html"
path = Path(path)
assert path.exists()
path.unlink()
with pytest.raises(ValueError):
path = s.export("test.py")
def test_neuron():
s = Scene(title="BR")
neuron = s.add(Neuron("tests/files/neuron1.swc"))
s.add(Neuron(Actor(neuron.mesh)))
s.add(Neuron(neuron.mesh))
Neuron(Sphere())
with pytest.raises(ValueError):
Neuron(1)
with pytest.raises(FileExistsError):
Neuron("tests/files/neuronsfsfs.swc")
with pytest.raises(NotImplementedError):
Neuron("tests/files/random_cells.h5")
del s
def test_gebe_expression_api(geapi):
s = Scene(title="BR")
geapi.get_gene_id_by_name(gene)
expids = geapi.get_gene_experiments(gene)
data = geapi.get_gene_data(gene, expids[0], use_cache=True)
# make actor
gene_actor = geapi.griddata_to_volume(
data, min_quantile=90, cmap="inferno"
)
assert isinstance(gene_actor, Actor)
assert gene_actor.name == gene
assert gene_actor.br_class == "Gene Data"
s.add(gene_actor)
s.render(interactive=False)
del s
"""
This example shows how to add a label to a renderend actor
"""
from brainrender import Scene
from rich import print
from myterial import orange
from pathlib import Path
print(f"[{orange}]Running example: {Path(__file__).name}")
# crate a scene and add brain regions
scene = Scene()
th, mos = scene.add_brain_region("TH", "MOs")
scene.add_label(th, "TH")
scene.add_label(mos, "My region")
# render
scene.render()
point = [14000 * fact, 4000, 6000]
plane = scene.atlas.get_plane(pos=point, norm=(1, 0, 0))
# slice
box = scene.get_actors(name="box")[0]
acts = [a for a in scene.actors if a != box]
scene.slice(plane, actors=acts)
# make new silhouettes
for act in scene.get_actors(br_class="brain region"):
act._needs_silhouette = True
# ------------------------------- Create scene ------------------------------- #
scene = Scene(inset=INSET)
scene.root._needs_silhouette = SILHOUETTE
# add transparent box around root to preserve camera position
root_box(scene)
# add all brain regions
mains = (
"Isocortex",
"HPF",
"STR",
"PAL",
"CB",
"MB",
"TH",
"HY",
from rich import print
from pathlib import Path
from brainrender import Scene
sys.path.append("./")
from paper.figures import INSET, SILHOUETTE
print("[bold red]Running: ", Path(__file__).name)
# camera settings
cam = {
"pos": (-20268, -6818, 14964),
"viewup": (0, -1, 0),
"clippingRange": (16954, 58963),
"focalPoint": (6489, 4329, -5556),
"distance": 35514,
}
# create scene
scene = Scene(inset=INSET, screenshots_folder="paper/screenshots")
scene.root._needs_silhouette = SILHOUETTE
# add brain regions
for reg, col in zip(("SCm", "SCs", "ZI"), (scmcol, scscol, zicol)):
scene.add_brain_region(reg, color=col, silhouette=SILHOUETTE)
# render
scene.render(zoom=1.75, camera=cam)
scene.screenshot(name="mouse_regions", scale=1)
brainrender.settings.SHOW_AXES = False
print("[bold red]Running: ", Path(__file__).name)
# camera settings
cam = {
"pos": (-16954, 2456, -3961),
"viewup": (0, -1, 0),
"clippingRange": (22401, 34813),
"focalPoint": (7265, 2199, -5258),
"distance": 24256,
}
# create scene
scene = Scene(inset=False, screenshots_folder="paper/screenshots", root=True)
scene.root._needs_silhouette = False
scene.root.alpha(0.5)
# add brain regions
pag = scene.add_brain_region("PAG", alpha=0.4, silhouette=False, color=pagcol)
scm = scene.add_brain_region("SCm", alpha=0.3, silhouette=False, color=scmcol)
# add neuron mesh
neuron = scene.add("paper/data/yulins_neuron.stl")
neuron.c(neuroncol)
# add sphere at soma location
soma_pos = [9350.51912036, 2344.33986638, 5311.18297796]
point = scene.add(Point(soma_pos, color=neuroncol, radius=25))
scene.add_silhouette(point, lw=1, color="k")
from brainrender import Scene, Animation
from benchmark.timer import Timer
# Create a brainrender scene
scene = Scene(title="brain regions", inset=False)
with Timer(scene, name="Animation"):
# Add brain regions
for br in ("TH", "MOs", "MOp", "CA1", "CB", "MB"):
scene.add_brain_region(br, silhouette=False)
anim = Animation(scene, "examples", "vid3")
# Specify camera position and zoom at some key frames
# each key frame defines the scene's state after n seconds have passed
anim.add_keyframe(0, camera="top", zoom=1.3)
anim.add_keyframe(1, camera="sagittal", zoom=2.1)
anim.add_keyframe(2, camera="frontal", zoom=3)
anim.add_keyframe(3, camera="frontal", zoom=2)
# Make videos
anim.make_video(duration=3, fps=10)
from pathlib import Path
# To measure distances and angles
save_folder = Path(
"/Users/federicoclaudi/Dropbox (UCL)/Rotation_vte/Presentations/Presentations/Fiete lab"
)
settings.SHOW_AXES = False
BREGMA = np.array([5400, 0, 0]) # AP # DV # ML
top = np.array([4.136, -2.106, 0]) * 1000 + BREGMA # AP ML DV
tip = np.array([5.507, -0.584, 6.489]) * 1000 + BREGMA
scene = Scene(
inset=False,
screenshots_folder=save_folder,
)
cun, grn, mos = scene.add_brain_region("CUN", "GRN", "MOs", alpha=0.7)
# CUN/GRN probe
tip[1] = tip[1] + scene.root.centerOfMass()[2]
top[1] = top[1] + scene.root.centerOfMass()[2]
top = top[[0, 2, 1]]
tip = tip[[0, 2, 1]]
scene.add(shapes.Cylinder(pos=[top, tip], c="k", r=50, alpha=1))
# MOs probe
mos_center = mos.centerOfMass() + np.array([1000, 0, -800])
for x in [-500, -1000, -1500, -2000]:
