def test_ar_calculation():
sheet = Sheet("test", *three_faces_sheet())
SheetGeometry.update_all(sheet)
sheet.face_df["AR"] = utils.ar_calculation(sheet, coords=["x", "y"])
sheet.vert_df["x"] = sheet.vert_df["x"] * 2
sheet.face_df["AR2"] = utils.ar_calculation(sheet, coords=["x", "y"])
assert_allclose(sheet.face_df["AR2"], 2 * sheet.face_df["AR"])
def test_spherical_update_height():
datasets, _ = three_faces_sheet(zaxis=True)
specs = config.geometry.spherical_sheet()
eptm = Sheet("3faces_3D", datasets, specs)
expected_rho = pd.Series([
0.0,
1.0,
1.7320381058163818,
1.9999559995159892,
1.732,
0.99997799975799462,
1.7320381058163818,
2.0,
1.7320381058163818,
0.99997799975799462,
1.732,
1.9999559995159892,
1.7320381058163818,
])
expected_height = expected_rho - eptm.vert_df["basal_shift"]
SheetGeometry.update_all(eptm)
assert all((eptm.vert_df["rho"] - expected_rho)**2 < TOLERANCE)
assert all((eptm.vert_df["height"] - expected_height)**2 < TOLERANCE)
def test_sheet_view():
sheet = Sheet("test", *three_faces_sheet())
SheetGeometry.update_all(sheet)
face_spec = {
"color": pd.Series(range(3)),
"color_range": (0, 3),
"visible": True,
"colormap": "Blues",
"epsilon": 0.1,
}
color = pd.DataFrame(np.zeros((sheet.Ne, 3)),
index=sheet.edge_df.index,
columns=["R", "G", "B"])
color.loc[0, "R"] = 0.8
edge_spec = {"color": color, "visible": True}
fig, (edge_mesh, face_mesh) = sheet_view(sheet,
face=face_spec,
edge=edge_spec)
assert face_mesh.color.shape == (39, 3)
assert face_mesh.triangles.shape == (18, 3)
assert face_mesh.lines is None
assert edge_mesh.triangles is None
assert edge_mesh.lines.shape == (18, 2)
sheet.face_df["visible"] = False
sheet.face_df.loc[0, "visible"] = True
fig, (edge_mesh, face_mesh) = sheet_view(sheet,
face=face_spec,
edge=edge_spec)
assert face_mesh.triangles.shape == (6, 3)
def test_sheet_view():
sheet = Sheet("test", *three_faces_sheet())
SheetGeometry.update_all(sheet)
face_spec = {
"color": pd.Series(range(3)),
"color_range": (0, 3),
"visible": True,
"colormap": "Blues",
"epsilon": 0.1,
}
color = pd.DataFrame(
np.zeros((sheet.Ne, 3)), index=sheet.edge_df.index, columns=["R", "G", "B"]
)
color.loc[0, "R"] = 0.8
edge_spec = {"color": color, "visible": True}
canvas, view = sheet_view(sheet, face=face_spec, edge=edge_spec, interactive=False)
content = view.scene.children
edge_mesh, face_mesh = content[-2:]
assert face_mesh.mesh_data.get_face_colors().shape == (18, 4)
assert face_mesh.mesh_data.get_faces().shape == (18, 3)
assert edge_mesh.pos.shape == (13, 3)
def test_length_grad():
sheet = Sheet("etst", *generation.three_faces_sheet())
SheetGeometry.update_all(sheet)
lg = length_grad(sheet)
assert np.all(lg.loc[0].values == np.array([-1, 0, 0]))
def test_rod_update_height():
pth = os.path.join(CURRENT_DIR, '../../stores/rod_sheet.hf5')
datasets = load_datasets(pth)
specs = config.geometry.rod_sheet()
sheet = Sheet('rod', datasets, specs)
SheetGeometry.update_all(sheet)
assert (sheet.vert_df.rho.mean() - 0.7895479495559642)**2 < TOLERANCE
def test_rod_update_height():
pth = os.path.join(stores_dir, "rod_sheet.hf5")
datasets = load_datasets(pth)
specs = config.geometry.rod_sheet()
sheet = Sheet("rod", datasets, specs)
SheetGeometry.update_all(sheet)
assert (sheet.vert_df.rho.mean() - 0.96074585429756632)**2 < TOLERANCE
def main():
# --------- Chargement d'un fichier HDF5 --------- #
dsets = hdf5.load_datasets("data/with_collisions.hf5",
data_names=["vert", "edge", "face"])
specs = config.geometry.cylindrical_sheet()
sheet = Sheet("ellipse", dsets, specs)
SheetGeometry.update_all(sheet)
list_intersected_facesolve_intersection(sheet)
def test_data_at_opposite_array():
sheet = Sheet("emin", *three_faces_sheet())
geom.update_all(sheet)
sheet.get_opposite()
opp = utils.data_at_opposite(sheet,
sheet.edge_df[["dx", "dy"]].to_numpy(),
free_value=None)
assert opp.shape == (sheet.Ne, 2)
assert_array_equal(opp.index, sheet.edge_df.index)
def test_data_at_opposite_df():
sheet = Sheet("emin", *three_faces_sheet())
geom.update_all(sheet)
sheet.get_opposite()
opp = utils.data_at_opposite(sheet,
sheet.edge_df[["dx", "dy"]],
free_value=None)
assert opp.shape == (sheet.Ne, 2)
assert list(opp.columns) == ["dx", "dy"]
def test_save_import_triangular_mesh():
sheet = Sheet("test", *three_faces_sheet())
fh = tempfile.mktemp(suffix=".obj")
meshes.save_triangular_mesh(fh, sheet)
data = meshes.import_triangular_mesh(fh)
sheet = Sheet('test', data)
geom.update_all(sheet)
assert sheet.Nf == 18
assert sheet.Ne == 54
assert sheet.Nv == 16
def test_get_phis():
pth = os.path.join(stores_dir, "rod_sheet.hf5")
datasets = load_datasets(pth)
specs = config.geometry.rod_sheet()
sheet = Sheet("rod", datasets, specs)
SheetGeometry.update_all(sheet)
sheet.edge_df["sphi"] = SheetGeometry.get_phis(sheet)
assert np.all(
sheet.edge_df.sort_values(["face", "sphi"]).groupby("face").apply(
lambda df: np.roll(df["trgt"], 1) == df["srce"]))
def get_ventral_patch(fname):
sim_dsets = hdf5.load_datasets(fname)
sheet = Sheet('morph', sim_dsets, config.geometry.flat_sheet())
to_crop = sheet.cut_out(
[[-300, 300], [sheet.vert_df.y.max() - 22,
sheet.vert_df.y.max() + 1], [-300, 300]], )
sheet.remove(to_crop)
sheet.vert_df[['x', 'y', 'z']] = sheet.vert_df[['x', 'z', 'y']]
SheetGeometry.update_all(sheet)
return sheet
def test_detection():
sheet = Sheet("crossed",
hdf5.load_datasets(Path(stores_dir) / "sheet6x5.hf5"))
sheet.vert_df.z = 5 * sheet.vert_df.x**2
# sheet.vert_df[sheet.coords] += np.random.normal(scale=0.001, size=(sheet.Nv, 3))
SheetGeometry.update_all(sheet)
sheet.vert_df.x -= 35 * (sheet.vert_df.x / 2)**3
SheetGeometry.update_all(sheet)
colliding_edges = set(collisions.self_intersections(sheet).flatten())
expected = {32, 1, 34, 9, 35}
assert colliding_edges == expected
def test_data_at_opposite():
sheet = Sheet("emin", *three_faces_sheet())
geom.update_all(sheet)
sheet.get_opposite()
opp = utils.data_at_opposite(sheet,
sheet.edge_df["length"],
free_value=None)
assert opp.shape == (sheet.Ne, )
assert opp.loc[0] == 1.0
assert ~np.isfinite(opp.loc[1])
opp = utils.data_at_opposite(sheet, sheet.edge_df["length"], free_value=-1)
assert opp.loc[1] == -1.0
def test_solving():
sheet = Sheet("crossed",
hdf5.load_datasets(Path(stores_dir) / "sheet6x5.hf5"))
sheet.vert_df.z = 5 * sheet.vert_df.x**2
SheetGeometry.update_all(sheet)
positions_buffer = sheet.vert_df[sheet.coords].copy()
sheet.vert_df.x -= 35 * (sheet.vert_df.x / 2)**3
SheetGeometry.update_all(sheet)
colliding_edges = collisions.self_intersections(sheet)
boxes = solvers.CollidingBoxes(sheet, positions_buffer, colliding_edges)
boxes.solve_collisions(shyness=0.01)
assert collisions.self_intersections(sheet).size == 0
assert sheet.vert_df.loc[[22, 12], "x"].diff().loc[12] == 0.01
def test_iso_solver():
pth = os.path.join(stores_dir, "rod_sheet.hf5")
datasets = load_datasets(pth)
specs = config.geometry.rod_sheet()
sheet = Sheet("rod", datasets, specs)
geom.reset_scafold(sheet)
geom.update_all(sheet)
dyn_specs = config.dynamics.quasistatic_sheet_spec()
dyn_specs["vert"]["basal_shift"] = 0.0
dyn_specs["face"]["prefered_vol"] = 1.0
sheet.update_specs(dyn_specs, reset=True)
geom.update_all(sheet)
res = bruteforce_isotropic_relax(sheet, geom, model)
assert_almost_equal(res["x"], 1.6001116383)
def test_scaled_unscaled():
sheet = Sheet("3faces_3D", *three_faces_sheet())
SheetGeometry.update_all(sheet)
def mean_area():
return sheet.face_df.area.mean()
prev_area = sheet.face_df.area.mean()
sc_area = utils.scaled_unscaled(mean_area, 2, sheet, SheetGeometry)
post_area = sheet.face_df.area.mean()
assert post_area == prev_area
assert_almost_equal(sc_area / post_area, 4.0)
def fails():
raise ValueError
with pytest.raises(ValueError):
utils.scaled_unscaled(fails, 2, sheet, SheetGeometry)
post_area = sheet.face_df.area.mean()
assert post_area == prev_area
def test_periodic_planar():
hdf_path = hdf5.load_datasets(
os.path.join(stores_dir, "planar_periodic8x8.hf5"))
specs = config.stores.planar_periodic8x8()
sheet = Sheet("periodic", hdf_path, specs)
PlanarGeometry.update_all(sheet)
assert sheet.edge_df.length.max() < 1.0
fsx = sheet.edge_df["fx"] - sheet.edge_df["sx"]
fsy = sheet.edge_df["fy"] - sheet.edge_df["sy"]
lai = (fsx**2 + fsy**2)**0.5
assert lai.max() < 0.7
assert sheet.face_df.area.max() < 1.2
assert sheet.face_df.area.min() > 0.8
sheet.update_specs(config.geometry.sheet_spec())
sheet = Sheet("2.5D", sheet.datasets, sheet.specs)
SheetGeometry.update_all(sheet)
assert sheet.edge_df.length.max() < 1.0
fsx = sheet.edge_df["fx"] - sheet.edge_df["sx"]
fsy = sheet.edge_df["fy"] - sheet.edge_df["sy"]
lai = (fsx**2 + fsy**2)**0.5
assert lai.max() < 0.7
assert sheet.face_df.area.max() < 1.2
assert sheet.face_df.area.min() > 0.8
def test_already():
# GH111
sheet = Sheet("crossed",
hdf5.load_datasets(Path(stores_dir) / "sheet6x5.hf5"))
sheet.vert_df.z = 5 * sheet.vert_df.x**2
SheetGeometry.update_all(sheet)
sheet.vert_df.x -= 35 * (sheet.vert_df.x / 2)**3
SheetGeometry.update_all(sheet)
positions_buffer = sheet.vert_df[sheet.coords].copy()
sheet.vert_df.x -= 0.1 * (sheet.vert_df.x / 2)**3
SheetGeometry.update_all(sheet)
colliding_edges = collisions.self_intersections(sheet)
boxes = solvers.CollidingBoxes(sheet, positions_buffer, colliding_edges)
res = boxes.solve_collisions(shyness=0.01)
colliding_edges = collisions.self_intersections(sheet)
assert len(colliding_edges) == 0