from scipy.spatial import Voronoi
from tyssue import generation
from tyssue.core.sheet import Sheet
from tyssue.generation import hexa_grid3d, from_3d_voronoi
from tyssue.generation import hexa_grid2d, from_2d_voronoi
from tyssue.generation import extrude, subdivide_faces
from tyssue import Epithelium, BulkGeometry, config
from tyssue.core.sheet import get_opposite
from pytest import raises
import numpy as np
import pandas as pd
def test_3faces():
datasets, _ = generation.three_faces_sheet()
assert datasets["edge"].shape[0] == 18
assert datasets["face"].shape[0] == 3
assert datasets["vert"].shape[0] == 13
def test_from_3d_voronoi():
grid = hexa_grid3d(6, 4, 3)
datasets = from_3d_voronoi(Voronoi(grid))
assert datasets["vert"].shape[0] == 139
assert datasets["edge"].shape[0] == 1272
assert datasets["face"].shape[0] == 141
assert datasets["cell"].shape[0] == 70
bulk = Epithelium("bulk", datasets, config.geometry.bulk_spec())
bulk.reset_index()
bulk.reset_topo()
BulkGeometry.update_all(bulk)
bulk.sanitize()
assert bulk.validate()
def test_from_2d_voronoi():
grid = hexa_grid2d(6, 4, 1, 1)
datasets = from_2d_voronoi(Voronoi(grid))
assert datasets["vert"].shape[0] == 32
assert datasets["edge"].shape[0] == 82
assert datasets["face"].shape[0] == 24
def test_extrude():
datasets, specs = generation.three_faces_sheet()
sheet = Sheet("test", datasets, specs)
extruded = extrude(sheet.datasets, method="translation")
assert extruded["cell"].shape[0] == 3
assert extruded["face"].shape[0] == 24
assert extruded["edge"].shape[0] == 108
assert extruded["vert"].shape[0] == 26
def test_subdivide():
datasets, specs = generation.three_faces_sheet()
sheet = Sheet("test", datasets, specs)
subdivided = subdivide_faces(sheet, [0])
assert subdivided["face"].shape[0] == 3
assert subdivided["edge"].shape[0] == 30
assert subdivided["vert"].shape[0] == 14
datasets_3d = extrude(datasets, method="translation")
sheet_3d = Sheet("test3d", datasets_3d, specs)
subdivided_3d = subdivide_faces(sheet_3d, [0])
assert subdivided_3d["face"].shape[0] == 24
assert subdivided_3d["edge"].shape[0] == 120
assert subdivided_3d["vert"].shape[0] == 27
assert subdivided_3d["cell"].shape[0] == 3
def test_extrude_invalid_method():
datasets, specs = generation.three_faces_sheet()
with raises(ValueError):
datasets_3d = extrude(datasets, method="invalid_method")
def test_hexagrid3d_noise():
np.random.seed(1)
grid = hexa_grid3d(6, 4, 3, noise=0.1)
datasets = from_3d_voronoi(Voronoi(grid))
assert datasets["vert"].shape[0] == 318
assert datasets["edge"].shape[0] == 3300
assert datasets["face"].shape[0] == 335
assert datasets["cell"].shape[0] == 72
def test_anchors():
datasets, specs = generation.three_faces_sheet()
sheet = Sheet("test_anchors", datasets, specs)
sheet.edge_df["opposite"] = get_opposite(sheet.edge_df)
expected_dict = {
18: [1, 13],
19: [2, 14],
20: [3, 15],
21: [4, 16],
22: [5, 17],
23: [6, 18],
24: [7, 19],
25: [8, 20],
26: [9, 21],
27: [10, 22],
28: [11, 23],
29: [12, 24],
}
expected_res = pd.DataFrame.from_dict(expected_dict, orient="index")
expected_res.columns = ["srce", "trgt"]
generation.create_anchors(sheet)
res_srce_trgt_anchors = sheet.edge_df.loc[18:, ["srce", "trgt"]]
assert res_srce_trgt_anchors.equals(expected_res)
def test_extract():
datasets, specs = generation.three_faces_sheet()
sheet = Sheet("test_sheet_extract_coordinate", datasets, specs)
sheet.face_df.loc[0, "is_alive"] = 0
subsheet = sheet.extract("is_alive")
assert subsheet.face_df["is_alive"].all()
assert subsheet.Nf == 2
def test_sheet_extract_coordinate():
grid = hexa_grid2d(6, 4, 3, 3)
datasets = from_2d_voronoi(Voronoi(grid))
sheet = Sheet("test_extract_bounding_box", datasets)
subsheet = sheet.extract_bounding_box(
[sheet.face_df["x"].min(), sheet.face_df["x"].max() / 2],
[sheet.face_df["y"].min(), sheet.face_df["y"].max() / 2],
)
assert subsheet.face_df["x"].max() <= sheet.face_df["x"].max() / 2
assert subsheet.face_df["x"].min() >= sheet.face_df["x"].min()
assert subsheet.face_df["y"].max() <= sheet.face_df["y"].max() / 2
assert subsheet.face_df["y"].min() >= sheet.face_df["y"].min()
assert subsheet.face_df["z"].max() <= sheet.face_df["z"].max()
assert subsheet.face_df["z"].min() >= sheet.face_df["z"].min()
