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adds zarr support #248

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merged 6 commits into from
Nov 18, 2021
Merged

adds zarr support #248

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8db5d68
adds zarr support
glyg Jul 7, 2021
7bc1286
removes flycheck file
glyg Jul 7, 2021
dfe05f9
adds flycheck to gitignore
glyg Jul 7, 2021
c9b4800
browse_history widget
glyg Sep 3, 2021
9d7a12b
fixes tests
glyg Sep 6, 2021
9e0440d
fix bad coordinates in history.retrieve
glyg Sep 6, 2021
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2 changes: 1 addition & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -80,4 +80,4 @@ dist/
*.blend[1-9]

## pytest
.pytest_cache
.pytest_cacheflycheck_*
1,516 changes: 758 additions & 758 deletions doc/bibliography/tyssue.bib
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65 changes: 64 additions & 1 deletion tests/core/test_history.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,9 @@
import pytest
import os
import pytest

from pathlib import Path

import numpy as np

from tyssue import Sheet, History, Epithelium, RNRGeometry
from tyssue.core.history import HistoryHdf5
Expand Down Expand Up @@ -63,6 +65,60 @@ def test_retrieve():
assert sheet_.datasets["face"].loc[0, "area"] == 100.0


def test_browse():
sheet = Sheet("3", *three_faces_sheet())
history = History(sheet)
for i in range(30):
history.record(i / 10)

times = [t for t, _ in history.browse()]
np.testing.assert_allclose(times, history.time_stamps)

times_areas = np.array(
[[t, s.face_df.loc[0, "area"]] for t, s in history.browse(2, 8, endpoint=True)]
)
assert times_areas.shape == (7, 2)
assert times_areas[0, 0] == history.time_stamps[2]
assert times_areas[-1, 0] == history.time_stamps[8]
assert set(times_areas[:, 0]).issubset(history.time_stamps)

times_areas = np.array(
[
[t, s.face_df.loc[0, "area"]]
for t, s in history.browse(2, 8, 4, endpoint=False)
]
)
assert times_areas.shape == (4, 2)
assert times_areas[0, 0] == history.time_stamps[2]
assert times_areas[-1, 0] == history.time_stamps[7]
assert set(times_areas[:, 0]).issubset(history.time_stamps)

times_areas = np.array(
[
[t, s.face_df.loc[0, "area"]]
for t, s in history.browse(2, 8, 4, endpoint=True)
]
)
assert times_areas.shape == (4, 2)
assert times_areas[0, 0] == history.time_stamps[2]
assert times_areas[-1, 0] == history.time_stamps[8]
assert set(times_areas[:, 0]).issubset(history.time_stamps)

times_areas = np.array(
[[t, s.face_df.loc[0, "area"]] for t, s in history.browse(2, 8, 10)]
)
assert times_areas.shape == (10, 2)
assert times_areas[0, 0] == history.time_stamps[2]
assert times_areas[-1, 0] == history.time_stamps[8]
assert set(times_areas[:, 0]).issubset(history.time_stamps)

times_areas = np.array(
[[t, s.edge_df.loc[0, "length"]] for t, s in history.browse(size=40)]
)
assert times_areas.shape == (40, 2)
assert set(times_areas[:, 0]) == set(history.time_stamps)


def test_overwrite_time():
sheet = Sheet("3", *three_faces_sheet())
history = History(sheet)
Expand Down Expand Up @@ -232,6 +288,13 @@ def test_historyHDF5_from_archive():
os.remove("test.hf5")


def test_retrieve_coords():
sheet = Sheet("3", *three_faces_sheet())
history = History(sheet)
history.record()
assert history.retrieve(0).coords == sheet.coords


def test_to_and_from_archive():

sheet = Sheet("3", *three_faces_sheet())
Expand Down
154 changes: 2 additions & 152 deletions tests/core/test_objects.py
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Expand Up @@ -492,159 +492,9 @@ def test_polygons():
fp = eptm.face_polygons()

eptm.reset_index(order=True)
expected_res = [
[
[0.0, 0.0, 0.0],
[1.0, 0.0, 0.0],
[1.5, 0.866, 0.0],
[1.0, 1.732, 0.0],
[0.0, 1.732, 0.0],
[-0.5, 0.866, 0.0],
],
[
[-1.5, -0.866, 0.0],
[-0.5, -0.866, 0.0],
[0.0, 0.0, 0.0],
[-0.5, 0.866, 0.0],
[-1.5, 0.866, 0.0],
[-2.0, 0.0, 0.0],
],
[
[0.0, -1.732, 0.0],
[1.0, -1.732, 0.0],
[1.5, -0.866, 0.0],
[1.0, 0.0, 0.0],
[0.0, 0.0, 0.0],
[-0.5, -0.866, 0.0],
],
[
[0.0, 0.0, 0.0],
[0.33333333, 0.0, 0.0],
[0.5, 0.28866667, 0.0],
[0.33333333, 0.57733333, 0.0],
[0.0, 0.57733333, 0.0],
[-0.16666667, 0.28866667, 0.0],
],
[
[-0.5, -0.28866667, 0.0],
[-0.16666667, -0.28866667, 0.0],
[0.0, 0.0, 0.0],
[-0.16666667, 0.28866667, 0.0],
[-0.5, 0.28866667, 0.0],
[-0.66666667, 0.0, 0.0],
],
[
[0.0, -0.57733333, 0.0],
[0.33333333, -0.57733333, 0.0],
[0.5, -0.28866667, 0.0],
[0.33333333, 0.0, 0.0],
[0.0, 0.0, 0.0],
[-0.16666667, -0.28866667, 0.0],
],
[[1.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.33333333, 0.0, 0.0]],
[
[0.5, 0.28866667, 0.0],
[0.33333333, 0.0, 0.0],
[1.0, 0.0, 0.0],
[1.5, 0.866, 0.0],
],
[
[0.33333333, 0.57733333, 0.0],
[0.5, 0.28866667, 0.0],
[1.5, 0.866, 0.0],
[1.0, 1.732, 0.0],
],
[
[0.0, 0.57733333, 0.0],
[0.33333333, 0.57733333, 0.0],
[1.0, 1.732, 0.0],
[0.0, 1.732, 0.0],
],
[
[-0.5, 0.866, 0.0],
[-0.16666667, 0.28866667, 0.0],
[0.0, 0.57733333, 0.0],
[0.0, 1.732, 0.0],
],
[
[0.0, 0.0, 0.0],
[-0.16666667, 0.28866667, 0.0],
[0.0, 0.0, 0.0],
[-0.5, 0.866, 0.0],
],
[
[0.0, 0.0, 0.0],
[0.0, 0.0, 0.0],
[-0.16666667, 0.28866667, 0.0],
[-0.5, 0.866, 0.0],
],
[
[-0.5, 0.28866667, 0.0],
[-0.16666667, 0.28866667, 0.0],
[-0.5, 0.866, 0.0],
[-1.5, 0.866, 0.0],
],
[
[-2.0, 0.0, 0.0],
[-0.66666667, 0.0, 0.0],
[-0.5, 0.28866667, 0.0],
[-1.5, 0.866, 0.0],
],
[
[-1.5, -0.866, 0.0],
[-0.5, -0.28866667, 0.0],
[-0.66666667, 0.0, 0.0],
[-2.0, 0.0, 0.0],
],
[
[-1.5, -0.866, 0.0],
[-0.5, -0.866, 0.0],
[-0.16666667, -0.28866667, 0.0],
[-0.5, -0.28866667, 0.0],
],
[
[-0.5, -0.866, 0.0],
[0.0, 0.0, 0.0],
[-0.16666667, -0.28866667, 0.0],
[0.0, 0.0, 0.0],
],
[
[-0.5, -0.866, 0.0],
[0.0, 0.0, 0.0],
[0.0, 0.0, 0.0],
[-0.16666667, -0.28866667, 0.0],
],
[
[0.0, -1.732, 0.0],
[0.0, -0.57733333, 0.0],
[-0.16666667, -0.28866667, 0.0],
[-0.5, -0.866, 0.0],
],
[
[0.0, -1.732, 0.0],
[1.0, -1.732, 0.0],
[0.33333333, -0.57733333, 0.0],
[0.0, -0.57733333, 0.0],
],
[
[1.0, -1.732, 0.0],
[1.5, -0.866, 0.0],
[0.5, -0.28866667, 0.0],
[0.33333333, -0.57733333, 0.0],
],
[
[1.5, -0.866, 0.0],
[1.0, 0.0, 0.0],
[0.33333333, 0.0, 0.0],
[0.5, -0.28866667, 0.0],
],
[[1.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.33333333, 0.0, 0.0], [0.0, 0.0, 0.0]],
]
expected_res = [np.array(poly) for poly in expected_res]

res = eptm.face_polygons(["x", "y", "z"])
for i in range(res.shape[0]):
np.testing.assert_almost_equal(expected_res[i], res[i], decimal=4)
shapes = res.apply(lambda s: s.shape in ((6, 3), (4, 3)))
assert all(shapes)


def test_face_polygons_exception():
Expand Down
23 changes: 9 additions & 14 deletions tests/draw/test_plt.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ def test_sheet_view(self):
0.0, 1.0, num=self.sheet.edge_df.shape[0]
)[::-1]

self.draw_specs["edge"]["visible"] = True
self.draw_specs["edge"]["visible"] = True
self.draw_specs["edge"]["color"] = self.sheet.edge_df["rand"] # [0, 0, 0, 1]
self.draw_specs["edge"]["alpha"] = 1.0
self.draw_specs["edge"]["color_range"] = 0, 3
Expand Down Expand Up @@ -145,13 +145,11 @@ def test_create_gif():
sheet.edge_df.loc[[1], "line_tension"] *= 8
res = solver.solve(0.5, dt=0.05)

with pytest.raises(ValueError):
create_gif(history, "frames.gif")
create_gif(history, "frames.gif", num_frames=5)
create_gif(history, "interval.gif", interval=(2, 4))

assert os.path.isfile("frames.gif") == True
assert os.path.isfile("interval.gif") == True
assert os.path.isfile("frames.gif")
assert os.path.isfile("interval.gif")

os.remove("frames.gif")
os.remove("interval.gif")
Expand All @@ -161,13 +159,10 @@ def test_plot_forces():
geom = SheetGeometry
model = PlanarModel
sheet = Sheet("3", *three_faces_sheet())
sheet.update_specs(model.specs)
sheet.update_specs(model.specs)
geom.update_all(sheet)
fig, ax = plot_forces(sheet,
geom,
model,
list('xy'),
0.05,
**{'extract': {'x_boundary': (-10, 10)}})

assert ax.lines[0].get_xydata().shape == (54, 2)
fig, ax = plot_forces(
sheet, geom, model, list("xy"), 0.05, **{"extract": {"x_boundary": (-10, 10)}}
)

assert ax.lines[0].get_xydata().shape == (54, 2)
25 changes: 25 additions & 0 deletions tests/io/test_hdf.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
import tempfile
import numpy as np
import pandas as pd

from tyssue.generation import three_faces_sheet
from tyssue import Sheet
from tyssue.io import hdf5


def test_save_datasets():
sheet = Sheet("test", *three_faces_sheet())
fh = tempfile.mktemp(suffix=".hdf5")
hdf5.save_datasets(fh, sheet)
with pd.HDFStore(fh) as st:
for key in sheet.datasets:
assert key in st


def test_load_datasets():
sheet = Sheet("test", *three_faces_sheet())
fh = tempfile.mktemp(suffix=".hdf5")
hdf5.save_datasets(fh, sheet)

datasets = hdf5.load_datasets(fh)
assert np.all(datasets["vert"][sheet.vert_df.columns] == sheet.vert_df)
31 changes: 31 additions & 0 deletions tests/io/test_zarr.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,31 @@
import tempfile
import numpy as np
import pandas as pd
import zarr as zr

from tyssue.generation import three_faces_sheet
from tyssue import Sheet
from tyssue.io import zarr


def test_save_datasets():
sheet = Sheet("test", *three_faces_sheet())
fh = tempfile.mktemp(suffix=".zarr")
zarr.save_datasets(fh, sheet)
with zr.open(fh) as st:
for key in sheet.datasets:
assert key in st


def test_load_datasets():
sheet = Sheet("test", *three_faces_sheet())
sheet.settings["test"] = 3
fh = tempfile.mktemp(suffix=".zarr")
zarr.save_datasets(fh, sheet)
datasets, settings = zarr.load_datasets(fh)
assert np.all(datasets["vert"][sheet.vert_df.columns] == sheet.vert_df)
assert settings == sheet.settings
sheet.settings["test"] = np.zeros(4)
zarr.save_datasets(fh, sheet)
datasets, settings = zarr.load_datasets(fh)
assert settings["test"] == [0.0, 0.0, 0.0, 0.0]
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