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Running on Zero
Running on Zero
| import numpy as np | |
| from cellquant.annotations import RasterAnnotation | |
| from cellquant.data import AugConfig, PatchSampler, make_targets | |
| def _raster(): | |
| inst = np.zeros((64, 64), np.int32) | |
| inst[10:30, 10:30] = 1 | |
| inst[30:50, 30:50] = 2 # touches instance 1 at a corner | |
| nos = np.zeros((64, 64), np.int32) | |
| nos[20:23, 20:23] = 1 | |
| nos[5:7, 50:52] = 2 | |
| return RasterAnnotation(inst, ["", "Cell, Nostril, Antibody +", "Cell, Antibody -"], nos, | |
| ["", "Nostril in Nucleus", "Nostril External of Nucleus"]) | |
| def test_make_targets_layout(): | |
| T = make_targets(_raster()) | |
| assert set(np.unique(T["cell3"])) == {0, 1, 2} | |
| assert ((T["cell3"] > 0) == (T["cellmask"] > 0)).all() | |
| # border ring is 3 px wide: a 20x20 square has 20*20 - 14*14 = 204 border px | |
| assert int((T["cell3"][10:30, 10:30] == 2).sum()) == 204 | |
| assert T["dist"].shape == T["cell3"].shape and T["dist"].dtype == np.float32 | |
| assert T["antibody"][15, 15] == 1 and T["antibody"][40, 40] == 0 | |
| assert T["cellnos"][15, 15] == 1 and T["cellnos"][40, 40] == 0 | |
| assert T["nos3"][21, 21] == 1 and T["nos3"][5, 50] == 2 and T["nos3"][0, 0] == 0 | |
| def test_sampler_batch_shapes_and_reproducibility(): | |
| img = (np.random.default_rng(0).random((64, 64, 3)) * 255).astype(np.uint8) | |
| T = make_targets(_raster()) | |
| cfg = AugConfig(crop=32) | |
| a = PatchSampler([img], [T], cfg, seed=3).batch(2) | |
| b = PatchSampler([img], [T], cfg, seed=3).batch(2) | |
| x, t = a | |
| assert x.shape == (2, 3, 32, 32) and x.min() >= 0 and x.max() <= 1 | |
| assert t["cell3"].shape == (2, 32, 32) and t["cell3"].dtype.is_floating_point is False | |
| assert np.allclose(x.numpy(), b[0].numpy()) | |
| assert all(np.array_equal(t[k].numpy(), b[1][k].numpy()) for k in t) | |