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refactor(grainstats): GrainStats.get_max_min_feret() > measure.feret #823

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Apr 17, 2024
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refactor(grainstats): GrainStats.get_max_min_feret() > measure.feret #823

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50c0c36
refactor(grainstats): GrainStats.get_max_min_feret() > measure.feret
ns-rse Mar 25, 2024
74916b1
Merge branch 'main' into ns-rse/748-grain-profiles-grainstats
ns-rse Apr 15, 2024
3130a7a
refactor(grainstats): GrainStats.get_max_min_feret() > measure.feret
ns-rse Mar 25, 2024
c7111af
refactor(grainstats): GrainStats.get_max_min_feret() > measure.feret
ns-rse Mar 25, 2024
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10 changes: 5 additions & 5 deletions tests/_regtest_outputs/test_grainstats_minicircle.test_grainstats_regression.out
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
centre_x centre_y radius_min radius_max radius_mean radius_median height_min height_max height_median height_mean volume area area_cartesian_bbox smallest_bounding_width smallest_bounding_length smallest_bounding_area aspect_ratio threshold max_feret min_feret image
molecule_number
0 7.500895e-08 4.775362e-08 4.044948e-09 2.542964e-08 1.600048e-08 1.647888e-08 1.006306e-09 2.696640e-09 1.597337e-09 1.596062e-09 1.084371e-24 6.794043e-16 1.319762e-15 2.053897e-08 5.037861e-08 1.034725e-15 2.452830 above 5.037861e-08 2.053897e-08 None
1 8.028649e-08 7.895237e-08 6.658610e-09 2.623645e-08 1.609777e-08 1.573693e-08 1.009513e-09 2.480685e-09 1.668932e-09 1.683197e-09 1.031843e-24 6.130257e-16 1.526707e-15 2.017441e-08 4.942135e-08 9.970467e-16 2.449704 above 4.987228e-08 2.017441e-08 None
2 4.001424e-08 7.585689e-08 9.745734e-09 2.369314e-08 1.746942e-08 1.818722e-08 1.006681e-09 2.139365e-09 1.646541e-09 1.598842e-09 1.123717e-24 7.028320e-16 1.546230e-15 3.359220e-08 4.149625e-08 1.393950e-15 1.235294 above 4.440534e-08 3.176819e-08 None
centre_x centre_y radius_min radius_max radius_mean radius_median height_min height_max height_median height_mean volume area area_cartesian_bbox smallest_bounding_width smallest_bounding_length smallest_bounding_area aspect_ratio threshold max_feret min_feret max_feret_coords min_feret_coords image
molecule_number
0 7.500895e-08 4.775362e-08 4.044948e-09 2.542964e-08 1.600048e-08 1.647888e-08 1.006306e-09 2.696640e-09 1.597337e-09 1.596062e-09 1.084371e-24 6.794043e-16 1.319762e-15 2.053897e-08 5.037861e-08 1.034725e-15 2.452830 above 5.037861e-08 2.053897e-08 [[10, 0], [5, 25]] [[10.1923076923077, 15.0384615384615], [0.0, 13.0]] None
1 8.028649e-08 7.895237e-08 6.658610e-09 2.623645e-08 1.609777e-08 1.573693e-08 1.009513e-09 2.480685e-09 1.668932e-09 1.683197e-09 1.031843e-24 6.130257e-16 1.526707e-15 2.017441e-08 4.942135e-08 9.970467e-16 2.449704 above 4.987228e-08 2.017441e-08 [[1, 1], [15, 22]] [[10.2518248175182, 6.6824817518248], [1.0, 11.0]] None
2 4.001424e-08 7.585689e-08 9.745734e-09 2.369314e-08 1.746942e-08 1.818722e-08 1.006681e-09 2.139365e-09 1.646541e-09 1.598842e-09 1.123717e-24 7.028320e-16 1.546230e-15 3.359220e-08 4.149625e-08 1.393950e-15 1.235294 above 4.440534e-08 3.176819e-08 [[21, 6], [0, 14]] [[11.1834319526627, 14.8402366863905], [5.0, 0.0]] None
12 changes: 6 additions & 6 deletions tests/_regtest_outputs/test_processing.test_process_scan_above.out
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
image_size_x_m image_size_y_m image_area_m2 image_size_x_px image_size_y_px image_area_px2 grains_number_above grains_per_m2_above grains_number_below grains_per_m2_below rms_roughness
image
image
minicircle_small 1.2646e-07 1.2646e-07 1.5993e-14 64 64 4096 3 1.8758e+14 0 0.0000e+00 6.8208e-10
centre_x centre_y radius_min radius_max radius_mean radius_median height_min height_max height_median height_mean volume area area_cartesian_bbox smallest_bounding_width smallest_bounding_length smallest_bounding_area aspect_ratio threshold max_feret min_feret image contour_length circular end_to_end_distance
molecule_number
0 7.5100e-08 4.7559e-08 3.9431e-09 2.5631e-08 1.6016e-08 1.6680e-08 9.1991e-10 2.6422e-09 1.5338e-09 1.5341e-09 1.0543e-24 6.8721e-16 1.3198e-15 2.0539e-08 5.0379e-08 1.0347e-15 2.4528e+00 above 5.0379e-08 2.0539e-08 minicircle_small 6.0226e-08 False 8.6738e-09
1 8.0241e-08 7.8677e-08 6.8951e-09 2.7188e-08 1.6272e-08 1.6263e-08 9.0630e-10 2.4586e-09 1.6144e-09 1.6264e-09 1.0352e-24 6.3645e-16 1.5931e-15 2.0174e-08 5.1212e-08 1.0332e-15 2.5385e+00 above 5.1262e-08 2.0174e-08 minicircle_small 6.6355e-08 True 0.0000e+00
2 4.0012e-08 7.5644e-08 9.9461e-09 2.3654e-08 1.7561e-08 1.8364e-08 9.0641e-10 2.1066e-09 1.5939e-09 1.5493e-09 1.1192e-24 7.2236e-16 1.5462e-15 3.3592e-08 4.1496e-08 1.3940e-15 1.2353e+00 above 4.4405e-08 3.2528e-08 minicircle_small 9.6106e-08 True 0.0000e+00
centre_x centre_y radius_min radius_max radius_mean radius_median height_min height_max height_median height_mean volume area area_cartesian_bbox smallest_bounding_width smallest_bounding_length smallest_bounding_area aspect_ratio threshold max_feret min_feret max_feret_coords min_feret_coords image contour_length circular end_to_end_distance
molecule_number
0 7.5100e-08 4.7559e-08 3.9431e-09 2.5631e-08 1.6016e-08 1.6680e-08 9.1991e-10 2.6422e-09 1.5338e-09 1.5341e-09 1.0543e-24 6.8721e-16 1.3198e-15 2.0539e-08 5.0379e-08 1.0347e-15 2.4528e+00 above 5.0379e-08 2.0539e-08 [[10, 0], [5, 25]] [[10.1923076923077, 15.0384615384615], [0.0, 13.0]] minicircle_small 6.0226e-08 False 8.6738e-09
1 8.0241e-08 7.8677e-08 6.8951e-09 2.7188e-08 1.6272e-08 1.6263e-08 9.0630e-10 2.4586e-09 1.6144e-09 1.6264e-09 1.0352e-24 6.3645e-16 1.5931e-15 2.0174e-08 5.1212e-08 1.0332e-15 2.5385e+00 above 5.1262e-08 2.0174e-08 [[2, 0], [14, 23]] [[10.2518248175182, 6.6824817518248], [1.0, 11.0]] minicircle_small 6.6355e-08 True 0.0000e+00
2 4.0012e-08 7.5644e-08 9.9461e-09 2.3654e-08 1.7561e-08 1.8364e-08 9.0641e-10 2.1066e-09 1.5939e-09 1.5493e-09 1.1192e-24 7.2236e-16 1.5462e-15 3.3592e-08 4.1496e-08 1.3940e-15 1.2353e+00 above 4.4405e-08 3.2528e-08 [[21, 6], [0, 14]] [[10.3313609467456, 15.1952662721894], [4.0, 0.0]] minicircle_small 9.6106e-08 True 0.0000e+00
8 changes: 4 additions & 4 deletions tests/_regtest_outputs/test_processing.test_process_scan_below.out
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
image_size_x_m image_size_y_m image_area_m2 image_size_x_px image_size_y_px image_area_px2 grains_number_above grains_per_m2_above grains_number_below grains_per_m2_below rms_roughness
image
image
minicircle_small 1.2646e-07 1.2646e-07 1.5993e-14 64 64 4096 0 0.0000e+00 1 6.2526e+13 6.8208e-10
centre_x centre_y radius_min radius_max radius_mean radius_median height_min height_max height_median height_mean volume area area_cartesian_bbox smallest_bounding_width smallest_bounding_length smallest_bounding_area aspect_ratio threshold max_feret min_feret image contour_length circular end_to_end_distance
molecule_number
0 3.2366e-08 1.4036e-08 7.7690e-10 1.2272e-08 6.4301e-09 6.4170e-09 -3.7937e-10 -2.1207e-10 -2.4477e-10 -2.6816e-10 -3.0364e-26 1.1323e-16 3.0066e-16 7.0841e-09 2.1505e-08 1.5234e-16 3.0357e+00 below 2.2092e-08 7.0841e-09 minicircle_small NaN NaN NaN
centre_x centre_y radius_min radius_max radius_mean radius_median height_min height_max height_median height_mean volume area area_cartesian_bbox smallest_bounding_width smallest_bounding_length smallest_bounding_area aspect_ratio threshold max_feret min_feret max_feret_coords min_feret_coords image contour_length circular end_to_end_distance
molecule_number
0 3.2366e-08 1.4036e-08 7.7690e-10 1.2272e-08 6.4301e-09 6.4170e-09 -3.7937e-10 -2.1207e-10 -2.4477e-10 -2.6816e-10 -3.0364e-26 1.1323e-16 3.0066e-16 7.0841e-09 2.1505e-08 1.5234e-16 3.0357e+00 below 2.2092e-08 7.0841e-09 [[10, 5], [0, 0]] [[5.7049180327869, 5.7540983606557], [8.0, 3.0]] minicircle_small NaN NaN NaN
14 changes: 7 additions & 7 deletions tests/_regtest_outputs/test_processing.test_process_scan_both.out
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
image_size_x_m image_size_y_m image_area_m2 image_size_x_px image_size_y_px image_area_px2 grains_number_above grains_per_m2_above grains_number_below grains_per_m2_below rms_roughness
image
image
minicircle_small 1.2646e-07 1.2646e-07 1.5993e-14 64 64 4096 3 1.8758e+14 1 6.2526e+13 6.8208e-10
centre_x centre_y radius_min radius_max radius_mean radius_median height_min height_max height_median height_mean volume area area_cartesian_bbox smallest_bounding_width smallest_bounding_length smallest_bounding_area aspect_ratio threshold max_feret min_feret image contour_length circular end_to_end_distance
molecule_number
0 3.2366e-08 1.4036e-08 7.7690e-10 1.2272e-08 6.4301e-09 6.4170e-09 -3.7937e-10 -2.1207e-10 -2.4477e-10 -2.6816e-10 -3.0364e-26 1.1323e-16 3.0066e-16 7.0841e-09 2.1505e-08 1.5234e-16 3.0357e+00 below 2.2092e-08 7.0841e-09 minicircle_small NaN NaN NaN
0 7.5100e-08 4.7559e-08 3.9431e-09 2.5631e-08 1.6016e-08 1.6680e-08 9.1991e-10 2.6422e-09 1.5338e-09 1.5341e-09 1.0543e-24 6.8721e-16 1.3198e-15 2.0539e-08 5.0379e-08 1.0347e-15 2.4528e+00 above 5.0379e-08 2.0539e-08 minicircle_small 6.0226e-08 0.0000e+00 8.6738e-09
1 8.0241e-08 7.8677e-08 6.8951e-09 2.7188e-08 1.6272e-08 1.6263e-08 9.0630e-10 2.4586e-09 1.6144e-09 1.6264e-09 1.0352e-24 6.3645e-16 1.5931e-15 2.0174e-08 5.1212e-08 1.0332e-15 2.5385e+00 above 5.1262e-08 2.0174e-08 minicircle_small 6.6355e-08 1.0000e+00 0.0000e+00
2 4.0012e-08 7.5644e-08 9.9461e-09 2.3654e-08 1.7561e-08 1.8364e-08 9.0641e-10 2.1066e-09 1.5939e-09 1.5493e-09 1.1192e-24 7.2236e-16 1.5462e-15 3.3592e-08 4.1496e-08 1.3940e-15 1.2353e+00 above 4.4405e-08 3.2528e-08 minicircle_small 9.6106e-08 1.0000e+00 0.0000e+00
centre_x centre_y radius_min radius_max radius_mean radius_median height_min height_max height_median height_mean volume area area_cartesian_bbox smallest_bounding_width smallest_bounding_length smallest_bounding_area aspect_ratio threshold max_feret min_feret max_feret_coords min_feret_coords image contour_length circular end_to_end_distance
molecule_number
0 3.2366e-08 1.4036e-08 7.7690e-10 1.2272e-08 6.4301e-09 6.4170e-09 -3.7937e-10 -2.1207e-10 -2.4477e-10 -2.6816e-10 -3.0364e-26 1.1323e-16 3.0066e-16 7.0841e-09 2.1505e-08 1.5234e-16 3.0357e+00 below 2.2092e-08 7.0841e-09 [[10, 5], [0, 0]] [[5.7049180327869, 5.7540983606557], [8.0, 3.0]] minicircle_small NaN NaN NaN
0 7.5100e-08 4.7559e-08 3.9431e-09 2.5631e-08 1.6016e-08 1.6680e-08 9.1991e-10 2.6422e-09 1.5338e-09 1.5341e-09 1.0543e-24 6.8721e-16 1.3198e-15 2.0539e-08 5.0379e-08 1.0347e-15 2.4528e+00 above 5.0379e-08 2.0539e-08 [[10, 0], [5, 25]] [[10.1923076923077, 15.0384615384615], [0.0, 13.0]] minicircle_small 6.0226e-08 0.0000e+00 8.6738e-09
1 8.0241e-08 7.8677e-08 6.8951e-09 2.7188e-08 1.6272e-08 1.6263e-08 9.0630e-10 2.4586e-09 1.6144e-09 1.6264e-09 1.0352e-24 6.3645e-16 1.5931e-15 2.0174e-08 5.1212e-08 1.0332e-15 2.5385e+00 above 5.1262e-08 2.0174e-08 [[2, 0], [14, 23]] [[10.2518248175182, 6.6824817518248], [1.0, 11.0]] minicircle_small 6.6355e-08 1.0000e+00 0.0000e+00
2 4.0012e-08 7.5644e-08 9.9461e-09 2.3654e-08 1.7561e-08 1.8364e-08 9.0641e-10 2.1066e-09 1.5939e-09 1.5493e-09 1.1192e-24 7.2236e-16 1.5462e-15 3.3592e-08 4.1496e-08 1.3940e-15 1.2353e+00 above 4.4405e-08 3.2528e-08 [[21, 6], [0, 14]] [[10.3313609467456, 15.1952662721894], [4.0, 0.0]] minicircle_small 9.6106e-08 1.0000e+00 0.0000e+00
84 changes: 0 additions & 84 deletions tests/test_grainstats.py
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Expand Up @@ -285,87 +285,3 @@ def test_get_cropped_region(grainstats: GrainStats, length, centre, img_len, exp
output = grainstats.get_cropped_region(image, length, centre)
assert output.shape == (2 * length + 1, 2 * length + 1)
assert output[expected[0], expected[1]] == 5


@pytest.mark.parametrize(
("base_point_1", "base_point_2", "top_point", "expected"),
[
(np.array([0, 0]), np.array([1, 0]), np.array([1, 1]), 1),
(np.array([0, 0]), np.array([5, 0]), np.array([2, 5]), 5),
(np.array([0, 0]), np.array([1, 0]), np.array([1, -1]), 1),
],
)
def test_grainstats_get_triangle_height(base_point_1, base_point_2, top_point, expected) -> None:
"""Tests the GrainStats.get_triangle_height method."""
assert GrainStats.get_triangle_height(base_point_1, base_point_2, top_point) == expected


@pytest.mark.parametrize(
("edge_points", "min_expected", "max_expected"),
[
pytest.param([[0, 0], [0, 1], [1, 0], [1, 1]], 1.0, 1.4142135623730951, id="square"),
pytest.param([[1, 1], [1, 2], [2, 1]], 0.7071067811865476, 1.4142135623730951, id="triangle (isosceles)"),
pytest.param([[0, 0], [1, 0], [0, 2]], 0.8944271909999159, 2.23606797749979, id="triangle"),
pytest.param([[0, 1], [1, 0], [1, 2], [2, 1]], 1.4142135623730951, 2.0, id="circle"),
pytest.param([[1, 2], [2, 1], [2, 4], [5, 2]], 2.4961508830135313, 4, id="quadrilateral"),
pytest.param(
[
[1, 3],
[1, 4],
[1, 5],
[1, 6],
[1, 7],
[2, 2],
[2, 8],
[3, 1],
[3, 9],
[4, 1],
[4, 9],
[5, 1],
[5, 9],
[6, 2],
[6, 8],
[7, 3],
[7, 4],
[7, 5],
[7, 6],
[7, 7],
],
6.0,
8.246211251235321,
id="horizontal ellipse",
),
pytest.param(
[
[1, 2],
[1, 3],
[1, 4],
[2, 1],
[2, 5],
[3, 2],
[3, 6],
[4, 3],
[4, 7],
[5, 4],
[5, 8],
[6, 5],
[6, 6],
[6, 7],
],
2.82842712474619,
7.615773105863909,
id="angled ellipse",
),
pytest.param(
[[1, 5], [2, 3], [2, 4], [3, 2], [4, 1], [5, 1], [6, 2], [6, 3], [7, 4], [7, 5], [7, 6], [8, 7], [8, 8]],
5.252257314388902,
8.06225774829855,
id="curved line",
),
],
)
def test_get_min_max_ferets(edge_points, min_expected, max_expected) -> None:
"""Tests the GrainStats.get_min_max_ferets method."""
min_feret, max_feret = GrainStats.get_max_min_ferets(edge_points)
np.testing.assert_almost_equal(min_feret, min_expected)
np.testing.assert_almost_equal(max_feret, max_expected)
4 changes: 2 additions & 2 deletions tests/test_processing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -419,7 +419,7 @@ def test_process_scan_align_grainstats_dnatracing(
)
tracing_to_check = ["contour_length", "circular", "end_to_end_distance"]

assert results.shape == (3, 25)
assert results.shape == (3, 27)
assert np.isnan(results.loc[2, "contour_length"])
assert np.isnan(sum(results.loc[2, tracing_to_check]))

Expand Down Expand Up @@ -497,7 +497,7 @@ def test_run_grainstats(process_scan_config: dict, tmp_path: Path) -> None:

assert isinstance(grainstats_df, pd.DataFrame)
assert grainstats_df.shape[0] == 13
assert len(grainstats_df.columns) == 21
assert len(grainstats_df.columns) == 23


def test_run_dnatracing(process_scan_config: dict, tmp_path: Path) -> None:
Expand Down
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