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refactor(grainstats): GrainStats.get_max_min_feret() > measure.feret
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Closes #798

Replaces the functionality for calculating minimum and maximum feret distances within the `GrainStats`  class with the
new `topostats.measure.feret.min_max_feret()`.

+ Reorder dictionary returned by `min_max_feret()`.
+ Dictionary is included in the `stats` dictionary built by `GrainStats` and saved as CSV.
+ Updates `tests/test_grainstats_minicircle.py::test_grainstats_regression` to include the co-ordinates.
+ Updates `tests/test_grainstats.py::test_process_scan*` to include co-ordinates.
+ Removes `GrainStats.get_max_min_feret()` and associated methods that are called as well as their tests.
+ Co-ordinates for min/max feret are included by default in HDF5 output now that they are part of the returned
  dataframe. These are rounded to 13 decimal places to address precision errors encountered on Windows machines running
  the test suite.

Will have to rethink/change how results are returned by `GraintStats` class if height profiles are to be
extracted. Probably most sensible to have profiling as a separate step conducted after GrainStats.
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ns-rse committed Apr 15, 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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@@ -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 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]] [[10.192307692307693, 15.038461538461537], [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]] [[10.251824817518248, 6.6824817518248185], [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]] [[11.183431952662723, 14.840236686390533], [5.0, 0.0]] 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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@@ -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 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]] [[10.192307692307693, 15.038461538461537], [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]] [[10.251824817518248, 6.6824817518248185], [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]] [[10.331360946745562, 15.195266272189349], [4.0, 0.0]] 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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@@ -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 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]] [[5.704918032786886, 5.754098360655739], [8.0, 3.0]] 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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@@ -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 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]] [[5.704918032786886, 5.754098360655739], [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]] [[10.192307692307693, 15.038461538461537], [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]] [[10.251824817518248, 6.6824817518248185], [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]] [[10.331360946745562, 15.195266272189349], [4.0, 0.0]] 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
24 changes: 15 additions & 9 deletions topostats/measure/feret.py
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Original file line number Diff line number Diff line change
Expand Up @@ -197,11 +197,15 @@ def rotating_calipers(points: npt.NDArray, axis: int = 0) -> Generator:
base2 = lower_hull[lower_index] # previous point on lower hull
apex = upper_hull[upper_index] # original upper caliper
counter += 1
yield triangle_height(base1, base2, apex), calipers, np.asarray(
[
list(_min_feret_coord(np.asarray(base1), np.asarray(base2), np.asarray(apex))),
apex,
]
yield (
triangle_height(base1, base2, apex),
calipers,
np.asarray(
[
list(_min_feret_coord(np.asarray(base1), np.asarray(base2), np.asarray(apex))),
apex,
]
),
)


Expand Down Expand Up @@ -324,7 +328,9 @@ def sort_clockwise(coordinates: npt.NDArray) -> npt.NDArray:
return coordinates[order]


def min_max_feret(points: npt.NDArray, axis: int = 0) -> dict[float, tuple[int, int], float, tuple[int, int]]:
def min_max_feret(
points: npt.NDArray, axis: int = 0, precision: int = 13
) -> dict[float, tuple[int, int], float, tuple[int, int]]:
"""
Given a list of 2-D points, returns the minimum and maximum feret diameters.
Expand Down Expand Up @@ -362,8 +368,8 @@ def min_max_feret(points: npt.NDArray, axis: int = 0) -> dict[float, tuple[int,
return {
"max_feret": sqrt(max_feret_sq),
"min_feret": min_feret,
"max_feret_coords": np.asarray(max_feret_coord),
"min_feret_coords": np.asarray(min_feret_coord),
"max_feret_coords": np.asarray(max_feret_coord).round(decimals=precision),
"min_feret_coords": np.asarray(min_feret_coord).round(decimals=precision),
}


Expand Down Expand Up @@ -434,7 +440,7 @@ def plot_feret( # pylint: disable=too-many-arguments,too-many-locals # noqa: C9
show: bool = False,
) -> None:
"""
Plot upper and lower convex hulls with rotating calipers and optionally the minimum feret distances.
Plot upper and lower convex hulls with rotating calipers and optionally the feret distances.
Plot varying levels of details in constructing convex hulls and deriving the minimum and maximum feret.
Expand Down

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