Refactor pipeline to use grain crop dictionaries

tests/_regtest_outputs/test_grainstats_minicircle.test_grainstats_regression.out

@@ -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
-grain_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      0.407692     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      0.408213     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      0.809524     above  4.440534e-08  3.176819e-08  None
+              class_number  subgrain_number      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
+grain_number                                                                                                                                                                                                                                                                                                                                                                   
+0                        1                0  3.548872e-08  9.122587e-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      0.407692     above  5.037861e-08  2.053897e-08  None
+1                        1                0  7.238244e-08  1.224246e-07  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      0.408213     above  4.987228e-08  2.017441e-08  None
+2                        1                0  7.755846e-08  1.272332e-07  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      0.809524     above  4.440534e-08  3.176819e-08  None

tests/_regtest_outputs/test_processing.test_process_scan_both.out

@@ -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                                                                                                                                                                                                               
 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  grain_number  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  grain_endpoints  grain_junctions  total_branch_lengths  grain_width_mean  total_contour_length  average_end_to_end_distance
-0 7.5100e-08 4.7559e-08             0  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    4.0769e-01     above 5.0379e-08 2.0539e-08  minicircle_small       1.0000e+00       1.0000e+00            8.4571e-08        8.2685e-09            6.5881e-08                   8.8370e-09
-1 8.0241e-08 7.8677e-08             1  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    3.9394e-01     above 5.1262e-08 2.0174e-08  minicircle_small       0.0000e+00       0.0000e+00            7.3054e-08        7.6154e-09            5.8272e-08                   0.0000e+00
-2 4.0012e-08 7.5644e-08             2  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    8.0952e-01     above 4.4405e-08 3.2528e-08  minicircle_small       0.0000e+00       0.0000e+00            1.0447e-07        7.8033e-09            8.7183e-08                   0.0000e+00
-3 3.2366e-08 1.4036e-08             0  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    3.2941e-01     below 2.2092e-08 7.0841e-09  minicircle_small              NaN              NaN                   NaN               NaN                   NaN                          NaN
+   class_number  subgrain_number  grain_number   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  grain_endpoints  grain_junctions  total_branch_lengths  grain_width_mean  total_contour_length  average_end_to_end_distance
+0             1                0             0 3.7555e-08 8.9055e-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    4.0769e-01     above 5.0379e-08 2.0539e-08  minicircle_small       1.0000e+00       1.0000e+00            8.5729e-08        9.5493e-09            6.7087e-08                   9.4020e-09
+1             1                0             1 7.4313e-08 8.8557e-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    3.9394e-01     above 5.1262e-08 2.0174e-08  minicircle_small       0.0000e+00       0.0000e+00            7.3054e-08        7.6878e-09            5.7989e-08                   0.0000e+00
+2             1                0             2 7.9532e-08 4.0076e-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    8.0952e-01     above 4.4405e-08 3.2528e-08  minicircle_small       0.0000e+00       0.0000e+00            1.0331e-07        7.8754e-09            8.5725e-08                   0.0000e+00
+3             1                0             0 2.0510e-08 2.9845e-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    3.2941e-01     below 2.2092e-08 7.0841e-09  minicircle_small              NaN              NaN                   NaN               NaN                   NaN                          NaN

tests/conftest.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import importlib.resources as pkg_resources
+import pickle
 from pathlib import Path
 from unittest.mock import MagicMock
 
@@ -16,7 +17,7 @@
 
 import topostats
 from topostats.filters import Filters
-from topostats.grains import Grains
+from topostats.grains import GrainCrop, Grains
 from topostats.grainstats import GrainStats
 from topostats.io import LoadScans, read_yaml
 from topostats.plotting import TopoSum
@@ -325,6 +326,59 @@ def random_grains(grains_config: dict, random_filters: Filters) -> Grains:
     return grains
 
 
+@pytest.fixture()
+def dummy_graincrop() -> GrainCrop:
+    """Dummy GrainCrop object for testing."""
+    image = np.random.random((10, 10)).astype(np.float32)
+    mask = np.stack(
+        arrays=[
+            np.array(
+                [
+                    [1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
+                    [1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
+                    [1, 1, 0, 0, 0, 0, 0, 0, 1, 1],
+                    [1, 1, 0, 0, 0, 0, 0, 0, 1, 1],
+                    [1, 1, 0, 0, 0, 0, 0, 0, 1, 1],
+                    [1, 1, 0, 0, 0, 0, 0, 0, 1, 1],
+                    [1, 1, 0, 0, 0, 0, 0, 0, 1, 1],
+                    [1, 1, 0, 0, 0, 0, 0, 0, 1, 1],
+                    [1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
+                    [1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
+                ]
+            ),
+            np.array(
+                [
+                    [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+                    [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+                    [0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
+                    [0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
+                    [0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
+                    [0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
+                    [0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
+                    [0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
+                    [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+                    [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+                ]
+            ),
+        ],
+        axis=-1,
+    )
+    return GrainCrop(
+        image=image,
+        mask=mask,
+        padding=2,
+        bbox=(1, 1, 12, 12),
+        pixel_to_nm_scaling=1.0,
+        filename="dummy",
+    )
+
+
+@pytest.fixture()
+def dummy_graincrops_dict(dummy_graincrop: GrainCrop) -> dict[int, GrainCrop]:
+    """Dummy dictionary of GrainCrop objects for testing."""
+    return {0: dummy_graincrop}
+
+
 @pytest.fixture()
 def small_array_filters(small_array: np.ndarray, load_scan: LoadScans, filter_config: dict) -> Grains:
     """Filters object based on small_array."""
@@ -588,6 +642,14 @@ def minicircle_grain_mask(minicircle_grain_threshold_abs: Grains) -> Grains:
     return minicircle_grain_threshold_abs
 
 
+@pytest.fixture()
+def minicircle_small_graincrops() -> dict[int, GrainCrop]:
+    """Dictionary of graincrops for the minicircle_small image."""
+    with open(RESOURCES / "minicircle_small_graincrops.pkl", "rb") as f:
+        graincrops = pickle.load(f)
+    return graincrops
+
+
 @pytest.fixture()
 def minicircle_grain_clear_border(minicircle_grain_mask: np.array) -> Grains:
     """Cleared borders."""
@@ -682,31 +744,26 @@ def minicircle_grain_coloured(minicircle_grain_labelled_post_removal: np.array)
 
 # Derive fixture for grainstats
 @pytest.fixture()
-def grainstats(image_random: np.array, grainstats_config: dict, tmp_path) -> GrainStats:
+def dummy_grainstats(
+    dummy_graincrops_dict: dict[int, GrainCrop], grainstats_config: dict, tmp_path: Path
+) -> GrainStats:
     """Grainstats class for testing functions."""
     return GrainStats(
-        image_random,
-        image_random,
-        pixel_to_nanometre_scaling=0.5,
+        grain_crops=dummy_graincrops_dict,
         base_output_dir=tmp_path,
         **grainstats_config,
     )
 
 
-# Minicircle
 @pytest.fixture()
 def minicircle_grainstats(
-    minicircle_grain_gaussian_filter: Filters,
-    minicircle_grain_labelled_post_removal: Grains,
-    load_scan: LoadScans,
+    minicircle_small_graincrops: dict[int, GrainCrop],
     grainstats_config: dict,
     tmp_path: Path,
 ) -> GrainStats:
     """GrainStats object."""
     return GrainStats(
-        data=minicircle_grain_gaussian_filter.images["gaussian_filtered"],
-        labelled_data=minicircle_grain_labelled_post_removal.directions["above"]["labelled_regions_02"],
-        pixel_to_nanometre_scaling=load_scan.pixel_to_nm_scaling,
+        grain_crops=minicircle_small_graincrops,
         base_output_dir=tmp_path,
         plot_opts={
             "grain_image": {"core_set": True},

tests/resources/tracing/nodestats/catenanes_nodestats_grainstats.csv

@@ -1,3 +1,3 @@
 ,image,grain_number,num_crossings,avg_crossing_confidence,min_crossing_confidence
-grain_0,test_image,0,4,0.4013589828832889,0.2129989376767838
-grain_1,test_image,1,4,0.3441057054647598,0.17063184531586506
+grain_0,test_image,0,4,0.21426594097881008,0.001258249874731443
+grain_1,test_image,1,4,0.21633024904748463,0.1026576999771045

tests/resources/tracing/ordered_tracing/catenanes_ordered_tracing_grainstats.csv

@@ -1,3 +1,3 @@
 ,image,grain_number,num_mols,writhe_string
 grain_0,catenane,0,2,++++
-grain_1,catenane,1,2,+-++
+grain_1,catenane,1,2,++++

tests/resources/tracing/ordered_tracing/catenanes_ordered_tracing_molstats.csv

@@ -1,5 +1,5 @@
 ,image,grain_number,molecule_number,circular,topology,topology_flip,processing
-0,catenane,0,0,True,L4a1,L2a1,nodestats
-1,catenane,0,1,True,L4a1,L2a1,nodestats
-2,catenane,1,0,True,L2a1,0_1U0_1,nodestats
-3,catenane,1,1,True,L2a1,0_1U0_1,nodestats
+0,catenane,0,0,True,4^2_1,2^2_1,nodestats
+1,catenane,0,1,True,4^2_1,2^2_1,nodestats
+2,catenane,1,0,True,4^2_1,2^2_1,nodestats
+3,catenane,1,1,True,4^2_1,2^2_1,nodestats