Add basic curvature

tests/test_plottingfuncs.py

@@ -77,6 +77,155 @@ def test_dilate_binary_image(binary_image: np.ndarray, dilation_iterations: int,
 rng = np.random.default_rng()
 
 
+@pytest.mark.mpl_image_compare(baseline_dir="resources/img/")
+def test_plot_curvatures(tmp_path: Path) -> None:
+    """Test plotting of curvatures."""
+    image = np.array(
+        [
+            [0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2],
+            [0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2],
+            [0.1, 0.2, 1.1, 1.1, 1.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2],
+            [0.1, 0.2, 1.1, 0.2, 1.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2],
+            [0.1, 0.2, 1.1, 1.1, 1.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2],
+            [0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2],
+            [0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2],
+            [0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2],
+            [0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.2, 0.1, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2],
+            [0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.2, 1.2, 1.1, 1.1, 1.1, 1.1, 0.2, 0.1],
+            [0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.2, 0.1, 0.1, 1.1, 1.1, 0.2, 0.1, 1.2, 1.1, 0.2],
+            [0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.2, 1.1, 0.2, 0.1, 0.2, 0.1, 1.1, 0.1],
+            [0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.2, 0.1, 0.1, 1.1, 0.1, 0.2, 0.1, 0.2, 1.1, 0.2],
+            [0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.2, 0.1, 1.1, 0.1, 0.2, 0.1, 1.1, 0.1],
+            [0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.2, 0.1, 0.1, 0.2, 1.1, 1.1, 1.1, 1.1, 0.1, 0.2],
+            [0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1],
+        ]
+    )
+
+    cropped_images = {
+        "grain_0": {
+            "original_image": np.array(
+                [
+                    [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+                    [0.0, 0.2, 0.1, 0.2, 0.1, 0.2, 0.0],
+                    [0.0, 0.2, 1.1, 1.1, 1.1, 0.2, 0.0],
+                    [0.0, 0.2, 1.1, 0.2, 1.1, 0.2, 0.0],
+                    [0.0, 0.2, 1.1, 1.1, 1.1, 0.2, 0.0],
+                    [0.0, 0.2, 0.1, 0.2, 0.1, 0.2, 0.0],
+                    [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+                ]
+            ),
+            "bbox": [1, 1, 5, 5],
+            "pad_width": 1,
+        },
+        "grain_1": {
+            "original_image": np.array(
+                [
+                    [0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2],
+                    [0.2, 1.2, 1.1, 1.1, 1.1, 1.1, 0.2, 0.1],
+                    [0.1, 1.1, 1.1, 0.2, 0.1, 1.2, 1.1, 0.2],
+                    [0.2, 1.1, 0.2, 0.1, 0.2, 0.1, 1.1, 0.1],
+                    [0.1, 1.1, 0.1, 0.2, 0.1, 0.2, 1.1, 0.2],
+                    [0.2, 0.1, 1.1, 0.1, 0.2, 0.1, 1.1, 0.1],
+                    [0.1, 0.2, 1.1, 1.1, 1.1, 1.1, 0.1, 0.2],
+                    [0.2, 0.1, 0.2, 0.1, 0.2, 0.1, 0.2, 0.1],
+                ]
+            ),
+            "bbox": [8, 8, 15, 15],
+            "pad_width": 0,
+        },
+    }
+
+    grains_curvture_stats_dict = {
+        "grain_0": {"mol_0": np.array([0.2, 0.0, 0.2, 0.0, 0.2, 0.0, 0.2, 0.0])},
+        "grain_1": {
+            "mol_0": np.array(
+                [
+                    0.1,
+                    0.2,
+                    0.1,
+                    0.2,
+                    0.1,
+                    0.2,
+                    0.1,
+                    0.2,
+                    0.1,
+                    0.2,
+                    0.1,
+                    0.2,
+                    0.1,
+                    0.2,
+                    0.1,
+                    0.2,
+                    0.1,
+                    0.2,
+                ]
+            )
+        },
+    }
+
+    all_grain_smoothed_data = {
+        "grain_0": {
+            "mol_0": {
+                "spline_coords": np.array(
+                    [
+                        [2.5, 2.5],
+                        [2.5, 3.5],
+                        [2.5, 4.5],
+                        [3.5, 4.5],
+                        [4.5, 4.5],
+                        [4.5, 3.5],
+                        [4.5, 2.5],
+                        [3.5, 2.5],
+                    ]
+                ),
+            },
+        },
+        "grain_1": {
+            "mol_0": {
+                "spline_coords": np.array(
+                    [
+                        [1.5, 1.5],
+                        [1.5, 2.5],
+                        [1.5, 3.5],
+                        [1.5, 4.5],
+                        [1.5, 5.5],
+                        [2.5, 5.5],
+                        [2.5, 6.5],
+                        [3.5, 6.5],
+                        [4.5, 6.5],
+                        [5.5, 6.5],
+                        [6.5, 5.5],
+                        [6.5, 4.5],
+                        [6.5, 3.5],
+                        [6.5, 2.5],
+                        [5.5, 2.5],
+                        [4.5, 1.5],
+                        [3.5, 1.5],
+                        [2.5, 1.5],
+                    ],
+                )
+            }
+        },
+    }
+
+    fig, _ = Images(
+        np.array([[0, 0], [0, 0]]),
+        output_dir=tmp_path,
+        filename="Curvature",
+        image_type="non-binary",
+        savefig_dpi=200,
+        core_set=True,
+    ).plot_curvatures(
+        image=image,
+        cropped_images=cropped_images,
+        grains_curvature_stats_dict=grains_curvture_stats_dict,
+        all_grain_smoothed_data=all_grain_smoothed_data,
+        colourmap_normalisation_bounds=[-0.2, 0.2],
+    )
+
+    return fig
+
+
 @pytest.mark.parametrize(
     ("masked_array", "axes_colorbar", "region_properties"),
     [(rng.random((10, 10)), True, None), (None, True, None), (None, False, True)],

tests/test_processing.py

@@ -48,6 +48,7 @@ def test_process_scan_below(regtest, tmp_path, process_scan_config: dict, load_s
         nodestats_config=process_scan_config["nodestats"],
         ordered_tracing_config=process_scan_config["ordered_tracing"],
         splining_config=process_scan_config["splining"],
+        curvature_config=process_scan_config["curvature"],
         plotting_config=process_scan_config["plotting"],
         output_dir=tmp_path,
     )
@@ -76,6 +77,7 @@ def test_process_scan_below_height_profiles(tmp_path, process_scan_config: dict,
         nodestats_config=process_scan_config["nodestats"],
         ordered_tracing_config=process_scan_config["ordered_tracing"],
         splining_config=process_scan_config["splining"],
+        curvature_config=process_scan_config["curvature"],
         plotting_config=process_scan_config["plotting"],
         output_dir=tmp_path,
     )
@@ -110,6 +112,7 @@ def test_process_scan_above(regtest, tmp_path, process_scan_config: dict, load_s
         nodestats_config=process_scan_config["nodestats"],
         ordered_tracing_config=process_scan_config["ordered_tracing"],
         splining_config=process_scan_config["splining"],
+        curvature_config=process_scan_config["curvature"],
         plotting_config=process_scan_config["plotting"],
         output_dir=tmp_path,
     )
@@ -136,6 +139,7 @@ def test_process_scan_above_height_profiles(tmp_path, process_scan_config: dict,
         nodestats_config=process_scan_config["nodestats"],
         ordered_tracing_config=process_scan_config["ordered_tracing"],
         splining_config=process_scan_config["splining"],
+        curvature_config=process_scan_config["curvature"],
         plotting_config=process_scan_config["plotting"],
         output_dir=tmp_path,
     )
@@ -172,6 +176,7 @@ def test_process_scan_both(regtest, tmp_path, process_scan_config: dict, load_sc
         nodestats_config=process_scan_config["nodestats"],
         ordered_tracing_config=process_scan_config["ordered_tracing"],
         splining_config=process_scan_config["splining"],
+        curvature_config=process_scan_config["curvature"],
         plotting_config=process_scan_config["plotting"],
         output_dir=tmp_path,
     )
@@ -226,6 +231,7 @@ def test_save_cropped_grains(
         nodestats_config=process_scan_config["nodestats"],
         ordered_tracing_config=process_scan_config["ordered_tracing"],
         splining_config=process_scan_config["splining"],
+        curvature_config=process_scan_config["curvature"],
         plotting_config=process_scan_config["plotting"],
         output_dir=tmp_path,
     )
@@ -274,6 +280,7 @@ def test_save_format(process_scan_config: dict, load_scan_data: LoadScans, tmp_p
         nodestats_config=process_scan_config["nodestats"],
         ordered_tracing_config=process_scan_config["ordered_tracing"],
         splining_config=process_scan_config["splining"],
+        curvature_config=process_scan_config["curvature"],
         plotting_config=process_scan_config["plotting"],
         output_dir=tmp_path,
     )
@@ -558,58 +565,76 @@ def test_check_run_steps(
         "nodestats_run",
         "ordered_tracing_run",
         "splining_run",
+        "curvature_run",
         "log_msg1",
         "log_msg2",
     ),
     [
         pytest.param(
-            False,
-            False,
-            False,
-            False,
-            False,
-            False,
-            False,
+            False,  # Filters
+            False,  # Grains
+            False,  # Grainstats
+            False,  # Disordered tracing
+            False,  # Nodestats
+            False,  # Ordered tracing
+            False,  # Splining
+            False,  # Curvature
             "You have not included running the initial filter stage.",
             "Please check your configuration file.",
             id="All stages are disabled",
         ),
         pytest.param(
-            True,
-            False,
-            False,
-            False,
-            False,
-            False,
-            False,
+            True,  # Filters
+            False,  # Grains
+            False,  # Grainstats
+            False,  # Disordered tracing
+            False,  # Nodestats
+            False,  # Ordered tracing
+            False,  # Splining
+            False,  # Curvature
             "Detection of grains disabled, GrainStats will not be run.",
             "",
             id="Only filtering enabled",
         ),
         pytest.param(
-            True,
-            True,
-            False,
-            False,
-            False,
-            False,
-            False,
+            True,  # Filters
+            True,  # Grains
+            False,  # Grainstats
+            False,  # Disordered tracing
+            False,  # Nodestats
+            False,  # Ordered tracing
+            False,  # Splining
+            False,  # Curvature
             "Calculation of grainstats disabled, returning empty dataframe and empty height_profiles.",
             "",
             id="Filtering and Grain enabled",
         ),
         pytest.param(
-            True,
-            True,
-            True,
-            False,
-            False,
-            False,
-            False,
+            True,  # Filter
+            True,  # Grains
+            True,  # Grainstats
+            False,  # Disordered Tracing
+            False,  # Nodestats
+            False,  # Ordered tracing
+            False,  # Splining
+            False,  # Curvature
             "Processing grain",
             "Calculation of Disordered Tracing disabled, returning empty dictionary.",
             id="Filtering, Grain and GrainStats enabled",
         ),
+        pytest.param(
+            True,  # Filter
+            True,  # Grains
+            True,  # Grainstats
+            True,  # Disordered Tracing
+            True,  # Nodestats
+            True,  # Ordered tracing
+            True,  # Splining
+            False,  # Curvature
+            "Processing grain",
+            "Calculation of Curvature Stats disabled, returning None.",
+            id="All stages enabled",
+        ),
         # @ns-rse 2024-09-13 : Parameters need updating so test is performed.
         # pytest.param(
         #     True,
@@ -633,6 +658,7 @@ def test_process_stages(
     nodestats_run: bool,
     ordered_tracing_run: bool,
     splining_run: bool,
+    curvature_run: bool,
     log_msg1: str,
     log_msg2: str,
     caplog,
@@ -652,6 +678,7 @@ def test_process_stages(
     process_scan_config["nodestats"]["run"] = nodestats_run
     process_scan_config["ordered_tracing"]["run"] = ordered_tracing_run
     process_scan_config["splining"]["run"] = splining_run
+    process_scan_config["curvature"]["run"] = curvature_run
     _, _, _, _, _, _ = process_scan(
         topostats_object=img_dic["minicircle_small"],
         base_dir=BASE_DIR,
@@ -662,6 +689,7 @@ def test_process_stages(
         nodestats_config=process_scan_config["nodestats"],
         ordered_tracing_config=process_scan_config["ordered_tracing"],
         splining_config=process_scan_config["splining"],
+        curvature_config=process_scan_config["curvature"],
         plotting_config=process_scan_config["plotting"],
         output_dir=tmp_path,
     )
@@ -685,6 +713,7 @@ def test_process_scan_no_grains(process_scan_config: dict, load_scan_data: LoadS
         nodestats_config=process_scan_config["nodestats"],
         ordered_tracing_config=process_scan_config["ordered_tracing"],
         splining_config=process_scan_config["splining"],
+        curvature_config=process_scan_config["curvature"],
         plotting_config=process_scan_config["plotting"],
         output_dir=tmp_path,
     )

topostats/default_config.yaml

@@ -99,6 +99,9 @@ splining:
   spline_linear_smoothing: 5.0 # The amount of smoothing to apply to linear features.
   spline_circular_smoothing: 5.0 # The amount of smoothing to apply to circular features.
   spline_degree: 3 # The polynomial degree of the spline.
+curvature:
+  run: true # Options : true, false
+  colourmap_normalisation_bounds: [-0.5, 0.5] # Radians per nm to normalise the colourmap to.
 plotting:
   run: true # Options : true, false
   style: topostats.mplstyle # Options : topostats.mplstyle or path to a matplotlibrc params file