TopoStats classes - Grains

The `Grains` class now works with `TopoStats` classes, however...because `GrainCrops` was used in `TopoStats` and this work meant `TopoStats` was used by `Grains` we introduced a circular dependency which Python, reasonably,  complains about. The solution has been to move the class definitions to their own modules `topostats.classes`, but that wasn't without some issues since there are static methods of the `Grains` class that were used _within_ `GrainCrop`. For now these have been moved to the `utils` module and I've started writing tests for them (as they didn't appear to have any).

As a consequence this commit has a lot of things moving around which _will_ make it a pain to review, but hopefully this will be worth it.

For now the whole test suite does _not_ pass all tests because the integration tests where the pipeline is run
end-to-end fails. No attempt has been made to correct this yet because ultimately we would like to simply update the `TopoStats` objects and pass them around and that will only be addressed once each processing step/class has been refactored to work with these.

Subsequent modules should be a little easier to refactor now that the circular dependencies have been broken.

Author: ns-rse

tests/conftest.py

@@ -19,8 +19,11 @@
 from skimage.morphology import skeletonize
 
 import topostats
+from topostats.classes import GrainCrop, GrainCropsDirection, ImageGrainCrops, TopoStats
 from topostats.filters import Filters
-from topostats.grains import GrainCrop, GrainCropsDirection, Grains, ImageGrainCrops
+
+# from topostats.grains import GrainCrop, GrainCropsDirection, Grains, ImageGrainCrops
+from topostats.grains import Grains
 from topostats.grainstats import GrainStats
 from topostats.io import LoadScans, read_yaml
 from topostats.plotting import TopoSum
@@ -472,7 +475,7 @@ def imagegraincrops_catenanes(graincrops_above_catenanes: GrainCropsDirection) -
 @pytest.fixture()
 def topostats_catenanes_2_4_0(imagegraincrops_catenanes) -> topostats.TopoStats:
     """TopoStats object of example catenanes."""
-    return topostats.TopoStats(
+    return TopoStats(
         image_grain_crops=imagegraincrops_catenanes,
         filename="example_catenanes.spm",
         pixel_to_nm_scaling=0.488,
@@ -514,7 +517,7 @@ def imagegraincrops_rep_int(graincrops_above_rep_int: GrainCropsDirection) -> Im
 @pytest.fixture()
 def topostats_rep_int_2_4_0(imagegraincrops_rep_int) -> topostats.TopoStats:
     """TopoStats object of example rep_int."""
-    return topostats.TopoStats(
+    return TopoStats(
         image_grain_crops=imagegraincrops_rep_int,
         filename="example_rep_int.spm",
         pixel_to_nm_scaling=0.488,
@@ -741,10 +744,16 @@ def minicircle_grain_gaussian_filter(minicircle_masked_quadratic_removal: Filter
 @pytest.fixture()
 def minicircle_grains(minicircle_grain_gaussian_filter: Filters, grains_config: dict) -> Grains:
     """Grains object based on filtered minicircle."""
-    return Grains(
+    # TEMPORARY - This will be replaced when we have all modules working and start passing around TopoStats objects in
+    # their entirety
+    topostats_object = TopoStats(
         image=minicircle_grain_gaussian_filter.images["gaussian_filtered"],
         filename=minicircle_grain_gaussian_filter.filename,
         pixel_to_nm_scaling=minicircle_grain_gaussian_filter.pixel_to_nm_scaling,
+        img_path=Path.cwd(),
+    )
+    return Grains(
+        topostats_object=topostats_object,
         **grains_config,
     )
 

tests/test_filters.py

@@ -6,7 +6,7 @@
 import pytest
 from skimage.filters import gaussian  # pylint: disable=no-name-in-module
 
-from topostats import TopoStats
+from topostats.classes import TopoStats
 from topostats.filters import Filters
 
 # pylint: disable=protected-access