Adds topological features into better tracing

pyproject.toml

@@ -54,6 +54,7 @@ dependencies = [
   "tifffile",
   "AFMReader",
   "tqdm",
+  "topoly",
 ]
 
 [project.optional-dependencies]

topostats/plotting_dictionary.yaml

@@ -125,18 +125,21 @@ mask_grains:
   filename: "17-mask_grains"
   title: "Mask for Grains"
   image_type: "binary"
+  mask_cmap: "binary"
   savefig_dpi: 100
   core_set: false
 labelled_regions_01:
   filename: "18-labelled_regions"
   title: "Labelled Regions"
   image_type: "binary"
+  mask_cmap: "rainbow"
   savefig_dpi: 100
   core_set: false
 tidied_border:
   filename: "19-tidy_borders"
   title: "Tidied Borders"
   image_type: "binary"
+  mask_cmap: "rainbow"
   savefig_dpi: 100
   core_set: false
 removed_noise:
@@ -178,6 +181,7 @@ coloured_boxes:
   filename: "25-labelled_image_bboxes"
   title: "Labelled Image with Bounding Boxes"
   image_type: "binary"
+  mask_cmap: "rainbow"
   savefig_dpi: 100
   core_set: false
 grain_image:
@@ -218,23 +222,30 @@ pruned_skeleton:
   mask_cmap: "blue"
   core_set: false
   savefig_dpi: 600
+branch_indexes:
+  filename: "23-segment_indexes"
+  title: "Skeleton Segment Indexes"
+  image_type: "non-binary"
+  mask_cmap: "viridis"
+  core_set: false
+  savefig_dpi: 600
 branch_types:
-  filename: "23-branch_types"
-  title: "Skeleton Branch Types"
+  filename: "24-segment_types"
+  title: "Skeleton Segment Types"
   image_type: "non-binary"
   mask_cmap: "viridis"
   core_set: false
   savefig_dpi: 600
 # Nodestats troubleshooting images
 convolved_skeletons:
-  filename: "24-convolved_skeleton"
+  filename: "25-convolved_skeleton"
   title: "Skeletons and Nodes"
   image_type: "non-binary"
   mask_cmap: "blue_purple_green"
   core_set: false
   savefig_dpi: 600
 node_centres:
-  filename: "25-node_centres"
+  filename: "26-node_centres"
   title: "Skeletons and Highlighted Nodes"
   image_type: "non-binary"
   mask_cmap: "blue_purple_green"
@@ -276,29 +287,29 @@ ordered_traces:
   core_set: false
   savefig_dpi: 600
 trace_segments:
-  filename: "26-trace_segments"
+  filename: "27-trace_segments"
   title: "Trace Segments"
   image_type: "non-binary"
   mask_cmap: "gist_rainbow"
   savefig_dpi: 600
   core_set: false
 over_under:
-  filename: "27-molecule_crossings"
+  filename: "28-molecule_crossings"
   title: "Visualised Molecule Crossings"
   image_type: "non-binary"
   mask_cmap: "blue_purple_green"
   core_set: false
   savefig_dpi: 600
 all_molecules:
-  filename: "28-all_molecules"
+  filename: "29-all_molecules"
   title: "Individual Molecules"
   image_type: "non-binary"
   mask_cmap: "blue_purple_green"
   savefig_dpi: 600
   core_set: false
 # Splining
 fitted_trace:
-  filename: "27-fitted-traces"
+  filename: "30-fitted-traces"
   title: "Fitted Trace"
   image_type: "non-binary"
   mask_cmap: "blue_purple_green"