Diagnostic plotting extension (#304)

* Update example notebook

* Fix validation function

* Initial diagnostic plotting

* DiagnosticPlot class

* Pre-commit changes

* Fix notebook image relative pathing

* Another fix to relative pathing

* Move images to a folder in `/example_workbooks`

* Update dependencies

* Changes to extension

* Fixes to notebook

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Add pinning for `jupyter_bokeh` to avoid unresolvable bug when using older versions

* Add offset for minimum point size in `nasc_map`

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Changes to diagnostic plotting functions

* Changes to diagnostic plotting notebook

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: brandynlucca

docs/_toc.yml

@@ -14,7 +14,8 @@ parts:
     sections:
     - file: example_notebooks/example_echopop_workflow
     - file: example_notebooks/report_generation
-    - file: example_notebooks/plotting.ipynb
+    - file: example_notebooks/plotting
+    - file: example_notebooks/diagnostic_plotting
   - file: theory
     title: Underlying theory
     sections:

docs/example_notebooks/diagnostic_plotting.ipynb

@@ -362,6 +362,9 @@ def krige(input_dict: dict, analysis_dict: dict, settings_dict: dict) -> tuple[p
         arguments and user-defined inputs.
     """
 
+    # Initialize kriging analysis dictionary
+    analysis_dict.update({"kriging": {}})
+
     # Validate cropping method parameters
     validated_cropping_methods = MeshCrop.create(**settings_dict["cropping_parameters"])
     # ---- Update the dictionary
@@ -419,7 +422,16 @@ def krige(input_dict: dict, analysis_dict: dict, settings_dict: dict) -> tuple[p
         )
     else:
         # ---- Compute the cropped mesh
-        mesh_full = crop_mesh(transect_data, mesh_data, validated_cropping_methods)
+        mesh_full, transect_mesh_regions = crop_mesh(
+            transect_data, mesh_data, validated_cropping_methods
+        )
+        # ---- Append 'transect_mesh_regions' to analysis variable
+        analysis_dict["kriging"].update(
+            {
+                "transect_mesh_regions_df": transect_mesh_regions,
+            }
+        )
+        # ---- Print message, if verbose
         if (settings_dict["verbose"]) and (
             validated_cropping_methods["crop_method"] == "convex_hull"
         ):
@@ -453,7 +465,7 @@ def krige(input_dict: dict, analysis_dict: dict, settings_dict: dict) -> tuple[p
         # -------- y
         mesh_full["y"] = mesh_full["latitude"]
     # --- Append to the analysis attribute
-    analysis_dict.update({"kriging": {"mesh_df": mesh_full, "transect_df": transect_data}})
+    analysis_dict["kriging"].update({"mesh_df": mesh_full, "transect_df": transect_data})
 
     # Kriged results
     kriged_results = kriging(

docs/example_notebooks/notebook_images/cropped_kriging_mesh_interactive.png

@@ -1,13 +1,17 @@
-from .survey_extensions import patch_generate_reports as generate_reports
+from .survey_extensions import (
+    patch_diagnostic_plots as diagnostic_plots,
+    patch_generate_reports as generate_reports,
+)
 
 
 # Flex patch import
 def import_all_patches():
+    diagnostic_plots()
     generate_reports()
 
 
 # ---- Automatic import for `import echopop.extensions`
 import_all_patches()
 
 # Exposed individual patches for selective importing
-__all__ = ["generate_reports"]
+__all__ = ["diagnostic_plots", "generate_reports"]