Added "trace_linewidth" parameter to make the spline and curvature thickness user defined for visibility

.pre-commit-config.yaml

@@ -7,6 +7,7 @@ repos:
       - id: check-merge-conflict
       - id: check-toml
       - id: check-yaml
+        args: ["--unsafe"]
       - id: debug-statements
       - id: end-of-file-fixer
         types: [python]

docs/api/logs/index.md

@@ -1,3 +1,3 @@
 # Logs API
 
-[`logs.py`](logs.md)
+[`logs.py`](logs.md)

docs/api/logs/logs.md

@@ -1,3 +1,3 @@
 # Log Modules
 
-::: topostats.logs.logs
+::: topostats.logs.logs

mkdocs.yml

@@ -59,14 +59,14 @@ nav:
       - Grainstats: api/grainstats.md
       - IO: api/io.md
       - Logs:
-        - api/logs/index.md
-        - Logs: api/logs/logs.md
+          - api/logs/index.md
+          - Logs: api/logs/logs.md
       - Measure:
-        - api/measure/index.md
-        - Curvature: api/measure/curvature.md
-        - Feret: api/measure/feret.md
-        - Geometry: api/measure/geometry.md
-        - Height Profiles: api/measure/height_profiles.md
+          - api/measure/index.md
+          - Curvature: api/measure/curvature.md
+          - Feret: api/measure/feret.md
+          - Geometry: api/measure/geometry.md
+          - Height Profiles: api/measure/height_profiles.md
       - Plotting: api/plotting.md
       - PlottingFuncs: api/plottingfuncs.md
       - Processing: api/processing.md
@@ -76,14 +76,14 @@ nav:
       - Theme: api/theme.md
       - Thresholds: api/thresholds.md
       - Tracing:
-        - api/tracing/index.md
-        - Disorderd Tracing: api/tracing/disordered_tracing.md
-        - NodeStats: api/tracing/nodestats.md
-        - Ordered Tracing: api/tracing/ordered_tracing.md
-        - Pruning: api/tracing/pruning.md
-        - Skeletonize: api/tracing/skeletonize.md
-        - Splining: api/tracing/splining.md
-        - Tracing Funcs: api/tracing/tracingfuncs.md
+          - api/tracing/index.md
+          - Disorderd Tracing: api/tracing/disordered_tracing.md
+          - NodeStats: api/tracing/nodestats.md
+          - Ordered Tracing: api/tracing/ordered_tracing.md
+          - Pruning: api/tracing/pruning.md
+          - Skeletonize: api/tracing/skeletonize.md
+          - Splining: api/tracing/splining.md
+          - Tracing Funcs: api/tracing/tracingfuncs.md
       - Utils: api/utils.md
       - Validation: api/validation.md
 
@@ -96,10 +96,10 @@ plugins:
   - search
   - mkdocstrings:
       handlers:
-       python:
-         options:
-           docstring_style: numpy
-           show_signature_annotations: true
+        python:
+          options:
+            docstring_style: numpy
+            show_signature_annotations: true
   - mike:
       version_selector: true
 

tests/__snapshots__/test_classes.ambr

@@ -1274,6 +1274,7 @@
         'savefig_dpi': 100,
         'savefig_format': None,
         'style': 'topostats.mplstyle',
+        'trace_linewidth': 1.0,
         'zrange': list([
           None,
           None,
@@ -2764,6 +2765,7 @@
         'savefig_dpi': 100,
         'savefig_format': None,
         'style': 'topostats.mplstyle',
+        'trace_linewidth': 1.0,
         'zrange': list([
           None,
           None,

topostats/default_config.yaml

@@ -125,6 +125,7 @@ plotting:
     # - curvature
   zrange: [null, null] # low and high height range for core images (can take [null, null]). low <= high
   colorbar: true # Options : true, false
+  trace_linewidth: 1.0 # Linewidth for spline and cuvature traces.
   axes: true # Options : true, false (due to off being a bool when parsed)
   num_ticks: [null, null] # Number of ticks to have along the x and y axes. Options : null (auto) or integer > 1
   cmap: null # Colormap/colourmap to use (default is 'nanoscope' which is used if null, other options are 'afmhot', 'viridis' etc.)

topostats/plottingfuncs.py

@@ -152,7 +152,9 @@ class Images:
     savefig_dpi : str | float, optional
         The resolution of the saved plot (default 'figure').
     number_grains : bool
-            Optionally number each grain in a plot.
+        Optionally number each grain in a plot.
+    trace_linewidth : float
+        Width of lines when plotting splines/curvature.
     """
 
     def __init__(
@@ -184,6 +186,7 @@ def __init__(
         histogram_bins: int | None = None,
         savefig_dpi: str | float | None = None,
         number_grains: bool = False,
+        trace_linewidth: float = 1.0,
     ) -> None:
         """
         Initialise the class.
@@ -251,6 +254,8 @@ def __init__(
             The resolution of the saved plot (default 'figure').
         number_grains : bool
             Optionally number each grain in a plot.
+        trace_linewidth : float
+            Width of lines when plotting splines/curvature.
         """
         if style is None:
             style = "topostats.mplstyle"
@@ -283,6 +288,7 @@ def __init__(
         self.histogram_bins = mpl.rcParams["hist.bins"] if histogram_bins is None else histogram_bins
         self.savefig_dpi = mpl.rcParams["savefig.dpi"] if savefig_dpi is None else savefig_dpi
         self.number_grains = number_grains
+        self.trace_linewidth = trace_linewidth
 
     def plot_histogram_and_save(self) -> tuple | None:
         """
@@ -386,9 +392,8 @@ def plot_curvatures(
                                         (image.shape[0] - (min_row + point[0])) * self.pixel_to_nm_scaling,
                                     ],
                                     color=color,
-                                    linewidth=1,
+                                    linewidth=self.trace_linewidth,
                                 )
-
             # save the figure
             plt.title(self.title)
             plt.xlabel("Nanometres")
@@ -472,9 +477,8 @@ def plot_curvatures_individual_grain(
                                 (grain_crop.image.shape[0] - point[0]) * self.pixel_to_nm_scaling,
                             ],
                             color=colour,
-                            linewidth=3,
+                            linewidth=self.trace_linewidth,
                         )
-
                 plt.title(self.title)
                 plt.xlabel("Nanometres")
                 plt.ylabel("Nanometres")
@@ -566,7 +570,7 @@ def save_figure(self):
                         grain_coords[:, 1] * self.pixel_to_nm_scaling,
                         (shape[0] - grain_coords[:, 0]) * self.pixel_to_nm_scaling,
                         c="c",
-                        linewidth=1,
+                        linewidth=self.trace_linewidth,
                     )
 
             plt.title(self.title)

topostats/validation.py

@@ -479,6 +479,11 @@ def validate_config(config: dict, schema: Schema, config_type: str) -> None:
                 False,
                 error=("Invalid value in config for 'plotting.number_grain_plots', valid values are 'True' or 'False'"),
             ),
+            "trace_linewidth": And(
+                Or(int, float),
+                lambda n: n > 0.0,
+                error=("Invalid value in config for 'plotting.trace_linewidth', valid values are int or float"),
+            ),
         },
         "summary_stats": {
             "run": Or(