WIP adding scale bars

brainglobe_template_builder/plots.py

@@ -215,6 +215,8 @@ def plot_orthographic(
     show_slices: list[int] | None = None,
     pad_sizes: list[tuple[int, int]] | None = None,
     mip_attenuation: float = 0.01,
+    scale_bar: bool = False,
+    resolution: float = 0.025,
     save_path: Path | None = None,
 ) -> tuple[plt.Figure, np.ndarray]:
     """Plot orthographic views of a 3D image,
@@ -258,6 +260,29 @@ def plot_orthographic(
             ax.axhline(slice_idxs[h], color="r", linestyle="--", alpha=0.5)
             ax.axvline(slice_idxs[v], color="r", linestyle="--", alpha=0.5)
 
+        # Add scale bar equal to 1mm to each view
+        if scale_bar:
+            bar_length = 1 / resolution
+            bar_x = frames[j].shape[1] - bar_length - 20
+            bar_y = frames[j].shape[0] - 10
+            ax.plot(
+                [bar_x, bar_x + bar_length],
+                [bar_y, bar_y],
+                color="w",
+                linewidth=2,
+                clip_on=False,
+            )
+            # Add the text on if it's the top view
+            if j == 3:
+                ax.text(
+                    bar_x + bar_length / 2,
+                    bar_y - 5,
+                    "1 mm",
+                    color="w",
+                    ha="center",
+                    va="bottom",
+                )
+
         ax = _clear_spines_and_ticks(ax)
 
     fig.subplots_adjust(
@@ -275,6 +300,8 @@ def plot_inset_comparison(
     y_min: int,
     x_min: int,
     size: int,
+    scale_bar: bool = False,
+    resolution: float = 0.025,
     save_path: Path | None = None,
 ):
     """Plot the same inset from two images side by side.
@@ -325,6 +352,27 @@ def plot_inset_comparison(
         ax.axis("off")
         ax.set_title(name)
 
+        if scale_bar:
+            bar_length = 1 / resolution
+            bar_x = img_inset.shape[1] - bar_length - 5
+            bar_y = img_inset.shape[0] - 5
+            ax.plot(
+                [bar_x, bar_x + bar_length],
+                [bar_y, bar_y],
+                color="w",
+                linewidth=2,
+                clip_on=False,
+            )
+            if i == 1:  # Add the text on the second image only
+                ax.text(
+                    bar_x + bar_length / 2,
+                    bar_y - 2.5,
+                    "1 mm",
+                    color="w",
+                    ha="center",
+                    va="bottom",
+                )
+
     fig.tight_layout()
     if save_path:
         save_figure(fig, save_path.parent, save_path.name.split(".")[0])

examples/plots/template_and_individual.py

@@ -25,7 +25,7 @@
 # Load matplotlib parameters (to allow for proper font export)
 plt.style.use(current_dir / "plots.mplstyle")
 # Load config file containing template building parameters
-config = load_config(current_dir / "config_25um.yaml")
+config = load_config(current_dir / "config_50um.yaml")
 
 # Setup directories based on config file
 atlas_dir, template_dir, plots_dir = setup_directories(config)
@@ -101,6 +101,8 @@
     show_slices=config["show_slices"],
     pad_sizes=pad_sizes,
     mip_attenuation=config["mip_attenuation"],
+    scale_bar=True,
+    resolution=config["resolution_um"] * 1e-3,  # convert to mm
     save_path=plots_dir / "final_template_orthographic",
 )
 print("Plotted final template in orthographic view")
@@ -116,6 +118,8 @@
         show_slices=config["show_slices"],
         pad_sizes=pad_sizes,
         mip_attenuation=config["mip_attenuation"],
+        scale_bar=True,
+        resolution=config["resolution_um"] * 1e-3,  # convert to mm
         save_path=plots_dir / f"{example_subject}_orthographic",
     )
     print(f"Plotted {example_subject} in orthographic view")
@@ -129,5 +133,7 @@
             img2=("template", template_img),
             **inset_param,
             save_path=plots_dir / plot_file_name,
+            scale_bar=True,
+            resolution=config["resolution_um"] * 1e-3,  # convert to mm
         )
     print(f"Plotted inset comparison between {example_subject} and template")