added script for generating napari 3D viewer screenshots

examples/plots/surface_views.py

@@ -0,0 +1,113 @@
+# %%
+from pathlib import Path
+
+import napari
+from brainglobe_utils.IO.image import load_any, load_nii
+
+# %%
+# Define input/output paths
+
+work_dir = Path.home() / "Dropbox/NIU/resources/figures/BlackCap_atlas_v1"
+out_dir = work_dir / "img"
+subject_id = "sub-BC73"
+subject_image_name = f"{subject_id}_asym-brain.nii.gz"
+subject_img_path = work_dir / "data" / subject_image_name
+
+brainglobe_dir = Path.home() / ".brainglobe"
+atlas_name = "oldenburg_blackcap_25um_v1.1"
+average_img_path = brainglobe_dir / atlas_name / "reference.tiff"
+
+# %%
+# Load the images
+
+subject_img = load_nii(subject_img_path, as_array=True, as_numpy=True)
+print("Loaded subject image: ", subject_image_name)
+print("Subject image shape: ", subject_img.shape)
+
+template_img = load_any(average_img_path)
+print("Loaded template image for ", atlas_name)
+print("Template image shape: ", template_img.shape)
+
+# %%
+# Start napari viewer
+viewer = napari.Viewer(ndisplay=3)
+
+# Shared options for image layers
+image_layer_opts = {
+    "rendering": "attenuated_mip",
+    "depiction": "volume",
+}
+
+# Define napari viewer angles for each camera view
+camera_views = dict(
+    front=(0, 0, 90),
+    back=(0, 180, 90),
+    top=(180, 0, 0),
+    bottom=(180, 180, 0),
+    left=(0, 90, 90),
+    right=(0, -90, 90),
+    oblique=(20, -40, 60),
+)
+
+# %%
+# Add the average template image to the viewer
+template_layer = viewer.add_image(
+    template_img,
+    name="average_template",
+    experimental_clipping_planes=[
+        {
+            "position": [210, 0, 0],
+            "normal": [1, 0, 0],
+            "enabled": True,
+        }
+    ],
+    **image_layer_opts,
+)
+
+# %%
+# Take screenshot of the viewer at each pre-defined angle
+for view_name, view_angles in camera_views.items():
+    template_layer.experimental_clipping_planes[0].enabled = (
+        True if view_name == "oblique" else False
+    )
+    template_layer.attenuation = 0.2 if view_name == "oblique" else 0.03
+
+    viewer.camera.angles = view_angles
+    viewer.screenshot(
+        out_dir / f"{template_layer.name}_view-{view_name}.png",
+        canvas_only=True,
+    )
+# Hide the template layer
+template_layer.visible = False
+
+# %%
+# Add the subject image to the viewer
+subject_layer = viewer.add_image(
+    subject_img,
+    name=subject_id,
+    contrast_limits=[50, 2000],
+    experimental_clipping_planes=[
+        {
+            "position": [205, 0, 0],
+            "normal": [1, 0, 0],
+            "enabled": True,
+        }
+    ],
+    **image_layer_opts,
+)
+
+# %%
+# Take screenshot of the viewer at each pre-defined angle
+for view_name, view_angles in camera_views.items():
+    subject_layer.experimental_clipping_planes[0].enabled = (
+        True if view_name == "oblique" else False
+    )
+    subject_layer.attenuation = 0.2 if view_name == "oblique" else 0.03
+
+    viewer.camera.angles = view_angles
+    viewer.screenshot(
+        out_dir / f"{subject_layer.name}_view-{view_name}.png",
+        canvas_only=True,
+    )
+
+# %%