feat: add points with properties

Author: seankmartin

examples/write_points_with_properties.py

@@ -0,0 +1,151 @@
+import argparse
+import os
+import shutil
+
+import neuroglancer
+import neuroglancer.cli
+import neuroglancer.static_file_server
+import neuroglancer.write_annotations
+import numpy as np
+
+
+def write_some_annotations(
+    output_dir: str, coordinate_space: neuroglancer.CoordinateSpace
+):
+    properties = [
+        neuroglancer.AnnotationPropertySpec(
+            id="color",
+            description="Color of the annotation",
+            type="rgb",
+            default="#ff0000",  # red
+        ),
+        neuroglancer.AnnotationPropertySpec(
+            id="size",
+            description="Size of the annotation",
+            type="float32",
+            default=10,
+        ),
+        neuroglancer.AnnotationPropertySpec(
+            id="p_int8",
+            type="int8",
+            default=10,
+        ),
+        neuroglancer.AnnotationPropertySpec(
+            id="p_uint8",
+            type="uint8",
+            default=10,
+        ),
+        neuroglancer.AnnotationPropertySpec(
+            id="rgba_color",
+            type="rgba",
+            default="#00ff00ff",  # green with full opacity
+        ),
+        neuroglancer.AnnotationPropertySpec(
+            id="p_enum1",
+            type="uint16",
+            default=0,
+            enum_values=[0, 1, 2, 3],
+            enum_labels=[
+                "Option 0",
+                "Option 1",
+                "Option 2",
+                "Option 3",
+            ],
+        ),
+        neuroglancer.AnnotationPropertySpec(
+            id="p_fnum32",
+            type="float32",
+            default=0.0,
+            description="A float number property",
+            enum_values=[0.0, 1.5, 2.6, 3.0],
+            enum_labels=[
+                "Zero",
+                "One and a half",
+                "Two point six",
+                "Three",
+            ],
+        ),
+    ]
+
+    writer = neuroglancer.write_annotations.AnnotationWriter(
+        coordinate_space=coordinate_space,
+        annotation_type="point",
+        properties=properties,
+    )
+
+    writer.add_point(
+        [20, 30, 40],
+        color=(0, 255, 0),  # RGB color
+        size=10,
+        p_int8=1,
+        p_uint8=2,
+        rgba_color=(0, 255, 0, 255),  # RGBA color with full opacity
+        p_enum1=1,
+        p_fnum32=1.5,
+    )
+    writer.add_point(
+        [50, 51, 52],
+        color=(255, 0, 0),  # RGB color
+        size=30,
+        p_int8=2,
+        p_uint8=3,
+        rgba_color=(255, 0, 0, 255),  # RGBA color with full opacity
+        p_enum1=2,
+        p_fnum32=2.6,
+    )
+    writer.add_point(
+        [40, 50, 52],
+        color=(0, 0, 255),  # RGB color
+        size=20,
+        p_int8=3,
+        p_uint8=4,
+        rgba_color=(0, 200, 255, 14),  # RGBA color with part opacity
+        p_enum1=3,
+        p_fnum32=3.0,
+    )
+    writer.add_point([40, 50, 52])
+    writer.write(os.path.join(output_dir, "point"))
+
+
+if __name__ == "__main__":
+    ap = argparse.ArgumentParser()
+    neuroglancer.cli.add_server_arguments(ap)
+    args = ap.parse_args()
+    neuroglancer.cli.handle_server_arguments(args)
+    viewer = neuroglancer.Viewer()
+
+    tempdir = "/tmp/neuroglancer_annotations"
+    if os.path.exists(tempdir):
+        shutil.rmtree(tempdir)
+    os.makedirs(tempdir)
+
+    coordinate_space = neuroglancer.CoordinateSpace(
+        names=["x", "y", "z"], units=["nm", "nm", "nm"], scales=[10, 10, 10]
+    )
+    write_some_annotations(output_dir=tempdir, coordinate_space=coordinate_space)
+
+    server = neuroglancer.static_file_server.StaticFileServer(
+        static_dir=tempdir, bind_address=args.bind_address or "127.0.0.1", daemon=True
+    )
+
+    with viewer.txn() as s:
+        s.layers["image"] = neuroglancer.ImageLayer(
+            source=neuroglancer.LocalVolume(
+                data=np.full(fill_value=200, shape=(100, 100, 100), dtype=np.uint8),
+                dimensions=coordinate_space,
+            ),
+        )
+        s.layers["points"] = neuroglancer.AnnotationLayer(
+            source=f"precomputed://{server.url}/point",
+            tab="rendering",
+            shader="""
+void main() {
+  setColor(prop_color());
+  setPointMarkerSize(prop_size());
+}
+        """,
+        )
+        s.selected_layer.layer = "points"
+        s.selected_layer.visible = True
+        s.show_slices = False
+    print(viewer)