Feat: Add Olfactory bulb (#19)

Author: arnaudon

atlas_placement_hints/app/metadata/olfactory_bulb_metadata.json

@@ -0,0 +1,15 @@
+{
+    "region": {
+        "name": "olfactory_bulb",
+        "query": "MOB",
+        "attribute": "acronym",
+        "with_descendants": true
+
+    },
+    "layers": {
+        "names": ["MOBgl", "MOBopl", "MOBmi", "MOBipl", "MOBgr"],
+        "queries": ["MOBgl", "MOBopl", "MOBmi", "MOBipl", "MOBgr"],
+        "attribute": "acronym",
+        "with_descendants": false
+    }
+}

atlas_placement_hints/app/placement_hints.py

@@ -340,3 +340,60 @@ def thalamus(
         output_dir,
         has_hemispheres=True,
     )
+
+
+@app.command()
+@verbose_option
+@common_atlas_options
+@click.option(
+    "--metadata-path",
+    type=EXISTING_FILE_PATH,
+    required=False,
+    help=(
+        "(Optional) Path to the metadata json file. Defaults to "
+        f"`{METADATA_REL_PATH / 'olfactory_bulb_metadata.json'}`"
+    ),
+    default=str(METADATA_PATH / "olfactory_bulb_metadata.json"),
+)
+@click.option(
+    "--direction-vectors-path",
+    type=EXISTING_FILE_PATH,
+    required=True,
+    help=("Path to the olfactory bulb direction vectors file, e.g., `direction_vectors.nrrd`."),
+)
+@click.option(
+    "--output-dir",
+    required=True,
+    help="path of the directory to write. It will be created if it doesn't exist.",
+)
+@log_args(L)
+def olfactory_bulb(
+    verbose, annotation_path, hierarchy_path, metadata_path, direction_vectors_path, output_dir
+):
+    """Generate and save the placement hints of the mouse olfactory bulb.
+    Placement hints are saved under the names sepecified in
+    `app/metadata/olfactory_bulb_metadata.json`.
+    Default to:
+    \b
+    - `[PH]y.nrrd`
+    - `[PH]MOBgl.nrrd`, `[PH]MOBgr.nrrd`, `[PH]MOBipl.nrrd`, `[PH]MOBmi.nrrd`, `[PH]MOBopl.nrrd`,
+    A report together with an nrrd volume on problematic distance computations are generated
+    in `output_dir` under the names:
+    \b
+    - `distance_report.json`
+    - `<olfactory_bulb>_problematic_voxel_mask.nrrd` (mask of the voxels for which the computed
+    placement hints cannot be trusted).  <olfactory_bulb> is the region name specified in
+    olfactory_bulb_metadata.json. Defaults to "olfactory_bulb".
+    The annotation file can contain the olfactory_bulb or a superset.
+    For the algorithm to work properly, some space should separate the boundary
+    of the olfactory_bulb from the boundary of its enclosing array.
+    """
+    set_verbose(L, verbose)
+
+    atlas = _create_layered_atlas(annotation_path, hierarchy_path, metadata_path)
+    _placement_hints(
+        atlas,
+        direction_vectors_path,
+        output_dir,
+        has_hemispheres=True,
+    )