Limit thalamus region dirvecs to specific regions (#27)

* Limit thalamus region dirvecs to specific regions

This replaces the region selection of what region direction-vectors are
made for in thalamus with a regular expression. This was scientifically
necessary for exclusion of the habenular and peripeduncular regions, and
code-wise so that the thalamus region selection regex can be harmonized
across all uses. For information on which regions were chosen and how
this list was created, see the internal BBP Confluence page located at
"Circuits > Mouse Thalamus > Atlas-based Whole-thalamus subregion
selection". This regex has been built from the region list of the
desired and present thalamus regions as of the "final" version of the
hierarchy and annotation built by the Atlas pipeline, which is the
output of the rule `split_barrel_ccfv3_l23split`.

* Fix tests and pass linting/etc.

My addition broke the tests because the thalamus regions in the tests
weren't included in my subregion query. This has been fixed.

I also made the changes necessary to pass all the `tox` tests, including
linting, formatting, and general tests.

* Synchronize thalamus regex with placement-hints

---------

Co-authored-by: Austin E. Soplata <[email protected]>

atlas_direction_vectors/thalamus.py

@@ -8,7 +8,7 @@
 
 import numpy as np
 from atlas_commons.typing import BoolArray, NDArray
-from atlas_commons.utils import get_region_mask
+from atlas_commons.utils import get_region_mask, query_region_mask
 from scipy.ndimage import correlate  # type: ignore
 from scipy.ndimage.morphology import generate_binary_structure  # type: ignore
 from voxcell import RegionMap, VoxelData
@@ -63,7 +63,19 @@ def compute_direction_vectors(
         as the input one. Voxels outside the thalamus have np.nan coordinates.
     """
 
-    thalamus_mask = get_region_mask("TH", brain_regions.raw, region_map)
+    # For information on which regions were chosen and how this list was created, see the internal
+    # BBP Confluence page located at "Circuits > Mouse Thalamus > Atlas-based Whole-thalamus
+    # subregion selection".
+    thalamus_query = {
+        "query": "@^(?:AD|AMd|AMv|AV|CL|CM|Eth|IAD|IAM|IGL|IMD|IntG|LD|LGd-co|LGd-ip|LGd-sh|LGv_O|"
+        + "LP|MD_O|MGd|MGm|MGv|PCN|PF|PIL|PO|POL|PR|PT|PVT|PoT|RE|RH|SGN|SMT|SPA|SPFm|SPFp|SubG|"
+        + "TH_O|VAL|VM|VPL|VPLpc|VPM|VPMpc|Xi)$",
+        "attribute": "acronym",
+        "with_descendants": False,
+    }
+
+    thalamus_mask = query_region_mask(thalamus_query, brain_regions.raw, region_map)
+
     reticular_nucleus_mask = get_region_mask("RT", brain_regions.raw, region_map)
     reticular_nucleus_complement_mask = np.logical_and(thalamus_mask, ~reticular_nucleus_mask)
     common_outer_boundary_mask = _get_common_outer_boundary(thalamus_mask, reticular_nucleus_mask)

tests/app/test_direction_vectors.py

@@ -20,7 +20,7 @@ def test_thalamus():
     with runner.isolated_filesystem():
         voxel_data = create_voxeldata(
             718,  # VPL, Ventral posterolateral nucleus of the thalamus
-            709,  # VPM, Ventral posteromedial nucleus of the thalamus
+            733,  # VPM, Ventral posteromedial nucleus of the thalamus
         )
         voxel_data.save_nrrd("annotation.nrrd")
         result = runner.invoke(

tests/test_thalamus.py

@@ -66,8 +66,8 @@ def test_get_common_outer_boundary():
 
 def test_compute_direction_vectors(region_map):
     voxel_data = create_voxeldata(
-        685,  # VM, Ventral medial nucleus of the thalamus
-        709,  # VP, Ventral posterior complex of the thalamus
+        718,  # VPL, Ventral posterolateral nucleus of the thalamus
+        733,  # VPM, Ventral posteromedial nucleus of the thalamus
     )
     with warnings.catch_warnings(record=True) as warnings_:
         direction_vectors = tested.compute_direction_vectors(region_map, voxel_data)