fix test

region_grower/synthesize_morphologies.py

@@ -140,12 +140,17 @@ def _parallel_wrapper(
                 if p not in ["x", "y", "z", "orientation", "mtype", "current_depth"]
             },
         )
+        use_boundary = False
+        if "atlas_info" in row and isinstance(row["atlas_info"], str):
+            use_boundary = True
         current_space_context = SpaceContext(
             layer_depths=row["layer_depths"],
             cortical_depths=cortical_depths[row["synthesis_region"]],
-            directions=row["directions"] if "directions" in row else None,
-            boundaries=row["boundaries"] if "boundaries" in row else None,
-            atlas_info=json.loads(row["atlas_info"]) if "atlas_info" in row else None,
+            directions=row["directions"] if "directions" in row and use_boundary else None,
+            boundaries=row["boundaries"] if "boundaries" in row and use_boundary else None,
+            atlas_info=json.loads(row["atlas_info"])
+            if "atlas_info" in row and use_boundary
+            else None,
             soma_position=current_cell.position,
             soma_depth=row["current_depth"],
         )
@@ -570,11 +575,11 @@ def assign_atlas_data(self, min_depth=25, max_depth=5000):  # pylint: disable=to
                 dtype=object,
             )
 
-            if "directions" in self.atlas.region_structure[_region]:
+            if "directions" in self.atlas.region_structure.get(_region, []):
                 self.cells_data.loc[region_mask, "directions"] = json.dumps(
                     self.atlas.region_structure[_region]["directions"]
                 )
-            if "boundaries" in self.atlas.region_structure[_region]:
+            if "boundaries" in self.atlas.region_structure.get(_region, []):
                 boundaries = self.atlas.region_structure[_region]["boundaries"]
                 for boundary in boundaries:
                     if not Path(boundary["path"]).is_absolute():
@@ -589,10 +594,9 @@ def assign_atlas_data(self, min_depth=25, max_depth=5000):  # pylint: disable=to
                         )
 
                 self.cells_data.loc[region_mask, "boundaries"] = json.dumps(boundaries)
-            if (
-                "directions" in self.atlas.region_structure[_region]
-                or "boundaries" in self.atlas.region_structure[_region]
-            ):
+            if "directions" in self.atlas.region_structure.get(
+                _region, []
+            ) or "boundaries" in self.atlas.region_structure.get(_region, []):
                 self.cells_data.loc[region_mask, "atlas_info"] = json.dumps(
                     {
                         "voxel_dimensions": self.atlas.brain_regions.voxel_dimensions.tolist(),

tests/data/apical.yaml

@@ -1,24 +1,24 @@
 14a03569d26b949692e5dfe8cb1855fe:
-- 4.3279709815979
-- 59.805320739746094
-- -0.6919530630111694
+- 4.327972412109375
+- 59.805328369140625
+- -0.69195556640625
 216363698b529b4a97b750923ceb3ffd:
 - -70.52275085449219
 - 129.78277587890625
-- -7.857072830200195
+- -7.8570709228515625
 4462ebfc5f915ef09cfbac6e7687a66e:
-- 1.484359622001648
-- 52.40570831298828
-- -4.806603908538818
+- 1.4843597412109375
+- 52.40570068359375
+- -4.806610107421875
 87751d4ca8501e2c44dcda6a797d76de:
-- 13.616881370544434
-- 252.8784942626953
-- 4.428127288818359
+- 13.61688232421875
+- 252.87850952148438
+- 4.428131103515625
 e3e70682c2094cac629f6fbed82c07cd:
-- -14.571318626403809
-- 114.34882354736328
-- 6.069221019744873
+- -14.571319580078125
+- 114.34881591796875
+- 6.0692138671875
 e8d79f49af6d114c4a6f188a424e617b:
 - -77.39925384521484
-- 345.1856994628906
-- -33.771915435791016
+- 345.18572998046875
+- -33.77191162109375

tests/data/apical_no_axon.yaml

@@ -1,56 +1,56 @@
 14a03569d26b949692e5dfe8cb1855fe:
-- 4.3279709815979
-- 59.805320739746094
-- -0.6919530630111694
+- 4.327972412109375
+- 59.805328369140625
+- -0.69195556640625
 216363698b529b4a97b750923ceb3ffd:
 - -70.52275085449219
 - 129.78277587890625
-- -7.857072830200195
+- -7.8570709228515625
 4462ebfc5f915ef09cfbac6e7687a66e:
-- 1.484359622001648
-- 52.40570831298828
-- -4.806603908538818
+- 1.4843597412109375
+- 52.40570068359375
+- -4.806610107421875
 5bc8fbbcbde5c0994164d8399f767c45:
-- 1.9180573225021362
-- 56.46493911743164
-- -4.888937473297119
+- 1.918060302734375
+- 56.464935302734375
+- -4.8889312744140625
 6018366cf658f7a75ed34fe53a096533:
-- -1.085249662399292
+- -1.0852508544921875
 - 57.62152099609375
 - -4.8218231201171875
 6513270e269e0d37f2a74de452e6b438:
-- 8.458586692810059
+- 8.458587646484375
 - 162.99160766601562
-- 4.474689960479736
+- 4.4746856689453125
 7b89296c6dcbac5008577eb1924770d3:
-- 0.7617863416671753
-- 57.46580123901367
-- 1.8977699279785156
+- 0.76177978515625
+- 57.465789794921875
+- 1.89776611328125
 87751d4ca8501e2c44dcda6a797d76de:
-- 13.616881370544434
-- 252.8784942626953
-- 4.428127288818359
+- 13.61688232421875
+- 252.87850952148438
+- 4.428131103515625
 b8a1abcd1a6916c74da4f9fc3c6da5d7:
 - -84.93132019042969
 - 116.4366455078125
-- -6.362834453582764
+- -6.3628387451171875
 cd613e30d8f16adf91b7584a2265b1f5:
 - -71.48829650878906
 - 137.7943115234375
-- -5.734889030456543
+- -5.734893798828125
 d95bafc8f2a4d27bdcf4bb99f4bea973:
-- 7.555803298950195
-- 96.93486785888672
-- 2.7653095722198486
+- 7.5558013916015625
+- 96.93487548828125
+- 2.7653045654296875
 db5b5fab8f4d3e27dda1494c73cf256d:
-- -3.1312777996063232
+- -3.1312713623046875
 - 57.919647216796875
-- -0.5503649115562439
+- -0.5503692626953125
 e3e70682c2094cac629f6fbed82c07cd:
-- -14.571318626403809
-- 114.34882354736328
-- 6.069221019744873
+- -14.571319580078125
+- 114.34881591796875
+- 6.0692138671875
 e8d79f49af6d114c4a6f188a424e617b:
 - -77.39925384521484
-- 345.1856994628906
-- -33.771915435791016
+- 345.18572998046875
+- -33.77191162109375

tests/data_factories.py

@@ -59,13 +59,13 @@ def generate_region_structure_boundary(
     """Generate region_structure file with boundary entries."""
     with open(region_structure_path, encoding="utf-8") as f:
         structure = yaml.safe_load(f)
-    structure["O0"]["boundaries"] = {"path": mesh}
+    structure["O0"]["boundaries"] = [{"path": mesh}]
 
     if with_sections:
-        structure["O0"]["boundaries"]["params_section"] = {"d_min": 5, "d_max": 50}
+        structure["O0"]["boundaries"][0]["params_section"] = {"d_min": 5, "d_max": 50}
 
     if with_trunks:
-        structure["O0"]["boundaries"]["params_trunk"] = {"d_min": 5, "d_max": 5000}
+        structure["O0"]["boundaries"][0]["params_trunk"] = {"d_min": 5, "d_max": 5000}
 
     with open(out_path, "w", encoding="utf-8") as f:
         yaml.dump(structure, f)