Fix: Update to 3d angles and latest neurots (#10)

BlueBrain · Dec 3, 2024 · 68f549b · 68f549b
1 parent dc9efef
commit 68f549b
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Showing 12 changed files with 233 additions and 235 deletions.
diff --git a/region_grower/context.py b/region_grower/context.py
@@ -43,7 +43,7 @@
 from neuroc.scale import scale_section  # noqa: E402 ; pylint: disable=C0413
 from neurots import NeuronGrower  # noqa: E402 ; pylint: disable=C0413
 from neurots import NeuroTSError  # noqa: E402 ; pylint: disable=C0413
-from neurots.utils import PIA_DIRECTION  # noqa: E402 ; pylint: disable=C0413
+from neurots.utils import Y_DIRECTION  # noqa: E402 ; pylint: disable=C0413
 from voxcell.cell_collection import CellCollection  # noqa: E402 ; pylint: disable=C0413
 
 from region_grower import RegionGrowerError  # noqa: E402 ; pylint: disable=C0413
@@ -85,7 +85,7 @@ def lookup_orientation(self, vector: Optional[Point] = None) -> np.array:
 
         If orientation is None, the direction is assumed towards the pia.
         """
-        return np.dot(self.orientation, vector)[0] if vector else PIA_DIRECTION
+        return np.dot(self.orientation, vector)[0] if vector else Y_DIRECTION
 
 
 @attr.s(auto_attribs=True)
@@ -197,7 +197,7 @@ def _correct_position_orientation_scaling(self, params_orig: Dict) -> Dict:
 
         for neurite_type in params["grow_types"]:
             if isinstance(params[neurite_type]["orientation"], dict):
-                params["pia_direction"] = self.cell.lookup_orientation(PIA_DIRECTION).tolist()
+                params["pia_direction"] = self.cell.lookup_orientation(Y_DIRECTION).tolist()
             if isinstance(params[neurite_type]["orientation"], list):
                 params[neurite_type]["orientation"] = [
                     self.cell.lookup_orientation(orient).tolist()
@@ -249,7 +249,7 @@ def _post_growth_rescaling(self, grower: NeuronGrower, params: Dict) -> None:
 
             scale = modify.output_scaling(
                 root_section,
-                self.cell.orientation.dot(PIA_DIRECTION)[0],
+                self.cell.orientation.dot(Y_DIRECTION)[0],
                 target_min_length=target_min_length,
                 target_max_length=target_max_length,
             )

diff --git a/setup.py b/setup.py
@@ -24,7 +24,7 @@
     "morph-tool[nrn]>=2.9,<3",
     "neuroc>=0.3,<1",
     "neurom>=3,<4",
-    "neurots>=3.6,<4",
+    "neurots>=3.7,<4",
     "numpy>=1.22",
     "pandas>=1.5.3",
     "tqdm>=4.28.1",

diff --git a/tests/data/apical.yaml b/tests/data/apical.yaml
@@ -1,24 +1,24 @@
 14a03569d26b949692e5dfe8cb1855fe:
-- 5.5464959144592285
-- 113.9891357421875
-- -2.365058422088623
+- 4.3279709815979
+- 59.805320739746094
+- -0.6919530630111694
 216363698b529b4a97b750923ceb3ffd:
-- -4.380718231201172
-- 116.65441131591797
-- 6.396718978881836
+- -70.52275085449219
+- 129.78277587890625
+- -7.857072830200195
 4462ebfc5f915ef09cfbac6e7687a66e:
-- -44.474491119384766
-- 68.06861877441406
-- -7.087465286254883
+- 1.484359622001648
+- 52.40570831298828
+- -4.806603908538818
 87751d4ca8501e2c44dcda6a797d76de:
-- 4.237551689147949
-- 369.3919677734375
-- -0.3368062376976013
+- 13.616881370544434
+- 252.8784942626953
+- 4.428127288818359
 e3e70682c2094cac629f6fbed82c07cd:
-- -5.780806541442871
-- 164.6251678466797
-- 0.9229676723480225
+- -14.571318626403809
+- 114.34882354736328
+- 6.069221019744873
 e8d79f49af6d114c4a6f188a424e617b:
-- -28.59885025024414
-- 215.1460723876953
-- -12.506669998168945
+- -77.39925384521484
+- 345.1856994628906
+- -33.771915435791016
diff --git a/tests/data/apical_NRN_sections.yaml b/tests/data/apical_NRN_sections.yaml
@@ -1,12 +1,12 @@
 14a03569d26b949692e5dfe8cb1855fe:
-- 9
+- 3
 216363698b529b4a97b750923ceb3ffd:
-- 9
+- 46
 4462ebfc5f915ef09cfbac6e7687a66e:
-- 12
+- 3
 87751d4ca8501e2c44dcda6a797d76de:
-- 35
+- 6
 e3e70682c2094cac629f6fbed82c07cd:
-- 50
+- 18
 e8d79f49af6d114c4a6f188a424e617b:
-- 20
+- 32
diff --git a/tests/data/apical_NRN_sections_no_axon.yaml b/tests/data/apical_NRN_sections_no_axon.yaml
@@ -1,28 +1,28 @@
 14a03569d26b949692e5dfe8cb1855fe:
-- 9
+- 3
 216363698b529b4a97b750923ceb3ffd:
-- 9
+- 46
 4462ebfc5f915ef09cfbac6e7687a66e:
-- 12
+- 3
 5bc8fbbcbde5c0994164d8399f767c45:
-- 12
+- 3
 6018366cf658f7a75ed34fe53a096533:
-- 49
+- 3
 6513270e269e0d37f2a74de452e6b438:
-- 5
+- 56
 7b89296c6dcbac5008577eb1924770d3:
-- 5
+- 3
 87751d4ca8501e2c44dcda6a797d76de:
-- 35
+- 6
 b8a1abcd1a6916c74da4f9fc3c6da5d7:
-- 10
+- 58
 cd613e30d8f16adf91b7584a2265b1f5:
-- 6
+- 46
 d95bafc8f2a4d27bdcf4bb99f4bea973:
-- 3
+- 11
 db5b5fab8f4d3e27dda1494c73cf256d:
-- 7
+- 5
 e3e70682c2094cac629f6fbed82c07cd:
-- 50
+- 18
 e8d79f49af6d114c4a6f188a424e617b:
-- 20
+- 32
diff --git a/tests/data/apical_no_axon.yaml b/tests/data/apical_no_axon.yaml
@@ -1,56 +1,56 @@
 14a03569d26b949692e5dfe8cb1855fe:
-- 5.5464959144592285
-- 113.9891357421875
-- -2.365058422088623
+- 4.3279709815979
+- 59.805320739746094
+- -0.6919530630111694
 216363698b529b4a97b750923ceb3ffd:
-- -4.380718231201172
-- 116.65441131591797
-- 6.396718978881836
+- -70.52275085449219
+- 129.78277587890625
+- -7.857072830200195
 4462ebfc5f915ef09cfbac6e7687a66e:
-- -44.474491119384766
-- 68.06861877441406
-- -7.087465286254883
+- 1.484359622001648
+- 52.40570831298828
+- -4.806603908538818
 5bc8fbbcbde5c0994164d8399f767c45:
-- -2.684163808822632
-- 112.33018493652344
-- 3.1389687061309814
+- 1.9180573225021362
+- 56.46493911743164
+- -4.888937473297119
 6018366cf658f7a75ed34fe53a096533:
-- -57.31629180908203
-- 105.37586975097656
-- -68.1922836303711
+- -1.085249662399292
+- 57.62152099609375
+- -4.8218231201171875
 6513270e269e0d37f2a74de452e6b438:
-- 0.15954150259494781
-- 112.9250717163086
-- -2.502075672149658
+- 8.458586692810059
+- 162.99160766601562
+- 4.474689960479736
 7b89296c6dcbac5008577eb1924770d3:
-- 0.4192541837692261
-- 57.192779541015625
-- 5.780771255493164
+- 0.7617863416671753
+- 57.46580123901367
+- 1.8977699279785156
 87751d4ca8501e2c44dcda6a797d76de:
-- 4.237551689147949
-- 369.3919677734375
-- -0.3368062376976013
+- 13.616881370544434
+- 252.8784942626953
+- 4.428127288818359
 b8a1abcd1a6916c74da4f9fc3c6da5d7:
-- -4.5237274169921875
-- 114.20574188232422
-- -1.732434630393982
+- -84.93132019042969
+- 116.4366455078125
+- -6.362834453582764
 cd613e30d8f16adf91b7584a2265b1f5:
-- -1.3810073137283325
-- 115.31499481201172
-- -1.1782004833221436
+- -71.48829650878906
+- 137.7943115234375
+- -5.734889030456543
 d95bafc8f2a4d27bdcf4bb99f4bea973:
-- 1.7359588146209717
-- 57.819026947021484
-- 0.7563515901565552
+- 7.555803298950195
+- 96.93486785888672
+- 2.7653095722198486
 db5b5fab8f4d3e27dda1494c73cf256d:
-- -45.093421936035156
-- 75.82533264160156
-- 6.015667915344238
+- -3.1312777996063232
+- 57.919647216796875
+- -0.5503649115562439
 e3e70682c2094cac629f6fbed82c07cd:
-- -5.780806541442871
-- 164.6251678466797
-- 0.9229676723480225
+- -14.571318626403809
+- 114.34882354736328
+- 6.069221019744873
 e8d79f49af6d114c4a6f188a424e617b:
-- -28.59885025024414
-- 215.1460723876953
-- -12.506669998168945
+- -77.39925384521484
+- 345.1856994628906
+- -33.771915435791016
diff --git a/tests/data/debug_data.pkl b/tests/data/debug_data.pkl
diff --git a/tests/data/parameters.json b/tests/data/parameters.json
@@ -7,13 +7,16 @@
                 "has_apical_tuft": true,
                 "metric": "path_distances",
                 "modify": null,
-                "orientation": [
-                    [
-                        0.0,
-                        1.0,
-                        0.0
-                    ]
-                ],
+                "orientation": {
+                    "mode": "normal_pia_constraint",
+                    "values": {
+                        "direction": {
+                            "mean": 0.0,
+                            "std": 0.0
+                        }
+                    }
+                },
+                "radius": 0.3,
                 "randomness": 0.15,
                 "step_size": {
                     "norm": {
@@ -30,7 +33,17 @@
                 "growth_method": "tmd",
                 "metric": "path_distances",
                 "modify": null,
-                "orientation": null,
+                "orientation": {
+                    "mode": "pia_constraint",
+                    "values": {
+                        "form": "step",
+                        "params": [
+                            0.44484279339093336,
+                            0.5461595884090537
+                        ]
+                    }
+                },
+                "radius": 0.3,
                 "randomness": 0.15,
                 "step_size": {
                     "norm": {
@@ -48,8 +61,8 @@
                     "axon": 0.6
             },
             "grow_types": [
-                "basal_dendrite",
-                "apical_dendrite"
+                "apical_dendrite",
+                "basal_dendrite"
             ],
             "origin": [
                 0.0,
@@ -66,13 +79,16 @@
                 "has_apical_tuft": true,
                 "metric": "path_distances",
                 "modify": null,
-                "orientation": [
-                    [
-                        0.0,
-                        1.0,
-                        0.0
-                    ]
-                ],
+                "orientation": {
+                    "mode": "normal_pia_constraint",
+                    "values": {
+                        "direction": {
+                            "mean": 0.0,
+                            "std": 0.0
+                        }
+                    }
+                },
+                "radius": 0.3,
                 "randomness": 0.15,
                 "step_size": {
                     "norm": {
@@ -89,7 +105,17 @@
                 "growth_method": "tmd",
                 "metric": "path_distances",
                 "modify": null,
-                "orientation": null,
+                "orientation": {
+                    "mode": "pia_constraint",
+                    "values": {
+                        "form": "step",
+                        "params": [
+                            0.44484279339093336,
+                            0.5461595884090537
+                        ]
+                    }
+                },
+                "radius": 0.3,
                 "randomness": 0.15,
                 "step_size": {
                     "norm": {
@@ -107,8 +133,8 @@
                     "axon": 0.6
             },
             "grow_types": [
-                "basal_dendrite",
-                "apical_dendrite"
+                "apical_dendrite",
+                "basal_dendrite"
             ],
             "origin": [
                 0.0,

diff --git a/tests/test_cli.py b/tests/test_cli.py
@@ -196,28 +196,28 @@ def test_synthesize_morphologies(
         )
         assert equal_infos.all()
         assert debug_data["apical_sections"].tolist() == [
-            [72],
+            [55],
             None,
-            [23],
+            [46],
             None,
-            [42],
+            [49],
             None,
-            [38],
+            [62],
             None,
-            [67],
-            [74],
+            [34],
+            [49],
         ]
         assert debug_data["apical_NRN_sections"].tolist() == [
-            [50],
+            [18],
             None,
-            [9],
+            [46],
             None,
-            [9],
+            [3],
             None,
-            [12],
+            [3],
             None,
-            [35],
-            [20],
+            [6],
+            [32],
         ]
 
         cols = ["apical_sections", "apical_NRN_sections", "apical_points", "debug_infos"]