From 47fd1ce6d4cd45e6e9197fc5f2778eb56f4fe76f Mon Sep 17 00:00:00 2001
From: arnaudon <alexis.arnaudon@epfl.ch>
Date: Wed, 4 Dec 2024 17:25:12 +0100
Subject: [PATCH] fix test

---
 region_grower/synthesize_morphologies.py |  22 ++--
 tests/data/apical.yaml                   |  30 ++---
 tests/data/apical_no_axon.yaml           |  62 +++++------
 tests/data/debug_data.pkl                | Bin 6720 -> 6930 bytes
 tests/data_factories.py                  |   6 +-
 tests/test_context.py                    | 134 +++++++++++++----------
 tests/test_synthesize_morphologies.py    |  64 +++--------
 7 files changed, 154 insertions(+), 164 deletions(-)

diff --git a/region_grower/synthesize_morphologies.py b/region_grower/synthesize_morphologies.py
index 052823b..ae11bea 100644
--- a/region_grower/synthesize_morphologies.py
+++ b/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(),
diff --git a/tests/data/apical.yaml b/tests/data/apical.yaml
index a27668e..283c669 100644
--- a/tests/data/apical.yaml
+++ b/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
diff --git a/tests/data/apical_no_axon.yaml b/tests/data/apical_no_axon.yaml
index 98737a0..5371cd3 100644
--- a/tests/data/apical_no_axon.yaml
+++ b/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
diff --git a/tests/data/debug_data.pkl b/tests/data/debug_data.pkl
index b521d09bf153f90e65b73070bdcf032598214882..404efd9d1ebf9d4de68a5afb80651163314d0507 100644
GIT binary patch
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diff --git a/tests/data_factories.py b/tests/data_factories.py
index 144b12b..1735b60 100644
--- a/tests/data_factories.py
+++ b/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)
diff --git a/tests/test_context.py b/tests/test_context.py
index 6e32b00..5b2e91a 100644
--- a/tests/test_context.py
+++ b/tests/test_context.py
@@ -89,6 +89,10 @@ def test_distance_to_constraint(self, space_context):
         assert space_context.distance_to_constraint(-100, {"layer": 6, "fraction": 0}) == -900
         assert space_context.distance_to_constraint(1000, {"layer": 6, "fraction": 0}) == 200
 
+        for i in [np.nan, None, []]:
+            space_context.layer_depths = i
+            assert space_context.distance_to_constraint(1000, {"layer": 6, "fraction": 0}) is None
+
     def test_indices_to_positions(self, space_context):
         pos = space_context.indices_to_positions([0, 0, 0])
         assert_array_equal(pos, [-1100.0, -100.0, -1000.0])
@@ -124,17 +128,18 @@ def test_context(self, cell_state, space_context, synthesis_parameters, computat
             "mode": "normal_pia_constraint",
             "values": {"direction": {"mean": 0.0, "std": 0.0}},
         }
+
         assert_array_almost_equal(
             result.neuron.soma.points,
             np.array(
                 [
-                    [-4.4719658e00, -5.5439525e00, 0.0000000e00],
-                    [7.6192994e00, 5.0967985e-01, 0.0000000e00],
-                    [2.7471251e00, 7.1250825e00, 0.0000000e00],
-                    [4.6759019e-16, 7.6363273e00, 0.0000000e00],
-                    [-5.3491087e00, 5.4498196e00, 0.0000000e00],
-                    [-7.3899293e00, -1.5310667e00, 0.0000000e00],
-                    [-6.1610136e00, -3.6210527e00, 0.0000000e00],
+                    [-4.4719658e00, -5.5439453e00, 0.0000000e00],
+                    [7.6192994e00, 5.0967407e-01, 0.0000000e00],
+                    [2.7471251e00, 7.1250916e00, 0.0000000e00],
+                    [4.6759019e-16, 7.6363220e00, 0.0000000e00],
+                    [-5.3491087e00, 5.4498291e00, 0.0000000e00],
+                    [-7.3899293e00, -1.5310669e00, 0.0000000e00],
+                    [-6.1610136e00, -3.6210632e00, 0.0000000e00],
                 ],
                 dtype=np.float32,
             ),
@@ -144,9 +149,9 @@ def test_context(self, cell_state, space_context, synthesis_parameters, computat
             next(result.neuron.iter()).points,
             np.array(
                 [
-                    [-7.3899293, -1.5310667, -1.165452],
-                    [-8.706363, -1.8038092, -1.3730644],
-                    [-10.090032, -2.006144, -1.4496313],
+                    [-7.389929294586182, -1.53106689453125, -1.165452003479004],
+                    [-8.7063627243042, -1.803802490234375, -1.373064398765564],
+                    [-10.090031623840332, -2.006134033203125, -1.4496313333511353],
                 ],
                 dtype=np.float32,
             ),
@@ -182,45 +187,40 @@ def test_context_external_diametrizer(
         result = context_worker.synthesize()
 
         assert_array_equal(result.apical_sections, np.array([48]))
-        assert_array_almost_equal(
-            result.apical_points,
-            np.array([[20.272340774536133, 266.1555480957031, 6.746281147003174]]),
-        )
+        assert_array_almost_equal(result.apical_points, np.array([[20.27234, 266.15558, 6.746281]]))
 
         # This tests that input orientations are not mutated by the synthesize() call
         assert_array_almost_equal(
             synthesis_parameters.tmd_parameters["apical_dendrite"]["orientation"], [[0.0, 1.0, 0.0]]
         )
-
         assert_array_almost_equal(
             result.neuron.soma.points,
             np.array(
                 [
-                    [-5.785500526428223, 4.9841227531433105, 0.0],
-                    [-7.5740227699279785, -0.9734848141670227, 0.0],
-                    [-1.966903805732727, -7.378671169281006, 0.0],
-                    [3.565324068069458, -6.752922534942627, 0.0],
-                    [7.266839027404785, -2.346604108810425, 0.0],
-                    [7.384983062744141, 1.059786081314087, 0.0],
-                    [6.818241119384766, 3.4387624263763428, 0.0],
-                    [4.675901919111924e-16, 7.636327266693115, 0.0],
+                    [-5.785500526428223, 4.984130859375, 0.0],
+                    [-7.5740227699279785, -0.973480224609375, 0.0],
+                    [-1.966903805732727, -7.378662109375, 0.0],
+                    [3.565324068069458, -6.7529296875, 0.0],
+                    [7.266839027404785, -2.34661865234375, 0.0],
+                    [7.384983062744141, 1.059783935546875, 0.0],
+                    [6.818241119384766, 3.438751220703125, 0.0],
+                    [4.675901919111924e-16, 7.636322021484375, 0.0],
                 ],
                 dtype=np.float32,
             ),
         )
 
         assert len(result.neuron.root_sections) == 4
-
         assert_array_almost_equal(
             next(result.neuron.iter()).points,
             np.array(
                 [
-                    [-1.8836766, -3.876395, 6.3038735],
-                    [-2.0679207, -4.2555485, 6.9204607],
-                    [-2.2532284, -4.607763, 7.632429],
-                    [-2.4301565, -5.4218144, 8.747698],
-                    [-2.7331889, -6.253548, 9.650066],
-                    [-2.960198, -6.9949017, 10.46672],
+                    [-1.8836766481399536, -3.87640380859375, 6.303873538970947],
+                    [-2.067920684814453, -4.25555419921875, 6.9204607009887695],
+                    [-2.2532284259796143, -4.607757568359375, 7.632429122924805],
+                    [-2.4301564693450928, -5.42181396484375, 8.747697830200195],
+                    [-2.7331888675689697, -6.2535400390625, 9.650066375732422],
+                    [-2.960197925567627, -6.994903564453125, 10.466719627380371],
                 ],
                 dtype=np.float32,
             ),
@@ -266,22 +266,22 @@ def test_scale(self, small_context_worker, tmd_parameters):
                 for neu in result1.neuron.root_sections
             ],
             [
-                [[-7.38993, -1.531067, -1.165452], [-10.090032, -2.006144, -1.449631]],
+                [[-7.38993, -1.531067, -1.165452], [-10.090032, -2.006134, -1.449631]],
                 [
-                    [0.0000000e00, 7.6363282e00, 0.0000000e00],
-                    [-1.3458900e-01, 1.0937219e01, -4.8300001e-04],
+                    [0.0000000e00, 7.6363220e00, 0.0000000e00],
+                    [-1.3458900e-01, 1.0937225e01, -4.8300001e-04],
                 ],
-                [[-4.471966, -5.543952, -2.753109], [-10.985586, -11.732729, -7.093396]],
-                [[-6.161014, -3.621053, -2.691354], [-13.246824, -8.409419, -7.309253]],
-                [[2.8443, 5.418238, -4.567948], [6.907934, 20.718624, -14.104201]],
-                [[-4.320479, 2.283079, 5.868092], [-14.584823, 10.624202, 20.95233]],
-                [[-1.976977, 0.131083, -7.374814], [-7.476844, -0.560946, -41.175533]],
+                [[-4.471966, -5.543946, -2.753109], [-10.985586, -11.732727, -7.093396]],
+                [[-6.161014, -3.621063, -2.691354], [-13.246824, -8.409424, -7.309253]],
+                [[2.8443, 5.418244, -4.567948], [6.907934, 20.718628, -14.104201]],
+                [[-4.320479, 2.283081, 5.868092], [-14.584823, 10.624207, 20.95233]],
+                [[-1.976977, 0.131073, -7.374814], [-7.476844, -0.560944, -41.175533]],
             ],
         )
 
         assert_array_equal(result1.apical_sections, np.array([29]))
         assert_array_almost_equal(
-            result1.apical_points, np.array([[5.711923, 56.423206, 4.124067]])
+            result1.apical_points, np.array([[5.711923, 56.423218, 4.124067]])
         )
 
         # Test with no hard limit scaling for basal
@@ -313,13 +313,13 @@ def test_scale(self, small_context_worker, tmd_parameters):
                 for neu in result2.neuron.root_sections
             ],
             [
-                [[-7.38993, -1.531067, -1.165452], [-10.090032, -2.006144, -1.449631]],
-                [[-4.471966, -5.543952, -2.753109], [-8.223286, -9.750789, -4.556392]],
-                [[-4.320479, 2.283079, 5.868092], [-7.893101, 5.56567, 11.433157]],
-                [[2.8443, 5.418238, -4.567948], [5.717189, 11.469478, -8.845925]],
-                [[0.0, 7.636328, 0.0], [-0.592816, 17.272392, 0.240599]],
-                [[-6.161014, -3.621053, -2.691354], [-14.194309, -7.956396, -5.834008]],
-                [[-1.976977, 0.131083, -7.374814], [-5.85143, 2.059288, -21.650974]],
+                [[-7.38993, -1.531067, -1.165452], [-10.090032, -2.006134, -1.449631]],
+                [[-4.471966, -5.543946, -2.753109], [-8.223286, -9.750793, -4.556392]],
+                [[-4.320479, 2.283081, 5.868092], [-7.893101, 5.565674, 11.433157]],
+                [[2.8443, 5.418244, -4.567948], [5.717189, 11.469482, -8.845925]],
+                [[0.0, 7.636322, 0.0], [-0.592816, 17.2724, 0.240599]],
+                [[-6.161014, -3.621063, -2.691354], [-14.194309, -7.95639, -5.834008]],
+                [[-1.976977, 0.131073, -7.374814], [-5.85143, 2.059296, -21.650974]],
             ],
         )
 
@@ -351,23 +351,41 @@ def test_scale(self, small_context_worker, tmd_parameters):
                 for neu in result3.neuron.root_sections
             ],
             [
-                [[-7.38993, -1.531067, -1.165452], [-10.090032, -2.006144, -1.449631]],
                 [
-                    [0.0000000e00, 7.6363282e00, 0.0000000e00],
-                    [-1.2766400e-01, 1.0767367e01, -4.5900000e-04],
+                    [-7.38992977142334, -1.5310670137405396, -1.165452003479004],
+                    [-10.090031623840332, -2.006134033203125, -1.4496309757232666],
+                ],
+                [
+                    [0.0, 7.636322021484375, 0.0],
+                    [-0.1276639997959137, 10.767373085021973, -0.00045900000259280205],
+                ],
+                [
+                    [-4.471965789794922, -5.543945789337158, -2.7531089782714844],
+                    [-10.985586166381836, -11.73272705078125, -7.093396186828613],
+                ],
+                [
+                    [-6.161014080047607, -3.621062994003296, -2.6913540363311768],
+                    [-13.246824264526367, -8.409423828125, -7.309253215789795],
+                ],
+                [
+                    [2.8443000316619873, 5.418243885040283, -4.567947864532471],
+                    [6.907934188842773, 20.7186279296875, -14.104201316833496],
+                ],
+                [
+                    [-4.320478916168213, 2.2830810546875, 5.868092060089111],
+                    [-14.584822654724121, 10.62420654296875, 20.952329635620117],
+                ],
+                [
+                    [-1.976976990699768, 0.131072998046875, -7.374814033508301],
+                    [-7.47684383392334, -0.5609440207481384, -41.175533294677734],
                 ],
-                [[-4.471966, -5.543952, -2.753109], [-10.985586, -11.732729, -7.093396]],
-                [[-6.161014, -3.621053, -2.691354], [-13.246824, -8.409419, -7.309253]],
-                [[2.8443, 5.418238, -4.567948], [6.907934, 20.718624, -14.104201]],
-                [[-4.320479, 2.283079, 5.868092], [-14.584823, 10.624202, 20.95233]],
-                [[-1.976977, 0.131083, -7.374814], [-7.476844, -0.560946, -41.175533]],
             ],
         )
 
         assert_array_equal(result3.apical_sections, np.array([29]))
         assert_array_almost_equal(
             result3.apical_points,
-            np.array([[5.418009, 53.912827, 3.911858]]),
+            np.array([[5.418009, 53.91283, 3.911858]]),
         )
 
         # Test scale computation
@@ -430,10 +448,6 @@ def test_scale(self, small_context_worker, tmd_parameters):
 
         params["basal_dendrite"]["orientation"] = {}
 
-        # pylint: disable=protected-access
-        fixed_params = small_context_worker._correct_position_orientation_scaling(params)
-        assert fixed_params["pia_direction"] == Y_DIRECTION
-
     def test_debug_scales(self, small_context_worker, tmd_parameters):
         """Test debug logger."""
         mtype = small_context_worker.cell.mtype
@@ -562,5 +576,5 @@ def test_retry(
 
         assert_array_equal(result.apical_sections, np.array([81]))
         assert_array_almost_equal(
-            result.apical_points, [[-109.65276, 181.05916, -94.54867]], decimal=5
+            result.apical_points, [[-109.65276, 181.05914, -94.54867]], decimal=5
         )
diff --git a/tests/test_synthesize_morphologies.py b/tests/test_synthesize_morphologies.py
index a741e64..831fa9a 100644
--- a/tests/test_synthesize_morphologies.py
+++ b/tests/test_synthesize_morphologies.py
@@ -181,6 +181,7 @@ def test_synthesize_empty_population(
         None,
         None,
         25,
+        DATA / "region_structure.yaml",
     )
     # Update population to make it empty
     cells = CellCollection.load(args["input_cells"])
@@ -308,16 +309,16 @@ def test_synthesize_skip_write(
         "e8d79f49af6d114c4a6f188a424e617b",
     ]
     assert [[i[0].tolist()] if i else i for i in res["apical_points"].tolist()] == [
-        [[-14.571318626403809, 114.34882354736328, 6.069221019744873]],
+        [[-14.571319580078125, 114.34881591796875, 6.0692138671875]],
         None,
-        [[-70.52275085449219, 129.78277587890625, -7.857072830200195]],
+        [[-70.52275085449219, 129.78277587890625, -7.8570709228515625]],
         None,
-        [[4.3279709815979, 59.805320739746094, -0.6919530630111694]],
+        [[4.327972412109375, 59.805328369140625, -0.69195556640625]],
         None,
-        [[1.484359622001648, 52.40570831298828, -4.806603908538818]],
+        [[1.4843597412109375, 52.40570068359375, -4.806610107421875]],
         None,
-        [[13.616881370544434, 252.8784942626953, 4.428127288818359]],
-        [[-77.39925384521484, 345.1856994628906, -33.771915435791016]],
+        [[13.61688232421875, 252.87850952148438, 4.428131103515625]],
+        [[-77.39925384521484, 345.18572998046875, -33.77191162109375]],
     ]
 
     # Check that the morphologies were not written
@@ -331,16 +332,12 @@ def test_synthesize_skip_write(
     ]
 
 
-@pytest.mark.parametrize("with_sections", [True, False])
-@pytest.mark.parametrize("with_trunks", [True, False])
 def test_synthesize_boundary(
     tmpdir,
     small_O1_path,
     input_cells,
     axon_morph_tsv,
     mesh,
-    with_sections,
-    with_trunks,
 ):  # pylint: disable=unused-argument,too-many-locals
     """Test morphology synthesis but skip write step."""
     with_axon = True
@@ -353,7 +350,7 @@ def test_synthesize_boundary(
 
     region_structure = "region_structure.yaml"
     generate_region_structure_boundary(
-        DATA / "region_structure.yaml", region_structure, mesh, with_sections, with_trunks
+        DATA / "region_structure.yaml", region_structure, mesh, with_sections=True, with_trunks=True
     )
     args = create_args(
         False,
@@ -382,45 +379,20 @@ def test_synthesize_boundary(
         None,
         "4462ebfc5f915ef09cfbac6e7687a66e",
         None,
+        "87751d4ca8501e2c44dcda6a797d76de",
+        "e8d79f49af6d114c4a6f188a424e617b",
     ]
-    if with_sections and with_trunks:
-        assert_allclose(res["apical_points"][0], [[16.126877, 160.5279, 22.8638]])
-        assert res["apical_points"][1] is None
-
-        assert_allclose(res["apical_points"][3], [[5.216095, 114.55658, -12.494751]])
-        assert res["apical_points"][4] is None
-
-        assert_allclose(res["apical_points"][6], [[4.36911, 55.535736, -6.2556915]])
-        assert res["apical_points"][7] is None
-
-        assert_allclose(res["apical_points"][9], [[-11.084274, 111.49124, 0.98043823]])
-        assert res["apical_points"][10] is None
-
-    if with_sections and not with_trunks:
-        assert_allclose(res["apical_points"][0], [[-0.29234314, 58.81488, 0.5384369]])
-        assert res["apical_points"][1] is None
-
-        assert_allclose(res["apical_points"][3], [[8.230438, 116.570435, -7.345169]])
-        assert res["apical_points"][4] is None
-
-        assert_allclose(res["apical_points"][6], [[11.181992, 96.11371, -12.706863]])
-        assert res["apical_points"][7] is None
-
-        assert_allclose(res["apical_points"][9], [[3.5267944, 164.42618, 1.2018433]])
-        assert res["apical_points"][10] is None
-
-    if not with_sections and with_trunks:
-        assert_allclose(res["apical_points"][0], [[8.792313, 131.91104, -4.2198334]])
-        assert res["apical_points"][1] is None
+    assert_allclose(res["apical_points"][0], [[19.211365, 92.61514, -6.3647766]])
+    assert res["apical_points"][1] is None
 
-        assert_allclose(res["apical_points"][3], [[2.0048676, 116.672, -5.334656]])
-        assert res["apical_points"][4] is None
+    assert_allclose(res["apical_points"][3], [[-2.7629395, 117.766846, 4.818283]])
+    assert res["apical_points"][4] is None
 
-        assert_allclose(res["apical_points"][6], [[-2.347641, 58.229614, -0.56985474]])
-        assert res["apical_points"][7] is None
+    assert_allclose(res["apical_points"][6], [[-76.63339, 141.26578, -1.3202515]])
+    assert res["apical_points"][7] is None
 
-        assert_allclose(res["apical_points"][9], [[6.861679, 112.31445, -13.528854]])
-        assert res["apical_points"][10] is None
+    assert_allclose(res["apical_points"][9], [[0.65127563, 58.166138, 0.24832153]])
+    assert res["apical_points"][10] is None
 
     # Check that the morphologies were not written
     res_files = tmpdir.listdir()