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@arnaudon
arnaudon committed Dec 2, 2024
1 parent fdd839c commit f486201
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Showing 2 changed files with 117 additions and 121 deletions.
66 changes: 46 additions & 20 deletions tests/data/parameters.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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": {
Expand All @@ -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": {
Expand All @@ -48,8 +61,8 @@
"axon": 0.6
},
"grow_types": [
"basal_dendrite",
"apical_dendrite"
"apical_dendrite",
"basal_dendrite"
],
"origin": [
0.0,
Expand All @@ -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": {
Expand All @@ -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": {
Expand All @@ -107,8 +133,8 @@
"axon": 0.6
},
"grow_types": [
"basal_dendrite",
"apical_dendrite"
"apical_dendrite",
"basal_dendrite"
],
"origin": [
0.0,
Expand Down
172 changes: 71 additions & 101 deletions tests/test_context.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -117,51 +117,47 @@ def test_context(

# Synthesize in L2
result = context_worker.synthesize()
assert_array_equal(result.apical_sections, np.array([48]))
assert_array_equal(result.apical_sections, np.array([53]))
assert_array_almost_equal(
result.apical_points,
np.array([[20.272340774536133, 266.1555480957031, 6.746281147003174]]),
result.apical_points, np.array([[3.35894, 203.65117, -8.5437]]), decimal=5
)

# 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 synthesis_parameters.tmd_parameters["apical_dendrite"]["orientation"] == {
"mode": "normal_pia_constraint",
"values": {"direction": {"mean": 0.0, "std": 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],
[-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],
],
dtype=np.float32,
),
)
assert len(result.neuron.root_sections) == 4
assert len(result.neuron.root_sections) == 7
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],
[-7.3899293, -1.5310667, -1.165452],
[-8.706363, -1.8038092, -1.3730644],
[-10.090032, -2.006144, -1.4496313],
],
dtype=np.float32,
),
)
assert_array_almost_equal(
next(result.neuron.iter()).diameters,
np.array([0.6, 0.6, 0.6, 0.6, 0.6, 0.6], dtype=np.float32),
np.array([0.6, 0.6, 0.6], dtype=np.float32),
)

def test_context_external_diametrizer(
Expand Down Expand Up @@ -258,42 +254,37 @@ def test_scale(self, small_context_worker, tmd_parameters):
result1 = small_context_worker.synthesize()

expected_types = [
SectionType.basal_dendrite,
SectionType.apical_dendrite,
SectionType.basal_dendrite,
SectionType.basal_dendrite,
SectionType.basal_dendrite,
SectionType.basal_dendrite,
SectionType.basal_dendrite,
]
assert [i.type for i in result1.neuron.root_sections] == expected_types

assert_array_almost_equal(
[ # Check only first and last points of neurites
np.around(np.array([neu.points[0], neu.points[-1]]), 6)
for neu in result1.neuron.root_sections
],
[
[[-7.38993, -1.531067, -1.165452], [-10.090032, -2.006144, -1.449631]],
[
[0.0, 7.636328220367432, 0.0],
[-0.05446799844503403, 9.565113067626953, -0.004176999907940626],
],
[
[-1.8836770057678223, -3.8763949871063232, 6.3038740158081055],
[-3.030216932296753, -6.87820291519165, 10.731352806091309],
],
[
[7.384983062744141, 1.0597859621047974, 1.6286120414733887],
[17.74557876586914, 0.2534179985523224, 3.5686450004577637],
],
[
[-3.335297107696533, 4.92931604385376, 4.784468173980713],
[-19.434040069580078, 27.80714988708496, 24.4342041015625],
[0.0000000e00, 7.6363282e00, 0.0000000e00],
[-1.3458900e-01, 1.0937219e01, -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]],
],
)

assert_array_equal(result1.apical_sections, np.array([25]))
assert_array_equal(result1.apical_sections, np.array([29]))
assert_array_almost_equal(
result1.apical_points,
np.array([[-25.359481811523438, 65.18755340576172, -6.167412757873535]]),
result1.apical_points, np.array([[5.711923, 56.423206, 4.124067]])
)

# Test with no hard limit scaling for basal
Expand All @@ -310,6 +301,9 @@ def test_scale(self, small_context_worker, tmd_parameters):
result2 = small_context_worker.synthesize()

basal_expected_types = [
SectionType.basal_dendrite,
SectionType.basal_dendrite,
SectionType.basal_dendrite,
SectionType.basal_dendrite,
SectionType.apical_dendrite,
SectionType.basal_dendrite,
Expand All @@ -322,22 +316,13 @@ def test_scale(self, small_context_worker, tmd_parameters):
for neu in result2.neuron.root_sections
],
[
[
[-1.8836770057678223, -3.8763949871063232, 6.3038740158081055],
[-2.4301559925079346, -5.42181396484375, 8.747697830200195],
],
[
[0.0, 7.636328220367432, 0.0],
[-0.17696000635623932, 10.314826011657715, 0.06906899809837341],
],
[
[7.384983062744141, 1.0597859621047974, 1.6286120414733887],
[13.206015586853027, 1.6560349464416504, 3.2374720573425293],
],
[
[-3.335297107696533, 4.92931604385376, 4.784468173980713],
[-10.385510444641113, 19.43812370300293, 19.94303321838379],
],
[[-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]],
],
)

Expand Down Expand Up @@ -369,29 +354,23 @@ 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]],
[
[0.0, 7.636328220367432, 0.0],
[-0.0517829991877079, 9.470013618469238, -0.003971000202000141],
],
[
[-1.8836770057678223, -3.8763949871063232, 6.3038740158081055],
[-3.030216932296753, -6.87820291519165, 10.731352806091309],
],
[
[7.384983062744141, 1.0597859621047974, 1.6286120414733887],
[17.74557876586914, 0.2534179985523224, 3.5686450004577637],
],
[
[-3.335297107696533, 4.92931604385376, 4.784468173980713],
[-19.434040069580078, 27.80714988708496, 24.4342041015625],
[0.0000000e00, 7.6363282e00, 0.0000000e00],
[-1.2766400e-01, 1.0767367e01, -4.5900000e-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]],
],
)

assert_array_equal(result3.apical_sections, np.array([25]))
assert_array_equal(result3.apical_sections, np.array([29]))
assert_array_almost_equal(
result3.apical_points,
np.array([[-24.10912322998047, 62.349971771240234, -5.8633270263671875]]),
np.array([[5.418009, 53.912827, 3.911858]]),
)

# Test scale computation
Expand Down Expand Up @@ -487,27 +466,6 @@ def test_debug_scales(self, small_context_worker, tmd_parameters):

expected_debug_infos = {
"input_scaling": {
"default_func": {
"inputs": {
"target_thickness": 300.0,
"reference_thickness": 314,
"min_target_thickness": 1.0,
},
"scaling": [
{
"max_ph": 126.96580088057513,
"scaling_ratio": 0.9554140127388535,
},
{
"max_ph": 139.93140451880743,
"scaling_ratio": 0.9554140127388535,
},
{
"max_ph": 143.28779114733433,
"scaling_ratio": 0.9554140127388535,
},
],
},
"target_func": {
"inputs": {
"fit_slope": 0.5,
Expand All @@ -517,17 +475,29 @@ def test_debug_scales(self, small_context_worker, tmd_parameters):
"min_target_path_distance": 1.0,
},
"scaling": [
{
"max_ph": 420.70512274498446,
"scaling_ratio": 0.18064909574697127,
}
{"max_ph": 380.2369655856533, "scaling_ratio": 0.19987535899604694}
],
},
"default_func": {
"inputs": {
"target_thickness": 300.0,
"reference_thickness": 314,
"min_target_thickness": 1.0,
},
"scaling": [
{"max_ph": 161.90961466339775, "scaling_ratio": 0.9554140127388535},
{"max_ph": 88.93359927070985, "scaling_ratio": 0.9554140127388535},
{"max_ph": 176.74138075182876, "scaling_ratio": 0.9554140127388535},
{"max_ph": 143.28779114733433, "scaling_ratio": 0.9554140127388535},
{"max_ph": 160.10899907966802, "scaling_ratio": 0.9554140127388535},
{"max_ph": 176.74138075182876, "scaling_ratio": 0.9554140127388535},
],
},
},
"neurite_hard_limit_rescaling": {
0: {
19: {
"neurite_type": "apical_dendrite",
"scale": 0.9506947194040978,
"scale": 0.9485438342260688,
"target_min_length": 70.0,
"target_max_length": 70.0,
"deleted": False,
Expand Down Expand Up @@ -593,7 +563,7 @@ def test_retry(
context_worker.internals.retries = 3
result = context_worker.synthesize()

assert_array_equal(result.apical_sections, np.array([72]))
assert_array_equal(result.apical_sections, np.array([81]))
assert_array_almost_equal(
result.apical_points, [[-74.1576919555664, 241.61322021484375, -26.836679458618164]]
result.apical_points, [[-109.65276, 181.05916, -94.54867]], decimal=5
)

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