Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix: Allow for normal orientation with basals #90

Merged
merged 5 commits into from
Sep 28, 2023
Merged

Fix: Allow for normal orientation with basals #90

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
7ca7884
Fix: Allow for normal orientation with basals
arnaudon Sep 28, 2023
eb56209
fix test
arnaudon Sep 28, 2023
0159359
remove print
arnaudon Sep 28, 2023
d547805
set for 2 apicals
arnaudon Sep 28, 2023
c351bf5
fix
arnaudon Sep 28, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
45 changes: 28 additions & 17 deletions neurots/generate/orientations.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -222,7 +222,7 @@ def _mode_uniform(self, _, tree_type):
[sample.sample_spherical_unit_vectors(rng=self._rng) for _ in range(n_orientations)]
)

def _mode_normal_pia_constraint(self, values_dict, _):
def _mode_normal_pia_constraint(self, values_dict, tree_type):
"""Returns orientations using normal/exp distribution along a direction.

The `direction` value should be a dict with two entries: `mean` and `std`. The mean is the
Expand All @@ -234,24 +234,35 @@ def _mode_normal_pia_constraint(self, values_dict, _):

Pia direction can be overwritten by the parameter 'pia_direction' value.
"""
means = values_dict["direction"]["mean"]
means = means if isinstance(means, list) else [means]
stds = values_dict["direction"]["std"]
stds = stds if isinstance(stds, list) else [stds]
thetas = []
for mean, std in zip(means, stds):
if mean == 0:
if std > 0:
thetas.append(np.clip(self._rng.exponential(std), 0, np.pi))
n_orientations = sample.n_neurites(self._distributions[tree_type]["num_trees"], self._rng)
if (
isinstance(values_dict["direction"]["mean"], list)
and len(values_dict["direction"]["mean"]) == n_orientations
):
# to force the direction of possibly 2 apicals, otherwise it is for basals
n_orientations = 1

angles = []
for _ in range(n_orientations):
means = values_dict["direction"]["mean"]
means = means if isinstance(means, list) else [means]
stds = values_dict["direction"]["std"]
stds = stds if isinstance(stds, list) else [stds]
thetas = []
for mean, std in zip(means, stds):
if mean == 0:
if std > 0:
thetas.append(np.clip(self._rng.exponential(std), 0, np.pi))
else:
thetas.append(0)
else:
thetas.append(0)
else:
thetas.append(np.clip(self._rng.normal(mean, std), 0, np.pi))
thetas.append(np.clip(self._rng.normal(mean, std), 0, np.pi))

phis = self._rng.uniform(0, 2 * np.pi, len(means))
return spherical_angles_to_pia_orientations(
phis, thetas, self._parameters.get("pia_direction", None)
)
phis = self._rng.uniform(0, 2 * np.pi, len(means))
angles += spherical_angles_to_pia_orientations(
phis, thetas, self._parameters.get("pia_direction", None)
).tolist()
return np.array(angles)

def _mode_pia_constraint(self, _, tree_type):
"""Create trunks from distribution of angles with pia (`[0 , 1, 0]`) direction.
Expand Down
6 changes: 3 additions & 3 deletions tests/test_orientations.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -366,7 +366,7 @@ def test_orientation_manager__mode_normal_pia_constraint():
om.compute_tree_type_orientations(tree_type)

actual = om.get_tree_type_orientations("apical_dendrite")
expected = np.array([[-0.0084249, 0.99768935, 0.06741643]])
expected = np.array([[0.09842876357405606, 0.9948066102055255, 0.025914991658764108]])
npt.assert_allclose(actual, expected, rtol=1e-5)

# make one along pia
Expand Down Expand Up @@ -400,7 +400,7 @@ def test_orientation_manager__mode_normal_pia_constraint():
om.compute_tree_type_orientations(tree_type)

actual = om.get_tree_type_orientations("apical_dendrite")
expected = np.array([[-0.10517952, 0.52968005, 0.84165095]])
expected = np.array([[0.8067661158336028, 0.5513710782140335, 0.21241084824428402]])
npt.assert_allclose(actual, expected, rtol=1e-5)

# test other pia direction
Expand All @@ -417,7 +417,7 @@ def test_orientation_manager__mode_normal_pia_constraint():
om.compute_tree_type_orientations(tree_type)

actual = om.get_tree_type_orientations("apical_dendrite")
expected = np.array([[0.52968, 0.10518, 0.841651]])
expected = np.array([[0.5513710782140335, -0.8067661158336028, 0.21241084824428402]])
npt.assert_allclose(actual, expected, rtol=1e-5)


Expand Down