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Faster _compute_region_cell_counts #72

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Mar 26, 2024
Merged

Faster _compute_region_cell_counts #72

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4044db5
Faster _compute_region_cell_counts
mgeplf Mar 1, 2024
7bbb615
switch to ValueToIndexVoxels in voxcell
mgeplf Mar 26, 2024
db6d8a1
review comments
mgeplf Mar 26, 2024
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22 changes: 12 additions & 10 deletions atlas_densities/densities/inhibitory_neuron_densities_optimization.py
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@
from atlas_commons.typing import AnnotationT, FloatArray
from scipy.optimize import linprog
from tqdm import tqdm
from voxcell import RegionMap
from voxcell import RegionMap, voxel_data

from atlas_densities.densities import utils
from atlas_densities.densities.inhibitory_neuron_densities_helper import (
Expand Down Expand Up @@ -199,16 +199,18 @@ def _compute_region_cell_counts(
... ...
The index is the sorted list of all region identifiers.
"""
vtiv = voxel_data.ValueToIndexVoxels(annotation)
density = vtiv.ravel(density)

id_counts = []
for id_ in tqdm(hierarchy_info.index):
mask = annotation == id_
id_counts.append(np.sum(density[mask]) * voxel_volume)
for id_ in hierarchy_info.index:
indices = vtiv.value_to_1d_indices(id_)
id_counts.append(np.sum(density[indices]) * voxel_volume)

result = pd.DataFrame(
{"brain_region": hierarchy_info["brain_region"], "cell_count": id_counts},
index=hierarchy_info.index,
)

return result


Expand Down Expand Up @@ -736,17 +738,17 @@ def create_inhibitory_neuron_densities( # pylint: disable=too-many-locals
hierarchy_info = utils.get_hierarchy_info(RegionMap.from_dict(hierarchy), root=region_name)
average_densities = _resize_average_densities(average_densities, hierarchy_info)

L.info("Initialization of the linear program: started")
region_counts, id_counts = _compute_initial_cell_counts(
annotation, voxel_volume, average_densities, hierarchy_info
)

L.info("Retrieving overall neuron counts in atomic 3D regions ...")
neuron_counts = _compute_region_cell_counts(
annotation, neuron_density, voxel_volume, hierarchy_info
)
assert np.all(neuron_counts["cell_count"] >= 0.0)

L.info("Initialization of the linear program: started")
region_counts, id_counts = _compute_initial_cell_counts(
annotation, voxel_volume, average_densities, hierarchy_info
)

L.info("Setting the known values ...")
x_result, deltas = set_known_values(region_counts, id_counts, hierarchy_info)
# We assume that if the cell count of `cell_type` in `region_name` is known with certainty
Expand Down
2 changes: 1 addition & 1 deletion setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@
# from the HiGHS library. We use the "highs" method in the densities module.
"scipy>=1.6.0",
"tqdm>=4.44.1",
"voxcell>=3.0.0",
"voxcell>=3.1.7",
],
extras_require={
"tests": [
Expand Down
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