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Add min_distance parameter to peak_local_max call #2008

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merged 3 commits into from
Dec 1, 2023
Merged

Add min_distance parameter to peak_local_max call #2008

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fecec0d
Add min_distance parameter to peak_local_max call
iimog Nov 14, 2023
b61b62e
Fix iss test
iimog Nov 23, 2023
947472f
Fix docker build
iimog Nov 23, 2023
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3 changes: 2 additions & 1 deletion REQUIREMENTS.txt
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Expand Up @@ -22,8 +22,9 @@ scipy
showit >= 1.1.4
slicedimage==4.1.1
sympy ~= 1.5.0
urllib3 <1.27, >=1.25.4
tqdm
trackpy
validators
xarray >= 0.14.1
ipywidgets
ipywidgets
1 change: 1 addition & 0 deletions starfish/core/morphology/Filter/min_distance_label.py
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Expand Up @@ -63,6 +63,7 @@ def run(
exclude_border=self._exclude_border,
footprint=footprint,
labels=np.asarray(mask),
min_distance=self._minimum_distance_xy,
)
local_maximum_mask = np.zeros_like(distance, dtype=bool)
local_maximum_mask[tuple(local_maximum.T)] = True
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6 changes: 3 additions & 3 deletions starfish/test/full_pipelines/api/test_iss_api.py
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Expand Up @@ -105,8 +105,8 @@ def test_iss_pipeline_cropped_data(tmpdir):

masks = iss.masks

# segmentation identifies only one cell
assert len(iss.watershed_markers) == 6
# segmentation identifies four cells
assert len(iss.watershed_markers) == 4

# assign targets
lab = AssignTargets.Label()
Expand Down Expand Up @@ -143,4 +143,4 @@ def test_iss_pipeline_cropped_data(tmpdir):
# test that nans were properly removed from the expression matrix
assert 'nan' not in expression_matrix.genes.data
# test the number of spots that did not decode per cell
assert np.array_equal(expression_matrix.number_of_undecoded_spots.data, [13, 1, 0, 36])
assert np.array_equal(expression_matrix.number_of_undecoded_spots.data, [13, 1, 36])
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