diff --git a/REQUIREMENTS.txt b/REQUIREMENTS.txt index e645accc3..25bbdf926 100644 --- a/REQUIREMENTS.txt +++ b/REQUIREMENTS.txt @@ -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 \ No newline at end of file +ipywidgets diff --git a/starfish/core/morphology/Filter/min_distance_label.py b/starfish/core/morphology/Filter/min_distance_label.py index 29f52e695..95ec9fb23 100644 --- a/starfish/core/morphology/Filter/min_distance_label.py +++ b/starfish/core/morphology/Filter/min_distance_label.py @@ -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 diff --git a/starfish/test/full_pipelines/api/test_iss_api.py b/starfish/test/full_pipelines/api/test_iss_api.py index 52cdeef75..601652246 100644 --- a/starfish/test/full_pipelines/api/test_iss_api.py +++ b/starfish/test/full_pipelines/api/test_iss_api.py @@ -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() @@ -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])