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Use connectivity for foreground components #60

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Use connectivity for foreground components #60

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7 changes: 5 additions & 2 deletions MetricsReloaded/utility/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -128,7 +128,10 @@ def border_map2(self):
return border

def foreground_component(self):
return ndimage.label(self.binary_map)
structure = ndimage.generate_binary_structure(
self.binary_map.ndim, self.connectivity
)
return ndimage.label(self.binary_map, structure=structure)

def list_foreground_component(self):
labels, _ = self.foreground_component()
Expand Down Expand Up @@ -536,4 +539,4 @@ def trapezoidal_integration(x, fx):
Reference
https://en.wikipedia.org/w/index.php?title=Trapezoidal_rule&oldid=1104074899#Non-uniform_grid
"""
return np.sum((fx[:-1] + fx[1:])/2 * (x[1:] - x[:-1]))
return np.sum((fx[:-1] + fx[1:])/2 * (x[1:] - x[:-1]))
15 changes: 13 additions & 2 deletions test/test_utility/test_utils.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
import pytest
import numpy as np
from numpy.testing import assert_allclose, assert_array_equal
from MetricsReloaded.utility.utils import intersection_boxes, guess_input_style, com_from_box, point_in_box, point_in_mask, area_box, compute_box, compute_center_of_mass, compute_skeleton, combine_df, distance_transform_edt, one_hot_encode, median_heuristic, box_ior, box_iou, union_boxes, max_x_at_y_less, min_x_at_y_less, skeletonize, trapezoidal_integration
from MetricsReloaded.utility.utils import intersection_boxes, guess_input_style, com_from_box, point_in_box, point_in_mask, area_box, compute_box, compute_center_of_mass, compute_skeleton, combine_df, distance_transform_edt, one_hot_encode, median_heuristic, box_ior, box_iou, union_boxes, max_x_at_y_less, min_x_at_y_less, skeletonize, trapezoidal_integration, MorphologyOps


box3 = [2,3, 4,4]
Expand Down Expand Up @@ -80,6 +80,17 @@ def test_compute_center_of_mass():
mask[4:6,4:5] = 1
assert_array_equal(compute_center_of_mass(mask),np.asarray([3.125, 4.9375]))

def test_foreground_component_uses_connectivity():
mask = np.zeros([2, 2])
mask[0, 0] = 1
mask[1, 1] = 1

_, nlabels_connectivity_1 = MorphologyOps(mask, 1).foreground_component()
_, nlabels_connectivity_2 = MorphologyOps(mask, 2).foreground_component()

assert nlabels_connectivity_1 == 2
assert nlabels_connectivity_2 == 1

def test_box_ior():
box1 = [3,5,5,7]
box2 = [3,4,4,6]
Expand Down Expand Up @@ -121,4 +132,4 @@ def test_min_x_at_y_less():
x = [1, 2, 1, 3, 4, 0, 1, 4, 5]
y = [1, 2, 3, 4, 5, 6, 7 ,8, 9]
assert min_x_at_y_less(np.asarray(x), np.asarray(y),6) == 0
#compute_skeleton, combine_df, distance_transform_edt, one_hot_encode, median_heuristic, max_x_at_y_less, min_x_at_y_less, skeletonize, trapezoidal_integration
#compute_skeleton, combine_df, distance_transform_edt, one_hot_encode, median_heuristic, max_x_at_y_less, min_x_at_y_less, skeletonize, trapezoidal_integration