fix segment

src/segment/seg.py

@@ -20,7 +20,7 @@ def crop_center(array):
 def segment_bf(well, thr=0.2, smooth=10, erode=10, fill=True, plot=False):
     '''
     Serments input 2d array using thresholded gradient with filling
-    Returns SegmentedImage object
+    Returns labels
     '''
     grad = multiwell.get_2d_gradient(well)
     sm = multiwell.gaussian_filter(grad, smooth)

src/tests/test_segment.py

@@ -6,21 +6,22 @@ from skimage.transform import rotate
 
 from segment import seg
 import logging
+from droplet_growth.mic import regionprops
 
 logging.basicConfig(level=logging.DEBUG)
 
 logger = logging.getLogger(__name__)
 
 
-# def test_segment():
-#     image = np.zeros((600, 600))
-#     cx, cy, b, a = 300, 350, 50, 100
-#     rr, cc = ellipse(cx, cy, b, a)
-#     image[rr, cc] = 1.0
+def test_segment():
+    image = np.zeros((600, 600))
+    cx, cy, b, a = 300, 350, 50, 100
+    rr, cc = ellipse(cx, cy, b, a)
+    image[rr, cc] = 1.0
 
-#     mask = seg.find_spheroid(image, plot=0)
-#     props = seg.get_props(mask)
-#     logger.debug(f"len(props) {len(props)}")
-#     np.testing.assert_almost_equal(
-#         props[0]["eccentricity"], (1 - b ** 2 / a ** 2) ** 0.5, 0.02
-#     )
+    mask = seg.segment_bf(image, plot=0)
+    props = regionprops(mask)
+    logger.debug(f"len(props) {len(props)}")
+    np.testing.assert_almost_equal(
+        props[0]["eccentricity"], (1 - b ** 2 / a ** 2) ** 0.5, 0.02
+    )