From 0b08d8ffccf201dc648833c7ee7c17199b5c8ed5 Mon Sep 17 00:00:00 2001
From: Andrey Aristov <aaristov@pasteur.fr>
Date: Wed, 25 May 2022 19:23:11 +0200
Subject: [PATCH] fix segment
---
src/segment/seg.py | 2 +-
src/tests/test_segment.py | 23 ++++++++++++-----------
2 files changed, 13 insertions(+), 12 deletions(-)
diff --git a/src/segment/seg.py b/src/segment/seg.py
index 74e09dd..da47812 100644
--- a/src/segment/seg.py
+++ b/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)
diff --git a/src/tests/test_segment.py b/src/tests/test_segment.py
index eeaf0c2..46abeba 100644
--- a/src/tests/test_segment.py
+++ b/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
+ )
--
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