Update measurement tests

Author: constantinpape

flamingo_tools/measurements.py

@@ -89,11 +89,11 @@ def intensity_measures(seg_id):
         return measures
 
     seg_ids = table.label_id.values
+    assert len(seg_ids) > 0, "The segmentation table is empty."
     n_threads = mp.cpu_count() if n_threads is None else n_threads
     with futures.ThreadPoolExecutor(n_threads) as pool:
         measures = list(tqdm(
-            pool.map(intensity_measures, seg_ids),
-            total=len(seg_ids), desc="Compute intensity measures"
+            pool.map(intensity_measures, seg_ids), total=len(seg_ids), desc="Compute intensity measures"
         ))
 
     # Create the result table and save it.

test/test_measurements.py

@@ -4,6 +4,8 @@
 
 import imageio.v3 as imageio
 import pandas as pd
+import numpy as np
+from skimage.measure import regionprops_table
 
 
 class TestMeasurements(unittest.TestCase):
@@ -41,6 +43,18 @@ def test_compute_object_measures(self):
         expected_shape = (n_objects, len(expected_columns))
         self.assertEqual(table.shape, expected_shape)
 
+        image = imageio.imread(self.image_path)
+        segmentation = imageio.imread(self.seg_path)
+        properties = ("label", "intensity_mean", "intensity_std", "intensity_min", "intensity_max")
+        expected_measures = regionprops_table(segmentation, intensity_image=image, properties=properties)
+        expected_measures = pd.DataFrame(expected_measures)
+
+        for (col, col_exp) in [
+            ("label_id", "label"), ("mean", "intensity_mean"), ("stdev", "intensity_std"),
+            ("min", "intensity_min"), ("max", "intensity_max"),
+        ]:
+            self.assertTrue(np.allclose(table[col].values, expected_measures[col_exp].values))
+
 
 if __name__ == "__main__":
     unittest.main()