Update measurement test

Author: constantinpape

flamingo_tools/test_data.py

@@ -2,15 +2,40 @@
 from typing import Tuple
 
 import imageio.v3 as imageio
-from skimage.data import binary_blobs
+import requests
+from skimage.data import binary_blobs, cells3d
 from skimage.measure import label
 
 from .segmentation.postprocessing import _compute_table
 
+SEGMENTATION_URL = "https://owncloud.gwdg.de/index.php/s/kwoGRYiJRRrswgw/download"
 
-def create_image_data_and_segmentation(
-    folder: str, size: int = 256
-) -> Tuple[str, str, str]:
+
+def get_test_volume_and_segmentation(folder: str) -> Tuple[str, str, str]:
+    os.makedirs(folder, exist_ok=True)
+
+    segmentation_path = os.path.join(folder, "segmentation.tif")
+    resp = requests.get(SEGMENTATION_URL)
+    resp.raise_for_status()
+
+    with open(segmentation_path, "wb") as f:
+        f.write(resp.content)
+
+    nuclei = cells3d()[20:40, 1]
+    segmentation = imageio.imread(segmentation_path)
+    assert nuclei.shape == segmentation.shape
+
+    image_path = os.path.join(folder, "image.tif")
+    imageio.imwrite(image_path, nuclei)
+
+    table_path = os.path.join(folder, "default.tsv")
+    table = _compute_table(segmentation, resolution=0.38)
+    table.to_csv(table_path, sep="\t", index=False)
+
+    return image_path, segmentation_path, table_path
+
+
+def create_image_data_and_segmentation(folder: str, size: int = 256) -> Tuple[str, str, str]:
     """Create test data containing an image, a corresponding segmentation and segmentation table.
 
     Args:

test/test_measurements.py

@@ -6,14 +6,13 @@
 import pandas as pd
 
 
-class TestDataConversion(unittest.TestCase):
+class TestMeasurements(unittest.TestCase):
     folder = "./tmp"
 
     def setUp(self):
-        from flamingo_tools.test_data import create_image_data_and_segmentation
+        from flamingo_tools.test_data import get_test_volume_and_segmentation
 
-        self.image_path, self.seg_path, self.table_path =\
-            create_image_data_and_segmentation(self.folder)
+        self.image_path, self.seg_path, self.table_path = get_test_volume_and_segmentation(self.folder)
 
     def tearDown(self):
         try: