coalesce all utils in wsi/utils.py; less exposed methods; more docstr…

…ings
rendeirolab · Mar 15, 2024 · 176877a · 176877a
1 parent 36403f2
commit 176877a
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Showing 8 changed files with 433 additions and 660 deletions.
diff --git a/wsi/WholeSlideImage.py b/wsi/WholeSlideImage.py
diff --git a/wsi/dataset_h5.py b/wsi/dataset_h5.py
diff --git a/wsi/file_utils.py b/wsi/file_utils.py
diff --git a/wsi/tests/test_wsi.py b/wsi/tests/test_wsi.py
@@ -1,14 +1,33 @@
+from pathlib import Path
+import tempfile
+import joblib
+
+import requests
 import pytest
 from wsi import WholeSlideImage
 import numpy as np
 
 
-@pytest.mark.wsi
-@pytest.mark.slow
-def test_whole_slide_image_inference():
+mem = joblib.Memory("cache", verbose=0)
+
+
+@pytest.fixture(scope="session")
+@mem.cache
+def get_test_slide():
     slide_file = "GTEX-O5YU-1426"
     url = f"https://brd.nci.nih.gov/brd/imagedownload/{slide_file}"
-    slide = WholeSlideImage(url)
+    path = Path(tempfile.NamedTemporaryFile().name)
+
+    with open(path, "wb") as file:
+        for chunk in requests.get(url, stream=True).iter_content(chunk_size=1024):
+            file.write(chunk)
+    return path
+
+
+@pytest.mark.wsi
+@pytest.mark.slow
+def test_whole_slide_image_inference(get_test_slide):
+    slide = WholeSlideImage(get_test_slide)
     slide.segment()
     slide.tile()
     feats, coords = slide.inference("resnet18")

diff --git a/wsi/util_classes.py b/wsi/util_classes.py