Setup script and cacheing for downloading test data for benchmarking

.github/workflows/ci.yml

@@ -60,6 +60,18 @@ jobs:
         with:
           fetch-depth: 50 # this is to make sure we obtain the target base commit
 
+      - uses: actions/cache@v3
+        id: cache
+        with:
+          path: downloads
+          key: ${{ hashFiles('scripts/download_samples.py') }}
+
+      - name: Download Samples
+        if: steps.cache.outputs.cache-hit != 'true'
+        run: |
+          pip install requests
+          python scripts/download_test_data.py
+
       - name: Set up Python
         uses: actions/setup-python@v5
         with:

scripts/download_test_data.py

@@ -0,0 +1,37 @@
+import os
+import urllib.request
+import zipfile
+from pathlib import Path
+
+ROOT_DIR = Path(__file__).resolve().parents[1]
+DATASETS = [
+    "http://data.celltrackingchallenge.net/training-datasets/Fluo-N2DL-HeLa.zip",
+    "http://data.celltrackingchallenge.net/training-datasets/PhC-C2DL-PSC.zip"
+    "http://data.celltrackingchallenge.net/training-datasets/Fluo-N3DH-CE.zip",
+]
+
+
+def download_gt_data(url, root_dir):
+    data_dir = os.path.join(root_dir, "downloads")
+
+    if not os.path.exists(data_dir):
+        os.mkdir(data_dir)
+
+    filename = url.split("/")[-1]
+    file_path = os.path.join(data_dir, filename)
+
+    if not os.path.exists(file_path):
+        urllib.request.urlretrieve(url, file_path)
+
+        # Unzip the data
+        with zipfile.ZipFile(file_path, "r") as zip_ref:
+            zip_ref.extractall(data_dir)
+
+
+def main():
+    for url in DATASETS:
+        download_gt_data(url, ROOT_DIR)
+
+
+if __name__ == "__main__":
+    main()

tests/bench.py

@@ -13,24 +13,26 @@
 from traccuracy.matchers import CTCMatcher, IOUMatcher
 from traccuracy.metrics import CTCMetrics, DivisionMetrics
 
-from tests.test_utils import download_gt_data, gt_data
-
 ROOT_DIR = Path(__file__).resolve().parents[1]
 TIMEOUT = 20
 
 
 @pytest.fixture(scope="module")
 def gt_data_2d():
-    url = "http://data.celltrackingchallenge.net/training-datasets/PhC-C2DL-PSC.zip"
     path = "downloads/Fluo-N2DL-HeLa/01_GT/TRA"
-    return gt_data(url, ROOT_DIR, path)
+    return load_ctc_data(
+        os.path.join(ROOT_DIR, path),
+        os.path.join(ROOT_DIR, path, "man_track.txt"),
+    )
 
 
 @pytest.fixture(scope="module")
 def gt_data_3d():
-    url = "http://data.celltrackingchallenge.net/training-datasets/Fluo-N3DH-CE.zip"
     path = "downloads/Fluo-N3DH-CE/01_GT/TRA"
-    return gt_data(url, ROOT_DIR, path)
+    return load_ctc_data(
+        os.path.join(ROOT_DIR, path),
+        os.path.join(ROOT_DIR, path, "man_track.txt"),
+    )
 
 
 @pytest.fixture(scope="module")
@@ -74,9 +76,7 @@ def test_load_gt_ctc_data(
     benchmark,
     dataset,
 ):
-    url = f"http://data.celltrackingchallenge.net/training-datasets/{dataset}.zip"
     path = f"downloads/{dataset}/01_GT/TRA"
-    download_gt_data(url, ROOT_DIR)
 
     benchmark.pedantic(
         load_ctc_data,