Merge pull request #182 from DiamondLightSource/zenodo_upd

updating zenodo doi and tests

Author: namannimmo10

.github/workflows/httomolibgpu_tests_run_iris.yml

@@ -21,10 +21,6 @@ jobs:
       - name: Checkout repository code
         uses: actions/checkout@v4
 
-      - name: Set up CUDA environment
-        run: |
-          echo "LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH" >> $GITHUB_ENV
-
       - name: Create conda environment
         uses: mamba-org/setup-micromamba@v1
         with:

.github/workflows/main-checks.yml

@@ -20,10 +20,6 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up CUDA environment
-        run: |
-          echo "LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH" >> $GITHUB_ENV
-
       - name: Create conda environment
         uses: mamba-org/setup-micromamba@v1
         with:

.scripts/download_zenodo.py

@@ -19,28 +19,30 @@ def calculate_md5(filename):
 
 def download_zenodo_files(output_dir: Path):
     """
-    Download all files from Zenodo record 14338424 and verify their checksums.
-    
+    Download all files from Zenodo record 14627503 and verify their checksums.
+
     Args:
         output_dir: Directory where files should be downloaded
     """
     try:
-        print("Fetching files from Zenodo record 14338424...")
-        with urllib.request.urlopen("https://zenodo.org/api/records/14338424") as response:
+        print("Fetching files from Zenodo record 14627503...")
+        with urllib.request.urlopen(
+            "https://zenodo.org/api/records/14627503"
+        ) as response:
             data = json.loads(response.read())
-        
+
         # Create output directory if it doesn't exist
         output_dir.mkdir(parents=True, exist_ok=True)
-        
+
         # Now 'files' is a list, not a dictionary
         for file_info in data["files"]:
             filename = file_info["key"]  # The 'key' is the filename
             output_file = output_dir / filename
             print(f"Downloading {filename}...")
             url = file_info["links"]["self"]  # The link to download the file
-            
+
             expected_md5 = file_info["checksum"].split(":")[1]  # Extract MD5 hash
-            
+
             # Download the file
             urllib.request.urlretrieve(url, output_file)
 
@@ -53,9 +55,9 @@ def download_zenodo_files(output_dir: Path):
                 print(f"Expected: {expected_md5}")
                 print(f"Got: {actual_md5}")
                 sys.exit(1)
-                
+
         print("\nAll files downloaded and verified successfully!")
-        
+
     except Exception as e:
         print(f"Error: {str(e)}", file=sys.stderr)
         sys.exit(1)
@@ -65,6 +67,6 @@ def download_zenodo_files(output_dir: Path):
     if len(sys.argv) != 2:
         print("Usage: download_zenodo.py <output_directory>")
         sys.exit(1)
-        
+
     output_dir = Path(sys.argv[1])
     download_zenodo_files(output_dir)

zenodo-tests/conftest.py

@@ -12,49 +12,50 @@ def test_data_path():
 
 
 @pytest.fixture(scope="session")
-def data_i12LFOV_file(test_data_path):
-    in_file = os.path.join(test_data_path, "i12LFOV.npz")
+def i12_dataset1_file(test_data_path):
+    in_file = os.path.join(test_data_path, "i12_dataset1.npz")
     return np.load(in_file)
 
 
-@pytest.fixture(scope="session")
-def data_i12_sandstone_file(test_data_path):
-    in_file = os.path.join(test_data_path, "i12_sandstone_50sinoslices.npz")
-    return np.load(in_file)
+@pytest.fixture
+def i12_dataset1(i12_dataset1_file):
+    return (
+        cp.asarray(i12_dataset1_file["projdata"]),
+        i12_dataset1_file["angles"],
+        cp.asarray(i12_dataset1_file["flats"]),
+        cp.asarray(i12_dataset1_file["darks"]),
+    )
 
 
 @pytest.fixture(scope="session")
-def data_geant4sim_file(test_data_path):
-    in_file = os.path.join(test_data_path, "geant4_640_540_proj360.npz")
+def i12_dataset2_file(test_data_path):
+    in_file = os.path.join(test_data_path, "i12_dataset2.npz")
     return np.load(in_file)
 
+
 @pytest.fixture
-def i12LFOV_data(data_i12LFOV_file):
+def i12_dataset2(i12_dataset2_file):
     return (
-        cp.asarray(data_i12LFOV_file["projdata"]),
-        data_i12LFOV_file["angles"],
-        cp.asarray(data_i12LFOV_file["flats"]),
-        cp.asarray(data_i12LFOV_file["darks"]),
+        cp.asarray(i12_dataset2_file["projdata"]),
+        i12_dataset2_file["angles"],
+        cp.asarray(i12_dataset2_file["flats"]),
+        cp.asarray(i12_dataset2_file["darks"]),
     )
 
 
-@pytest.fixture
-def i12sandstone_data(data_i12_sandstone_file):
-    return (
-        cp.asarray(data_i12_sandstone_file["projdata"]),
-        data_i12_sandstone_file["angles"],
-        cp.asarray(data_i12_sandstone_file["flats"]),
-        cp.asarray(data_i12_sandstone_file["darks"]),
-    )
+@pytest.fixture(scope="session")
+def geant4_dataset1_file(test_data_path):
+    in_file = os.path.join(test_data_path, "geant4_dataset1.npz")
+    return np.load(in_file)
 
 
 @pytest.fixture
-def geantsim_data(data_geant4sim_file):
+def geant4_dataset1(geant4_dataset1_file):
     return (
-        cp.asarray(data_geant4sim_file["projdata"]),
-        data_geant4sim_file["angles"],
-        cp.asarray(data_geant4sim_file["flats"]),
-        cp.asarray(data_geant4sim_file["darks"]),
+        cp.asarray(geant4_dataset1_file["projdata"]),
+        geant4_dataset1_file["angles"],
+        cp.asarray(geant4_dataset1_file["flats"]),
+        cp.asarray(geant4_dataset1_file["darks"]),
     )
 
 

zenodo-tests/test_recon/test_rotation.py

@@ -6,11 +6,11 @@
 from httomolibgpu.recon.rotation import find_center_vo
 
 
-def test_center_vo_i12LFOV(i12LFOV_data, ensure_clean_memory):
-    projdata = i12LFOV_data[0]
-    flats = i12LFOV_data[2]
-    darks = i12LFOV_data[3]
-    del i12LFOV_data
+def test_center_vo_i12_dataset2(i12_dataset2, ensure_clean_memory):
+    projdata = i12_dataset2[0]
+    flats = i12_dataset2[2]
+    darks = i12_dataset2[3]
+    del i12_dataset2
 
     data_normalised = normalize(projdata, flats, darks, minus_log=False)
     del flats, darks, projdata
@@ -22,11 +22,11 @@ def test_center_vo_i12LFOV(i12LFOV_data, ensure_clean_memory):
     assert cor.dtype == np.float32
 
 
-def test_center_vo_average_i12LFOV(i12LFOV_data, ensure_clean_memory):
-    projdata = i12LFOV_data[0]
-    flats = i12LFOV_data[2]
-    darks = i12LFOV_data[3]
-    del i12LFOV_data
+def test_center_vo_average_i12_dataset2(i12_dataset2, ensure_clean_memory):
+    projdata = i12_dataset2[0]
+    flats = i12_dataset2[2]
+    darks = i12_dataset2[3]
+    del i12_dataset2
 
     data_normalised = normalize(projdata, flats, darks, minus_log=False)
     del flats, darks, projdata
@@ -37,11 +37,11 @@ def test_center_vo_average_i12LFOV(i12LFOV_data, ensure_clean_memory):
     assert cor.dtype == np.float32
 
 
-def test_center_vo_i12_sandstone(i12sandstone_data, ensure_clean_memory):
-    projdata = i12sandstone_data[0]
-    flats = i12sandstone_data[2]
-    darks = i12sandstone_data[3]
-    del i12sandstone_data
+def test_center_vo_i12_dataset1(i12_dataset1, ensure_clean_memory):
+    projdata = i12_dataset1[0]
+    flats = i12_dataset1[2]
+    darks = i12_dataset1[3]
+    del i12_dataset1
 
     data_normalised = normalize(projdata, flats, darks, minus_log=True)
     del flats, darks, projdata
@@ -53,11 +53,11 @@ def test_center_vo_i12_sandstone(i12sandstone_data, ensure_clean_memory):
     assert cor.dtype == np.float32
 
 
-def test_center_vo_i12_geantsim(geantsim_data, ensure_clean_memory):
-    projdata = geantsim_data[0]
-    flats = geantsim_data[2]
-    darks = geantsim_data[3]
-    del geantsim_data
+def test_center_vo_geant4_dataset1(geant4_dataset1, ensure_clean_memory):
+    projdata = geant4_dataset1[0]
+    flats = geant4_dataset1[2]
+    darks = geant4_dataset1[3]
+    del geant4_dataset1
 
     data_normalised = normalize(projdata, flats, darks, minus_log=True)
     del flats, darks, projdata