Added Jola's IO fix for corrupted MRC files

src/caked/dataloader.py

@@ -312,8 +312,12 @@ def read(self, filename):
             return np.load(filename)
 
         if self.datatype == "mrc":
-            with mrcfile.open(filename) as f:
-                return np.array(f.data)
+            try:
+                with mrcfile.open(filename) as f:
+                    return np.array(f.data)
+            except ValueError as exc:
+                msg = f"File {filename} is corrupted."
+                raise ValueError(msg) from exc
 
         else:
             msg = "Currently we only support mrcfile and numpy arrays."

tests/corrupt.mrc

@@ -0,0 +1 @@
+This file is corrupt to test the exception throw.

tests/test_disk_io.py

@@ -12,6 +12,7 @@
 ORIG_DIR = Path.cwd()
 TEST_DATA_MRC = Path(testdata_mrc.__file__).parent
 TEST_DATA_NPY = Path(testdata_npy.__file__).parent
+TEST_CORRUPT = Path(__file__).parent / "corrupt.mrc"
 DISK_PIPELINE = "disk"
 DATASET_SIZE_ALL = None
 DATASET_SIZE_SOME = 3
@@ -366,3 +367,13 @@ def test_drop_last():
     )
     assert loader_train_false.drop_last
     assert loader_val_false.drop_last
+
+
+def test_corrupt_mrcfile():
+    """
+    Test that corrupt mrcfiles are not loaded and throw an exception.
+    """
+    test_dataset = DiskDataset(paths=TEST_DATA_MRC, datatype=DATATYPE_MRC)
+    assert isinstance(test_dataset, DiskDataset)
+    with pytest.raises(Exception, match=r".* corrupted."):
+        test_dataset.read(TEST_CORRUPT)