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NeurodataWithoutBorders · Jul 20, 2024 · 18e3ecc · 18e3ecc
1 parent b7fb391
commit 18e3ecc
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Showing 2 changed files with 14 additions and 6 deletions.
diff --git a/lindi/LindiH5ZarrStore/LindiH5ZarrStore.py b/lindi/LindiH5ZarrStore/LindiH5ZarrStore.py
@@ -226,7 +226,10 @@ def close(self):
     def __getitem__(self, key):
         val = self._get_helper(key)
 
-        # Here's the hack
+        # If the key is a chunk and it's smaller than the expected size, then we
+        # need to pad it with zeros. This can happen if this is the final chunk
+        # in a contiguous hdf5 dataset. See
+        # https://github.com/NeurodataWithoutBorders/lindi/pull/84
         base_key = key.split('/')[-1]
         if val and _is_chunk_base_key(base_key):
             parent_key = key.split('/')[:-1]
@@ -238,9 +241,10 @@ def __getitem__(self, key):
                 chunk_shape = zarray['chunks']
                 dtype = zarray['dtype']
                 expected_chunk_size = int(np.prod(chunk_shape)) * _get_itemsize(dtype)
-                if len(val) != expected_chunk_size:
-                    # we need to pad it
+                if len(val) < expected_chunk_size:
                     val = _pad_chunk(val, expected_chunk_size)
+                elif len(val) > expected_chunk_size:
+                    raise Exception(f"Chunk size is larger than expected: {len(val)} > {expected_chunk_size}")
 
         return val
 

diff --git a/lindi/LindiH5pyFile/LindiReferenceFileSystemStore.py b/lindi/LindiH5pyFile/LindiReferenceFileSystemStore.py
@@ -124,7 +124,10 @@ def __contains__(self, key: object):
     def __getitem__(self, key: str):
         val = self._get_helper(key)
 
-        # Here's the hack
+        # If the key is a chunk and it's smaller than the expected size, then we
+        # need to pad it with zeros. This can happen if this is the final chunk
+        # in a contiguous hdf5 dataset. See
+        # https://github.com/NeurodataWithoutBorders/lindi/pull/84
         base_key = key.split('/')[-1]
         if val and _is_chunk_base_key(base_key):
             parent_key = key.split('/')[:-1]
@@ -136,9 +139,10 @@ def __getitem__(self, key: str):
                 chunk_shape = zarray['chunks']
                 dtype = zarray['dtype']
                 expected_chunk_size = int(np.prod(chunk_shape)) * _get_itemsize(dtype)
-                if len(val) != expected_chunk_size:
-                    # we need to pad it
+                if len(val) < expected_chunk_size:
                     val = _pad_chunk(val, expected_chunk_size)
+                elif len(val) > expected_chunk_size:
+                    raise Exception(f"Chunk size is larger than expected: {len(val)} > {expected_chunk_size}")
 
         return val