Merge pull request #40 from HumanBrainProject/fixes_for_upstream_updates

Fixes for upstream updates of NumPy and Nibabel

Author: ylep

src/neuroglancer_scripts/_compressed_segmentation.py

@@ -79,6 +79,7 @@ def _encode_channel(chunk_channel, block_size):
         (lookup_table, encoded_values) = np.unique(
             block, return_inverse=True, return_counts=False)
         bits = number_of_encoding_bits(len(lookup_table))
+        encoded_values = encoded_values.ravel()  # Numpy 2.0 compat
 
         # Write look-up table to the buffer (or re-use another one)
         lut_bytes = lookup_table.astype(block.dtype).tobytes()

src/neuroglancer_scripts/volume_reader.py

@@ -127,7 +127,7 @@ def nibabel_image_to_info(img,
 }}""".format(num_channels=shape[3] if len(shape) >= 4 else 1,
              data_type=guessed_dtype,
              size=list(shape[:3]),
-             resolution=[vs * 1000000 for vs in voxel_sizes[:3]])
+             resolution=[float(vs * 1_000_000) for vs in voxel_sizes[:3]])
 
     info = json.loads(formatted_info)  # ensure well-formed JSON