[Bug report] - numpy.frombuffer buffer size error

[lpjiang97]

I did a fresh install of iblenv on a M2 MacBook running MacOS 15.3 but got an error when loading spikes:

from one.api import ONE
from brainbox.io.one import SpikeSortingLoader

one = ONE(
    base_url='https://openalyx.internationalbrainlab.org',
    password='international',
    silent=True,
)
eid = 'caa5dddc-9290-4e27-9f5e-575ba3598614'
pids, probes = one.eid2pid(eid)
loader = SpikeSortingLoader(one=one, pid=pids[0], eid=eid)

The code above produced the following error:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[5], line 1
----> 1 loader = SpikeSortingLoader(one=one, pid=pids[0], eid=eid)

File <string>:18, in __init__(self, one, atlas, pid, eid, pname, session_path, collections, datasets, files, raw_data_files, collection, histology, spike_sorter, spike_sorting_path, _sync)

File ~/.miniconda3/envs/iblenv/lib/python3.10/site-packages/brainbox/io/one.py:839, in SpikeSortingLoader.__post_init__(self)
    837 self.datasets = self.one.list_datasets(self.eid)
    838 if self.atlas is None:
--> 839     self.atlas = AllenAtlas()
    840 self.files = {}
    841 self.raw_data_files = []

File ~/.miniconda3/envs/iblenv/lib/python3.10/site-packages/iblatlas/atlas.py:1388, in AllenAtlas.__init__(self, res_um, scaling, mock, hist_path)
   1386     # loads the files
   1387     label = self._read_volume(file_label_remap)
-> 1388     image = self._read_volume(hist_path)
   1390 super().__init__(image, label, dxyz, regions, ibregma, dims2xyz=dims2xyz, xyz2dims=xyz2dims)

File ~/.miniconda3/envs/iblenv/lib/python3.10/site-packages/iblatlas/atlas.py:1395, in AllenAtlas._read_volume(file_volume)
   1392 @staticmethod
   1393 def _read_volume(file_volume):
   1394     if file_volume.suffix == '.nrrd':
-> 1395         volume, _ = nrrd.read(file_volume, index_order='C')  # ml, dv, ap
   1396         # we want the coronal slice to be the most contiguous
   1397         volume = np.transpose(volume, (2, 0, 1))  # image[iap, iml, idv]

File ~/.miniconda3/envs/iblenv/lib/python3.10/site-packages/nrrd/reader.py:526, in read(filename, custom_field_map, index_order)
    524 with open(filename, 'rb') as fh:
    525     header = read_header(fh, custom_field_map)
--> 526     data = read_data(header, fh, filename, index_order)
    528 return data, header

File ~/.miniconda3/envs/iblenv/lib/python3.10/site-packages/nrrd/reader.py:465, in read_data(header, fh, filename, index_order)
    461     del compressed_data
    463     # Byte skip is applied AFTER the decompression. Skip first x bytes of the decompressed data and parse it using
    464     # NumPy
--> 465     data = np.frombuffer(decompressed_data[byte_skip:], dtype)
    467 # Close the file if we opened it
    468 if data_filename is not None:

ValueError: buffer size must be a multiple of element size

To Reproduce

1. A fresh install of iblenv
2. Run the code snippet above

Expected behavior
A spike loader created without errors.

Hardware info

• Apple M2 Max
• OS: MacOS 15.3

pip freeze outputs

alabaster==1.0.0
anyio==4.8.0
appdirs==1.4.4
appnope==0.1.4
apptools==5.3.0
argon2-cffi==23.1.0
argon2-cffi-bindings==21.2.0
arrow==1.3.0
asttokens==3.0.0
async-lru==2.0.4
attrs==25.1.0
babel==2.17.0
beautifulsoup4==4.13.3
bleach==6.2.0
blinker==1.9.0
boto3==1.37.4
botocore==1.37.4
certifi==2025.1.31
cffi==1.17.1
charset-normalizer==3.4.1
click==8.1.8
cloudpickle==3.1.1
colorcet==3.1.0
colorlog==6.9.0
comm==0.2.2
contourpy==1.3.1
cryptography==44.0.1
cycler==0.12.1
Cython==3.0.12
dask==2025.2.0
dataclasses==0.6
datajoint==0.14.3
debugpy==1.8.12
decorator==5.2.1
defusedxml==0.7.1
docutils==0.21.2
easyqc==1.0.0
exceptiongroup==1.2.2
executing==2.2.0
Faker==36.1.1
fastjsonschema==2.21.1
figrid==0.1.7
flake8==7.1.2
Flask==3.1.0
fonttools==4.56.0
fqdn==1.5.1
fsspec==2025.2.0
globus-sdk==3.50.0
graphviz==0.20.3
h11==0.14.0
h5py==3.13.0
httpcore==1.0.7
httpx==0.28.1
ibl-neuropixel==1.6.2
ibl-style==0.1.0
-e git+https://github.com/int-brain-lab/iblapps@3bc02a225ad26faa44f4be3b0fa0fa3ab2d6ad27#egg=iblapps
iblatlas==0.5.6
ibllib==3.2.0
iblqt==0.4.2
iblutil==1.14.0
idna==3.10
imagecodecs==2024.12.30
imageio==2.37.0
imagesize==1.4.1
importlib_metadata==8.6.1
iniconfig==2.0.0
ipykernel==6.29.5
ipython==8.33.0
ipywidgets==8.1.5
isoduration==20.11.0
itsdangerous==2.2.0
jedi==0.19.2
Jinja2==3.1.5
jmespath==1.0.1
joblib==1.4.2
json5==0.10.0
jsonpointer==3.0.0
jsonschema==4.23.0
jsonschema-specifications==2024.10.1
jupyter==1.1.1
jupyter-console==6.6.3
jupyter-events==0.12.0
jupyter-lsp==2.2.5
jupyter_client==8.6.3
jupyter_core==5.7.2
jupyter_server==2.15.0
jupyter_server_terminals==0.5.3
jupyterlab==4.3.5
jupyterlab_pygments==0.3.0
jupyterlab_server==2.27.3
jupyterlab_widgets==3.0.13
kiwisolver==1.4.8
lazy_loader==0.4
llvmlite==0.44.0
locket==1.0.0
MarkupSafe==3.0.2
matplotlib==3.10.1
matplotlib-inline==0.1.7
mccabe==0.7.0
minio==7.2.15
mistune==3.1.2
mtscomp==1.0.2
narwhals==1.28.0
nbclient==0.10.2
nbconvert==7.16.6
nbformat==5.10.4
nest-asyncio==1.6.0
networkx==3.4.2
notebook==7.3.2
notebook_shim==0.2.4
npTDMS==1.10.0
numba==0.61.0
numpy==1.26.4
ONE-api==3.0.0
opencv-python==4.11.0.86
opencv-python-headless==4.11.0.86
otumat==0.3.1
overrides==7.7.0
packaging==24.2
pandas==2.2.3
pandocfilters==1.5.1
parso==0.8.4
partd==1.4.2
patsy==1.0.1
pexpect==4.9.0
phylib==2.6.0
pillow==11.1.0
platformdirs==4.3.6
plotly==6.0.0
pluggy==1.5.0
prometheus_client==0.21.1
prompt_toolkit==3.0.50
psutil==7.0.0
Psychofit==1.0.0.post0
ptyprocess==0.7.0
pure_eval==0.2.3
pyarrow==19.0.1
pycodestyle==2.12.1
pycparser==2.22
pycryptodome==3.21.0
pydot==3.0.4
pyerf==1.0.1
pyflakes==3.2.0
Pygments==2.19.1
PyJWT==2.10.1
PyMySQL==1.1.1
pynrrd==1.1.3
PyOpenGL==3.1.9
pyparsing==3.2.1
PyQt5==5.15.11
PyQt5-Qt5==5.15.16
PyQt5_sip==12.17.0
pyqtgraph==0.13.7
pytest==8.3.4
python-dateutil==2.9.0.post0
python-json-logger==3.2.1
pytz==2025.1
PyYAML==6.0.2
pyzmq==26.2.1
QtPy==2.4.3
referencing==0.36.2
requests==2.32.3
rfc3339-validator==0.1.4
rfc3986-validator==0.1.1
rpds-py==0.23.1
ruff==0.9.9
s3transfer==0.11.3
scikit-image==0.25.2
scikit-learn==1.6.1
scikits.bootstrap==1.1.0
scipy==1.15.2
seaborn==0.13.2
Send2Trash==1.8.3
SimpleITK==2.4.1
six==1.17.0
slidingRP==1.1.1
sniffio==1.3.1
snowballstemmer==2.2.0
soundfile==0.13.1
soupsieve==2.6
sparse==0.15.5
Sphinx==8.1.3
sphinx-gallery==0.19.0
sphinxcontrib-applehelp==2.0.0
sphinxcontrib-devhelp==2.0.0
sphinxcontrib-htmlhelp==2.1.0
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==2.0.0
sphinxcontrib-serializinghtml==2.0.0
stack-data==0.6.3
statsmodels==0.14.4
terminado==0.18.1
threadpoolctl==3.5.0
tifffile==2025.2.18
tinycss2==1.4.0
tomli==2.2.1
toolz==1.0.0
tornado==6.4.2
tqdm==4.67.1
traitlets==5.14.3
traits==7.0.2
types-python-dateutil==2.9.0.20241206
typing_extensions==4.12.2
tzdata==2025.1
uri-template==1.3.0
urllib3==2.3.0
watchdog==6.0.0
wcwidth==0.2.13
webcolors==24.11.1
webencodings==0.5.1
websocket-client==1.8.0
Werkzeug==3.1.3
widgetsnbextension==4.0.13
zipp==3.21.0