Project-MONAI / Project-MONAI/MONAI
ValueError: compressor cannot be used for arrays with zarr_format 3
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Description
======================================================================
ERROR: test_zarr_avg_merger_patches_13 (tests.inferers.test_zarr_avg_merger.ZarrAvgMergerTests.test_zarr_avg_merger_patches_13)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.11.12/x64/lib/python3.11/site-packages/parameterized/parameterized.py", line 620, in standalone_func
return func(*(a + p.args), **p.kwargs, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/MONAI/MONAI/tests/inferers/test_zarr_avg_merger.py", line 301, in test_zarr_avg_merger_patches
merger = ZarrAvgMerger(**arguments)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/MONAI/MONAI/monai/utils/module.py", line 477, in _wrapper
return call_obj(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/MONAI/MONAI/monai/inferers/merger.py", line 273, in __init__
self.output = zarr.empty(
^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.12/x64/lib/python3.11/site-packages/zarr/api/synchronous.py", line 1151, in empty
return Array(sync(async_api.empty(shape, **kwargs)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.12/x64/lib/python3.11/site-packages/zarr/core/sync.py", line 163, in sync
raise return_result
File "/opt/hostedtoolcache/Python/3.11.12/x64/lib/python3.11/site-packages/zarr/core/sync.py", line 119, in _runner
return await coro
^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.12/x64/lib/python3.11/site-packages/zarr/api/asynchronous.py", line 1097, in empty
return await create(shape=shape, fill_value=None, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.12/x64/lib/python3.11/site-packages/zarr/api/asynchronous.py", line 1055, in create
return await AsyncArray._create(
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.12/x64/lib/python3.11/site-packages/zarr/core/array.py", line 600, in _create
raise ValueError(
ValueError: compressor cannot be used for arrays with zarr_format 3. Use bytes-to-bytes codecs instead.
======================================================================
ERROR: test_zarr_avg_merger_patches_14 (tests.inferers.test_zarr_avg_merger.ZarrAvgMergerTests.test_zarr_avg_merger_patches_14)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.11.12/x64/lib/python3.11/site-packages/parameterized/parameterized.py", line 620, in standalone_func
return func(*(a + p.args), **p.kwargs, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/MONAI/MONAI/tests/inferers/test_zarr_avg_merger.py", line 301, in test_zarr_avg_merger_patches
merger = ZarrAvgMerger(**arguments)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/MONAI/MONAI/monai/utils/module.py", line 477, in _wrapper
return call_obj(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/MONAI/MONAI/monai/inferers/merger.py", line 273, in __init__
self.output = zarr.empty(
^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.12/x64/lib/python3.11/site-packages/zarr/api/synchronous.py", line 1151, in empty
return Array(sync(async_api.empty(shape, **kwargs)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.12/x64/lib/python3.11/site-packages/zarr/core/sync.py", line 163, in sync
raise return_result
File "/opt/hostedtoolcache/Python/3.11.12/x64/lib/python3.11/site-packages/zarr/core/sync.py", line 119, in _runner
return await coro
^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.12/x64/lib/python3.11/site-packages/zarr/api/asynchronous.py", line 1097, in empty
return await create(shape=shape, fill_value=None, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.12/x64/lib/python3.11/site-packages/zarr/api/asynchronous.py", line 1055, in create
return await AsyncArray._create(
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.12/x64/lib/python3.11/site-packages/zarr/core/array.py", line 600, in _create
raise ValueError(
ValueError: compressor cannot be used for arrays with zarr_format 3. Use bytes-to-bytes codecs instead.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start in monai/inferers/merger.py around the ZarrAvgMerger constructor and reproduce the failure with tests/inferers/test_zarr_avg_merger.py. Check how the output array is created and compare it with the failing Zarr API message. Done means the affected parameterized tests pass without the compressor and zarr_format error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data, testing-qa
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Active
- Clarity
- Mostly clear
- Newbie friendliness
- 68/100