將 .h5 (HDF5) 文件轉換為 .zarr 格式時出現 TypeError

Question

我正在嘗試將 .h5 文件轉換為 .zarr 格式，但出現以下錯誤

TypeError: Object of type bytes_ is not JSON serializable

我在下面發布我的代碼

import h5py
import zarr
from sys import stdout

source = h5py.File('file.h5', 'r')
dest = zarr.open('file.zarr', 'w')
zarr.convenience.copy_all(source, dest, log=stdout, dry_run=False, if_exists='replace')

我檢查了 zarr 文檔，一些 github 問題，但無法弄清楚如何解決這個錯誤。

我正在添加我已經看過但找不到（或說實話）任何東西的鏈接

https://zarr.readthedocs.io/en/stable/api/convenience.html#zarr.convenience.copy_all

https://github.com/zarr-developers/zarr-python/issues/87

這是錯誤的回溯

Traceback (most recent call last):
  File "/home/prk/Documents/IISER-stuff/scripts/h5_to_zarr.py", line 8, in <module>
    zarr.convenience.copy_all(source, dest, log=stdout, dry_run=False, if_exists='replace')
  File "/home/prk/Documents/IISER-stuff/venv/lib/python3.8/site-packages/zarr/convenience.py", line 1063, in copy_all
    c, s, b = _copy(
  File "/home/prk/Documents/IISER-stuff/venv/lib/python3.8/site-packages/zarr/convenience.py", line 903, in _copy
    ds.attrs.update(source.attrs)
  File "/home/prk/Documents/IISER-stuff/venv/lib/python3.8/site-packages/zarr/attrs.py", line 120, in update
    self._write_op(self._update_nosync, *args, **kwargs)
  File "/home/prk/Documents/IISER-stuff/venv/lib/python3.8/site-packages/zarr/attrs.py", line 74, in _write_op
    return f(*args, **kwargs)
  File "/home/prk/Documents/IISER-stuff/venv/lib/python3.8/site-packages/zarr/attrs.py", line 131, in _update_nosync
    self._put_nosync(d)
  File "/home/prk/Documents/IISER-stuff/venv/lib/python3.8/site-packages/zarr/attrs.py", line 113, in _put_nosync
    self.store[self.key] = json_dumps(d)
  File "/home/prk/Documents/IISER-stuff/venv/lib/python3.8/site-packages/zarr/util.py", line 24, in json_dumps
    return json.dumps(o, indent=4, sort_keys=True, ensure_ascii=True,
  File "/usr/lib/python3.8/json/__init__.py", line 234, in dumps
    return cls(
  File "/usr/lib/python3.8/json/encoder.py", line 201, in encode
    chunks = list(chunks)
  File "/usr/lib/python3.8/json/encoder.py", line 431, in _iterencode
    yield from _iterencode_dict(o, _current_indent_level)
  File "/usr/lib/python3.8/json/encoder.py", line 405, in _iterencode_dict
    yield from chunks
  File "/usr/lib/python3.8/json/encoder.py", line 438, in _iterencode
    o = _default(o)
  File "/usr/lib/python3.8/json/encoder.py", line 179, in default
    raise TypeError(f'Object of type {o.__class__.__name__} '
TypeError: Object of type bytes_ is not JSON serializable

Answer 1

你有資源來試試這個命令行工具： https://github.com/saalfeldlab/n5-utils

安裝后調用

n5-copy -i file.h5 -o file.zarr

JSON 導出器處理字節元數據的方式可能只是一個小故障，這至少可以為您提供所需的副本。