Fail to read ome_metadata from certain czi files

[manerotoni]

Describe the Bug

Data recorded with a Zeiss LSM880 ZEN black Airyscan detector
Data Airy Processed with ZEN blue 3.8.89. It is a multiposition TZYX.

Attached is the metadata as extracted with Bioformats imageJ

Original Metadata - TCZYX_live_3scenes.zip

The error is also mentioned in https://forum.image.sc/t/extract-elapsed-time-timestamp-from-czi-metadata/84700/10

When performing

img = bioio.BioImage(fpath)
img.ome_metadata

I get the following error from ome_metadata and at a certain point it seems that bioio-czi.utils.transform_metadata_with_xslt unable to parse. Ideally it should just try and pass.

C:\Users\apoliti\Miniconda3\envs\chunk_format_kosti\lib\site-packages\xsdata\formats\converter.py:108: ConverterWarning: Failed to convert value `` to one of (<class 'float'>,)
  warnings.warn(
C:\Users\apoliti\Miniconda3\envs\chunk_format_kosti\lib\site-packages\pydantic\main.py:212: UserWarning: Casting invalid LightSourceID 'MTBLKM980LaserLine488' to 'LightSource:0'
  validated_self = self.__pydantic_validator__.validate_python(data, self_instance=self)
Traceback (most recent call last):
  File "D:\Code\chunkformat\test\test_util.py", line 28, in <module>
    img.ome_metadata
  File "C:\Users\apoliti\Miniconda3\envs\chunk_format_kosti\lib\site-packages\bioio\bio_image.py", line 943, in ome_metadata
    return self.reader.ome_metadata
  File "C:\Users\apoliti\Miniconda3\envs\chunk_format_kosti\lib\site-packages\bioio_czi\reader.py", line 912, in ome_metadata
    return metadata_utils.transform_metadata_with_xslt(
  File "C:\Users\apoliti\Miniconda3\envs\chunk_format_kosti\lib\site-packages\bioio_czi\utils.py", line 144, in transform_metadata_with_xslt
    ome = OME.from_xml(str(ome_etree))
  File "C:\Users\apoliti\Miniconda3\envs\chunk_format_kosti\lib\site-packages\ome_types\_mixins\_base_type.py", line 192, in from_xml
    return cast(T, from_xml(xml, **kwargs))
  File "C:\Users\apoliti\Miniconda3\envs\chunk_format_kosti\lib\site-packages\ome_types\_conversion.py", line 132, in from_xml
    return parser.parse(xml_2016, OME_type)
  File "C:\Users\apoliti\Miniconda3\envs\chunk_format_kosti\lib\site-packages\xsdata\formats\dataclass\parsers\bases.py", line 56, in parse
    result = handler.parse(source)
  File "C:\Users\apoliti\Miniconda3\envs\chunk_format_kosti\lib\site-packages\xsdata\formats\dataclass\parsers\handlers\lxml.py", line 40, in parse
    return self.process_context(ctx)
  File "C:\Users\apoliti\Miniconda3\envs\chunk_format_kosti\lib\site-packages\xsdata\formats\dataclass\parsers\handlers\lxml.py", line 62, in process_context
    self.parser.end(
  File "C:\Users\apoliti\Miniconda3\envs\chunk_format_kosti\lib\site-packages\xsdata\formats\dataclass\parsers\bases.py", line 151, in end
    return item.bind(qname, text, tail, objects)
  File "C:\Users\apoliti\Miniconda3\envs\chunk_format_kosti\lib\site-packages\xsdata\formats\dataclass\parsers\nodes\element.py", line 105, in bind
    obj = self.config.class_factory(self.meta.clazz, params)
  File "C:\Users\apoliti\Miniconda3\envs\chunk_format_kosti\lib\site-packages\xsdata\formats\dataclass\parsers\config.py", line 19, in default_class_factory
    return cls(**params)  # type: ignore
  File "C:\Users\apoliti\Miniconda3\envs\chunk_format_kosti\lib\site-packages\ome_types\_mixins\_kinded.py", line 20, in __init__
    return super().__init__(**data)
  File "C:\Users\apoliti\Miniconda3\envs\chunk_format_kosti\lib\site-packages\ome_types\_mixins\_base_type.py", line 104, in __init__
    super().__init__(**data)
  File "C:\Users\apoliti\Miniconda3\envs\chunk_format_kosti\lib\site-packages\pydantic\main.py", line 212, in __init__
    validated_self = self.__pydantic_validator__.validate_python(data, self_instance=self)
pydantic_core._pydantic_core.ValidationError: 1 validation error for Laser
wavelength
  Input should be a valid number, unable to parse string as a number [type=float_parsing, input_value='', input_type=str]
    For further information visit https://errors.pydantic.dev/2.9/v/float_parsing

Expected Behavior

No error

Reproduction

The data set is too big. I have to generate a smaller set. I do not see the behavior with all files. It seems something specific with the data set acquired on a particular machine and processed with a particular software.

Environment

• OS Version: windows 1-
• bioio-czi Version: 1.0.1

[BrianWhitneyAI]

@manerotoni Thank you for submitting this! If I am understanding your issue correctly you want to try to access .ome_metadata for your czi, bioio-czi fails to interpret this metadata and raises an error.

This is a little confusing but for our czi plugin .ome_metadata is just a transformation of the existing .metadata field using the xslt file.

    @property
    def ome_metadata(self) -> OME:
        return metadata_utils.transform_metadata_with_xslt(
            self.metadata,
            Path(__file__).parent / "czi-to-ome-xslt/xslt/czi-to-ome.xsl",
        )

so if you wanted the unprocessed metadata you can just access .metadata . Otherwise I think raising an error here makes sense as we could not get to a OME metadata output. Let me know what you think!