aicsimageio.metadata package

Submodules

aicsimageio.metadata.utils module

aicsimageio.metadata.utils.bioformats_ome(path: Union[str, Path], original_meta: bool = False) → OME[source]

Retrieve OME meta from any compatible file, using bioformats.

Note: this function requires the bioformats_jar package to be installed.

Parameters

  • path (str or Path) – path to image

  • original_meta (bool, optional) – whether to also retrieve the proprietary metadata as structured annotations in the OME output, by default False

Returns

OME – The parsed metadata object.

Return type

ome_types.OME

Raises

  • ImportError – if bioformats_jar is not installed.

  • ValidationError – if ome_types.cannot parse the xml in the file

aicsimageio.metadata.utils.clean_ome_xml_for_known_issues(xml: str) → str[source]

Clean an OME XML string for known issues created by AICS or MicroManager systems and tools.

Commonly this is used for cleaning a file produced by AICS prior to noticing the issue (2021), or for other users of aicsimageio as a whole prior to 4.x series of releases.

The result of this function should be an OME XML string that is relatively the same (no major pieces missing) but that validates against the reference OME XSD.

Parameters

xml (str) – The OME XML string to clean for errors.

Returns

cleaned_xml – The cleaned OME XML string.

Return type

str

Raises

ValueError – Provided XML does not contain a namespace.

aicsimageio.metadata.utils.dtype_to_ome_type(npdtype: dtype) → PixelType[source]

Convert numpy dtype to OME PixelType

Parameters

npdtype (numpy.dtype) – A numpy datatype.

Returns

ome_type – One of the supported OME Pixels types

Return type

PixelType

Raises

ValueError – No matching pixel type for provided numpy type.

aicsimageio.metadata.utils.generate_ome_channel_id(image_id: str, channel_id: Union[str, int]) → str[source]

Naively generates the standard OME channel ID using a provided ID.

Parameters

  • image_id (str) – An image id to pull the image specific index from. See: generate_ome_image_id for more details.

  • channel_id (Union[str, int]) – A string or int representing the ID for a channel. In the context of the usage of this function, this is usually used with the index of the channel.

Returns

ome_channel_id – The OME standard for channel IDs.

Return type

str

Notes

ImageIds are usually: “Image:0”, “Image:1”, or “Image:N”, ChannelIds are usually the combination of image index + channel index – “Channel:0:0” for the first channel of the first image for example.

aicsimageio.metadata.utils.generate_ome_detector_id(detector_id: Union[str, int]) → str[source]

Naively generates the standard OME detector ID using a provided ID.

Parameters

detector_id (Union[str, int]) – A string or int representing the ID for a detector.

Returns

ome_detector_id – The OME standard for detector IDs.

Return type

str

aicsimageio.metadata.utils.generate_ome_image_id(image_id: Union[str, int]) → str[source]

Naively generates the standard OME image ID using a provided ID.

Parameters

image_id (Union[str, int]) – A string or int representing the ID for an image. In the context of the usage of this function, this is usually used with the index of the scene / image.

Returns

ome_image_id – The OME standard for image IDs.

Return type

str

aicsimageio.metadata.utils.generate_ome_instrument_id(instrument_id: Union[str, int]) → str[source]

Naively generates the standard OME instrument ID using a provided ID.

Parameters

instrument_id (Union[str, int]) – A string or int representing the ID for an instrument.

Returns

ome_instrument_id – The OME standard for instrument IDs.

Return type

str

aicsimageio.metadata.utils.get_coords_from_ome(ome: OME, scene_index: int) → Dict[str, Union[List[Any], ndarray, Array, Any]][source]

Process the OME metadata to retrieve the coordinate planes.

Parameters

  • ome (OME) – A constructed OME object to retrieve data from.

  • scene_index (int) – The current operating scene index to pull metadata from.

Returns

coords – The coordinate planes / data for each dimension.

Return type

Dict[str, Union[List[Any], Union[types.ArrayLike, Any]]]

aicsimageio.metadata.utils.get_dims_from_ome(ome: OME, scene_index: int) → List[str][source]

Process the OME metadata to retrieve the dimension names.

Parameters

  • ome (OME) – A constructed OME object to retrieve data from.

  • scene_index (int) – The current operating scene index to pull metadata from.

Returns

dims – The dimension names pulled from the OME metadata.

Return type

List[str]

aicsimageio.metadata.utils.ome_to_numpy_dtype(ome_type: PixelType) → dtype[source]

Convert OME PixelType to numpy dtype

Parameters

ome_type (PixelType) – One of the supported OME Pixels types

Returns

npdtype – A numpy datatype.

Return type

numpy.dtype

Raises

ValueError – No matching numpy type for the provided pixel type.

aicsimageio.metadata.utils.physical_pixel_sizes(ome: OME, scene: int = 0) → PhysicalPixelSizes[source]
Returns

sizes – Using available metadata, the floats representing physical pixel sizes for dimensions Z, Y, and X.

Return type

PhysicalPixelSizes

Notes

We currently do not handle unit attachment to these values. Please see the file metadata for unit information.

aicsimageio.metadata.utils.transform_metadata_with_xslt(tree: Element, xslt: Union[str, Path]) → OME[source]

Given an in-memory metadata Element and a path to an XSLT file, convert metadata to OME.

Parameters

  • tree (ET.Element) – The metadata tree to convert.

  • xslt (PathLike) – Path to the XSLT file.

Returns

ome – The generated / translated OME metadata.

Return type

OME

Notes

This function will briefly update your processes current working directory to the directory that stores the XSLT file.

Module contents