large_image_converter package

Submodules

large_image_converter.format_aperio module

large_image_converter.format_aperio.adjust_params(geospatial, params, **kwargs)[source]

Adjust options for aperio format.

Parameters
  • geospatial – True if the source is geospatial.

  • params – the conversion options. Possibly modified.

Returns

suffix: the recommended suffix for the new file.

large_image_converter.format_aperio.create_thumbnail_and_label(tempPath, info, ifdCount, needsLabel, labelPosition, **kwargs)[source]

Create a thumbnail and, optionally, label image for the aperio file.

Parameters
  • tempPath – a temporary file in a temporary directory.

  • info – the tifftools info that will be written to the tiff tile; modified.

  • ifdCount – the number of ifds in the first tiled image. This is 1 if there are subifds.

  • needsLabel – true if a label image needs to be added.

  • labelPosition – the position in the ifd list where a label image should be inserted.

large_image_converter.format_aperio.modify_tiff_before_write(info, ifdIndices, tempPath, lidata, **kwargs)[source]

Adjust the metadata and ifds for a tiff file to make it compatible with Aperio (svs).

Aperio files are tiff files which are stored without subifds in the order full res, optional thumbnail, half res, quarter res, …, full res, half res, quarter res, …, label, macro. All ifds have an ImageDescription that start with an aperio header followed by some dimension information and then an option key-.value list

Parameters
  • info – the tifftools info that will be written to the tiff tile; modified.

  • ifdIndices – the 0-based index of the full resolution ifd of each frame followed by the ifd of the first associated image.

  • tempPath – a temporary file in a temporary directory.

  • lidata – large_image data including metadata and associated images.

large_image_converter.format_aperio.modify_tiled_ifd(info, ifd, idx, ifdIndices, lidata, liDesc, **kwargs)[source]

Modify a tiled image to add aperio metadata and ensure tags are set appropriately.

Parameters
  • info – the tifftools info that will be written to the tiff tile; modified.

  • ifd – the full resolution ifd as read by tifftools.

  • idx – index of this ifd.

  • ifdIndices – the 0-based index of the full resolution ifd of each frame followed by the ifd of the first associated image.

  • lidata – large_image data including metadata and associated images.

  • liDesc – the parsed json from the original large_image_converter description.

large_image_converter.format_aperio.modify_vips_image_before_output(image, convertParams, **kwargs)[source]

Make sure the vips image is either 1 or 3 bands.

Parameters
  • image – a vips image.

  • convertParams – the parameters that will be used for compression.

Returns

a vips image.

Module contents

large_image_converter.convert(inputPath, outputPath=None, **kwargs)[source]

Take a source input file and output a pyramidal tiff file.

Parameters
  • inputPath – the path to the input file or base file of a set.

  • outputPath – the path of the output file.

Optional parameters that can be specified in kwargs:

Parameters
  • tileSize – the horizontal and vertical tile size.

  • format – one of ‘tiff’ or ‘aperio’. Default is ‘tiff’.

  • onlyFrame – None for all frames or the 0-based frame number to just convert a single frame of the source.

  • compression – one of ‘jpeg’, ‘deflate’ (zip), ‘lzw’, ‘packbits’, ‘zstd’, or ‘none’.

  • quality – a jpeg or webp quality passed to vips. 0 is small, 100 is high quality. 90 or above is recommended. For webp, 0 is lossless.

  • level – compression level for zstd, 1-22 (default is 10) and deflate, 1-9.

  • predictor – one of ‘none’, ‘horizontal’, ‘float’, or ‘yes’ used for lzw and deflate. Default is horizontal for non-geospatial data and yes for geospatial.

  • psnr – psnr value for jp2k, higher results in large files. 0 is lossless.

  • cr – jp2k compression ratio. 1 is lossless, 100 will try to make a file 1% the size of the original, etc.

  • subifds – if True (the default), when creating a multi-frame file, store lower resolution tiles in sub-ifds. If False, store all data in primary ifds.

  • overwrite – if not True, throw an exception if the output path already exists.

Additional optional parameters:

Parameters
  • geospatial – if not None, a boolean indicating if this file is geospatial. If not specified or None, this will be checked.

  • _concurrency – the number of cpus to use during conversion. None to use the logical cpu count.

Returns

outputPath if successful

large_image_converter.format_hook(funcname, *args, **kwargs)[source]

Call a function specific to a file format.

Parameters
  • funcname – name of the function.

  • args – parameters to pass to the function.

  • kwargs – parameters to pass to the function.

Returns

dependent on the function. False to indicate no further processing should be done.

large_image_converter.is_geospatial(path)[source]

Check if a path is likely to be a geospatial file.

Parameters

path – The path to the file

Returns

True if geospatial.

large_image_converter.is_vips(path)[source]

Check if a path is readable by vips.

Parameters

path – The path to the file

Returns

True if readable by vips.

large_image_converter.json_serial(obj)[source]

Fallback serializier for json. This serializes datetime objects to iso format.

Parameters

obj – an object to serialize.

Returns

a serialized string.