bioio_base

• bioio_base package
  • Submodules
  • bioio_base.benchmark module
    • BenchmarkDefinition
      • BenchmarkDefinition.prefix
      • BenchmarkDefinition.test
    • benchmark()
    • benchmark_test()
    • cleanup()
  • bioio_base.constants module
  • bioio_base.dimensions module
    • DimensionNames
      • DimensionNames.Channel
      • DimensionNames.MosaicTile
      • DimensionNames.Samples
      • DimensionNames.SpatialX
      • DimensionNames.SpatialY
      • DimensionNames.SpatialZ
      • DimensionNames.Time
    • Dimensions
      • Dimensions.items()
      • Dimensions.order
      • Dimensions.shape
  • bioio_base.exceptions module
    • ConflictingArgumentsError
    • InvalidDimensionOrderingError
    • UnexpectedShapeError
    • UnsupportedFileFormatError
  • bioio_base.image_container module
    • ImageContainer
      • ImageContainer.channel_names
      • ImageContainer.current_resolution_level
      • ImageContainer.current_scene
      • ImageContainer.current_scene_index
      • ImageContainer.dask_data
      • ImageContainer.data
      • ImageContainer.dims
      • ImageContainer.dtype
      • ImageContainer.get_image_dask_data()
      • ImageContainer.get_image_data()
      • ImageContainer.metadata
      • ImageContainer.physical_pixel_sizes
      • ImageContainer.resolution_levels
      • ImageContainer.scale
      • ImageContainer.scenes
      • ImageContainer.set_resolution_level()
      • ImageContainer.set_scene()
      • ImageContainer.shape
      • ImageContainer.standard_metadata
      • ImageContainer.time_interval
      • ImageContainer.xarray_dask_data
      • ImageContainer.xarray_data
  • bioio_base.io module
    • pathlike_to_fs()
  • bioio_base.noop_reader module
    • NoopReader
      • NoopReader.scenes
  • bioio_base.reader module
    • Reader
      • Reader.channel_names
      • Reader.current_resolution_level
      • Reader.current_scene
      • Reader.current_scene_index
      • Reader.dask_data
      • Reader.data
      • Reader.dims
      • Reader.dtype
      • Reader.get_dask_stack()
      • Reader.get_image_dask_data()
      • Reader.get_image_data()
      • Reader.get_mosaic_tile_position()
      • Reader.get_mosaic_tile_positions()
      • Reader.get_stack()
      • Reader.get_xarray_dask_stack()
      • Reader.get_xarray_stack()
      • Reader.is_supported_image()
      • Reader.metadata
      • Reader.mosaic_dask_data
      • Reader.mosaic_data
      • Reader.mosaic_tile_dims
      • Reader.mosaic_xarray_dask_data
      • Reader.mosaic_xarray_data
      • Reader.ome_metadata
      • Reader.physical_pixel_sizes
      • Reader.resolution_level_dims
      • Reader.resolution_levels
      • Reader.scale
      • Reader.scenes
      • Reader.set_resolution_level()
      • Reader.set_scene()
      • Reader.shape
      • Reader.standard_metadata
      • Reader.time_interval
      • Reader.xarray_dask_data
      • Reader.xarray_data
  • bioio_base.reader_metadata module
    • ReaderMetadata
      • ReaderMetadata.get_reader()
      • ReaderMetadata.get_supported_extensions()
  • bioio_base.standard_metadata module
    • StandardMetadata
      • StandardMetadata.FIELD_LABELS
      • StandardMetadata.binning
      • StandardMetadata.column
      • StandardMetadata.dimensions_present
      • StandardMetadata.image_size_c
      • StandardMetadata.image_size_t
      • StandardMetadata.image_size_x
      • StandardMetadata.image_size_y
      • StandardMetadata.image_size_z
      • StandardMetadata.imaged_by
      • StandardMetadata.imaging_datetime
      • StandardMetadata.objective
      • StandardMetadata.pixel_size_x
      • StandardMetadata.pixel_size_y
      • StandardMetadata.pixel_size_z
      • StandardMetadata.position_index
      • StandardMetadata.row
      • StandardMetadata.timelapse
      • StandardMetadata.timelapse_interval
      • StandardMetadata.to_dict()
      • StandardMetadata.total_time_duration
    • binning()
    • imaged_by()
    • imaging_datetime()
    • objective()
    • timelapse_interval()
    • total_time_duration()
  • bioio_base.test_utilities module
    • check_can_serialize_image_container()
    • check_local_file_not_open()
    • run_image_container_checks()
    • run_image_file_checks()
    • run_multi_scene_image_read_checks()
    • run_no_scene_name_image_read_checks()
    • run_reader_mosaic_checks()
  • bioio_base.transforms module
    • generate_stack()
    • reduce_to_slice()
    • reshape_data()
    • transpose_to_dims()
  • bioio_base.types module
    • PhysicalPixelSizes
      • PhysicalPixelSizes.X
      • PhysicalPixelSizes.Y
      • PhysicalPixelSizes.Z
    • Scale
      • Scale.C
      • Scale.T
      • Scale.X
      • Scale.Y
      • Scale.Z
  • bioio_base.writer module
    • Writer
      • Writer.save()
  • Module contents