pandora2d.multiscale.check_configuration

This module contains functions allowing to check the configuration given to MVP pipeline.

Attributes

`multiscale_configuration_schema`
`pandora2d_configuration_schema`
`default_configuration_multiscale`

Functions

`tiff_area`(→ int)	Return tiff area for a given tif file_path
`get_tif_files_list`(→ List[pathlib.Path])	Return list of tif files in pyramid repository
`get_tif_shape_list`(→ List[Tuple])	Return list of tif files shape (height, width)
`is_repository_with_tif_file`(→ bool)	Check if the given path leads to a repository containing at least one readable tif file.
`is_json_file`(→ bool)	Check if the given path refers to a JSON file.
`check_pyramid_repositories`(first_pyramid_path, ...)	Check if first and second pyramid repositories contain the same number of tif files.
`check_mask_pyramid_repositories`(→ None)	Check if mask pyramid repository contains the same number of tif files as image pyramid repository.
`get_multiscale_config`(→ Dict[str, dict])	Get the multiscale configuration
`check_multiscale_section`(→ Dict[str, dict])	Check multiscale section of configuration
`get_pandora2d_config`(→ Dict[str, dict])	Get the pandora2d configuration
`check_pandora2d_section`(→ None)	Check pandora2d section of configuration
`update_pyramid_configuration`(→ None)	Update pyramid configurations with list of tif files sorted by ascending size
`check_conf`(→ Dict[str, dict])	Check multiscale configuration

Module Contents

pandora2d.multiscale.check_configuration.tiff_area(file_path: pathlib.Path | str) → int[source]

Return tiff area for a given tif file_path

Parameters:: file_path – path to tif file
Returns:: tif area width*height

pandora2d.multiscale.check_configuration.get_tif_files_list(path: pathlib.Path) → List[pathlib.Path][source]

Return list of tif files in pyramid repository sorted by file area

Parameters:: path – path to pyramid repository
Returns:: list of tif files sorted by size (width*height)

pandora2d.multiscale.check_configuration.get_tif_shape_list(tif_files_list: List[pathlib.Path]) → List[Tuple][source]

Return list of tif files shape (height, width)

Parameters:: tif_files_list – list of path to tif files
Returns:: list of shape (height, width) for each tif file in tif_files_list

pandora2d.multiscale.check_configuration.is_repository_with_tif_file(path: os.PathLike | str) → bool[source]

Check if the given path leads to a repository containing at least one readable tif file.

Parameters:: path – path to a repository
Returns:: whether the path refers to a valid repository or not

pandora2d.multiscale.check_configuration.is_json_file(path: str | pathlib.Path) → bool[source]

Check if the given path refers to a JSON file.

Parameters:: path – path to a JSON file
Returns:: whether the path refers to a JSON file or not

pandora2d.multiscale.check_configuration.check_pyramid_repositories(first_pyramid_path: str | pathlib.Path, second_pyramid_path: str | pathlib.Path)[source]

Check if first and second pyramid repositories contain the same number of tif files. Check if tif files have correct suffix.

This method is used to check that the left and right image pyramids contain the same number of images, and that, if masks are specified, there are as many masks as there are images in the pyramids.

Parameters:

first_pyramid_path – path to first pyramid repository
second_pyramid_path – path to second pyramid repository

pandora2d.multiscale.check_configuration.check_mask_pyramid_repositories(user_cfg: Dict) → None[source]

Check if mask pyramid repository contains the same number of tif files as image pyramid repository. Check if tif files have correct suffix.

Parameters:: user_cfg – user configuration

pandora2d.multiscale.check_configuration.get_multiscale_config(user_cfg: Dict[str, dict]) → Dict[str, dict][source]

Get the multiscale configuration

Parameters:: user_cfg – user configuration
Return cfg:: partial configuration

pandora2d.multiscale.check_configuration.check_multiscale_section(user_cfg) → Dict[str, dict][source]

Check multiscale section of configuration

Parameters:: user_cfg – user configuration
Returns:: cfg: checked multiscale configuration

pandora2d.multiscale.check_configuration.get_pandora2d_config(user_cfg: Dict[str, dict]) → Dict[str, dict][source]

Get the pandora2d configuration

Parameters:: user_cfg – user configuration
Return cfg:: partial configuration

pandora2d.multiscale.check_configuration.check_pandora2d_section(user_cfg) → None[source]

Check pandora2d section of configuration

Parameters:: user_cfg – user configuration
Returns:: cfg: checked pandora2d configuration

pandora2d.multiscale.check_configuration.update_pyramid_configuration(cfg_multiscale: Dict) → None[source]

Update pyramid configurations with list of tif files sorted by ascending size instead of path to pyramid repository.

Parameters:: cfg_multiscale – multiscale configuration

pandora2d.multiscale.check_configuration.check_conf(user_cfg: Dict) → Dict[str, dict][source]

Check multiscale configuration

Parameters:: user_cfg – user configuration
Returns:: cfg: checked multiscale configuration

pandora2d.multiscale.check_configuration.multiscale_configuration_schema[source]

pandora2d.multiscale.check_configuration.pandora2d_configuration_schema[source]

pandora2d.multiscale.check_configuration.default_configuration_multiscale[source]