assets_constants

CHANNELS_ASSETS_TYPES_CONFIG = {'aligned': {'basename': '<moving_channel,S>_to_<fixed_channel,S>/result.<N,1>', 'file_format_category': 'elastix_image', 'relevant_pipelines': ['registration'], 'resource_type': 'elastix'}, 'background': {'file_format_category': 'image', 'relevant_pipelines': ['CellMap', 'TubeMap', 'AxonMap'], 'resource_type': 'processed'}, 'binary': {'file_format_category': 'image', 'relevant_pipelines': ['TubeMap', 'AxonMap', 'TractMap'], 'resource_type': 'results', 'sub_types': ['status', 'smoothed', 'filled', 'deep_filled', 'postprocessed', 'combined', 'final', 'vesselize', 'median', 'pixels_raw', 'coordinates_transformed', 'coordinates_raw', 'labels']}, 'cells': {'file_format_category': 'table', 'relevant_pipelines': ['CellMap'], 'resource_type': 'results', 'sub_types': ['raw', 'filtered', 'shape', 'bkg']}, 'cells_stats': {'extensions': ['.csv', '.feather'], 'file_format_category': 'table', 'relevant_pipelines': ['CellMap'], 'resource_type': 'results'}, 'colocalization': {'file_format_category': 'table', 'relevant_pipelines': ['Colocalization'], 'resource_type': 'results', 'sub_types': ['report', 'filtered_report']}, 'density': {'file_format_category': 'portable_image', 'relevant_pipelines': ['CellMap', 'TubeMap', 'AxonMap', 'TractMap'], 'resource_type': 'results', 'sub_types': ['counts', 'intensities', 'branches']}, 'fixed_landmarks': {'basename': '<moving_channel,S>_to_<fixed_channel,S>/<fixed_channel,S>_landmarks', 'file_format_category': 'elastix_points', 'relevant_pipelines': ['registration'], 'resource_type': 'elastix'}, 'graph': {'file_format_category': 'graph', 'relevant_pipelines': ['TubeMap', 'AxonMap'], 'resource_type': 'graphs', 'sub_types': ['raw', 'cleaned', 'reduced', 'annotated', 'updated']}, 'layout': {'file_format_category': 'layout', 'relevant_pipelines': ['stitching'], 'resource_type': 'processed', 'sub_types': ['aligned', 'aligned_axis', 'placed']}, 'moving_landmarks': {'basename': '<moving_channel,S>_to_<fixed_channel,S>/<moving_channel,S>_landmarks', 'file_format_category': 'elastix_points', 'relevant_pipelines': ['registration'], 'resource_type': 'elastix'}, 'raw': {'file_format_category': 'image', 'relevant_pipelines': ['all'], 'resource_type': 'raw'}, 'resampled': {'file_format_category': 'portable_image', 'relevant_pipelines': ['registration'], 'resource_type': 'processed'}, 'skeleton': {'file_format_category': 'image', 'relevant_pipelines': ['TubeMap', 'AxonMap'], 'resource_type': 'results'}, 'stitched': {'file_format_category': 'image', 'relevant_pipelines': ['stitching'], 'resource_type': 'processed'}, 'tract_voxels': {'file_format_category': 'table', 'relevant_pipelines': ['TractMap'], 'resource_type': 'results', 'sub_types': ['raw', 'filtered', 'shape']}, 'vertices': {'extensions': ['.feather'], 'file_format_category': 'table', 'relevant_pipelines': ['TubeMap'], 'resource_type': 'results'}}

Assets that are not channel specific but global per sample.

CHECKSUM_ALGORITHMS = ('md5', 'sha1', 'sha256', 'sha512')

Mapping of resource types to the folder where they are stored.

Warning

Folders are relative to the root folder of the sample by default but can be absolute paths in which case they are used as is, ignoring the root folder of the sample.

DATA_CONTENT_TYPES = [None, 'undefined', 'no-pipeline', 'compound', 'colocalization', 'autofluorescence', 'nuclei', 'cells', 'vessels', 'veins', 'arteries', 'axons', 'atlas', 'myelin']

Assets that are channel specific. They may or may not make sense for a given channel based on the pipeline(s) relevant for that channel.

RESOURCE_TYPE_TO_FOLDER = {'atlas': 'atlas', 'config_snapshots': 'config_snapshots', 'data': '', 'elastix': '', 'graphs': '', 'logs': '', 'processed': '', 'raw': '', 'results': ''}

Mapping of content types (i.e. intrinsic labels) to the pipeline(s) that are relevant for that content type.