diff --git a/db/cellstar_db/models.py b/db/cellstar_db/models.py index e21f200a..da63455f 100644 --- a/db/cellstar_db/models.py +++ b/db/cellstar_db/models.py @@ -84,15 +84,9 @@ class VolumeExtraData(TypedDict): class SegmentationExtraData(TypedDict): voxel_size: list[float, float, float] | None - # map segmentation number (dimension) in case of >3D array (e.g. OMETIFF) - # or in case segmentation ids are given as numbers by default - # to segmentation id (string) segmentation_ids_mapping: dict[str, str] | None - # lattice_id (artificial, keys from segmentation_ids_mapping) - # to dict with keys = segment ids and values = segment names? - # could work, easier than modify descriptions via preprocessor command - # CURRENTLY IS A KEY THAT IS PROVIDED IN SEGMENTATION_IDS_MAPPING - segment_ids_to_segment_names_mapping: dict[str, dict[str, str]] | None + # NOTE: CURRENTLY IS A KEY THAT IS PROVIDED IN SEGMENTATION_IDS_MAPPING + custom_segment_ids_mapping: dict[str, dict[str, str]] | None # could have key = "ometiff" dataset_specific_data: object | None @@ -101,10 +95,6 @@ class ExtraData(TypedDict): entry_metadata: Optional[EntryMetadata] volume: Optional[VolumeExtraData] segmentation: Optional[SegmentationExtraData] - # for custom things - # metadata: Optional[object] - # dataset_specific_data: Optional[object] - # METADATA DATA MODEL diff --git a/docs/docs/preprocessor/preprocess.md b/docs/docs/preprocessor/preprocess.md index 2e446485..00b8f554 100644 --- a/docs/docs/preprocessor/preprocess.md +++ b/docs/docs/preprocessor/preprocess.md @@ -20,7 +20,7 @@ The `preprocess` command of `preprocessor/cellstar_preprocessor/preprocess.py` s |`--working-folder` | path to directory where temporary files will be stored during the build process | |`--db-path` | path to folder with database | |`--input-path` | Path to input file. Should be provided for each input file separately (see examples) | - |`--input-kind` | Kind of input file. One of the following: [map\|sff\|omezarr\|mask\|application_specific_segmentation\|custom_annotations\|nii_volume\|nii_segmentation\|geometric_segmentation\|star_file_geometric_segmentation\|ometiff_image\|ometiff_segmentation\|extra_data]. See examples for more details. | + |`--input-kind` | Kind of input file. One of the following: [map\|sff\|omezarr\|mask\|application_specific_segmentation\|custom_annotations\|nii_volume\|nii_segmentation\|geometric_segmentation\|ometiff_image\|ometiff_segmentation\|extra_data]. See examples for more details. | As one can see, `preprocess` command has two possible modes for the `preprocess`: `add` and `extend`. diff --git a/preprocessor/cellstar_preprocessor/model/input.py b/preprocessor/cellstar_preprocessor/model/input.py index 5ef56561..e7685eb5 100644 --- a/preprocessor/cellstar_preprocessor/model/input.py +++ b/preprocessor/cellstar_preprocessor/model/input.py @@ -31,7 +31,6 @@ class InputKind(str, Enum): nii_volume = "nii_volume" nii_segmentation = "nii_segmentation" geometric_segmentation = "geometric_segmentation" - star_file_geometric_segmentation = "star_file_geometric_segmentation" ometiff_image = "ometiff_image" ometiff_segmentation = "ometiff_segmentation" # allencell_metadata_csv = 'extra_data'