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'