Minor fixes

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
 

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: <code>[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]</code>. See examples for more details. |
+  |`--input-kind` | Kind of input file. One of the following: <code>[map\|sff\|omezarr\|mask\|application_specific_segmentation\|custom_annotations\|nii_volume\|nii_segmentation\|geometric_segmentation\|ometiff_image\|ometiff_segmentation\|extra_data]</code>. See examples for more details. |
 
 
 As one can see, `preprocess` command has two possible modes for the `preprocess`: `add` and `extend`.

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'