From fb67ee8253ee91322629e32e02d8a3eda22c0e62 Mon Sep 17 00:00:00 2001
From: Aliaksei <52605565+aliaksei-chareshneu@users.noreply.github.com>
Date: Mon, 23 Sep 2024 15:20:04 +0200
Subject: [PATCH 1/3] Update input.py

---
 preprocessor/cellstar_preprocessor/model/input.py | 1 -
 1 file changed, 1 deletion(-)

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'

From ba032f495e579a501db6cbc138c255475233a486 Mon Sep 17 00:00:00 2001
From: Aliaksei <52605565+aliaksei-chareshneu@users.noreply.github.com>
Date: Mon, 23 Sep 2024 15:24:57 +0200
Subject: [PATCH 2/3] remove deprecated type

remove deprecated type
---
 docs/docs/preprocessor/preprocess.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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: <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`.

From b2b61dbd7283c3f9e521e05395e4e5cfe28936f4 Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Wed, 25 Sep 2024 09:01:00 +0200
Subject: [PATCH 3/3] fix naming; remove comments

---
 db/cellstar_db/models.py | 14 ++------------
 1 file changed, 2 insertions(+), 12 deletions(-)

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