changes requested by Luca

quentinblampey · Feb 25, 2024 · c436785 · c436785
1 parent 3b3763b
commit c436785
Show file tree

Hide file tree

Showing 4 changed files with 13 additions and 12 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,3 +13,4 @@ and this project adheres to [Semantic Versioning][].
 ### Added
 
 -   Basic tool, preprocessing and plotting functions
+-   An experimental loader to load elemental ISS data objects, e.g. raw.tif, label.tif and anndata.h5ad
diff --git a/docs/api.md b/docs/api.md
@@ -20,4 +20,6 @@ I/O for the `spatialdata` project.
     steinbock
     merscope
     mcmicro
+
+    experimental - iss
 ```
diff --git a/src/spatialdata_io/__init__.py b/src/spatialdata_io/__init__.py
@@ -3,7 +3,6 @@
 from spatialdata_io.readers.codex import codex
 from spatialdata_io.readers.cosmx import cosmx
 from spatialdata_io.readers.curio import curio
-from spatialdata_io.readers.experimental.iss import iss
 from spatialdata_io.readers.mcmicro import mcmicro
 from spatialdata_io.readers.merscope import merscope
 from spatialdata_io.readers.steinbock import steinbock
@@ -18,7 +17,6 @@
     "cosmx",
     "mcmicro",
     "steinbock",
-    "iss",
     "merscope",
 ]
 

diff --git a/src/spatialdata_io/readers/experimental/iss.py b/src/spatialdata_io/readers/experimental/iss.py
@@ -40,21 +40,21 @@ def iss(
 
     Parameters
     ----------
-    path : str or Path
+    path
         Path to the directory containing the data.
-    raw_relative_path : str or Path
+    raw_relative_path
         Relative path to the raw raster image file.
-    label_relative_path : str or Path
+    label_relative_path
         Relative path to the label image file.
-    h5ad_relative_path : str or Path
+    h5ad_relative_path
         Relative path to the counts and metadata file.
-    dataset_id : str
+    dataset_id
         Dataset identifier.
-    imread_kwargs : Mapping[str, Any], optional
+    imread_kwargs
         Keyword arguments passed to :func:`dask_image.imread.imread`.
-    image_models_kwargs : Mapping[str, Any], optional
+    image_models_kwargs
         Keyword arguments passed to :class:`spatialdata.models.Image2DModel`.
-    label_models_kwargs : Mapping[str, Any], optional
+    label_models_kwargs
         Keyword arguments passed to :class:`spatialdata.models.Label2DModel`.
 
     Returns
@@ -77,7 +77,7 @@ def iss(
 
     label_image_parsed = Labels2DModel.parse(
         label_image,
-        scale_factors=[2, 4, 8, 16],
+        scale_factors=[2, 2, 2, 2],
         transformations={"global": transform_original},
         **label_models_kwargs,
     )
@@ -87,7 +87,7 @@ def iss(
 
     raw_image_parsed = Image2DModel.parse(
         raw_image,
-        scale_factors=[2, 4, 8, 16],
+        scale_factors=[2, 2, 2, 2],
         transformations={"global": transform_original},
         **image_models_kwargs,
     )