fix visium axes ordering for many versions AND cytassist. (#94)

* update

* update precomit

* fix precommit

.gitignore

@@ -30,3 +30,4 @@ __pycache__/
 
 # other
 _version.py
+.code-workspace

.pre-commit-config.yaml

@@ -7,11 +7,11 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
     - repo: https://github.com/psf/black
-      rev: 23.10.1
+      rev: 23.11.0
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v3.0.3
+      rev: v3.1.0
       hooks:
           - id: prettier
     - repo: https://github.com/asottile/blacken-docs
@@ -23,7 +23,7 @@ repos:
       hooks:
           - id: isort
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.6.1
+      rev: v1.7.1
       hooks:
           - id: mypy
             additional_dependencies: [numpy, types-PyYAML]

src/spatialdata_io/readers/_utils/_utils.py

@@ -10,7 +10,7 @@
 
 from spatialdata_io.readers._utils._read_10x_h5 import _read_10x_h5
 
-PathLike = Union[os.PathLike, str]
+PathLike = Union[os.PathLike, str]  # type:ignore[type-arg]
 
 try:
     from numpy.typing import NDArray

src/spatialdata_io/readers/visium.py

@@ -141,7 +141,7 @@ def visium(
     elif (path / "spatial" / VisiumKeys.SPOTS_FILE_2).exists() or (
         tissue_positions_file is not None and str(VisiumKeys.SPOTS_FILE_2) in str(tissue_positions_file)
     ):
-        read_coords = partial(pd.read_csv, header=1, index_col=0)
+        read_coords = partial(pd.read_csv, header=0, index_col=0)
         tissue_positions_file = (
             path / "spatial" / VisiumKeys.SPOTS_FILE_2
             if tissue_positions_file is None
@@ -151,7 +151,13 @@ def visium(
         raise ValueError(f"Cannot find `tissue_positions` file in `{path}`.")
     coords = read_coords(tissue_positions_file)
 
-    coords.columns = ["in_tissue", "array_row", "array_col", "pxl_col_in_fullres", "pxl_row_in_fullres"]
+    # to handle spaceranger_version < 2.0.0, where no column names are provided
+    # in fact, from spaceranger 2.0.0, the column names are provided in the file, and
+    # are "pxl_col_in_fullres", "pxl_row_in_fullres" are inverted.
+    # But, in the case of CytAssist, the column names provided but the image is flipped
+    # so we need to invert the columns.
+    if "in_tissue" not in coords.columns or "CytAssist" in str(fullres_image_file):
+        coords.columns = ["in_tissue", "array_row", "array_col", "pxl_col_in_fullres", "pxl_row_in_fullres"]
 
     adata.obs = pd.merge(adata.obs, coords, how="left", left_index=True, right_index=True)
     coords = adata.obs[[VisiumKeys.SPOTS_X, VisiumKeys.SPOTS_Y]].values