Merge pull request #200 from scverse/fix/visium_old_data_with_header

Fixes header bug Visium data #146

src/spatialdata_io/readers/visium.py

@@ -4,7 +4,6 @@
 import os
 import re
 from collections.abc import Mapping
-from functools import partial
 from pathlib import Path
 from types import MappingProxyType
 from typing import Any
@@ -138,7 +137,6 @@ def visium(
     if (path / "spatial" / VisiumKeys.SPOTS_FILE_1).exists() or (
         tissue_positions_file is not None and str(VisiumKeys.SPOTS_FILE_1) in str(tissue_positions_file)
     ):
-        read_coords = partial(pd.read_csv, header=None, index_col=0)
         tissue_positions_file = (
             path / "spatial" / VisiumKeys.SPOTS_FILE_1
             if tissue_positions_file is None
@@ -147,19 +145,25 @@ 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=0, index_col=0)
         tissue_positions_file = (
             path / "spatial" / VisiumKeys.SPOTS_FILE_2
             if tissue_positions_file is None
             else path / tissue_positions_file
         )
     else:
         raise ValueError(f"Cannot find `tissue_positions` file in `{path}`.")
-    coords = read_coords(tissue_positions_file)
+    coords = pd.read_csv(tissue_positions_file, header=None, index_col=0)
 
-    # to handle spaceranger_version < 2.0.0, where no column names are provided
-    if "in_tissue" not in coords.columns:
-        coords.columns = ["in_tissue", "array_row", "array_col", "pxl_row_in_fullres", "pxl_col_in_fullres"]
+    if tissue_positions_file.name == VisiumKeys.SPOTS_FILE_1:
+        # spaceranger_version < 2.0.0 but header detected: https://github.com/scverse/spatialdata-io/issues/146
+        if "in_tissue" in coords.iloc[0].tolist():
+            coords = pd.read_csv(tissue_positions_file, header=0, index_col=0)
+        else:
+            assert "in_tissue" not in coords.columns
+            coords.columns = ["in_tissue", "array_row", "array_col", "pxl_row_in_fullres", "pxl_col_in_fullres"]
+    else:
+        assert tissue_positions_file.name == VisiumKeys.SPOTS_FILE_2
+        coords = pd.read_csv(tissue_positions_file, header=0, index_col=0)
 
     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