Merge pull request #215 from scverse/fix/no_transformations_visium_hd

LucaMarconato · web-flow · commit ea0441c53f35 · 2024-10-31T01:40:00.000+09:00
Visium hd: get transformation matrices only if images are parsed
diff --git a/src/spatialdata_io/readers/visium_hd.py b/src/spatialdata_io/readers/visium_hd.py
@@ -107,7 +107,6 @@ def load_image(path: Path, suffix: str, scale_factors: list[int] | None = None)
         )
 
     metadata, hd_layout = _parse_metadata(path, filename_prefix)
-    transform_matrices = _get_transform_matrices(metadata, hd_layout)
     file_format = hd_layout[VisiumHDKeys.FILE_FORMAT]
     if file_format != "1.0":
         warnings.warn(
@@ -347,6 +346,7 @@ def _get_bins(path: Path) -> list[str]:
             suffix="_cytassist_image",
         )
         image = images[dataset_id + "_cytassist_image"]
+        transform_matrices = _get_transform_matrices(metadata, hd_layout)
         affine0 = transform_matrices["cytassist_colrow_to_spot_colrow"]
         affine1 = transform_matrices["spot_colrow_to_microscope_colrow"]
         set_transformation(image, Sequence([affine0, affine1]), "global")

Original file line number	Diff line number	Diff line change
`@@ -107,7 +107,6 @@ def load_image(path: Path, suffix: str, scale_factors: list[int] \| None = None)`
`107`	`107`	`)`
`108`	`108`
`109`	`109`	`metadata, hd_layout = _parse_metadata(path, filename_prefix)`
`110`		`- transform_matrices = _get_transform_matrices(metadata, hd_layout)`
`111`	`110`	`file_format = hd_layout[VisiumHDKeys.FILE_FORMAT]`
`112`	`111`	`if file_format != "1.0":`
`113`	`112`	`warnings.warn(`
`@@ -347,6 +346,7 @@ def _get_bins(path: Path) -> list[str]:`
`347`	`346`	`suffix="_cytassist_image",`
`348`	`347`	`)`
`349`	`348`	`image = images[dataset_id + "_cytassist_image"]`
	`349`	`+ transform_matrices = _get_transform_matrices(metadata, hd_layout)`
`350`	`350`	`affine0 = transform_matrices["cytassist_colrow_to_spot_colrow"]`
`351`	`351`	`affine1 = transform_matrices["spot_colrow_to_microscope_colrow"]`
`352`	`352`	`set_transformation(image, Sequence([affine0, affine1]), "global")`