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Include dataset id in visium HD reader #278

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Merged
merged 2 commits into from
Feb 23, 2025
Merged

Include dataset id in visium HD reader #278

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47deae2
Include dataset id in visium HD reader
grst Feb 17, 2025
abe3d64
Merge branch 'main' into coord-system-names
LucaMarconato Feb 23, 2025
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19 changes: 12 additions & 7 deletions src/spatialdata_io/readers/visium_hd.py
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Original file line number Diff line number Diff line change
Expand Up @@ -242,9 +242,9 @@ def _get_bins(path_bins: Path) -> list[str]:
shapes_name = dataset_id + "_" + bin_size_str
radius = scalefactors[VisiumHDKeys.SCALEFACTORS_SPOT_DIAMETER_FULLRES] / 2.0
transformations = {
"global": transform_original,
"downscaled_hires": transform_hires,
"downscaled_lowres": transform_lowres,
dataset_id: transform_original,
f"{dataset_id}_downscaled_hires": transform_hires,
f"{dataset_id}_downscaled_lowres": transform_lowres,
}
circles = ShapesModel.parse(
adata.obsm["spatial"],
Expand Down Expand Up @@ -322,7 +322,10 @@ def _get_bins(path_bins: Path) -> list[str]:
)
set_transformation(
images[dataset_id + "_hires_image"],
{"downscaled_hires": Identity(), "global": transform_hires.inverse()},
{
f"{dataset_id}_downscaled_hires": Identity(),
dataset_id: transform_hires.inverse(),
},
set_all=True,
)

Expand All @@ -340,7 +343,10 @@ def _get_bins(path_bins: Path) -> list[str]:
)
set_transformation(
images[dataset_id + "_lowres_image"],
{"downscaled_lowres": Identity(), "global": transform_lowres.inverse()},
{
f"{dataset_id}_downscaled_lowres": Identity(),
dataset_id: transform_lowres.inverse(),
},
set_all=True,
)

Expand All @@ -365,7 +371,7 @@ def _get_bins(path_bins: Path) -> list[str]:
projective /= projective[2, 2]
if _projective_matrix_is_affine(projective):
affine = Affine(projective, input_axes=("x", "y"), output_axes=("x", "y"))
set_transformation(image, affine, "global")
set_transformation(image, affine, dataset_id)
else:
# the projective matrix is not affine, we will separate the affine part and the projective shift, and apply
# the projective shift to the image
Expand Down Expand Up @@ -413,7 +419,6 @@ def _get_bins(path_bins: Path) -> list[str]:

if annotate_table_by_labels:
for bin_size_str in bin_sizes:

shapes_name = dataset_id + "_" + bin_size_str

# add labels layer (rasterized bins).
Expand Down
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