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fix visium hd wrong global coordinate system #303

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Merged
melonora merged 1 commit into from
Apr 16, 2025
Merged

fix visium hd wrong global coordinate system #303

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12 changes: 9 additions & 3 deletions src/spatialdata_io/readers/visium_hd.py
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Original file line number Diff line number Diff line change
Expand Up @@ -379,7 +379,7 @@ def _get_bins(path_bins: Path) -> list[str]:
affine = Affine(affine_matrix, input_axes=("x", "y"), output_axes=("x", "y"))

# determine the size of the transformed image
bounding_box = get_extent(image)
bounding_box = get_extent(image, coordinate_system=dataset_id)
x0, x1 = bounding_box["x"]
y0, y1 = bounding_box["y"]
x1 -= 1
Expand Down Expand Up @@ -410,7 +410,7 @@ def _get_bins(path_bins: Path) -> list[str]:
numpy_data, ProjectiveTransform(projective_shift).inverse, output_shape=transformed_shape, order=1
)
warped = np.round(warped * 255).astype(np.uint8)
warped = Image2DModel.parse(warped, dims=("y", "x", "c"), transformations={"global": affine}, rgb=True)
warped = Image2DModel.parse(warped, dims=("y", "x", "c"), transformations={dataset_id: affine}, rgb=True)

# we replace the cytassist image with the warped image
images[dataset_id + "_cytassist_image"] = warped
Expand Down Expand Up @@ -484,7 +484,13 @@ def _load_image(
), "When the image is not in RGB, the first dimension should be the number of channels."

image = DataArray(data, dims=("c", "y", "x"))
parsed = Image2DModel.parse(image, scale_factors=scale_factors, rgb=None, **image_models_kwargs)
parsed = Image2DModel.parse(
image,
scale_factors=scale_factors,
rgb=None,
transformations={dataset_id: Identity()},
**image_models_kwargs,
)
images[dataset_id + suffix] = parsed
else:
warnings.warn(f"File {path} does not exist, skipping it.", UserWarning, stacklevel=2)
Expand Down
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