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Commit b9b1865

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xyi
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raise max images size and manually set chunk size
1 parent 3dc01c9 commit b9b1865

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Lines changed: 5 additions & 1 deletion

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  • src/spatialdata_io/readers

src/spatialdata_io/readers/g4x.py

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,6 +7,7 @@
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import dask.dataframe as dd
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import numpy as np
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import glymur
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import PIL
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from anndata.io import read_h5ad
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from dask.array.image import imread
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from spatialdata import SpatialData, to_polygons
@@ -22,9 +23,12 @@
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from spatialdata_io._constants._constants import G4XKeys
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from spatialdata_io._docs import inject_docs
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PIL.Image.MAX_IMAGE_PIXELS = 500000000
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__all__ = ["g4x"]
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@inject_docs(xx=G4XKeys)
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def g4x(
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input_path: str | Path,
@@ -355,7 +359,7 @@ def _write_he(
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kwargs["scale_factors"] = (
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[2, 2, 2] if "scale_factors" not in kwargs else kwargs["scale_factors"]
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)
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kwargs["chunks"] = "auto" if "chunks" not in kwargs else kwargs["chunks"]
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kwargs["chunks"] = [1, 1024, 1024] if "chunks" not in kwargs else kwargs["chunks"]
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sdata[img_key] = Image2DModel.parse(img, **kwargs)
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logger.debug(f"Writing Image2DModel for {img_key}")
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sdata.write_element(img_key)

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