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Fixes dtype('>u2') key error when extracting 2d image #82

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Oct 2, 2023
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Fixes dtype('>u2') key error when extracting 2d image #82

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15 changes: 8 additions & 7 deletions pytools/HedwigZarrImage.py
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Original file line number Diff line number Diff line change
Expand Up @@ -157,17 +157,18 @@ def extract_2d(

zarr_request_size = [1, 0, 1, target_size_y * size_factor, target_size_x * size_factor]

arr = self._ome_ngff_get_array_from_size(zarr_request_size)
logger.debug(arr.info)
z_arr = self._ome_ngff_get_array_from_size(zarr_request_size)
logger.debug(z_arr.info)

arr = dask.array.from_zarr(arr.astype(arr.dtype.newbyteorder("=")))
d_arr = dask.array.from_zarr(z_arr)
d_arr = d_arr.astype(d_arr.dtype.newbyteorder("="))
if is_vector:
arr = dask.array.squeeze(arr, axis=(0, 2)) # Output CYX
arr = dask.array.moveaxis(arr, 0, -1) # transpose to YXC
d_arr = dask.array.squeeze(d_arr, axis=(0, 2)) # Output CYX
d_arr = dask.array.moveaxis(d_arr, 0, -1) # transpose to YXC
else:
arr = dask.array.squeeze(arr, axis=(0, 1, 2))
d_arr = dask.array.squeeze(d_arr, axis=(0, 1, 2))

img = sitk.GetImageFromArray(arr.compute(), isVector=is_vector)
img = sitk.GetImageFromArray(d_arr.compute(), isVector=is_vector)

logger.debug(img)

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