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fixes spacing/orientation xform ordering #3802

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Merged
wyli merged 2 commits into from
Feb 14, 2022
Merged

fixes spacing/orientation xform ordering #3802

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21c9dbc
following https://github.com/Project-MONAI/tutorials/issues/545
wyli Feb 14, 2022
58a9323
Merge branch 'dev' into fix-orientation
wyli Feb 14, 2022
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2 changes: 1 addition & 1 deletion docs/source/highlights.md
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Expand Up @@ -472,8 +472,8 @@ For example:
train_transforms = [
LoadImaged(...),
AddChanneld(...),
Spacingd(...),
Orientationd(...),
Spacingd(...),
ScaleIntensityRanged(...),
EnsureTyped(..., data_type="tensor"),
ToDeviced(..., device="cuda:0"),
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2 changes: 1 addition & 1 deletion monai/apps/deepgrow/dataset.py
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Expand Up @@ -126,8 +126,8 @@ def _default_transforms(image_key, label_key, pixdim):
[
LoadImaged(keys=keys),
AsChannelFirstd(keys=keys),
Spacingd(keys=keys, pixdim=pixdim, mode=mode),
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Orientationd(keys=keys, axcodes="RAS"),
Spacingd(keys=keys, pixdim=pixdim, mode=mode),
]
)

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4 changes: 4 additions & 0 deletions monai/transforms/spatial/dictionary.py
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Expand Up @@ -464,6 +464,10 @@ class Orientationd(MapTransform, InvertibleTransform):

After reorienting the input array, this transform will write the new affine
to the `affine` field of metadata which is formed by ``key_{meta_key_postfix}``.

This transform assumes the channel-first input format.
In the case of using this transform for normalizing the orientations of images,
it should be used before any anisotropic spatial transforms.
"""

backend = Orientation.backend
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