nifti saver squeeze dims#1680
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rijobro merged 2 commits intoProject-MONAI:masterfrom Mar 3, 2021
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Signed-off-by: Richard Brown <[email protected]>
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fixes #1677. |
wyli
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thanks! looks good to me. (there's a similar workaround in niftynet https://github.com/NifTK/NiftyNet/blob/935bf4334cd00fa9f9d50f6a95ddcbfdde4031e0/niftynet/io/misc_io.py#L441-L450 proposed by @hjmjohnson )
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for the file path, I think it's originally from Clara Train where we want to save some other relevant predictions along with each |
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Fixes #1678.
Description
Currently
NiftiSaver(therefore defaultSaveImageandSaveImaged) saves images as(H,W,D,C), even if input image had no channel dimension, or was only a 2D image.This PR allows users to squeeze trailing singleton dimensions. If C==1, image will be saved as
(H,W,D). If D is also == 1, image will be saved as(H,W). If D==1, but C>1, image will still be saved as(H,W,D,C)(to avoid channel dimension being interpreted as depth).I also changed the saved path fromEDIT: I reverted this for backwards compatibility, but I still find it ugly./some/path/filename/filename.nii.gzto/some/path/filename.nii.gz, as I assumed the former was a mistake. I can undo this if it was intentional.Status
Ready
Types of changes
./runtests.sh --codeformat --coverage../runtests.sh --quick.make htmlcommand in thedocs/folder.