481 rotation of output images in prostate mri anatomy #482
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481-Rotation of output images in prostate_mri_anatomy - The transformations applied to the test data during preprocessing are not reversed during postprocessing. Thus, the resulting predictions have a different rotation compared to the original images and labels. I added an 'invertd()' function that reverses all the traceable transformations in the preprocessing. - Running the inference on a PC without a GPU leads to an error because the handlers function 'CheckpointLoader' attempts to load the model onto the GPU. I set the map_location argument to torch.device(device) so that it automatically loads the model onto the CPU when a GPU is not available. - Additionally, I changed some of the config directories as they were referring to the validation dataset rather than the test dataset. Signed-off-by: FaresAlMohamad <[email protected]>
updated version and changelog after adding an invertd transformation to postprocessing, setting the map_location argument of the checkpointloader in handlers to torch.devide(device) for CPU compatibility and changing some directories. The changes are documented in the history of the inference.json file of prostate_mri_anatomy. Signed-off-by: FaresAlMohamad <[email protected]>
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wyli
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Aug 28, 2023
Signed-off-by: Yiheng Wang <[email protected]>
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wyli
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Aug 29, 2023
yiheng-wang-nv
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Jul 29, 2024
) ### Description 481-Rotation of output images in prostate_mri_anatomy - The transformations applied to the test data during preprocessing are not reversed during postprocessing. Thus, the resulting predictions have a different rotation compared to the original images and labels. I added an 'invertd()' function that reverses all the traceable transformations in the preprocessing. - Running the inference on a PC without a GPU leads to an error because the handlers function 'CheckpointLoader' attempts to load the model onto the GPU. I set the map_location argument to torch.device(device) so that it automatically loads the model onto the CPU when a GPU is not available. - Additionally, I changed some of the config directories as they were referring to the validation dataset rather than the test dataset. ### Status Ready ### Please ensure all the checkboxes: <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Codeformat tests passed locally by running `./runtests.sh --codeformat`. - [x] Update `version` and `changelog` in `metadata.json` if changing an existing bundle. - [x] Please ensure the naming rules in config files meet our requirements (please refer to: `CONTRIBUTING.md`). - [x] Ensure versions of packages such as `monai`, `pytorch` and `numpy` are correct in `metadata.json`. - [x] Descriptions should be consistent with the content, such as `eval_metrics` of the provided weights and TorchScript modules. - [x] Files larger than 25MB are excluded and replaced by providing download links in `large_file.yml`. - [x] Avoid using path that contains personal information within config files (such as use `/home/your_name/` for `"bundle_root"`). --------- Signed-off-by: FaresAlMohamad <[email protected]>
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Description
481-Rotation of output images in prostate_mri_anatomy
Status
Ready
Please ensure all the checkboxes:
./runtests.sh --codeformat.versionandchangeloginmetadata.jsonif changing an existing bundle.CONTRIBUTING.md).monai,pytorchandnumpyare correct inmetadata.json.eval_metricsof the provided weights and TorchScript modules.large_file.yml./home/your_name/for"bundle_root").