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Update run_with_minimal_input.md
Add "testing" set to datalist description Signed-off-by: Daniël Nobbe <[email protected]>
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auto3dseg/docs/run_with_minimal_input.md

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@@ -29,12 +29,19 @@ For the AutoRunner, you only need the `training` field with its list of training
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{"image": "/path/to/image_1.nii.gz", "label": "/path/to/label_1.nii.gz"},
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{"image": "/path/to/image_2.nii.gz", "label": "/path/to/label_2.nii.gz"},
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...
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],
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"testing":
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[
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"/path/to/test_image_1.nii.gz",
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"/path/to/test_image_2.nii.gz",
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...
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]
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}
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```
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In each training item, you can add a `fold` field (with an integer starting at 0) to pre-specify the cross-validation folds, otherwise the AutoRunner will generate its own folds (always 5). All trained algorithms will use the same generated or pre-specified folds, the file can be found in the `work_dir` folder that the AutoRunner generates.
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If you have a validation set, you can include it under a `validation` key with the same format as the `training` list. This will disable cross-validation.
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If you have a validation set, you can include it under a `validation` key with the same format as the `training` list. This will disable cross-validation.
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A "testing" list can also be added, which only requires the image files, not the labels. If it is included, the AutoRunner will output predictions on the testing set after training.
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It is recommended to add a `name` field and any other metadata fields that allow you to track which version of your dataset the models are trained on.
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Save the file to `./datalist.json`.

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