diff --git a/CHANGELOG.md b/CHANGELOG.md index 35f86f040..1fba73d8f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ created. ## Upcoming ### Added +- ([#544](https://github.com/microsoft/InnerEye-DeepLearning/pull/544)) Add documentation for segmentation model evaluation. - ([#465](https://github.com/microsoft/InnerEye-DeepLearning/pull/465/)) Adding ability to run segmentation inference module on test data with partial ground truth files. (Also [522](https://github.com/microsoft/InnerEye-DeepLearning/pull/522).) - ([#502](https://github.com/microsoft/InnerEye-DeepLearning/pull/502)) More flags for fine control of when to run inference. diff --git a/docs/move_model.md b/docs/move_model.md index 3734d02ee..4d34d1d41 100644 --- a/docs/move_model.md +++ b/docs/move_model.md @@ -10,14 +10,19 @@ training time: If you want to export a model from one Workspace to another you can use the following command to download and upload a model from an AzureML workspace. This script does not use settings.yml, it uses interactive authentication, and the -workspace specified in the parameters. The model will be written to the path in --path parameter with two folders one -for the `MODEL` and one for the `ENVIRONMENT` files. +workspace specified in the parameters. -- Download to - path: `python InnerEye/Scripts/move_model.py -a download --path ./ --workspace_name "" --resource_group "" --subscription_id "" --model_id "name:version"` +- Download to path: -- Upload from - path: `python InnerEye/Scripts/move_model.py - upload --path ./ --workspace_name "" --resource_group "" --subscription_id "" --model_id "name:version"` +`python InnerEye/Scripts/move_model.py -a download --path ./ --workspace_name "" --resource_group "" --subscription_id "" --model_id "name:version"` + + The model will be downloaded to a subfolder called `name_version` (based on the `--model_id` parameter) of the path in `--path` parameter. For example, with `--model_id "my_model:100` this will be `my_model_100`. The subfolder will contain two folders: one for the `MODEL` and one for the `ENVIRONMENT` files. + +- Upload from path: + +`python InnerEye/Scripts/move_model.py -a upload --path ./ --workspace_name "" --resource_group "" --subscription_id "" --model_id "name:version"` + +The model is expected to be in the format above, i.e. contained in a subfolder called `name_version` of the path in `--path` parameter. The model will be automatically given the next available `id` once uploaded to the workspace. For example, if `my_model:100` already exists then it will be called `my_model:101`. Once in place you may want to run inference on the model with partial test data, i.e. test data from patients for whom -some of the labels are missing. Normally inference on partial test data would raise an exception. To allow inference to continue over partial test data add the flag `--allow_incomplete_labels` to your inference call, for example `python InnerEye/ML/runner.py --allow_incomplete_labels --train=False --azureml --model= --run_recovery_id=` \ No newline at end of file +some of the labels are missing. Normally inference on partial test data would raise an exception. To allow inference to continue over partial test data add the flag `--allow_incomplete_labels` to your inference call, for example `python InnerEye/ML/runner.py --allow_incomplete_labels --no-train --azureml --model= --run_recovery_id=` \ No newline at end of file