From cc62c1371bee5939ae3570b9faa0aef8bfdee961 Mon Sep 17 00:00:00 2001 From: Jonathan Tripp Date: Fri, 16 Jul 2021 15:06:03 +0100 Subject: [PATCH 1/4] Typo in docs for move movel --- docs/move_model.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/move_model.md b/docs/move_model.md index 3734d02ee..e3e703eee 100644 --- a/docs/move_model.md +++ b/docs/move_model.md @@ -17,7 +17,7 @@ for the `MODEL` and one for the `ENVIRONMENT` files. path: `python InnerEye/Scripts/move_model.py -a download --path ./ --workspace_name "" --resource_group "" --subscription_id "" --model_id "name:version"` - Upload from - path: `python InnerEye/Scripts/move_model.py - upload --path ./ --workspace_name "" --resource_group "" --subscription_id "" --model_id "name:version"` + path: `python InnerEye/Scripts/move_model.py -a upload --path ./ --workspace_name "" --resource_group "" --subscription_id "" --model_id "name:version"` 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 From 65a8ea85ed7611088c2b136de6f24f2a713c4e3c Mon Sep 17 00:00:00 2001 From: Jonathan Tripp Date: Fri, 16 Jul 2021 15:11:38 +0100 Subject: [PATCH 2/4] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) 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. From 119640d9743dda00fee5f60ea4d18e8c7f232a72 Mon Sep 17 00:00:00 2001 From: Jonathan Tripp Date: Fri, 16 Jul 2021 15:33:27 +0100 Subject: [PATCH 3/4] Expand explanation of move_model --- docs/move_model.md | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/docs/move_model.md b/docs/move_model.md index e3e703eee..ee36982fd 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 -a 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 From 91beef508b0d3e34dfcd895aac62958fc48a7fc4 Mon Sep 17 00:00:00 2001 From: Jonathan Tripp Date: Mon, 19 Jul 2021 13:22:32 +0100 Subject: [PATCH 4/4] Use --no- flag option --- docs/move_model.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/move_model.md b/docs/move_model.md index ee36982fd..4d34d1d41 100644 --- a/docs/move_model.md +++ b/docs/move_model.md @@ -25,4 +25,4 @@ workspace specified in the parameters. 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