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Update auto3dseg algorithm templates#184

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dongyang0122 merged 4 commits intoProject-MONAI:mainfrom
dongyang0122:auto3dseg_update_scripts
Feb 10, 2023
Merged

Update auto3dseg algorithm templates#184
dongyang0122 merged 4 commits intoProject-MONAI:mainfrom
dongyang0122:auto3dseg_update_scripts

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@dongyang0122
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Update auto3dseg algorithm templates for performance (accuracy) and efficiency improvement.

dongy added 2 commits January 19, 2023 12:19
Signed-off-by: dongy <[email protected]>
Signed-off-by: dongy <[email protected]>
@mingxin-zheng
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I would like to hear @Nic-Ma 's thought on the ConfigParser. Since we already use num_epochs_per_validation in lots of places, such as the unit tests of MONAI, tutorials of Auto3DSeg, I feel hesitated to make such change.

@Nic-Ma
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Nic-Ma commented Feb 2, 2023

Hi @dongyang0122 @mingxin-zheng ,

I tried to reproduce the issue with below config:

{
    "data": [1, 2],
    "data_per_batch": 2,
    "transform": {
        "_target_": "Compose",
        "transforms": [
            {"_target_": "LoadImaged", "keys": "image"},
            {"_target_": "RandTorchVisiond", "keys": "@##0#keys", "name": "ColorJitter", "brightness": 0.25},
        ],
    },
    "dataset": {"_target_": "Dataset", "data": "@data", "transform": "@transform"},
    "dataloader": {
        "_target_": "DataLoader",
        "dataset": "@##dataset",
        "batch_size": "@data_per_batch",
        "collate_fn": "$monai.data.list_data_collate",
    },
}

But seems the first 2 lines can be parsed OK:

"data": [1, 2],
"data_per_batch": 2

Could you please help provide a simple program to reproduce the issue you asked?

Thanks.

Signed-off-by: dongy <[email protected]>
@mingxin-zheng
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Hi @dongyang0122 , if the fix in the dev branch has resolved the issue of num_epoch_*, can we revert the name of the variable back to num_epochs_per_validation?

@dongyang0122
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Hi @dongyang0122 , if the fix in the dev branch has resolved the issue of num_epoch_*, can we revert the name of the variable back to num_epochs_per_validation?

If we convert it back to previous name, then we have to inform users to install monai from the dev branch. I feel it adds another layer of complexity for general users. how about converting it back once the changes are reflected in the installation via pip install monai? and meanwhile we can merge the changes at the moment.

Signed-off-by: dongy <[email protected]>
@dongyang0122 dongyang0122 merged commit 922ac66 into Project-MONAI:main Feb 10, 2023
wyli pushed a commit to Project-MONAI/MONAI that referenced this pull request Mar 15, 2023
Signed-off-by: Mingxin Zheng
<[email protected]>

Fixes #5972 .

### Description
Fix and New Feature included:
- fix cache rate:
Project-MONAI/research-contributions#173
- typo fix
Project-MONAI/research-contributions#178
- scheduler step fix
Project-MONAI/research-contributions#182
- enhancement
Project-MONAI/research-contributions#184
- Fixed pretrain weight loading
Project-MONAI/research-contributions#202

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [x] `python tests/test_integration_autorunner.py` succeeded locally

---------

Signed-off-by: Mingxin Zheng <[email protected]>
@dongyang0122 dongyang0122 deleted the auto3dseg_update_scripts branch June 5, 2023 13:27
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3 participants