add checkpoint
Browse files- inference.json +40 -11
inference.json
CHANGED
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@@ -1,6 +1,9 @@
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{
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"dataset_dir": "/workspace/data/
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"device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
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"network_def": {
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"_target_": "UNet",
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"spatial_dims": 3,
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@@ -34,6 +37,17 @@
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"_target_": "EnsureChannelFirstd",
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"keys": "image"
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},
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{
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"_target_": "ScaleIntensityRanged",
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"keys": "image",
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@@ -49,17 +63,9 @@
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}
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]
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},
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"datalist": {
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"_target_": "DatasetFunc",
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"data": "$@dataset_dir + '/dataset.json'",
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"func": "$monai.data.load_decathlon_datalist",
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"is_segmentation": true,
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"data_list_key": "test",
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"base_dir": "@dataset_dir"
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},
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"dataset": {
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"_target_": "Dataset",
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"data": "@datalist",
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"transform": "@preprocessing"
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},
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"dataloader": {
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@@ -87,6 +93,15 @@
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"keys": "pred",
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"softmax": true
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},
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{
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"_target_": "AsDiscreted",
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"keys": "pred",
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@@ -95,11 +110,24 @@
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{
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"_target_": "SaveImaged",
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"keys": "pred",
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"meta_keys": "
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"output_dir": "eval"
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}
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]
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},
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"evaluator": {
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"_target_": "SupervisedEvaluator",
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"device": "@device",
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@@ -107,6 +135,7 @@
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"network": "@network",
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"inferer": "@inferer",
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"postprocessing": "@postprocessing",
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"amp": false
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}
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}
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{
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"dataset_dir": "/workspace/data/Task09_Spleen",
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"ckpt_path": "/workspace/data//spleen_segmentation/models/model.pt",
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"log": "$__import__('logging').basicConfig(level=20)",
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"device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
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"datalist": "$list(sorted(__import__('glob').glob(@dataset_dir + '/imagesTs/*.nii.gz')))",
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"network_def": {
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"_target_": "UNet",
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"spatial_dims": 3,
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"_target_": "EnsureChannelFirstd",
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"keys": "image"
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},
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{
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"_target_": "Orientationd",
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"keys": "image",
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"axcodes": "RAS"
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},
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{
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"_target_": "Spacingd",
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"keys": "image",
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"pixdim": [1.5, 1.5, 2.0],
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"mode": "bilinear"
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},
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{
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"_target_": "ScaleIntensityRanged",
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"keys": "image",
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}
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]
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},
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"dataset": {
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"_target_": "Dataset",
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"data": "$[{'image': i} for i in @datalist]",
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"transform": "@preprocessing"
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},
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"dataloader": {
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"keys": "pred",
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"softmax": true
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},
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{
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"_target_": "Invertd",
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"keys": "pred",
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"transform": "@preprocessing",
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"orig_keys": "image",
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"meta_key_postfix": "meta_dict",
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"nearest_interp": false,
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"to_tensor": true
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},
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{
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"_target_": "AsDiscreted",
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"keys": "pred",
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{
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"_target_": "SaveImaged",
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"keys": "pred",
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"meta_keys": "pred_meta_dict",
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"output_dir": "eval"
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}
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]
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},
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"handlers": [
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{
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"_target_": "CheckpointLoader",
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"_disabled_": "$not __import__('os').path.exists(@ckpt_path)",
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"load_path": "@ckpt_path",
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"load_dict": {"model": "@network"}
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},
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{
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"_target_": "StatsHandler",
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"_disabled_": "@log",
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"iteration_log": false
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}
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],
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"evaluator": {
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"_target_": "SupervisedEvaluator",
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"device": "@device",
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"network": "@network",
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"inferer": "@inferer",
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"postprocessing": "@postprocessing",
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"val_handlers": "@handlers",
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"amp": false
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}
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}
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