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{
"imports": [
"$import torch",
"$import json",
"$import ignite"
],
"bundle_root": "/workspace/bundle/endoscopic_inbody_classification",
"ckpt_dir": "$@bundle_root + '/models'",
"output_dir": "$@bundle_root + '/eval'",
"dataset_dir": "/workspace/data/endoscopic_inbody_classification",
"train_json": "$@bundle_root+'/label/train_samples.json'",
"val_json": "$@bundle_root+'/label/val_samples.json'",
"train_fp": "$open(@train_json,'r', encoding='utf8')",
"train_dict": "$json.load(@train_fp)",
"train_close": "$@train_fp.close()",
"val_fp": "$open(@val_json,'r', encoding='utf8')",
"val_dict": "$json.load(@val_fp)",
"val_interval": 1,
"val_close": "$@val_fp.close()",
"device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
"network_def": {
"_target_": "SEResNet50",
"spatial_dims": 2,
"in_channels": 3,
"num_classes": 2
},
"network": "$@network_def.to(@device)",
"loss": {
"_target_": "torch.nn.CrossEntropyLoss",
"reduction": "sum"
},
"optimizer": {
"_target_": "torch.optim.Adam",
"params": "$@network.parameters()",
"lr": 0.001
},
"train": {
"deterministic_transforms": [
{
"_target_": "LoadImaged",
"keys": "image"
},
{
"_target_": "ToTensord",
"keys": "label"
},
{
"_target_": "AsChannelFirstd",
"keys": "image"
},
{
"_target_": "Resized",
"keys": "image",
"spatial_size": [
256,
256
],
"mode": "bilinear"
},
{
"_target_": "CastToTyped",
"dtype": "$torch.float32",
"keys": "image"
},
{
"_target_": "NormalizeIntensityd",
"nonzero": true,
"channel_wise": true,
"keys": "image"
},
{
"_target_": "EnsureTyped",
"keys": "image"
}
],
"random_transforms": [
{
"_target_": "RandRotated",
"range_x": 0.3,
"prob": 0.2,
"mode": "bilinear",
"keys": "image"
},
{
"_target_": "RandScaleIntensityd",
"factors": 0.3,
"prob": 0.5,
"keys": "image"
},
{
"_target_": "RandShiftIntensityd",
"offsets": 0.1,
"prob": 0.5,
"keys": "image"
},
{
"_target_": "RandGaussianNoised",
"std": 0.01,
"prob": 0.15,
"keys": "image"
},
{
"_target_": "RandFlipd",
"spatial_axis": 0,
"prob": 0.5,
"keys": "image"
},
{
"_target_": "RandFlipd",
"spatial_axis": 1,
"prob": 0.5,
"keys": "image"
}
],
"preprocessing": {
"_target_": "Compose",
"transforms": "$@train#deterministic_transforms + @train#random_transforms"
},
"dataset": {
"_target_": "Dataset",
"data": "@train_dict",
"transform": "@train#preprocessing"
},
"dataloader": {
"_target_": "DataLoader",
"dataset": "@train#dataset",
"batch_size": 64,
"shuffle": true,
"num_workers": 4
},
"inferer": {
"_target_": "SimpleInferer"
},
"handlers": [
{
"_target_": "ValidationHandler",
"validator": "@validate#evaluator",
"epoch_level": true,
"interval": "@val_interval"
},
{
"_target_": "StatsHandler",
"tag_name": "train_loss",
"output_transform": "$monai.handlers.from_engine(['loss'], first=True)"
},
{
"_target_": "TensorBoardStatsHandler",
"log_dir": "@output_dir",
"tag_name": "train_loss",
"output_transform": "$monai.handlers.from_engine(['loss'], first=True)"
}
],
"key_metric": {
"train_accu": {
"_target_": "ignite.metrics.Accuracy",
"output_transform": "$monai.handlers.from_engine(['pred', 'label'])"
}
},
"postprocessing": {
"_target_": "Compose",
"transforms": [
{
"_target_": "AsDiscreted",
"argmax": [
true,
false
],
"to_onehot": [
2,
2
],
"keys": [
"pred",
"label"
]
}
]
},
"trainer": {
"_target_": "SupervisedTrainer",
"max_epochs": 25,
"device": "@device",
"train_data_loader": "@train#dataloader",
"network": "@network",
"loss_function": "@loss",
"optimizer": "@optimizer",
"inferer": "@train#inferer",
"postprocessing": "@train#postprocessing",
"key_train_metric": "@train#key_metric",
"train_handlers": "@train#handlers"
}
},
"validate": {
"preprocessing": {
"_target_": "Compose",
"transforms": "%train#deterministic_transforms"
},
"dataset": {
"_target_": "Dataset",
"data": "@val_dict",
"transform": "@validate#preprocessing"
},
"dataloader": {
"_target_": "DataLoader",
"dataset": "@validate#dataset",
"batch_size": 64,
"shuffle": false,
"num_workers": 4
},
"inferer": {
"_target_": "SimpleInferer"
},
"postprocessing": {
"_target_": "Compose",
"transforms": "%train#postprocessing"
},
"handlers": [
{
"_target_": "StatsHandler",
"iteration_log": false
},
{
"_target_": "TensorBoardStatsHandler",
"log_dir": "@output_dir",
"iteration_log": false
},
{
"_target_": "CheckpointSaver",
"save_dir": "@ckpt_dir",
"save_dict": {
"model": "@network"
},
"save_key_metric": true,
"key_metric_filename": "model.pt"
}
],
"key_metric": {
"val_accu": {
"_target_": "ignite.metrics.Accuracy",
"output_transform": "$monai.handlers.from_engine(['pred', 'label'])"
}
},
"evaluator": {
"_target_": "SupervisedEvaluator",
"device": "@device",
"val_data_loader": "@validate#dataloader",
"network": "@network",
"inferer": "@validate#inferer",
"postprocessing": "@validate#postprocessing",
"key_val_metric": "@validate#key_metric",
"val_handlers": "@validate#handlers"
}
},
"training": [
"$monai.utils.set_determinism(seed=0)",
"$setattr(torch.backends.cudnn, 'benchmark', True)",
"$@train#trainer.run()"
]
}
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