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{
"imports": [
"$import glob",
"$import ignite",
"$import json",
"$import pathlib",
"$import os"
],
"bundle_root": "/workspace/data/pathology_nuclei_classification",
"ckpt_dir": "$@bundle_root + '/models'",
"output_dir": "$@bundle_root + '/eval'",
"dataset_dir": "/workspace/data/CoNSePNuclei",
"dataset_json": "$@dataset_dir + '/dataset.json'",
"train_datalist": "$json.loads(pathlib.Path(@dataset_json).read_text())['training']",
"val_datalist": "$json.loads(pathlib.Path(@dataset_json).read_text())['validation']",
"val_interval": 1,
"device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
"network_def": {
"_target_": "DenseNet121",
"spatial_dims": 2,
"in_channels": 4,
"out_channels": 4
},
"network": "$@network_def.to(@device)",
"loss": {
"_target_": "torch.nn.CrossEntropyLoss"
},
"optimizer": {
"_target_": "torch.optim.Adam",
"params": "[email protected]()",
"lr": 0.0001
},
"max_epochs": 50,
"train": {
"preprocessing": {
"_target_": "Compose",
"transforms": [
{
"_target_": "LoadImaged",
"keys": [
"image",
"label"
],
"dtype": "uint8"
},
{
"_target_": "EnsureChannelFirstd",
"keys": [
"image",
"label"
]
},
{
"_target_": "SplitLabeld",
"keys": "label",
"mask_value": "",
"others_value": 255,
"to_binary_mask": false
},
{
"_target_": "RandTorchVisiond",
"keys": "image",
"name": "ColorJitter",
"brightness": 0.25,
"contrast": 0.75,
"saturation": 0.25,
"hue": 0.04
},
{
"_target_": "RandFlipd",
"keys": [
"image",
"label",
"others"
],
"prob": 0.5
},
{
"_target_": "RandRotate90d",
"keys": [
"image",
"label",
"others"
],
"prob": 0.5
},
{
"_target_": "ScaleIntensityRanged",
"keys": "image",
"a_min": 0.0,
"a_max": 255.0,
"b_min": -1.0,
"b_max": 1.0
},
{
"_target_": "AddLabelAsGuidanced",
"keys": "image",
"source": "label"
},
{
"_target_": "SetLabelClassd",
"keys": "label",
"offset": -1
},
{
"_target_": "SelectItemsd",
"keys": [
"image",
"label"
]
}
]
},
"dataset": {
"_target_": "CacheDataset",
"data": "@train_datalist",
"transform": "@train#preprocessing",
"cache_rate": 1.0,
"num_workers": 4
},
"dataloader": {
"_target_": "DataLoader",
"dataset": "@train#dataset",
"batch_size": 64,
"shuffle": true,
"num_workers": 4
},
"inferer": {
"_target_": "SimpleInferer"
},
"postprocessing": {
"_target_": "Compose",
"transforms": [
{
"_target_": "Activationsd",
"keys": "pred",
"softmax": true
},
{
"_target_": "AsDiscreted",
"keys": [
"pred",
"label"
],
"argmax": [
true,
false
],
"to_onehot": 4
},
{
"_target_": "ToTensord",
"keys": [
"pred",
"label"
],
"device": "@device"
}
]
},
"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)"
},
{
"_target_": "scripts.TensorBoardImageHandler",
"class_names": {
"0": "Other",
"1": "Inflammatory",
"2": "Epithelial",
"3": "Spindle-Shaped"
},
"log_dir": "@output_dir",
"batch_limit": 4,
"tag_name": "train"
}
],
"key_metric": {
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"_target_": "ConfusionMatrix",
"metric_name": "f1 score",
"output_transform": "$monai.handlers.from_engine(['pred', 'label'])"
}
},
"trainer": {
"_target_": "SupervisedTrainer",
"max_epochs": "@max_epochs",
"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",
"amp": true
}
},
"validate": {
"preprocessing": {
"_target_": "Compose",
"transforms": [
{
"_target_": "LoadImaged",
"keys": [
"image",
"label"
],
"dtype": "uint8"
},
{
"_target_": "EnsureChannelFirstd",
"keys": [
"image",
"label"
]
},
{
"_target_": "SplitLabeld",
"keys": "label",
"mask_value": "",
"others_value": 255,
"to_binary_mask": false
},
{
"_target_": "ScaleIntensityRanged",
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"a_min": 0.0,
"a_max": 255.0,
"b_min": -1.0,
"b_max": 1.0
},
{
"_target_": "AddLabelAsGuidanced",
"keys": "image",
"source": "label"
},
{
"_target_": "SetLabelClassd",
"keys": "label",
"offset": -1
},
{
"_target_": "SelectItemsd",
"keys": [
"image",
"label",
"image_meta_dict"
]
}
]
},
"dataset": {
"_target_": "CacheDataset",
"data": "@val_datalist",
"transform": "@validate#preprocessing",
"cache_rate": 1.0
},
"dataloader": {
"_target_": "DataLoader",
"dataset": "@validate#dataset",
"batch_size": 64,
"shuffle": false,
"num_workers": 4
},
"inferer": {
"_target_": "SimpleInferer"
},
"postprocessing": "%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"
},
{
"_target_": "scripts.TensorBoardImageHandler",
"class_names": {
"0": "Other",
"1": "Inflammatory",
"2": "Epithelial",
"3": "Spindle-Shaped"
},
"log_dir": "@output_dir",
"batch_limit": 8,
"tag_name": "val"
}
],
"key_metric": {
"val_f1": {
"_target_": "ConfusionMatrix",
"metric_name": "f1 score",
"output_transform": "$monai.handlers.from_engine(['pred', 'label'])"
}
},
"additional_metrics": {
"val_accuracy": {
"_target_": "ignite.metrics.Accuracy",
"output_transform": "$monai.handlers.from_engine(['pred', 'label'])"
}
},
"evaluator": {
"_target_": "SupervisedEvaluator",
"device": "@device",
"val_data_loader": "@validate#dataloader",
"network": "@network",
"inferer": "@validate#inferer",
"postprocessing": "@validate#postprocessing",
"key_val_metric": "@validate#key_metric",
"additional_metrics": "@validate#additional_metrics",
"val_handlers": "@validate#handlers",
"amp": true
}
},
"training": [
"$import sys",
"$sys.path.append(@bundle_root)",
"$monai.utils.set_determinism(seed=123)",
"$setattr(torch.backends.cudnn, 'benchmark', True)",
"$@train#trainer.run()"
]
}
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