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{
"imports": [
"$import glob",
"$import os"
],
"bundle_root": ".",
"ckpt_dir": "$@bundle_root + '/models'",
"output_dir": "$@bundle_root + '/eval'",
"data_list_file_path": "$@bundle_root + '/LUNA16_datasplit/dataset_fold0.json'",
"dataset_dir": "/datasets/LUNA16_Images_resample",
"train_datalist": "$monai.data.load_decathlon_datalist(@data_list_file_path, is_segmentation=True, data_list_key='training', base_dir=@dataset_dir)",
"device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
"epochs": 300,
"val_interval": 5,
"learning_rate": 0.01,
"amp": true,
"batch_size": 4,
"patch_size": [
192,
192,
80
],
"val_patch_size": [
512,
512,
192
],
"anchor_generator": {
"_target_": "monai.apps.detection.utils.anchor_utils.AnchorGeneratorWithAnchorShape",
"feature_map_scales": [
1,
2,
4
],
"base_anchor_shapes": [
[
6,
8,
4
],
[
8,
6,
5
],
[
10,
10,
6
]
]
},
"backbone": "$monai.networks.nets.resnet.resnet50(spatial_dims=3,n_input_channels=1,conv1_t_stride=[2,2,1],conv1_t_size=[7,7,7])",
"feature_extractor": "$monai.apps.detection.networks.retinanet_network.resnet_fpn_feature_extractor(@backbone,3,False,[1,2],None)",
"network_def": {
"_target_": "RetinaNet",
"spatial_dims": 3,
"num_classes": 1,
"num_anchors": 3,
"feature_extractor": "@feature_extractor",
"size_divisible": [
16,
16,
8
]
},
"network": "$@network_def.to(@device)",
"detector": {
"_target_": "RetinaNetDetector",
"network": "@network",
"anchor_generator": "@anchor_generator",
"debug": false
},
"detector_ops": [
"$@detector.set_atss_matcher(num_candidates=4, center_in_gt=False)",
"$@detector.set_hard_negative_sampler(batch_size_per_image=64,positive_fraction=0.3,pool_size=20,min_neg=16)",
"$@detector.set_target_keys(box_key='box', label_key='label')",
"$@detector.set_box_selector_parameters(score_thresh=0.02,topk_candidates_per_level=1000,nms_thresh=0.22,detections_per_img=300)",
"$@detector.set_sliding_window_inferer(roi_size=@val_patch_size,overlap=0.25,sw_batch_size=1,mode='constant',device='cpu')"
],
"optimizer": {
"_target_": "torch.optim.SGD",
"params": "$@detector.network.parameters()",
"lr": "@learning_rate",
"momentum": 0.9,
"weight_decay": 3e-05,
"nesterov": true
},
"after_scheduler": {
"_target_": "torch.optim.lr_scheduler.StepLR",
"optimizer": "@optimizer",
"step_size": 160,
"gamma": 0.1
},
"lr_scheduler": {
"_target_": "scripts.warmup_scheduler.GradualWarmupScheduler",
"optimizer": "@optimizer",
"multiplier": 1,
"total_epoch": 10,
"after_scheduler": "@after_scheduler"
},
"train": {
"preprocessing_transforms": [
{
"_target_": "LoadImaged",
"keys": "image"
},
{
"_target_": "EnsureChannelFirstd",
"keys": "image"
},
{
"_target_": "EnsureTyped",
"keys": [
"image",
"box"
]
},
{
"_target_": "EnsureTyped",
"keys": "label",
"dtype": "$torch.long"
},
{
"_target_": "Orientationd",
"keys": "image",
"axcodes": "RAS"
},
{
"_target_": "ScaleIntensityRanged",
"keys": "image",
"a_min": -1024.0,
"a_max": 300.0,
"b_min": 0.0,
"b_max": 1.0,
"clip": true
},
{
"_target_": "ConvertBoxToStandardModed",
"box_keys": "box",
"mode": "cccwhd"
},
{
"_target_": "AffineBoxToImageCoordinated",
"box_keys": "box",
"box_ref_image_keys": "image",
"affine_lps_to_ras": true
}
],
"random_transforms": [
{
"_target_": "RandCropBoxByPosNegLabeld",
"image_keys": "image",
"box_keys": "box",
"label_keys": "label",
"spatial_size": "@patch_size",
"whole_box": true,
"num_samples": "@batch_size",
"pos": 1,
"neg": 1
},
{
"_target_": "RandZoomBoxd",
"image_keys": "image",
"box_keys": "box",
"label_keys": "label",
"box_ref_image_keys": "image",
"prob": 0.2,
"min_zoom": 0.7,
"max_zoom": 1.4,
"padding_mode": "constant",
"keep_size": true
},
{
"_target_": "ClipBoxToImaged",
"box_keys": "box",
"label_keys": "label",
"box_ref_image_keys": "image",
"remove_empty": true
},
{
"_target_": "RandFlipBoxd",
"image_keys": "image",
"box_keys": "box",
"box_ref_image_keys": "image",
"prob": 0.5,
"spatial_axis": 0
},
{
"_target_": "RandFlipBoxd",
"image_keys": "image",
"box_keys": "box",
"box_ref_image_keys": "image",
"prob": 0.5,
"spatial_axis": 1
},
{
"_target_": "RandFlipBoxd",
"image_keys": "image",
"box_keys": "box",
"box_ref_image_keys": "image",
"prob": 0.5,
"spatial_axis": 2
},
{
"_target_": "RandRotateBox90d",
"image_keys": "image",
"box_keys": "box",
"box_ref_image_keys": "image",
"prob": 0.75,
"max_k": 3,
"spatial_axes": [
0,
1
]
},
{
"_target_": "BoxToMaskd",
"box_keys": "box",
"label_keys": "label",
"box_mask_keys": "box_mask",
"box_ref_image_keys": "image",
"min_fg_label": 0,
"ellipse_mask": true
},
{
"_target_": "RandRotated",
"keys": [
"image",
"box_mask"
],
"mode": [
"nearest",
"nearest"
],
"prob": 0.2,
"range_x": 0.5236,
"range_y": 0.5236,
"range_z": 0.5236,
"keep_size": true,
"padding_mode": "zeros"
},
{
"_target_": "MaskToBoxd",
"box_keys": [
"box"
],
"label_keys": [
"label"
],
"box_mask_keys": [
"box_mask"
],
"min_fg_label": 0
},
{
"_target_": "DeleteItemsd",
"keys": "box_mask"
},
{
"_target_": "RandGaussianNoised",
"keys": "image",
"prob": 0.1,
"mean": 0.0,
"std": 0.1
},
{
"_target_": "RandGaussianSmoothd",
"keys": "image",
"prob": 0.1,
"sigma_x": [
0.5,
1.0
],
"sigma_y": [
0.5,
1.0
],
"sigma_z": [
0.5,
1.0
]
},
{
"_target_": "RandScaleIntensityd",
"keys": "image",
"factors": 0.25,
"prob": 0.15
},
{
"_target_": "RandShiftIntensityd",
"keys": "image",
"offsets": 0.1,
"prob": 0.15
},
{
"_target_": "RandAdjustContrastd",
"keys": "image",
"prob": 0.3,
"gamma": [
0.7,
1.5
]
}
],
"final_transforms": [
{
"_target_": "EnsureTyped",
"keys": [
"image",
"box"
]
},
{
"_target_": "EnsureTyped",
"keys": "label",
"dtype": "$torch.long"
},
{
"_target_": "ToTensord",
"keys": [
"image",
"box",
"label"
]
}
],
"preprocessing": {
"_target_": "Compose",
"transforms": "$@train#preprocessing_transforms + @train#random_transforms + @train#final_transforms"
},
"dataset": {
"_target_": "Dataset",
"data": "$@train_datalist[: int(0.95 * len(@train_datalist))]",
"transform": "@train#preprocessing"
},
"dataloader": {
"_target_": "DataLoader",
"dataset": "@train#dataset",
"batch_size": 1,
"shuffle": true,
"num_workers": 4,
"collate_fn": "$monai.data.utils.no_collation"
},
"handlers": [
{
"_target_": "LrScheduleHandler",
"lr_scheduler": "@lr_scheduler",
"print_lr": true
},
{
"_target_": "ValidationHandler",
"validator": "@validate#evaluator",
"epoch_level": true,
"interval": "@val_interval"
},
{
"_target_": "StatsHandler",
"tag_name": "train_loss",
"output_transform": "$lambda x: monai.handlers.from_engine(['loss'], first=True)(x)[0]"
},
{
"_target_": "TensorBoardStatsHandler",
"log_dir": "@output_dir",
"tag_name": "train_loss",
"output_transform": "$lambda x: monai.handlers.from_engine(['loss'], first=True)(x)[0]"
}
],
"trainer": {
"_target_": "scripts.trainer.DetectionTrainer",
"_requires_": "@detector_ops",
"max_epochs": "@epochs",
"device": "@device",
"train_data_loader": "@train#dataloader",
"detector": "@detector",
"optimizer": "@optimizer",
"train_handlers": "@train#handlers",
"amp": "@amp"
}
},
"validate": {
"preprocessing": {
"_target_": "Compose",
"transforms": "$@train#preprocessing_transforms + @train#final_transforms"
},
"dataset": {
"_target_": "Dataset",
"data": "$@train_datalist[int(0.95 * len(@train_datalist)): ]",
"transform": "@validate#preprocessing"
},
"dataloader": {
"_target_": "DataLoader",
"dataset": "@validate#dataset",
"batch_size": 1,
"shuffle": false,
"num_workers": 2,
"collate_fn": "$monai.data.utils.no_collation"
},
"inferer": {
"_target_": "scripts.detection_inferer.RetinaNetInferer",
"detector": "@detector"
},
"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_coco": {
"_target_": "scripts.cocometric_ignite.IgniteCocoMetric",
"coco_metric_monai": "$monai.apps.detection.metrics.coco.COCOMetric(classes=['nodule'], iou_list=[0.1], max_detection=[100])",
"output_transform": "$monai.handlers.from_engine(['pred', 'label'])",
"box_key": "box",
"label_key": "label",
"pred_score_key": "label_scores",
"reduce_scalar": true
}
},
"evaluator": {
"_target_": "scripts.evaluator.DetectionEvaluator",
"_requires_": "@detector_ops",
"device": "@device",
"val_data_loader": "@validate#dataloader",
"network": "@network",
"inferer": "@validate#inferer",
"key_val_metric": "@validate#key_metric",
"val_handlers": "@validate#handlers",
"amp": "@amp"
}
},
"initialize": [
"$monai.utils.set_determinism(seed=0)"
],
"run": [
"$@train#trainer.run()"
]
}
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