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{
"whether_raw_luna16": false,
"whether_resampled_luna16": "$(not @whether_raw_luna16)",
"imports": [
"$import glob",
"$import numpy",
"$import os"
],
"bundle_root": ".",
"image_key": "image",
"ckpt_dir": "$@bundle_root + '/models'",
"output_dir": "$@bundle_root + '/eval'",
"output_filename": "result_luna16_fold0.json",
"data_list_file_path": "$@bundle_root + '/LUNA16_datasplit/dataset_fold0.json'",
"dataset_dir": "/datasets/LUNA16_Images_resample",
"test_datalist": "$monai.data.load_decathlon_datalist(@data_list_file_path, is_segmentation=True, data_list_key='validation', base_dir=@dataset_dir)",
"device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
"amp": true,
"load_pretrain": true,
"spatial_dims": 3,
"num_classes": 1,
"force_sliding_window": false,
"size_divisible": [
16,
16,
8
],
"infer_patch_size": [
512,
512,
192
],
"anchor_generator": {
"_target_": "monai.apps.detection.utils.anchor_utils.AnchorGeneratorWithAnchorShape",
"feature_map_scales": [
1,
2,
4
],
"base_anchor_shapes": [
[
6,
8,
4
],
[
8,
6,
5
],
[
10,
10,
6
]
]
},
"backbone": "$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": "$monai.apps.detection.networks.retinanet_network.resnet_fpn_feature_extractor(@backbone,3,False,[1,2],None)",
"network_def": {
"_target_": "RetinaNet",
"spatial_dims": "@spatial_dims",
"num_classes": "@num_classes",
"num_anchors": 3,
"feature_extractor": "@feature_extractor",
"size_divisible": "@size_divisible",
"use_list_output": false
},
"network": "$@network_def.to(@device)",
"detector": {
"_target_": "RetinaNetDetector",
"network": "@network",
"anchor_generator": "@anchor_generator",
"debug": false,
"spatial_dims": "@spatial_dims",
"num_classes": "@num_classes",
"size_divisible": "@size_divisible"
},
"detector_ops": [
"$@detector.set_target_keys(box_key='box', label_key='label')",
"$@detector.set_box_selector_parameters(score_thresh=0.02,topk_candidates_per_level=1000,nms_thresh=0.22,detections_per_img=300)",
"$@detector.set_sliding_window_inferer(roi_size=@infer_patch_size,overlap=0.25,sw_batch_size=1,mode='constant',device='cpu')"
],
"preprocessing": {
"_target_": "Compose",
"transforms": [
{
"_target_": "LoadImaged",
"keys": "@image_key",
"_disabled_": "@whether_raw_luna16"
},
{
"_target_": "LoadImaged",
"keys": "@image_key",
"reader": "itkreader",
"affine_lps_to_ras": true,
"_disabled_": "@whether_resampled_luna16"
},
{
"_target_": "EnsureChannelFirstd",
"keys": "@image_key"
},
{
"_target_": "Orientationd",
"keys": "@image_key",
"axcodes": "RAS"
},
{
"_target_": "Spacingd",
"keys": "@image_key",
"pixdim": [
0.703125,
0.703125,
1.25
],
"_disabled_": "@whether_resampled_luna16"
},
{
"_target_": "ScaleIntensityRanged",
"keys": "@image_key",
"a_min": -1024.0,
"a_max": 300.0,
"b_min": 0.0,
"b_max": 1.0,
"clip": true
},
{
"_target_": "EnsureTyped",
"keys": "@image_key"
}
]
},
"dataset": {
"_target_": "Dataset",
"data": "$@test_datalist",
"transform": "@preprocessing"
},
"dataloader": {
"_target_": "DataLoader",
"dataset": "@dataset",
"batch_size": 1,
"shuffle": false,
"num_workers": 4,
"collate_fn": "$monai.data.utils.no_collation"
},
"inferer": {
"_target_": "scripts.detection_inferer.RetinaNetInferer",
"detector": "@detector",
"force_sliding_window": "@force_sliding_window"
},
"postprocessing": {
"_target_": "Compose",
"transforms": [
{
"_target_": "ClipBoxToImaged",
"box_keys": "box",
"label_keys": "label",
"box_ref_image_keys": "@image_key",
"remove_empty": true
},
{
"_target_": "AffineBoxToWorldCoordinated",
"box_keys": "box",
"box_ref_image_keys": "@image_key",
"affine_lps_to_ras": true
},
{
"_target_": "ConvertBoxModed",
"box_keys": "box",
"src_mode": "xyzxyz",
"dst_mode": "cccwhd"
},
{
"_target_": "DeleteItemsd",
"keys": [
"@image_key"
]
}
]
},
"handlers": [
{
"_target_": "StatsHandler",
"iteration_log": false
},
{
"_target_": "scripts.detection_saver.DetectionSaver",
"output_dir": "@output_dir",
"filename": "@output_filename",
"batch_transform": "$lambda x: [xx['image'].meta for xx in x]",
"output_transform": "$lambda x: [@postprocessing({**xx['pred'],'image':xx['image']}) for xx in x]",
"pred_box_key": "box",
"pred_label_key": "label",
"pred_score_key": "label_scores"
}
],
"evaluator": {
"_target_": "scripts.evaluator.DetectionEvaluator",
"_requires_": "@detector_ops",
"device": "@device",
"val_data_loader": "@dataloader",
"network": "@network",
"inferer": "@inferer",
"val_handlers": "@handlers",
"amp": "@amp"
},
"checkpointloader": {
"_target_": "CheckpointLoader",
"load_path": "$@bundle_root + '/models/model.pt'",
"load_dict": {
"model": "@network"
}
},
"initialize": [
"$setattr(torch.backends.cudnn, 'benchmark', True)",
"$@checkpointloader(@evaluator) if @load_pretrain else None"
],
"run": [
"$@evaluator.run()"
]
}
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