[54a97f]: / configs / inference.json

Download this file

139 lines (138 with data), 3.8 kB

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
{
"imports": [
"$import glob",
"$import os"
],
"bundle_root": ".",
"output_dir": "$@bundle_root + '/eval'",
"dataset_dir": "/workspace/data/endoscopic_tool_dataset",
"datalist": "$list(sorted(glob.glob(os.path.join(@dataset_dir,'test', '*', '*[!seg].jpg'))))",
"device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
"network_def": {
"_target_": "FlexibleUNet",
"in_channels": 3,
"out_channels": 2,
"backbone": "efficientnet-b2",
"spatial_dims": 2,
"pretrained": false,
"is_pad": false,
"pre_conv": null
},
"network": "$@network_def.to(@device)",
"preprocessing": {
"_target_": "Compose",
"transforms": [
{
"_target_": "LoadImaged",
"keys": "image",
"image_only": false
},
{
"_target_": "EnsureChannelFirstd",
"keys": "image",
"channel_dim": -1
},
{
"_target_": "Resized",
"keys": [
"image"
],
"spatial_size": [
736,
480
],
"mode": [
"bilinear"
]
},
{
"_target_": "ScaleIntensityd",
"keys": [
"image"
]
}
]
},
"dataset": {
"_target_": "Dataset",
"data": "$[{'image': i} for i in @datalist]",
"transform": "@preprocessing"
},
"dataloader": {
"_target_": "DataLoader",
"dataset": "@dataset",
"batch_size": 1,
"shuffle": false,
"num_workers": 4
},
"inferer": {
"_target_": "SimpleInferer"
},
"postprocessing": {
"_target_": "Compose",
"transforms": [
{
"_target_": "Invertd",
"keys": "pred",
"transform": "@preprocessing",
"orig_keys": "image",
"meta_key_postfix": "meta_dict",
"nearest_interp": false,
"to_tensor": true
},
{
"_target_": "AsDiscreted",
"argmax": true,
"to_onehot": 2,
"keys": [
"pred"
]
},
{
"_target_": "Lambdad",
"keys": [
"pred"
],
"func": "$lambda x : x[1:]"
},
{
"_target_": "SaveImaged",
"keys": "pred",
"meta_keys": "pred_meta_dict",
"output_dir": "@output_dir",
"output_ext": ".png",
"scale": 255,
"squeeze_end_dims": true
}
]
},
"handlers": [
{
"_target_": "CheckpointLoader",
"load_path": "$@bundle_root + '/models/model.pt'",
"load_dict": {
"model": "@network"
},
"map_location": "@device"
},
{
"_target_": "StatsHandler",
"iteration_log": false
}
],
"evaluator": {
"_target_": "SupervisedEvaluator",
"device": "@device",
"val_data_loader": "@dataloader",
"network": "@network",
"inferer": "@inferer",
"postprocessing": "@postprocessing",
"val_handlers": "@handlers"
},
"initialize": [
"$monai.utils.set_determinism(seed=123)"
],
"run": [
"$@evaluator.run()"
]
}