configs/inference_autoencoder.json

{
    "imports": [
        "$import torch",
        "$from datetime import datetime",
        "$from pathlib import Path",
        "$from PIL import Image",
        "$from scripts.utils import visualize_2d_image"
    ],
    "bundle_root": ".",
    "model_dir": "$@bundle_root + '/models'",
    "dataset_dir": "/workspace/data/medical",
    "output_dir": "$@bundle_root + '/output'",
    "create_output_dir": "$Path(@output_dir).mkdir(exist_ok=True)",
    "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
    "output_postfix": "$datetime.now().strftime('%Y%m%d_%H%M%S')",
    "channel": 0,
    "spatial_dims": 2,
    "image_channels": 1,
    "latent_channels": 1,
    "infer_patch_size": [
        240,
        240
    ],
    "infer_batch_size_img": 1,
    "infer_batch_size_slice": 1,
    "autoencoder_def": {
        "_target_": "monai.networks.nets.autoencoderkl.AutoencoderKL",
        "spatial_dims": "@spatial_dims",
        "in_channels": "@image_channels",
        "out_channels": "@image_channels",
        "latent_channels": "@latent_channels",
        "channels": [
            64,
            128,
            256
        ],
        "num_res_blocks": 2,
        "norm_num_groups": 32,
        "norm_eps": 1e-06,
        "attention_levels": [
            false,
            false,
            false
        ],
        "with_encoder_nonlocal_attn": true,
        "with_decoder_nonlocal_attn": true,
        "include_fc": false
    },
    "load_autoencoder_path": "$@bundle_root + '/models/model_autoencoder.pt'",
    "load_autoencoder": "$@autoencoder_def.load_old_state_dict(torch.load(@load_autoencoder_path))",
    "autoencoder": "$@autoencoder_def.to(@device)",
    "preprocessing_transforms": [
        {
            "_target_": "LoadImaged",
            "keys": "image"
        },
        {
            "_target_": "EnsureChannelFirstd",
            "keys": "image"
        },
        {
            "_target_": "Lambdad",
            "keys": "image",
            "func": "$lambda x: x[@channel, :, :, :]"
        },
        {
            "_target_": "EnsureChannelFirstd",
            "keys": "image",
            "channel_dim": "no_channel"
        },
        {
            "_target_": "EnsureTyped",
            "keys": "image"
        },
        {
            "_target_": "Orientationd",
            "keys": "image",
            "axcodes": "RAS"
        },
        {
            "_target_": "CenterSpatialCropd",
            "keys": "image",
            "roi_size": "$[@infer_patch_size[0], @infer_patch_size[1], 20]"
        },
        {
            "_target_": "ScaleIntensityRangePercentilesd",
            "keys": "image",
            "lower": 0,
            "upper": 100,
            "b_min": 0,
            "b_max": 1
        }
    ],
    "crop_transforms": [
        {
            "_target_": "DivisiblePadd",
            "keys": "image",
            "k": [
                4,
                4,
                1
            ]
        },
        {
            "_target_": "RandSpatialCropSamplesd",
            "keys": "image",
            "random_size": false,
            "roi_size": "$[@infer_patch_size[0], @infer_patch_size[1], 1]",
            "num_samples": "@infer_batch_size_slice"
        },
        {
            "_target_": "SqueezeDimd",
            "keys": "image",
            "dim": 3
        }
    ],
    "final_transforms": [
        {
            "_target_": "ScaleIntensityRangePercentilesd",
            "keys": "image",
            "lower": 0,
            "upper": 100,
            "b_min": 0,
            "b_max": 1
        }
    ],
    "preprocessing": {
        "_target_": "Compose",
        "transforms": "$@preprocessing_transforms + @crop_transforms + @final_transforms"
    },
    "dataset": {
        "_target_": "monai.apps.DecathlonDataset",
        "root_dir": "@dataset_dir",
        "task": "Task01_BrainTumour",
        "section": "validation",
        "cache_rate": 0.0,
        "num_workers": 8,
        "download": false,
        "transform": "@preprocessing"
    },
    "dataloader": {
        "_target_": "DataLoader",
        "dataset": "@dataset",
        "batch_size": 1,
        "shuffle": true,
        "num_workers": 0
    },
    "recon_img_pil": "$Image.fromarray(visualize_2d_image(@recon_img), 'RGB')",
    "orig_img_pil": "$Image.fromarray(visualize_2d_image(@input_img[0,0,...]), 'RGB')",
    "input_img": "$monai.utils.first(@dataloader)['image'].to(@device)",
    "recon_img": "$@autoencoder(@input_img)[0][0,0,...]",
    "run": [
        "$@create_output_dir",
        "$@load_autoencoder",
        "$@orig_img_pil.save(@output_dir+'/orig_img_'+@output_postfix+'.png')",
        "$@recon_img_pil.save(@output_dir+'/recon_img_'+@output_postfix+'.png')"
    ]
}