diff --git a/model-zoo/models/mednist_ddpm/bundle/configs/common.yaml b/model-zoo/models/mednist_ddpm/bundle/configs/common.yaml index e48b917b..c6073eb5 100644 --- a/model-zoo/models/mednist_ddpm/bundle/configs/common.yaml +++ b/model-zoo/models/mednist_ddpm/bundle/configs/common.yaml @@ -1,6 +1,6 @@ # This file defines common definitions used in training and inference, most importantly the network definition -imports: +imports: - $import os - $import datetime - $import torch @@ -27,8 +27,8 @@ network_def: attention_levels: [false, true, true] num_res_blocks: 1 num_head_channels: 128 - -network: $@network_def.to(@device) + +network: $@network_def.to(@device) bundle_root: . ckpt_path: $@bundle_root + '/models/model.pt' @@ -54,8 +54,7 @@ base_transforms: scheduler: _target_: generative.networks.schedulers.DDPMScheduler num_train_timesteps: '@num_train_timesteps' - + inferer: _target_: generative.inferers.DiffusionInferer scheduler: '@scheduler' - \ No newline at end of file diff --git a/model-zoo/models/mednist_ddpm/bundle/configs/infer.yaml b/model-zoo/models/mednist_ddpm/bundle/configs/infer.yaml index f140c3b6..46297e18 100644 --- a/model-zoo/models/mednist_ddpm/bundle/configs/infer.yaml +++ b/model-zoo/models/mednist_ddpm/bundle/configs/infer.yaml @@ -35,4 +35,4 @@ testing: #alternative version which saves to a jpg file testing_jpg: - '@load_state' -- '$@save_trans(@sample(@noise.to(@device))[0])' \ No newline at end of file +- '$@save_trans(@sample(@noise.to(@device))[0])' diff --git a/model-zoo/models/mednist_ddpm/bundle/configs/logging.conf b/model-zoo/models/mednist_ddpm/bundle/configs/logging.conf index db85a0b9..91c1a21c 100644 --- a/model-zoo/models/mednist_ddpm/bundle/configs/logging.conf +++ b/model-zoo/models/mednist_ddpm/bundle/configs/logging.conf @@ -18,4 +18,4 @@ formatter=fullFormatter args=(sys.stdout,) [formatter_fullFormatter] -format=%(asctime)s - %(name)s - %(levelname)s - %(message)s \ No newline at end of file +format=%(asctime)s - %(name)s - %(levelname)s - %(message)s diff --git a/model-zoo/models/mednist_ddpm/bundle/configs/metadata.json b/model-zoo/models/mednist_ddpm/bundle/configs/metadata.json index aef66f9f..1e657634 100644 --- a/model-zoo/models/mednist_ddpm/bundle/configs/metadata.json +++ b/model-zoo/models/mednist_ddpm/bundle/configs/metadata.json @@ -7,7 +7,9 @@ "monai_version": "1.0.0", "pytorch_version": "1.10.2", "numpy_version": "1.21.2", - "optional_packages_version": {"generative":"0.1.0"}, + "optional_packages_version": { + "generative": "0.1.0" + }, "task": "MedNIST Hand Generation", "description": "", "authors": "Walter Hugo Lopez Pinaya, Mark Graham, and Eric Kerfoot", diff --git a/model-zoo/models/mednist_ddpm/bundle/configs/train.yaml b/model-zoo/models/mednist_ddpm/bundle/configs/train.yaml index 459e23bd..919e3a21 100644 --- a/model-zoo/models/mednist_ddpm/bundle/configs/train.yaml +++ b/model-zoo/models/mednist_ddpm/bundle/configs/train.yaml @@ -4,7 +4,7 @@ output_dir: $datetime.datetime.now().strftime('./results/output_%y%m%d_%H%M%S') dataset_dir: ./data -train_data: +train_data: _target_ : MedNISTDataset root_dir: '@dataset_dir' section: training @@ -12,7 +12,7 @@ train_data: progress: false seed: 0 -val_data: +val_data: _target_ : MedNISTDataset root_dir: '@dataset_dir' section: validation @@ -37,7 +37,7 @@ save_interval: 5 train_transforms: - _target_: RandAffined keys: '@image' - rotate_range: + rotate_range: - ['$-np.pi / 36', '$np.pi / 36'] - ['$-np.pi / 36', '$np.pi / 36'] translate_range: @@ -49,14 +49,14 @@ train_transforms: spatial_size: [64, 64] padding_mode: "zeros" prob: '@rand_prob' - + train_ds: _target_: Dataset data: $@train_datalist transform: _target_: Compose transforms: '$@base_transforms + @train_transforms' - + train_loader: _target_: ThreadDataLoader dataset: '@train_ds' @@ -65,7 +65,7 @@ train_loader: num_workers: '@num_workers' use_thread_workers: '@use_thread_workers' persistent_workers: '$@num_workers > 0' - shuffle: true + shuffle: true val_ds: _target_: Dataset @@ -73,7 +73,7 @@ val_ds: transform: _target_: Compose transforms: '@base_transforms' - + val_loader: _target_: DataLoader dataset: '@val_ds' @@ -81,19 +81,19 @@ val_loader: num_workers: '@num_workers' persistent_workers: '$@num_workers > 0' shuffle: false - + lossfn: _target_: torch.nn.MSELoss - + optimizer: _target_: torch.optim.Adam params: $@network.parameters() lr: '@lr' - + prepare_batch: _target_: generative.engines.DiffusionPrepareBatch num_train_timesteps: '@num_train_timesteps' - + val_handlers: - _target_: StatsHandler name: train_log @@ -114,7 +114,7 @@ evaluator: output_transform: $monai.handlers.from_engine([@pred, @label]) metric_cmp_fn: '$scripts.inv_metric_cmp_fn' val_handlers: '$list(filter(bool, @val_handlers))' - + handlers: - _target_: CheckpointLoader _disabled_: $not os.path.exists(@ckpt_path) @@ -144,14 +144,14 @@ trainer: optimizer: '@optimizer' inferer: '@inferer' prepare_batch: '@prepare_batch' - key_train_metric: + key_train_metric: train_acc: _target_: MeanSquaredError output_transform: $monai.handlers.from_engine([@pred, @label]) metric_cmp_fn: '$scripts.inv_metric_cmp_fn' train_handlers: '$list(filter(bool, @handlers))' amp: '@use_amp' - -training: + +training: - '$monai.utils.set_determinism(0)' - '$@trainer.run()' diff --git a/model-zoo/models/mednist_ddpm/bundle/configs/train_multigpu.yaml b/model-zoo/models/mednist_ddpm/bundle/configs/train_multigpu.yaml index 2811612f..51f5acf4 100644 --- a/model-zoo/models/mednist_ddpm/bundle/configs/train_multigpu.yaml +++ b/model-zoo/models/mednist_ddpm/bundle/configs/train_multigpu.yaml @@ -21,10 +21,10 @@ vsampler: shuffle: false val_loader#sampler: '@vsampler' -training: +training: - $import torch.distributed as dist - $dist.init_process_group(backend='nccl') - $torch.cuda.set_device(@device) - $monai.utils.set_determinism(seed=123), - $@trainer.run() -- $dist.destroy_process_group() \ No newline at end of file +- $dist.destroy_process_group() diff --git a/model-zoo/models/mednist_ddpm/bundle/docs/sub_train_multigpu.sh b/model-zoo/models/mednist_ddpm/bundle/docs/sub_train_multigpu.sh index 7c424af0..4d5f6af0 100644 --- a/model-zoo/models/mednist_ddpm/bundle/docs/sub_train_multigpu.sh +++ b/model-zoo/models/mednist_ddpm/bundle/docs/sub_train_multigpu.sh @@ -33,4 +33,4 @@ torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run training --config_file "$CONFIG" \ --logging_file "$BUNDLE/configs/logging.conf" \ --bundle_root "$BUNDLE" \ - --dataset_dir "$DATASET" \ No newline at end of file + --dataset_dir "$DATASET"