configs/train.yaml

---
imports:
- "$import glob"
- "$import json"
- "$import os"
- "$import ignite"
- "$from scipy import ndimage"
- "$import scripts.monai_utils"
- "$import scripts.lr_scheduler"
- "$import monai.apps.deepedit.transforms"
workflow_type: train
input_channels: 1
output_channels: 4
output_classes: 4
#arch_ckpt_path: "$@bundle_root + '/models/dynunet_FT.pt'"
#arch_ckpt: "$torch.load(@arch_ckpt_path, map_location=torch.device('cuda'))"
bundle_root: "."
ckpt_dir: "$@bundle_root + '/models'"
output_dir: "$@bundle_root + '/eval'"
dataset_dir: "/processed/Public/CT_TotalSegmentator/TS_split/test/"  #"/workspace/data"
data_list_file_path: "$@bundle_root + '/configs/TS_test.json'"
train_datalist: "$monai.data.load_decathlon_datalist(@data_list_file_path, data_list_key='training')"
val_datalist: "$monai.data.load_decathlon_datalist(@data_list_file_path, data_list_key='validation')"
n_gpu: 0
device: "$torch.device('cuda:' + str(@n_gpu) if torch.cuda.is_available() else 'cpu')"
spatial_size:
- 96
- 96
- 96
spatial_dims: "$len(@spatial_size)"
labels:
  background: 0
  liver: 1
  spleen: 2
  pancreas: 3
network_def:
  _target_: monai.networks.nets.DynUNet
  spatial_dims: "@spatial_dims"
  in_channels: "@input_channels"
  out_channels: "@output_channels"
  kernel_size:
  - 3
  - 3
  - 3
  - 3
  - 3
  - 3
  strides:
  - 1
  - 2
  - 2
  - 2
  - 2
  -
    - 2
    - 2
    - 1
  upsample_kernel_size:
  - 2
  - 2
  - 2
  - 2
  -
    - 2
    - 2
    - 1
  norm_name: "instance"
  deep_supervision: false
  res_block: true
network: "$@network_def.to(@device)"
loss:
    _target_: DiceCELoss
    include_background: false
    to_onehot_y: true
    softmax: true
    squared_pred: true
    batch: true
    smooth_nr: 1.0e-06
    smooth_dr: 1.0e-06
optimizer:
  _target_: torch.optim.AdamW
  params: "$@network.parameters()"
  weight_decay: 1.0e-05
  lr: 0.00005
max_epochs: 15
lr_scheduler:
  _target_: scripts.lr_scheduler.LinearWarmupCosineAnnealingLR
  optimizer: "@optimizer"
  warmup_epochs: 10
  warmup_start_lr: 0.0000005
  eta_min: 1.0e-08
  max_epochs: "@max_epochs"
image_key: image
label_key: label
val_interval: 2
train:
  deterministic_transforms:
  - _target_: LoadImaged
    keys:
    - "@image_key"
    - "@label_key"
    reader: ITKReader
  - _target_: EnsureChannelFirstd
    keys:
    - "@image_key"
    - "@label_key"
  - _target_: Orientationd
    keys:
    - "@image_key"
    - "@label_key"
    axcodes: RAS
  - _target_: Spacingd
    keys:
    - "@image_key"
    - "@label_key"
    pixdim:
    - 1.5
    - 1.5
    - 3.0
    mode:
    - bilinear
    - nearest
  - _target_: scripts.monai_utils.AddLabelNamesd
    keys: "@label_key"
    label_names: "@labels"
  - _target_: ScaleIntensityRanged
    keys: "@image_key"
    a_min: -250
    a_max: 400
    b_min: 0
    b_max: 1
    clip: true
  - _target_: CropForegroundd
    keys:
    - "@image_key"
    - "@label_key"
    source_key: "@image_key"
    mode:
    - "minimum"
    - "minimum"
  - _target_: EnsureTyped
    keys:
    - "@image_key"
    - "@label_key"
  - _target_: CastToTyped
    keys: "@image_key"
    dtype: "$torch.float32"
  random_transforms:
  - _target_: RandCropByLabelClassesd
    keys:
    - "@image_key"
    - "@label_key"
    label_key: "@label_key" # label4crop
    spatial_size: "@spatial_size"
    num_classes: 4
    ratios: null
    allow_smaller: true
    num_samples: 8
#   - _target_: RandSpatialCropSamplesd
#     keys:
#     - "@image_key"
#     - "@label_key"
#     roi_size: "$[int(x * 0.75) for x in @spatial_size]"
#     num_samples: 1
#     max_roi_size: "@spatial_size"
#     random_center: true
#     random_size: true
#     allow_missing_keys: false
  - _target_: SpatialPadd
    keys:
    - "@image_key"
    - "@label_key"
    spatial_size: "@spatial_size"
    method: "symmetric"
    mode:
    - "minimum"
    - "minimum"
    allow_missing_keys: false
  - _target_: RandRotate90d
    keys:
    - "@image_key"
    - "@label_key"
    prob: 0.5
    max_k: 3
    allow_missing_keys: false
#   - _target_: SelectItemsd
#     keys:
#     - "@image_key"
#     - "@label_key"
#     - "label_names"
  - _target_: CastToTyped
    keys:
    - "@image_key"
    - "@label_key"
    dtype:
    - "$torch.float32"
    - "$torch.uint8"
  - _target_: ToTensord
    keys:
    - "@image_key"
    - "@label_key"
  preprocessing:
    _target_: Compose
    transforms: "$@train#deterministic_transforms + @train#random_transforms"
  dataset:
    _target_: PersistentDataset
    data: "@train_datalist"
    transform: "@train#preprocessing"
    cache_dir: "$@bundle_root + '/cache'"
  dataloader:
    _target_: DataLoader
    dataset: "@train#dataset"
    batch_size: 1
    shuffle: true
    num_workers: 4
  inferer:
    _target_: SimpleInferer
  postprocessing:
    _target_: Compose
    transforms:
    - _target_: Activationsd
      keys: pred
      softmax: true
    - _target_: AsDiscreted
      keys:
      - pred
      - label
      argmax:
      - true
      - false
      to_onehot:
      - "@output_classes"
      - "@output_classes"
    - _target_: scripts.monai_utils.SplitPredsLabeld
      keys: pred
#   dice_function:
#     _target_: "$engine.state.metrics['train_dice']"
  handlers:
  - _target_: LrScheduleHandler
    lr_scheduler: "@lr_scheduler"
    print_lr: true
#     step_transform: "@dice_function"
  - _target_: ValidationHandler
    validator: "@validate#evaluator"
    epoch_level: true
    interval: "@val_interval"
  - _target_: StatsHandler
    tag_name: train_loss
    output_transform: "$monai.handlers.from_engine(['loss'], first=True)"
  - _target_: TensorBoardStatsHandler
    log_dir: "@output_dir"
    tag_name: train_loss
    output_transform: "$monai.handlers.from_engine(['loss'], first=True)"
  key_metric:
    train_dice:
      _target_: MeanDice
      output_transform: "$monai.handlers.from_engine(['pred', 'label'])"
      include_background: false
  additional_metrics:
    liver_dice:
      _target_: monai.handlers.MeanDice
      output_transform: "$monai.handlers.from_engine(['pred_liver', 'label_liver'])"
      include_background: false
    spleen_dice:
      _target_: monai.handlers.MeanDice
      output_transform: "$monai.handlers.from_engine(['pred_spleen', 'label_spleen'])"
      include_background: false
    pancreas_dice:
      _target_: monai.handlers.MeanDice
      output_transform: "$monai.handlers.from_engine(['pred_pancreas', 'label_pancreas'])"
      include_background: false
  trainer:
    _target_: SupervisedTrainer
    device: "@device"
    max_epochs: "@max_epochs"
    train_data_loader: "@train#dataloader"
    network: "@network"
    loss_function: "@loss"
   # train_interaction: null
    optimizer: "@optimizer"
    inferer: "@train#inferer"
    postprocessing: "@train#postprocessing"
    key_train_metric: "@train#key_metric"
    additional_metrics: "@train#additional_metrics"
    train_handlers: "@train#handlers"
    amp: true
validate:
  preprocessing:
    _target_: Compose
    transforms: "%train#deterministic_transforms"
  dataset:
    # _target_: CacheDataset
    # data: "@val_datalist"
    # transform: "@validate#preprocessing"
    # cache_rate: 0.025
    _target_: PersistentDataset
    data: "@val_datalist"
    transform: "@validate#preprocessing"
    cache_dir: "$@bundle_root + '/cache'"
  dataloader:
    _target_: DataLoader
    dataset: "@validate#dataset"
    batch_size: 1
    shuffle: false
    num_workers: 4
  inferer:
    _target_: SlidingWindowInferer
    roi_size: "@spatial_size"
    sw_batch_size: 4
    mode: "constant"
    overlap: 0.5
  postprocessing: "%train#postprocessing"
  handlers:
  - _target_: StatsHandler
    iteration_log: false
  - _target_: TensorBoardStatsHandler
    log_dir: "@output_dir"
    iteration_log: false
  - _target_: CheckpointSaver
    save_dir: "@ckpt_dir"
    save_dict:
        model: "@network"
    save_key_metric: true
    key_metric_filename: model_latest.pt
  key_metric:
    val_dice:
      _target_: MeanDice
      output_transform: "$monai.handlers.from_engine(['pred', 'label'])"
      include_background: false
  additional_metrics:
    val_liver_dice:
      _target_: monai.handlers.MeanDice
      output_transform: "$monai.handlers.from_engine(['pred_liver', 'label_liver'])"
      include_background: false
    val_spleen_dice:
      _target_: monai.handlers.MeanDice
      output_transform: "$monai.handlers.from_engine(['pred_spleen', 'label_spleen'])"
      include_background: false
    val_pancreas_dice:
      _target_: monai.handlers.MeanDice
      output_transform: "$monai.handlers.from_engine(['pred_pancreas', 'label_pancreas'])"
      include_background: false
  evaluator:
    _target_: SupervisedEvaluator
    device: "@device"
    val_data_loader: "@validate#dataloader"
    network: "@network"
    inferer: "@validate#inferer"
    postprocessing: "@validate#postprocessing"
    key_val_metric: "@validate#key_metric"
    #additional_metrics: "@validate#additional_metrics"
    val_handlers: "@validate#handlers"
    amp: true
initialize:
- "$monai.utils.set_determinism(seed=123)"
run:
- "$print('Training started... ')"
- "$print('output_channels: ', @output_channels )"
- "$print('spatial_dims: ', @spatial_dims)"
- "$print('Labels dict: ', @labels)"
- "$@train#trainer.run()"