backbone:
  num_of_channels: 64
  block_str:
  - T1L1G1T1L1G1
  - T1L1G1T1L1G1
  block:
    cell:
      attention_type: conv
      mixer_type: conv
      window_size:
      - 8
      - 8
      - 16
      patch_size:
      - 4
      - 4
      - 2
      window_sizing_method: mixed
      n_head: 64
      scale_ratio_in_mixer: 4.0
      normalize_Q_K: true
      cosine_att: true
      att_with_relative_position_bias: true
      att_dropout_p: 0.0
      dropout_p: 0.1
      att_with_output_proj: true
      norm_mode: layer
      activation_func: prelu
      upsample_method: linear
      with_timer: false
      temporal:
        _target_: ifm.model.config.TemporalAttentionConfig
        stride_qk:
        - 1
        - 1
        - 1
      spatial_local:
        _target_: ifm.model.config.SpatialLocalConfig
      spatial_global:
        _target_: ifm.model.config.SpatialGlobalConfig
        shuffle_in_window: false
      convoluation:
        _target_: ifm.model.config.ConvolutionConfig
        conv_type: conv3d
      spatial_local_3d:
        _target_: ifm.model.config.SpatialLocal3DConfig
      spatial_global_3d:
        _target_: ifm.model.config.SpatialGlobal3DConfig
        shuffle_in_window: false
      spatial_vit:
        _target_: ifm.model.config.SpatialViTConfig
      vit_3d:
        _target_: ifm.model.config.ViT3DConfig
      swin_3d:
        _target_: ifm.model.config.Swin3DConfig
    _target_: ifm.model.config.BlockConfig
    cell_type: sequential
    block_dense_connection: false
  _target_: ifm.model.config.HRNetConfig
  name: HRnet
  num_resolution_levels: 2
optim:
  lr: 1.0e-05
  weight_decay: 0.0
  name: sophia
  beta1: 0.9
  beta2: 0.999
  eps: 1.0e-08
  rho: 0.01
scheduler:
  name: OneCycleLR
  pct_start: 0.3
  anneal_strategy: cos
  div_factor: 25
dataset:
  _target_: ifm.mri.denoising.data.MRIDenoisingDataset
  cutout_shape:
  - 64
  - 64
  - 16
  repetition: 1
  min_noise_level: 0.1
  max_noise_level: 128.0
  kspace_filter_sigma:
  - 0.8
  - 1.0
  - 1.5
  - 2.0
  - 2.25
  kspace_filter_sigma_T:
  - 0.25
  - 0.5
  - 0.65
  - 0.85
  - 1.0
  - 1.5
  - 2.0
  - 2.25
  prob_apply_filter_T: 0.2
  pf_filter_ratio:
  - 1.0
  - 0.875
  - 0.75
  - 0.625
  phase_resolution_ratio:
  - 1.0
  - 0.75
  - 0.65
  - 0.55
  readout_resolution_ratio:
  - 1.0
  - 0.75
  - 0.65
  - 0.55
  only_white_noise: false
  ignore_gmap: false
  add_noise: true
  add_salt_pepper: true
  salt_pepper_amount: 0.4
  salt_pepper_prob: 0.4
  add_poisson: true
  poisson_prob: 0.4
  shuffle_along_3rd_dim: true
  shuffle_along_3rd_dim_prob: 0.1
  matrix_size_adjust_ratio:
  - 0.5
  - 0.75
  - 1.0
  - 1.25
  - 1.5
  matrix_size_adjust_prob: 0.5
  resolution_reduction_prob: 0.0
  single_frame_mode: true
  single_frame_mode_prob: 0.1
  dicom_mode: false
trainer:
  _target_: lightning.Trainer
  max_epochs: 320
  precision: 32
  devices: 8
  accelerator: gpu
  strategy: ddp
  num_nodes: 2
  gradient_clip_val: 1.0
  accumulate_grad_batches: 1
  log_every_n_steps: 200
  enable_progress_bar: true
  enable_model_summary: true
  enable_checkpointing: true
  check_val_every_n_epoch: 16
  val_check_interval: 1.0
  fast_dev_run: false
  overfit_batches: 0.0
  limit_train_batches: 1.0
  limit_val_batches: 1.0
  limit_test_batches: 1.0
  deterministic: false
  benchmark: true
  profiler: null
logging:
  project: ifm-mri-denoising
  run_name: ifm-mri-denoising-medium-no-epoch
  output_dir: /data/ifm-mri-denoising/ifm-mri-denoising_20251004_025430/ifm-mri-denoising-medium-no-epoch
  wandb_entity: biomed-signal-processing
  wandb_dir: /data/ifm-mri-denoising/ifm-mri-denoising_20251004_025430/ifm-mri-denoising-medium-no-epoch/wandb
  use_wandb: true
  save_ckpt_every_n_epochs: 16
  save_batches_to_output_dir: false
  log_train_batches: 16
  log_val_batches: 16
  log_test_batches: 32
tyger:
  mode: false
  dop: 8
step_mode:
  total_steps: 0
  steps_to_report: 200
  steps_to_timing: 1000
  steps_to_validate: 10000
  steps_to_save_ckpts: 20000
train_data_dir: /data/imaging-fm-projects/mri/denoising/data/whole/tra
test_data_dir: /data/imaging-fm-projects/mri/denoising/data/whole/test
seed: 3360635092
max_epochs: 320
batch_size: 2
num_workers: 8
prefetch_factor: 8
loss:
- mse
- perpendicular
- perceptual
- charbonnier
- gaussian3d
loss_weights:
- 1.0
- 1.0
- 1.0
- 1.0
- 1.0
val_data_portion: 0.02
overlap_for_inference:
- 16
- 16
- 8
device_mesh:
- 8
- 2
date: rank_0_955201_02-55-13-20251004
rank: 0
global_rank: 0
rank_str: "\e[34m\e[47mrank 0, global_rank 0 \e[0m"
device: cuda:0
yaml_file: null
log_file_name: null
ddp: true