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@@ -33,3 +33,6 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.zst filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
+large/snraware_large_model.pts filter=lfs diff=lfs merge=lfs -text
+medium/snraware_medium_model.pts filter=lfs diff=lfs merge=lfs -text
+small/snraware_small_model.pts filter=lfs diff=lfs merge=lfs -text

large/snraware_large_model.pts

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:505e0614b4a86de9c6546c22eed3c546b99fc07966e1fed0401a3364cbeffdee
+size 469738706

large/snraware_large_model.yaml

@@ -0,0 +1,215 @@
+backbone:
+  num_of_channels: 64
+  block_str:
+  - T1L1G1T1L1G1T1L1G1T1L1G1
+  - T1L1G1T1L1G1T1L1G1T1L1G1
+  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-large-no-epoch
+  output_dir: /data/ifm-mri-denoising/ifm-mri-denoising_20251004_025456/ifm-mri-denoising-large-no-epoch
+  wandb_entity: biomed-signal-processing
+  wandb_dir: /data/ifm-mri-denoising/ifm-mri-denoising_20251004_025456/ifm-mri-denoising-large-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: 3782770815
+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_544387_02-57-14-20251004
+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

medium/snraware_medium_model.pts

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+version https://git-lfs.github.com/spec/v1
+oid sha256:cd504782790b55b4e15422e18c34cac548182ee6aecf0aec4c4fb770de1c3b39
+size 235485912

medium/snraware_medium_model.yaml

@@ -0,0 +1,215 @@
+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

small/snraware_small_model.pts

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:672d9583e85ec9f418695fdf73180daed47b885bc9804291d9dc0ad02219ad91
+size 118325006

small/snraware_small_model.yaml

@@ -0,0 +1,207 @@
+backbone:
+  num_of_channels: 64
+  block_str:
+  - T1L1G1
+  - T1L1G1
+  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: 1
+  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-small-no-epoch
+  output_dir: /data1/inference_time/models/small
+  wandb_entity: biomed-signal-processing
+  wandb_dir: /data1/inference_time/models/small/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: 20000
+  steps_to_validate: 5000
+  steps_to_save_ckpts: 5000
+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: null
+max_epochs: 320
+batch_size: 4
+num_workers: 4
+prefetch_factor: 8
+loss:
+- mse
+- perpendicular
+- perceptual
+- charbonnier
+- gaussian3d
+loss_weights:
+- 1.0
+- 1.0
+- 1.0
+- 1.0
+- 1.0
+val_data_portion: 0.05
+overlap_for_inference:
+- 16
+- 16
+- 8
+device_mesh:
+- 8
+- 2