Replace configs with minimal inference-only YAMLs (no training/validation)

medl_ads_1d.yaml

@@ -1,240 +1,65 @@
 model:
-  model_name: medl.medl.MEDL3D
-  engine_name: null
-  iterations: 3
-  num_layers: 3
-  unet_num_filters: 18
-  unet_num_pool_layers: 4
-  unet_dropout: 0.0
-  unet_norm: false
+    model_name: medl.medl.MEDL3D
+    iterations: 3
+    num_layers: 3
+    unet_num_filters: 18
+    unet_num_pool_layers: 4
+    unet_dropout: 0.0
+    unet_norm: false
 additional_models:
-  sampling_model:
-    model_name: adaptive.policy.StraightThroughPolicy
-    engine_name: null
-    sampling_dimension: ONE_D
-    st_slope: 10.0
-    st_clamp: false
-    use_softplus: true
-    slope: 10.0
-    fix_sign_leakage: true
-    acceleration: null
-    kspace_shape:
-    - 12
-    - 512
-    - 246
-    num_layers: 2
-    kspace_sampler: false
-    sampler_detach_mask: false
-    sampler_chans: 16
-    sampler_num_pool_layers: 3
-    sampler_fc_size: 128
-    sampler_drop_prob: 0.0
-    sampler_num_fc_layers: 3
-    sampler_activation: LEAKY_RELU
-    sampling_type: STATIC
-    num_time_steps: null
-    num_slices: null
-  sensitivity_model:
-    model_name: unet.unet_2d.UnetModel2d
-    engine_name: null
-    in_channels: 2
-    out_channels: 2
-    num_filters: 16
-    num_pool_layers: 4
-    dropout_probability: 0.0
+    sampling_model:
+        model_name: adaptive.policy.StraightThroughPolicy
+        sampling_dimension: ONE_D
+        st_slope: 10.0
+        st_clamp: false
+        use_softplus: true
+        slope: 10.0
+        fix_sign_leakage: true
+        kspace_shape:
+            - 12
+            - 512
+            - 246
+        num_layers: 2
+        kspace_sampler: false
+        sampler_detach_mask: false
+        sampler_chans: 16
+        sampler_num_pool_layers: 3
+        sampler_fc_size: 128
+        sampler_drop_prob: 0.0
+        sampler_num_fc_layers: 3
+        sampler_activation: LEAKY_RELU
+        sampling_type: STATIC
+    sensitivity_model:
+        model_name: unet.unet_2d.UnetModel2d
+        in_channels: 2
+        out_channels: 2
+        num_filters: 16
+        num_pool_layers: 4
+        dropout_probability: 0.0
 physics:
-  forward_operator: fft2
-  backward_operator: ifft2
-  use_noise_matrix: false
-  noise_matrix_scaling: 1.0
-training:
-  datasets:
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: train
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIRandom
-        accelerations:
-        - 4.0327
-        - 6
-        - 8.2
-        center_fractions:
-        - 0.04
-        - 0.04
-        - 0.04
-      use_seed: false
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: true
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.5
-  model_checkpoint: null
-  optimizer: Adam
-  lr: 0.003
-  weight_decay: 0.0
-  batch_size: 1
-  lr_step_size: 10000
-  lr_gamma: 0.8
-  lr_warmup_iter: 2000
-  swa_start_iter: null
-  num_iterations: 60001
-  validation_steps: 4000
-  gradient_steps: 1
-  gradient_clipping: 0.0
-  gradient_debug: false
-  loss:
-    crop: null
-    losses:
-    - function: l2_loss
-      multiplier: 1
-  checkpointer:
-    checkpoint_steps: 2000
-  metrics: []
-  regularizers: []
-validation:
-  datasets:
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: val-4x
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIRandom
-        accelerations:
-        - 4.0327
-        center_fractions:
-        - 0.04
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: true
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.0
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: val-6x
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIRandom
-        accelerations:
-        - 6
-        center_fractions:
-        - 0.04
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: true
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.0
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: val-8x
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIRandom
-        accelerations:
-        - 8.2
-        center_fractions:
-        - 0.04
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: true
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.0
-  batch_size: 1
-  metrics:
-  - fastmri_ssim
-  - fastmri_psnr
-  regularizers: []
-  crop: header
+    forward_operator: fft2
+    backward_operator: ifft2
 inference:
-  dataset:
-    name: CMRxRecon
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIRandom
-        accelerations:
-        - 4.0327
-        center_fractions:
-        - 0.04
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: true
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.0
-    text_description: inference
-    data_root: null
-    filenames_filter: null
-    filenames_lists: null
-    filenames_lists_root: null
-    kspace_key: kspace_full
-    compute_mask: false
-    extra_keys: null
-    kspace_context: time
-  batch_size: 1
-  metrics:
-  - fastmri_ssim
-  - fastmri_psnr
-  - fastmri_nmse
-  crop: header
-logging:
-  log_as_image: null
-  tensorboard:
-    num_images: 4
+    batch_size: 1
+    crop: header
+    dataset:
+        name: CMRxRecon
+        transforms:
+            use_seed: true
+            delete_kspace: false
+            masking:
+                name: FastMRIRandom
+                accelerations:
+                    - 4.0327
+                center_fractions:
+                    - 0.04
+            cropping:
+                image_center_crop: false
+            sensitivity_map_estimation:
+                estimate_sensitivity_maps: true
+            normalization:
+                scaling_key: acs_kspace
+                scale_percentile: 0.995
+        kspace_key: kspace_full
+        compute_mask: false
+        kspace_context: time

medl_ads_1d_frame.yaml

@@ -1,352 +1,64 @@
 model:
-  model_name: medl.medl.MEDL3D
-  engine_name: null
-  iterations: 3
-  num_layers: 3
-  unet_num_filters: 18
-  unet_num_pool_layers: 4
-  unet_dropout: 0.0
-  unet_norm: false
+    model_name: medl.medl.MEDL3D
+    iterations: 3
+    num_layers: 3
+    unet_num_filters: 18
+    unet_num_pool_layers: 4
+    unet_dropout: 0.0
+    unet_norm: false
 additional_models:
-  sampling_model:
-    model_name: adaptive.policy.StraightThroughPolicy
-    engine_name: null
-    sampling_dimension: ONE_D
-    st_slope: 10.0
-    st_clamp: false
-    use_softplus: true
-    slope: 10.0
-    fix_sign_leakage: true
-    acceleration: null
-    kspace_shape:
-    - 512
-    - 246
-    num_layers: 2
-    kspace_sampler: false
-    sampler_detach_mask: false
-    sampler_chans: 16
-    sampler_num_pool_layers: 3
-    sampler_fc_size: 128
-    sampler_drop_prob: 0.0
-    sampler_num_fc_layers: 3
-    sampler_activation: LEAKY_RELU
-    sampling_type: DYNAMIC_2D
-    num_time_steps: 12
-    num_slices: null
-  sensitivity_model:
-    model_name: unet.unet_2d.UnetModel2d
-    engine_name: null
-    in_channels: 2
-    out_channels: 2
-    num_filters: 16
-    num_pool_layers: 4
-    dropout_probability: 0.0
+    sampling_model:
+        model_name: adaptive.policy.StraightThroughPolicy
+        sampling_dimension: ONE_D
+        st_slope: 10.0
+        st_clamp: false
+        use_softplus: true
+        slope: 10.0
+        fix_sign_leakage: true
+        kspace_shape:
+            - 512
+            - 246
+        num_layers: 2
+        kspace_sampler: false
+        sampler_detach_mask: false
+        sampler_chans: 16
+        sampler_num_pool_layers: 3
+        sampler_fc_size: 128
+        sampler_drop_prob: 0.0
+        sampler_num_fc_layers: 3
+        sampler_activation: LEAKY_RELU
+        sampling_type: DYNAMIC_2D
+        num_time_steps: 12
+    sensitivity_model:
+        model_name: unet.unet_2d.UnetModel2d
+        in_channels: 2
+        out_channels: 2
+        num_filters: 16
+        num_pool_layers: 4
+        dropout_probability: 0.0
 physics:
-  forward_operator: fft2
-  backward_operator: ifft2
-  use_noise_matrix: false
-  noise_matrix_scaling: 1.0
-training:
-  datasets:
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: train-4x
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIRandom
-        mode: DYNAMIC
-        accelerations:
-        - 4.0327
-        center_fractions:
-        - 0.04
-      use_seed: false
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: true
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.5
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: train-6x
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIRandom
-        mode: DYNAMIC
-        accelerations:
-        - 6
-        center_fractions:
-        - 0.04
-      use_seed: false
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: true
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.5
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: train-8x
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIRandom
-        mode: DYNAMIC
-        accelerations:
-        - 8.2
-        center_fractions:
-        - 0.04
-      use_seed: false
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: true
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.5
-  model_checkpoint: null
-  optimizer: Adam
-  lr: 0.003
-  weight_decay: 0.0
-  batch_size: 1
-  lr_step_size: 10000
-  lr_gamma: 0.8
-  lr_warmup_iter: 2000
-  swa_start_iter: null
-  num_iterations: 60001
-  validation_steps: 10000
-  gradient_steps: 1
-  gradient_clipping: 0.0
-  gradient_debug: false
-  loss:
-    crop: null
-    losses:
-    - function: l2_loss
-      multiplier: 1
-  checkpointer:
-    checkpoint_steps: 2000
-  metrics: []
-  regularizers: []
-validation:
-  datasets:
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: val-4x
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIRandom
-        mode: DYNAMIC
-        accelerations:
-        - 4.0327
-        center_fractions:
-        - 0.04
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: true
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.0
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: val-6x
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIRandom
-        mode: DYNAMIC
-        accelerations:
-        - 6
-        center_fractions:
-        - 0.04
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: true
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.0
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: val-8x
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIRandom
-        mode: DYNAMIC
-        accelerations:
-        - 8.2
-        center_fractions:
-        - 0.04
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: true
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.0
-  batch_size: 1
-  metrics:
-  - fastmri_ssim
-  - fastmri_psnr
-  regularizers: []
-  crop: null
+    forward_operator: fft2
+    backward_operator: ifft2
 inference:
-  dataset:
-    name: CMRxRecon
-    transforms:
-      masking:
-        name: FastMRIRandom
-        accelerations:
-        - 8.2
-        center_fractions:
-        - 0.04
-        mode: DYNAMIC
-        val_accelerations:
-        - 5.0
-        - 10.0
-        val_center_fractions:
-        - 0.1
-        - 0.05
-        range_mode: DISCRETE
-      target_acceleration: null
-      cropping:
-        crop: null
-        crop_type: uniform
-        image_center_crop: false
-      augmentation:
-        rescale: null
-        rescale_mode: NEAREST
-        rescale_2d_if_3d: false
-        pad:
-        - 512
-        - 246
-      random_augmentations:
-        random_rotation_degrees:
-        - -90
-        - 90
-        random_rotation_probability: 0.0
-        random_flip_type: RANDOM
-        random_flip_probability: 0.0
-        random_reverse_probability: 0.0
-      padding_eps: 0.0
-      estimate_body_coil_image: false
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-        sensitivity_maps_type: RSS_ESTIMATE
-        sensitivity_maps_espirit_threshold: 0.05
-        sensitivity_maps_espirit_kernel_size: 6
-        sensitivity_maps_espirit_crop: 0.95
-        sensitivity_maps_espirit_max_iters: 30
-        sensitivity_maps_gaussian: 0.7
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      use_acs_as_mask: true
-      delete_acs_mask: false
-      delete_kspace: false
-      image_recon_type: RSS
-      compress_coils: null
-      pad_coils: null
-      registration:
-        registration: false
-        registration_simulate_reference: null
-        registration_simulate_elastic_sigma: 3.0
-        registration_simulate_elastic_points: 3
-        registration_simulate_elastic_rotate: 0.0
-        registration_simulate_elastic_zoom: 0.0
-        registration_estimate_displacement: true
-        registration_simulate_reference_from_key_index: 0
-        registration_moving_key: TARGET
-        demons_filter_type: SYMMETRIC_FORCES
-        demons_num_iterations: 100
-        demons_smooth_displacement_field: true
-        demons_standard_deviations: 1.5
-        demons_intensity_difference_threshold: null
-        demons_maximum_rms_error: null
-      use_seed: true
-      transforms_type: SUPERVISED
-      mask_split_ratio:
-      - 0.4
-      mask_split_acs_region:
-      - 0
-      - 0
-      mask_split_keep_acs: false
-      mask_split_type: GAUSSIAN
-      mask_split_gaussian_std: 3.0
-      mask_split_half_direction: VERTICAL
-    text_description: inference-8x
-    data_root: null
-    filenames_filter: null
-    filenames_lists: null
-    filenames_lists_root: null
-    kspace_key: kspace_full
-    compute_mask: false
-    extra_keys: null
-    kspace_context: time
-  batch_size: 1
-  metrics:
-  - fastmri_ssim
-  - fastmri_psnr
-  - fastmri_nmse
-  crop: null
-logging:
-  log_as_image: null
-  tensorboard:
-    num_images: 4
+    batch_size: 1
+    dataset:
+        name: CMRxRecon
+        transforms:
+            use_seed: true
+            delete_kspace: false
+            masking:
+                name: FastMRIRandom
+                accelerations:
+                    - 8.2
+                center_fractions:
+                    - 0.04
+            cropping:
+                image_center_crop: false
+            sensitivity_map_estimation:
+                estimate_sensitivity_maps: true
+            normalization:
+                scaling_key: acs_kspace
+                scale_percentile: 0.995
+        kspace_key: kspace_full
+        compute_mask: false
+        kspace_context: time

medl_ads_1d_frame_init2.yaml

@@ -1,267 +1,62 @@
 model:
-  model_name: medl.medl.MEDL3D
-  engine_name: null
-  iterations: 3
-  num_layers: 3
-  unet_num_filters: 18
-  unet_num_pool_layers: 4
-  unet_dropout: 0.0
-  unet_norm: false
+    model_name: medl.medl.MEDL3D
+    iterations: 3
+    num_layers: 3
+    unet_num_filters: 18
+    unet_num_pool_layers: 4
+    unet_dropout: 0.0
+    unet_norm: false
 additional_models:
-  sampling_model:
-    model_name: adaptive.policy.StraightThroughPolicy
-    sampling_dimension: ONE_D
-    st_slope: 10.0
-    st_clamp: false
-    use_softplus: true
-    slope: 10.0
-    fix_sign_leakage: true
-    acceleration: null
-    kspace_shape:
-    - 512
-    - 246
-    num_layers: 2
-    kspace_sampler: false
-    sampler_detach_mask: false
-    sampler_chans: 16
-    sampler_num_pool_layers: 3
-    sampler_fc_size: 128
-    sampler_drop_prob: 0.0
-    sampler_num_fc_layers: 3
-    sampler_activation: LEAKY_RELU
-    sampling_type: DYNAMIC_2D
-    num_time_steps: 12
-    num_slices: null
-    engine_name: null
-  sensitivity_model:
-    model_name: unet.unet_2d.UnetModel2d
-    engine_name: null
-    in_channels: 2
-    out_channels: 2
-    num_filters: 16
-    num_pool_layers: 4
-    dropout_probability: 0.0
+    sampling_model:
+        model_name: adaptive.policy.StraightThroughPolicy
+        sampling_dimension: ONE_D
+        st_slope: 10.0
+        st_clamp: false
+        use_softplus: true
+        slope: 10.0
+        fix_sign_leakage: true
+        kspace_shape:
+            - 512
+            - 246
+        num_layers: 2
+        kspace_sampler: false
+        sampler_detach_mask: false
+        sampler_chans: 16
+        sampler_num_pool_layers: 3
+        sampler_fc_size: 128
+        sampler_drop_prob: 0.0
+        sampler_num_fc_layers: 3
+        sampler_activation: LEAKY_RELU
+        sampling_type: DYNAMIC_2D
+        num_time_steps: 12
+    sensitivity_model:
+        model_name: unet.unet_2d.UnetModel2d
+        in_channels: 2
+        out_channels: 2
+        num_filters: 16
+        num_pool_layers: 4
+        dropout_probability: 0.0
 physics:
-  forward_operator: fft2
-  backward_operator: ifft2
-  use_noise_matrix: false
-  noise_matrix_scaling: 1.0
-training:
-  datasets:
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: train-4x
-    transforms:
-      masking:
-        name: FastMRIEquispaced
-        accelerations:
-        - 6
-        center_fractions:
-        - 0.04
-      target_acceleration: 4.0327
-      dynamic_mask: true
-      use_seed: false
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: false
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: train-6x
-    transforms:
-      masking:
-        name: FastMRIEquispaced
-        accelerations:
-        - 8.2
-        center_fractions:
-        - 0.04
-      target_acceleration: 6
-      dynamic_mask: true
-      use_seed: false
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: false
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: train-8x
-    transforms:
-      masking:
-        name: FastMRIEquispaced
-        accelerations:
-        - 10.25
-        center_fractions:
-        - 0.04
-      target_acceleration: 8.2
-      dynamic_mask: true
-      use_seed: false
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: false
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-  model_checkpoint: null
-  optimizer: Adam
-  lr: 0.003
-  weight_decay: 0.0
-  batch_size: 1
-  lr_step_size: 10000
-  lr_gamma: 0.8
-  lr_warmup_iter: 2000
-  swa_start_iter: null
-  num_iterations: 60021
-  validation_steps: 4000
-  gradient_steps: 1
-  gradient_clipping: 0.0
-  gradient_debug: false
-  loss:
-    crop: null
-    losses:
-    - function: l2_loss
-      multiplier: 1
-  checkpointer:
-    checkpoint_steps: 2000
-  metrics: []
-  regularizers: []
-validation:
-  datasets:
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: val-4x
-    transforms:
-      masking:
-        name: FastMRIEquispaced
-        accelerations:
-        - 6
-        center_fractions:
-        - 0.04
-      target_acceleration: 4
-      dynamic_mask: true
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: false
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: val-6x
-    transforms:
-      masking:
-        name: FastMRIEquispaced
-        accelerations:
-        - 8.2
-        center_fractions:
-        - 0.04
-      target_acceleration: 6
-      dynamic_mask: true
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: false
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: val-8x
-    transforms:
-      masking:
-        name: FastMRIEquispaced
-        accelerations:
-        - 10.25
-        center_fractions:
-        - 0.04
-      target_acceleration: 8.2
-      dynamic_mask: true
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: false
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-  batch_size: 1
-  metrics:
-  - fastmri_ssim
-  - fastmri_psnr
-  regularizers: []
-  crop: header
+    forward_operator: fft2
+    backward_operator: ifft2
 inference:
-  dataset:
-    name: CMRxRecon
-    transforms:
-      masking:
-        name: FastMRIEquispaced
-        accelerations:
-        - 6
-        center_fractions:
-        - 0.04
-      target_acceleration: 4.0327
-      dynamic_mask: true
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: false
-      padding_eps: 0.0
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-  batch_size: 1
-  crop: header
-  metrics:
-  - fastmri_ssim
-  - fastmri_psnr
-  - fastmri_nmse
-logging:
-  log_as_image: null
-  tensorboard:
-    num_images: 4
+    batch_size: 1
+    crop: header
+    dataset:
+        name: CMRxRecon
+        transforms:
+            use_seed: true
+            delete_kspace: false
+            masking:
+                name: FastMRIEquispaced
+                accelerations:
+                    - 6
+                center_fractions:
+                    - 0.04
+            cropping:
+                image_center_crop: false
+            sensitivity_map_estimation:
+                estimate_sensitivity_maps: true
+            normalization:
+                scaling_key: acs_kspace
+                scale_percentile: 0.995

medl_ads_1d_init2.yaml

@@ -1,291 +1,64 @@
 model:
-  model_name: medl.medl.MEDL3D
-  engine_name: null
-  iterations: 3
-  num_layers: 3
-  unet_num_filters: 18
-  unet_num_pool_layers: 4
-  unet_dropout: 0.0
-  unet_norm: false
+    model_name: medl.medl.MEDL3D
+    iterations: 3
+    num_layers: 3
+    unet_num_filters: 18
+    unet_num_pool_layers: 4
+    unet_dropout: 0.0
+    unet_norm: false
 additional_models:
-  sampling_model:
-    model_name: adaptive.policy.StraightThroughPolicy
-    engine_name: null
-    sampling_dimension: ONE_D
-    st_slope: 10.0
-    st_clamp: false
-    use_softplus: true
-    slope: 10.0
-    fix_sign_leakage: true
-    acceleration: null
-    kspace_shape:
-    - 12
-    - 512
-    - 246
-    num_layers: 2
-    kspace_sampler: false
-    sampler_detach_mask: false
-    sampler_chans: 16
-    sampler_num_pool_layers: 3
-    sampler_fc_size: 128
-    sampler_drop_prob: 0.0
-    sampler_num_fc_layers: 3
-    sampler_activation: LEAKY_RELU
-    sampling_type: STATIC
-    num_time_steps: null
-    num_slices: null
-  sensitivity_model:
-    model_name: unet.unet_2d.UnetModel2d
-    engine_name: null
-    in_channels: 2
-    out_channels: 2
-    num_filters: 16
-    num_pool_layers: 4
-    dropout_probability: 0.0
+    sampling_model:
+        model_name: adaptive.policy.StraightThroughPolicy
+        sampling_dimension: ONE_D
+        st_slope: 10.0
+        st_clamp: false
+        use_softplus: true
+        slope: 10.0
+        fix_sign_leakage: true
+        kspace_shape:
+            - 12
+            - 512
+            - 246
+        num_layers: 2
+        kspace_sampler: false
+        sampler_detach_mask: false
+        sampler_chans: 16
+        sampler_num_pool_layers: 3
+        sampler_fc_size: 128
+        sampler_drop_prob: 0.0
+        sampler_num_fc_layers: 3
+        sampler_activation: LEAKY_RELU
+        sampling_type: STATIC
+    sensitivity_model:
+        model_name: unet.unet_2d.UnetModel2d
+        in_channels: 2
+        out_channels: 2
+        num_filters: 16
+        num_pool_layers: 4
+        dropout_probability: 0.0
 physics:
-  forward_operator: fft2
-  backward_operator: ifft2
-  use_noise_matrix: false
-  noise_matrix_scaling: 1.0
-training:
-  datasets:
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: train-4x
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIEquispaced
-        accelerations:
-        - 6
-        center_fractions:
-        - 0.04
-      use_seed: false
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: false
-      target_acceleration: 4.0327
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.5
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: train-8x
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIEquispaced
-        accelerations:
-        - 8.2
-        center_fractions:
-        - 0.04
-      use_seed: false
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: false
-      target_acceleration: 6
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.5
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: train-8x
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIEquispaced
-        accelerations:
-        - 10.25
-        center_fractions:
-        - 0.04
-      use_seed: false
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: false
-      target_acceleration: 8.2
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.5
-  model_checkpoint: null
-  optimizer: Adam
-  lr: 0.003
-  weight_decay: 0.0
-  batch_size: 1
-  lr_step_size: 10000
-  lr_gamma: 0.8
-  lr_warmup_iter: 2000
-  swa_start_iter: null
-  num_iterations: 60001
-  validation_steps: 4000
-  gradient_steps: 1
-  gradient_clipping: 0.0
-  gradient_debug: false
-  loss:
-    crop: null
-    losses:
-    - function: l2_loss
-      multiplier: 1
-  checkpointer:
-    checkpoint_steps: 2000
-  metrics: []
-  regularizers: []
-validation:
-  datasets:
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: val-4x
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIEquispaced
-        accelerations:
-        - 6
-        center_fractions:
-        - 0.04
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: false
-      target_acceleration: 4
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.0
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: val-6x
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIEquispaced
-        accelerations:
-        - 8.2
-        center_fractions:
-        - 0.04
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: false
-      target_acceleration: 6
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.0
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: val-8x
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIEquispaced
-        accelerations:
-        - 10.25
-        center_fractions:
-        - 0.04
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: false
-      target_acceleration: 8.2
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.0
-  batch_size: 1
-  metrics:
-  - fastmri_ssim
-  - fastmri_psnr
-  regularizers: []
-  crop: header
+    forward_operator: fft2
+    backward_operator: ifft2
 inference:
-  dataset:
-    name: CMRxRecon
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIEquispaced
-        accelerations:
-        - 6
-        center_fractions:
-        - 0.04
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: false
-      target_acceleration: 4.0327
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.0
-    text_description: inference
-    kspace_context: time
-    kspace_key: kspace_full
-  batch_size: 1
-  crop: header
-  metrics:
-  - fastmri_ssim
-  - fastmri_psnr
-  - fastmri_nmse
-logging:
-  log_as_image: null
-  tensorboard:
-    num_images: 4
+    batch_size: 1
+    crop: header
+    dataset:
+        name: CMRxRecon
+        transforms:
+            use_seed: true
+            delete_kspace: false
+            masking:
+                name: FastMRIEquispaced
+                accelerations:
+                    - 6
+                center_fractions:
+                    - 0.04
+            cropping:
+                image_center_crop: false
+            sensitivity_map_estimation:
+                estimate_sensitivity_maps: true
+            normalization:
+                scaling_key: acs_kspace
+                scale_percentile: 0.995
+        kspace_context: time
+        kspace_key: kspace_full

medl_ads_2d.yaml

@@ -1,211 +1,62 @@
 model:
-  model_name: medl.medl.MEDL3D
-  engine_name: null
-  iterations: 3
-  num_layers: 3
-  unet_num_filters: 18
-  unet_num_pool_layers: 4
-  unet_dropout: 0.0
-  unet_norm: false
+    model_name: medl.medl.MEDL3D
+    iterations: 3
+    num_layers: 3
+    unet_num_filters: 18
+    unet_num_pool_layers: 4
+    unet_dropout: 0.0
+    unet_norm: false
 additional_models:
-  sampling_model:
-    model_name: adaptive.policy.StraightThroughPolicy
-    sampling_dimension: TWO_D
-    st_slope: 10.0
-    st_clamp: false
-    use_softplus: true
-    slope: 10.0
-    fix_sign_leakage: true
-    acceleration: null
-    kspace_shape:
-    - 12
-    - 512
-    - 246
-    num_layers: 2
-    kspace_sampler: false
-    sampler_detach_mask: false
-    sampler_chans: 16
-    sampler_num_pool_layers: 3
-    sampler_fc_size: 128
-    sampler_drop_prob: 0.0
-    sampler_num_fc_layers: 3
-    sampler_activation: LEAKY_RELU
-    sampling_type: STATIC
-    num_time_steps: null
-    num_slices: null
-    engine_name: null
-  sensitivity_model:
-    model_name: unet.unet_2d.UnetModel2d
-    engine_name: null
-    in_channels: 2
-    out_channels: 2
-    num_filters: 16
-    num_pool_layers: 4
-    dropout_probability: 0.0
+    sampling_model:
+        model_name: adaptive.policy.StraightThroughPolicy
+        sampling_dimension: TWO_D
+        st_slope: 10.0
+        st_clamp: false
+        use_softplus: true
+        slope: 10.0
+        fix_sign_leakage: true
+        kspace_shape:
+            - 12
+            - 512
+            - 246
+        num_layers: 2
+        kspace_sampler: false
+        sampler_detach_mask: false
+        sampler_chans: 16
+        sampler_num_pool_layers: 3
+        sampler_fc_size: 128
+        sampler_drop_prob: 0.0
+        sampler_num_fc_layers: 3
+        sampler_activation: LEAKY_RELU
+        sampling_type: STATIC
+    sensitivity_model:
+        model_name: unet.unet_2d.UnetModel2d
+        in_channels: 2
+        out_channels: 2
+        num_filters: 16
+        num_pool_layers: 4
+        dropout_probability: 0.0
 physics:
-  forward_operator: fft2
-  backward_operator: ifft2
-  use_noise_matrix: false
-  noise_matrix_scaling: 1.0
-training:
-  datasets:
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: train
-    transforms:
-      masking:
-        name: Gaussian2D
-        accelerations:
-        - 4.0327
-        - 6
-        - 8.2
-        center_fractions:
-        - 0.04
-        - 0.04
-        - 0.04
-      use_seed: false
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: true
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-  model_checkpoint: null
-  optimizer: Adam
-  lr: 0.003
-  weight_decay: 0.0
-  batch_size: 1
-  lr_step_size: 10000
-  lr_gamma: 0.8
-  lr_warmup_iter: 2000
-  swa_start_iter: null
-  num_iterations: 60001
-  validation_steps: 4000
-  gradient_steps: 1
-  gradient_clipping: 0.0
-  gradient_debug: false
-  loss:
-    crop: null
-    losses:
-    - function: l2_loss
-      multiplier: 1
-  checkpointer:
-    checkpoint_steps: 2000
-  metrics: []
-  regularizers: []
-validation:
-  datasets:
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: val-4x
-    transforms:
-      masking:
-        name: Gaussian2D
-        accelerations:
-        - 4.0327
-        center_fractions:
-        - 0.04
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: true
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: val-6x
-    transforms:
-      masking:
-        name: Gaussian2D
-        accelerations:
-        - 6
-        center_fractions:
-        - 0.04
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: true
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: val-8x
-    transforms:
-      masking:
-        name: Gaussian2D
-        accelerations:
-        - 8.2
-        center_fractions:
-        - 0.04
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: true
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-  batch_size: 1
-  metrics:
-  - fastmri_ssim
-  - fastmri_psnr
-  regularizers: []
-  crop: header
+    forward_operator: fft2
+    backward_operator: ifft2
 inference:
-  dataset:
-    name: CMRxRecon
-    transforms:
-      masking:
-        name: Gaussian2D
-        accelerations:
-        - 4.0327
-        center_fractions:
-        - 0.04
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: true
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-  batch_size: 1
-  crop: header
-  metrics:
-  - fastmri_ssim
-  - fastmri_psnr
-  - fastmri_nmse
-logging:
-  log_as_image: null
-  tensorboard:
-    num_images: 4
+    batch_size: 1
+    crop: header
+    dataset:
+        name: CMRxRecon
+        transforms:
+            use_seed: true
+            delete_kspace: false
+            masking:
+                name: Gaussian2D
+                accelerations:
+                    - 4.0327
+                center_fractions:
+                    - 0.04
+            cropping:
+                image_center_crop: false
+            sensitivity_map_estimation:
+                estimate_sensitivity_maps: true
+            normalization:
+                scaling_key: acs_kspace
+                scale_percentile: 0.995

medl_ads_2d_frame.yaml

@@ -1,252 +1,61 @@
 model:
-  model_name: medl.medl.MEDL3D
-  engine_name: null
-  iterations: 3
-  num_layers: 3
-  unet_num_filters: 18
-  unet_num_pool_layers: 4
-  unet_dropout: 0.0
-  unet_norm: false
+    model_name: medl.medl.MEDL3D
+    iterations: 3
+    num_layers: 3
+    unet_num_filters: 18
+    unet_num_pool_layers: 4
+    unet_dropout: 0.0
+    unet_norm: false
 additional_models:
-  sampling_model:
-    model_name: adaptive.policy.StraightThroughPolicy
-    sampling_dimension: TWO_D
-    st_slope: 10.0
-    st_clamp: false
-    use_softplus: true
-    slope: 10.0
-    fix_sign_leakage: true
-    acceleration: null
-    kspace_shape:
-    - 512
-    - 246
-    num_layers: 2
-    kspace_sampler: false
-    sampler_detach_mask: false
-    sampler_chans: 16
-    sampler_num_pool_layers: 3
-    sampler_fc_size: 128
-    sampler_drop_prob: 0.0
-    sampler_num_fc_layers: 3
-    sampler_activation: LEAKY_RELU
-    sampling_type: DYNAMIC_2D
-    num_time_steps: 12
-    num_slices: null
-    engine_name: null
-  sensitivity_model:
-    model_name: unet.unet_2d.UnetModel2d
-    engine_name: null
-    in_channels: 2
-    out_channels: 2
-    num_filters: 16
-    num_pool_layers: 4
-    dropout_probability: 0.0
+    sampling_model:
+        model_name: adaptive.policy.StraightThroughPolicy
+        sampling_dimension: TWO_D
+        st_slope: 10.0
+        st_clamp: false
+        use_softplus: true
+        slope: 10.0
+        fix_sign_leakage: true
+        kspace_shape:
+            - 512
+            - 246
+        num_layers: 2
+        kspace_sampler: false
+        sampler_detach_mask: false
+        sampler_chans: 16
+        sampler_num_pool_layers: 3
+        sampler_fc_size: 128
+        sampler_drop_prob: 0.0
+        sampler_num_fc_layers: 3
+        sampler_activation: LEAKY_RELU
+        sampling_type: DYNAMIC_2D
+        num_time_steps: 12
+    sensitivity_model:
+        model_name: unet.unet_2d.UnetModel2d
+        in_channels: 2
+        out_channels: 2
+        num_filters: 16
+        num_pool_layers: 4
+        dropout_probability: 0.0
 physics:
-  forward_operator: fft2
-  backward_operator: ifft2
-  use_noise_matrix: false
-  noise_matrix_scaling: 1.0
-training:
-  datasets:
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: train-4x
-    transforms:
-      masking:
-        name: Gaussian2D
-        accelerations:
-        - 4.0327
-        center_fractions:
-        - 0.04
-      use_seed: false
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: true
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: train-6x
-    transforms:
-      masking:
-        name: Gaussian2D
-        accelerations:
-        - 6
-        center_fractions:
-        - 0.04
-      use_seed: false
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: true
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: train-8x
-    transforms:
-      masking:
-        name: Gaussian2D
-        accelerations:
-        - 8.2
-        center_fractions:
-        - 0.04
-      use_seed: false
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: true
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-  model_checkpoint: null
-  optimizer: Adam
-  lr: 0.003
-  weight_decay: 0.0
-  batch_size: 1
-  lr_step_size: 10000
-  lr_gamma: 0.8
-  lr_warmup_iter: 2000
-  swa_start_iter: null
-  num_iterations: 60001
-  validation_steps: 4000
-  gradient_steps: 1
-  gradient_clipping: 0.0
-  gradient_debug: false
-  loss:
-    crop: null
-    losses:
-    - function: l2_loss
-      multiplier: 1
-  checkpointer:
-    checkpoint_steps: 2000
-  metrics: []
-  regularizers: []
-validation:
-  datasets:
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: val-4x
-    transforms:
-      masking:
-        name: Gaussian2D
-        accelerations:
-        - 4.0327
-        center_fractions:
-        - 0.04
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: true
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: val-6x
-    transforms:
-      masking:
-        name: Gaussian2D
-        accelerations:
-        - 6
-        center_fractions:
-        - 0.04
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: true
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: val-8x
-    transforms:
-      masking:
-        name: Gaussian2D
-        accelerations:
-        - 8.2
-        center_fractions:
-        - 0.04
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: true
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-  batch_size: 1
-  metrics:
-  - fastmri_ssim
-  - fastmri_psnr
-  regularizers: []
-  crop: header
+    forward_operator: fft2
+    backward_operator: ifft2
 inference:
-  dataset:
-    name: CMRxRecon
-    transforms:
-      masking:
-        name: Gaussian2D
-        accelerations:
-        - 4.0327
-        center_fractions:
-        - 0.04
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: true
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-  batch_size: 1
-  crop: null
-  metrics:
-  - fastmri_ssim
-  - fastmri_psnr
-  - fastmri_nmse
-logging:
-  log_as_image: null
-  tensorboard:
-    num_images: 4
+    batch_size: 1
+    dataset:
+        name: CMRxRecon
+        transforms:
+            use_seed: true
+            delete_kspace: false
+            masking:
+                name: Gaussian2D
+                accelerations:
+                    - 4.0327
+                center_fractions:
+                    - 0.04
+            cropping:
+                image_center_crop: false
+            sensitivity_map_estimation:
+                estimate_sensitivity_maps: true
+            normalization:
+                scaling_key: acs_kspace
+                scale_percentile: 0.995

vsharp_ads_1d.yaml

@@ -1,21 +1,20 @@
 model:
     model_name: vsharp.vsharp.VSharpNet3D
-    engine_name:
     num_steps: 8
     num_steps_dc_gd: 8
     image_init: SENSE
     no_parameter_sharing: true
     auxiliary_steps: -1
     initializer_channels:
-      - 32
-      - 32
-      - 64
-      - 64
+        - 32
+        - 32
+        - 64
+        - 64
     initializer_dilations:
-      - 1
-      - 1
-      - 2
-      - 4
+        - 1
+        - 1
+        - 2
+        - 4
     initializer_multiscale: 1
     initializer_activation: PRELU
     unet_num_filters: 16
@@ -25,18 +24,16 @@ model:
 additional_models:
     sampling_model:
         model_name: adaptive.policy.StraightThroughPolicy
-        engine_name:
         sampling_dimension: ONE_D
         st_slope: 10.0
         st_clamp: false
         use_softplus: true
         slope: 10.0
         fix_sign_leakage: true
-        acceleration:
         kspace_shape:
-          - 12
-          - 512
-          - 246
+            - 12
+            - 512
+            - 246
         num_layers: 1
         kspace_sampler: false
         sampler_detach_mask: false
@@ -47,11 +44,8 @@ additional_models:
         sampler_num_fc_layers: 3
         sampler_activation: LEAKY_RELU
         sampling_type: STATIC
-        num_time_steps:
-        num_slices:
     sensitivity_model:
         model_name: unet.unet_2d.UnetModel2d
-        engine_name:
         in_channels: 2
         out_channels: 2
         num_filters: 16
@@ -60,204 +54,27 @@ additional_models:
 physics:
     forward_operator: fft2
     backward_operator: ifft2
-    use_noise_matrix: false
-    noise_matrix_scaling: 1.0
-training:
-    datasets:
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: train
-        transforms:
-            padding_eps: 0.0
-            masking:
-                name: FastMRIRandom
-                accelerations:
-                  - 4.0327
-                  - 6
-                  - 8.2
-                center_fractions:
-                  - 0.04
-                  - 0.04
-                  - 0.04
-            use_seed: false
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: true
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-            random_augmentations:
-                random_rotation_probability: 0.0
-                random_flip_probability: 0.5
-    model_checkpoint:
-    optimizer: Adam
-    lr: 0.003
-    weight_decay: 0.0
-    batch_size: 1
-    lr_step_size: 10000
-    lr_gamma: 0.8
-    lr_warmup_iter: 2000
-    swa_start_iter:
-    num_iterations: 60001
-    validation_steps: 4000
-    gradient_steps: 1
-    gradient_clipping: 0.0
-    gradient_debug: false
-    loss:
-        crop:
-        losses:
-          - function: l1_loss
-            multiplier: 1
-          - function: ssim_loss
-            multiplier: 1
-          - function: ssim_3d_loss
-            multiplier: 1
-          - function: hfen_l1_norm_loss
-            multiplier: 1
-          - function: kspace_nmae_loss
-            multiplier: 3
-    checkpointer:
-        checkpoint_steps: 2000
-    metrics: []
-    regularizers: []
-validation:
-    datasets:
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: val-4x
-        transforms:
-            padding_eps: 0.0
-            masking:
-                name: FastMRIRandom
-                accelerations:
-                  - 4.0327
-                center_fractions:
-                  - 0.04
-            use_seed: true
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: true
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-            random_augmentations:
-                random_rotation_probability: 0.0
-                random_flip_probability: 0.0
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: val-6x
-        transforms:
-            padding_eps: 0.0
-            masking:
-                name: FastMRIRandom
-                accelerations:
-                  - 6
-                center_fractions:
-                  - 0.04
-            use_seed: true
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: true
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-            random_augmentations:
-                random_rotation_probability: 0.0
-                random_flip_probability: 0.0
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: val-8x
-        transforms:
-            padding_eps: 0.0
-            masking:
-                name: FastMRIRandom
-                accelerations:
-                  - 8.2
-                center_fractions:
-                  - 0.04
-            use_seed: true
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: true
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-            random_augmentations:
-                random_rotation_probability: 0.0
-                random_flip_probability: 0.0
+inference:
     batch_size: 1
-    metrics:
-      - fastmri_ssim
-      - fastmri_psnr
-    regularizers: []
     crop: header
-inference:
     dataset:
         name: CMRxRecon
         transforms:
-            padding_eps: 0.0
+            use_seed: true
+            delete_kspace: false
             masking:
                 name: FastMRIRandom
                 accelerations:
-                  - 4.0327
+                    - 4.0327
                 center_fractions:
-                  - 0.04
-            use_seed: true
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: true
-            augmentation:
-                pad:
-                  - 512
-                  - 246
+                    - 0.04
+            cropping:
+                image_center_crop: false
             sensitivity_map_estimation:
                 estimate_sensitivity_maps: true
             normalization:
                 scaling_key: acs_kspace
                 scale_percentile: 0.995
-            random_augmentations:
-                random_rotation_probability: 0.0
-                random_flip_probability: 0.0
-        text_description: inference
-        data_root:
-        filenames_filter:
-        filenames_lists:
-        filenames_lists_root:
         kspace_key: kspace_full
         compute_mask: false
-        extra_keys:
         kspace_context: time
-    batch_size: 1
-    metrics:
-      - fastmri_ssim
-      - fastmri_psnr
-      - fastmri_nmse
-    crop: header
-logging:
-    log_as_image:
-    tensorboard:
-        num_images: 4

vsharp_ads_1d_frame.yaml

@@ -1,21 +1,20 @@
 model:
     model_name: vsharp.vsharp.VSharpNet3D
-    engine_name:
     num_steps: 8
     num_steps_dc_gd: 8
     image_init: SENSE
     no_parameter_sharing: true
     auxiliary_steps: -1
     initializer_channels:
-      - 32
-      - 32
-      - 64
-      - 64
+        - 32
+        - 32
+        - 64
+        - 64
     initializer_dilations:
-      - 1
-      - 1
-      - 2
-      - 4
+        - 1
+        - 1
+        - 2
+        - 4
     initializer_multiscale: 1
     initializer_activation: PRELU
     unet_num_filters: 16
@@ -25,17 +24,15 @@ model:
 additional_models:
     sampling_model:
         model_name: adaptive.policy.StraightThroughPolicy
-        engine_name:
         sampling_dimension: ONE_D
         st_slope: 10.0
         st_clamp: false
         use_softplus: true
         slope: 10.0
         fix_sign_leakage: true
-        acceleration:
         kspace_shape:
-          - 512
-          - 246
+            - 512
+            - 246
         num_layers: 1
         kspace_sampler: false
         sampler_detach_mask: false
@@ -47,10 +44,8 @@ additional_models:
         sampler_activation: LEAKY_RELU
         sampling_type: DYNAMIC_2D
         num_time_steps: 12
-        num_slices:
     sensitivity_model:
         model_name: unet.unet_2d.UnetModel2d
-        engine_name:
         in_channels: 2
         out_channels: 2
         num_filters: 16
@@ -59,317 +54,26 @@ additional_models:
 physics:
     forward_operator: fft2
     backward_operator: ifft2
-    use_noise_matrix: false
-    noise_matrix_scaling: 1.0
-training:
-    datasets:
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: train-4x
-        transforms:
-            padding_eps: 0.0
-            masking:
-                name: FastMRIRandom
-                mode: DYNAMIC
-                accelerations:
-                  - 4.0327
-                center_fractions:
-                  - 0.04
-            use_seed: false
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: true
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-            random_augmentations:
-                random_rotation_probability: 0.0
-                random_flip_probability: 0.5
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: train-6x
-        transforms:
-            padding_eps: 0.0
-            masking:
-                name: FastMRIRandom
-                mode: DYNAMIC
-                accelerations:
-                  - 6
-                center_fractions:
-                  - 0.04
-            use_seed: false
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: true
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-            random_augmentations:
-                random_rotation_probability: 0.0
-                random_flip_probability: 0.5
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: train-8x
-        transforms:
-            padding_eps: 0.0
-            masking:
-                name: FastMRIRandom
-                mode: DYNAMIC
-                accelerations:
-                  - 8.2
-                center_fractions:
-                  - 0.04
-            use_seed: false
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: true
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-            random_augmentations:
-                random_rotation_probability: 0.0
-                random_flip_probability: 0.5
-    model_checkpoint:
-    optimizer: Adam
-    lr: 0.003
-    weight_decay: 0.0
-    batch_size: 1
-    lr_step_size: 10000
-    lr_gamma: 0.8
-    lr_warmup_iter: 2000
-    swa_start_iter:
-    num_iterations: 60001
-    validation_steps: 10000
-    gradient_steps: 1
-    gradient_clipping: 0.0
-    gradient_debug: false
-    loss:
-        crop:
-        losses:
-          - function: l1_loss
-            multiplier: 1
-          - function: ssim_loss
-            multiplier: 1
-          - function: ssim_3d_loss
-            multiplier: 1
-          - function: hfen_l1_norm_loss
-            multiplier: 1
-          - function: kspace_nmae_loss
-            multiplier: 3
-    checkpointer:
-        checkpoint_steps: 2000
-    metrics: []
-    regularizers: []
-validation:
-    datasets:
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: val-4x
-        transforms:
-            padding_eps: 0.0
-            masking:
-                name: FastMRIRandom
-                mode: DYNAMIC
-                accelerations:
-                  - 4.0327
-                center_fractions:
-                  - 0.04
-            use_seed: true
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: true
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-            random_augmentations:
-                random_rotation_probability: 0.0
-                random_flip_probability: 0.0
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: val-6x
-        transforms:
-            padding_eps: 0.0
-            masking:
-                name: FastMRIRandom
-                mode: DYNAMIC
-                accelerations:
-                  - 6
-                center_fractions:
-                  - 0.04
-            use_seed: true
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: true
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-            random_augmentations:
-                random_rotation_probability: 0.0
-                random_flip_probability: 0.0
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: val-8x
-        transforms:
-            padding_eps: 0.0
-            masking:
-                name: FastMRIRandom
-                mode: DYNAMIC
-                accelerations:
-                  - 8.2
-                center_fractions:
-                  - 0.04
-            use_seed: true
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: true
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-            random_augmentations:
-                random_rotation_probability: 0.0
-                random_flip_probability: 0.0
-    batch_size: 1
-    metrics:
-      - fastmri_ssim
-      - fastmri_psnr
-    regularizers: []
-    crop:
 inference:
+    batch_size: 1
     dataset:
         name: CMRxRecon
         transforms:
+            use_seed: true
+            delete_kspace: false
             masking:
                 name: FastMRIRandom
                 accelerations:
-                  - 8.2
+                    - 8.2
                 center_fractions:
-                  - 0.04
-                mode: DYNAMIC
-                val_accelerations:
-                  - 5.0
-                  - 10.0
-                val_center_fractions:
-                  - 0.1
-                  - 0.05
-                range_mode: DISCRETE
-            target_acceleration:
+                    - 0.04
             cropping:
-                crop:
-                crop_type: uniform
                 image_center_crop: false
-            augmentation:
-                rescale:
-                rescale_mode: NEAREST
-                rescale_2d_if_3d: false
-                pad:
-                  - 512
-                  - 246
-            random_augmentations:
-                random_rotation_degrees:
-                  - -90
-                  - 90
-                random_rotation_probability: 0.0
-                random_flip_type: RANDOM
-                random_flip_probability: 0.0
-                random_reverse_probability: 0.0
-            padding_eps: 0.0
-            estimate_body_coil_image: false
             sensitivity_map_estimation:
                 estimate_sensitivity_maps: true
-                sensitivity_maps_type: RSS_ESTIMATE
-                sensitivity_maps_espirit_threshold: 0.05
-                sensitivity_maps_espirit_kernel_size: 6
-                sensitivity_maps_espirit_crop: 0.95
-                sensitivity_maps_espirit_max_iters: 30
-                sensitivity_maps_gaussian: 0.7
             normalization:
                 scaling_key: acs_kspace
                 scale_percentile: 0.995
-            use_acs_as_mask: true
-            delete_acs_mask: false
-            delete_kspace: false
-            image_recon_type: RSS
-            compress_coils:
-            pad_coils:
-            registration:
-                registration: false
-                registration_simulate_reference:
-                registration_simulate_elastic_sigma: 3.0
-                registration_simulate_elastic_points: 3
-                registration_simulate_elastic_rotate: 0.0
-                registration_simulate_elastic_zoom: 0.0
-                registration_estimate_displacement: true
-                registration_simulate_reference_from_key_index: 0
-                registration_moving_key: TARGET
-                demons_filter_type: SYMMETRIC_FORCES
-                demons_num_iterations: 100
-                demons_smooth_displacement_field: true
-                demons_standard_deviations: 1.5
-                demons_intensity_difference_threshold:
-                demons_maximum_rms_error:
-            use_seed: true
-            transforms_type: SUPERVISED
-            mask_split_ratio:
-              - 0.4
-            mask_split_acs_region:
-              - 0
-              - 0
-            mask_split_keep_acs: false
-            mask_split_type: GAUSSIAN
-            mask_split_gaussian_std: 3.0
-            mask_split_half_direction: VERTICAL
-        text_description: inference-8x
-        data_root:
-        filenames_filter:
-        filenames_lists:
-        filenames_lists_root:
         kspace_key: kspace_full
         compute_mask: false
-        extra_keys:
         kspace_context: time
-    batch_size: 1
-    metrics:
-      - fastmri_ssim
-      - fastmri_psnr
-      - fastmri_nmse
-    crop:
-logging:
-    log_as_image:
-    tensorboard:
-        num_images: 4

vsharp_ads_1d_frame_init2.yaml

@@ -6,15 +6,15 @@ model:
     no_parameter_sharing: true
     auxiliary_steps: -1
     initializer_channels:
-      - 32
-      - 32
-      - 64
-      - 64
+        - 32
+        - 32
+        - 64
+        - 64
     initializer_dilations:
-      - 1
-      - 1
-      - 2
-      - 4
+        - 1
+        - 1
+        - 2
+        - 4
     initializer_multiscale: 1
     initializer_activation: PRELU
     unet_num_filters: 16
@@ -30,10 +30,9 @@ additional_models:
         use_softplus: true
         slope: 10.0
         fix_sign_leakage: true
-        acceleration:
         kspace_shape:
-          - 512
-          - 246
+            - 512
+            - 246
         num_layers: 1
         kspace_sampler: false
         sampler_detach_mask: false
@@ -45,7 +44,6 @@ additional_models:
         sampler_activation: LEAKY_RELU
         sampling_type: DYNAMIC_2D
         num_time_steps: 12
-        num_slices:
     sensitivity_model:
         model_name: unet.unet_2d.UnetModel2d
         in_channels: 2
@@ -56,234 +54,24 @@ additional_models:
 physics:
     forward_operator: fft2
     backward_operator: ifft2
-    use_noise_matrix: false
-    noise_matrix_scaling: 1.0
-training:
-    datasets:
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: train-4x
-        transforms:
-            masking:
-                name: FastMRIEquispaced
-                accelerations:
-                  - 6
-                center_fractions:
-                  - 0.04
-            target_acceleration: 4.0327
-            dynamic_mask: true
-            use_seed: false
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: false
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: train-6x
-        transforms:
-            masking:
-                name: FastMRIEquispaced
-                accelerations:
-                  - 8.2
-                center_fractions:
-                  - 0.04
-            target_acceleration: 6
-            dynamic_mask: true
-            use_seed: false
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: false
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: train-8x
-        transforms:
-            masking:
-                name: FastMRIEquispaced
-                accelerations:
-                  - 10.25
-                center_fractions:
-                  - 0.04
-            target_acceleration: 8.2
-            dynamic_mask: true
-            use_seed: false
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: false
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-    model_checkpoint:
-    optimizer: Adam
-    lr: 0.003
-    weight_decay: 0.0
-    batch_size: 1
-    lr_step_size: 10000
-    lr_gamma: 0.8
-    lr_warmup_iter: 2000
-    swa_start_iter:
-    num_iterations: 60021
-    validation_steps: 4000
-    gradient_steps: 1
-    gradient_clipping: 0.0
-    gradient_debug: false
-    loss:
-        crop:
-        losses:
-          - function: l1_loss
-            multiplier: 1
-          - function: ssim_loss
-            multiplier: 1
-          - function: ssim_3d_loss
-            multiplier: 1
-          - function: hfen_l1_norm_loss
-            multiplier: 1
-          - function: kspace_nmae_loss
-            multiplier: 3
-    checkpointer:
-        checkpoint_steps: 2000
-    metrics: []
-    regularizers: []
-validation:
-    datasets:
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: val-4x
-        transforms:
-            masking:
-                name: FastMRIEquispaced
-                accelerations:
-                  - 6
-                center_fractions:
-                  - 0.04
-            target_acceleration: 4
-            dynamic_mask: true
-            use_seed: true
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: false
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: val-6x
-        transforms:
-            masking:
-                name: FastMRIEquispaced
-                accelerations:
-                  - 8.2
-                center_fractions:
-                  - 0.04
-            target_acceleration: 6
-            dynamic_mask: true
-            use_seed: true
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: false
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: val-8x
-        transforms:
-            masking:
-                name: FastMRIEquispaced
-                accelerations:
-                  - 10.25
-                center_fractions:
-                  - 0.04
-            target_acceleration: 8.2
-            dynamic_mask: true
-            use_seed: true
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: false
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
+inference:
     batch_size: 1
-    metrics:
-      - fastmri_ssim
-      - fastmri_psnr
-    regularizers: []
     crop: header
-inference:
     dataset:
         name: CMRxRecon
         transforms:
+            use_seed: true
+            delete_kspace: false
             masking:
                 name: FastMRIEquispaced
                 accelerations:
-                  - 6
+                    - 6
                 center_fractions:
-                  - 0.04
-            # Match kosmos inference target_accelerations: [4.0327].
-            target_acceleration: 4.0327
-            dynamic_mask: true
-            use_seed: true
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: false
-            # Kosmos inference used compute_and_apply_padding: false.
-            padding_eps: 0.0
-            augmentation:
-                pad:
-                  - 512
-                  - 246
+                    - 0.04
+            cropping:
+                image_center_crop: false
             sensitivity_map_estimation:
                 estimate_sensitivity_maps: true
             normalization:
                 scaling_key: acs_kspace
                 scale_percentile: 0.995
-    batch_size: 1
-    crop: header
-    metrics:
-      - fastmri_ssim
-      - fastmri_psnr
-      - fastmri_nmse
-logging:
-    log_as_image:
-    tensorboard:
-        num_images: 4

vsharp_ads_1d_init2.yaml

@@ -1,314 +1,79 @@
 model:
-  model_name: vsharp.vsharp.VSharpNet3D
-  engine_name: null
-  num_steps: 8
-  num_steps_dc_gd: 8
-  image_init: SENSE
-  no_parameter_sharing: true
-  auxiliary_steps: -1
-  initializer_channels:
-  - 32
-  - 32
-  - 64
-  - 64
-  initializer_dilations:
-  - 1
-  - 1
-  - 2
-  - 4
-  initializer_multiscale: 1
-  initializer_activation: PRELU
-  unet_num_filters: 16
-  unet_num_pool_layers: 4
-  unet_dropout: 0.0
-  unet_norm: false
+    model_name: vsharp.vsharp.VSharpNet3D
+    num_steps: 8
+    num_steps_dc_gd: 8
+    image_init: SENSE
+    no_parameter_sharing: true
+    auxiliary_steps: -1
+    initializer_channels:
+        - 32
+        - 32
+        - 64
+        - 64
+    initializer_dilations:
+        - 1
+        - 1
+        - 2
+        - 4
+    initializer_multiscale: 1
+    initializer_activation: PRELU
+    unet_num_filters: 16
+    unet_num_pool_layers: 4
+    unet_dropout: 0.0
+    unet_norm: false
 additional_models:
-  sampling_model:
-    model_name: adaptive.policy.StraightThroughPolicy
-    engine_name: null
-    sampling_dimension: ONE_D
-    st_slope: 10.0
-    st_clamp: false
-    use_softplus: true
-    slope: 10.0
-    fix_sign_leakage: true
-    acceleration: null
-    kspace_shape:
-    - 12
-    - 512
-    - 246
-    num_layers: 1
-    kspace_sampler: false
-    sampler_detach_mask: false
-    sampler_chans: 16
-    sampler_num_pool_layers: 3
-    sampler_fc_size: 128
-    sampler_drop_prob: 0.0
-    sampler_num_fc_layers: 3
-    sampler_activation: LEAKY_RELU
-    sampling_type: STATIC
-    num_time_steps: null
-    num_slices: null
-  sensitivity_model:
-    model_name: unet.unet_2d.UnetModel2d
-    engine_name: null
-    in_channels: 2
-    out_channels: 2
-    num_filters: 16
-    num_pool_layers: 4
-    dropout_probability: 0.0
+    sampling_model:
+        model_name: adaptive.policy.StraightThroughPolicy
+        sampling_dimension: ONE_D
+        st_slope: 10.0
+        st_clamp: false
+        use_softplus: true
+        slope: 10.0
+        fix_sign_leakage: true
+        kspace_shape:
+            - 12
+            - 512
+            - 246
+        num_layers: 1
+        kspace_sampler: false
+        sampler_detach_mask: false
+        sampler_chans: 16
+        sampler_num_pool_layers: 3
+        sampler_fc_size: 128
+        sampler_drop_prob: 0.0
+        sampler_num_fc_layers: 3
+        sampler_activation: LEAKY_RELU
+        sampling_type: STATIC
+    sensitivity_model:
+        model_name: unet.unet_2d.UnetModel2d
+        in_channels: 2
+        out_channels: 2
+        num_filters: 16
+        num_pool_layers: 4
+        dropout_probability: 0.0
 physics:
-  forward_operator: fft2
-  backward_operator: ifft2
-  use_noise_matrix: false
-  noise_matrix_scaling: 1.0
-training:
-  datasets:
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: train-4x
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIEquispaced
-        accelerations:
-        - 6
-        center_fractions:
-        - 0.04
-      use_seed: false
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: false
-      target_acceleration: 4.0327
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.5
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: train-8x
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIEquispaced
-        accelerations:
-        - 8.2
-        center_fractions:
-        - 0.04
-      use_seed: false
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: false
-      target_acceleration: 6
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.5
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: train-8x
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIEquispaced
-        accelerations:
-        - 10.25
-        center_fractions:
-        - 0.04
-      use_seed: false
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: false
-      target_acceleration: 8.2
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.5
-  model_checkpoint: null
-  optimizer: Adam
-  lr: 0.003
-  weight_decay: 0.0
-  batch_size: 1
-  lr_step_size: 10000
-  lr_gamma: 0.8
-  lr_warmup_iter: 2000
-  swa_start_iter: null
-  num_iterations: 60001
-  validation_steps: 4000
-  gradient_steps: 1
-  gradient_clipping: 0.0
-  gradient_debug: false
-  loss:
-    crop: null
-    losses:
-    - function: l1_loss
-      multiplier: 1
-    - function: ssim_loss
-      multiplier: 1
-    - function: ssim_3d_loss
-      multiplier: 1
-    - function: hfen_l1_norm_loss
-      multiplier: 1
-    - function: kspace_nmae_loss
-      multiplier: 3
-  checkpointer:
-    checkpoint_steps: 2000
-  metrics: []
-  regularizers: []
-validation:
-  datasets:
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: val-4x
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIEquispaced
-        accelerations:
-        - 6
-        center_fractions:
-        - 0.04
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: false
-      target_acceleration: 4
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.0
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: val-6x
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIEquispaced
-        accelerations:
-        - 8.2
-        center_fractions:
-        - 0.04
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: false
-      target_acceleration: 6
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.0
-  - name: CMRxRecon
-    kspace_context: time
-    text_description: val-8x
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIEquispaced
-        accelerations:
-        - 10.25
-        center_fractions:
-        - 0.04
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: false
-      target_acceleration: 8.2
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.0
-  batch_size: 1
-  metrics:
-  - fastmri_ssim
-  - fastmri_psnr
-  regularizers: []
-  crop: header
+    forward_operator: fft2
+    backward_operator: ifft2
 inference:
-  dataset:
-    name: CMRxRecon
-    transforms:
-      padding_eps: 0.0
-      masking:
-        name: FastMRIEquispaced
-        accelerations:
-        - 6
-        center_fractions:
-        - 0.04
-      use_seed: true
-      delete_kspace: false
-      delete_acs_mask: false
-      use_acs_as_mask: false
-      target_acceleration: 4.0327
-      augmentation:
-        pad:
-        - 512
-        - 246
-      sensitivity_map_estimation:
-        estimate_sensitivity_maps: true
-      normalization:
-        scaling_key: acs_kspace
-        scale_percentile: 0.995
-      random_augmentations:
-        random_rotation_probability: 0.0
-        random_flip_probability: 0.0
-    text_description: inference
-    kspace_context: time
-    kspace_key: kspace_full
-  batch_size: 1
-  crop: header
-  metrics:
-  - fastmri_ssim
-  - fastmri_psnr
-  - fastmri_nmse
-logging:
-  log_as_image: null
-  tensorboard:
-    num_images: 4
+    batch_size: 1
+    crop: header
+    dataset:
+        name: CMRxRecon
+        transforms:
+            use_seed: true
+            delete_kspace: false
+            masking:
+                name: FastMRIEquispaced
+                accelerations:
+                    - 6
+                center_fractions:
+                    - 0.04
+            cropping:
+                image_center_crop: false
+            sensitivity_map_estimation:
+                estimate_sensitivity_maps: true
+            normalization:
+                scaling_key: acs_kspace
+                scale_percentile: 0.995
+        kspace_context: time
+        kspace_key: kspace_full

vsharp_ads_2d.yaml

@@ -6,15 +6,15 @@ model:
     no_parameter_sharing: true
     auxiliary_steps: -1
     initializer_channels:
-      - 32
-      - 32
-      - 64
-      - 64
+        - 32
+        - 32
+        - 64
+        - 64
     initializer_dilations:
-      - 1
-      - 1
-      - 2
-      - 4
+        - 1
+        - 1
+        - 2
+        - 4
     initializer_multiscale: 1
     initializer_activation: PRELU
     unet_num_filters: 16
@@ -30,11 +30,10 @@ additional_models:
         use_softplus: true
         slope: 10.0
         fix_sign_leakage: true
-        acceleration:
         kspace_shape:
-          - 12
-          - 512
-          - 246
+            - 12
+            - 512
+            - 246
         num_layers: 1
         kspace_sampler: false
         sampler_detach_mask: false
@@ -45,8 +44,6 @@ additional_models:
         sampler_num_fc_layers: 3
         sampler_activation: LEAKY_RELU
         sampling_type: STATIC
-        num_time_steps:
-        num_slices:
     sensitivity_model:
         model_name: unet.unet_2d.UnetModel2d
         in_channels: 2
@@ -57,175 +54,24 @@ additional_models:
 physics:
     forward_operator: fft2
     backward_operator: ifft2
-    use_noise_matrix: false
-    noise_matrix_scaling: 1.0
-training:
-    datasets:
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: train
-        transforms:
-            masking:
-                name: Gaussian2D
-                accelerations:
-                  - 4.0327
-                  - 6
-                  - 8.2
-                center_fractions:
-                  - 0.04
-                  - 0.04
-                  - 0.04
-            use_seed: false
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: true
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-    model_checkpoint:
-    optimizer: Adam
-    lr: 0.003
-    weight_decay: 0.0
-    batch_size: 1
-    lr_step_size: 10000
-    lr_gamma: 0.8
-    lr_warmup_iter: 2000
-    swa_start_iter:
-    num_iterations: 60001
-    validation_steps: 4000
-    gradient_steps: 1
-    gradient_clipping: 0.0
-    gradient_debug: false
-    loss:
-        crop:
-        losses:
-          - function: l1_loss
-            multiplier: 1
-          - function: ssim_loss
-            multiplier: 1
-          - function: ssim_3d_loss
-            multiplier: 1
-          - function: hfen_l1_norm_loss
-            multiplier: 1
-          - function: kspace_nmae_loss
-            multiplier: 3
-    checkpointer:
-        checkpoint_steps: 2000
-    metrics: []
-    regularizers: []
-validation:
-    datasets:
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: val-4x
-        transforms:
-            masking:
-                name: Gaussian2D
-                accelerations:
-                  - 4.0327
-                center_fractions:
-                  - 0.04
-            use_seed: true
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: true
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: val-6x
-        transforms:
-            masking:
-                name: Gaussian2D
-                accelerations:
-                  - 6
-                center_fractions:
-                  - 0.04
-            use_seed: true
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: true
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: val-8x
-        transforms:
-            masking:
-                name: Gaussian2D
-                accelerations:
-                  - 8.2
-                center_fractions:
-                  - 0.04
-            use_seed: true
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: true
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
+inference:
     batch_size: 1
-    metrics:
-      - fastmri_ssim
-      - fastmri_psnr
-    regularizers: []
     crop: header
-inference:
     dataset:
         name: CMRxRecon
         transforms:
+            use_seed: true
+            delete_kspace: false
             masking:
                 name: Gaussian2D
                 accelerations:
-                  - 4.0327
+                    - 4.0327
                 center_fractions:
-                  - 0.04
-            use_seed: true
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: true
-            augmentation:
-                pad:
-                  - 512
-                  - 246
+                    - 0.04
+            cropping:
+                image_center_crop: false
             sensitivity_map_estimation:
                 estimate_sensitivity_maps: true
             normalization:
                 scaling_key: acs_kspace
                 scale_percentile: 0.995
-    batch_size: 1
-    crop: header
-    metrics:
-      - fastmri_ssim
-      - fastmri_psnr
-      - fastmri_nmse
-logging:
-    log_as_image:
-    tensorboard:
-        num_images: 4

vsharp_ads_2d_frame.yaml

@@ -6,15 +6,15 @@ model:
     no_parameter_sharing: true
     auxiliary_steps: -1
     initializer_channels:
-      - 32
-      - 32
-      - 64
-      - 64
+        - 32
+        - 32
+        - 64
+        - 64
     initializer_dilations:
-      - 1
-      - 1
-      - 2
-      - 4
+        - 1
+        - 1
+        - 2
+        - 4
     initializer_multiscale: 1
     initializer_activation: PRELU
     unet_num_filters: 16
@@ -30,10 +30,9 @@ additional_models:
         use_softplus: true
         slope: 10.0
         fix_sign_leakage: true
-        acceleration:
         kspace_shape:
-          - 512
-          - 246
+            - 512
+            - 246
         num_layers: 1
         kspace_sampler: false
         sampler_detach_mask: false
@@ -45,7 +44,6 @@ additional_models:
         sampler_activation: LEAKY_RELU
         sampling_type: DYNAMIC_2D
         num_time_steps: 12
-        num_slices:
     sensitivity_model:
         model_name: unet.unet_2d.UnetModel2d
         in_channels: 2
@@ -56,217 +54,23 @@ additional_models:
 physics:
     forward_operator: fft2
     backward_operator: ifft2
-    use_noise_matrix: false
-    noise_matrix_scaling: 1.0
-training:
-    datasets:
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: train-4x
-        transforms:
-            masking:
-                name: Gaussian2D
-                accelerations:
-                  - 4.0327
-                center_fractions:
-                  - 0.04
-            use_seed: false
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: true
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: train-6x
-        transforms:
-            masking:
-                name: Gaussian2D
-                accelerations:
-                  - 6
-                center_fractions:
-                  - 0.04
-            use_seed: false
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: true
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: train-8x
-        transforms:
-            masking:
-                name: Gaussian2D
-                accelerations:
-                  - 8.2
-                center_fractions:
-                  - 0.04
-            use_seed: false
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: true
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-    model_checkpoint:
-    optimizer: Adam
-    lr: 0.003
-    weight_decay: 0.0
-    batch_size: 1
-    lr_step_size: 10000
-    lr_gamma: 0.8
-    lr_warmup_iter: 2000
-    swa_start_iter:
-    num_iterations: 60001
-    validation_steps: 4000
-    gradient_steps: 1
-    gradient_clipping: 0.0
-    gradient_debug: false
-    loss:
-        crop:
-        losses:
-          - function: l1_loss
-            multiplier: 1
-          - function: ssim_loss
-            multiplier: 1
-          - function: ssim_3d_loss
-            multiplier: 1
-          - function: hfen_l1_norm_loss
-            multiplier: 1
-          - function: kspace_nmae_loss
-            multiplier: 3
-    checkpointer:
-        checkpoint_steps: 2000
-    metrics: []
-    regularizers: []
-validation:
-    datasets:
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: val-4x
-        transforms:
-            masking:
-                name: Gaussian2D
-                accelerations:
-                  - 4.0327
-                center_fractions:
-                  - 0.04
-            use_seed: true
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: true
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: val-6x
-        transforms:
-            masking:
-                name: Gaussian2D
-                accelerations:
-                  - 6
-                center_fractions:
-                  - 0.04
-            use_seed: true
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: true
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-      - name: CMRxRecon
-        kspace_context: time
-        text_description: val-8x
-        transforms:
-            masking:
-                name: Gaussian2D
-                accelerations:
-                  - 8.2
-                center_fractions:
-                  - 0.04
-            use_seed: true
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: true
-            augmentation:
-                pad:
-                  - 512
-                  - 246
-            sensitivity_map_estimation:
-                estimate_sensitivity_maps: true
-            normalization:
-                scaling_key: acs_kspace
-                scale_percentile: 0.995
-    batch_size: 1
-    metrics:
-      - fastmri_ssim
-      - fastmri_psnr
-    regularizers: []
-    crop: header
 inference:
+    batch_size: 1
     dataset:
         name: CMRxRecon
         transforms:
+            use_seed: true
+            delete_kspace: false
             masking:
                 name: Gaussian2D
                 accelerations:
-                  - 4.0327
+                    - 4.0327
                 center_fractions:
-                  - 0.04
-            use_seed: true
-            delete_kspace: false
-            delete_acs_mask: false
-            use_acs_as_mask: true
-            augmentation:
-                pad:
-                  - 512
-                  - 246
+                    - 0.04
+            cropping:
+                image_center_crop: false
             sensitivity_map_estimation:
                 estimate_sensitivity_maps: true
             normalization:
                 scaling_key: acs_kspace
                 scale_percentile: 0.995
-    batch_size: 1
-    crop:
-    metrics:
-      - fastmri_ssim
-      - fastmri_psnr
-      - fastmri_nmse
-logging:
-    log_as_image:
-    tensorboard:
-        num_images: 4