---
imports:
  - "$from scipy import ndimage"
arch_ckpt_path: models
amp: true
data_file_base_dir: /workspace/data/msd/Task07_Pancreas
data_list_file_path: configs/dataset_0.json
determ: true
input_channels: 1
learning_rate: 0.025
learning_rate_arch: 0.001
learning_rate_milestones:
- 0.4
- 0.8
num_images_per_batch: 1
num_epochs: 1430
num_epochs_per_validation: 100
num_epochs_warmup: 715
num_patches_per_image: 1
num_sw_batch_size: 6
output_classes: 3
overlap_ratio: 0.625
patch_size:
- 96
- 96
- 96
patch_size_valid:
- 96
- 96
- 96
ram_cost_factor: 0.8
image_key: image
label_key: label
transform_train:
  _target_: Compose
  transforms:
  - _target_: LoadImaged
    keys:
    - "@image_key"
    - "@label_key"
  - _target_: EnsureChannelFirstd
    keys:
    - "@image_key"
    - "@label_key"
  - _target_: Orientationd
    keys:
    - "@image_key"
    - "@label_key"
    axcodes: RAS
  - _target_: Spacingd
    keys:
    - "@image_key"
    - "@label_key"
    pixdim:
    - 1
    - 1
    - 1
    mode:
    - bilinear
    - nearest
    align_corners:
    - true
    - true
  - _target_: CastToTyped
    keys: "@image_key"
    dtype: "$torch.float32"
  - _target_: ScaleIntensityRanged
    keys: "@image_key"
    a_min: -87
    a_max: 199
    b_min: 0
    b_max: 1
    clip: true
  - _target_: CastToTyped
    keys:
    - "@image_key"
    - "@label_key"
    dtype:
    - "$np.float16"
    - "$np.uint8"
  - _target_: CopyItemsd
    keys: "@label_key"
    times: 1
    names:
    - label4crop
  - _target_: Lambdad
    keys: label4crop
    func: "$lambda x, s=@output_classes: np.concatenate(tuple([ndimage.binary_dilation((x==_k).astype(x.dtype), iterations=48).astype(float) for _k in range(s)]), axis=0)"
    overwrite: true
  - _target_: EnsureTyped
    keys:
    - "@image_key"
    - "@label_key"
  - _target_: CastToTyped
    keys: "@image_key"
    dtype: "$torch.float32"
  - _target_: SpatialPadd
    keys:
    - "@image_key"
    - "@label_key"
    - label4crop
    spatial_size: "@patch_size"
    mode:
    - reflect
    - constant
    - constant
  - _target_: RandCropByLabelClassesd
    keys:
    - "@image_key"
    - "@label_key"
    label_key: label4crop
    num_classes: "@output_classes"
    ratios: "$[1,] * @output_classes"
    spatial_size: "@patch_size"
    num_samples: "@num_patches_per_image"
  - _target_: Lambdad
    keys: label4crop
    func: "$lambda x: 0"
  - _target_: RandRotated
    keys:
    - "@image_key"
    - "@label_key"
    range_x: 0.3
    range_y: 0.3
    range_z: 0.3
    mode:
    - bilinear
    - nearest
    prob: 0.2
  - _target_: RandZoomd
    keys:
    - "@image_key"
    - "@label_key"
    min_zoom: 0.8
    max_zoom: 1.2
    mode:
    - trilinear
    - nearest
    align_corners:
    - null
    - null
    prob: 0.16
  - _target_: RandGaussianSmoothd
    keys: "@image_key"
    sigma_x:
    - 0.5
    - 1.15
    sigma_y:
    - 0.5
    - 1.15
    sigma_z:
    - 0.5
    - 1.15
    prob: 0.15
  - _target_: RandScaleIntensityd
    keys: "@image_key"
    factors: 0.3
    prob: 0.5
  - _target_: RandShiftIntensityd
    keys: "@image_key"
    offsets: 0.1
    prob: 0.5
  - _target_: RandGaussianNoised
    keys: "@image_key"
    std: 0.01
    prob: 0.15
  - _target_: RandFlipd
    keys:
    - "@image_key"
    - "@label_key"
    spatial_axis: 0
    prob: 0.5
  - _target_: RandFlipd
    keys:
    - "@image_key"
    - "@label_key"
    spatial_axis: 1
    prob: 0.5
  - _target_: RandFlipd
    keys:
    - "@image_key"
    - "@label_key"
    spatial_axis: 2
    prob: 0.5
  - _target_: CastToTyped
    keys:
    - "@image_key"
    - "@label_key"
    dtype:
    - "$torch.float32"
    - "$torch.uint8"
  - _target_: ToTensord
    keys:
    - "@image_key"
    - "@label_key"
transform_validation:
  _target_: Compose
  transforms:
  - _target_: LoadImaged
    keys:
    - "@image_key"
    - "@label_key"
  - _target_: EnsureChannelFirstd
    keys:
    - "@image_key"
    - "@label_key"
  - _target_: Orientationd
    keys:
    - "@image_key"
    - "@label_key"
    axcodes: RAS
  - _target_: Spacingd
    keys:
    - "@image_key"
    - "@label_key"
    pixdim:
    - 1
    - 1
    - 1
    mode:
    - bilinear
    - nearest
    align_corners:
    - true
    - true
  - _target_: CastToTyped
    keys: "@image_key"
    dtype: "$torch.float32"
  - _target_: ScaleIntensityRanged
    keys: "@image_key"
    a_min: -87
    a_max: 199
    b_min: 0
    b_max: 1
    clip: true
  - _target_: CastToTyped
    keys:
    - "@image_key"
    - "@label_key"
    dtype:
    - "$np.float16"
    - "$np.uint8"
  - _target_: CastToTyped
    keys:
    - "@image_key"
    - "@label_key"
    dtype:
    - "$torch.float32"
    - "$torch.uint8"
  - _target_: ToTensord
    keys:
    - "@image_key"
    - "@label_key"
loss:
  _target_: DiceCELoss
  include_background: false
  to_onehot_y: true
  softmax: true
  squared_pred: true
  batch: true
  smooth_nr: 0.00001
  smooth_dr: 0.00001
dints_space:
  _target_: monai.networks.nets.TopologySearch
  channel_mul: 0.5
  num_blocks: 12
  num_depths: 4
  use_downsample: true
  device: "$torch.device('cuda')"
network:
  _target_: monai.networks.nets.DiNTS
  dints_space: "@dints_space"
  in_channels: "@input_channels"
  num_classes: "@output_classes"
  use_downsample: true