train_config.yml

# Trained on data from the 2018 Kaggle Data Science Bowl: https://www.kaggle.com/c/data-science-bowl-2018/data
manual_seed: 0
model:
  name: UNet2D
  in_channels: 1
  out_channels: 1
  # use Groupnorm instead of Batchnorm for DSB; Batchnorm introduces artifacts around nuclei due to the difference
  # in intensity distribution between images with large and small cells
  layer_order: gcr
  num_groups: 8
  f_maps: [32, 64, 128]
  #conv_padding: 0
  final_sigmoid: true
  is_segmentation: true
trainer:
  checkpoint_dir: '/home/adrian/Datasets/DSB2018'
  resume: null
  validate_after_iters: 250
  log_after_iters: 250
  max_num_epochs: 10000
  max_num_iterations: 150000
  eval_score_higher_is_better: True
optimizer:
  learning_rate: 0.0002
  weight_decay: 0.00001
loss:
  name: BCEDiceLoss
  skip_last_target: true
eval_metric:
  name: BlobsAveragePrecision
  use_last_target: true
  metric: 'ap'
lr_scheduler:
  name: ReduceLROnPlateau
  mode: max
  factor: 0.2
  patience: 30
loaders:
  dataset: DSB2018Dataset
  batch_size: 32
  num_workers: 8
  train:
    file_paths:
      - '/home/adrian/Datasets/DSB2018/train'

    transformer:
      raw:
        - name: CropToFixed
          size: [256, 256]
        - name: Standardize
        - name: RandomFlip
        - name: RandomRotate90
        - name: RandomRotate
          axes: [[2, 1]]
          angle_spectrum: 30
          mode: reflect
        - name: ElasticDeformation
          spline_order: 3
          execution_probability: 0.2
        - name: AdditiveGaussianNoise
          execution_probability: 0.1
        - name: AdditivePoissonNoise
          execution_probability: 0.1
        - name: ToTensor
          expand_dims: true
      label:
        - name: CropToFixed
          size: [256, 256]
        - name: RandomFlip
        - name: RandomRotate90
        - name: RandomRotate
          axes: [[2, 1]]
          angle_spectrum: 30
          mode: reflect
        - name: ElasticDeformation
          spline_order: 0
          execution_probability: 0.2
        - name: Relabel
        - name: BlobsToMask
          append_label: true
        - name: ToTensor
          expand_dims: true
  val:
    file_paths:
      - '/home/adrian/Datasets/DSB2018/train'

    transformer:
      raw:
        - name: CropToFixed
          size: [256, 256]
          centered: true
        - name: Standardize
        - name: ToTensor
          expand_dims: true
      label:
        - name: CropToFixed
          size: [256, 256]
          # always get the same crop for validation
          centered: true
        - name: Relabel
        - name: BlobsToMask
          append_label: true
        - name: ToTensor
          expand_dims: true