config.yaml

# diffinfinite
is_diffinfinite: True # we are not extracting from svs files
patching_enabled: True
diffinfinite_macro_path: diffinfinite_macropatches/
diffinfinite_out_path: diffinfinite_out/
diffclasses: 10
out_patch_size: 256
grayscale_patches: False
using_masks: True
generate_color_mapped_masks: True

cmap_whole_masks: True
cmap_whole_masks_out: whole_cmaps/

split:
  enabled: True
  factor: 4
  presplit_out_path: presplit_out/
  gen_color_mapped_submasks: True
  patched_split_out: patched_presplit_out/

annotator:
  enabled: True
  strategy: 'TopKLabeling'  # [TopKLabeling, TopKThrLabeling]
  k: 4
  thr: 0.1
  compute_perc_by_ignoring_unknown_class: True
  csv_filename: 'annotator.csv'
  plot_class_distribution: True
  balancer:
    enabled: True
    strategy: 'RandomUnderSampler'  # [RandomUnderSampler, RandomOverSampler, SMOTE]

# traditional scans
h5_source_path: dest/patches/
slide_ext: '.svs' # unused
hdf_extension: .h5
target_patch_size: 256
wsi_output_path: out/
limit: 100  # limit = -1 disables the limit, default: -1

transforms:
  prewhiten: False
  using_imagenet: False