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vista2d

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vista2d
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imports:
  - $import os

# seed: 28022024 # uncommend for deterministic results (but slower)
seed: null

bundle_root: "."
ckpt_path: $os.path.join(@bundle_root, "models")  # location to save checkpoints
output_dir: $os.path.join(@bundle_root, "eval")  # location to save events and logs
log_output_file: $os.path.join(@output_dir, "vista_cell.log")

mlflow_tracking_uri: null                     # enable mlflow logging, e.g. $@ckpt_path + '/mlruns/ or "http://127.0.0.1:8080" or a remote url
mlflow_log_system_metrics: true               # log system metrics to mlflow (requires: pip install psutil pynvml)
mlflow_run_name: null                         # optional name of the current run

ckpt_save: true                               # save checkpoints periodically
amp: true
amp_dtype: "float16" #float16 or bfloat16 (Ampere or newer)
channels_last: true
compile: false # complie the model for faster processing

start_epoch: 0
run_final_testing: true
use_weighted_sampler: false                   # only applicable when using several dataset jsons for data_list_files

pretrained_ckpt_name: null
pretrained_ckpt_path: null

# for commandline setting of a single dataset
datalist: datalists/cellpose_datalist.json
basedir: /cellpose_dataset
data_list_files:
  - {datalist: "@datalist", basedir: "@basedir"}


fold: 0
learning_rate: 0.01  # try 1.0e-4 if using AdamW
quick: false  # whether to use a small subset of data for quick testing
roi_size: [256, 256]

train:
  skip: false
  handlers: []
  trainer:
    num_warmup_epochs: 3
    max_epochs: 200
    num_epochs_per_saving: 1
    num_epochs_per_validation: null
  num_workers: 4
  batch_size: 1
  dataset:
    preprocessing:
      roi_size: "@roi_size"
    data:
      key: null # set to 'testing' to use this subset in periodic validations, instead of the the validation set
      data_list_files: "@data_list_files"

dataset:
  data:
    key: "testing"
    data_list_files: "@data_list_files"

validate:
  grouping: true
  evaluator:
    postprocessing: "@postprocessing"
  dataset:
    data: "@dataset#data"
  batch_size: 1
  num_workers: 4
  preprocessing: null
  postprocessing: null
  inferer: null
  handlers: null
  key_metric: null

infer:
  evaluator:
    postprocessing: "@postprocessing"
  dataset:
    data: "@dataset#data"


device: "$torch.device(('cuda:' + os.environ.get('LOCAL_RANK', '0')) if torch.cuda.is_available() else 'cpu')"
network_def:
  _target_: monai.networks.nets.cell_sam_wrapper.CellSamWrapper
  checkpoint: $os.path.join(@ckpt_path, "sam_vit_b_01ec64.pth")
network: $@network_def.to(@device)

loss_function:
  _target_: scripts.components.CellLoss

key_metric:
  _target_: scripts.components.CellAcc

# optimizer:
#   _target_: torch.optim.AdamW
#   params: $@network.parameters()
#   lr: "@learning_rate"
#   weight_decay: 1.0e-5

optimizer:
  _target_: torch.optim.SGD
  params: $@network.parameters()
  momentum: 0.9
  lr: "@learning_rate"
  weight_decay: 1.0e-5

lr_scheduler:
  _target_: monai.optimizers.lr_scheduler.WarmupCosineSchedule
  optimizer: "@optimizer"
  warmup_steps: "@train#trainer#num_warmup_epochs"
  warmup_multiplier: 0.1
  t_total: "@train#trainer#max_epochs"

inferer:
  sliding_inferer:
    _target_: monai.inferers.SlidingWindowInfererAdapt
    roi_size: "@roi_size"
    sw_batch_size: 1
    overlap: 0.625
    mode: "gaussian"
    cache_roi_weight_map: true
    progress: false

image_saver:
  _target_: scripts.components.SaveTiffd
  keys: "seg"
  output_dir: "@output_dir"
  nested_folder: false

postprocessing:
  _target_: monai.transforms.Compose
  transforms:
    - "@image_saver"