config.yaml

hydra:
  run:
    dir: ./results/${hydra.runtime.choices.experiment}/${now:%Y-%m-%d}/${now:%H-%M-%S}
  sweep:
    dir: ./results/${hydra.runtime.choices.experiment}/${now:%Y-%m-%d}/${now:%H-%M-%S}
    subdir: ${hydra.job.num}_${hydra.job.override_dirname}
  verbose:
    - pelphix
    - perphix
    # - deepdrr

defaults:
  - _self_ # makes it so the subconfigs override the primary
  - experiment: train
  - scheduler: step
  - backbone: unet
  - optimizer: adam

  # Use the configured logging.
  - override hydra/job_logging: rich

# Universal variables across experiments
experiment:
  seed: 1234
  onedrive_dir: ${onedrive_dir}
  nmdid_dir: ${nmdid_dir}
  skip_download: ${skip_download}

onedrive_dir: ~/datasets/OneDrive
nmdid_dir: sambhav/NMDID-ARCADE
pelvis_annotations_dir: 2023-03-12_pelvis-annotations_ssm
skip_download: True
num_workers: 0
num_procedures: 10000

# vis
fps: 2
show: True

# SSM parameters
n_points: 5000
pelvis_n_points: 10000
n_components: 40


_device_translation_min: 5
_device_translation_max: 100
_device_angulation_max: 45
_wire_translation_min: 2
_wire_translation_max: 15
_wire_angulation_max: 45


# Generating the Pelphix dataset.
sim:
  root: ${onedrive_dir}/datasets/Pelphix
  nmdid_root: ${onedrive_dir}/${nmdid_dir}
  pelvis_annotations_dir: ${onedrive_dir}/${nmdid_dir}/${pelvis_annotations_dir}
  num_val: 10
  scan_name: THIN_BONE_TORSO
  image_size:
    - ${image_size}
    - ${image_size}
  max_procedure_length: 1000
  num_procedures: ${num_procedures}
  overwrite: ${overwrite}
  cache_dir: ${hydra:runtime.cwd}/cache/pelphix
  num_workers: ${num_workers}
  uniform_wire_movement: False

  skill_factor: [0.1, 0.3]
  view_skill_factor: [0.6, 0.8]
  view_tolerance:
    # in degrees.
    # ap: 3
    # lateral: 5
    # inlet: 3
    # outlet: 5
    # oblique_left: 3
    # oblique_right: 3
    # teardrop_left: 2
    # teardrop_right: 2
    ap: 2
    lateral: 2
    inlet: 2
    outlet: 2
    oblique_left: 2
    oblique_right: 2
    teardrop_left: 1
    teardrop_right: 1
  corridor_radii:
    s1_left: 5
    s1_right: 5
    s1: 5
    s2: 5
    ramus_left: 3
    ramus_right: 3
    teardrop_left: 8
    teardrop_right: 8
  random_translation_bounds:
    min:
      device:
        ap: ${_device_translation_min}
        lateral: ${_device_translation_min}
        inlet: ${_device_translation_min}
        outlet: ${_device_translation_min}
        oblique_left: ${_device_translation_min}
        oblique_right: ${_device_translation_min}
        teardrop_left: ${_device_translation_min}
        teardrop_right: ${_device_translation_min}
      wire:
        ap: ${_wire_translation_min}
        lateral: ${_wire_translation_min}
        inlet: ${_wire_translation_min}
        outlet: ${_wire_translation_min}
        oblique_left: ${_wire_translation_min}
        oblique_right: ${_wire_translation_min}
        teardrop_left: ${_wire_translation_min}
        teardrop_right: ${_wire_translation_min}
    max:
      device:
        ap: ${_device_translation_max}
        lateral: ${_device_translation_max}
        inlet: ${_device_translation_max}
        outlet: ${_device_translation_max}
        oblique_left: ${_device_translation_max}
        oblique_right: ${_device_translation_max}
        teardrop_left: ${_device_translation_max}
        teardrop_right: ${_device_translation_max}
      wire:
        ap: ${_wire_translation_max}
        lateral: ${_wire_translation_max}
        inlet: ${_wire_translation_max}
        outlet: ${_wire_translation_max}
        oblique_left: ${_wire_translation_max}
        oblique_right: ${_wire_translation_max}
        teardrop_left: ${_wire_translation_max}
        teardrop_right: ${_wire_translation_max}
  random_angulation_bounds:
    min:
      device:
        ap: 2
        lateral: 2
        inlet: 2
        outlet: 2
        oblique_left: 2
        oblique_right: 2
        teardrop_left: 2
        teardrop_right: 2
      wire:
        ap: 5
        lateral: 5
        inlet: 5
        outlet: 5
        oblique_left: 5
        oblique_right: 5
        teardrop_left: 5
        teardrop_right: 5
    max:
      device:
        ap: ${_device_angulation_max}
        lateral: ${_device_angulation_max}
        inlet: ${_device_angulation_max}
        outlet: ${_device_angulation_max}
        oblique_left: ${_device_angulation_max}
        oblique_right: ${_device_angulation_max}
        teardrop_left: ${_device_angulation_max}
        teardrop_right: ${_device_angulation_max}
      wire:
        ap: ${_wire_angulation_max}
        lateral: ${_wire_angulation_max}
        inlet: ${_wire_angulation_max}
        outlet: ${_wire_angulation_max}
        oblique_left: ${_wire_angulation_max}
        oblique_right: ${_wire_angulation_max}
        teardrop_left: ${_wire_angulation_max}
        teardrop_right: ${_wire_angulation_max}

# Other experimental variables
overwrite: False

gpus: 1
eval_only: False
image_size: 224 # 384
onedrive:
  syncdir: ${onedrive_dir}

# Set to the output dir for a previous run to continue.
output_dir: output
batch_size: 2
base_lr: 0.00025

# path to transformer checkpoint, for resuming training or for testing
ckpt: null 

transformer:
  d_model: 512
  nhead: 8
  dim_feedforward: 2048
  num_layers: 6
  dropout: 0.5

data_num_workers: 2
dataloader:
  batch_size: ${batch_size}
  num_workers: ${data_num_workers}
  drop_last: False


trainer:
  devices: ${gpus}
  accelerator: gpu
  strategy: auto
  deterministic: True
  precision: 16 # 32 # 32 might be needed because embedded features are large (usually in range (-25, 25)).
  max_epochs: 200
  gradient_clip_val: 5 # 0.5
  log_every_n_steps: 10
  # find_unused_parameters: False

### Testing on Cadaver/patient Data ###
# Path to results directory (e.g. where checkpoint can be found) and results/visualizations will be save.
# If provided, and ckpt is not provided, will load the latest checkpoint from the results directory.
results_dir: "." 

liverpool:
  root_in_onedrive: datasets/2023-02-09_cadaver_liverpool/2023-02-16_percutaneous-fixation_conventional # in onedrive
  root: ${onedrive_dir}/${liverpool.root_in_onedrive}
  annotations_dir: ${liverpool.root}/annotations
  csv_path: ${liverpool.root}/sequences.csv
  image_dir: ${liverpool.root}/OrthoTrauma (20130116)

# Training the U-Net
weights_only: False
unet_seq_len: 48
unet_module:
  supercategories: ["task", "activity", "acquisition", "frame"]
  supercategory_num_classes: [8,3,8,2]
  num_seg_classes: 17
  num_keypoints: 16
  unet: ${backbone}
  transformer: ${transformer}
  optimizer: ${optimizer}
  scheduler: ${scheduler}
  use_keypoints: True
  use_segmentations: True
  filter_preds: False

unet_image_size: 224
triplets: True
sequences_train:
  seq_len: ${unet_seq_len}
  train: true
  image_size: ${unet_image_size}
  triplets: ${triplets}
  configs:
    - loader: load
      config:
        annotation_path: ${sim.root}/annotations/pelphix_000338_train.json
        image_dir: ${sim.root}/pelphix_000338_train
    - loader: load
      config:
        annotation_path: ${sim.root}/annotations/pelphix_000339_train.json
        image_dir: ${sim.root}/pelphix_000339_train

sequences_val:
  seq_len: ${unet_seq_len}
  train: false
  image_size: ${unet_image_size}
  triplets: ${triplets}
  configs:
    - loader: load
      config:
        annotation_path: ${sim.root}/annotations/pelphix_000338_val.json
        image_dir: ${sim.root}/pelphix_000338_val
    - loader: load
      config:
        annotation_path: ${sim.root}/annotations/pelphix_000339_val.json
        image_dir: ${sim.root}/pelphix_000339_val


sequences_test:
  seq_len: ${unet_seq_len} # 300 rather than 100?
  train: false
  image_size: ${unet_image_size}
  fliph: true
  triplets: ${triplets}
  overlap: 0.5
  configs:
    - loader: from_csv
      config:
        image_dir: ${liverpool.image_dir}
        annotations_dir: ${liverpool.annotations_dir}
        csv_path: ${liverpool.csv_path}
        name: liverpool
        use_previous: false