params.yml

paths:
  dir_video_exp: /n/data1/hms/neurobio/sabatini/gyu/github_clone/z_position_tracker/tester/exp
  path_video_stack: /n/data1/hms/neurobio/sabatini/gyu/github_clone/z_position_tracker/tester/stack/zstack_815_00001_00001.tif
  dir_save: /n/data1/hms/neurobio/sabatini/gyu/github_clone/z_position_tracker/tester/save
import_tiff:
  downsample_factors: [1,1,1]
  clip_zero: True
  verbose: True
dense_to_sparse:
  inherit_metadata: False
  kwargs:
    num_frames_per_slice: 60   # Only matters when inherit_metadata is False
    num_slices: 25   # Only matters when inherit_metadata is False
    num_volumes: 10   # Only matters when inherit_metadata is False
    step_size_um: 0.8   # Only matters when inherit_metadata is False
    frames_to_discard_per_slice: 30
    sparse_step_size_um: 0.8
    verbose: True
z_tracking:
  files_per_job: -1   # -1 submits a job per each tiff file. n (type:int) submits jobs, each tracks n tiff files. 0 submits 1 job only, tracks every tiff files.
  kwargs:
    clip_zero: True
    downsample_factors: [1,1,1]
    bandpass_spatialFs_bounds: [0.02, 0.3]   # List works; If not, will be casted as tuple in main code
    order_butter: 5
    use_GPU: True
    batch_size: 70
    resample_factor: 100
    sig: 4.0
    verbose: True