[FEATURE REQUEST] Better documentation on the config file

[phisanti]

I was just wondering if it could be possible to get a better documentation on what it is and what it does each of the parameters of the config file. What happens if I decrease or increase such and such parameter and many such a cases. I took a look at this link, and only found an example of the config file, but no explanation:

"MotionModel": {
  "name": "cell_motion",
  "dt": 1.0,
  "measurements": 3,
  "states": 6,
  "accuracy": 7.5,
  "prob_not_assign": 0.1,
  "max_lost": 5,
  "A": {
    "matrix": [1,0,0,1,0,0,
               0,1,0,0,1,0,
               0,0,1,0,0,1,
               0,0,0,1,0,0,
               0,0,0,0,1,0,
               0,0,0,0,0,1]
  },
  "H": {
    "matrix": [1,0,0,0,0,0,
               0,1,0,0,0,0,
               0,0,1,0,0,0]
  },
  "P": {
    "sigma": 150.0,
    "matrix": [0.1,0,0,0,0,0,
               0,0.1,0,0,0,0,
               0,0,0.1,0,0,0,
               0,0,0,1,0,0,
               0,0,0,0,1,0,
               0,0,0,0,0,1]
  },
  "G": {
    "sigma": 15.0,
    "matrix": [0.5,0.5,0.5,1,1,1]

  },
  "R": {
    "sigma": 5.0,
    "matrix": [1,0,0,
               0,1,0,
               0,0,1]
  }
}

"HypothesisModel": {
  "name": "cell_hypothesis",
  "hypotheses": ["P_FP", "P_init", "P_term", "P_link", "P_branch", "P_dead"],
  "lambda_time": 5.0,
  "lambda_dist": 5.0,
  "lambda_link": 5.0,
  "lambda_branch": 5.0,
  "eta": 1e-10,
  "theta_dist": 5.0,
  "theta_time": 5.0,
  "dist_thresh": 10,
  "time_thresh": 3,
  "apop_thresh": 2,
  "segmentation_miss_rate": 0.1,
  "apoptosis_rate": 0.1,
  "relax": false
}

My goal is to track single cell bacteria with the option to divide and some of them die, so not sure how should I modify the file.

[zichael-ang]

Just wanted to add here: extra validation on the config file would also be helpful. I've been dealing with btrack crashing my kernel for a week now until I figured I'd try a different config and now it works. Would like to be able to check for malformed configs/validate configs.