Update the input parameter file with one section by routine

[XDevos]

With version 0.8.1 of pyHiM, the infoList.json are structured like:

{
  "acquisition": {
      ...
  },
  "zProject": {
      ...
  },
  "alignImages": {
      ...
  },
  "segmentedObjects": {
      ...
  },
  "buildsPWDmatrix": {
      ...
  }
}

Expected structure for parameters.json ( = infoList.json) like this (names can change):

{
  "acquisition": {
      ...
  },
  "project": {
      ...
  },
  "register_global": {
      ...
  },
  "register_local": {
      ...
  },
  "mask_2d": {
      ...
  },
  "localize_2d": {
      ...
  },
  "mask_3d": {
      ...
  },
  "localize_3d": {
      ...
  },
  "filter_localizations": {
      ...
  },
  "correct_localizations": {
      ...
  },
  "build_traces": {
      ...
  },
  "build_matrix": {
      ...
  }
}