The Config File

To start the program, it is necessary to define a configuration file. You can get a config file here. However, the best place to find the latest examples of config files is on the Github Repository. The idea behind the config file is that it makes it transparent both to the end user and to the developer the different settings available throughout the program.

The example config files only show the minimum possible contents. You are free to add as many entries as you would like. However, they are not going to be displayed in the GUI, nor will be used automatically. They will, however, be stored as metadata together with all the files. You could use the config file in order to annotate your experiments, for example.

The Format

The config file is formatted as a YAML file. These files are very easy to transform into python dictionaries and are very easy to type. So, for example, to change how the tracking algorithm works, one would change the following lines:

    diameter: 11  # Diameter of the particles (in pixels) to track, has to be an odd number
    invert: False
    minmass: 100

Note that for the file to make sense, it has to be indexed with 2 spaces. When reading it, it automatically converts some data types. For example, diameter will be available as config['tracking']['locate']['diameter'] and will be of type integer. invert will be a boolean, etc. If the data type is not clear, the default is a string. So, for example:

  exposure_time: 30ms # Initial exposure time (in ms)

Will generate a config['camera']['exposure_time'] of type string, that will need to be transformed to a quantity later on. Note also that comments are ignored (after the # nothing is read).