Parameters conversion to make an App run on BL

When an App is registered on Brainlife, a config.json is automatically created based on the info the App creator enters via the BL GUI. There are four types of parameters:

NUMBER
STRING
ENUM
BOOL

So, it is impossible to enter a list of int or a numpy nd.array for instance. So, the values must be converted.

Apr 22, 2021 For now, we have decided not to read and convert Python dictionaries, so the BL user won’t be able to give a dictionary as a parameter value. However, he can use a dictionary if he uses the App locally (see Parameters conversion when the App runs locally).

Jun 8, 2021 Python dictionaries are used in app-temporal-filtering to define optionally the parameters of an IIR filter, but also in app-make-epochs to define the threshold values for each type of channel to use to detect bad channels. So, it is important to find a way to make possible to use dictionaries on BL.

Case of a numpy.nd.array

It is impossible to enter a np.nd.array in BL. So we register such parameter as a STRING and ask the user to enter floats separated by a comma: 10, 15, 20. In the config.json, such parameter will be written as:

{
"param_notch_widths": "10, 15, 20"
}

It was decided to enter numpy.nd.array this way on BL to differentiate it from the way it was entered in the config.json.example when the App is run locally (see Parameters conversion when the App runs locally) and it is easier to convert it into a numpy.nd.array.

In the Python file, we added:

if isinstance(config['param_notch_widths'], str):
    config['param_notch_widths'] = list(map(float, config['param_notch_widths'].split(', ')))
    config['param_notch_widths'] = np.array(config['param_notch_widths'])

Case of a slice

It is also impossible to enter directly a slice on BL. So we enter the parameter as a STRING. In the config.json, such parameter is written as follows:

{
config['param_picks_by_channel_indices']: "0, 10, 2"
}

This parameter is entered the same way as a numpy.nd.array. So far it is not an issue because no parameter is either a numpy.nd.array or a slice.

In the Python file, we added:

Case of a tuple

A tuple can not be entered on BL. So we registered the parameter as a STRING. In the config.json, such parameter is written as follows:

To convert it into a tuple, in the Python file we added:

The first step is to convert it into a list and then convert the elements of the list into the right type. For tuple parameters in which their elements are the same type, there is no need to compute the two list comprehensions:

Case of a list of integers/floats or strings

On Brainlife, when we enter a list, we have to use the type STRING and so the list is considered as a string, so they need to be converted.

Indeed, a list of floats or integers are written as follows in the config.json:

and a list of str:

So, we first need to convert it into a list and then convert the elements of the list into the right type.

For a list of strings:

If you want to convert it into a list of floats or ints, just replace str in list(map(str, picks.split(', '))) by the type you want.

If the list is empty, the user must enter []. In the Python code it will be converted into an empty list:

Cases when a parameter can be two types

When the App is run locally, this configuration is not an issue, but on Brainlife when you define the parameter, it must be either a STRING, a NUMBER, a BOOLEAN, or an ENUM.

Case when a parameter is either a str or a float/int

When a parameter can be both a str or a float/ int, we registered it as a STRING on BL, and then we convert it into a float or int.

But we must be careful: we only want to convert a str into float/int when the App runs on BL. For instance the parameter param_filter_length can be “auto”, a str with the duration in s, or ms, or a int. So to be sure that the conversion into float happens only on Brainlife and only when the user does want to use a float:

Case when a parameter is either a str or a bool

When a parameter can be both a str or a bool, we registered it as a STRING or ENUM on BL (either way, it is considered as a str), and then we convert it into a bool.

For instance the parameter param_proj can be “delayed”, or a bool. So, we registered it as an ENUM parameter and convert "True” and “False“ into a bool: