[FEATURE] Configure settings without cloning repo

[jesse-wei]

Settings are intended to be configured via the JSON config files gui_config.json and cli_config.json.

However, those files have to be in the directory NR is run from to be discovered. For now, this means cloning the repo.

When installing via pip and running from a Python terminal, those files may not exist. In that case, NR will grab the default gui_config.json and cli_config.json from the installed package, which the user can't easily find and edit.

Here's the code in constants.py that does this:

JSON_CLI_CONFIG_PATH: Path = Path("cli_config.json")
"""Settings that configure cli_settings.py."""
if not JSON_CLI_CONFIG_PATH.exists():
    # __name__ will get to the utils module
    # and cli_config.json is at root directory
    JSON_CLI_CONFIG_PATH = Path(
        pkg_resources.resource_filename(__name__, "../../cli_config.json")
    )

JSON_GUI_CONFIG_PATH: Path = Path("gui_config.json")
"""Settings that configure gui_settings.py."""
if not JSON_GUI_CONFIG_PATH.exists():
    # __name__ will get to the utils module
    # and gui_config.json is at root directory
    JSON_GUI_CONFIG_PATH = Path(
        pkg_resources.resource_filename(__name__, "../../gui_config.json")
    )

One solution would be to create an importable function (in NeuroRuler.__init__) that puts these files in cwd so that the user can edit and re-run GUI or CLI. Then these settings will persist as long as the user runs from that directory.

One could also create a function that simply modifies values in gui_settings.py or cli_settings.py.

[jesse-wei]

File > Import MRI Settings accepts a NeuroRuler JSON in this format (the format that NR exports):

{
    "input_image_path": "/Users/jesse/Documents/GitHub/COMP523/NeuroRuler/data/150649_V06_t1w.nrrd",
    "output_contoured_slice_path": "/Users/jesse/Documents/GitHub/COMP523/NeuroRuler/output/150649_V06_t1w/150649_V06_t1w_contoured.png",
    "x_rotation": 0,
    "y_rotation": 0,
    "z_rotation": 0,
    "slice": 79,
    "smoothing_conductance": 3.0,
    "smoothing_iterations": 5,
    "smoothing_time_step": 0.0625,
    "filter_option": "Otsu",
    "upper_binary_threshold": 200.0,
    "lower_binary_threshold": 0.0,
    "circumference": 433.57236555037326
}

However, the import_json function could be improved to also accept the gui_config.json file.

Not sure what would have to happen after parsing the settings there. The app might need to restart?