Design Pattern

Command design pattern:

The code is designed around the command design pattern.

Each core function is designed to act on numpy arrays or nibabel instances, and it is tested on dummy examples.

The facade methods, acting on paths to the images in nifti format, access the core method and return another image as output.

An instances of the class LabelsManager access the nifty images through their paths, and apply to their data each of the specified tools.

For example to apply the tool relabel under tools.manipulations.relabel to the input files file{1..10}.nii.gz in the folder input_folder and save the relabelled segmentations in the output_folder you can do:

lt = LABelsToolkit(input_folder, output_folder)

for i in range(1, 11):
    input_file_name = 'file{}.nii.gz'.format(i)
    output_file_name = 'file{}.nii.gz'.format(i)
    lt.manipulate.relabel(input_file_name, output_file_name,
                          [1, 2, 3, 4, 5, 6], [2, 3, 4, 5, 6, 7])