.. _Getting started:

Installation
============

Pypi soon, clone for the moment and install the requirements.

Hello, World!
=============

This example shows the basic usage of segmentation_RT::

    #import
    import os
    from segmentation_rt.dl.dataloader import DatasetPatch, DatasetSingle
    from segmentation_rt.dl.model import Model
    from segmentation_rt.mask2rs import RTStruct
    from segmentation_rt.rs2mask import Dataset

    # dataset
    structures = ["Heart", "Breast L", "Breast R"]
    dataset = Dataset('data/data', 'data/DIBH_dataset', structures)
    dataset.make()

    # training
    root_training = 'data/DIBH_dataset/'
    checkpoints_dir = 'checkpoints/'
    name = 'DIBH'

    expr_dir = os.path.join(checkpoints_dir, name)
    dataset = DatasetPatch(root_training, structures, 0.9, batch_size=4)
    training_loader_patches, validation_loader_patches = dataset.get_loaders()
    model = Model(expr_dir, structures, n_blocks=9, niter=150, niter_decay=50)
    model.train(training_loader_patches, validation_loader_patches)

    # testing
    expr_dir = os.path.join(checkpoints_dir, name)
    model = Model(expr_dir, structures,  n_blocks=9)
    root_prediction = 'prediction/ct/'
    pred_data_loader = DatasetSingle(root_prediction, structures)
    fake_segmentation = model.test(pred_data_loader, export_path='prediction/143012/', save=True)

    # rtstruct
    ct_path = os.path.join('prediction/143012/ct/')
    mask = os.path.join('prediction/143012/fake_segmentation.nii')

    struct = RTStruct(ct_path, mask, structures)
    struct.create()
    struct.save()