from brats_toolkit.preprocessor import Preprocessor

# instantiate
prep = Preprocessor()

# define inputs
examName = "TCGA-DU-7294"
t1File = "example_data/input_preprocessor_single_processing/TCGA-DU-7294/TCGA-DU-7294-T1.nii.gz"
t1cFile = "example_data/input_preprocessor_single_processing/TCGA-DU-7294/TCGA-DU-7294-T1c.nii.gz"
t2File = "example_data/input_preprocessor_single_processing/TCGA-DU-7294/TCGA-DU-7294-T2.nii.gz"
flaFile = "example_data/input_preprocessor_single_processing/TCGA-DU-7294/TCGA-DU-7294-FLAIR.nii.gz"

# define outputs
outputDir = "example_data/output_preprocessor_single/TCGA-DU-7294"

# execute it
prep.single_preprocess(
    t1File=t1File,
    t1cFile=t1cFile,
    t2File=t2File,
    flaFile=flaFile,
    outputFolder=outputDir,
    # this way the brain extraction will run on cpu
    mode="cpu",
    confirm=True,
    skipUpdate=False,
    gpuid="0",
)