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",

)