Models:
Samuel Callahan
SCallahan/
BraTS-Toolkit
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[ab8281]: / 1_segmentation.py

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import datetime



from brats_toolkit.segmentor import Segmentor



# log

starttime = str(datetime.datetime.now().time())

print("*** starting at", starttime, "***")



# instantiate

seg = Segmentor(verbose=True)



# input files

t1File = "example_data/output_preprocessor_single/TCGA-DU-7294/hdbet_brats-space/TCGA-DU-7294_hdbet_brats_t1.nii.gz"

t1cFile = "example_data/output_preprocessor_single/TCGA-DU-7294/hdbet_brats-space/TCGA-DU-7294_hdbet_brats_t1c.nii.gz"

t2File = "example_data/output_preprocessor_single/TCGA-DU-7294/hdbet_brats-space/TCGA-DU-7294_hdbet_brats_t2.nii.gz"

flaFile = "example_data/output_preprocessor_single/TCGA-DU-7294/hdbet_brats-space/TCGA-DU-7294_hdbet_brats_fla.nii.gz"



# output

outputFolder = "example_data/output_segmentor/TCGA-DU-7294/"



# algorithms we want to select for segmentation



# 2019 algorithms

# cids = ["mic-dkfz", "scan", "xfeng", "lfb_rwth", "zyx_2019", "scan_2019"]



# 2020 algorithms

cids = ["isen-20", "hnfnetv1-20", "yixinmpl-20", "sanet0-20", "scan-20"]



# execute it

for cid in cids:

    try:

        outputFile = outputFolder + cid + ".nii.gz"

        seg.segment(

            t1=t1File,

            t2=t2File,

            t1c=t1cFile,

            fla=flaFile,

            cid=cid,

            outputPath=outputFile,

        )



    except Exception as e:

        print("error:", str(e))

        print("error occured for:", cid)



# log

endtime = str(datetime.datetime.now().time())

print("*** finished at:", endtime, "***")