bratsPreprocessor.py

#!/usr/bin/env python3.8
# -*- coding: utf-8 -*-
"""
Created on Wed Feb  1 09:50:09 2023

@author: useradmin
"""


    
    
    
    

def checkFileFound(file):
    try:       
        f = open(file, 'r')
        f.close()
    except IOError:
        print('file not found')
    
    



def main(dirPath, dirName, Flair, T1, T1c, T2):
    from brats_toolkit.preprocessor import Preprocessor
    # instantiate
    prep = Preprocessor()
   
    print("assigning files to variable")
    
    t1File = T1
    checkFileFound(t1File)
    
    
    t1cFile = T1c
    checkFileFound(t1cFile)
    
    t2File = T2
    checkFileFound(t2File)
    
    flaFile = Flair
    checkFileFound(flaFile)
    
    print(t1File, t1cFile, t2File, flaFile)
    # define outputs
    outputDir = dirPath+"/output"
    print(outputDir)
    # execute it
    prep.single_preprocess(t1File=t1File, t1cFile=t1cFile, t2File=t2File, flaFile=flaFile, outputFolder=outputDir, mode="gpu", confirm=True, skipUpdate=False, gpuid='0')
 
    

    

if __name__ == "__main__":
    import sys
    print("I am here ............................................",sys.argv[0],"...",sys.argv[1],"...", sys.argv[2],".....\nflair", sys.argv[3], "..\nt1", sys.argv[4], "\nt1c..",sys.argv[5],"\nt2..", sys.argv[6])
    examName = sys.argv[2]
    print(examName)
    f = open(sys.argv[1]+"/bratPreprocesstestout.txt", 'w')
    print("file open")
    sys.stdout = f
    main(sys.argv[1], sys.argv[2], sys.argv[3],  sys.argv[4], sys.argv[5], sys.argv[6])
    #f.close()