dicom_to_nifti.py

#author @t_sanf

from parsing_VOI import *
import pydicom
import math
import nibabel
import re
import dicom2nifti
import shutil


class Dicom2Nifti():

    def __init__(self):
        self.basePATH = r''
        self.databases=['']

    def dicom_to_nifti(self,t2_only=True):
        '''
        convert all dicom files in each database to .nifti format
        :return:
        '''

        databases = self.databases

        if t2_only==True:
            series_all=['t2']
        else:
            series_all=['t2','adc','highb']

        exception_logger=[]
        for database in databases:
            for patient in self.check_for_nifti_completion():
                print("converting files to nifti for patient {}".format(patient))

                #make nifti file if one does not already exist
                if not os.path.exists(os.path.join(self.basePATH, database, patient, 'nifti')):
                    os.mkdir(os.path.join(self.basePATH, database, patient, 'nifti'))

                for series in series_all:
                    #account for aligned data structure
                    if series=='t2':
                        dicom_name = series; nifti_name = series

                    if series=='adc' or series=='highb':
                        nifti_name=series
                        dicom_name = os.path.join(series, 'aligned')

                    #make folder if not already made:
                    if not os.path.exists(os.path.join(self.basePATH,database,patient,'nifti',nifti_name)):
                        os.mkdir(os.path.join(self.basePATH,database,patient,'nifti',nifti_name))

                    dicom_directory=os.path.join(self.basePATH,database,patient,'dicoms',dicom_name)
                    nifti_directory=os.path.join(self.basePATH, database, patient, 'nifti', nifti_name)

                    dicom2nifti.convert_directory(dicom_directory, nifti_directory, reorient=False)

        print("the following patients still need to be processed {}".format(exception_logger))


    def check_for_nifti_completion(self):
        '''iterate over files and check if files have been converted from dicom to nifti format for all series'''

        need_to_process=[]
        for database in self.databases:
            for patient in os.listdir(os.path.join(self.basePATH,database)):
                if not os.path.exists(os.path.join(self.basePATH, database, patient, 'nifti')):
                    need_to_process+=[patient]

                elif os.path.exists(os.path.join(self.basePATH, database, patient, 'nifti')):
                    for val in ['t2', 'adc', 'highb']:
                        file=os.path.join(self.basePATH, database, patient, 'nifti')
                        if not os.path.isdir(os.path.join(file,val)):
                            need_to_process += [patient]
                        elif os.path.isdir(os.path.join(file,val)):
                            if len(os.listdir(os.path.join(file, val))) == 0:
                                need_to_process += [patient]

                print("patient {} has already had dicoms converted to nifti".format(patient))

            print('total of {} patients to convert to nifti masks'.format(len(set(need_to_process))))
            return set(need_to_process)

    def remove_nifti_files(self,database):
        '''iterate over files and remove emtpy nifti files (if there is an error)'''

        need_to_process=[]
        for patient in os.listdir(os.path.join(self.basePATH,database)):
            print(patient)
            if os.path.exists(os.path.join(self.basePATH, database, patient, 'nifti')):
                shutil.rmtree(os.path.join(self.basePATH, database, patient, 'nifti'))
                print('removing data for patient {}'.format(patient))



if __name__=='__main__':
    c=Dicom2Nifti()
    c.dicom_to_nifti()