def main(mp_rage_images_folder, pet_images_folder, segmented_regions_folder,
         output_folder):
    mp_rage_images = FileUtils.get_files_name_in(mp_rage_images_folder)

    for mp_rage_image in mp_rage_images:
        try:
            patient_id = FileUtils.extract_patient_id_from(mp_rage_image)
            pet_image = FileUtils.get_file_of_patient_with_id_from_folder(
                patient_id, pet_images_folder)
            subject_folder = os.path.join(output_folder, patient_id)

            # Register the mp rage to the pet space
            CoRegistrationProcessFactory.create_co_registration_process_with(
                mp_rage_image, pet_image, subject_folder).run()

            segmented_regions_image = FileUtils.get_file_of_patient_with_id_from_folder(
                patient_id, segmented_regions_folder)

            transformation_matrix_path = \
                CoRegistrationProcessFactory.get_transformation_matrix_file_name_from(subject_folder, mp_rage_image)

            # Register the mask to the subject space using the transformation matrix
            CoRegistrationProcessFactory \
                .create_co_registration_process_with(segmented_regions_image, pet_image, subject_folder,
                                                     transformation_matrix_path).run()
        except IndexError as e:
            print("Unable to read file for patient with id {}".format(
                patient_id))
コード例 #2
0
def main(subjects_folder_path, masks_folder_path, template_path,
         output_folder):
    subjects = FileUtils.get_files_name_in(subjects_folder_path)
    masks = FileUtils.get_files_name_in(masks_folder_path)

    for subject in subjects:
        patient_id = FileUtils.extract_patient_id_from(subject)
        subject_folder = os.path.join(output_folder, patient_id)

        # Register the template to the subject space
        CoRegistrationProcessFactory.create_co_registration_process_with(
            template_path, subject, subject_folder).run()
        for mask in masks:
            transformation_matrix_path = \
                CoRegistrationProcessFactory.get_transformation_matrix_file_name_from(subject_folder, template_path)

            # Register the mask to the subject space using the transformation matrix
            CoRegistrationProcessFactory \
                .create_co_registration_process_with(mask, subject, subject_folder, transformation_matrix_path).run()