base.py 文件源码

def post_process_segmentation(input_scan, options, save_nifti = True):
    """
    Post-process the probabilistic segmentation using parameters t_bin and l_min
    t_bin: threshold to binarize the output segmentations 
    l_min: minimum lesion volume

    Inputs: 
    - input_scan: probabilistic input image (segmentation)
    - options dictionary
    - save_nifti: save the result as nifti 

    Output:
    - output_scan: final binarized segmentation 
    """

    from scipy import ndimage

    t_bin = options['t_bin']
    l_min = options['l_min']
    output_scan = np.zeros_like(input_scan)

    # threshold input segmentation
    t_segmentation = input_scan >= t_bin

    # filter candidates by size and store those > l_min
    labels, num_labels = ndimage.label(t_segmentation)
    label_list = np.unique(labels)
    num_elements_by_lesion = ndimage.labeled_comprehension(t_segmentation, labels, label_list, np.sum, float, 0)

    for l in range(len(num_elements_by_lesion)):
        if num_elements_by_lesion[l]>l_min:
            # assign voxels to output
            current_voxels = np.stack(np.where(labels == l), axis =1)
            output_scan[current_voxels[:,0], current_voxels[:,1], current_voxels[:,2]] = 1

    #save the output segmentation as Nifti1Image
    if save_nifti:
        nifti_out = nib.Nifti1Image(output_scan, np.eye(4))
        nifti_out.to_filename(os.path.join(options['test_folder'], options['test_scan'], options['experiment'], options['test_name']))

    return output_scan