GenCT-ageencoder/mask_generation.py

### Tumor Generateion
import random
import cv2
import elasticdeform
import numpy as np
from scipy.ndimage import gaussian_filter


def generate_prob_function(mask_shape):
    sigma = np.random.uniform(3,15)
    # uniform noise generate
    a = np.random.uniform(0, 1, size=(mask_shape[0],mask_shape[1],mask_shape[2]))

    # Gaussian filter
    # this taks some time
    a_2 = gaussian_filter(a, sigma=sigma)

    scale = np.random.uniform(0.19, 0.21)
    base = np.random.uniform(0.04, 0.06)
    a =  scale * (a_2 - np.min(a_2)) / (np.max(a_2) - np.min(a_2)) + base

    return a

# Step 1: Random select (numbers) location for tumor.
def random_select(mask_scan):
    # we first find z index and then sample point with z slice
    z_start, z_end = np.where(np.any(mask_scan, axis=(0, 1)))[0][[0, -1]]

    # we need to strict number z's position (0.3 - 0.7 in the middle of liver)
    z = round(random.uniform(0.3, 0.7) * (z_end - z_start)) + z_start

    liver_mask = mask_scan[..., z]

    # erode the mask (we don't want the edge points)
    kernel = np.ones((5,5), dtype=np.uint8)
    liver_mask = cv2.erode(liver_mask, kernel, iterations=1)

    coordinates = np.argwhere(liver_mask == 1)
    random_index = np.random.randint(0, len(coordinates))
    xyz = coordinates[random_index].tolist() # get x,y
    xyz.append(z)
    potential_points = xyz

    return potential_points

# Step 2 : generate the ellipsoid
def get_ellipsoid(x, y, z):
    """"
    x, y, z is the radius of this ellipsoid in x, y, z direction respectly.
    """
    sh = (4*x, 4*y, 4*z)
    out = np.zeros(sh, int)
    aux = np.zeros(sh)
    radii = np.array([x, y, z])
    com = np.array([2*x, 2*y, 2*z])  # center point

    # calculate the ellipsoid 
    bboxl = np.floor(com-radii).clip(0,None).astype(int)
    bboxh = (np.ceil(com+radii)+1).clip(None, sh).astype(int)
    roi = out[tuple(map(slice,bboxl,bboxh))]
    roiaux = aux[tuple(map(slice,bboxl,bboxh))]
    logrid = *map(np.square,np.ogrid[tuple(
            map(slice,(bboxl-com)/radii,(bboxh-com-1)/radii,1j*(bboxh-bboxl)))]),
    dst = (1-sum(logrid)).clip(0,None)
    mask = dst>roiaux
    roi[mask] = 1
    np.copyto(roiaux,dst,where=mask)

    return out

def get_fixed_geo(mask_scan, tumor_type):

    enlarge_x, enlarge_y, enlarge_z = 160, 160, 160
    geo_mask = np.zeros((mask_scan.shape[0] + enlarge_x, mask_scan.shape[1] + enlarge_y, mask_scan.shape[2] + enlarge_z), dtype=np.int8)
    # texture_map = np.zeros((mask_scan.shape[0] + enlarge_x, mask_scan.shape[1] + enlarge_y, mask_scan.shape[2] + enlarge_z), dtype=np.float16)
    tiny_radius, small_radius, medium_radius, large_radius = 4, 8, 16, 32

    if tumor_type == 'tiny':
        num_tumor = random.randint(3,10)
        for _ in range(num_tumor):
            # Tiny tumor
            x = random.randint(int(0.75*tiny_radius), int(1.25*tiny_radius))
            y = random.randint(int(0.75*tiny_radius), int(1.25*tiny_radius))
            z = random.randint(int(0.75*tiny_radius), int(1.25*tiny_radius))
            sigma = random.uniform(0.5,1)
            
            geo = get_ellipsoid(x, y, z)
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,1))
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(1,2))
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,2))
            point = random_select(mask_scan)
            new_point = [point[0] + enlarge_x//2, point[1] + enlarge_y//2, point[2] + enlarge_z//2]
            x_low, x_high = new_point[0] - geo.shape[0]//2, new_point[0] + geo.shape[0]//2 
            y_low, y_high = new_point[1] - geo.shape[1]//2, new_point[1] + geo.shape[1]//2 
            z_low, z_high = new_point[2] - geo.shape[2]//2, new_point[2] + geo.shape[2]//2 
            
            # paste small tumor geo into test sample
            geo_mask[x_low:x_high, y_low:y_high, z_low:z_high] += geo

    if tumor_type == 'small':
        num_tumor = random.randint(3,10)
        for _ in range(num_tumor):
            # Small tumor
            x = random.randint(int(0.75*small_radius), int(1.25*small_radius))
            y = random.randint(int(0.75*small_radius), int(1.25*small_radius))
            z = random.randint(int(0.75*small_radius), int(1.25*small_radius))
            sigma = random.randint(1, 2)
            
            geo = get_ellipsoid(x, y, z)
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,1))
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(1,2))
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,2))
            # texture = get_texture((4*x, 4*y, 4*z))
            point = random_select(mask_scan)
            new_point = [point[0] + enlarge_x//2, point[1] + enlarge_y//2, point[2] + enlarge_z//2]
            x_low, x_high = new_point[0] - geo.shape[0]//2, new_point[0] + geo.shape[0]//2 
            y_low, y_high = new_point[1] - geo.shape[1]//2, new_point[1] + geo.shape[1]//2 
            z_low, z_high = new_point[2] - geo.shape[2]//2, new_point[2] + geo.shape[2]//2 
            
            # paste small tumor geo into test sample
            geo_mask[x_low:x_high, y_low:y_high, z_low:z_high] += geo
            # texture_map[x_low:x_high, y_low:y_high, z_low:z_high] = texture

    if tumor_type == 'medium':
        num_tumor = random.randint(2, 5)
        for _ in range(num_tumor):
            # medium tumor
            x = random.randint(int(0.75*medium_radius), int(1.25*medium_radius))
            y = random.randint(int(0.75*medium_radius), int(1.25*medium_radius))
            z = random.randint(int(0.75*medium_radius), int(1.25*medium_radius))
            sigma = random.randint(3, 6)
            
            geo = get_ellipsoid(x, y, z)
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,1))
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(1,2))
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,2))
            # texture = get_texture((4*x, 4*y, 4*z))
            point = random_select(mask_scan)
            new_point = [point[0] + enlarge_x//2, point[1] + enlarge_y//2, point[2] + enlarge_z//2]
            x_low, x_high = new_point[0] - geo.shape[0]//2, new_point[0] + geo.shape[0]//2 
            y_low, y_high = new_point[1] - geo.shape[1]//2, new_point[1] + geo.shape[1]//2 
            z_low, z_high = new_point[2] - geo.shape[2]//2, new_point[2] + geo.shape[2]//2 
            
            # paste medium tumor geo into test sample
            geo_mask[x_low:x_high, y_low:y_high, z_low:z_high] += geo
            # texture_map[x_low:x_high, y_low:y_high, z_low:z_high] = texture

    if tumor_type == 'large':
        num_tumor = random.randint(1,3)
        for _ in range(num_tumor):
            # Large tumor
            x = random.randint(int(0.75*large_radius), int(1.25*large_radius))
            y = random.randint(int(0.75*large_radius), int(1.25*large_radius))
            z = random.randint(int(0.75*large_radius), int(1.25*large_radius))
            sigma = random.randint(5, 10)
            
            geo = get_ellipsoid(x, y, z)
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,1))
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(1,2))
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,2))
            # texture = get_texture((4*x, 4*y, 4*z))
            point = random_select(mask_scan)
            new_point = [point[0] + enlarge_x//2, point[1] + enlarge_y//2, point[2] + enlarge_z//2]
            x_low, x_high = new_point[0] - geo.shape[0]//2, new_point[0] + geo.shape[0]//2 
            y_low, y_high = new_point[1] - geo.shape[1]//2, new_point[1] + geo.shape[1]//2 
            z_low, z_high = new_point[2] - geo.shape[2]//2, new_point[2] + geo.shape[2]//2 
            
            # paste small tumor geo into test sample
            geo_mask[x_low:x_high, y_low:y_high, z_low:z_high] += geo
            # texture_map[x_low:x_high, y_low:y_high, z_low:z_high] = texture

    if tumor_type == "mix":
        # tiny
        num_tumor = random.randint(3,10)
        for _ in range(num_tumor):
            # Tiny tumor
            x = random.randint(int(0.75*tiny_radius), int(1.25*tiny_radius))
            y = random.randint(int(0.75*tiny_radius), int(1.25*tiny_radius))
            z = random.randint(int(0.75*tiny_radius), int(1.25*tiny_radius))
            sigma = random.uniform(0.5,1)
            
            geo = get_ellipsoid(x, y, z)
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,1))
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(1,2))
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,2))
            point = random_select(mask_scan)
            new_point = [point[0] + enlarge_x//2, point[1] + enlarge_y//2, point[2] + enlarge_z//2]
            x_low, x_high = new_point[0] - geo.shape[0]//2, new_point[0] + geo.shape[0]//2 
            y_low, y_high = new_point[1] - geo.shape[1]//2, new_point[1] + geo.shape[1]//2 
            z_low, z_high = new_point[2] - geo.shape[2]//2, new_point[2] + geo.shape[2]//2 
            
            # paste small tumor geo into test sample
            geo_mask[x_low:x_high, y_low:y_high, z_low:z_high] += geo

        # small
        num_tumor = random.randint(5,10)
        for _ in range(num_tumor):
            # Small tumor
            x = random.randint(int(0.75*small_radius), int(1.25*small_radius))
            y = random.randint(int(0.75*small_radius), int(1.25*small_radius))
            z = random.randint(int(0.75*small_radius), int(1.25*small_radius))
            sigma = random.randint(1, 2)
        
            geo = get_ellipsoid(x, y, z)
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,1))
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(1,2))
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,2))
            # texture = get_texture((4*x, 4*y, 4*z))
            point = random_select(mask_scan)
            new_point = [point[0] + enlarge_x//2, point[1] + enlarge_y//2, point[2] + enlarge_z//2]
            x_low, x_high = new_point[0] - geo.shape[0]//2, new_point[0] + geo.shape[0]//2 
            y_low, y_high = new_point[1] - geo.shape[1]//2, new_point[1] + geo.shape[1]//2 
            z_low, z_high = new_point[2] - geo.shape[2]//2, new_point[2] + geo.shape[2]//2 
            
            # paste small tumor geo into test sample
            geo_mask[x_low:x_high, y_low:y_high, z_low:z_high] += geo
            # texture_map[x_low:x_high, y_low:y_high, z_low:z_high] = texture
            
        # medium
        num_tumor = random.randint(2, 5)
        for _ in range(num_tumor):
            # medium tumor
            x = random.randint(int(0.75*medium_radius), int(1.25*medium_radius))
            y = random.randint(int(0.75*medium_radius), int(1.25*medium_radius))
            z = random.randint(int(0.75*medium_radius), int(1.25*medium_radius))
            sigma = random.randint(3, 6)
            
            geo = get_ellipsoid(x, y, z)
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,1))
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(1,2))
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,2))
            # texture = get_texture((4*x, 4*y, 4*z))
            point = random_select(mask_scan)
            new_point = [point[0] + enlarge_x//2, point[1] + enlarge_y//2, point[2] + enlarge_z//2]
            x_low, x_high = new_point[0] - geo.shape[0]//2, new_point[0] + geo.shape[0]//2 
            y_low, y_high = new_point[1] - geo.shape[1]//2, new_point[1] + geo.shape[1]//2 
            z_low, z_high = new_point[2] - geo.shape[2]//2, new_point[2] + geo.shape[2]//2 
            
            # paste medium tumor geo into test sample
            geo_mask[x_low:x_high, y_low:y_high, z_low:z_high] += geo
            # texture_map[x_low:x_high, y_low:y_high, z_low:z_high] = texture

        # large
        num_tumor = random.randint(1,3)
        for _ in range(num_tumor):
            # Large tumor
            x = random.randint(int(0.75*large_radius), int(1.25*large_radius))
            y = random.randint(int(0.75*large_radius), int(1.25*large_radius))
            z = random.randint(int(0.75*large_radius), int(1.25*large_radius))
            sigma = random.randint(5, 10)
            geo = get_ellipsoid(x, y, z)
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,1))
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(1,2))
            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,2))
            # texture = get_texture((4*x, 4*y, 4*z))
            point = random_select(mask_scan)
            new_point = [point[0] + enlarge_x//2, point[1] + enlarge_y//2, point[2] + enlarge_z//2]
            x_low, x_high = new_point[0] - geo.shape[0]//2, new_point[0] + geo.shape[0]//2 
            y_low, y_high = new_point[1] - geo.shape[1]//2, new_point[1] + geo.shape[1]//2 
            z_low, z_high = new_point[2] - geo.shape[2]//2, new_point[2] + geo.shape[2]//2 
            
            # paste small tumor geo into test sample
            geo_mask[x_low:x_high, y_low:y_high, z_low:z_high] += geo
            # texture_map[x_low:x_high, y_low:y_high, z_low:z_high] = texture

    geo_mask = geo_mask[enlarge_x//2:-enlarge_x//2, enlarge_y//2:-enlarge_y//2, enlarge_z//2:-enlarge_z//2]
    # texture_map = texture_map[enlarge_x//2:-enlarge_x//2, enlarge_y//2:-enlarge_y//2, enlarge_z//2:-enlarge_z//2]
    geo_mask = (geo_mask * mask_scan) >=1
    
    return geo_mask


def SynthesisTumor(mask_scan, tumor_type, texture):
    # for speed_generate_tumor, we only send the liver part into the generate program
    x_start, x_end = np.where(np.any(mask_scan, axis=(1, 2)))[0][[0, -1]]
    y_start, y_end = np.where(np.any(mask_scan, axis=(0, 2)))[0][[0, -1]]
    z_start, z_end = np.where(np.any(mask_scan, axis=(0, 1)))[0][[0, -1]]

    # shrink the boundary
    x_start, x_end = max(0, x_start+1), min(mask_scan.shape[0], x_end-1)
    y_start, y_end = max(0, y_start+1), min(mask_scan.shape[1], y_end-1)
    z_start, z_end = max(0, z_start+1), min(mask_scan.shape[2], z_end-1)

    liver_mask = get_fixed_geo(mask_scan, tumor_type)

    mask_scan[x_start:x_end, y_start:y_end, z_start:z_end] = liver_mask

    return mask_scan

if __name__ == 'main':
    geo_mask = get_fixed_geo(mask_scan, tumor_type)