def test_3d_energy_decrease():
a_black = np.zeros((5, 5, 5)).astype(np.uint8)
a_black[2, 2, 2] = 255
a_white = invert(a_black)
assert_array_less(
meijering(a_black, black_ridges=True).std(), a_black.std())
assert_array_less(
meijering(a_white, black_ridges=False).std(), a_white.std())
assert_array_less(
sato(a_black, black_ridges=True, mode='reflect').std(), a_black.std())
assert_array_less(
sato(a_white, black_ridges=False, mode='reflect').std(), a_white.std())
assert_array_less(frangi(a_black, black_ridges=True).std(), a_black.std())
assert_array_less(frangi(a_white, black_ridges=False).std(), a_white.std())
assert_array_less(
hessian(a_black, black_ridges=True, mode='reflect').std(),
a_black.std())
assert_array_less(
hessian(a_white, black_ridges=False, mode='reflect').std(),
a_white.std())
def test_2d_linearity():
a_black = np.ones((3, 3)).astype(np.uint8)
a_white = invert(a_black)
assert_allclose(meijering(1 * a_black, black_ridges=True),
meijering(10 * a_black, black_ridges=True),
atol=1e-3)
assert_allclose(meijering(1 * a_white, black_ridges=False),
meijering(10 * a_white, black_ridges=False),
atol=1e-3)
assert_allclose(sato(1 * a_black, black_ridges=True),
sato(10 * a_black, black_ridges=True),
atol=1e-3)
assert_allclose(sato(1 * a_white, black_ridges=False),
sato(10 * a_white, black_ridges=False),
atol=1e-3)
assert_allclose(frangi(1 * a_black, black_ridges=True),
frangi(10 * a_black, black_ridges=True),
atol=1e-3)
assert_allclose(frangi(1 * a_white, black_ridges=False),
frangi(10 * a_white, black_ridges=False),
atol=1e-3)
assert_allclose(hessian(1 * a_black, black_ridges=True),
hessian(10 * a_black, black_ridges=True),
atol=1e-3)
assert_allclose(hessian(1 * a_white, black_ridges=False),
hessian(10 * a_white, black_ridges=False),
atol=1e-3)
def test_3d_linearity():
# Note: last axis intentionally not size 3 to avoid 2D+RGB autodetection
# warning from an internal call to `skimage.filters.gaussian`.
a_black = np.ones((3, 3, 5)).astype(np.uint8)
a_white = invert(a_black)
assert_allclose(meijering(1 * a_black, black_ridges=True),
meijering(10 * a_black, black_ridges=True),
atol=1e-3)
assert_allclose(meijering(1 * a_white, black_ridges=False),
meijering(10 * a_white, black_ridges=False),
atol=1e-3)
assert_allclose(sato(1 * a_black, black_ridges=True, mode='reflect'),
sato(10 * a_black, black_ridges=True, mode='reflect'),
atol=1e-3)
assert_allclose(sato(1 * a_white, black_ridges=False, mode='reflect'),
sato(10 * a_white, black_ridges=False, mode='reflect'),
atol=1e-3)
assert_allclose(frangi(1 * a_black, black_ridges=True),
frangi(10 * a_black, black_ridges=True),
atol=1e-3)
assert_allclose(frangi(1 * a_white, black_ridges=False),
frangi(10 * a_white, black_ridges=False),
atol=1e-3)
assert_allclose(hessian(1 * a_black, black_ridges=True, mode='reflect'),
hessian(10 * a_black, black_ridges=True, mode='reflect'),
atol=1e-3)
assert_allclose(hessian(1 * a_white, black_ridges=False, mode='reflect'),
hessian(10 * a_white, black_ridges=False, mode='reflect'),
atol=1e-3)
def sato(image): image= data.coins() image = filters.sato(image, sigmas=range(1, 10, 2), black_ridges=True, mode=None, cval=0) cmap = plt.cm.gray fig, axes = plt.subplots(1, 1, squeeze=False) axes[0, 0].imshow(image, cmap=cmap, aspect='auto') plt.tight_layout() plt.show()
def apply(self, c):
if self.filter_name == "frangi":
return frangi(c)
if self.filter_name == "hessian":
return hessian(c)
if self.filter_name == "sato":
return sato(c)
raise ValueError("FilterName - {} - not known".format(
self.filter_name))
def test_2d_cropped_camera_image():
a_black = crop(camera(), ((206, 206), (206, 206)))
a_white = invert(a_black)
zeros = np.zeros((100, 100))
ones = np.ones((100, 100))
assert_allclose(meijering(a_black, black_ridges=True),
meijering(a_white, black_ridges=False))
assert_allclose(sato(a_black, black_ridges=True),
sato(a_white, black_ridges=False))
assert_allclose(frangi(a_black, black_ridges=True), zeros, atol=1e-3)
assert_allclose(frangi(a_white, black_ridges=False), zeros, atol=1e-3)
assert_allclose(hessian(a_black, black_ridges=True), ones, atol=1 - 1e-7)
assert_allclose(hessian(a_white, black_ridges=False), ones, atol=1 - 1e-7)
def satoFilter():
global filterimage
imgFilter4 = filters.sato(img,
sigmas=range(1, 10, 2),
black_ridges=True,
mode=None,
cval=0)
filterimage = imgFilter4
io.imshow(imgFilter4)
io.show()
def test_2d_null_matrix():
a_black = np.zeros((3, 3)).astype(np.uint8)
a_white = invert(a_black)
zeros = np.zeros((3, 3))
ones = np.ones((3, 3))
assert_equal(meijering(a_black, black_ridges=True), ones)
assert_equal(meijering(a_white, black_ridges=False), ones)
assert_equal(sato(a_black, black_ridges=True), zeros)
assert_equal(sato(a_white, black_ridges=False), zeros)
assert_allclose(frangi(a_black, black_ridges=True), zeros, atol=1e-3)
assert_allclose(frangi(a_white, black_ridges=False), zeros, atol=1e-3)
assert_equal(hessian(a_black, black_ridges=False), ones)
assert_equal(hessian(a_white, black_ridges=True), ones)
def test_3d_null_matrix():
# Note: last axis intentionally not size 3 to avoid 2D+RGB autodetection
# warning from an internal call to `skimage.filters.gaussian`.
a_black = np.zeros((3, 3, 5)).astype(np.uint8)
a_white = invert(a_black)
zeros = np.zeros((3, 3, 5))
ones = np.ones((3, 3, 5))
assert_allclose(meijering(a_black, black_ridges=True), zeros, atol=1e-1)
assert_allclose(meijering(a_white, black_ridges=False), zeros, atol=1e-1)
assert_equal(sato(a_black, black_ridges=True, mode='reflect'), zeros)
assert_equal(sato(a_white, black_ridges=False, mode='reflect'), zeros)
assert_allclose(frangi(a_black, black_ridges=True), zeros, atol=1e-3)
assert_allclose(frangi(a_white, black_ridges=False), zeros, atol=1e-3)
assert_equal(hessian(a_black, black_ridges=False, mode='reflect'), ones)
assert_equal(hessian(a_white, black_ridges=True, mode='reflect'), ones)
def test_3d_cropped_camera_image():
a_black = crop(camera(), ((200, 212), (100, 312)))
a_black = np.dstack([a_black, a_black, a_black])
a_white = invert(a_black)
zeros = np.zeros((100, 100, 3))
ones = np.ones((100, 100, 3))
assert_allclose(meijering(a_black, black_ridges=True),
meijering(a_white, black_ridges=False))
assert_allclose(sato(a_black, black_ridges=True, mode='reflect'),
sato(a_white, black_ridges=False, mode='reflect'))
assert_allclose(frangi(a_black, black_ridges=True), zeros, atol=1e-3)
assert_allclose(frangi(a_white, black_ridges=False), zeros, atol=1e-3)
assert_allclose(hessian(a_black, black_ridges=True, mode='reflect'),
ones, atol=1 - 1e-7)
assert_allclose(hessian(a_white, black_ridges=False, mode='reflect'),
ones, atol=1 - 1e-7)
def get_text(im=None):
"""
Extract digits using tesseract
"""
sato_res = sato(im, mode='reflect')
im_filt = img_as_ubyte(sato_res)
val = threshold_otsu(im_filt)
im_filt = img_as_ubyte(im_filt >= val)
custom_config = r'-c tessedit_char_whitelist=0123456789. --psm 5 -l letsgodigital'
res = pytesseract.image_to_string(im_filt, config=custom_config)
return res
def setup(self):
retina = color.rgb2gray(data.retina())
t0, _ = filters.threshold_multiotsu(retina, classes=3)
mask = (retina > t0)
vessels = filters.sato(retina, sigmas=range(1, 10)) * mask
thresholded = filters.apply_hysteresis_threshold(vessels, 0.01, 0.03)
labeled = ndi.label(thresholded)[0]
largest_nonzero_label = np.argmax(np.bincount(labeled[labeled > 0]))
binary = (labeled == largest_nonzero_label)
self.skeleton = morphology.skeletonize(binary)
labeled2 = ndi.label(thresholded[::2, ::2])[0]
largest_nonzero_label2 = np.argmax(np.bincount(labeled2[labeled2 > 0]))
binary2 = (labeled2 == largest_nonzero_label2)
small_skeleton = morphology.skeletonize(binary2)
self.g, self.n = graph.pixel_graph(small_skeleton, connectivity=2)
def __call__(self, img):
"""
:param img: input image
:returns tubular features image
"""
if len(img.shape) == 3:
layers = img.shape[2]
else:
img = img[..., np.newaxis]
layers = 1
sato = np.zeros(img.shape)
for i in range(layers):
sato[..., i] = filters.sato(img[..., i],
black_ridges=self.black,
sigmas=self.sigmas,
mode="reflect")
return sato
def retina_speed_image():
with warnings.catch_warnings():
warnings.simplefilter('ignore', RuntimeWarning)
image_data = rescale(rgb2gray(retina())[260:1280, 90:800], 0.5)
speed_data = sato(image_data)
return speed_data
def obtenerImagenes(filename, wPath, tmpPath):
# Redes Convolucionales
Seg_model = Segmentation_model_2()
Seg_model.load_weights(wPath, by_name=True)
in_img = plt.imread(filename, 3) / 255
in_img = tf.image.resize(in_img, (64*9, 64*9))
n_img = tf.image.resize(in_img, (64*9, 64*9))
in_img = tf.stack([in_img, n_img], axis=0)
salida = Seg_model(in_img, training = False)
res = salida[0,...]
res = tf.image.resize(res, (584, 565))
res = res.numpy()
res = res.reshape(584,565)
binary = res > .1
binary_clean = morphology.remove_small_objects(binary, 3000)
prueba = np.clip(res,0 , 1)
cv2.imwrite(tmpPath + "/deepSeg.png", binary_clean * 255)
# Filtro de Sato
image = cv2.imread(filename, 0)
ring = np.zeros((584,565))
rr, cc = circle(292, 282, 250, shape=(image.shape))
ring[rr, cc] = 1
elevation_map = sobel(image)
satoi = sato(image)
thresh = threshold_li(satoi)
binary = satoi > thresh
frgi = frangi(image)
threshF = threshold_li(frgi)
bF = frgi * 100000 > .03
bF = morphology.remove_small_objects(bF, 3000)
bF = bF * ring #imagen segmentada 1
binary_clean = morphology.remove_small_objects(binary, 3000)
l_binary_clean = morphology.label(binary_clean, return_num=True, connectivity=1)
binary_f = binary_clean * ring # segmentada 2, solo arterias principales
cv2.imwrite(tmpPath + "/SatoSeg.png", bF * 255)
shape = binary_f.shape
a = shape[0]/2 - 1
b = shape[1] + 1 /2
centro_ = (233, 291)
x_1 = y_2 = y_3 = px = i = lado = 0
y_1 = a
#primer pixel blanco centro
while px != 1:
px = binary_f[int(a)][i]
i = i + 1
x_1 = i
if x_1 > shape[1] / 2:
lado = 0
i = shape[1] - 1
px = 0
while px != 1:
px = binary_f[int(a)][i]
i = i - 1
else:
lado = 1
if lado == 0:
b = (shape[1] + 1) / 4
b = (b * 3) - 20
else:
b = ((shape[1] + 1) / 4) + 20
x_1 = i
x_2 = b
x_3 = x_2
px, i = [0, 0]
#primer pixel blanco arriba
while px != 1:
px = binary_f[i][int(b)]
i = i + 1
y_2 = i
px, i = [0, shape[0] - 1]
#primer pixel blanco abajo
while px != 1:
px = binary_f[i][int(b)]
i = i - 1
y_3 = i
if x_1 < shape[1] / 2:
lado = 1
punto1 = (int(x_1), int(y_1))
punto2 = (int(x_2), int(y_2))
punto3 = (int(x_3), int(y_3))
centro = [b, a]
color = (0, 0, 255)
# Para calculo de angulos Tan(x) = CatetoOpuesto / CatetoAdyacente
ca = np.abs(centro[0] - x_1)
co1 = np.abs(centro[1] - y_2)
co2 = np.abs(centro[1] - y_3)
ca_ = (int(centro[0]), int(y_1)) # coordernadas para impresion
co_ = (int(centro[0]), y_2) # coordernadas para impresion
img2 = (binary_f * 255) + image
l = cv2.line(img2, punto1, punto2, color, 5)
l = cv2.line(l, punto1, punto3, color, 5)
l = cv2.line(l, punto1, ca_, color, 2)
l = cv2.line(l, ca_, co_, color, 2)
l = cv2.circle(l, punto1, 30, color, 2)
angulo1 = np.rad2deg(np.arctan(co1 / ca)) # x = arcTan((Co/Ca))
angulo2 = np.rad2deg(np.arctan(co2 / ca))
angulo = np.abs(angulo1) + np.abs(angulo2)
cv2.putText(l, "{0:.7}".format(angulo), centro_, cv2.QT_FONT_NORMAL, 0.8, (0,0,0), 2, cv2.LINE_AA)
cv2.imwrite(tmpPath + "/lineas.png", l)
def run(self, ips, snap, img, para = None): rst = sato(snap, range(para['start'], para['end'], para['step']), black_ridges=para['bridges']) img[:] = scale(rst, ips.range[0], ips.range[1])
def sat(image):
return sato(image)
def run(self, ips, imgs, para=None):
IPy.show_img(
sato(imgs,
range(para['start'], para['end'], para['step']),
black_ridges=para['bridges']), ips.title + '-sato')
def filter(original_images, transformation):
"""
:param original_images:
:param transformation:
:return:
"""
nb_images, img_rows, img_cols, nb_channels = original_images.shape
transformed_images = []
if (transformation == TRANSFORMATION.filter_sobel):
for img in original_images:
if (nb_channels == 3):
img = cv2.cvtColor(img, cv2.COLOR_RGB2GRAY)
img = img.reshape(img_rows, img_cols)
img_trans = filters.sobel(img)
if (nb_channels == 3):
img_trans = cv2.cvtColor(img_trans, cv2.COLOR_GRAY2RGB)
transformed_images.append(img_trans)
elif (transformation == TRANSFORMATION.filter_median):
for img in original_images:
img_trans = ndimage.median_filter(img, size=3)
transformed_images.append(img_trans)
elif (transformation == TRANSFORMATION.filter_minimum):
for img in original_images:
img_trans = ndimage.minimum_filter(img, size=3)
transformed_images.append(img_trans)
elif (transformation == TRANSFORMATION.filter_maximum):
for img in original_images:
img_trans = ndimage.maximum_filter(img, size=3)
transformed_images.append(img_trans)
elif (transformation == TRANSFORMATION.filter_gaussian):
for img in original_images:
img_trans = ndimage.gaussian_filter(img, sigma=1)
transformed_images.append(img_trans)
elif (transformation == TRANSFORMATION.filter_rank):
for img in original_images:
img_trans = ndimage.rank_filter(img, rank=15, size=3)
transformed_images.append(img_trans)
elif (transformation == TRANSFORMATION.filter_entropy):
for img in original_images:
radius = 2
if (nb_channels == 3):
radius = 1
img = cv2.cvtColor(img, cv2.COLOR_RGB2GRAY)
img = img.reshape(img_rows, img_cols)
"""
requires values in range [-1., 1.]
"""
img = (img - 0.5) * 2.
"""
skimage-entropy function returns values in float64,
however opencv only supports float32.
"""
img_trans = np.float32(
filters.rank.entropy(img, disk(radius=radius)))
"""
rescale back into range [0., 1.]
"""
img_trans = (img_trans / 2.) + 0.5
if (nb_channels == 3):
img_trans = cv2.cvtColor(img_trans, cv2.COLOR_GRAY2RGB)
transformed_images.append(img_trans)
elif (transformation == TRANSFORMATION.filter_roberts):
for img in original_images:
if (nb_channels == 3):
img = cv2.cvtColor(img, cv2.COLOR_RGB2GRAY)
img = img.reshape(img_rows, img_cols)
img_trans = roberts(img)
if (nb_channels == 3):
img_trans = cv2.cvtColor(img_trans, cv2.COLOR_GRAY2RGB)
transformed_images.append(img_trans)
elif (transformation == TRANSFORMATION.filter_scharr):
for img in original_images:
if (nb_channels == 3):
img = cv2.cvtColor(img, cv2.COLOR_RGB2GRAY)
img = img.reshape(img_rows, img_cols)
img_trans = scharr(img)
if (nb_channels == 3):
img_trans = cv2.cvtColor(img_trans, cv2.COLOR_GRAY2RGB)
transformed_images.append(img_trans)
elif (transformation == TRANSFORMATION.filter_prewitt):
for img in original_images:
if (nb_channels == 3):
img = cv2.cvtColor(img, cv2.COLOR_RGB2GRAY)
img = img.reshape(img_rows, img_cols)
img_trans = prewitt(img)
if (nb_channels == 3):
img_trans = cv2.cvtColor(img_trans, cv2.COLOR_GRAY2RGB)
transformed_images.append(img_trans)
elif (transformation == TRANSFORMATION.filter_meijering):
for img in original_images:
if nb_channels == 1:
img = cv2.cvtColor(img, cv2.COLOR_GRAY2RGB)
img_trans = meijering(img, sigmas=[0.01])
if nb_channels == 1:
img_trans = img_trans[:, :, 1]
transformed_images.append(img_trans)
elif (transformation == TRANSFORMATION.filter_sato):
for img in original_images:
img_trans = sato(img)
transformed_images.append(img_trans)
elif (transformation == TRANSFORMATION.filter_frangi):
for img in original_images:
img_trans = frangi(img)
transformed_images.append(img_trans)
elif (transformation == TRANSFORMATION.filter_hessian):
for img in original_images:
img_trans = hessian(img)
transformed_images.append(img_trans)
elif (transformation == TRANSFORMATION.filter_skeletonize):
for img in original_images:
img = invert(img)
img = img.reshape((img_rows, img_cols))
img = skeletonize(img)
transformed_images.append(img)
elif (transformation == TRANSFORMATION.filter_thin):
for img in original_images:
img = img.reshape(img_rows, img_cols)
img = thin(img, max_iter=100)
transformed_images.append(img)
else:
raise ValueError('{} is not supported.'.format(transformation))
transformed_images = np.stack(transformed_images, axis=0)
if (nb_channels == 1):
# reshape a 3d to a 4d
transformed_images = transformed_images.reshape(
(nb_images, img_rows, img_cols, nb_channels))
return transformed_images
#ridge detection
from skimage import io, filters, feature
import matplotlib.pyplot as plt
from skimage.color import rgb2gray
from skimage.util import invert
import cv2
from skimage.filters import meijering, sato, frangi, hessian
img = io.imread("Classified image 1.jpg")
#img = rgb2gray(invert(img))
img = rgb2gray(img)
meijering_img = meijering(img)
sato_img = sato(img)
frangi_img = frangi(img)
hessian_img = hessian(img)
fig = plt.figure(figsize=(20, 20))
#ax1 = fig.add_subplot(2,2,1)
#ax1.imshow(img, cmap="gray")
#ax1.title.set_text("Input Image")
ax1 = fig.add_subplot(2, 2, 1)
ax1.imshow(hessian_img, cmap="gray")
ax1.title.set_text("Hessian")
ax2 = fig.add_subplot(2, 2, 2)
ax2.imshow(meijering_img, cmap="gray")
def noisy_mountains_2():
rand_color = randomcolor.RandomColor()
size_x = 20
size_y = 20
upscale_factor = 10
n_labels = 4
sigma = 1
buffer = 0.0005
hsv_index = 1
segment_spacing = [10, 10]
image_rgb = np.random.uniform(0, 1, (size_x, size_y, 3))
labels = np.random.randint(n_labels + 1, size=(
size_x, size_y)) * np.random.randint(0, 2, size=(size_x, size_y))
# segment random image
segments = random_walker(
image_rgb,
labels,
multichannel=True,
beta=250,
copy=False,
spacing=segment_spacing,
)
all_colors = np.array(
rand_color.generate(hue="purple", count=n_labels,
format_='Array_rgb')) / 256.
for color_index in np.unique(segments):
color_hsv = color.rgb2hsv(all_colors[color_index - 1])
color_hsv[2] = 0.3 + (color_index - 1) * 0.4 / n_labels
color_rgb = color.hsv2rgb(color_hsv)
image_rgb[segments == color_index] = color_rgb
# transform segmented image so it is large, preserving blobs, and blurry
image_rgb = rescale(image_rgb,
upscale_factor,
anti_aliasing=False,
multichannel=True)
image_rgb = gaussian(image_rgb, sigma=sigma, multichannel=True)
image_hsv = color.rgb2hsv(image_rgb)
plt.figure()
plt.imshow(image_rgb)
plt.show()
for pix_frac in [0.9]:
total_pixels_switched = int(image_rgb.shape[0] * image_rgb.shape[0] *
pix_frac)
print(total_pixels_switched)
for _ in range(total_pixels_switched):
rand_x, rand_y = np.random.choice(
image_hsv.shape[0]), np.random.choice(image_hsv.shape[1])
orig_rgb = image_rgb[rand_x, rand_y]
rand_value = image_hsv[rand_x, rand_y, hsv_index]
x, y = np.where((rand_value *
(1 + 0.5 * buffer) >= image_hsv[:, :, hsv_index])
& (rand_value *
(1 - 2 * buffer) < image_hsv[:, :, hsv_index]))
if len(x) == 0:
continue
idx = np.random.choice(len(x))
update_rgb = image_rgb[x[idx], y[idx]]
image_rgb[x[idx], y[idx]] = orig_rgb
image_rgb[rand_x, rand_y] = update_rgb
plt.figure()
plt.title(pix_frac)
plt.imshow(image_rgb)
plt.show()
plt.figure()
plt.imshow(image_rgb)
plt.show()
# filtered_img = prewitt_v(color.rgb2hsv(image_rgb)[:, :, 0])
# filtered_img = meijering(color.rgb2hsv(image_rgb)[:, :, 0])
filtered_img = sato(color.rgb2hsv(image_rgb)[:, :, 0])
# filtered_img = frangi(color.rgb2hsv(image_rgb)[:, :, 0])
plt.figure()
plt.imshow(filtered_img)
plt.show()
filtered_img = filtered_img
filtered_img = (filtered_img + np.abs(np.min(filtered_img))
) / np.max(filtered_img + np.abs(np.min(filtered_img)))
filtered_img += 0.8
plt.figure()
plt.imshow(filtered_img, cmap='gray')
plt.colorbar()
plt.show()
num_erosions = 5
eroded_image = hessian(color.rgb2hsv(image_rgb)[:, :, 0])
eroded_aug = np.zeros_like(eroded_image)
for n in range(num_erosions):
eroded_aug += 1 * eroded_image
eroded_image = erosion(eroded_image)
plt.figure()
plt.imshow(image_rgb)
plt.show()
image_hsv = color.rgb2hsv(image_rgb)
image_hsv[:, :, 2] *= filtered_img
image_hsv[:, :, 2] *= 1 - (0.3 * eroded_aug / np.max(eroded_aug))
image_rgb_shadow_aug = color.hsv2rgb(image_hsv)
plt.figure()
plt.imshow(image_rgb_shadow_aug)
plt.show()
def sato_filter(filename):
img = asarray(Image.open(filename))
img = rgb2gray(img)
img = filters.sato(img)
plt.imsave(filename, img, cmap="gray")
return filename
def run(img, **args):
if len(img.shape) > 2 and img.shape[2] == 4:
img = color.rgba2rgb(img)
if len(img.shape) == 2:
img = color.gray2rgb(img)
return to_base64(sato(color.rgb2gray(img), **args))
def detectNeedle(self, magnitudevolume, phasevolume, truePhasePoint,
maskThreshold, ridgeOperator, slice_index):
#magnitude volume
magn_imageData = magnitudevolume.GetImageData()
magn_rows, magn_cols, magn_zed = magn_imageData.GetDimensions()
magn_scalars = magn_imageData.GetPointData().GetScalars()
magn_imageOrigin = magnitudevolume.GetOrigin()
magn_imageSpacing = magnitudevolume.GetSpacing()
magn_matrix = vtk.vtkMatrix4x4()
magnitudevolume.GetIJKToRASMatrix(magn_matrix)
# magnitudevolume.CreateDefaultDisplayNodes()
# phase volume
phase_imageData = phasevolume.GetImageData()
phase_rows, phase_cols, phase_zed = phase_imageData.GetDimensions()
phase_scalars = phase_imageData.GetPointData().GetScalars()
#Convert vtk to numpy
magn_array = numpy_support.vtk_to_numpy(magn_scalars)
numpy_magn = magn_array.reshape(magn_zed, magn_rows, magn_cols)
phase_array = numpy_support.vtk_to_numpy(phase_scalars)
numpy_phase = phase_array.reshape(phase_zed, phase_rows, phase_cols)
# slice = int(slice_number)
# slice = (slice_index)
# maskThreshold = int(maskThreshold)
#2D Slice Selector
### 3 3D values are : numpy_magn , numpy_phase, mask
numpy_magn = numpy_magn[slice_index, :, :]
numpy_phase = numpy_phase[slice_index, :, :]
#mask = mask[slice,:,:]
numpy_magn_sliced = numpy_magn.astype(np.uint8)
#mask thresholding
img = cv2.pyrDown(numpy_magn_sliced)
_, threshed = cv2.threshold(numpy_magn_sliced, maskThreshold, 255,
cv2.THRESH_BINARY)
contours, _ = cv2.findContours(threshed, cv2.RETR_TREE,
cv2.CHAIN_APPROX_SIMPLE)
#find maximum contour and draw
cmax = max(contours, key=cv2.contourArea)
epsilon = 0.002 * cv2.arcLength(cmax, True)
approx = cv2.approxPolyDP(cmax, epsilon, True)
cv2.drawContours(numpy_magn_sliced, [approx], -1, (0, 255, 0), 3)
width, height = numpy_magn_sliced.shape
#fill maximum contour and draw
mask = np.zeros([width, height, 3], dtype=np.uint8)
cv2.fillPoly(mask, pts=[cmax], color=(255, 255, 255))
mask = mask[:, :, 0]
#phase_cropped
phase_cropped = cv2.bitwise_and(numpy_phase, numpy_phase, mask=mask)
phase_cropped = np.expand_dims(phase_cropped, axis=0)
node = slicer.vtkMRMLScalarVolumeNode()
node.SetName('phase_cropped')
slicer.mrmlScene.AddNode(node)
slicer.util.updateVolumeFromArray(node, phase_cropped)
node.SetOrigin(magn_imageOrigin)
node.SetSpacing(magn_imageSpacing)
node.SetIJKToRASDirectionMatrix(magn_matrix)
unwrapped_phase = slicer.vtkMRMLScalarVolumeNode()
unwrapped_phase.SetName('unwrapped_phase')
slicer.mrmlScene.AddNode(unwrapped_phase)
#
# Run phase unwrapping module
#
parameter_name = slicer.mrmlScene.GetNodeByID(
'vtkMRMLCommandLineModuleNode1')
if parameter_name is None:
slicer.cli.createNode(slicer.modules.phaseunwrapping)
else:
pass
cli_input = slicer.util.getFirstNodeByName('phase_cropped')
cli_output = slicer.util.getNode('unwrapped_phase')
cli_params = {
'inputVolume': cli_input,
'outputVolume': cli_output,
'truePhase': truePhasePoint
}
self.cliParamNode = slicer.cli.runSync(slicer.modules.phaseunwrapping,
node=self.cliParamNode,
parameters=cli_params)
pu_imageData = unwrapped_phase.GetImageData()
pu_rows, pu_cols, pu_zed = pu_imageData.GetDimensions()
pu_scalars = pu_imageData.GetPointData().GetScalars()
pu_NumpyArray = numpy_support.vtk_to_numpy(pu_scalars)
phaseunwrapped = pu_NumpyArray.reshape(pu_zed, pu_rows, pu_cols)
# for debug
self.phaseunwrapped_numpy = pu_NumpyArray.reshape(pu_cols, pu_rows)
#Delete unwrapped_phase after I get the information from it
# delete_unwrapped = slicer.mrmlScene.GetFirstNodeByName('Phase Unwrapping')
# slicer.mrmlScene.RemoveNode(delete_unwrapped)
I = phaseunwrapped.squeeze()
A = np.fft.fft2(I)
A1 = np.fft.fftshift(A)
# Image size
[M, N] = A.shape
# filter size parameter
R = 10
X = np.arange(0, N, 1)
Y = np.arange(0, M, 1)
[X, Y] = np.meshgrid(X, Y)
Cx = 0.5 * N
Cy = 0.5 * M
Lo = np.exp(-(((X - Cx)**2) + ((Y - Cy)**2)) / ((2 * R)**2))
Hi = 1 - Lo
J = A1 * Lo
J1 = np.fft.ifftshift(J)
B1 = np.fft.ifft2(J1)
K = A1 * Hi
K1 = np.fft.ifftshift(K)
B2 = np.fft.ifft2(K1)
B2 = np.real(B2)
#Remove border for false positive
border_size = 20
top, bottom, left, right = [border_size] * 4
mask_borderless = cv2.copyMakeBorder(mask, top, bottom, left, right,
cv2.BORDER_CONSTANT, (0, 0, 0))
kernel = np.ones((5, 5), np.uint8)
mask_borderless = cv2.erode(mask_borderless, kernel, iterations=5)
mask_borderless = ndimage.binary_fill_holes(mask_borderless).astype(
np.uint8)
x, y = mask_borderless.shape
mask_borderless = mask_borderless[0 + border_size:y - border_size,
0 + border_size:x - border_size]
B2 = cv2.bitwise_and(B2, B2, mask=mask_borderless)
# for debug
self.mask_borderless = mask_borderless
# ridgeOperator = int(ridgeOperator)
meiji = sato(B2,
sigmas=(ridgeOperator, ridgeOperator),
black_ridges=True)
#(minVal, maxVal, minLoc, maxLoc) = cv2.minMaxLoc(meiji)
result2 = np.reshape(meiji, meiji.shape[0] * meiji.shape[1])
ids = np.argpartition(result2, -51)[-51:]
sort = ids[np.argsort(result2[ids])[::-1]]
(y1, x1) = np.unravel_index(sort[0], meiji.shape) # best match
self.meiji = meiji
point = (x1, y1)
coords = [x1, y1, slice_index]
circle1 = plt.Circle(point, 2, color='red')
self.x1 = x1
self.y1 = y1
# Find or create MRML transform node
transformNode = None
try:
transformNode = slicer.util.getNode('TipTransform')
except slicer.util.MRMLNodeNotFoundException as exc:
transformNode = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLLinearTransformNode')
transformNode.SetName("TipTransform")
transformNode.SetAndObserveMatrixTransformToParent(magn_matrix)
# Fiducial Creation
fidNode1 = None
try:
fidNode1 = slicer.util.getNode('needle_tip')
except slicer.util.MRMLNodeNotFoundException as exc:
fidNode1 = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLMarkupsFiducialNode", "needle_tip")
fidNode1.RemoveAllMarkups()
# fidNode1.CreateDefaultDisplayNodes()
# fidNode1.SetMaximumNumberOfControlPoints(1)
fidNode1.AddFiducialFromArray(coords)
fidNode1.SetAndObserveTransformNodeID(transformNode.GetID())
###TODO: dont delete the volume after use. create a checkpoint to update on only one volume
delete_wrapped = slicer.mrmlScene.GetFirstNodeByName('phase_cropped')
slicer.mrmlScene.RemoveNode(delete_wrapped)
delete_unwrapped = slicer.mrmlScene.GetFirstNodeByName(
'unwrapped_phase')
slicer.mrmlScene.RemoveNode(delete_unwrapped)
#print ("Needle tip location",y1,x1)
#self.counter = 0
return True
def vectorize_lines(im: np.ndarray, threshold: float = 0.15, min_length=5):
"""
Vectorizes lines from a binarized array.
Args:
im (np.ndarray): Array of shape (3, H, W) with the first dimension
being probabilities for (start_separators,
end_separators, baseline).
threshold (float): Threshold for baseline blob detection.
min_length (int): Minimal length of output baselines.
Returns:
[[x0, y0, ... xn, yn], [xm, ym, ..., xk, yk], ... ]
A list of lists containing the points of all baseline polylines.
"""
# split into baseline and separator map
st_map = im[0]
end_map = im[1]
sep_map = st_map + end_map
bl_map = im[2]
bl_map = filters.sato(bl_map, black_ridges=False, mode='constant')
bin_bl_map = bl_map > threshold
# skeletonize
line_skel = skeletonize(bin_bl_map)
# find end points
kernel = np.array([[1, 1, 1], [1, 10, 1], [1, 1, 1]])
line_extrema = np.transpose(
np.where(
(convolve2d(line_skel, kernel, mode='same') == 11) * line_skel))
class LineMCP(MCP_Connect):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.connections = dict()
self.scores = defaultdict(lambda: np.inf)
def create_connection(self, id1, id2, pos1, pos2, cost1, cost2):
k = (min(id1, id2), max(id1, id2))
s = cost1 + cost2
if self.scores[k] > s:
self.connections[k] = (pos1, pos2, s)
self.scores[k] = s
def get_connections(self):
results = []
for k, (pos1, pos2, s) in self.connections.items():
results.append(
np.concatenate(
[self.traceback(pos1),
self.traceback(pos2)[::-1]]))
return results
def goal_reached(self, int_index, float_cumcost):
return 2 if float_cumcost else 0
mcp = LineMCP(~line_skel)
try:
mcp.find_costs(line_extrema)
except ValueError as e:
return []
lines = [
approximate_polygon(line, 3).tolist()
for line in mcp.get_connections()
]
# extend baselines to blob boundary
lines = _extend_boundaries(lines, bin_bl_map)
# orient lines
f_st_map = maximum_filter(st_map, size=20)
f_end_map = maximum_filter(end_map, size=20)
oriented_lines = []
for bl in lines:
l_end = tuple(bl[0])
r_end = tuple(bl[-1])
if f_st_map[l_end] - f_end_map[l_end] > 0.2 and f_st_map[
r_end] - f_end_map[r_end] < -0.2:
pass
elif f_st_map[l_end] - f_end_map[l_end] < -0.2 and f_st_map[
r_end] - f_end_map[r_end] > 0.2:
bl = bl[::-1]
else:
logger.debug(
'Insufficient marker confidences in output. Defaulting to upright line.'
)
if bl[0][1] > bl[-1][1]:
bl = bl[::-1]
if geom.LineString(bl).length >= min_length:
oriented_lines.append([x[::-1] for x in bl])
return oriented_lines
def tubeness(image, sigma_max=3):
"""Wrapper around the scikit-image sato tubeness filter"""
tube = sato(image, sigmas=range(1, sigma_max + 1), black_ridges=False)
return tube
def buttonSave(arg):
copy = arg[1]
imageTemp = arg[2]
filterTry = filterVar.get()
if (filterTry == 1):
copy = cv2.GaussianBlur(copy, (5, 5), 0)
elif (filterTry == 2):
copy = cv2.Canny(copy, 100, 150)
elif (filterTry == 3):
copy = filters.roberts(imageTemp)
elif (filterTry == 4):
copy = filters.sato(imageTemp)
elif (filterTry == 5):
copy = filters.scharr(imageTemp)
elif (filterTry == 6):
copy = filters.sobel(imageTemp)
elif (filterTry == 7):
copy = filters.unsharp_mask(copy, radius=30, amount=3)
elif (filterTry == 8):
#copy = filters.median(imageTemp, disk(5))
b, g, r = cv2.split(copy)
b = filters.median(b, disk(5))
g = filters.median(g, disk(5))
r = filters.median(r, disk(5))
copy = cv2.merge((b, g, r))
elif (filterTry == 9):
copy = filters.prewitt(imageTemp)
elif (filterTry == 10):
copy = filters.rank.modal(imageTemp, disk(5))
flag = 0
if (np.ndim(copy) == 2):
flag = 0
else:
flag = 1
if (hEsitleme.get() or hGrafik.get()):
if (flag):
copy = cv2.cvtColor(copy, cv2.COLOR_BGR2GRAY)
if (hGrafik.get()):
plt.hist(copy.ravel(), 256, [0, 256])
plt.show()
if (hEsitleme.get()):
copy = cv2.equalizeHist(copy)
if (uzaysalVars[0].get()):
reScaleRatio = float(uzaysalVarsInputs[0].get())
if (np.ndim(copy) == 3):
b, g, r = cv2.split(copy)
b = transform.rescale(b, reScaleRatio)
g = transform.rescale(g, reScaleRatio)
r = transform.rescale(r, reScaleRatio)
copy = cv2.merge((b, g, r))
else:
copy = transform.rescale(copy, reScaleRatio)
if (uzaysalVars[1].get()):
resizeY = float(uzaysalVarsInputs[1].get())
resizeX = float(uzaysalVarsInputs[2].get())
if (np.ndim(copy) == 3):
b, g, r = cv2.split(copy)
b = transform.resize(
b, (b.shape[0] // resizeX, b.shape[1] // resizeY),
anti_aliasing=True)
g = transform.resize(
g, (g.shape[0] // resizeX, g.shape[1] // resizeY),
anti_aliasing=True)
r = transform.resize(
r, (r.shape[0] // resizeX, r.shape[1] // resizeY),
anti_aliasing=True)
copy = cv2.merge((b, g, r))
else:
copy = transform.resize(
copy, (copy.shape[0] // resizeX, copy.shape[1] // resizeY),
anti_aliasing=True)
if (uzaysalVars[2].get()):
copy = transform.swirl(copy, rotation=0, strength=10, radius=120)
if (uzaysalVars[3].get()):
copy = transform.rotate(copy,
int(uzaysalVarsInputs[3].get()),
resize=True)
if (uzaysalVars[4].get()):
copy = copy[:, ::-1]
if (yogunlukVars[0].get() or yogunlukVars[1].get()):
if (yogunlukVars[0].get()):
startINX = int(yogunlukVars[2].get())
finishINX = int(yogunlukVars[3].get())
copy = exposure.rescale_intensity(copy,
in_range=(startINX,
finishINX))
if (yogunlukVars[1].get()):
startOUTX = int(yogunlukVars[4].get())
finishOUTX = int(yogunlukVars[5].get())
copy = exposure.rescale_intensity(copy,
out_range=(startOUTX,
finishOUTX))
morfoTry = morfVar.get()
morfoGirisN = 0
if (np.ndim(copy) == 3):
morfoGirisN = 1
if (morfoTry == 1):
if (morfoGirisN):
b, g, r = cv2.split(copy)
b = morphology.area_closing(b, 128, 9)
g = morphology.area_closing(g, 128, 9)
r = morphology.area_closing(r, 128, 9)
copy = cv2.merge((b, g, r))
else:
copy = morphology.area_closing(copy)
elif (morfoTry == 2):
if (morfoGirisN):
b, g, r = cv2.split(copy)
b = morphology.area_opening(b, 128, 9)
g = morphology.area_opening(g, 128, 9)
r = morphology.area_opening(r, 128, 9)
copy = cv2.merge((b, g, r))
else:
copy = morphology.area_opening(copy)
elif (morfoTry == 3):
if (morfoGirisN):
b, g, r = cv2.split(copy)
b = morphology.erosion(b, disk(6))
g = morphology.erosion(g, disk(6))
r = morphology.erosion(r, disk(6))
copy = cv2.merge((b, g, r))
else:
copy = morphology.erosion(copy, disk(6))
elif (morfoTry == 4):
if (morfoGirisN):
b, g, r = cv2.split(copy)
b = morphology.dilation(b, disk(6))
g = morphology.dilation(g, disk(6))
r = morphology.dilation(r, disk(6))
copy = cv2.merge((b, g, r))
else:
copy = morphology.dilation(copy, disk(6))
elif (morfoTry == 5):
if (morfoGirisN):
b, g, r = cv2.split(copy)
b = morphology.opening(b, disk(6))
g = morphology.opening(g, disk(6))
r = morphology.opening(r, disk(6))
copy = cv2.merge((b, g, r))
else:
copy = morphology.opening(copy, disk(6))
elif (morfoTry == 6):
if (morfoGirisN):
b, g, r = cv2.split(copy)
b = morphology.closing(b, disk(6))
g = morphology.opening(g, disk(6))
r = morphology.opening(r, disk(6))
copy = cv2.merge((b, g, r))
else:
copy = morphology.opening(copy, disk(6))
elif (morfoTry == 7):
if (morfoGirisN):
b, g, r = cv2.split(copy)
b = morphology.white_tophat(b, disk(6))
g = morphology.white_tophat(g, disk(6))
r = morphology.white_tophat(r, disk(6))
copy = cv2.merge((b, g, r))
else:
copy = morphology.white_tophat(copy, disk(6))
elif (morfoTry == 8):
if (morfoGirisN):
b, g, r = cv2.split(copy)
b = morphology.black_tophat(b, disk(6))
g = morphology.black_tophat(g, disk(6))
r = morphology.black_tophat(r, disk(6))
copy = cv2.merge((b, g, r))
else:
copy = morphology.black_tophat(copy, disk(6))
elif (morfoTry == 10):
if (morfoGirisN):
copy = cv2.cvtColor(copy, cv2.COLOR_BGR2GRAY)
copy = exposure.rescale_intensity(copy)
local_maxima = extrema.local_maxima(copy)
label_maxima = measure.label(local_maxima)
copy = color.label2rgb(label_maxima,
copy,
alpha=0.7,
bg_label=0,
bg_color=None,
colors=[(1, 0, 0)])
elif (morfoTry == 9):
if (morfoGirisN):
copy = cv2.cvtColor(copy, cv2.COLOR_BGR2GRAY)
copy = exposure.rescale_intensity(copy)
h = 0.05
h_maxima = extrema.h_maxima(copy, h)
label_h_maxima = measure.label(h_maxima)
copy = color.label2rgb(label_h_maxima,
copy,
alpha=0.7,
bg_label=0,
bg_color=None,
colors=[(1, 0, 0)])
arg[1] = copy
arg[2] = imageTemp
cv2.imshow("org", copy)
cv2.waitKey(0)
cv2.destroyAllWindows()
"""
def run(self, ips, imgs, para=None):
imgs[:] = sato(imgs,
range(para['start'], para['end'], para['step']),
black_ridges=para['bridges'])
def sato_filter(im, sigmas):
'''Enter function general description + arguments'''
im_sato = sato(im,sigmas=sigmas,mode='reflect',black_ridges=False)
return im_sato
def bonus(use_naive=False):
"""
Fair compare.
https://github.com/orobix/retina-unet/blob/master/src/retinaNN_predict.py
"""
from sklearn.metrics import confusion_matrix
from sklearn.metrics import precision_recall_curve
from sklearn.metrics import jaccard_score
from sklearn.metrics import f1_score
y_pred, y_true = [], []
for filename in sorted(glob("idx*_s64_out1_p.png")):
if not use_naive:
y_pred.append(io.imread(filename, as_gray=True))
else:
from skimage.filters import sato
kwargs = {"sigmas": [1], "black_ridges": 1}
raw = io.imread(filename.replace("1_p", "3_x"), as_gray=True)
img = sato(raw, **kwargs)
# plt.figure()
# plt.imshow(img)
# plt.show()
y_pred.append(img)
y_true.append(io.imread(filename.replace("1_p", "2_y"), as_gray=True))
y_pred, y_true = np.array(y_pred), np.array(y_true)
if use_naive:
y_pred = RetinalDataset.normalize(np.array(y_pred)) / 255
print(y_true.shape, y_pred.shape)
for i in range(len(y_pred)):
print(i, "DICE", dice_loss_1(y_pred[i], y_true[i]))
# Confusion matrix
threshold_confusion = 0.8
print(y_true.max(), y_pred.max())
print(y_true.shape, y_pred.shape)
y_pred = np.where(y_pred > threshold_confusion, 1, 0).astype(int)
y_true = y_true.astype(int)
# plt.figure()
# plt.imshow(y_pred[0])
# plt.show()
def __specific(A, B, name="?"):
A, B = A.flatten(), B.flatten()
print(f"=== \033[90m(name={name})\033[0m ===")
confusion = confusion_matrix(A, B)
print(confusion)
accuracy = 0
if float(np.sum(confusion)) != 0:
accuracy = float(confusion[0, 0] + confusion[1, 1]) / float(
np.sum(confusion))
print("Global Accuracy: " + str(accuracy))
specificity = 0
if float(confusion[0, 0] + confusion[0, 1]) != 0:
specificity = float(
confusion[0, 0]) / float(confusion[0, 0] + confusion[0, 1])
print("Specificity: " + str(specificity))
sensitivity = 0
if float(confusion[1, 1] + confusion[1, 0]) != 0:
sensitivity = float(
confusion[1, 1]) / float(confusion[1, 1] + confusion[1, 0])
print("Sensitivity: " + str(sensitivity))
precision = 0
if float(confusion[1, 1] + confusion[0, 1]) != 0:
precision = float(
confusion[1, 1]) / float(confusion[1, 1] + confusion[0, 1])
print("Precision: " + str(precision))
# F1 score
F1_score = f1_score(A,
B,
labels=None,
average="binary",
sample_weight=None)
print("F1 score (F-measure): " + str(F1_score))
# Jaccard similarity index
jaccard_index = jaccard_score(A, B, average="binary")
print("Jaccard similarity score: " + str(jaccard_index))
__specific(y_true, y_pred, name="all")
for idx in range(y_pred.shape[0]):
__specific(y_true[idx], y_pred[idx], name=idx)