def fun_estrella_cil_vol(tam_base):
aux = morphology.star(tam_base[0] / 3)
tam_aux = aux.shape
Salida_Base = np.zeros((tam_aux[0], tam_aux[1], tam_base[2]))
# Slice-wise drawing
for i in range(0, tam_base[2] - 1):
Salida_Base[:, :, i] = morphology.star(tam_base[0] / 3)
return Salida_Base
def _star_kernel(m, n):
c = m + m // 2 - n - n // 2
outer_star = star(m)
inner_star = np.zeros_like(outer_star)
inner_star[c: -c, c: -c] = star(n)
outer_weight = 1.0 / (np.sum(outer_star - inner_star))
inner_weight = 1.0 / np.sum(inner_star)
bfilter = (outer_weight * outer_star -
(outer_weight + inner_weight) * inner_star)
return bfilter
def _star_kernel(m, n):
c = m + m // 2 - n - n // 2
outer_star = star(m)
inner_star = np.zeros_like(outer_star)
inner_star[c:-c, c:-c] = star(n)
outer_weight = 1.0 / (np.sum(outer_star - inner_star))
inner_weight = 1.0 / np.sum(inner_star)
bfilter = (outer_weight * outer_star -
(outer_weight + inner_weight) * inner_star)
return bfilter
def fun_estrella_rot_vol(tam_base):
aux = morphology.star(tam_base / 3)
tam_aux = aux.shape
Salida_Base = np.zeros((tam_aux[0], tam_aux[0], tam_aux[0]))
# I create a star in the center of the volume, wich must be a cube
Salida_Base[:, :, tam_base / 2] = morphology.star(tam_base / 3)
Salida_aux = Salida_Base
# Now I rotate it over its X axis
for i in range(0, 360, 1):
Salida_Base = Salida_Base + fun_rotar_vol(Salida_aux, 0, i, 0)
# Saturate output...
Salida_Base[np.where(Salida_Base > 1)] = 1
return Salida_Base
def _threshold_downsample_lvl(self, lvl_img):
"""Generates thresholded overview image.
Args:
wsi: An openslide image instance.
Returns:
A 2D numpy array of binary image
"""
# calculate the overview level size and retrieve the image
downsample_img = lvl_img.convert('HSV')
downsample_img = np.array(downsample_img)
# dilate image and then threshold the image
schannel = downsample_img[:, :, 1]
schannel = dilation(schannel, star(3))
schannel = ndimage.gaussian_filter(schannel, sigma=(5, 5), order=0)
threshold_global = threshold_otsu(schannel)
schannel[schannel > threshold_global] = 255
schannel[schannel <= threshold_global] = 0
#import scipy.misc # check the result
#scipy.misc.imsave('outfile.jpg', schannel)
return schannel
def erosion(self):
image = self.image
se = star(5)
ero = morphology.erosion(image, se)
self.plotResult(ero, 'Erosion')
cv2.imwrite('./Results/{}-erosion-star5.png'.format(self.name_file), ero)
def starMask(maskImg, star_size):
boxsize = maskImg.get_xsize()
maskArray = EMNumPy.em2numpy(maskImg)
if (boxsize <= star_size):
print "ERROR: star size is larger than the boxsize of particles."
sys.exit()
#from skimage.morphology import star
#Generates a star shaped structuring element that has 8 vertices and is an overlap of square of size 2*a + 1 with its 45 degree rotated version.
#The slanted sides are 45 or 135 degrees to the horizontal axis.
starArray = star(star_size, dtype=np.uint8)
m, n = starArray.shape
assert m==n
if (m%2 == 0):
pad_before = (boxsize - m)/2
pad_after = (boxsize - m)/2
else:
pad_before = (boxsize - m)/2
pad_after = (boxsize - m)/2+1
starArrayPad = np.pad(starArray, (pad_before, pad_after), mode='constant')
starImg = EMNumPy.numpy2em(starArrayPad)
return starImg
def _threshold_downsample_level(self, img):
"""Generates thresholded overview image.
Args:
wsi: An openslide image instance.
Returns:
A 2D numpy array of binary image
"""
# calculate the overview level size and retrieve the image
img_hsv = img.convert('HSV')
img_hsv_np = np.array(img_hsv)
# dilate image and then threshold the image
schannel = img_hsv_np[:, :, 1]
mask = np.zeros(schannel.shape)
schannel = dilation(schannel, star(3))
schannel = ndimage.gaussian_filter(schannel, sigma=(5, 5), order=0)
threshold_global = threshold_otsu(schannel)
# schannel[schannel > threshold_global] = 255
# schannel[schannel <= threshold_global] = 0
mask[schannel > threshold_global] = SELECTED
mask[schannel <= threshold_global] = BACKGROUND
# import scipy.misc # check the result
# scipy.misc.imsave('outfile.jpg', schannel)
return mask
def create_mask(img):
mask = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
mask = normalize(mask, 0.28, 98)
mask[mask[:, :] > 0.0] = 1
mask = erosion(mask, star(9))
mask = erosion(mask, disk(9))
return invert(mask)
def seg(img):
img_np = np.asarray(img)
img_np_g = img_np[:, :, 1]
shape = img_np_g.shape
mask = np.ones(shape).astype(np.uint8)
searched = np.zeros((shape)).astype(np.uint8)
coor = []
init_val = 0
def inRange(val):
return val >= init_val - 10 and val <= init_val + 10
def addSeed_initVal():
sums = 0
for idx in range(shape[0]):
coor.append({'x': idx, 'y': 0})
searched[idx, 0] = 1
sums += img_np_g[idx, 0]
return sums / shape[0]
def isPixel(x, y):
return (x >= 0 and x < shape[0]) and (y >= 0 and y < shape[1])
def deal(x, y):
if isPixel(x, y) and not searched[x, y] and inRange(img_np_g[x, y]):
coor.append({'x': x, 'y': y})
searched[x, y] = 1
mask[x, y] = 0
init_val = addSeed_initVal()
print('init val: %d' % init_val)
while coor != []:
x = coor[0]['x']
y = coor[0]['y']
if x == 0: deal(x, y)
del coor[0]
deal(x + 1, y)
deal(x, y + 1)
deal(x - 1, y)
deal(x, y - 1)
mask = opening(mask, star(5))
mask = erosion(mask, star(3))
return mask
def Dilation(img, dil=1, device=None):
bs = img.shape[0]
img = img.detach().cpu().numpy()
img_dil = np.zeros_like(img)
for i in range(bs):
img_dil[i, 0] = binary_dilation(img[i, 0], selem=star(dil))
return torch.tensor(img_dil).to(device) if device else torch.tensor(
img_dil)
def threshold_segmentation(img):
# calculate the overview level size and retrieve the image
img_hsv = img.convert('HSV')
img_hsv_np = np.array(img_hsv)
# dilate image and then threshold the image
schannel = img_hsv_np[:, :, 1]
mask = np.zeros(schannel.shape)
schannel = dilation(schannel, star(3))
schannel = ndimage.gaussian_filter(schannel, sigma=(5, 5), order=0)
threshold_global = threshold_otsu(schannel)
mask[schannel > threshold_global] = FOREGROUND
mask[schannel <= threshold_global] = BACKGROUND
return mask
def objects():
from skimage.morphology import (square, rectangle, diamond, disk, cube,
octahedron, ball, octagon, star)
from mpl_toolkits.mplot3d import Axes3D
# Generate 2D and 3D structuring elements.
struc_2d = {
"square(15)": square(15),
"rectangle(15, 10)": rectangle(15, 10),
"diamond(7)": diamond(7),
"disk(7)": disk(7),
"octagon(7, 4)": octagon(7, 4),
"star(5)": star(5)
}
struc_3d = {
"cube(11)": cube(11),
"octahedron(5)": octahedron(5),
"ball(5)": ball(5)
}
# Visualize the elements.
fig = plt.figure(figsize=(8, 8))
idx = 1
for title, struc in struc_2d.items():
ax = fig.add_subplot(3, 3, idx)
ax.imshow(struc, cmap="Paired", vmin=0, vmax=12)
for i in range(struc.shape[0]):
for j in range(struc.shape[1]):
ax.text(j, i, struc[i, j], ha="center", va="center", color="w")
ax.set_axis_off()
ax.set_title(title)
idx += 1
for title, struc in struc_3d.items():
ax = fig.add_subplot(3, 3, idx, projection=Axes3D.name)
ax.voxels(struc)
ax.set_title(title)
idx += 1
fig.tight_layout()
plt.show()
def se(self):
fig = plt.figure(figsize=(10, 5))
a = fig.add_subplot(1, 3, 1)
plt.imshow(disk(5), cmap=plt.cm.gray)
a.set_title('Disk 5px ')
plt.axis('off')
a = fig.add_subplot(1, 3, 2)
plt.imshow(square(5), cmap=plt.cm.gray)
a.set_title('Square 5px')
plt.axis('off')
a = fig.add_subplot(1, 3, 3)
plt.imshow(star(5), cmap=plt.cm.gray)
a.set_title('Star 5px')
plt.axis('off')
plt.tight_layout()
plt.savefig('./Results/se.png')
plt.show()
def task1():
img = mimg.imread("bw1.bmp")
new_img1 = binary_erosion(img, selem=square(width=30))
new_img2 = binary_erosion(img, selem=rectangle(width=30, height=20))
new_img3 = binary_erosion(img, selem=diamond(radius=5))
new_img4 = binary_erosion(img, selem=disk(radius=15))
new_img5 = binary_erosion(img, selem=star(a=10))
new_img6 = binary_erosion(img, selem=octagon(m=10, n=20))
new_img7 = binary_dilation(img, )
fig, ax = plt.subplots(1, 8)
show(ax[0], img, "original")
show(ax[1], new_img1, "BE square")
show(ax[2], new_img2, "BE rectangle")
show(ax[3], new_img3, "BE diamond")
show(ax[4], new_img4, "BE disk")
show(ax[5], new_img5, "BE star")
show(ax[6], new_img6, "BE octagon")
show(ax[7], new_img2, "binary_dilation")
plt.show()
def __init__(self,
images_dir,
masks_dir,
img_transform,
mask_transform,
test=False,
sample_size=(1024, 1024),
dil=star(0),
inv=False,
preprocessing_fn=None):
self.images_dir = images_dir
self.masks_dir = masks_dir
self.images_titles = sorted(os.listdir(self.images_dir))
self.masks_titles = sorted(os.listdir(self.masks_dir))
self.img_transform = img_transform
self.mask_transform = mask_transform
self.preprocessing_fn = preprocessing_fn
self.sample_size = sample_size
self.test = test
self.dil = dil
self.inv = inv
def generate_labels(mask_gt, mask_p, sigma=0.5, tr=1):
'''
Generate labels for discriminator input
'''
gt_dil = binary_dilation(mask_gt,selem=star(1))
skel_gt = make_skeleton(mask_gt, sigma=sigma, tr=tr)
T_0 = gt_dil * mask_p
labels0 = torch.zeros((8,8))
for i in range(8):
for j in range(8):
prop_patch = T_0[i*32:(i+1)*32, j*32:(j+1)*32]
patch = np.array(skel_gt[i*32:(i+1)*32, j*32:(j+1)*32], dtype=np.uint8)
paths = find_paths(patch)
labels0[i,j] = assing_label(prop_patch, paths)
labels = [labels0]
for i in range(3):
labels.append(generate_sublabels(labels[-1]))
return labels
def binarize_image(image):
edges = canny(image/255., sigma=0.001)
fullim = closing(edges, selem=star(1))
filled_im = binary_fill_holes(fullim)
clean_im2 = remove_small_objects(filled_im, min_size=350)
# implementation of watershed
padw = 150
cleanpad = pad(clean_im2, ((padw, padw),), mode='constant')
distance = ndi.distance_transform_edt(cleanpad)
local_maxi = peak_local_max(distance, indices=False,
footprint=np.ones((90, 90)),
labels=cleanpad)
markers = ndi.label(local_maxi)[0]
labels = watershed(-distance, markers, mask=cleanpad)
labels = labels[padw:-padw, padw:-padw]
label_edge = scharr(labels)
label_edge = label_edge < 0.0000000000001
split_cells = np.logical_and(label_edge, clean_im2)
split_cells = remove_small_objects(split_cells, min_size=350)
return split_cells
def find_objects(imgs, masks, filenames):
for i, img in enumerate(imgs):
temp = rgb2gray(img)
edges = canny(temp, mask=masks[i], sigma=2)
labeled_image, num_labels = label(edges, return_num=True)
remove_obj = remove_small_objects(labeled_image)
boundaries = find_boundaries(remove_obj)
temp = ndi.binary_closing(boundaries, star(1))
temp = ndi.binary_fill_holes(temp)
labeled_image, num_labels = label(temp, return_num=True)
remove_obj = remove_small_objects(labeled_image, 1000)
remove_obj, num_labels = label(remove_obj, return_num=True)
regions = regionprops(remove_obj)
remove_obj = ndi.binary_erosion(remove_obj, square(2))
remove_obj = ndi.binary_erosion(remove_obj, disk(2))
# additional removing for case, when small object were receive after erosion
remove_obj = remove_small_objects(remove_obj, 1000)
remove_obj, num_labels = label(remove_obj, return_num=True)
contours = find_contours(remove_obj, 0.9, fully_connected='high')
# Display the image and plot all contours found
fig, ax = plt.subplots()
ax.imshow(imgs[i], interpolation='nearest', cmap=plt.cm.gray)
for n, contour in enumerate(contours):
ax.plot(contour[:, 1], contour[:, 0], linewidth=1)
compact_value = regions[n].area / (regions[n].perimeter)**2
if compact_value > 0.07 and regions[n].solidity > 0.985:
continue
if compact_value > 0.06 and regions[
n].solidity > 0.985 and regions[n].eccentricity > 0.8:
continue
if regions[n].solidity > 0.95:
added_text = 'C'
tolerance_value = 7
else:
added_text = ''
tolerance_value = 5.5
res = approximate_polygon(contour, tolerance=tolerance_value)
text = 'P' + str(len(res) - 1) + added_text
coords = regions[n].centroid
ax.text(coords[1] - 10,
coords[0] - 10,
text,
style='italic',
color='red',
fontsize=8,
bbox={
'facecolor': 'white',
'alpha': 0.5,
'pad': 3
})
ax.plot(res[:, 1], res[:, 0], linewidth=2)
out_filename = filenames[i][:-4] + '_out.png'
fig.savefig(out_filename)
ax.axis('image')
ax.set_xticks([])
ax.set_yticks([])
plt.show()
128, 192, 0, 128, 64, 128, 128, 192, 128, 128, 0, 64, 0, 128, 64, 0, 0,
192, 0, 128, 192, 0, 0, 64, 128
]
zero_pad = 256 * 3 - len(palette)
for i in range(zero_pad):
palette.append(0)
selems = [
sm.square(7),
sm.square(15),
sm.square(23),
sm.disk(7),
sm.disk(15),
sm.disk(23),
sm.star(7),
sm.star(15),
sm.star(23)
]
def colorize_mask(mask):
# mask: numpy array of the mask
new_mask = Image.fromarray(mask.astype(np.uint8)).convert('P')
new_mask.putpalette(palette)
return new_mask
def make_dataset(mode):
assert mode in ['train', 'val', 'test']
from skimage.morphology import binary_erosion, binary_dilation, binary_opening, binary_closing, square, rectangle, disk, star
from skimage import io
import matplotlib.pyplot as plt
path = "images/lab5/bw2.bmp"
image = io.imread(path)
openingBin = []
closingBin = []
opening = []
closing = []
salems = [square(5), rectangle(3, 5), disk(3), star(3)]
for i in range(4):
# binary_opening
# binary_closing
openingBin.insert(i, binary_opening(image, salems[i]))
closingBin.insert(i, binary_closing(openingBin[i], salems[i]))
# opening
# closing
newImage = binary_erosion(image, salems[i])
newImage = binary_dilation(newImage, salems[i])
opening.insert(i, newImage)
newImage = binary_dilation(opening[i], salems[i])
newImage = binary_erosion(newImage, salems[i])
closing.insert(i, newImage)
plt.gray()
def create_mask(img):
img = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
img = normalize(img)
img = contrast(img, 0.0)
img = erosion(img, star(3))
return invert(img)
tamaño = 10
img = imread('circunferencias.png')
noisy_image = rgb2gray(img)
binaria = 0.25 <= noisy_image
binaria = ~binaria
# Erosion y dilatación
if opcion == 0:
erosionada = erosion(binaria, disk(tamaño))
imagen_final = dilation(erosionada, disk(tamaño))
if opcion == 1:
erosionada = erosion(binaria, octagon(tamaño, int(tamaño / 2)))
imagen_final = dilation(erosionada, octagon(tamaño, int(tamaño / 2)))
if opcion == 2:
erosionada = erosion(binaria, square(tamaño))
imagen_final = dilation(erosionada, square(tamaño))
if opcion == 3:
erosionada = erosion(binaria, star(tamaño))
imagen_final = dilation(erosionada, star(tamaño))
#Gaurdado de imagenes
plt.imshow(binaria, cmap='gray', vmin=0, vmax=1)
plt.title('Binaria')
plt.show()
plt.imshow(erosionada, cmap='gray', vmin=0, vmax=1)
plt.title('Tratada')
plt.show()
plt.imshow(imagen_final, cmap='gray', vmin=0, vmax=1)
plt.title('Tratada')
plt.show()
cv2.imwrite('imagen.png', imagen_final)
max(0, y - box_size):y + box_size,
max(0, x - box_size):x + box_size]) #copy is critical
out[out != val] = 0
return out.astype('uint8')
if __name__ == '__main__':
#goal is to generate noise, ask if objects are linear or spherical and exclude based on some feature
dims = (1, 500, 500, 500)
#choice of obejct
selem = ball(9)
selem = cube(9)
selem = cylinder(9, 9)
selem = np.asarray([star(9) for xx in range(9)])
#dilate
src = dilate_with_element(
generate_random_points(dims, numpoints=20)[0], selem)
lbl = ndi.label(src)
centers = ndi.measurements.center_of_mass(src, lbl[0],
range(1, lbl[1] + 1))
plt.imshow(np.max(src, 0))
plt.imshow(np.max(lbl[0], 0))
##
lbl_vol = np.copy(lbl[0])
lbl_vol[lbl[0] > 0] = 1
sitk.Show(sitk.GetImageFromArray(lbl_vol))
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from skimage.morphology import (square, rectangle, diamond, disk, cube,
octahedron, ball, octagon, star)
# Generate 2D and 3D structuring elements.
struc_2d = {
"square(15)": square(15),
"rectangle(15, 10)": rectangle(15, 10),
"diamond(7)": diamond(7),
"disk(7)": disk(7),
"octagon(7, 4)": octagon(7, 4),
"star(5)": star(5)
}
struc_3d = {
"cube(11)": cube(11),
"octahedron(5)": octahedron(5),
"ball(5)": ball(5)
}
# Visualize the elements.
fig = plt.figure(figsize=(8, 8))
idx = 1
for title, struc in struc_2d.items():
ax = fig.add_subplot(3, 3, idx)
ax.imshow(struc, cmap="Paired", vmin=0, vmax=12)
def dilation(self):
image = self.image
se = star(5)
dil = morphology.dilation(image, se)
self.plotResult(dil, 'Dilation')
def element(self) -> np.array:
return morphology.star(self.a)
plt.imshow(np.hstack([255 - img, 255 - img_e, 255 - img_d]), cmap='gray')
plt.title(
"disk(5), iteration: " + str(i + 1), {
'fontsize': 28,
'fontweight': 'bold',
'verticalalignment': 'baseline',
'horizontalalignment': 'center'
})
plt.axis('off')
plt.show()
img_e = img.copy()
img_d = img.copy()
for i in range(0, 3):
img_e = erosion(img_e.copy(), star(5))
img_d = dilation(img_d.copy(), star(5))
plt.imshow(np.hstack([255 - img, 255 - img_e, 255 - img_d]), cmap='gray')
plt.title(
"star(5), iteration: " + str(i + 1), {
'fontsize': 28,
'fontweight': 'bold',
'verticalalignment': 'baseline',
'horizontalalignment': 'center'
})
plt.axis('off')
plt.show()
img_e = img.copy()
img_d = img.copy()
for i in range(0, 3):
def _seg_dfs(self, img):
img_np = np.asarray(img)
img_np_g = img_np[:, :, 1]
shape = img_np_g.shape
mask = np.ones(shape).astype(np.uint8) * SELECTED
searched = np.zeros((shape)).astype(np.bool)
coor = []
init_val = 0
def inRange(val):
return val >= init_val - 10 and val <= init_val + 10
def addSeed_initVal():
val1 = img_np_g[:, 0].mean()
val2 = img_np_g[0, :].mean()
val3 = img_np_g[:, shape[1]-1].mean()
val4 = img_np_g[shape[0]-1, 0].mean()
val = np.max((val1, val2, val3, val4))
for idx in range(shape[0]):
# L
coor.append({'x': idx, 'y': 0})
searched[idx, 0] = True
# R
coor.append({'x': idx, 'y': shape[1]-1})
searched[idx, shape[1]-1] = True
for idx in range(shape[1]):
# U
coor.append({'x': 0, 'y': idx})
searched[0, idx] = True
# D
coor.append({'x': shape[0]-1, 'y': idx})
searched[shape[0]-1, idx] = True
return val
def isPixel(x, y):
return (x >= 0 and x < shape[0]) and (y >= 0 and y < shape[1])
def deal(x, y):
if isPixel(x, y) and not searched[x, y] and inRange(img_np_g[x, y]):
coor.append({'x': x, 'y': y})
searched[x, y] = True
mask[x, y] = BACKGROUND
init_val = addSeed_initVal()
# print('init val: %d' % init_val)
while coor != []:
x = coor[0]['x']
y = coor[0]['y']
if x == 0 or y == 0\
or x == shape[0]-1 or y == shape[1]-1:
deal(x, y)
del coor[0]
deal(x + 1, y)
deal(x, y + 1)
deal(x - 1, y)
deal(x, y - 1)
mask = opening(mask, star(5))
# mask = erosion(mask, star(3))
mask = dilation(mask, star(3))
return mask
img = sk.io.imread('teeth.jpg', True)
grey = img.copy()
img_t = cv2.threshold(255*grey, 160, 170, cv2.THRESH_BINARY_INV)[1]
img_tmp = 255 -img_t
plt.axis('off')
plt.imshow(img_tmp, cmap='gray')
plt.show()
img_e = binary_dilation(img_t, rectangle(2,3))
img_tmp = 255- 255*img_e
plt.imshow(img_tmp, cmap='gray')
plt.show()
img_e = binary_closing(img_e, rectangle(8,2))
img_tmp = 255- 255*img_e
plt.imshow(img_tmp, cmap='gray')
plt.show()
img_e = binary_dilation(img_e, octagon(10,2))
img_tmp = 255- 255*img_e
plt.imshow(img_tmp, cmap='gray')
plt.show()
img_e = binary_dilation(img_e, star(8))
img_tmp = 255- 255*img_e
plt.imshow(img_tmp, cmap='gray')
plt.show()
for i in range(3):
img_e = binary_erosion(img_e, star(3 + i))
img_e = 255- 255*img_e
plt.imshow(img_e, cmap='gray')
plt.axis('off')
plt.show()