### Scale-Space Blob Detection

Implementing a Laplacian blob detector in python from scratch

Features generated from Harris Corner Detector are not invariant to scale. For feature tracking, we need features which are invariant to affine transformations. Laplacian blob detector is one of the basic methods which generates features that are invariant to scaling.

**The idea** of a Laplacian blob detector is to convolve the image with a “blob filter” at multiple scales and look for extrema of filter response in the resulting scale space.

**Blob Filter:**

This filter generated by double derivating Gaussian filter along x and y-axis and adding them. Above is also known as Laplacian of Gaussian.

The output of the LOG filter is maximum when there is a corner in an image.

We want to find the characteristic scale of the blob, by convolving the image with different sigmas. But as we increase the sigma the response of blob filter with image decreases due to which we might not able to find a better scale. To reduce this effect we multiply the LOG filter σ square. This process is known as scale normalization.

The Laplacian archives maximum response for the binary circle of radius r is at σ=1.414*r

Above are some of the basics of the blob filter. The whole process boils down to two steps

- Convolve image with scale-normalized Laplacian at several scales (different scales means different sigma)
- Find maxima of squared Laplacian response in scale-space

**Code for Laplacian Blob Detection**

The code has four main steps:

- Generation of LOG filters
- Convolving the images with Gaussian filters
- Finding the maximum peak
- Drawing the blobs.

**Generation of LOG filter**

import cv2

from pylab import *

import numpy as np

import matplotlib.pyplot as plt

img = cv2.imread("sunflowers.jpg",0) #gray scale conversion

from scipy import ndimage

from scipy.ndimage import filters

from scipy import spatial

k = 1.414

sigma = 1.0

img = img/255.0 #image normalization

def LoG(sigma):

#window size

n = np.ceil(sigma*6)

y,x = np.ogrid[-n//2:n//2+1,-n//2:n//2+1]

y_filter = np.exp(-(y*y/(2.*sigma*sigma)))

x_filter = np.exp(-(x*x/(2.*sigma*sigma)))

final_filter = (-(2*sigma**2) + (x*x + y*y) ) * (x_filter*y_filter) * (1/(2*np.pi*sigma**4))

return final_filter

LoG function takes sigma as input and generates a filter of size 6*sigma(best option).

**Convolving the images with Gaussian filters**

The images are convolved with different LOG filters

def LoG_convolve(img):

log_images = [] #to store responses

for i in range(0,9):

y = np.power(k,i)

sigma_1 = sigma*y #sigma

filter_log = LoG(sigma_1) #filter generation

image = cv2.filter2D(img,-1,filter_log) # convolving image

image = np.pad(image,((1,1),(1,1)),'constant') #padding

image = np.square(image) # squaring the response

log_images.append(image)

log_image_np = np.array([i for i in log_images]) # storing the #in numpy array

return log_image_np

log_image_np = LoG_convolve(img)

#print(log_image_np.shape)

To choose different sigma, I have multiplied sigma with k^i.The dimension of the log_image_np array will be z*image_height*image_width.where z represents the kth power that is multiplied to sigma.

In the above function, I have generated only 9 filters the plot of 9 filters are

**Finding the maximum peak**

def detect_blob(log_image_np):

co_ordinates = [] #to store co ordinates

(h,w) = img.shape

for i in range(1,h):

for j in range(1,w):

slice_img = log_image_np[:,i-1:i+2,j-1:j+2] #9*3*3 slice

result = np.amax(slice_img) #finding maximum

if result >= 0.03: #threshold

z,x,y = np.unravel_index(slice_img.argmax(),slice_img.shape)

co_ordinates.append((i+x-1,j+y-1,k**z*sigma)) #finding co-rdinates

return co_ordinates

co_ordinates = list(set(detect_blob(log_image_np)))

At each pixel 3×3 neighborhood is considered in all scales which gives the 9x3x3 matrix. The maximum peak of the matrix is given by the maximum value of the matrix.

For every pixel, there will be a maximum. But not all pixels contribute to blobs. So we need to eliminate them by thresholding the peaks. This threshold is found by trial and error method.

If the maximum value is greater than the threshold then the point is considered and coordinate is stored.

(z,x,y) is the coordinates of the sliced image so we need to change them to original image coordinates. After changing them we will store them in the co_ordinates list and plot them.

fig, ax = plt.subplots()

nh,nw = img.shape

count = 0

ax.imshow(img, interpolation='nearest',cmap="gray")

for blob in co_ordinates:

y,x,r = blob

c = plt.Circle((x, y), r*1.414, color='red', linewidth=1.5, fill=False)

ax.add_patch(c)

ax.plot()

plt.show()

The above code draws the blob at each point in the stored list.

Result

In the above image, we can find many blobs are overlapping. To reduce overlapped blobs we will find the area of overlap between blobs. If the area is greater than the threshold the blob with the smaller radius will be discarded.

#provided in scipy doucumentaion

def blob_overlap(blob1, blob2):

n_dim = len(blob1) - 1

root_ndim = sqrt(n_dim)

#print(n_dim)

# radius of two blobs

r1 = blob1[-1] * root_ndim

r2 = blob2[-1] * root_ndim

d = sqrt(np.sum((blob1[:-1] - blob2[:-1])**2))

#no overlap between two blobs

if d > r1 + r2:

return 0

# one blob is inside the other, the smaller blob must die

elif d <= abs(r1 - r2):

return 1

else:

#computing the area of overlap between blobs

ratio1 = (d ** 2 + r1 ** 2 - r2 ** 2) / (2 * d * r1)

ratio1 = np.clip(ratio1, -1, 1)

acos1 = math.acos(ratio1)

ratio2 = (d ** 2 + r2 ** 2 - r1 ** 2) / (2 * d * r2)

ratio2 = np.clip(ratio2, -1, 1)

acos2 = math.acos(ratio2)

a = -d + r2 + r1

b = d - r2 + r1

c = d + r2 - r1

d = d + r2 + r1

area = (r1 ** 2 * acos1 + r2 ** 2 * acos2 -0.5 * sqrt(abs(a * b * c * d)))

return area/(math.pi * (min(r1, r2) ** 2))

def redundancy(blobs_array, overlap):

sigma = blobs_array[:, -1].max()

distance = 2 * sigma * sqrt(blobs_array.shape[1] - 1)

tree = spatial.cKDTree(blobs_array[:, :-1])

pairs = np.array(list(tree.query_pairs(distance)))

if len(pairs) == 0:

return blobs_array

else:

for (i, j) in pairs:

blob1, blob2 = blobs_array[i], blobs_array[j]

if blob_overlap(blob1, blob2) > overlap:

if blob1[-1] > blob2[-1]:

blob2[-1] = 0

else:

blob1[-1] = 0

return np.array([b for b in blobs_array if b[-1] > 0])

co_ordinates = np.array(co_ordinates)

co_ordinates = redundancy(co_ordinates,0.5)

After removing overlapped blobs the output is

We can see that most of the blobs have been eliminated.

Link for the code in Github.

Thanks for reading. Any suggestions would be appreciated.

## 1 Comment

## Python Lover · January 23, 2020 at 1:20 pm

Awesome post! Keep up the great work! 🙂