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Original image 1
Original image 2
I am trying to match two microscopy images (please see the attached file). However, the matches are horrible and the homography matrix produces an unacceptable result. Is there a way to improve this registration?
import cv2 # Imports the Open CV2 module for image manipulation.
import numpy as np # Imports the numpy module for numerical manipulation.
from tkinter import Tk # Imports tkinter for the creation of a graphic user interface.
from tkinter.filedialog import askopenfilename # Imports the filedialog window from tkinter
Tk().withdraw()
filename1 = askopenfilename(title='Select the skewed file')
Tk().withdraw()
filename2 = askopenfilename(title='Select the original file')
img1 = cv2.imread(filename1)
img2 = cv2.imread(filename2)
img1 = cv2.cvtColor(img1, cv2.COLOR_BGR2GRAY)
img2 = cv2.cvtColor(img2, cv2.COLOR_BGR2GRAY)
orb = cv2.ORB_create(nfeatures=10000)
kp1, des1 = orb.detectAndCompute(img1, None)
kp2, des2 = orb.detectAndCompute(img2, None)
matcher = cv2.DescriptorMatcher_create(cv2.DESCRIPTOR_MATCHER_BRUTEFORCE_HAMMING)
matches = matcher.match(des1, des2, None)
matches = sorted(matches, key = lambda x:x.distance)
points1 = np.zeros((len(matches), 2), dtype=np.float32)
points2 = np.zeros((len(matches), 2), dtype=np.float32)
for i, match in enumerate(matches):
points1[i, :] = kp1[match.queryIdx].pt
points2[i, :] = kp2[match.trainIdx].pt
h, mask = cv2.findHomography(points1, points2, cv2.RANSAC)
height, width = img2.shape
im1Reg = cv2.warpPerspective(img1, h, (width, height))
img3 = cv2.drawKeypoints(img1, kp1, None, flags=0)
img4 = cv2.drawKeypoints(img2, kp2, None, flags=0)
img5 = cv2.drawMatches(img1, kp1, img2, kp2, matches[:10], None)
img = np.dstack((im1Reg, img2, im1Reg))
cv2.imshow("Shifted", img3)
cv2.imshow("Original", img4)
cv2.imshow("Matches", img5)
cv2.imshow("Registered", im1Reg)
cv2.imshow("Merged", img)
cv2.waitKey(0)
Image showing the matches I get
(I may be wrong, since haven't dealt with microscopy image processing and there must exist commonly spread ways to solve typical problems in the area, you should investigate this area if it's not a toy project).
In my opinion you should try another decision to solve your problem instead of using any kind of point-feature-based image descriptors (ORB, SURF etc.).
First of all, not all of them provide subpixel accuracy you may need in processing microscopy images. But the main reason is the math behind that descriptors. Refer to any CV book or paper.
Here is the link to ORB-descriptor paper. Notice images authors use for matching detected points. Good points are one on edges and corners of the image so it's can be used to match objects of sharp and outstanding shape.
Well-known example:
Matched points are on letters (unique shape) and textured drawing.
Try to detect plain green textbook (without any letters and anything on its cover) with this tool and you will fail.
So I think that your images are not one can be processed this way (since objects are not sharp in shape, not textured and very close to each other). It would be hard even for man's eye to match similar circles (in case of less obvious example, e.g. shift one view left/right a little).
But what I notice at glance, your image can be greatly described by circles on it. Hough-based circle detection is much easier (both for understanding and computing) and what is really important, it can give almost 100% accuracy on such images. You can easily operate with circles number, size, position etc.
Though, microscopy CV is a separate area with its own common tools to use and there might be lots of pros and cons to use Hough or something else. But at first glance it seemed to be much more accurate choose than point features description.
i've been trying to match a scanned formular with its empty template. The goal is to rotate and scale it to match the template.
Source (left), template (right)
Match (left), Homography warp (right)
The template does not contain any very specific logo, fixation cross or rectangular frame that would conveniently help me with feature or pattern matching. Even worse, the scanned formular can be skewed, altered and contains handwritten signatures and stamps.
My approach, after unsuccessfully testing ORB feature matching, was to concentrate on the shape of the formular (lines and column).
The pictures I provide here are obtained by reconstituting lines after a segment detection (LSD) with a certain minimum size. Most of what remains for source and template is the document layout itself.
In the following script (that should work out of the box along with pictures), I attempt to do ORB feature matching, but fail to make it work because it is concentrating on edges and not on the document layout.
import cv2 # using opencv-python v3.4
import numpy as np
from imutils import resize
# alining image using ORB descriptors, then homography warp
def align_images(im1, im2,MAX_MATCHES=5000,GOOD_MATCH_PERCENT = 0.15):
# Detect ORB features and compute descriptors.
orb = cv2.ORB_create(MAX_MATCHES)
keypoints1, descriptors1 = orb.detectAndCompute(im1, None)
keypoints2, descriptors2 = orb.detectAndCompute(im2, None)
# Match features.
matcher = cv2.DescriptorMatcher_create(cv2.DESCRIPTOR_MATCHER_BRUTEFORCE_HAMMING)
matches = matcher.match(descriptors1, descriptors2, None)
# Sort matches by score
matches.sort(key=lambda x: x.distance, reverse=False)
# Remove not so good matches
numGoodMatches = int(len(matches) * GOOD_MATCH_PERCENT)
matches = matches[:numGoodMatches]
# Draw top matches
imMatches = cv2.drawMatches(im1, keypoints1, im2, keypoints2, matches, None)
# Extract location of good matches
points1 = np.zeros((len(matches), 2), dtype=np.float32)
points2 = np.zeros((len(matches), 2), dtype=np.float32)
for i, match in enumerate(matches):
points1[i, :] = keypoints1[match.queryIdx].pt
points2[i, :] = keypoints2[match.trainIdx].pt
# Find homography
h, mask = cv2.findHomography(points1, points2, cv2.RANSAC)
# Use homography
if len(im2.shape) == 2:
height, width = im2.shape
else:
height, width, channels = im2.shape
im1Reg = cv2.warpPerspective(im1, h, (width, height))
return im1Reg, h, imMatches
template_fn = './stack/template.jpg'
image_fn = './stack/image.jpg'
im = cv2.imread(image_fn, cv2.IMREAD_GRAYSCALE)
template = cv2.imread(template_fn, cv2.IMREAD_GRAYSCALE)
# aligh images
imReg, h, matches = align_images(template,im)
# display output
cv2.imshow('im',im)
cv2.imshow('template',template)
cv2.imshow('matches',matches)
cv2.imshow('result',imReg)
cv2.waitKey(0)
cv2.destroyAllWindows()
Is there any way to make the pattern matching algorithm work on the image on the left (source)? (another idea was to leave only lines intersections)
Alternatively, I have been trying to do scale and rotation invariant pattern matching for loops and while keeping max correlation, but it is way too resource consuming and not very reliable.
I'm therefore looking for hints in the right direction using opencv.
SOLUTION
The issue was about reducing the image to what really matters: the layout.
Also, ORB was not appropriate since it is not as robust (rotation and size invariant) as SIFT and AKAZE are.
I proceeded as follows:
convert the images to black and white
use line segment detection and filter lines shorter than 1/60th of the width
reconstruct the image from segments (line width does not have a big impact)
(optional: resize the pictures to speed up the rest)
apply a Gaussian transformation on the line reconstruction, 1/25th of the width
detect and match features using SIFT (patented) or AKAZE (free) algorithm
find a homography and warp the source picture to match the template
Matches for AKAZE
Matches for SIFT
I noted:
the layout of the template has to match, otherwise it will only stick to what it recognizes
line detection is better with higher resolution, then downsizing is possible since Gaussian are applied
SIFT produces more features and seems more reliable than AKAZE
I have a 512x512 image which gave 6109 SIFT keypoints.
Now, I rotated it then I got 6070 SIFT keypoints.
I tried following
import cv2
import numpy as np
np.set_printoptions(threshold=np.nan)
img = cv2.imread('home.jpg')
gray= cv2.cvtColor(img,cv2.COLOR_BGR2GRAY)
sift = cv2.xfeatures2d.SIFT_create()
kp,des = sift.detectAndCompute(gray,None)
print('kp',len(kp))
print('des',des.shape)
for i in range(len(kp)):
print('x ',kp[i].pt[0])
print('y ',kp[i].pt[1])
print('size',kp[i].size)
print('response',kp[i].response)
print('descriptor',np.sort(des[i]))
print('\n')
Send the output to a text file.
Now I did the same with rotated image.
You must have noticed that I am sorting the 128 value descriptor before writing it in file so that on rotation if order of values changes in descriptor then still there will be match.
My conclusion is that among those 12179 descriptors(6070+6109), only two were identical. Rest differed atleast by one number,usually by many I saw.
Can you suggest a python code that will show the x,y coordinates of correspondences between the two images ?
Also, there is something fundamentally wrong i must be doing here in comparing descriptors.Please point that out .
Thanks
Why are you sorting the descriptor? 128-dimensional descriptor is something that describes the feature keypoint(as the name suggests). By sorting you are essentially losing the description of your key points/features.
Searching for an identical descriptor is not a good way to find correspondence. You have to find descriptors with minimum Euclidean distance(or some other distance measure), to get correspondence. There are many algorithms for that in opencv like Brute force matches or knn based matcher or flann based matcher. YOu have to give the descriptor as input to these matcher(do not modify your decsriptor values by sorting or some other opertation)
For example
kp1, des1 = sift.detectAndCompute(img1,None)
kp2, des2 = sift.detectAndCompute(img2,None)
# BFMatcher with default params
bf = cv2.BFMatcher()
matches = bf.knnMatch(des1,des2, k=2)
matches will have index for correspondences and distance between those correspondences
You can get sort this matches based on matches.distance
and get x and y coordinate using matches.queryIdx and matches.trainIdx
you can get x and y location using kp1[matches[idx].trainIdx] and kp2[matches[idx].queryIdx]
this is implementation of details provided by Garvita Tiwari.
I am using python 2.7.12 with opencv 3.4.1
import cv2
import numpy as np
src_img = cv2.imread('src.jpg')
test_img = cv2.imread('test.jpg')
src_gray= cv2.cvtColor(src_img,cv2.COLOR_BGR2GRAY)
test_gray= cv2.cvtColor(test_img,cv2.COLOR_BGR2GRAY)
sift = cv2.xfeatures2d.SIFT_create()
src_kp,src_desc = sift.detectAndCompute(src_gray,None)
test_kp,test_desc = sift.detectAndCompute(test_gray,None)
bf = cv2.BFMatcher()
matches = bf.knnMatch(src_desc,test_desc, k=2)
good = []
for m,n in matches:
if m.distance < 0.75*n.distance:
good.append([m])
print 'so the correspondences are'
for i in range(len(good)):
print int(src_kp[good[i][0].queryIdx].pt[0]),int(src_kp[good[i][0].queryIdx].pt[1]) ,'->',int(test_kp[good[i][0].trainIdx].pt[0]) ,int(test_kp[good[i][0].trainIdx].pt[1])
I have to stitch two or more images together using python and openCV.
I found this code for finding keypoints and matches, but I don't know how to continue.
Help me please!
import numpy as np
import cv2
MIN_MATCH_COUNT = 10
img1 = cv2.imread('a.jpg',0) # queryImage
img2 = cv2.imread('b.jpg',0) # trainImage
# Initiate SIFT detector
sift = cv2.SIFT()
# find the keypoints and descriptors with SIFT
kp1, des1 = sift.detectAndCompute(img1,None)
kp2, des2 = sift.detectAndCompute(img2,None)
FLANN_INDEX_KDTREE = 0
index_params = dict(algorithm = FLANN_INDEX_KDTREE, trees = 5)
search_params = dict(checks = 50)
flann = cv2.FlannBasedMatcher(index_params, search_params)
matches = flann.knnMatch(des1,des2,k=2)
# store all the good matches as per Lowe's ratio test.
good = []
for m,n in matches:
if m.distance < 0.7*n.distance:
good.append(m)
Your question is not very clear, but I assume what you mean is that you have a bunch of images and you want to have opencv find the corresponding landmarks and then warp/scale each picture so that they can form one big image.
A method without using the stitcher class, basically looping over pictures and determining the best fitting one each iteration, is documented in this github code
One approach to image stitching consists of the following steps.
Firstly, as you've already figured out, you need a feature point detector and the some way to find correspondences between feature points on both images. It's typically a good idea to eliminate a lot of correspondences because they will likely contain a lot of noise. A super simple way to eliminate a lot of noise is to look for symmetry in the matches.
This is roughly what your code does up to this point.
Next, to stitch images together, you need to warp one of the images to match the perspective of the other image. This is done by estimating the homography using the correspondences. Because your correspondences will still likely contain a lot of noise, we typically use RANSAC to robustly estimate the homography.
A quick google search provides many examples of this being implemented.
I am just doing an example of feature detection in OpenCV. This example is shown below. It is giving me the following error
module' object has no attribute 'drawMatches'
I have checked the OpenCV Docs and am not sure why I'm getting this error. Does anyone know why?
import numpy as np
import cv2
import matplotlib.pyplot as plt
img1 = cv2.imread('box.png',0) # queryImage
img2 = cv2.imread('box_in_scene.png',0) # trainImage
# Initiate SIFT detector
orb = cv2.ORB()
# find the keypoints and descriptors with SIFT
kp1, des1 = orb.detectAndCompute(img1,None)
kp2, des2 = orb.detectAndCompute(img2,None)
# create BFMatcher object
bf = cv2.BFMatcher(cv2.NORM_HAMMING, crossCheck=True)
# Match descriptors.
matches = bf.match(des1,des2)
# Draw first 10 matches.
img3 = cv2.drawMatches(img1,kp1,img2,kp2,matches[:10], flags=2)
plt.imshow(img3),plt.show()
Error:
Traceback (most recent call last):
File "match.py", line 22, in <module>
img3 = cv2.drawMatches(img1,kp1,img2,kp2,matches[:10], flags=2)
AttributeError: 'module' object has no attribute 'drawMatches'
I am late to the party as well, but I installed OpenCV 2.4.9 for Mac OS X, and the drawMatches function doesn't exist in my distribution. I've also tried the second approach with find_obj and that didn't work for me either. With that, I decided to write my own implementation of it that mimics drawMatches to the best of my ability and this is what I've produced.
I've provided my own images where one is of a camera man, and the other one is the same image but rotated by 55 degrees counterclockwise.
The basics of what I wrote is that I allocate an output RGB image where the amount of rows is the maximum of the two images to accommodate for placing both of the images in the output image and the columns are simply the summation of both the columns together. Be advised that I assume that both images are grayscale.
I place each image in their corresponding spots, then run through a loop of all of the matched keypoints. I extract which keypoints matched between the two images, then extract their (x,y) coordinates. I draw circles at each of the detected locations, then draw a line connecting these circles together.
Bear in mind that the detected keypoint in the second image is with respect to its own coordinate system. If you want to place this in the final output image, you need to offset the column coordinate by the amount of columns from the first image so that the column coordinate is with respect to the coordinate system of the output image.
Without further ado:
import numpy as np
import cv2
def drawMatches(img1, kp1, img2, kp2, matches):
"""
My own implementation of cv2.drawMatches as OpenCV 2.4.9
does not have this function available but it's supported in
OpenCV 3.0.0
This function takes in two images with their associated
keypoints, as well as a list of DMatch data structure (matches)
that contains which keypoints matched in which images.
An image will be produced where a montage is shown with
the first image followed by the second image beside it.
Keypoints are delineated with circles, while lines are connected
between matching keypoints.
img1,img2 - Grayscale images
kp1,kp2 - Detected list of keypoints through any of the OpenCV keypoint
detection algorithms
matches - A list of matches of corresponding keypoints through any
OpenCV keypoint matching algorithm
"""
# Create a new output image that concatenates the two images together
# (a.k.a) a montage
rows1 = img1.shape[0]
cols1 = img1.shape[1]
rows2 = img2.shape[0]
cols2 = img2.shape[1]
# Create the output image
# The rows of the output are the largest between the two images
# and the columns are simply the sum of the two together
# The intent is to make this a colour image, so make this 3 channels
out = np.zeros((max([rows1,rows2]),cols1+cols2,3), dtype='uint8')
# Place the first image to the left
out[:rows1,:cols1] = np.dstack([img1, img1, img1])
# Place the next image to the right of it
out[:rows2,cols1:] = np.dstack([img2, img2, img2])
# For each pair of points we have between both images
# draw circles, then connect a line between them
for mat in matches:
# Get the matching keypoints for each of the images
img1_idx = mat.queryIdx
img2_idx = mat.trainIdx
# x - columns
# y - rows
(x1,y1) = kp1[img1_idx].pt
(x2,y2) = kp2[img2_idx].pt
# Draw a small circle at both co-ordinates
# radius 4
# colour blue
# thickness = 1
cv2.circle(out, (int(x1),int(y1)), 4, (255, 0, 0), 1)
cv2.circle(out, (int(x2)+cols1,int(y2)), 4, (255, 0, 0), 1)
# Draw a line in between the two points
# thickness = 1
# colour blue
cv2.line(out, (int(x1),int(y1)), (int(x2)+cols1,int(y2)), (255,0,0), 1)
# Show the image
cv2.imshow('Matched Features', out)
cv2.waitKey(0)
cv2.destroyWindow('Matched Features')
# Also return the image if you'd like a copy
return out
To illustrate that this works, here are the two images that I used:
I used OpenCV's ORB detector to detect the keypoints, and used the normalized Hamming distance as the distance measure for similarity as this is a binary descriptor. As such:
import numpy as np
import cv2
img1 = cv2.imread('cameraman.png', 0) # Original image - ensure grayscale
img2 = cv2.imread('cameraman_rot55.png', 0) # Rotated image - ensure grayscale
# Create ORB detector with 1000 keypoints with a scaling pyramid factor
# of 1.2
orb = cv2.ORB(1000, 1.2)
# Detect keypoints of original image
(kp1,des1) = orb.detectAndCompute(img1, None)
# Detect keypoints of rotated image
(kp2,des2) = orb.detectAndCompute(img2, None)
# Create matcher
bf = cv2.BFMatcher(cv2.NORM_HAMMING, crossCheck=True)
# Do matching
matches = bf.match(des1,des2)
# Sort the matches based on distance. Least distance
# is better
matches = sorted(matches, key=lambda val: val.distance)
# Show only the top 10 matches - also save a copy for use later
out = drawMatches(img1, kp1, img2, kp2, matches[:10])
This is the image I get:
To use with knnMatch from cv2.BFMatcher
I'd like to make a note where the above code only works if you assume that the matches appear in a 1D list. However, if you decide to use the knnMatch method from cv2.BFMatcher for example, what is returned is a list of lists. Specifically, given the descriptors in img1 called des1 and the descriptors in img2 called des2, each element in the list returned from knnMatch is another list of k matches from des2 which are the closest to each descriptor in des1. Therefore, the first element from the output of knnMatch is a list of k matches from des2 which were the closest to the first descriptor found in des1. The second element from the output of knnMatch is a list of k matches from des2 which were the closest to the second descriptor found in des1 and so on.
To make the most sense of knnMatch, you must limit the total amount of neighbours to match to k=2. The reason why is because you want to use at least two matched points for each source point available to verify the quality of the match and if the quality is good enough, you'll want to use these to draw your matches and show them on the screen. You can use a very simple ratio test (credit goes to David Lowe) to ensure that for a point, we see that the distance / dissimilarity in matching to the best point is much smaller than the distance / dissimilarity in matching to the second best point. We can capture this by finding the ratio of the distance of the best matched point to the second best matched point. The ratio should be small to illustrate that a point to its best matched point is unambiguous. If the ratio is close to 1, this means that both matches are equally as "good" and thus ambiguous so we should not include these. We can think of this as an outlier rejection technique. Therefore, to turn what is returned from knnMatch to what is required with the code I wrote above, iterate through the matches, use the above ratio test and check if it passes. If it does, add the first matched keypoint to a new list.
Assuming that you created all of the variables like you did before declaring the BFMatcher instance, you'd now do this to adapt the knnMatch method for using drawMatches:
# Create matcher
bf = cv2.BFMatcher(cv2.NORM_HAMMING, crossCheck=True)
# Perform KNN matching
matches = bf.knnMatch(des1, des2, k=2)
# Apply ratio test
good = []
for m,n in matches:
if m.distance / n.distance < 0.75: # Or you can do m.distance < 0.75 * n.distance
# Add the match for point m to the best
good.append(m)
# Or do a list comprehension
#good = [m for (m,n) in matches if m.distance < 0.75*n.distance]
# Now perform drawMatches
out = drawMatches(img1, kp1, img2, kp2, good)
As you iterate over the matches list, m and n should be the match between a point from des1 and its best match (m) and its second best match (n) both from des2. If we see that the ratio is small, we'll add this best match between the two points (m) to a final list. The ratio that I have, 0.75, is a parameter that needs tuning so if you're not getting good results, play around with this until you do. However, values between 0.7 to 0.8 are a good start.
I want to attribute the above modifications to user #ryanmeasel and the answer that these modifications were found is in his post: OpenCV Python : No drawMatchesknn function.
The drawMatches Function is not part of the Python interface.
As you can see in the docs, it is only defined for C++ at the moment.
Excerpt from the docs:
C++: void drawMatches(const Mat& img1, const vector<KeyPoint>& keypoints1, const Mat& img2, const vector<KeyPoint>& keypoints2, const vector<DMatch>& matches1to2, Mat& outImg, const Scalar& matchColor=Scalar::all(-1), const Scalar& singlePointColor=Scalar::all(-1), const vector<char>& matchesMask=vector<char>(), int flags=DrawMatchesFlags::DEFAULT )
C++: void drawMatches(const Mat& img1, const vector<KeyPoint>& keypoints1, const Mat& img2, const vector<KeyPoint>& keypoints2, const vector<vector<DMatch>>& matches1to2, Mat& outImg, const Scalar& matchColor=Scalar::all(-1), const Scalar& singlePointColor=Scalar::all(-1), const vector<vector<char>>& matchesMask=vector<vector<char> >(), int flags=DrawMatchesFlags::DEFAULT )
If the function had a Python interface, you would find something like this:
Python: cv2.drawMatches(img1, keypoints1, [...])
EDIT
There actually was a commit that introduced this function 5 months ago. However, it is not (yet) in the official documentation.
Make sure you are using the newest OpenCV Version (2.4.7).
For sake of completeness the Functions interface for OpenCV 3.0.0 will looks like this:
cv2.drawMatches(img1, keypoints1, img2, keypoints2, matches1to2[, outImg[, matchColor[, singlePointColor[, matchesMask[, flags]]]]]) → outImg
I know this question has an accepted answer that is correct, but if you are using OpenCV 2.4.8 and not 3.0(-dev), a workaround could be to use some functions from the included samples found in opencv\sources\samples\python2\find_obj
import cv2
from find_obj import filter_matches,explore_match
img1 = cv2.imread('../c/box.png',0) # queryImage
img2 = cv2.imread('../c/box_in_scene.png',0) # trainImage
# Initiate SIFT detector
orb = cv2.ORB()
# find the keypoints and descriptors with SIFT
kp1, des1 = orb.detectAndCompute(img1,None)
kp2, des2 = orb.detectAndCompute(img2,None)
# create BFMatcher object
bf = cv2.BFMatcher(cv2.NORM_HAMMING)#, crossCheck=True)
matches = bf.knnMatch(des1, trainDescriptors = des2, k = 2)
p1, p2, kp_pairs = filter_matches(kp1, kp2, matches)
explore_match('find_obj', img1,img2,kp_pairs)#cv2 shows image
cv2.waitKey()
cv2.destroyAllWindows()
This is the output image: