I'm trying to implement a paper. In it I need to calculate the centre of gravity and second order moment of an image.
The equations of centre of gravity and second order moment are respectively given as:
Im having trouble trying to code this in Matlab ss from what I understand p(x,y) is the pixel of the image, but I'm having trouble what y represents and how would I implement in in the sum function. This is my implementation of the first equation but since I did not incorporate the y in there I'm sure the result given is wrong.
img = imread(path);
m = numel(img);
cog = sum(img(:))/m;
i think, m should be the maximum of y, because f2 is a function of x which means in Matlab it should be a vector.
try this code to implement f2:
img = magic(10)
m = 10;
temp = 0;
for y = 1:m
temp = temp+y*img(:,y);
%temp = temp+y*img(y,:); % depends on your image coordinates system
end
f2 = temp/m
Try the following code that uses vectorized anonymous functions.
% Read the image into an array (3 dimensions).
% Note: you may need to convert to doubles
img = im2double(imread(path));
% Get the size (may need to switch m and n).
[m, n, o] = size(img);
% Create y vector
y = 1:m;
% Create functions (not sure how you want to handle the RGB values).
f2 = #(x, p) sum(y.*p(x,:,1)/m);
f3 = #(x, p) sum(y.^2.*p(x,:,1)/(m^2));
% Call the functions
x = 10; % Some pixel x position
f2_result = f2(x, img);
f3_result = f3(x, img);
Note: I may have the x and y switched depending on the orientation of your image. If that's the case then switch things around like this:
[n, m, o] = size(img);
...
f2 = #(x, p) sum(y.*p(:,x)/m);
etc...
I'm not at work so I can't run the im2double function (don't have the library) but I think it will work.
Related
Currently I have been working on obtaining the length of a curve, with the following code I have managed to get the length of a curve present in an image.
test image one curve
Then I paste the code that I used to get the length of the curve of a simple image. What I did is the following:
I got the columns and rows of the image
I got the columns in x and the rows in y
I obtained the coefficients of the curve, based on the formula of the
parable
Build the equation
Implement the arc length formula to obtain the length of the curve
grayImage = imread(fullFileName);
[rows, columns, numberOfColorBands] = size(grayImage);
if numberOfColorBands > 1
grayImage = grayImage(:, :, 2); % Take green channel.
end
subplot(2, 2, 1);
imshow(grayImage, []);
% Get the rows (y) and columns (x).
[rows, columns] = find(binaryImage);
coefficients = polyfit(columns, rows, 2); % Gets coefficients of the formula.
% Fit a curve to 500 points in the range that x has.
fittedX = linspace(min(columns), max(columns), 500);
% Now get the y values.
fittedY = polyval(coefficients, fittedX);
% Plot the fitting:
subplot(2,2,3:4);
plot(fittedX, fittedY, 'b-', 'linewidth', 4);
grid on;
xlabel('X', 'FontSize', fontSize);
ylabel('Y', 'FontSize', fontSize);
% Overlay the original points in red.
hold on;
plot(columns, rows, 'r+', 'LineWidth', 2, 'MarkerSize', 10)
formula = poly2sym([coefficients(1),coefficients(2),coefficients(3)]);
% formulaD = vpa(formula)
df=diff(formula);
df = df^2;
f= (sqrt(1+df));
i = int(f,min(columns),max(columns));
j = double(i);
disp(j);
Now I have the image 2 which has n curves, I do not know how I can do to get the length of each curve
test image n curves
I suggest you to look at Hough Transformation:
https://uk.mathworks.com/help/images/hough-transform.html
You will need Image Processing Toolbox. Otherwise, you have to develop your own logic.
https://en.wikipedia.org/wiki/Hough_transform
Update 1
I had a two-hour thinking about your problem and I'm only able to extract the first curve. The problem is to locate the starting points of the curves. Anyway, here is the code I come up with and hopefully will give you some ideas for further development.
clc;clear;close all;
grayImage = imread('2.png');
[rows, columns, numberOfColorBands] = size(grayImage);
if numberOfColorBands > 1
grayImage = grayImage(:, :, 2); % Take green channel.
end
% find edge.
bw = edge(grayImage,'canny');
imshow(bw);
[x, y] = find(bw == 1);
P = [x,y];
% For each point, find a point that is of distance 1 or sqrt(2) to it, i.e.
% find its connectivity.
cP = cell(1,length(x));
for i = 1:length(x)
px = x(i);
py = y(i);
dx = x - px*ones(size(x));
dy = y - py*ones(size(y));
distances = (dx.^2 + dy.^2).^0.5;
cP{i} = [x(distances == 1), y(distances == 1);
x(distances == sqrt(2)), y(distances == sqrt(2))];
end
% pick the first point and a second point that is connected to it.
fP = P(1,:);
Q(1,:) = fP;
Q(2,:) = cP{1}(1,:);
m = 2;
while true
% take the previous point from point set Q, when current point is
% Q(m,1)
pP = Q(m-1,:);
% find the index of the current point in point set P.
i = find(P(:,1) == Q(m,1) & P(:,2) == Q(m,2));
% Find the distances from the previous points to all points connected
% to the current point.
dx = cP{i}(:,1) - pP(1)*ones(length(cP{i}),1);
dy = cP{i}(:,2) - pP(2)*ones(length(cP{i}),1);
distances = (dx.^2 + dy.^2).^0.5;
% Take the farthest point as the next point.
m = m+1;
p_cache = cP{i}(find(distances==max(distances),1),:);
% Calculate the distance of this point to the first point.
distance = ((p_cache(1) - fP(1))^2 + (p_cache(2) - fP(2))^2).^0.5;
if distance == 0 || distance == 1
break;
else
Q(m,:) = p_cache;
end
end
% By now we should have built the ordered point set Q for the first curve.
% However, there is a significant weakness and this weakness prevents us to
% build the second curve.
Update 2
Some more work since the last update. I'm able to separate each curve now. The only problem I can see here is to have a good curve fitting. I would suggest B-spline or Bezier curves than polynomial fit. I think I will stop here and leave you to figure out the rest. Hope this helps.
Note that the following script uses Image Processing Toolbox to find the edges of the curves.
clc;clear;close all;
grayImage = imread('2.png');
[rows, columns, numberOfColorBands] = size(grayImage);
if numberOfColorBands > 1
grayImage = grayImage(:, :, 2); % Take green channel.
end
% find edge.
bw = edge(grayImage,'canny');
imshow(bw);
[x, y] = find(bw == 1);
P = [x,y];
% For each point, find a point that is of distance 1 or sqrt(2) to it, i.e.
% find its connectivity.
cP =[0,0]; % add a place holder
for i = 1:length(x)
px = x(i);
py = y(i);
dx = x - px*ones(size(x));
dy = y - py*ones(size(y));
distances = (dx.^2 + dy.^2).^0.5;
c = [find(distances == 1); find(distances == sqrt(2))];
cP(end+1:end+length(c),:) = [ones(length(c),1)*i, c];
end
cP (1,:) = [];% remove the place holder
% remove duplicates
cP = unique(sort(cP,2),'rows');
% seperating curves
Q{1} = cP(1,:);
for i = 2:length(cP)
cp = cP(i,:);
% search for points in cp in Q.
for j = 1:length(Q)
check = ismember(cp,Q{j});
if ~any(check) && j == length(Q) % if neither has been saved in Q
Q{end+1} = cp;
break;
elseif sum(check) == 2 % if both points cp has been saved in Q
break;
elseif sum(check) == 1 % if only one of the points exists in Q, add the one missing.
Q{j} = [Q{j}, cp(~check)];
break;
end
end
% review sets in Q, merge the ones having common points
for j = 1:length(Q)-1
q = Q{j};
for m = j+1:length(Q)
check = ismember(q,Q{m});
if sum(check)>=1 % if there are common points
Q{m} = [Q{m}, q(~check)]; % merge
Q{j} = []; % delete the merged set
break;
end
end
end
Q = Q(~cellfun('isempty',Q)); % remove empty cells;
end
% each cell in Q represents a curve. Note that points are not ordered.
figure;hold on;axis equal;grid on;
for i = 1:length(Q)
x_ = x(Q{i});
y_ = y(Q{i});
coefficients = polyfit(y_, x_, 3); % Gets coefficients of the formula.
% Fit a curve to 500 points in the range that x has.
fittedX = linspace(min(y_), max(y_), 500);
% Now get the y values.
fittedY = polyval(coefficients, fittedX);
plot(fittedX, fittedY, 'b-', 'linewidth', 4);
% Overlay the original points in red.
plot(y_, x_, 'r.', 'LineWidth', 2, 'MarkerSize', 1)
formula = poly2sym([coefficients(1),coefficients(2),coefficients(3)]);
% formulaD = vpa(formula)
df=diff(formula);
lengthOfCurve(i) = double(int((sqrt(1+df^2)),min(y_),max(y_)));
end
Result:
You can get a good approximation of the arc lengths using regionprops to estimate the perimeter of each region (i.e. arc) and then dividing that by 2. Here's how you would do this (requires the Image Processing Toolbox):
img = imread('6khWw.png'); % Load sample RGB image
bw = ~imbinarize(rgb2gray(img)); % Convert to grayscale, then binary, then invert it
data = regionprops(bw, 'PixelList', 'Perimeter'); % Get perimeter (and pixel coordinate
% list, for plotting later)
lens = [data.Perimeter]./2; % Compute lengths
imshow(bw) % Plot image
hold on;
for iLine = 1:numel(data),
xy = mean(data(iLine).PixelList); % Get mean of coordinates
text(xy(1), xy(2), num2str(lens(iLine), '%.2f'), 'Color', 'r'); % Plot text
end
And here's the plot this makes:
As a sanity check, we can use a simple test image to see how good an approximation this gives us:
testImage = zeros(100); % 100-by-100 image
testImage(5:95, 5) = 1; % Add a vertical line, 91 pixels long
testImage(5, 10:90) = 1; % Add a horizontal line, 81 pixels long
testImage(2020:101:6060) = 1; % Add a diagonal line 41-by-41 pixels
testImage = logical(imdilate(testImage, strel('disk', 1))); % Thicken lines slightly
Running the above code on this image, we get the following:
As you can see the horizontal and vertical line lengths come out close to what we expect, and the diagonal line is a little bit more than sqrt(2)*41 due to the dilation step extending its length slightly.
I try with this post but i don´t understand so much, but the idea Colours123 sounds great, this post talk about GUI https://www.mathworks.com/matlabcentral/fileexchange/24195-gui-utility-to-extract-x--y-data-series-from-matlab-figures
I think that you should go through the image and ask if there is a '1' if yes, ask the following and thus identify the beginning of a curve, get the length and save it in a BD, I am not very good with the code , But that's my idea
I have to use an inverse filter to remove the blurring from this image
.
Unfortunately, I have to figure out the transfer function H of the imaging
system used to get these sharper images, It should be Gaussian. So, I should determine the approximate width of the Gaussian by trying different Gaussian widths in an inverse filter and judging which resulting images look the “best”.
The best result will be optimally sharp – i.e., edges will look sharp but will not have visible ringing.
I tried by using 3 approaches:
I created a transfer function with N dimensions (odd number, for simplicity), by creating a grid of N dimensions, and then applying the Gaussian function to this grid. After that, we add zeroes to this transfer function in order to get the same size as the original image. However, after applying the filter to the original image, I just see noise (too many artifacts).
I created the transfer function with size as high as the original image, by creating a grid of the same size as the original image. If sigma is too small, then the PSF FFT magnitude is wide. Otherwise it gets thinner. If sigma is small, then the image is even more blurred, but if we set a very high sigma value then we get the same image (not better at all).
I used the fspecial function, playing with sizes of sigma and h. But still I do not get anything sharper than the original blurred image.
Any ideas?
Here is the code used for creating the transfer function in Approach 1:
%Create Gaussian Filter
function h = transfer_function(N, sigma, I) %N is the dimension of the kernel
%create a 2D-grid that is the same size as the Gaussian filter matrix
grid = -floor(N/2) : floor(N/2);
[x, y] = meshgrid(grid, grid);
arg = -(x.*x + y.*y)/(2*sigma*sigma);
h = exp(arg); %gaussian 2D-function
kernel = h/sum(h(:)); %Normalize so that total weight equals 1
[rows,cols] = size(I);
add_zeros_w = (rows - N)/2;
add_zeros_h = (cols - N)/2;
h = padarray(kernel,[add_zeros_w add_zeros_h],0,'both'); % h = kernel_final_matrix
end
And this is the code for every approach:
I = imread('lena_blur.jpg');
I1 = rgb2gray(I);
figure(1),
I1 = double(I1);
%---------------Approach 1
% N = 5; %Dimension Assume is an odd number
% sigma = 20; %The bigger number, the thinner the PSF in FREQ
% H = transfer_function(N, sigma, I1);
%I1=I1(2:end,2:end); %To simplify operations
imagesc(I1); colormap('gray'); title('Original Blurred Image')
I_fft = fftshift(fft2(I1)); %Shift the image in Fourier domain to let its DC part in the center of the image
% %FILTER-----------Approach 2---------------
% N = 5; %Dimension Assume is an odd number
% sigma = 20; %The bigger number, the thinner the PSF in FREQ
%
%
% [x,y] = meshgrid(-size(I,2)/2:size(I,2)/2-1, -size(I,1)/2:size(I,1)/2-1);
% H = exp(-(x.^2+y.^2)*sigma/2);
% %// Normalize so that total area (sum of all weights) is 1
% H = H /sum(H(:));
%
% %Avoid zero freqs
% for i = 1:size(I,2) %Cols
% for j = 1:size(I,1) %Rows
% if (H(i,j) == 0)
% H(i,j) = 1e-8;
% end
% end
% end
%
% [rows columns z] = size(I);
% G_filter_fft = fft2(H,rows,columns);
%FILTER---------------------------------
%Filter--------- Aproach 3------------
N = 21; %Dimension Assume is an odd number
sigma = 1.25; %The bigger number, the thinner the PSF in FREQ
H = fspecial('gaussian',N,sigma)
[rows columns z] = size(I);
G_filter_fft = fft2(H,rows,columns);
%Filter--------- Aproach 3------------
%DISPLAY FFT PSF MAGNITUDE
figure(2),
imshow(fftshift(abs(G_filter_fft)),[]); title('FFT PSF magnitude 2D');
% Yest = Y_blurred/Gaussian_Filter
I_restoration_fft = I_fft./G_filter_fft;
I_restoration = (ifft2(I_restoration_fft));
I_restoration = abs(I_restoration);
I_fft = abs(I_fft);
% Display of Frequency domain (To compare with the slides)
figure(3),
subplot(1,3,1);
imagesc(I_fft);colormap('gray');title('|DFT Blurred Image|')
subplot(1,3,2)
imshow(log(fftshift(abs(G_filter_fft))+1),[]) ;title('| Log DFT Point Spread Function + 1|');
subplot(1,3,3)
imagesc(abs(I_restoration_fft));colormap('gray'); title('|DFT Deblurred|')
% imshow(log(I_restoration+1),[])
%Display PSF FFT in 3D
figure(4)
hf_abs = abs(G_filter_fft);
%270x270
surf([-134:135]/135,[-134:135]/135,fftshift(hf_abs));
% surf([-134:134]/134,[-134:134]/134,fftshift(hf_abs));
shading interp, camlight, colormap jet
xlabel('PSF FFT magnitude')
%Display Result (it should be the de-blurred image)
figure(5),
%imshow(fftshift(I_restoration));
imagesc(I_restoration);colormap('gray'); title('Deblurred Image')
%Pseudo Inverse restoration
% cam_pinv = real(ifft2((abs(G_filter_fft) > 0.1).*I_fft./G_filter_fft));
% imshow(fftshift(cam_pinv));
% xlabel('pseudo-inverse restoration')
A possible solution is deconvwr. I will first show its performance starting from an undistorted lena image. So, I know exactly the gaussian blurring function. Note that setting estimated_nsr to zero will destroy the performance completely due to quantisation noise.
I_ori = imread('lenaTest3.jpg'); % Download an original undistorted lena file
N = 19;
sigma = 5;
H = fspecial('gaussian',N,sigma)
estimated_nsr = 0.05;
I = imfilter(I_ori, H)
wnr3 = deconvwnr(I, H, estimated_nsr);
figure
subplot(1, 4, 1);
imshow(I_ori)
subplot(1, 4, 2);
imshow(I)
subplot(1, 4, 3);
imshow(wnr3)
title('Restoration of Blurred, Noisy Image Using Estimated NSR');
subplot(1, 4, 4);
imshow(H, []);
The best parameters I found for your problem by trial and error.
N = 19;
sigma = 2;
H = fspecial('gaussian',N,sigma)
estimated_nsr = 0.05;
EDIT: calculating exactly the used blurring filter
If you download an undistorted lena (I_original_fft), you can calculate the used blurring filter as follows:
G_filter_fft = I_fft./I_original_fft
the following procedure is shutting dow my Rstudio: I understand is any of the akima or rgl packages or both. How to solve this? data here
s=read.csv("GRVMAX tadpoles.csv")
require(nlme)
t=s[s$SPP== levels(s$SPP)[1],]
head(t)
t=na.omit(t)
t$TEM=as.numeric(as.character(t$TEM))
library(akima)
x=t$TEM
y=t$value
z=t$time
spline <- with(t,interp(x,y,z,duplicate="median",linear=T))
# rotatable 3D plot of points and spline surface
library(rgl)
open3d(scale=c(1/diff(range(x)),1/diff(range(y)),1/diff(range(z))))
with(spline,surface3d(as.character(x),y,z, col))
points3d(x,y,z, add=T)
title3d(xlab="temperature",ylab="performance",zlab="time")
axes3d()
interp() causes the problem. I think the reason is that scale of y is much different from x (the algorithm of interp() is basically for contour of spatial map). So interp() run when you give y changed scale. (Note; I did y*10 and output/10 but maybe it is a rough scale change. It whoud be better to concider methods of changing scale)
library(nlme); library(akima); library(rgl)
s = read.csv("GRVMAX tadpoles.csv")
t = s[s$SPP == levels(s$SPP)[1],]
t = na.omit(t)
head(t)
t$TEM = as.numeric(as.character(t$TEM))
x = t$TEM
y = t$value * 10 # scale change
z = t$time
spline <- interp(x, y, z, duplicate = "median", linear = T) # with() is unnecessary
spline$y <- spline$y / 10 # rescale
y <- y / 10 # rescale
open3d() # Is scale needed ??
# persp3d() can directly take interp.obj as an argument
persp3d(spline, col = "blue", alpha = 0.5, axes = F, xlab="", ylab="", zlab="")
points3d(x, y, z, add=T)
title3d(xlab="temperature", ylab="performance", zlab="time")
axes3d()
I am having some problems in matlab i don't understand. The following piece of code analyses a collection of images, and should return a coherent image (and always did).
But since I've put an if-condition in the second for-loop (for optimisation purposes) it returns an interlaced image.
I don't understand why, and am getting ready to throw my computer out the window. I suspect it has something to do with ind2sub, but as far as i can see everything is working just fine! Does anyone know why it's doing this?
function imageMedoid(imageList, resizeFolder, outputFolder, x, y)
% local variables
medoidImage = zeros([1, y*x, 3]);
alphaImage = zeros([y x]);
medoidContainer = zeros([y*x, length(imageList), 3]);
% loop through all images in the resizeFolder
for i=1:length(imageList)
% get filename and load image and alpha channel
fname = imageList(i).name;
[container, ~, alpha] = imread([resizeFolder fname]);
% convert alpha channel to zeros and ones, add to alphaImage
alphaImage = alphaImage + (double(alpha) / 255);
% add (r,g,b) values to medoidContainer and reshape to single line
medoidContainer(:, i, :) = reshape(im2double(container), [y*x 3]);
end
% loop through every pixel
for i=1:(y * x)
% convert i to coordinates for alphaImage
[xCoord, yCoord] = ind2sub([x y],i);
if alphaImage(yCoord, xCoord) == 0
% write default value to medoidImage if alpha is zero
medoidImage(1, i, 1:3) = 0;
else
% calculate distances between all values for current pixel
distances = pdist(squeeze(medoidContainer(i,:,1:3)));
% convert found distances to matrix of distances
distanceMatrix = squareform(distances);
% find index of image with the medoid value
[~, j] = min(mean(distanceMatrix,2));
% write found medoid value to medoidImage
medoidImage(1, i, 1:3) = medoidContainer(i, j, 1:3);
end
end
% replace values larger than one (in alpha channel) by one
alphaImage(alphaImage > 1) = 1;
% reshape image to original proportions
medoidImage = reshape(medoidImage, y, x, 3);
% save medoid image
imwrite(medoidImage, [outputFolder 'medoid_modified.png'], 'Alpha', alphaImage);
end
I didn't include the whole code, just this function (for brevity's sake), if anyone needs more (for a better understanding of it), please let me know and i'll include it.
When you call ind2sub, you give the size [x y], but the actual size of alphaImage is [y x] so you are not indexing the correct location with xCoord and yCoord.
I am plotting a 7x7 pixel 'image' in MATLAB, using the imagesc command:
imagesc(conf_matrix, [0 1]);
This represents a confusion matrix, between seven different objects. I have a thumbnail picture of each of the seven objects that I would like to use as the axes tick labels. Is there an easy way to do this?
I don't know an easy way. The axes properties XtickLabel which determines the labels, can only be strings.
If you want a not-so-easy way, you could do something in the spirit of the following non-complete (in the sense of a non-complete solution) code, creating one label:
h = imagesc(rand(7,7));
axh = gca;
figh = gcf;
xticks = get(gca,'xtick');
yticks = get(gca,'ytick');
set(gca,'XTickLabel','');
set(gca,'YTickLabel','');
pos = get(axh,'position'); % position of current axes in parent figure
pic = imread('coins.png');
x = pos(1);
y = pos(2);
dlta = (pos(3)-pos(1)) / length(xticks); % square size in units of parant figure
% create image label
lblAx = axes('parent',figh,'position',[x+dlta/4,y-dlta/2,dlta/2,dlta/2]);
imagesc(pic,'parent',lblAx)
axis(lblAx,'off')
One problem is that the label will have the same colormap of the original image.
#Itmar Katz gives a solution very close to what I want to do, which I've marked as 'accepted'. In the meantime, I made this dirty solution using subplots, which I've given here for completeness. It only works up to a certain size input matrix though, and only displays well when the figure is square.
conf_mat = randn(5);
A = imread('peppers.png');
tick_images = {A, A, A, A, A};
n = length(conf_mat) + 1;
% plotting axis labels at left and top
for i = 1:(n-1)
subplot(n, n, i + 1);
imshow(tick_images{i});
subplot(n, n, i * n + 1);
imshow(tick_images{i});
end
% generating logical array for where the confusion matrix should be
idx = 1:(n*n);
idx(1:n) = 0;
idx(mod(idx, n)==1) = 0;
% plotting the confusion matrix
subplot(n, n, find(idx~=0));
imshow(conf_mat);
axis image
colormap(gray)