Plot over an image background in MATLAB - image

I'd like to plot a graph over an image. I followed this tutorial to Plot over an image background in MATLAB and it works fine:
% replace with an image of your choice
img = imread('myimage.png');
% set the range of the axes
% The image will be stretched to this.
min_x = 0;
max_x = 8;
min_y = 0;
max_y = 6;
% make data to plot - just a line.
x = min_x:max_x;
y = (6/8)*x;
imagesc([min_x max_x], [min_y max_y], img);
hold on;
plot(x,y,'b-*','linewidth',1.5);
But when I apply the procedure to my study case, it doesn't work. I'd like to do something like:
I = imread('img_png.png'); % here I load the image
DEM = GRIDobj('srtm_bigtujunga30m_utm11.tif');
FD = FLOWobj(DEM,'preprocess','c');
S = STREAMobj(FD,flowacc(FD)>1000);
% with the last 3 lines I calculated the stream network on a geographic area using the TopoToolBox
imagesc(I);
hold on
plot(S)
The aim is to plot the stream network over the satellite image of the same area.
The only difference between the two examples that doesn't let the code working is in the plot line, in the first case "plot(x,y)" works, in the other one "plot(S)" doesn't.
Thanks guys.
This is the satellite image, imagesc(I)

It is possible that the plot method of the STREAMobj performs it's own custom plotting including creating new figures, axes, toggling hold states, etc. Because you can't easily control what their plot routine does, it's likely easier to flip the order of your plotting so that you plot your stuff after the toolbox plots the STREAMobj. This way you have completely control over how your image is added.
% Plot the STREAMobj
hlines = plot(S);
% Make sure we plot on the same axes
hax = ancestor(hlines, 'axes');
% Make sure that we can add more plot objects
hold(hax, 'on')
% Plot your image data on the same axes
imagesc(I, 'Parent', hax)

Maybe I am preaching to the choir or overlooking something here but the example you used actually mapped the image to the data range of the plot, hence the lines:
% set the range of the axes
% The image will be stretched to this.
min_x = 0;
max_x = 8;
min_y = 0;
max_y = 6;
imagesc([min_x max_x], [min_y max_y], img);
where you directly plot your image
imagesc(I);
If now your data coordinates and your image coordinates are vastly different you either see one or the other.

Thanks guys, I solved in this way:
I = imread('orto.png'); % satellite image loading
DEM = GRIDobj('demF1.tif');
FD = FLOWobj(DEM,'preprocess','c');
S = STREAMobj(FD,flowacc(FD)>1000); % Stream network extraction
x = S.x; % [node attribute] x-coordinate vector
y = S.y; % [node attribute] y-coordinate vector
min_x = min(x);
max_x = max(x);
min_y = min(y);
max_y = max(y);
imagesc([min_x max_x], [min_y max_y], I);
hold on
plot(S);
Here's the resulting image: stream network over the satellite image
Actually the stream network doesn't match the satellite image just because I'm temporarily using different images and DEM.

Related

To show/join Two Images Simultaneously in Matlab's slider?

I cannot make too big file (like tried here) so I need to show only portions at a time.
However, I cannot make the transfer from one file to another smooth in Matlab.
I am trying to expand the solution of the thread To refresh imshow in Matlab? for two images. The problem is the ending of image A and start of the image B. Now, I have an interruption in the flow, which I do not like because I cannot show two images at the same time without an interruption.
In the example here, it is not needed to filter the axes.
Code
iterationCounter=1;
hFig=figure('Menubar','none', 'NumberTitle','off', 'Color','k');
while(iterationCounter < 7)
filenamePng=fullfile(homedir, '/Images/Raw/', iterationCounter, '.png');
imgRGB=imread(filenamePng);
% https://stackoverflow.com/a/29952648/54964
%%// create sliding-window video
len = 40*2^3;
signal = imgRGB(:,1:end,:);
hImg = imshow(signal(:,1:1+len,:), ...
'InitialMagnification',100, 'Border','tight');
vid = VideoWriter('signal.avi');
vid.Quality = 100;
vid.FrameRate = 60;
open(vid);
M = size(signal,2);
for k=1:M-len
set(hImg, 'CData',signal(:,k:k+len,:))
writeVideo(vid, getframe());
end
iterationCounter=iterationCounter+1;
end
close(vid);
Output for Image A and Image B
where there is an interruption in the slider after each image.
The picture is just a screenshot of two images: beginning and ending of the slider. The blue area is just OS X GUI but still indicates that there is a gap and interruption between the start and end.
How can show/join two images simultaneously in Matlab's slider?
In order to display multiple images side by side in this scrolling window, I think the easiest approach is to actually load all of the images upfront into an array that is [nRows x (nColumns * nImages) x 3] and then just use the original code to scroll through this.
hFig=figure('Menubar','none', 'NumberTitle','off', 'Color','k');
signal = [];
% Load all the images into one "long" image
for k = 1:7
filename = fullfile(homedir, sprintf('%d.png', k));
img = imread(filename);
signal = cat(2, signal, img);
end
%%// create sliding-window video
windowWidth = 320; % Width in pixels
hImg = imshow(signal(:,1:1 + windowWidth,:), ...
'InitialMagnification',100, 'Border','tight');
vid = VideoWriter('signal.avi');
vid.Quality = 100;
vid.FrameRate = 60;
open(vid);
M = size(signal,2);
for k = 1:(M - windowWidth)
set(hImg, 'CData',signal(:,k:k + windowWidth,:))
writeVideo(vid, getframe());
end
close(vid);
The command imagesc is a low-level image command where Suever's proposal does not work.
A general approach to remove padding/margins/background is to use
<plot imshow imagesc ...>
set(gca,'position',[0 0 1 1],'units','normalized')

Plotting a 2D Moving Image in MatLab [duplicate]

I'm trying to plot small images on a larger plot... Actually its isomap algorithm, I got many points, now each point correspond to some image, I know which image is it... The porblem is how to load that image and plot on the graph?
One more thing I have to plot both image and the points, so, basically the images will overlap the points.
Certainly, the type of image given here
Something like this should get you started. You can use the low-level version of the image function to draw onto a set of axes.
% Define some random data
N = 5;
x = rand(N, 1);
y = rand(N, 1);
% Load an image
rgb = imread('ngc6543a.jpg');
% Draw a scatter plot
scatter(x, y);
axis([0 1 0 1]);
% Offsets of image from associated point
dx = 0.02;
dy = 0.02;
width = 0.1;
height = size(rgb, 1) / size(rgb, 2) * width;
for i = 1:N
image('CData', rgb,...
'XData', [x(i)-dx x(i)-(dx+width)],...
'YData', [y(i)-dy y(i)-(dy+height)]);
end

Connect disjoint edges in binary image

I performed some operations on an image of a cube and I obtained a binary image of the edges of the cube which are disconnected at some places.The image I obtained is shown below:
I want to join the sides to make it a closed figure.I have tried the following:
BW = im2bw(image,0.5);
BW = imdilate(BW,strel('square',5));
figure,imshow(BW);
But this only thickens the image.It does not connect the edges.I have also tried bwmorph() and various other functions, but it is not working.Can anyone please suggest any function or steps to connect the edges? Thank you
This could be one approach -
%// Read in the input image
img = im2bw(imread('http://i.imgur.com/Bl7zhcn.jpg'));
%// There seems to be white border, which seems to be non-intended and
%// therefore could be removed
img = img(5:end-4,5:end-4);
%// Thin input binary image, find the endpoints in it and connect them
im1 = bwmorph(img,'thin',Inf);
[x,y] = find(bwmorph(im1,'endpoints'));
for iter = 1:numel(x)-1
two_pts = [y(iter) x(iter) y(iter+1) x(iter+1)];
shapeInserter = vision.ShapeInserter('Shape', 'Lines', 'BorderColor', 'White');
rectangle = int32(two_pts);
im1 = step(shapeInserter, im1, rectangle);
end
figure,imshow(im1),title('Thinned endpoints connected image')
%// Dilate the output image a bit
se = strel('diamond', 1);
im2 = imdilate(im1,se);
figure,imshow(im2),title('Dilated Thinned endpoints connected image')
%// Get a convex shaped blob from the endpoints connected and dilate image
im3 = bwconvhull(im2,'objects',4);
figure,imshow(im3),title('Convex blob corresponding to previous output')
%// Detect the boundary of the convex shaped blob and
%// "attach" to the input image to get the final output
im4 = bwboundaries(im3);
idx = im4{:};
im5 = false(size(im3));
im5(sub2ind(size(im5),idx(:,1),idx(:,2))) = 1;
img_out = img;
img_out(im5==1 & img==0)=1;
figure,imshow(img_out),title('Final output')
Debug images -
I used the above code to write the following one.I haven't tested it on many images and it may not be as efficient as the one above but it executes faster comparatively.So I thought I would post it as a solution.
I = imread('image.jpg'); % your original image
I=im2bw(I);
figure,imshow(I)
I= I(5:end-4,5:end-4);
im1 = bwmorph(I,'thin',Inf);
[x,y] = find(bwmorph(im1,'endpoints'));
for iter = 1:numel(x)-1
im1=linept(im1, x(iter), y(iter), x(iter+1), y(iter+1));
end
im2=imfill(im1,'holes');
figure,imshow(im2);
BW = edge(im2);
figure,imshow(BW);
se = strel('diamond', 1);
im3 = imdilate(BW,se);
figure,imshow(im3);
The final result is this:
I got the "linept" function from here:http://in.mathworks.com/matlabcentral/fileexchange/4177-connect-two-pixels

matlab plot graph of data over an image

What I would like to do is plot an image of a graph (from say a pdf file or a scanned image). Next, I would like to overlay an axis on the graph in the image, and then plot data on that axis (over the image).
Using imtool, I know the coordinates of the graph in the image (x range = ~52-355 pixels, and y range = 23(top) - 262(bottom) pixels in this case).
This is what I have tried:
I = imread('C:\MATLAB\R2014a\help\images\ref\ftrans2_fig.png');
I = squeeze(uint8(mean(I,3)));
figure, imshow(I)
[rows, cols] = size(I);
x_data = (-1 : .01 : +1)';
y_data = 1 - x_data.^2;
h1 = axes('Position',([52, 23, 355-52, 262-23] ./ [cols, rows, cols, rows] ));
set(h1, 'Color', 'none')
hold on
plot(x_data, y_data, '-rx')
Question: Knowing the pixel coordinates of the graph in the image, how do I determine the proper position of the axis in the figure, (my code fails to account for the actual size of the figure box, the gray border around the image). I have to do this for several images and sets of data, so I would like an automated method, assuming I find the coordinates of the graphs in the image ahead of time.
Thanks for your reply! (1st time posting, please be kind)
You may be able to solve your problem by forcing the image onto the same axis as the plot. Try this:
I = imread('C:\MATLAB\R2014a\help\images\ref\ftrans2_fig.png');
I = squeeze(uint8(mean(I,3)));
[rows, cols] = size(I);
x_data = (-1 : .01 : +1)';
y_data = 1 - x_data.^2;
h1 = axes('Position',([52, 23, 355-52, 262-23] ./ [cols, rows, cols, rows] ));
set(h1, 'Color', 'none')
hold on
image(I, 'Parent', h1);
plot(h1, x_data, y_data, '-rx')
That should at ensure that the plot axis and the image axis have the same origin, as they will be one and the same. You may need to adjust your sizing code. Let me know if that doesn't do it for you.
Good Luck!
I think I have it figured out.
It would have been easier if I could use:
figure, h1=imshow(I)
get(h1,'Position')
but that results in "The name 'Position' is not an accessible property for an instance of class 'image'."
Instead, this appears to work:
I = imread('C:\MATLAB\R2014a\help\images\ref\ftrans2_fig.png');
I = squeeze(uint8(mean(I,3)));
in_mag = 300;
figure, imshow(I, 'Border', 'tight', 'InitialMagnification', in_mag)
[rows, cols] = size(I);
x_data = (-1 : .01 : +1)';
y_data = 1 - x_data.^2;
% Coord of graph in image pixels
x_0 = 50; x_max = 354; y_0 = 262; y_max = 23;
h1 = axes('Position',([x_0, rows-y_0, x_max-x_0, y_0-y_max] ...
./ [cols, rows, cols, rows] ));
set(h1,'Color','none')
hold on
plot(x_data, y_data, '-rx')
ylim([0,1.4])
set(gca,'YColor', [0 0 1], 'XColor', [0 0 1])
However, if anybody has a better idea, I would be very happy to explore it!
Thanks

How to reconstruct an image using rgb values of all pixels in Matlab

I am trying to read an image using imread then, save the RGB values of all of the pixels in an array. And finally, be able to recreate this image using only the RGB values.
This is the for loop that saves all of the RGB values of each pixel.
A=imread('image.jpg');
N=2500; %the image dimensions are 50x50
i=1;
rgbValues = zeros(N, 3);
for x = 1:50
for y = 1:50
rgbValues(i,:) = A(x,y,:);
i=i+1;
end
end
Now, how am I able to recreate this image if I have all of the rgb values saved.
A direct way to do this is:
ny = 50;
nx = 50;
recreatedImage = zeros(ny,nx,3, 'uint8');
for ind = 1:3
recreatedImage(:,:, ind) = ( reshape(rgbValues(:, ind), nx, ny))';
end
As Natan indicated, reshape will work also but you have to do this:
recreatedImage=reshape(rgbValues,[ny,nx,3]);
Which is, unfortunately, transposed so you will need to work it to get it rotated back up.
You might consider swapping your x and y values in your for loop so you iterate over all y and then all x values---because this is how MATLAB stores the data and you can change the above code to:
for ind = 1:3
recreatedImage(:,:, ind) = ( reshape(rgbValues(:, ind), ny, nx));
end
(edit) and then the direct reshape works as well:
rgbValuesBacktoShape=reshape(rgbValues,[50,50,3]);

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