Read coordinates on a txt file and plot them over an image.

Dear all,

I made a program that reads some coordinates (x, y) of a text file and plot the points over a gray image. The problem is that the 'y' coordinates are inverted. This problem doesn't happen when I draw a regular plot (without reading from a file).

How can I fix this issue?

Thanks in advance,

[KSSV]

How you have plotted (x,y) in regular plot? It should not effect whether you read from file or plot directly. Show us code.

[Gabriel]

It is quite simple, indeed:

[x, y] = textread('coordfile.txt', '%f , %f');
imshow(img, []), hold on;
plot(x, y, 'r*')

I tried to use "flipud" but it didn't solve the problem.

[Image Analyst]

Gabriel, do you want your x axis to be at the top of your image, with rising y values going downward? Or do you want your x axis to be at the bottom of your image, with rising y values going upward? And do you like the way your image is displayed, or do you wish the top were at the bottom and vice versa?

Answer 1

[Stephen23]

Images are referenced to the top left of the image (due to traditions related to the scanning of a CRT), so this is how all image handling programs work with them. MATLAB simply follows this standard.

People who are used to plotting data relative to an x-axis at the bottom of their plot might get a bit confused, but need to learn that images use a different standard.

A simple internet search shows many questions already dealing with this topic, e.g.:

https://www.mathworks.com/matlabcentral/answers/94170-how-can-i-reverse-the-y-axis-when-i-use-the-image-or-imagesc-function-to-display-an-image-in-matlab

and is also explained in the documentation for the relevant functions, e.g. imagesc:

"The high-level version of imagesc calls newplot before plotting and sets these axes properties: ... YDir to 'reverse'. Values along the y-axis increase from top to bottom."

[Gabriel]

Actually I tried to use fipud but it didn't solve the problem...

I can't just use imagesc because the function that draws the image and plot the coordinates appears in many other parts of the code and can't be changed.

I created a short example to illustrate the problem:

[x, y] = textread('coordfile.txt', '%f , %f');
imshow(img, []), hold on;
plot(flipud(x), flipud(y), 'r*')

[Stephen23]

@Gabriel: flipud cannot "solve" this for you. Think about what flipud actually does: it does not change the positions of values inside the axes. It just rearranges your input data, which makes no difference at all to where it gets plotted. As this example demonstrates:

 plot([0;1],[3;4]) % your original plot
 plot([1;0;,[4;3]) % after |flipud|

Note that the points themselves are exactly the same as before. You have not changed where they are relative to the y-axis.

You should change the YDir property, or adjust your data to be relative to the top of the plot. There may be other solutions.

[Guillaume]

plot(x, size(img, 1) - y, 'r*')

would solve the problem quickly

[Stelios Fanourakis]

Hey I am doing something similar but I cannot take anything as a result. I use

filePatternu = fullfile(destinationFolder, '*.dcm'); allFiles = dir(filePatternu);

for k= 2: 1: length(allFiles) baseFileName = allFiles(k).name; % e.g. "1.png" fullFileName = fullfile(destinationFolder, baseFileName); I = dicomread(fullFileName); % img respresents input image. pause(2) [x, y] = textread('imgpositions.txt', '%f , %f'); figure imshow(I, [x y]) drawnow; end

Although, I get no error still I get no image