courbe de suivie des pixels dans les images

hi , I have 25 MRI images (dicom) as input. I select 6 fixed point (x, y) and I keep the location of these pixels for the other images. I want to plot the progression curve of these pixels in the 25 images.

I want to display the curve of each image in the same plot but by different colors .how to program that?

i use this code :

rep = uigetdir;
Imgs = dir(rep);
thisname = Imgs(3).name;
[path,name,ext]=fileparts(thisname);
ext=strcat('*',ext);
chemin = fullfile(rep,ext);
list = dir(chemin);
nbr_images= numel(list);
for n=1:25
k=dicomread(fullfile(rep, list(n).name));
end;
IM=double(k);
axes(handles.axes1);imshow(IM,[]);
impixelinfo;
[xi,yi]=getpts

  IM=dicomread(fullfile(rep, list(1).name))
IM(1,1,numel(list))=0; %extend array to fit all slices
for n=2:numel(list)
    IM(:,:,n)=dicomread(fullfile(rep, list(n).name));
end
for k=1:6
     for n=1:25
     column= round(xi(k));
    row= round(yi(k));
     intensityProfile(k)=squeeze(IM(column,row));
 axes(handles.axes2);plot(intensityProfile,'b*-');
   end
    
 end

[Walter Roberson]

ep = uigetdir;

It looks like one letter got dropped, and that should be

rep = uigetdir;

Answer 1

[Image Analyst]

Pass in the color of the line:

plotColors = 'rgbcmyk'; % Whatever you want.
for k = 1 : 6
    plot(intensityProfile, '*-', 'Color', plotColors(k), 'LineWidth', 3);
end

[Amal Felhi]

i want every curve has a color not every point ,i want 25 curves from the 25 images

[Image Analyst]

Amal, try this. You can see that for every one of the 25 slices I measure the intensity of the 6 points and plot a curve with 6 points. So 25 curves, each in a different color. Is this what you want?

clc;    % Clear the command window.
close all;  % Close all figures (except those of imtool.)
clear;  % Erase all existing variables. Or clearvars if you want.
workspace;  % Make sure the workspace panel is showing.
format short g;
format compact;
fontSize = 18;
fprintf('Beginning to run %s.m ...\n', mfilename);

%===========================================================
% Create sample volumetric image.
numSlices = 25;
IM = repmat(imread('cameraman.tif'), [1, 1, 25]);
% Add some noise so every slice is not the same.
IM = uint8(double(IM) + 40 * rand(size(IM)));
whos IM

%===========================================================
% Now we have our image and we can begin.
% Display last image.
subplot(2, 1, 1);
imshow(IM(:, :, end));
impixelinfo;
g = gcf;
g.WindowState = 'maximized';
title('Draw 6 points.  Type Enter when done');
uiwait(msgbox('Draw 6 points.  Type Enter when done'));
[xi,yi] = getpts()
% Label the points.
for k = 1 : length(xi)
	hold on;
	plot(xi(k), yi(k), 'y.', 'MarkerSize', 20)
	str = sprintf(' Point #%d', k);
	text(xi(k), yi(k), str, 'VerticalAlignment', 'middle', 'FontSize', 18, 'FontWeight', 'bold', 'Color', 'y');
end
columns = round(xi);
rows = round(yi);
numSlices = size(IM, 3);
numPoints = length(xi);
legendStrings = cell(numSlices, 1);

%===========================================================
% Now we can plot the colors of the 6 points for each slice.
subplot(2, 1, 2);
% Create the colors
plotColors = jet(numSlices); % or 'rgbcmyk'; % Whatever you want.
% if you use 'rgbcmyk', then use plotColors(k) below.
for slice = 1 : numSlices
	% For each slice, get the intensity at the 6 points and plot them.
	fprintf('Getting profile at all %d points through slice #%d.\n', numPoints, slice);
	for k = 1 : numPoints
		intensityProfile(k) = IM(rows(k), columns(k), slice);
	end
	% Plot the 6 points for this slice.
	fprintf('    The color of line #%d is (%.2f, %.2f, %.2f).\n', slice, plotColors(slice, :));
	plot(intensityProfile, '-', 'Color', plotColors(slice, :), 'LineWidth', 1);
	hold on;
	legendStrings{slice} = sprintf('Slice #%d', slice);
end
grid on;
xlabel('Slice Number', 'FontSize', fontSize);
ylabel('Gray Level', 'FontSize', fontSize);
legend(legendStrings);
fprintf('Done running %s.m.\n', mfilename);

[Amal Felhi]

thank you it works

[Amal Felhi]

I have another problem if you can help me please

i use this code:

rep = uigetdir;
Imgs = dir(rep);
thisname = Imgs(3).name;
[path,name,ext]=fileparts(thisname);
ext=strcat('*',ext);
chemin = fullfile(rep,ext);
list = dir(chemin);
nbr_images= numel(list);
for n=1:25
k=dicomread(fullfile(rep, list(n).name));
end;
IM=double(k);
figure(1),imshow(IM,[]);
impixelinfo;

[xi1,yi1] = getpts()
[xi2,yi2] = getpts()
[xi3,yi3] = getpts()
x1= round(xi1);
y1= round(yi1);

    x2= round(xi2);
    y2= round(yi2);
    
    x3= round(xi3);
    y3= round(yi3);
    
IM=dicomread(fullfile(rep, list(1).name))
IM(1,1,numel(list))=0; %extend array to fit all slices
for n=2:numel(list)
    IM(:,:,n)=dicomread(fullfile(rep, list(n).name));
end


for n=1:25
    X1=squeeze(IM(x1,y1,:));
    X2=squeeze(IM(x2,y2,:));
    X3=squeeze(IM(x3,y3,:));
   figure(1), plot(X1,'b*-');
   xlabel('Cycle cardiaque');
ylabel('intensité');
title('Courbe six segments');
    set(gca,'Xtick',1:1:25); 
    set(gca,'Ytick',0:10:255); 
   figure(2), plot(X2,'b*-');
   xlabel('Cycle cardiaque');
ylabel('intensité');
title('Courbe six segments');
    set(gca,'Xtick',1:1:25); 
    set(gca,'Ytick',0:10:255); 
       figure(3), plot(X3,'b*-');
   xlabel('Cycle cardiaque');
ylabel('intensité');
title('Courbe six segments');
    set(gca,'Xtick',1:1:25); 
    set(gca,'Ytick',0:10:255); 
    end

i get these curves:

I want to display them in the same curve with different colors.

[Walter Roberson]

Do not call figure() then. But you will need hold on

[Amal Felhi]

thank u it works

Answer 2

[Walter Roberson]

for n=1:25
k=dicomread(fullfile(rep, list(n).name));
end;

Why do you read all of them but immediately throw all of them away except the last of them?

IM(1,1,numel(list))=0; %extend array to fit all slices

you use numel(list) repeatedly, but you already assigned

nbr_images= numel(list);

It is not clear why you do not use the variable instead of numel(list) later ?

     intensityProfile(k)=squeeze(IM(column,row));

n should be part of your indexing, probably on both sides. And you probably should hold off the plot at that point until after the for k loop.

[Amal Felhi]

i read all of them because i need all the pictures.

I want to select the 6 points from a single image then I draw the curve of these 6 points for the 25 images in 25 curves

[Walter Roberson]

for n=1:25

Okay, you loop 25 times

k=dicomread(fullfile(rep, list(n).name));

You construct a file name, and ask dicomread to read the file. The result of reading the file overwrites all of the variable k

end;

When n = 1, you read a file and stored it in k. When n = 2, you read a file, and stored it in k, throwing away what was already in k . This just wastes time unless you are in a loop in which you are carefully testing ahead of time that all of the files are truly readable.

[Amal Felhi]

okay I will try