image stack display in matlab using a slider - image

I have a 3 dimension matrix of data (a stack of images across a dimension, time for example.
I want to display an image, and have a slider below to navigate across the images.
I wrote a piece of code which works, but it's bulky and kinda ugly I think...I want to write a clean function and so I would like to know if anyone know of a cleaner, nicer way to do it.
Here is my code:
interv = [min max]; % interval for image visualization
imagesc(Temps_visu,X*100,squeeze(X,Y,MyMatrix(:,:,1)),interv);
title('My Title');
xlabel('X (cm)');
ylabel('Y (cm)');
pos = get(gca,'position');
% slider position
Newpos = [pos(1) pos(2)-0.1 pos(3) 0.05];
pp = 1;
% callback slider
S = ['pp=floor(get(gcbo,''value''));imagesc(Temps_visu,X*100,squeeze(X,Y,MyMatrix(:,:,1)),interv));' ...
'set_axes_elasto;title(''My Title'');disp(pp);'];
Mz = size(MyMatrix,3);
% Creating Uicontrol
h = uicontrol('style','slider',...
'units','normalized',...
'position',Newpos,...
'callback',S,...
'min',1,'max',Mz,...
'value',pp,...
'sliderstep',[1/(Mz-1) 10/(Mz-1)]);

Here is a way to do it using a listener object for smooth visualization of your stack. I made up a dummy stack using grayscale variations of the same image (i.e. only 4 frames) but the principle will be the same for your application. Notice that I use imshow to display the images, but using imagesc as you do won't cause any problem.
The code is commented so hopefully this is clear enough. If not please don't hesitate to ask for help!
Code:
function SliderDemo
clc
clear all
NumFrames = 4; %// Check below for dummy 4D matrix/image sequence
hFig = figure('Position',[100 100 500 500],'Units','normalized');
handles.axes1 = axes('Units','normalized','Position',[.2 .2 .6 .6]);
%// Create slider and listener object for smooth visualization
handles.SliderFrame = uicontrol('Style','slider','Position',[60 20 400 50],'Min',1,'Max',NumFrames,'Value',1,'SliderStep',[1/NumFrames 2/NumFrames],'Callback',#XSliderCallback);
handles.SliderxListener = addlistener(handles.SliderFrame,'Value','PostSet',#(s,e) XListenerCallBack);
handles.Text1 = uicontrol('Style','Text','Position',[180 420 60 30],'String','Current frame');
handles.Edit1 = uicontrol('Style','Edit','Position',[250 420 100 30],'String','1');
%// Create dummy image sequence, here 4D sequence of grayscale images.
MyImage = imread('peppers.png');
MyMatrix = cat(4,rgb2gray(MyImage),MyImage(:,:,1),MyImage(:,:,2),MyImage(:,:,3));
%// Use setappdata to store the image stack and in callbacks, use getappdata to retrieve it and use it. Check the docs for the calling syntax.
setappdata(hFig,'MyMatrix',MyMatrix); %// You could use %//setappdata(0,'MyMatrix',MyMatrix) to store in the base workspace.
%// Display 1st frame
imshow(MyMatrix(:,:,:,1))
%// IMPORTANT. Update handles structure.
guidata(hFig,handles);
%// Listener callback, executed when you drag the slider.
function XListenerCallBack
%// Retrieve handles structure. Used to let MATLAB recognize the
%// edit box, slider and all UI components.
handles = guidata(gcf);
%// Here retrieve MyMatrix using getappdata.
MyMatrix = getappdata(hFig,'MyMatrix');
%// Get current frame
CurrentFrame = round((get(handles.SliderFrame,'Value')));
set(handles.Edit1,'String',num2str(CurrentFrame));
%// Display appropriate frame.
imshow(MyMatrix(:,:,:,CurrentFrame),'Parent',handles.axes1);
guidata(hFig,handles);
end
%// Slider callback; executed when the slider is release or you press
%// the arrows.
function XSliderCallback(~,~)
handles = guidata(gcf);
%// Here retrieve MyMatrix using getappdata.
MyMatrix = getappdata(hFig,'MyMatrix');
CurrentFrame = round((get(handles.SliderFrame,'Value')));
set(handles.Edit1,'String',num2str(CurrentFrame));
imshow(MyMatrix(:,:,:,CurrentFrame),'Parent',handles.axes1);
guidata(hFig,handles);
end
end
The figure looks like this:
Hope that helps!

Related

MATLAB: How to change pixel values after using VideoReader

I'm trying to read a video file using VideoReader and change some pixel values and save it back to the video file. I can easily change the matrix values but how do I save it back into the video file?
obj = VideoReader('DemoClip.asf');
imageData = read(obj);
imageData(17,32,:) = 65;
Here is a way to do it using videoWriter. The code is commented; if something is unclear please ask. I used the demo xylophone.mp4 file from Mathworks.
clear
clc
close all
xyloObj = VideoReader('xylophone.mp4');
imageData = read(xyloObj);
%// Open writer object
writerObj = VideoWriter('NewVideo.avi');
open(writerObj);
%// Show 1st frame
hIm = imshow(imageData(:,:,:,1));
for k = 1:size(imageData,4)
%// Change pixel values
imageData(1:200,1:200,:,k) = uint8(0);
%// Refresh cdata property. Faster than calling repetitevely imshow
set(hIm,'CData',imageData(:,:,:,k));
drawnow
frame = getframe;
%// Write to video file
writeVideo(writerObj,frame);
end
close(writerObj);
Sample frame of the resulting video:

Motion History Image (MHI) in Matlab

My project is to detect human activity through stored video clips.
I am successfully able to do the following:
Get the Motion History Image (MHI) from a video using OpenCV
Train and classify the set of images using Matlab
However, I want to use Matlab in order to get the Motion History Image (MHI). Is it possible, and if yes can someone guide me? Thank you.
I have attached a sample Motion History Image (MHI)
I have used the following code for MHI:
http://www.ece.iastate.edu/~alexs/classes/2007_Fall_401/code/09_MotionHistory/motempl.c
MHI is just a ways of implementing motion detection (and uses silhouettes as the basis of it).
Let suppose that the silhouette of the most recent object has been created. It also uses a timestamp to identify if the current silhouette is recent or not. The older silhouettes have to be compared with the current silhouette in order to achieve movement detection. Hence, earlier silhouettes are also saved in the image, with an earlier timestamp.
MHI describes the changes of some moving objects over the image sequence. Basically, you should only maintain an image where every pixel encodes a time information - whether the silhouette is recent or not or where the movement occurs at a given time.
Therefore the implementation of MHI is very simple e.g.:
function MHI = MHI(fg)
% Initialize the output, MHI a.k.a. H(x,y,t,T)
MHI = fg;
% Define MHI parameter T
T = 15; % # of frames being considered; maximal value of MHI.
% Load the first frame
frame1 = fg{1};
% Get dimensions of the frames
[y_max x_max] = size(frame1);
% Compute H(x,y,1,T) (the first MHI)
MHI{1} = fg{1} .* T;
% Start global loop for each frame
for frameIndex = 2:length(fg)
%Load current frame from image cell
frame = fg{frameIndex};
% Begin looping through each point
for y = 1:y_max
for x = 1:x_max
if (frame(y,x) == 255)
MHI{frameIndex}(y,x) = T;
else
if (MHI{frameIndex-1}(y,x) > 1)
MHI{frameIndex}(y,x) = MHI{frameIndex-1}(y,x) - 1;
else
MHI{frameIndex}(y,x) = 0;
end
end
end
end
end
Code from: https://searchcode.com/codesearch/view/8509149/
Update #1:
Try to draw it as follows:
% showMHI.m
% Input frame number and motion history vector to display normalized MHI
% at the specified frame.
function showMHI(n, motion_history)
frameDisp = motion_history{n};
frameDisp = double(frameDisp);
frameDisp = frameDisp ./ 15;
figure, imshow(frameDisp)
title('MHI Image');

Change Range Of Displayed Pixel Values from Command Line?

I'm working with some MRI data in Matlab 2014b, but the data is formed of intensity values not RGB. To get around this I use the code below to form a movie out of the MRI frames (I'm working on dynamic data here)
My problem is that the images need to have altered display values for the pixels, as the default only displays between -Inf and Inf, and I need between 0 and 0.25 to get a sensible image out of my data.
Are there any ways to pass that change from the script in to the movie, and then to write to file? I can only seem to do this per image in implay, and I'd like an automated way to edit each image and then store as a frame for a movie..?
%Code for producing movie.
graymap = gray(256);
for i = 1:32
a(:,:,i) = cmunique(Reformed_Data_Colourmap(:,:,i));
end
for i = 1:32
b = im2frame(a(:,:,i),graymap);
a(:,:,1) = ((b.cdata));
image(a(:,:,1))
colormap 'gray'
%The change needs to be here, to display pixel values from 0 to 0.25, to allow for a sensible image from the MR data.
frames(1,i) = getframe;
end
movie(frames)
The solution is provided:
for i = 1:32
b = im2frame(a(:,:,i),graymap);
a(:,:,1) = ((b.cdata));
clims = [0 250];
%image(a(:,:,1),clims)
colormap 'gray'
imagesc(a(:,:,1),clims);
%set('window', [0 400])
frames(1,i) = getframe;
end
clims solves the issue.

How to make gif images from a set of images in matlab?

How to make '.gif' image from a set of '.jpg' images (say: I1.jpg, I2.jpg,..., I10.jpg) in matlab?
Ok here is a simple example. I got an image with a unicorn on it and remove 2 part to create 3 different images, just for the sake of creating an animated gif. Here is what it looks like:
clear
clc
%// Image source: http:\\giantbomb.com
A = rgb2gray(imread('Unicorn1.jpg'));
B = rgb2gray(imread('Unicorn2.jpg'));
C = rgb2gray(imread('Unicorn3.jpg'));
ImageCell = {A;B;C};
figure;
subplot(131)
imshow(A)
subplot(132)
imshow(B)
subplot(133)
imshow(C)
%// Just to show what the images look like (I removed spots to make sure there was an animation created):
%// Create file name.
FileName = 'UnicornAnimation.gif';
for k = 1:numel(ImageCell)
if k ==1
%// For 1st image, start the 'LoopCount'.
imwrite(ImageCell{k},FileName,'gif','LoopCount',Inf,'DelayTime',1);
else
imwrite(ImageCell{k},FileName,'gif','WriteMode','append','DelayTime',1);
end
end
As you see, its not that different from the example on the Mathworks website. Here my images are in a cell array but yours might be in a regular array or something else.That should work fine; when I open 'UnicornAnimation.gif' it is indeed a nice animation!
Hope that helps!

Matlab: How can I display several outputs in the same image?

Let's say my image is img=zeros(100,100,3), my outputs are several ellipse which i get using a created function [ret]=draw_ellipse(x,y,a,b,angle,color,img), I can display one ellipse using imshow(ret).For the moment, I'm trying to show serval ellipse in the image. But i don't know how to code it. will ‘for loop’ work or I need to hold them?
If this is related to what you were doing in your previous question, then what you need to do is to pass the result of one iteration as input to the next.
So assuming that the function [ret]=draw_ellipse(x,y,a,b,angle,color,img) you mentioned takes as input an image img and returns the same image with an ellipse drawn on it, you could do this:
%# ellipses parameters
%#x = {..}; y = {..};
%#a = {..}; b = {..};
%#angle = {..}; color = {..};
img = zeros(200,100,'uint8'); %# image to start with
for i=1:10
img = draw_ellipse(x{i},y{i}, a{i},b{i}, angle{i}, color{i}, img);
end
imshow(img)
I'm a bit unsure of what you want. You want to show several ellipse in one image, like plotting several graphs with hold on?
There is no equivalent command for images, but a simple solution is to add the ellipses into one image and show that one:
several_ellipse = ellipse1 + ellipse2 + ellipse3;
imshow(several_ellipse)
Presumably you want to pass ret as the final input to the next call to draw_ellipse.

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