Dimension of a TIF file as “420x560x3” - Matlab to

Question

I am trying to create a movie in Matlab using series of functions under VideoWriter function. My code is somewhat like one shown below:

vidObj=VideoWriter('movie.avi');
open(vidObj);

for i=1:N %N is number of frames

[nx,ny]=coordinates(Lx,Ly,Nx,Ny,[x(i),-y(i)]);
%Lx and Ly refer to the length and height in meters. 
%Nx and Ny are number of pixels (boxes) and fit into the respective L's. 
%If Lx=10e-6 , with Nx=5, there will be 5 pixels in x dimension,
%each of length 2e-6 m.
[xf,yf]=ndgrid(nx,ny);
zf=zeros(size(xf))+z(i);    

% generate a frame here
[E,H]=nfmie(an,bn,xf,yf,zf,rad,ns,nm,lambda,tf_flag,cc_flag);
Ecc=sqrt(real(E(:,:,1)).^2+real(E(:,:,2)).^2+real(E(:,:,3)).^2+imag(E(:,:,1)).^2+imag(E(:,:,2)).^2+imag(E(:,:,3)).^2);
clf
imagesc(nx/rad,ny/rad,Ecc)
rectangle('Position',[-rad(end),-rad(end),dia(end),dia(end)],'Curvature',[1,1]);
axis image;
axis off;
currFrame=getframe(gcf);
writeVideo(vidObj,currFrame);
end
close(vidObj);
return

This generated a movie called movie.avi. However, the movie (and the tif images generated from command window) has the dimensions of "420x560x3".

edit: the tif's are generated from the movie.avi using the following code:

obj = VideoReader('movie.avi');
vid = read(obj);
frames = obj.NumberOfFrames;
for x = 1 : frames
    imwrite(vid(:,:,:,x),strcat('frame-',num2str(x),'.tif'));
end

I am trying to use these images in another software, IDL, following: read Part 1 of this link

However, when runs on IDL, it detects the dimensions as [3x420x560], and therefore generates a really weird image when I run the normalization.

1. How do I fix this? Is using imwrite going to help?
2. I was able to successfully open the .tif in IDL, but it shows that the 420x560 is actually an image including an external grey boundary.

How do I remove this boundary? I tried seeing through my functions and they were fine. (I think)

I apologize in advance for asking so many questions. I am very new to this and need help. Thank you once again

Answer 1

I think that the grey boundary around your image is due to the fact that when the code grabs the frame (using getframe) it is being passed the handle to the current figure (gcf) which includes the grey boundary around the image. Try instead using the handle to the current axis

currFrame=getframe(gca);

I tried this and with gca there was no grey boundary around the image when I tried the

image(currFrame.cdata);

When I retrieved the frame, the data within that corresponded to the image was reduced in dimension. I'm not sure why the code does this but an alternative to getframe is to do the following

I           = imread('someImage.jpg');
h           = imagesc(I);
imageScData = get(h,'CData');
frameData   = im2frame(imageScData);

Naturally, you won't have the first two lines since you are building your image at each iteration of the for loop. But I did notice that size(frameData.cdata)==size(I) - so no reduction.

You also mention how IDL (which I've never used) is reading in the files incorrectly or rather that the image dimensions are detected incorrectly. How are you writing out the image to a tif file? (I didn't see any MATLAB code above, like imwrite, indicating this.)

Answer 2

To fix interleave problem, i.e., 3 x 420 x 560 vs 420 vs 3 x 560 vs 420 x 560 x 3, when reading in IDL, use the INTERLEAVE keyword to READ_TIFF to specify how you want the result:

IDL> im = read_tiff(filename, interleave=2)