I am attempting to make a movie from a 3d matrix, which is made multiple 2d matrices and the third dimension is time.
I have read the following question witch is pretty much the same and I have attempted to do the same. How to make a video from a 3d matrix in matlab
The 3d matrix I want to play is stored in a object instanced A.
a.movie; % 3D matrix
X = permute(a.movie,[1 2 4 3]); % 4D matrix
movie = immovie(X,map); % map is the colormap you want to use
implay(movie);
I would like to know why should a.movie be permuted? And what is the map referred?
How can I define 0 as blue and 100 as red?
The post you linked us to exactly answers that. immovie expects a m x n x 1 x k matrix where m and n are the rows and columns of 1 slice from your 3D matrix, and k is the number of slices. You currently have your 3D matrix set up to be m x n x k. Therefore, by permuting, you are artificially creating a 4D matrix from your 3D original matrix. Simply put, you can think of your 3D matrix as having a singleton 4D dimension: m x n x k x 1. The job of permute here is to swap the 3rd and 4th dimension - that's why you see the [1 2 4 3] vector in the permute call. The first and second dimensions represent the rows and columns, and you leave those empty.
Now that answers the permute question. The map is defined as a colour map. This maps each value in your 3D matrix to a unique colour. Basically, the colour map is a M x 3 matrix where row in this matrix corresponds to a unique colour. Each column represents a colour channel. Therefore, the first column represents the proportion of red you want, the second channel is the proportion of green and the last is the proportion of blue. Keep in mind that these colours should be normalized between [0,1].
The goal of the colour map is to take each value in your 3D matrix, and figure out which colour that value maps to. The way to do this is to use each value in your 3D matrix exactly as it is and use this to access the row of the colour map. This row gives you the colours you want. Now, I'm assuming that your values in the 3D matrix span from 0 to 100.
If you want the colours to span between blue and red. The blue colour has an exact colour of RGB = (0,0,1) assuming normalized coordinates and similarly, the red represents the exact colour of RGB = (1,0,0). Therefore, start off with RGB = (0,0,1), then start linearly increasing the red component while linearly decreasing the blue component until the red is 1 and the blue is 0.
What we can do is figure out how many unique values there are in your matrix, then we can create our colour map that way so we can ensure that each value in your matrix gets assigned to one colour. However, this will require that a.movie be redefined to ensure that we can assign a value to a colour.
Therefore, I'd create your colour map like this:
[unq,~,id] = unique(a.movie);
movie_IDs = reshape(id, size(a.movie));
M = numel(unq);
map = [linspace(1,0,M).', zeros(M,1), linspace(0,1,M).'];
Now, go ahead and use map with the above code to create your movie.
X = permute(movie_IDs,[1 2 4 3]); % 4D matrix
movie = immovie(X,map); % map is the colormap you want to use
implay(movie);
However, the colour map you're looking at is the jet colour map. Therefore, you can simply just create a jet colour map:
map = jet(M);
However, you must make sure you run through each value in a.movie and assign a unique integer to each value to ensure that there are no gaps in your data and every value gets assigned to a new value that goes up from 1 to M in order for the movie to properly access the right colour.
MATLAB has a bunch of built-in colour maps for you to use if you don't feel like designing your own colour map. http://www.mathworks.com/help/matlab/ref/colormap.html#inputarg_map - However, from what I see in your post, making the colour map is what you want to do.