random sampling from a 3-way data cube - matlab

imagine a 2 x 2 x 2 three-way data cube:
data = [1 2; 3 4];
data(:,:,2) = [5 6; 7 8]
I wish to generate a row-column slice from this cube (i.e. a 2x2 matrix) in which each element of the slice is obtained by randomly sampling its 3-mode fiber (i.e. an nth mode fiber is a vector running along the nth mode/dimension/way. There are 4 3-mode fibers in this cube, one of them is f1 = [1 5], another one is f2 = [2 6] and so on). For example, one slice could turn out to be:
slice = [5 2; 3 4]
a different sampling might lead to the slice:
slice = [1 2; 7 8]
Is there a quick way to do this?
I tried using slice = datasample(data,1,3) but this function randomly picks a row-column slice from the cube (i.e. either, slice = [1 2; 3 4] or [5 6; 7 8]).

If I understand correctly, then it's quite simple actually. You have four 3-mode fibers and you wish to construct a 2x2 matrix where each element was sampled from the corresponding fiber.
So, you need to sample 4 times (one for each fiber) one element out of 2 (each fiber has two elements):
>> [h w fiberSize] = size(data); % make the solution more general
>> fIdx = randsample( fiberSize, h*w ); % sample with replacements
After sampling we construct the slice, for simplicity I'll "flatten" the 3D data into a 2D matrix
>> fData = reshape( data, [], fiberSize );
>> slice = fData( sub2ind( [h*w fiberSize], 1:(h*w), fIdx ) );
>> slice = reshape( slice, [h w] ); % shape the slice

The following solution is valid for any cube size. No toolbox required.
N = size(data,1); %//length of side of cube
r = randi(N,1,N^2)-1; %//this is the random sampling
data_permuted = permute(data,[3 1 2]); %//permute so that sampling is along first dim
slice = data_permuted((1:N:N^3)+r); %//sample using linear indexing
slice = reshape(slice.',N,N); %//reshape into a matrix

Try this solution for any nmode (e.g. nmode=3 is the 3-mode):
data = cat(3,[1 2; 3 4],[5 6; 7 8]);
nmode = 3;
Dn = size(data,nmode);
modeSampleInds = randi(Dn,1,numel(data)/Dn); % here is the random sample
dp = reshape(permute(data,[nmode setdiff(1:ndims(data),nmode)]), Dn, []);
outSize = size(data); outSize(nmode)=1;
slice = reshape(dp(sub2ind(size(dp),modeSampleInds,1:size(dp,2))),outSize)
Note that this does not require the Statistics Toolbox. It is also completely generalized for any matrix size, number of dimension, and "N-mode fiber".
I'd be glad to explain each line if needed.

Related

extract 3D matrix's columns based on "surface" values - vectorization

I have an NxMxK matrix A
A = [1 2 1; 1 1 2];
A = cat(3, A, [3 3 3; 3 3 3])
A(:,:,1) =
1 2 1
1 1 2
A(:,:,2) =
3 3 3
3 3 3
and I want to create a YxK 2D matrix B where K is the number of elements of A(:,:,1)==2:
k=0;
for ii=1:size(A,1)
for jj=1:size(A,2)
if A(ii,jj)==2
k=k+1;
B(k,:) = A(ii,jj,:);
end
end
end
Is there a way of vectorizing this code?
My attempt was to find the indices of A(:,:,1)==2 and then try to select the whole column but I do not know how to do it:
inds = find(A(:,:,1)==2)
B = A(inds,:) %this line does not make sense
EDIT
Preallocating B helps:
inds=find(A(:,:,1)==2);
B=NaN(numel(inds),size(A,3));
k=0;
for ii=1:size(A,1)
for jj=1:size(A,2)
if A(ii,jj)==2
k=k+1;
B(k,:) = squeeze(A(ii,jj,:));
end
end
end
But still not vectorized.
You can reshape matrix A to a (N*M)xK 2D matrix.
A = [1 2 1; 1 1 2];
A = cat(3, A, [3 3 3; 3 3 3]);
A_ = reshape(A,numel(A(:,:,1)),size(A,3));
B = A_(A_(:,1)==2,:);
Your first attempt at vectorization is almost right. Just don't use find, but use the logical matrix for indexing.
inds = A(:,:,1)==2;
The inds matrix is 2D, not 3D, so we use repmat to repeat its values along the 3rd dimension:
K = size(A,3);
inds = repmat(inds,1,1,K); % or simply cat(3,inds,inds) if K==2
B = A(inds);
The result is a column vector of size Y*K, not a matrix of size YxK, we can use reshape to fix that:
B = reshape(B,[],K);
I guess this answer is similar to Anthony's, except the indexing and the reshaping are reversed. I didn't really notice the similarity until after I wrote it down. I guess also Anthony's is a little shorter. :/

matlab remove for loop in matrix computation

I'm working on a problem on Matlab according to Matrix. I think my code could be improved by remove the for loop. But I really don't know how to fix this one. Can anyone help me, please?
the code is:
K = 3;
X = [1 2; 3 4; 5 6; 7 8];
idx = [1;2;3;1];
for i = 1:K
ids = (idx == i);
centroids(i,:) = sum(bsxfun(#times, X, ids))./ sum(ids);
end
in this code, data points X is 4x2. There are K=3 centroids, so the centroids is a matrix of 3x2. This code is part of a K-mean function, which is using data points and their closest centroids to find new position of centroids.
I want to make the code as something without the FOR loop, maybe beginning like this:
ids = bsxfun(#eq, idx, 1:K);
centroids = ..............
You can avoid the bsxfun by using logical indexing, this seems to be a worthwhile performance increase, at least for small matrices X. It is best for small K, and for a small number of rows of X.
K = 3;
X = [1 2; 3 4; 5 6; 7 8];
idx = [1;2;3;1];
centroids=zeros(K,2);
for i = 1:K
ids = (idx == i);
centroids(i,:) = sum(X(ids,:),1)./sum(ids);
end
If X has a large number of rows, this method is fastest:
K = 3;
X = [1 2; 3 4; 5 6; 7 8];
idx = [1;2;3;1];
centroids=zeros(K,2);
t=bsxfun(#eq,idx,1:K);
centroids=bsxfun(#rdivide,t.'*X,sum(t).');
And if K is very large, Luis' accumarray method is fastest.
You could apply accumarray. Note that accumarray only works when X is a column. So, if X has two columns, you can call accumarray twice:
centroids(:,1) = accumarray(idx, X(:,1), [], #mean)
centroids(:,2) = accumarray(idx, X(:,2), [], #mean)
Alternatively, if X contains two columns of real numbers, you can use complex to "pack" the two columns into one complex column, and then unpack the results:
centroids = accumarray(idx, complex(X(:,1),X(:,2)), [], #mean);
centroids = [ real(centroids) imag(centroids)];
If X has an arbitrary number of columns, possibly with complex numbers, you can loop over columns:
centroids = NaN(K, size(X,2)); %// preallocate
for col = 1:size(X,2);
centroids(:,col) = accumarray(idx, X(:,col), [], #mean);
end

pick random numbers in certain range from vector

how would you use randperm to randomly pick three numbers out of a range of 5 in a vector?
i have a vector like this:
A = [1 2 3 4 5 6 7 8 9 10]
now from every 5 consecutive values i want to randomly pick 3 of them:
A_result = [1 3 5 6 7 9]
any help is appreciated!
This one uses different random indices in every 5-group.
A = [1 2 3 4 5 6 7 8 9 10]
B = reshape(A,5,[]) % (5 x 2)
ind = cell2mat(arrayfun(#(x)sort(randperm(5,3))',1:size(B,2),'UniformOutput',false)) % (3 x 2), row indices into B
ind = bsxfun(#plus,ind,size(B,1)*(0:size(B,2)-1)) % (3 x 2), linear indices into B
C = B(ind) % (3 x 2) result
C(:)' % result vector
Every sort(randperm(5,3))' call generates a random column vector with 3 ascending numbers from 1 to 5, like [1;3;4] or [2;4;5]. arrayfun with the dummy argument x calls this 2 times in this example, because A consists of 2 sub-vectors of length 5. With the argument 'Uniform output' set to false, it generates a cell array of these random vectors, and cell2mat converts it to the (3 x 2)-matrix ind. The bsxfun call converts the values in the matrix ind to a matrix of linear indices into matrix B or A.
For your (900 x 25)-matrix, do
A = rand(900,25); % (900 x 25)
B = A'; % (25 x 900)
ind = cell2mat(arrayfun(#(x)sort(randperm(25,17))',1:size(B,2),'UniformOutput',false)); % (17 x 900), row indices into B
ind = bsxfun(#plus,ind,size(B,1)*(0:size(B,2)-1)); % (17 x 900), linear indices into B
C = B(ind); % (17 x 900), result
You can use reshape and randsample
rA = reshape( A, 5, [] ); % groups of 5 in a a row
A_result = rA( randsample( 5, 3, false ), : );
A_result = reshape( A_result, 1, [] );
You can pre-generate all possible picking patterns, and then randomly select one such pattern for each group. This approach is suitable for small group sizes, otherwise it may use a lot of memory.
A = 1:10; %// example data
n = 5; %// group size. Assumed to divide numel(A)
k = 3; %// how many to pick from each group
S = numel(A);
patterns = nchoosek(1:n, k); %// all possible picking patterns
K = size(patterns, 1);
p = randi(K, S/n, 1); %// generate random indices for patterns
pick = bsxfun(#plus, patterns(p,:).', (0:n:S-1)); %'// to linear indices
A_result = A(pick(:));

How to represent a vector as a matrix?

I have a vector of length 3. i want to represent it as a matrix of dimension 4*2. ie) if the length of vector is n then matrix should be of dimension (n+1)*2. The matrix should have elements arranged as follows:
Vector= [2 3 4]
Matrix = [0 2;2 3;3 4;4 0]
You can solve your problem easily with simple operations:
vector = [2 3 4];
matrix = [0 vector; vector 0]';
' is used to transpose the matrix.
Additionally there are two useful functions in Matlab to manipulate matrices and vectors:
reshape()
repmat()
The command reshape from Matlab is the basis of my answer to your question:
B = reshape(A,m,n) returns the m-by-n matrix B whose elements are taken column-wise from A. An error results if A does not have m*n elements (from the official Matlab help).
You basically add zeros at the beginning and at the end and then have every number in the vector occur twice (if you "unfold"/reshape the matrix). So lets construct the desired matrix by reversing this description:
%set input vector
v = [2 3 4];
%"double" the numbers, v_ is my temporary storage variable
v_ = [v; v];
%align all numbers along one dimension
v_ = reshape(v_, 2*length(v), 1)
%add zeros at beginning and end
v_ = [0 v_ 0];
%procude final matrix
m = reshape(v_, length(v)+1, 2);
in short
%set input vector
v = [2 3 4];
%"double" the numbers, v_ is my temporary storage variable
%all values are aligned as row vector
%zeros are added at beginning and end
v_ = [0, v, v, 0];
%produce final matrix
m = reshape(v_, length(v)+1, 2);
I haven't checked it, since I don't have a Matlab at hand right now, but you should get the idea.
Edit
The answer by 13aumi manages this task even without the reshape command. However, you need to pay close attention to the shape of v (row- vs- column-vector).

Getting the N-dimensional product of vectors

I am trying to write code to get the 'N-dimensional product' of vectors. So for example, if I have 2 vectors of length L, x & y, then the '2-dimensional product' is simply the regular vector product, R=x*y', so that each entry of R, R(i,j) is the product of the i'th element of x and the j'th element of y, aka R(i,j)=x(i)*y(j).
The problem is how to elegantly generalize this in matlab for arbitrary dimensions. This is I had 3 vectors, x,y,z, I want the 3 dimensional array, R, such that R(i,j,k)=x(i)*y(j)*z(k).
Same thing for 4 vectors, x1,x2,x3,x4: R(i1,i2,i3,i4)=x1(i1)*x2(i2)*x3(i3)*x4(i4), etc...
Also, I do NOT know the number of dimensions beforehand. The code must be able to handle an arbitrary number of input vectors, and the number of input vectors corresponds to the dimensionality of the final answer.
Is there any easy matlab trick to do this and avoid going through each element of R specifically?
Thanks!
I think by "regular vector product" you mean outer product.
In any case, you can use the ndgrid function. I like this more than using bsxfun as it's a little more straightforward.
% make some vectors
w = 1:10;
x = w+1;
y = x+1;
z = y+1;
vecs = {w,x,y,z};
nvecs = length(vecs);
[grids{1:nvecs}] = ndgrid(vecs{:});
R = grids{1};
for i=2:nvecs
R = R .* grids{i};
end;
% Check results
for i=1:10
for j=1:10
for k=1:10
for l=1:10
V(i,j,k,l) = R(i,j,k,l) == w(i)*x(j)*y(k)*z(l);
end;
end;
end;
end;
all(V(:))
ans = 1
The built-in function bsxfun is a fast utility that should be able to help. It is designed to perform 2 input functions on a per-element basis for two inputs with mismatching dimensions. Singletons dimensions are expanded, and non-singleton dimensions need to match. (It sounds confusing, but once grok'd it useful in many ways.)
As I understand your problem, you can adjust the dimension shape of each vector to define the dimension that it should be defined across. Then use nested bsxfun calls to perform the multiplication.
Example code follows:
%Some inputs, N-by-1 vectors
x = [1; 3; 9];
y = [1; 2; 4];
z = [1; 5];
%The computation you describe, using nested BSXFUN calls
bsxfun(#times, bsxfun(#times, ... %Nested BSX fun calls, 1 per dimension
x, ... % First argument, in dimension 1
permute(y,2:-1:1) ) , ... % Second argument, permuited to dimension 2
permute(z,3:-1:1) ) % Third argument, permuted to dimension 3
%Result
% ans(:,:,1) =
% 1 2 4
% 3 6 12
% 9 18 36
% ans(:,:,2) =
% 5 10 20
% 15 30 60
% 45 90 180
To handle an arbitrary number of dimensions, this can be expanded using a recursive or loop construct. The loop would look something like this:
allInputs = {[1; 3; 9], [1; 2; 4], [1; 5]};
accumulatedResult = allInputs {1};
for ix = 2:length(allInputs)
accumulatedResult = bsxfun(#times, ...
accumulatedResult, ...
permute(allInputs{ix},ix:-1:1));
end