I have got the following code. I need to rewrite it without looping. How should I do it?
l1 = [1 2 3 2 1];
l2 = [3 4 4 5 4];
A = zeros(5,5);
for i=1:5
A(i, l1(i):l2(i)) = 1;
end
A
You can use bsxfun -
I = 1:5 % Array corresponding to iterator : "for i=1:5"
out = bsxfun(#le,l1(:),I) & bsxfun(#ge,l2(:),I)
If you need a double datatype array, convert to double, like so -
out_double = double(out)
Add one more into the mix then! This one simply uses a cumsum to generate all the 1s - so it does not use the : operator at all - It's also fully parallel :D
l1 = [1 2 3 2 1];
l2 = [3 4 4 5 4];
A = zeros(5,5);
L1 = l1+(1:5)*5-5; %Convert to matrix location index
L2 = l2+(1:5)*5-5; %Convert to matrix location index
A(L1) = 1; %Place 1 in that location
A(L2) = 1; %Place 1 in that location
B = cumsum(A,1) ==1 ; %So fast
Answer = (A|B)'; %Lightning fast
Answer =
1 1 1 0 0
0 1 1 1 0
0 0 1 1 0
0 1 1 1 1
1 1 1 1 0
Here is how you could build the matrix without using a loop.
% Our starting values
l1 = [1 2 3 2 1];
l2 = [3 4 4 5 4];
% Coordinate grid of the right size (we don't need r, but I keep it there for illustration)
[r,c] = ndgrid(1:5);
% Build the logical index based on our lower and upper bounds on the column indices
idx_l1=bsxfun(#ge,c,l1');
idx_l2=bsxfun(#le,c,l2');
% The result
A = zeros(size(idx_l1));
A(idx_l1&idx_l2)=1
You may need something like [r,c] = ndgrid(1:numel(l1),1:10).
Also if your matrix size is truly huge and memory becomes an issue, you may want to stick to a loop anyway, but for 'normal size' this could be faster.
There should be some skepticism in every vectorization. If you measure the time actually your loop is faster than the given answers, mostly because you only perform in place write.
Here is another one that would probably get faster for larger sizes but I haven't tested:
tic
myind = [];
for i = 1:5
myind = [myind (5*(i-1))+[l1(i):l2(i)]];
end
A(myind) = 1;
toc
gives the transposed A because of the linear indexing order.
Related
I'm performing input-output calculations in Octave. I have several matrices/vectors in the formula:
F = f' * (I-A)^-1 * Y
All vectors probably contain zeroes. I would like to omit them from the calculation and just return 0 instead. Any help would be greatly appreciated!
Miranda
What do you mean when you say "omit them"?
If you want to remove zeros from a vector you can do this:
octave:1> x=[1,2,0,3,4,0,5];
octave:2> x(find(x==0))=[]
x =
1 2 3 4 5
The logic is: x==0 will test each element of x (in this case the test is if it equals zero) and will return a vector of 0's and 1's (0 if the test is false for that element and 1 otherwise)
So:
octave:1> x=[1,2,0,3,4,0,5];
octave:2> x==0
ans =
0 0 1 0 0 1 0
The find() function will return the index value of any non-zero element of it's argument, hence:
octave:3> find(x==0)
ans =
3 6
And then you are just indexing and removing when you do something like:
octave:5> x([3, 6]) = []
x =
1 2 3 4 5
But instead you do it with the output of the find() function (which is the vector [3,6] in this case)
You can do the same for matrices:
octave:7> A = [1,2,0;4,5,0]
A =
1 2 0
4 5 0
octave:8> A(find(A==0))=[]
A =
1
4
2
5
Then use the reshape() function to turn it back into a matrix.
I'm trying to create a function that is able to go through a row vector and output the possible combinations of an n choose k without recursion.
For example: 3 choose 2 on [a,b,c] outputs [a,b; a,c; b,c]
I found this: How to loop through all the combinations of e.g. 48 choose 5 which shows how to do it for a fixed n choose k and this: https://codereview.stackexchange.com/questions/7001/generating-all-combinations-of-an-array which shows how to get all possible combinations. Using the latter code, I managed to make a very simple and inefficient function in matlab which returned the result:
function [ combi ] = NCK(x,k)
%x - row vector of inputs
%k - number of elements in the combinations
combi = [];
letLen = 2^length(x);
for i = 0:letLen-1
temp=[0];
a=1;
for j=0:length(x)-1
if (bitand(i,2^j))
temp(k) = x(j+1);
a=a+1;
end
end
if (nnz(temp) == k)
combi=[combi; derp];
end
end
combi = sortrows(combi);
end
This works well for very small vectors, but I need this to be able to work with vectors of at least 50 in length. I've found many examples of how to do this recursively, but is there an efficient way to do this without recursion and still be able to do variable sized vectors and ks?
Here's a simple function that will take a permutation of k ones and n-k zeros and return the next combination of nchoosek. It's completely independent of the values of n and k, taking the values directly from the input array.
function [nextc] = nextComb(oldc)
nextc = [];
o = find(oldc, 1); %// find the first one
z = find(~oldc(o+1:end), 1) + o; %// find the first zero *after* the first one
if length(z) > 0
nextc = oldc;
nextc(1:z-1) = 0;
nextc(z) = 1; %// make the first zero a one
nextc(1:nnz(oldc(1:z-2))) = 1; %// move previous ones to the beginning
else
nextc = zeros(size(oldc));
nextc(1:nnz(oldc)) = 1; %// start over
end
end
(Note that the else clause is only necessary if you want the combinations to wrap around from the last combination to the first.)
If you call this function with, for example:
A = [1 1 1 1 1 0 1 0 0 1 1]
nextCombination = nextComb(A)
the output will be:
A =
1 1 1 1 1 0 1 0 0 1 1
nextCombination =
1 1 1 1 0 1 1 0 0 1 1
You can then use this as a mask into your alphabet (or whatever elements you want combinations of).
C = ['a' 'b' 'c' 'd' 'e' 'f' 'g' 'h' 'i' 'j' 'k']
C(find(nextCombination))
ans = abcdegjk
The first combination in this ordering is
1 1 1 1 1 1 1 1 0 0 0
and the last is
0 0 0 1 1 1 1 1 1 1 1
To generate the first combination programatically,
n = 11; k = 8;
nextCombination = zeros(1,n);
nextCombination(1:k) = 1;
Now you can iterate through the combinations (or however many you're willing to wait for):
for c = 2:nchoosek(n,k) %// start from 2; we already have 1
nextCombination = nextComb(A);
%// do something with the combination...
end
For your example above:
nextCombination = [1 1 0];
C(find(nextCombination))
for c = 2:nchoosek(3,2)
nextCombination = nextComb(nextCombination);
C(find(nextCombination))
end
ans = ab
ans = ac
ans = bc
Note: I've updated the code; I had forgotten to include the line to move all of the 1's that occur prior to the swapped digits to the beginning of the array. The current code (in addition to being corrected above) is on ideone here. Output for 4 choose 2 is:
allCombs =
1 2
1 3
2 3
1 4
2 4
3 4
I have a problem with sorting some finance data based on firmnumbers. So given is a matrix that looks like:
[1 3 4 7;
1 2 7 8;
2 3 7 8;]
On Matlab i would like the matrix to be sorted as follows:
[1 0 3 4 7 0;
1 2 0 0 7 8;
0 2 3 0 7 8;]
So basically every column needs to consist of 1 type of number.
I have tried many things but i cant get the matrix sorted properly.
A = [1 3 4 7;
1 2 7 8;
2 3 7 8;]
%// Get a unique list of numbers in the order that you want them to appear as the new columns
U = unique(A(:))'
%'//For each column (of your output, same as columns of U), find which rows have that number. Do this by making A 3D so that bsxfun compares each element with each element
temp1 = bsxfun(#eq,permute(A,[1,3,2]),U)
%// Consolidate this into a boolean matrix with the right dimensions and 1 where you'll have a number in your final answer
temp2 = any(temp1,3)
%// Finally multiply each line with U
bsxfun(#times, temp2, U)
So you can do that all in one line but I broke it up to make it easier to understand. I suggest you run each line and look at the output to see how it works. It might seem complicated but it's worthwhile getting to understand bsxfun as it's a really useful function. The first use which also uses permute is a bit more tricky so I suggest you first make sure you understand that last line and then work backwards.
What you are asking can also be seen as an histogram
A = [1 3 4 7;
1 2 7 8;
2 3 7 8;]
uniquevalues = unique(A(:))
N = histc(A,uniquevalues' ,2) %//'
B = bsxfun(#times,N,uniquevalues') %//'
%// bsxfun can replace the following instructions:
%//(the instructions are equivalent only when each value appears only once per row )
%// B = repmat(uniquevalues', size(A,1),1)
%// B(N==0) = 0
Answer without assumptions - Simplified
I did not feel comfortable with my old answer that makes the assumption of everything being an integer and removed the possibility of duplicates, so I came up with a different solution based on #lib's suggestion of using a histogram and counting method.
The only case I can see this not working for is if a 0 is entered. you will end up with a column of all zeros, which one might interpret as all rows initially containing a zero, but that would be incorrect. you could uses nan instead of zeros in that case, but not sure what this data is being put into, and if it that processing would freak out.
EDITED
Includes sorting of secondary matrix, B, along with A.
A = [-1 3 4 7 9; 0 2 2 7 8.2; 2 3 5 9 8];
B = [5 4 3 2 1; 1 2 3 4 5; 10 9 8 7 6];
keys = unique(A);
[counts,bin] = histc(A,transpose(unique(A)),2);
A_sorted = cell(size(A,1),1);
for ii = 1:size(A,1)
for jj = 1:numel(keys)
temp = zeros(1,max(counts(:,jj)));
temp(1:counts(ii,jj)) = keys(jj);
A_sorted{ii} = [A_sorted{ii},temp];
end
end
A_sorted = cell2mat(A_sorted);
B_sorted = nan(size(A_sorted));
for ii = 1:size(bin,1)
for jj = 1:size(bin,2)
idx = bin(ii,jj);
while ~isnan(B_sorted(ii,idx))
idx = idx+1;
end
B_sorted(ii,idx) = B(ii,jj);
end
end
B_sorted(isnan(B_sorted)) = 0
You can create at the beginning a matrix with 9 columns , and treat the values in your original matrix as column indexes.
A = [1 3 4 7;
1 2 7 8;
2 3 7 8;]
B = zeros(3,max(A(:)))
for i = 1:size(A,1)
B(i,A(i,:)) = A(i,:)
end
B(:,~any(B,1)) = []
I have a 3D image, divided into contiguous regions where each voxel has the same value. The value assigned to this region is unique to the region and serves as a label. The example image below describes the 2D case:
1 1 1 1 2 2 2
1 1 1 2 2 2 3
Im = 1 4 1 2 2 3 3
4 4 4 4 3 3 3
4 4 4 4 3 3 3
I want to create a graph describing adjaciency between these regions. In the above case, this would be:
0 1 0 1
A = 1 0 1 1
0 1 0 1
1 1 1 0
I'm looking for a speedy solution to do this for large 3D images in MATLAB. I came up with a solution that iterates over all regions, which takes 0.05s per iteration - unfortunately, this will take over half an hour for an image with 32'000 regions. Does anybody now a more elegant way of doing this? I'm posting the current algorithm below:
labels = unique(Im); % assuming labels go continuously from 1 to N
A = zeros(labels);
for ii=labels
% border mask to find neighbourhood
dil = imdilate( Im==ii, ones(3,3,3) );
border = dil - (Im==ii);
neighLabels = unique( Im(border>0) );
A(ii,neighLabels) = 1;
end
imdilate is the bottleneck I would like to avoid.
Thank you for your help!
I came up with a solution which is a combination of Divakar's and teng's answers, as well as my own modifications and I generalised it to the 2D or 3D case.
To make it more efficient, I should probably pre-allocate the r and c, but in the meantime, this is the runtime:
For a 3D image of dimension 117x159x126 and 32000 separate regions: 0.79s
For the above 2D example: 0.004671s with this solution, 0.002136s with Divakar's solution, 0.03995s with teng's solution.
I haven't tried extending the winner (Divakar) to the 3D case, though!
noDims = length(size(Im));
validim = ones(size(Im))>0;
labels = unique(Im);
if noDims == 3
Im = padarray(Im,[1 1 1],'replicate', 'post');
shifts = {[-1 0 0] [0 -1 0] [0 0 -1]};
elseif noDims == 2
Im = padarray(Im,[1 1],'replicate', 'post');
shifts = {[-1 0] [0 -1]};
end
% get value of the neighbors for each pixel
% by shifting the image in each direction
r=[]; c=[];
for i = 1:numel(shifts)
tmp = circshift(Im,shifts{i});
r = [r ; Im(validim)];
c = [c ; tmp(validim)];
end
A = sparse(r,c,ones(size(r)), numel(labels), numel(labels) );
% make symmetric, delete diagonal
A = (A+A')>0;
A(1:size(A,1)+1:end)=0;
Thanks for the help!
Try this out -
Im = padarray(Im,[1 1],'replicate');
labels = unique(Im);
box1 = [-size(Im,1)-1 -size(Im,1) -size(Im,1)+1 -1 1 size(Im,1)-1 size(Im,1) size(Im,1)+1];
mat1 = NaN(numel(labels),numel(labels));
for k2=1:numel(labels)
a1 = find(Im==k2);
for k1=1:numel(labels)
a2 = find(Im==k1);
t1 = bsxfun(#plus,a1,box1);
t2 = bsxfun(#eq,t1,permute(a2,[3 2 1]));
mat1(k2,k1) = any(t2(:));
end
end
mat1(1:size(mat1,1)+1:end)=0;
If it works for you, share with us the runtimes as comparison? Would love to see if the coffee brews any faster than half an hour!
Below is my attempt.
Im = [1 1 1 1 2 2 2;
1 1 1 2 2 2 3;
1 4 1 2 2 3 3;
4 4 4 4 3 3 3;
4 4 4 4 3 3 3];
% mark the borders
validim = zeros(size(Im));
validim(2:end-1,2:end-1) = 1;
% get value of the 4-neighbors for each pixel
% by shifting the images 4 times in each direction
numNeighbors = 4;
adj = zeros([prod(size(Im)),numNeighbors]);
shifts = {[0 1] [0 -1] [1 0] [-1 0]};
for i = 1:numNeighbors
tmp = circshift(Im,shifts{i});
tmp(validim == 0) = nan;
adj(:,i) = tmp(:);
end
% mark neighbors where it does not eq Im
imDuplicates = repmat(Im(:),[1 numNeighbors]);
nonequals = adj ~= imDuplicates;
% neglect the border
nonequals(isnan(adj)) = 0;
% get these neighbor values and the corresponding Im value
compared = [imDuplicates(nonequals == 1) adj(nonequals == 1)];
% construct your 'A' % possibly could be more optimized here.
labels = unique(Im);
A = zeros(numel(labels));
for i = 1:size(compared,1)
A(compared(i,1),compared(i,2)) = 1;
end
#Lisa
Yours reasoning is elegant, though it obviously gives wrong answers for labels on the edges.
Try this simple label matrix:
Im =
1 2 2
3 3 3
3 4 4
The resulting adjacency matrix , according to your code is:
A =
0 1 1 0
1 0 1 1
1 1 0 1
0 1 1 0
which claims an adjacency between labels "2" and "4": obviously wrong. This happens simply because you are reading padded Im labels based on "validim" indices, which now doesn't match the new Im and goes all the way down to the lower borders.
Suppose I have this matrix:
matrix = [2 2; 2 3; 3 4; 4 5]
And now I'd like to filter out all rows which do not begin with an even number to produce
[2 2; 2 3; 4 5]
Is there a high-level procedure for doing this, or do I have to code for it?
You can get a logical index for the rows whose first element is even, and use : to select all the columns. Here's how it's done, line by line:
octave> matrix = [2 2; 2 3; 3 4; 4 5]
matrix =
2 2
2 3
3 4
4 5
octave> ! mod (matrix(:,1), 2)
ans =
1
1
0
1
octave> matrix(! mod (matrix(:,1), 2),:)
ans =
2 2
2 3
4 5
EDIT: in the comments below it was asked for other selection methods. I'm unaware of any specific function for it, but the thing above is indexing with a function:
even_rows = matrix(! mod (matrix(:,1), 2), :) # first element is even
s3_rows = matrix(matrix(:,1) == 3, :); # first element is 3
int_rows = matrix(fix (matrix(:,1)), == matrix(:,1), :); # first element is an integer
IF there was a function, one would still have to write the function, it wouldn't be any easier shorter or easier to read. But if you want to write a function, you could:
function selec = select_rows (func, mt)
selec = mt(func (mt(:,1)),:);
endfunction
even_rows = select_rows (#(x) ! mod (x, 2), matrix);
se_rows = select_rows (#(x) x == 3, matrix);
int_rows = select_rows (#(x) fix (x) == x, matrix);
EDIT2: to have the rows that have already matched, simply keep track of them on the mask. Example:
mask = ! mod (matrix(:,1), 2); # mask for even numbers
even = matrix(mask,:);
mask = ! mask & matrix(:,1) == 3; # mask for left overs starting with a 3
s3 = matrix(mask,:);
rest = matrix(! mask, :); # get the leftovers
As above, you could write a function that does it. It would take a matrix as the first argument plus any number of function handles. It would iterate over the function handles modifying the mask everytime and filling a cell array with the matrices.