Apologies for the awkward title, here is a more specific description of the problem. I have a large (e.g. 10^6 x 10^6) sparse symmetric matrix which defines bonds between nodes.
e.g. The matrix A = [0 1 0 0 0; 1 0 0 2 3; 0 0 0 4 0; 0 2 4 0 5; 0 3 0 5 0] would describe a 5-node system, such that nodes 1 and 2 are connected by bond number A(1,2) = 1, nodes 3 and 4 are connected by bond number A(3,4) = 4, etc.
I want to form two new matrices. The first, B, would list the nodes connected to each node (i.e. each row i of B has elements given by find(A(i,:)), and padded with zeros at the end if necessary) and the second, C, would list the bonds connected to that node (i.e. each row i of C has elements given by nonzeros(A(i,:)), again padded if necessary).
e.g. for the matrix A above, I would want to form B = [2 0 0; 1 4 5; 4 0 0; 2 3 5; 2 4 0] and C = [1 0 0; 1 2 3; 4 0 0; 2 4 5; 3 5 0]
The current code is:
B=zeros(length(A), max(sum(spones(A))))
C=zeros(length(A), max(sum(spones(A))))
for i=1:length(A)
B(i,1:length(find(A(i,:)))) = find(A(i,:));
C(i,1:length(nonzeros(A(i,:)))) = nonzeros(A(i,:));
end
which works, but is slow for large length(A). I have tried other formulations, but they all include for loops and don't give much improvement.
How do I do this without looping through the rows?
Hmm. Not sure how to vectorize (find returns linear indices when given a matrix, which is not what you want), but have you tried this:
B=zeros(length(A), 0);
C=zeros(length(A), 0);
for i=1:length(A)
Bi = find(A(i,:));
B(i,1:length(Bi)) = Bi;
Ci = nonzeros(A(i,:));
C(i,1:length(Ci)) = Ci;
end
I made two changes:
removed call to spones (seems unnecessary; the performance hit needed to expand the # of columns in B and C is probably minimal)
cached result of find() and nonzeros() so they're not called twice
I know it's hard to read, but that code is a vectorized version of your code:
[ i j k ] = find(A);
A2=(A~=0);
j2=nonzeros(cumsum(A2,2).*A2);
C2=accumarray([i,j2],k)
k2=nonzeros(bsxfun(#times,1:size(A,2),A2));
B2=accumarray([i,j2],k2);
Try it and tell me if it works for you.
Related
I am trying to compare two vectors of different size. For instance when I run the code below:
A = [1 4 3 7 9];
B = [1 2 3 4 5 6 7 8 9];
myPadded = [A zeros(1,4)];
C = ismember(myPadded,B)
I get the following output:
C = 1 1 1 1 1 0 0 0 0
However, I want an output that will reflect the positions of the compared values, hence, I would like an output that is displayed as follows:
C = 1 0 1 1 0 0 1 0 1
Please, I need some help :)
There are 2 points. First, you are writing the inputs of ismember in the wrong order. Additionally, you do not need to grow your matrix. Simply try ismember(B, A) and you will get what you expect.
The function ismember(myPadded, B) returns a vector the same size of myPadded, indicating if the i-th element of myPadded is present in B.
To get what you want, just invert parameter order: ismember(B, myPadded).
A quick way of doing this is to use logical indexing. This will only work if the last digit of B is included in A.
A = [1 4 3 7 9];
c(A) = 1; % or true.
An assumption here is that you want to subindex a vector 1:N, so that B always is B = 1:N. In case the last digit is not one this is easy to fix. Just remember to return all to its previous state after you are done. It will be 2 rows extra though.
This solution is meant as a special case working on a very common problem.
New to MatLab here (R2015a, Mac OS 10.10.5), and hoping to find a solution to this indexing problem.
I want to change the values of a large 2D matrix, based on one vector of row indices and one of column indices. For a very simple example, if I have a 3 x 2 matrix of zeros:
A = zeros(3, 2)
0 0
0 0
0 0
I want to change A(1, 1) = 1, and A(2, 2) = 1, and A(3, 1) = 1, such that A is now
1 0
0 1
1 0
And I want to do this using vectors to indicate the row and column indices:
rows = [1 2 3];
cols = [1 2 1];
Is there a way to do this without looping? Remember, this is a toy example that needs to work on a very large 2D matrix. For extra credit, can I also include a vector that indicates which value to insert, instead of fixing it at 1?
My looping approach is easy, but slow:
for i = 1:length(rows)
A(rows(i), cols(i)) = 1;
end
sub2ind can help here,
A = zeros(3,2)
rows = [1 2 3];
cols = [1 2 1];
A(sub2ind(size(A),rows,cols))=1
A =
1 0
0 1
1 0
with a vector to 'insert'
b = [1,2,3];
A(sub2ind(size(A),rows,cols))=b
A =
1 0
0 2
3 0
I found this answer online when checking on the speed of sub2ind.
idx = rows + (cols - 1) * size(A, 1);
therefore
A(idx) = 1 % or b
5 tests on a big matrix (~ 5 second operations) shows it's 20% faster than sub2ind.
There is code for an n-dimensional problem here too.
What you have is basically a sparse definition of a matrix. Thus, an alternative to sub2ind is sparse. It will create a sparse matrix, use full to convert it to a full matrix.
A=full(sparse(rows,cols,1,3,2))
I'm having a few issues getting MATLAB to do what I want.
say I have a matrix x = [1 2 3 4; 1 4 4 5; 6 4 1 4]
I'm trying to write code that will go through the matrix and change each 4 to a 5, so it modifies the input matrix
I've tried a few things:
while index <= numel(x)
if index == 4
index = 5;
end
index = index + 1;
end
for item = x
if item == 4
item = 5;
end
end
the simplest thing i tried was
for item = x
if item == 4
item = 5;
end
end
i noticed by looking at the workspace that the value of item did indeed change but the value of x (the matrix) stayed the same.
How do I get the output that i'm looking for?
If you just want to change all the 4s to 5s then:
x(x==4)=5
basically x==4 will result in a logical matrix with 1s everywhere there was a 4 in x:
[0 0 0 1
0 1 1 0
0 1 0 1]
We then use logical index to only affect the values of x where those 1s are and change them all to 5s.
If you wanted to do this using a loop (which I highly recommend against) then you can do this:
for index = 1:numel(x)
if x(index) == 4
x(index) = 5;
end
end
Short answer to achieve what you want:
x(x==4) = 5
Answer to why your code doesn't do what you expected:
You are changing the item to a 5. But that item is a new variable, it does not point to the same item in your matrix x. Hence the original matrix x remains unchanged.
Hi I have the following matrix:
A= 1 2 3;
0 4 0;
1 0 9
I want matrix A to be:
A= 1 2 3;
1 4 9
PS - semicolon represents the end of each column and new column starts.
How can I do that in Matlab 2014a? Any help?
Thanks
The problem you run into with your problem statement is the fact that you don't know the shape of the "squeezed" matrix ahead of time - and in particular, you cannot know whether the number of nonzero elements is a multiple of either the rows or columns of the original matrix.
As was pointed out, there is a simple function, nonzeros, that returns the nonzero elements of the input, ordered by columns. In your case,
A = [1 2 3;
0 4 0;
1 0 9];
B = nonzeros(A)
produces
1
1
2
4
3
9
What you wanted was
1 2 3
1 4 9
which happens to be what you get when you "squeeze out" the zeros by column. This would be obtained (when the number of zeros in each column is the same) with
reshape(B, 2, 3);
I think it would be better to assume that the number of elements may not be the same in each column - then you need to create a sparse array. That is actually very easy:
S = sparse(A);
The resulting object S is a sparse array - that is, it contains only the non-zero elements. It is very efficient (both for storage and computation) when lots of elements are zero: once more than 1/3 of the elements are nonzero it quickly becomes slower / bigger. But it has the advantage of maintaining the shape of your matrix regardless of the distribution of zeros.
A more robust solution would have to check the number of nonzero elements in each column and decide what the shape of the final matrix will be:
cc = sum(A~=0);
will count the number of nonzero elements in each column of the matrix.
nmin = min(cc);
nmax = max(cc);
finds the smallest and largest number of nonzero elements in any column
[i j s] = find(A); % the i, j coordinates and value of nonzero elements of A
nc = size(A, 2); % number of columns
B = zeros(nmax, nc);
for k = 1:nc
B(1:cc(k), k) = s(j == k);
end
Now B has all the nonzero elements: for columns with fewer nonzero elements, there will be zero padding at the end. Finally you can decide if / how much you want to trim your matrix B - if you want to have no zeros at all, you will need to trim some values from the longer columns. For example:
B = B(1:nmin, :);
Simple solution:
A = [1 2 3;0 4 0;1 0 9]
A =
1 2 3
0 4 0
1 0 9
A(A==0) = [];
A =
1 1 2 4 3 9
reshape(A,2,3)
ans =
1 2 3
1 4 9
It's very simple though and might be slow. Do you need to perform this operation on very large/many matrices?
From your question it's not clear what you want (how to arrange the non-zero values, specially if the number of zeros in each column is not the same). Maybe this:
A = reshape(nonzeros(A),[],size(A,2));
Matlab's logical indexing is extremely powerful. The best way to do this is create a logical array:
>> lZeros = A==0
then use this logical array to index into A and delete these zeros
>> A(lZeros) = []
Finally, reshape the array to your desired size using the built in reshape command
>> A = reshape(A, 2, 3)
I have a vector like this:
A = [1 2 1 1 1 4 5 0 0 1 2 0 2 3 2 2 2 0 0 0 0 33]
I would like to count how many GROUPS of non zero elements it contains and save them.
so I want to isolate:
[1 2 1 1 1 4 5]
[1 2]
[2 3 2 2 2]
[33]
and then count the groups (they should be 4) :)
Can you help me please?
Thanks
To count your groups, a fast vectorized method using logical indexing is:
count = sum(diff([A 0]==0)==1)
This assumes that A is a row vector as in your example. This works with no zeros, all zeros, the empty vector, and several other test cases I tried.
To obtain your groups of values themselves, you can use a variation to my answer to a similar question:
a0 = (A~=0);
d = diff(a0);
start = find([a0(1) d]==1) % Start index of each group
len = find([d -a0(end)]==-1)-start+1 % Length, number of indexes in each group
In your case it might make sense to replace len with
finish = find([d -a0(end)]==-1) % Last index of each group
The length of start, len, and finish should be the same as the value of count so you could just use this if you need to do the breaking up. You can then use start and len (or finish) to store your groups in a cell array or struct or some other ragged array. For example:
count = length(start);
B = cell(count,1);
for i = 1:count
B{i} = A(start(i):finish(i));
end