How to improve sparse array indexed assignment in MATLAB?
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Hi, how can I improve indexed assignment to a sparse matrix? Please refer to line 29 and 31 of the attached code that is simply trying to read the attached txt file and put +1 for positive values and -1 for negative values and generate a matrix. How can I speed it up? Thanks.
An example function call will be: A= cnf_to_A('quinn.txt');
2 个评论
David Hill
2022-3-2
In the example you create a 16x18 sparse array. Do not understand where to index your -1/+1 values into.
回答(2 个)
David Hill
2022-3-3
s=readmatrix('quinn.txt','Range','C3:D3');
r=readmatrix('quinn.txt','NumHeaderLines',3);
X=sparse(s(2),s(1));
ra=abs(r(:,1:2));
rv=ones(size(ra));
rv(r<0)=-1;
linIndex=s(2)*(ra-1)+(1:s(2))'.*[1 1];
X(linIndex(:))=rv(:);
5 个评论
David Hill
2022-3-3
Try this:
File='irregular.txt';
fid=fopen(File);
count=1;
while ~feof(fid)
tline = fgetl(fid);
tline = strtrim(tline);
if (tline(1)=='p' || tline(1)=='P')
c=count;
elseif (tline(1)=='c' || tline(1)=='C')
cc=count;
end
count=count+1;
end
fclose(fid);
s=readmatrix(File,'Range',sprintf('C%d:D%d',c,c));
r=readmatrix(File,'NumHeaderLines',max(c,cc));
X=sparse(s(2),s(1));
ra=abs(r);
rv=ones(size(ra));
rv(r<0)=-1;
linIndex=s(2)*(ra-1)+(1:s(2))'.*ones(1,size(ra,2));
linIndex=linIndex(linIndex>0);
rv=rv(~isnan(r)&r~=0);
X(linIndex)=rv;
Matt J
2022-3-3
编辑:Matt J
2022-3-3
Assigning into an existing sparse matrix is fundamentally a slow thing. If you are creating a matrix from scratch, use the sparse() command, not assignment:
Jdata=[
1 2 0
-2 -4 0
3 4 0
-4 -5 0
5 -6 0
6 -7 0
6 7 0
7 -16 0
8 -9 0
-8 -14 0
9 10 0
9 -10 0
-10 -11 0
10 12 0
11 12 0
13 14 0
14 -15 0
15 16 0];
N=size(Jdata,1);
rows=(1:N)';
I=[rows,rows];
J=abs(Jdata(:,1:2));
S=sign(Jdata(:,1:2));
A=sparse(I,J,S);
spy(A)
3 个评论
Matt J
2022-3-3
编辑:Matt J
2022-3-3
Thank you very much. This code is giving me error:
I fixed it.
Also, as I am discussing with @David Hill above, the data is not always regular like this, it can be irregular too:
That's not really an important aspect. You would need to build I,J,S differently in the irregular case, but the point about avoiding assignment is the same.
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