I have two geotiff images (saying "A" and "B") imported in Matlab as matrices with Geotiffread. One has different values, while the second has only 0 and 255s.
What I'd like to do is replacing all the 255s with the values inside the other image (or matrix), according to their positions.
A and B differs in size, but they have the same projections.
I tried this:
A (A== 255)= B;
the output is the error:
??? In an assignment A(:) = B, the number of elements in A and B must be the same.
Else, I also tried with the logical approach:
if A== 255
A= B;
end
and nothing happens.
Is there a way to replace the values of A with values of B according to a specific value and the position in the referenced space?
As darthbith put in his comment, you need to make sure that the number of entries you want to replace is the same as the number values you are putting in.
By doing A(A==255)=B you are trying to put the entire matrix B into the subset of A that equals 255.
However, if, as you said, the projections are the same, you can simply do A(A==255) = B(A==255), under the assumption that B is larger or the same size as A.
Some sample code to provide a proof of concept.
A = randi([0,10],10,10);
B = randi([0,4],15,15);
C = A % copy original A matrix for comparison later
A(A==5) = B(A==5); % replace values
C==A % compare original and new
This example code creates two matrices, A is a 10x10 and B is a 15x15 and replaces all values that equal 5 in A with the corresponding values in B. This is shown to be true by doing C==A which shows where the new matrix and the old matrix vary, proving replacement did happen.
It seems to me that you are trying to mask an image with a binary mask. You can do this:
BW = im2bw(B,0.5);
A=A.*BW;
hope it helps
Try A(A==255) = B(A==255). The error is telling you that when you try to assign values to the elements of an array, you cannot give it any more or fewer values than you are trying to assign.
Also, regarding the if statement: if A==255 means the same as if all(A==255), as in, if any elements of A are not 255, false is returned. You can check this at the command line.
If you're really desperate, you can use a pair of nested for loops to achieve this (assuming A and B are the same size and shape):
[a,b] = size(A);
for ii = 1:a
for jj = 1:b
if A(ii,jj) == 255
A(ii,jj) = B(ii,jj);
end
end
end
Related
This piece of code is part of a larger function. I already created a list of molecular weights and I also defined a list of all the fragments in my data.
I'm trying to figure out how I can go through the list of fragments, calculate their molecular weight and check if it matches the number in the other list. If it matches, the sequence is appended into an empty list.
combs = [397.47, 2267.58, 475.63, 647.68]
fragments = ['SKEPFKTRIDKKPCDHNTEPYMSGGNY', 'KMITKARPGCMHQMGEY', 'AINV', 'QIQD', 'YAINVMQCL', 'IEEATHMTPCYELHGLRWV', 'MQCL', 'HMTPCYELHGLRWV', 'DHTAQPCRSWPMDYPLT', 'IEEATHM', 'MVGKMDMLEQYA', 'GWPDII', 'QIQDY', 'TPCYELHGLRWVQIQDYA', 'HGLRWVQIQDYAINV', 'KKKNARKW', 'TPCYELHGLRWV']
frags = []
for c in combs:
for f in fragments:
if c == SeqUtils.molecular_weight(f, 'protein', circular = True):
frags.append(f)
print(frags)
I'm guessing I don't fully know how the SeqUtils.molecular_weight command works in Python, but if there is another way that would also be great.
You are comparing floating point values for equality. That is bound to fail. You always have to account for some degree of error when dealing with floating point values. In this particular case you also have to take into account the error margin of the input values.
So do not compare floats like this
x == y
but instead like this
abs(x - y) < epsilon
where epsilon is some carefully selected arbitrary number.
I did two slight modifications to your code: I swapped the order of the f and the c loop to be able to store the calculated value of w. And I append the value of w to the list frags as well in order to better understand what is happening.
Your modified code now looks like this:
from Bio import SeqUtils
combs = [397.47, 2267.58, 475.63, 647.68]
fragments = ['SKEPFKTRIDKKPCDHNTEPYMSGGNY', 'KMITKARPGCMHQMGEY', 'AINV', 'QIQD', 'YAINVMQCL', 'IEEATHMTPCYELHGLRWV',
'MQCL', 'HMTPCYELHGLRWV', 'DHTAQPCRSWPMDYPLT', 'IEEATHM', 'MVGKMDMLEQYA', 'GWPDII', 'QIQDY',
'TPCYELHGLRWVQIQDYA', 'HGLRWVQIQDYAINV', 'KKKNARKW', 'TPCYELHGLRWV']
frags = []
threshold = 0.5
for f in fragments:
w = SeqUtils.molecular_weight(f, 'protein', circular=True)
for c in combs:
if abs(c - w) < threshold:
frags.append((f, w))
print(frags)
This prints the result
[('AINV', 397.46909999999997), ('IEEATHMTPCYELHGLRWV', 2267.5843), ('MQCL', 475.6257), ('QIQDY', 647.6766)]
As you can see, the first value for the weight differs from the reference value by about 0.0009. That's why you did not catch it with your approach.
Lets say I have a matrix x=[ 1 2 1 2 1 2 1 2 3 4 5 ]. To look at its histogram, I can do h=hist(x).
Now, h with retrieve a matrix consisting only the number of occurrences and does not store the original value to which it occurred.
What I want is something like a function which takes a value from x and returns number of occurrences of it. Having said that, what one thing histeq does should we admire is, it automatically scales nearest values according!
How should solve this issue? How exactly people do it?
My reason of interest is in images:
Lets say I have an image. I want to find all number of occurrences of a chrominance value of image.
I'm not really shure what you are looking for, but if you ant to use hist to count the number of occurences, use:
[h,c]=hist(x,sort(unique(x)))
Otherwise hist uses ranges defined by centers. The second output argument returns the corresponding number.
hist has a second return value that will be the bin centers xc corresponding to the counts n returned in form of the first return value: [n, xc] = hist(x). You should have a careful look at the reference which describes a large number of optional arguments that control the behavior of hist. However, hist is way too mighty for your specific problem.
To simply count the number of occurrences of a specific value, you could simply use something like sum(x(:) == 42). The colon operator will linearize your image matrix, the equals operator will yield a list of boolean values with 1 for each element of x that was 42, and thus sum will yield the total number of these occurrences.
An alternative to hist / histc is to use bsxfun:
n = unique(x(:)).'; %'// values contained in x. x can have any number of dims
y = sum(bsxfun(#eq, x(:), n)); %// count for each value
I am a new student learning to use Matlab.
Could anyone please tell me is there a faster way possibly without loops:
to assign for each row only two values 1, -1 into different positions of a big sparse matrix.
My code to build a bimatrix or bibimatrix for the MILP problem of condition :
f^k_{ij} <= y_{ij} for every arc (i,j) and all k ~=r; in a multi-commodity flow model.
Naive approach:
bimatrix=[];
% create each row and then add to bimatrix
newrow4= zeros(1,n*(n+1)^2);
for k=1:n
for i=0:n
for j=1: n
if j~=i
%change value of some positions to -1 and 1
newrow4(i*n^2+(j-1)*n+k)=1;
newrow4((n+1)*n^2+i*n+j)=-1;
% add to bimatrix
bimatrix=[bimatrix; newrow4];
% change newrow4 back to zeros row.
newrow4(i*n^2+(j-1)*n+k)=0;
newrow4((n+1)*n^2+i*n+j)=0;
end
end
end
end
OR:
% Generate the big sparse matrix first.
bibimatrix=zeros(n^3 ,n*(n+1)^2);
t=1;
for k=1:n
for i=0:n
for j=1: n
if j~=i
%Change 2 positions in each row to -1 and 1 in each row.
bibimatrix(t,i*n^2+(j-1)*n+k)=1;
bibimatrix(t,(n+1)*n^2+i*n+j)=-1;
t=t+1
end
end
end
end
With these above code in Matlab, the time to generate this matrix, with n~12, is more than 3s. I need to generate a larger matrix in less time.
Thank you.
Suggestion: Use sparse matrices.
You should be able to create two vectors containing the column number where you want your +1 and -1 in each row. Let's call these two vectors vec_1 and vec_2. You should be able to do this without loops (if not, I still think the procedure below will be faster).
Let the size of your matrix be (max_row X max_col). Then you can create your matrix like this:
bibimatrix = sparse(1:max_row,vec_1,1,max_row,max_col);
bibimatrix = bibimatrix + sparse(1:max_row, vec_2,-1,max_row,max_col)
If you want to see the entire matrix (which you don't, since it's huge) you can write: full(bibimatrix).
EDIT:
You may also do it this way:
col_vec = [vec_1, vec_2];
row_vec = [1:max_row, 1:max_row];
s = [ones(1,max_row), -1*ones(1,max_row)];
bibimatrix = sparse(row_vec, col_vec, s, max_row, max_col)
Disclaimer: I don't have MATLAB available, so it might not be error-free.
I am working on image processing. I want to add the difference of pixels of two images.
Suppose I have two images A, and B. I pick the first pixel of both images and store the difference value. I want to add this difference value to next pixel-difference. I try using this code, but it is not working. How can I do it?
A = imread('sub2.jpg');
B = imread('sub1.jpg');
tic
[rows cols] = size(A);
diff1 = 0;
for x = 1:rows
for y = 1:cols
diff = A(x,y)-B(x,y);
diff1 = diff1+diff;
end
end
disp(diff1);
toc
You can do it in one line as follows:
sum(sum(imsubtract(A-B)))
imsubtract subtracts two images and saves the difference in a matrix with the same size as A. Then, sum takes the sum of the result.
If you need absolute differences, you may use imabsdiff instead of imsubtract.
Note that the values of the differences are in 0 and 255. If you want negative instances, then you should directly subtract the matrices as A-B.
Looks okay though, but you're better off with:
diff1 = sum(sum(A-B));
or if B is larger than A:
diff1 = sum(sum(A-B(1:size(A,1),1:size(A,2))));
This gives just one value (as your code does), I'm not sure if that really is what you want..
How can I select some parts of an matrix and cut the single dimensions?
Example: B = zeros(100,100,3,'double');
When I select B(2,3,:) I get a 1x1x3 matrix as result - this is not the expected result, because for some operations (like norm) I need a vector as result. To handle this problem I used squeeze, but this operations seems to be very time consuming, especially when heavily used.
How can I select only the vector and 'cut' the single dimensions?
In your case you could use the colon operator, like this:
x = B(2,3,:);
x = x(:);
This places all elements of X into a number-of-elements by 1 vector.
You could also permute the dimensions to bring the non-singleton one to front. Either:
>> permute(B(2,3,:),[3 1 2])
ans =
0.97059
0.69483
0.2551
or
>> permute(B(2,3,:),[1 3 2])
ans =
0.97059 0.69483 0.2551
depending on whether you want a row or a column vector.