I am a beginner in Matlab and have not been able to find an answer to my question so far. Your help will definitely be very much appreciated.
I have 70 matrices (100x100), named SUBJ_1, SUBJ_2 etc. I would like to create a loop so that I would calculate some metrics (i.e. max and min values) for each matrix, and save the output in a 70x2 result matrix (where each row would correspond to the consecutively named SUBJ_ matrix).
I am struggling with both stages - how to use the names of individual variables in a 'for' loop and how to properly save individual outputs in a combined array.
Many thanks and all the best!
Don't use such variable names, create a big cell array named SUBJ and put each Matrix in it.
r=zeros(numel(SUBJ),2)
for idx=1:numel(SUBJ)
r(idx,1)=min(min(SUBJ{idx}))
r(idx,2)=max(max(SUBJ{idx}))
end
min and max are called twice because first call creates maximum among rows, second call among columns.
Even though this is in principle possible in Matlab, I would not recommend it: too slow and cumbersome to implement.
You could instead use a 3-D matrix (100x100x70) SUBJ which would contain all the SUBJ_1 etc. in one matrix. This would allow you to calculate min/max etc. with just one line of code. Matlab will take care of the loops internally:
OUTPUT(:,1) = min(min(SUBJ,[],1)[],2);
OUTPUT(:,2) = max(max(SUBJ,[],1)[],2);
Like this, OUTPUT(1,1) contains min(min(SUBJ(:,:,1))) and so on...
As to how to use the names of individual variables in a 'for' loop, here gives an example:
SUBJ = [];
for idx = 1:70
term = eval(['SUBJ_',num2str(idx)]);
SUBJ = [SUBJ; max(max(term)),min(min(term))];
end
Related
I have a dataset of n nifti (.nii) images. Ideally, I'd like to be able to get the value of the same voxel/element from each image, and apply a function to the n data points. I'd like to do this for each voxel/element across the whole image, so that I can reconvert the result back into .nii format.
I've used the Tools for NIfTI and ANALYZE image toolbox to load my images:
data(1)=load_nii('C:\file1.nii');
data(2)=load_nii('C:\file2.nii');
...
data(n)=load_nii('C:\filen.nii');
From which I obtain a struct object with each sub-field containing one loaded nifti. Each of these has a subfield 'img' corresponding to the image data I want to work on. The problem comes from trying to select a given xyz within each img field of data(1) to data(n). As I discovered, it isn't possible to select in this way:
data(:).img(x,y,z)
or
data(1:n).img(x,y,z)
because matlab doesn't support it. The contents of the first brackets have to be scalar for the call to work. The solution from googling around seems to be a loop that creates a temporary variable:
for z = 1:nz
for x = 1:nx
for y = 1:ny
for i=1:n;
points(i)=data(i).img(x,y,z);
end
[p1(x,y,z,:),~,p2(x,y,z)] = fit_data(a,points,b);
end
end
end
which works, but takes too long (several days) for a single set of images given the size of nx, ny, nz (several hundred each).
I've been looking for a solution to speed up the code, which I believe depends on removing those loops by vectorisation, preselecting the img fields (via getfield ?)and concatenating them, and applying something like arrayfun/cellfun/structfun, but i'm frankly a bit lost on how to do it. I can only think of ways to pre-select which themselves require loops, which seems to defeat the purpose of the exercise (though a solution with fewer loops, or fewer nested loops at least, might do it), or fun into the same problem that calls like data(:).img(x,y,z) dont work. googling around again is throwing up ways to select and concatenate fields within a struct, or a given field across multiple structs. But I can't find anything for my problem: select an element from a non-scalar sub-field in a sub-struct of a struct object (with the minimum of loops). Finally I need the output to be in the form of a matrix that the toolbox above can turn back into a nifti.
Any and all suggestions, clues, hints and help greatly appreciated!
You can concatenate images as a 4D array and use linear indexes to speed up calculations:
img = cat(4,data.img);
p1 = zeros(nx,ny,nz,n);
p2 = zeros(nx,ny,nz);
sz = ny*nx*nz;
for k = 1 : sz
points = img(k:sz:end);
[p1(k:sz:end),~,p2(k)] = fit_data(a,points,b);
end
I am storing the field variables calculated in a for loop in a vector by appending the values, However I would like to preallocate first for performance. I tried to vectorize this operation but it does not give me what I would like to accomplish. I have put the example of the operation below. How do I do the preallocation in this? For speed.
j=('load raw.mat');
var=fields(j);
val_mat=[];
kk=fieldnames(j);
for i=(length(kk)-Var_no)+1:Var_no+(length(kk)-Var_no)
val_mat=[val_mat j.(var{i})];
end
Based on your code it looks like you are trying to grab all variables stored in raw.mat and concatenate them. To do this, you can replace the loop with struct2cell to convert all field values to a cell array of values and then use cat to concatenate them
data = load('raw.mat');
values = struct2cell(data);
val_mat = cat(2, values{:});
Since we have removed the loop, there is no need to pre-allocate.
I've also taken the liberty to rewrite your code as valid MATLAB code.
I have the results from an iterative process, where the results from each iteration is placed beside eachother, like this:
res =
43.7826 38.8460 38.6889 38.6912 38.6915
107.0735 98.5577 98.1212 98.1170 98.1175
-134.6218 -131.6938 -131.5378 -131.5352 -131.5352
-105.9498 -103.1403 -102.9195 -102.9139 -102.9139
What I want to do is create one matrix that shows the difference between each column, and one matrix that shows the percentage change from one column to the next.
This is obviously simple to do using loops, but is there a clever way to do this without loops (maybe using some built-in Matlab functions)?
Thanks.
The command diff(...) performes the difference:
diff_res = diff(res,1,2)
in this case the difference of the first order in the second dimension (columns).
After you can compute the percentage:
per_res = diff_res(:,1:4)./res(:,1:4).*100
I am trying to use MATLAB in order to generate a variable whose elements are either 0 or 1. I want to define this variable using some kind of concatenation (equivalent of Java string append) so that I can add as many 0's and 1's according to some upper limit.
I can only think of using a for loop to append values to an existing variable. Something like
variable=1;
for i=1:N
if ( i%2==0)
variable = variable.append('0')
else
variable = variable.append('1')
i=i+1;
end
Is there a better way to do this?
In MATLAB, you can almost always avoid a loop by treating arrays in a vectorized way.
The result of pseudo-code you provided can be obtained in a single line as:
variable = mod((1:N),2);
The above line generates a row vector [1,2,...,N] (with the code (1:N), use (1:N)' if you need a column vector) and the mod function (as most MATLAB functions) is applied to each element when it receives an array.
That's not valid Matlab code:
The % indicates the start of a comment, hence introducing a syntax error.
There is no append method (at least not for arrays).
Theres no need to increment the index in a for loop.
Aside of that it's a bad idea to have Matlab "grow" variables, as memory needs to be reallocated at each time, slowing it down considerably. The correct approach is:
variable=zeros(N,1);
for i=1:N
variable(i)=mod(i,2);
end
If you really do want to grow variables (some times it is inevitable) you can use this:
variable=[variable;1];
Use ; for appending rows, use , for appending columns (does the same as vertcat and horzcat). Use cat if you have more than 2 dimensions in your array.
I run through a for loop, each time extracting certain elements of an array, say element1, element2, etc. How do I then pool all of the elements I've extracted together so that I have a list of them?
John covered the basics of for loops, so...
Note that matlab code is often more efficient if you vectorize it instead of using loops (this is less true than it used to be). For example, if in your loop you're just grabbing the first value in every row of a matrix, instead of looping you can do:
yourValues = theMatrix(:,1)
Where the solo : operator indicates "every possible value for this index". If you're just starting out in matlab it is definitely worthwhile to read up on matrix indexing in matlab (among other topics).
Build the list as you go:
for i = 1:whatever
' pick out theValue
yourList(i) = theValue
end
I'm assuming that you pick out one element per loop iteration. If not, just maintain a counter and use that instead of i.
Also, I'm not assuming you're pulling out your elements from the same position in your array each time through the loop. If you're doing that, then look into Donnie's suggestion.
In MATLAB, you can always perform a loop operation. But the recommended "MATLAB" way is to avoid looping:
Suppose you want to get the subset of array items
destArray = [];
for k=1:numel(sourceArray)
if isGoodMatch(sourceArray(k))
destArray = [destArray, sourceArray(k)]; % This will create a warning about resizing
end
end
You perform the same task without looping:
matches = arrayfun(#(a) isGoodMatch(a), sourceArray); % returns a vector of bools
destArray = sourceArray(matches);