I have the following problem:
I have two arrays called Variable_1 and Variable_2 (same size 8x3, only different values). I need to make calculations with the values inside the array and store the result in a new array. The calculation is the same for both arrays.
Right now, I solved it with 2 for-loops.
for i = 1:size(Variable_1,1)
Calculation_1 = 5 * Variable_1(i,1);
Result_1(i,:) = Calculation_1;
end
for i = 1:size(Variable_2,1)
Calculation_2 = 5 * Variable_2(i,1);
Result_2(i,:) = Calculation_2;
end
I want to get rid of two separate for-loops and do it with one loop or a loop in a loop. The name "Variable_x" needs to be kinda dynamical. It is different for every run in the outer for-loop. First, it is Variable_1 and matlab has to look in the array "Variable_1" at position i. Later, it is Variable_2 and it has to look in another array, here called "Variable_2".
I know that I shouldn't use dynamic variables and however I didn't found a solution anyway. Maybe it works with Cellarrays but I dont't know exactly how I use them in this specific case.
It is kinda hard to explain, so feel free to ask questions if you have one. I am really looking forward for any suggestions.
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
To process data in MATLAB I have to execute a certain function, let's call it function(). Since there is much data to be processed, like large array Time or Voltage (but many more) I execute those one by one like this:
TimeNew = function(Time);
VoltageNew = function(Voltage);
... etc
So this is done around 10 times. Moreover, I have to do such a thing multiple times, resulting in around 30 lines of code which all do the same thing but to a different variable.
Is there a way to optimize this? I am using the most recent version of MATLAB (2015b) and have all toolboxes installed.
A possible solution could be to store the input array into a struct, them use that struct as input of the function.
In the function you can identify the number and content of each field by using fieldnames and getfiled built-in function.
The function could return a structure as output whose names can be made the same as the ones of the input struct.
In the example below, three arrays are generated and the function siply compute their square.
var_1=1:10;
var_2=11:20;
var_3=21:30;
str_in=struct('var_1',var_1,'var_2',var_2,'var_3',var_3)
str_out=my_function(str_in)
The function
function [str_out]=my_function(str_in)
f_names=fieldnames(str_in)
n_fields=length(f_names);
for i=1:n_fields
x=getfield(str_in,f_names{i})
str_out.(f_names{i})=x.^2;
end
Hope this helps.
Qapla'
You could try cellfun
allResultsAsACell = cellfun(#function, {Time,Voltage,...,varN});
This is equivalent to
allResultsAsACell{1} = function(Time);
allResultsAsACell{2} = function(Voltage);
...
allResultsAsACell{N} = function{VarN};
The issue is just matching up the indices with the values. I'm sure you could code those in as well if you needed (e.g. timeInd = 1; voltageInd =2; ...)
To see more on the cellfun method, type
help cellfun
into your MATLAB terminal.
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
This question already has answers here:
Dynamic variables matlab
(2 answers)
Closed 8 years ago.
I was wondering how I can use a for loop to create multiple matrix when given a certain number.
Such as If 3 was given I would need three matricies called: C1, C2 and C3.
k = 3
for i = 1:K
C... = [ ]
end
Not sure how to implement this.
The first thing coming in mind is the eval function mentioned by Dennis Jaheruddin, and yes, it is bad practice. So does the documentation say:
Why Avoid the eval Function?
Although the eval function is very powerful and flexible, it not
always the best solution to a programming problem. Code that calls
eval is often less efficient and more difficult to read and debug than
code that uses other functions or language constructs. For example:
MATLAB® compiles code the first time you run it to enhance performance for future runs. However, because code in an eval
statement can change at run time, it is not compiled.
Code within an eval statement can unexpectedly create or assign to a variable already in the current workspace, overwriting existing
data.
Concatenating strings within an eval statement is often difficult to read. Other language constructs can simplify the syntax in your
code.
The "safer" alternative is the function assignin:
The following will do exactly what you want:
letter = 'C';
numbers = 1:3;
arrayfun(#(x) assignin('base',[letter num2str(x)],[]),numbers)
I know cases where you need to create variables likes this, but in most cases it is better and more convenient to use cell arrays or structs.
The trick is to use a cell array:
k=3
C=cell(k,1)
for t=1:k
C{t}= rand(t)
end
If each matrix is of equal size, you would probably just want a three dimensional matrix rather than a cell array.
You now have one cell array,but can access the matrices like this:
C{2} %Access the second matrix.
The use of eval is almost inevitable in this case:
k = 3;
for i = 1:k
eval(sprintf('C%d = [];', i));
end;
Mind you that generating variable names for data storage rather than indexing them (numerically -- see the solution of Dennis Jaheruddin based on cell arrays -- or creating a dynamic struct with named fields that store the data) is almost always a bad idea. Unless you do so to cope up with some weird scripts that you don't want to / cannot modify that need some variables already created in the global workspace.
For classification I'm building a number of models for a classifier in MATLAB. I use the class ClassificationKNN for this.
I would very much like to store multiple models (or objects of this class) inside a matrix.
Normally you could access and create matrices inside a matrix with the curly braces ({}).
My loop looks like this:
models = []
for i = 1:length(x)
models = [models, {ClassificationKNN.fit(x,y)}]
end
Unfortunately this returns a matrix models of size (1,3) but all cells are empty which means the models are lost...
How can I make sure every model is stored in a matrix? I need to do this because I need all models later in my calculations and the position in the matrix is important...
Any ideas?
You want a cell array of models, right? It sure looks that way, if that will work try this:
models = {}
for ii = 1:length(x)
models = [models, {ClassificationKNN.fit(x,y)}]
end
Also, you loop through calling ClassificationKNN.fit(x,y) with the same arguments every time, is this just a test, or pseudo-code for an example. Like the comment says, it's best to preallocate like:
models = cell(length(x),1);
for ii = 1:length(x)
models{ii} = ClassificationKNN.fit(x,y);
end
But, either way is likely fine.
Thanks to macduffs post I finally figured out what was going on. Whilest reading his proposition I realised that that indeed should be the correct way if getting a cell array of objects.
After trying it, the array again seemed empty when opening it in the variable editor. I tried calling the first cell in the array to see if it was indeed empty and it was not. It returned the object I had stored in it. This means the question was answered.
I then reverted back to my own method to see if that worked as well and it did. When calling a cell it also returned an object.
Bottom line:
Do not trust the variable editor ^^.