My data is x,y co-ordinates in multiple files
a=dir('*.mat')
b={a(:).name}
to load the filenames in a cell array
How do I use a loop to sequentially load one column of data from each file into consecutive rows of a new/separate array......?
I've been doing it individually using e.g.
Load(example1.mat)
A(:,1)=AB(:,1)
Load(example2.mat)
A(:,2)=AB(:,1)
Load(example3.mat)
A(:,3)=AB(:,1)
Obviously very primitive and time consuming!!
My Matlab skills are weak so any advice gratefully received
Cheers
Many thanks again, I'm still figuring out how to read the code but I used it like this;
a=dir('*.mat');
b={a(:).name};
test1=zeros(numel(b),1765);
for k=1:numel(b) S=load(b{k});
I then used the following code to create a PCA cluster plot
test1(k,:)=S.AB(:,2); end [wcoeff,score,latent,tsquared,explained] = pca(test1,... 'VariableWeights','variance');
c3 = wcoeff(:,1:3) coefforth = inv(diag(std(test1)))*wcoeff; I = c3'*c3 cscores = zscore(test1)*coefforth;
figure() plot(score(:,1),score(:,2),'+') xlabel('1st Principal Component') ylabel('2nd Principal Component') –
I was using 'gname' to label the points on the cluster plot but found that the point were simply labelled from 1 to the number of rows in the array.....I was going to ask you about this but I found out simply through trial and error if I used 'gname(b)' this labels the points with the .names listed in b.....
However the clusterplot starts to look very busy/messy once I have labelled quite a few points so now I am wondering is is possible to extract the filenames into a list by dragging round or selecting a few points, I think it is possible as I have read a few related topics.....but any tips/advice around gname or labelled/extracting labels from clusterplots would be greatly appreciated. Apologies again for my formatting I'm still getting used to this website!!!
Here is a way to do it. Hopefully I got what you wanted correctly :)
The code is commented but please ask any questions if something is unclear.
a=dir('*.mat');
b={a(:).name};
%// Initialize the output array. Here SomeNumber depends on the size of your data in AB.
A = zeros(numel(b),SomeNumber);
%// Loop through each 'example.mat' file
for k = 1:numel(b)
%// ===========
%// Here you could do either of the following:
1)
%// Create a name to load with sprintf. It does not require a or b.
NameToLoad = sprintf('example%i.mat',k);
%// Load the data
S = load(NameToLoad);
2)
%// Load directly from b:
S = load(b{k});
%// ===========
%// Now S is a structure containing every variable from the exampleX.mat file.
%// You can access the data using dot notation.
%// Store the data into rows of A
A(k,:) = S.AB(:,1);
end
Hope that is what you meant!
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 a total beginner in MATLAB and I hope to find some help here. I have some model prediction results for 80 individuals alltogether in one large matrix. I need to extract the data for each individual from the big matrix, assign them in a new variable/matrix, do some extra calculations and then plot certain information as needed.
To do so, I am trying to write a script with a loop function but in a complicated, or maybe more accurately: in a primitive way!
Simplified Example:
My matrix is called: All_Indi_Data .... its dimension is: 600 rows x 21 columns
%Column 1: grouping variable (e.g., code or ID with values 1,2,3,4,5, etc.);
%Column 2: independent var.;
%Column 3: t;
%Column 4: OBS;
%Column 5: PRED;
i= length (All_Indi_Data);
%% First Indi.
q=1; % indicating the ID of the indi for which I want to extract the data
j=1; % variable added to insure writing start from the first row
for r=1:i
if All_Indi_Data (r,1)==q
Indi_1 (j,1:21) = All_Indi_Data (r,1:21)
j=j+1
end
end
%% Second Indi.
q=q+1
j=1
for r=1:i
if All_Indi_Data (r,1)==q
Indi_2 (j,1:21) = All_Indi_Data (r,1:21)
j=j+1
end
end
.
.
.
1) My first question is: can I allocate these data in new variables (Indi_1, Indi_2, ect.) in a more simple way with or without the loop function?!!! I would appreciate your help a lot.
2) Is there any code or any way to plot these selected parts (according to the grouping variable, e.g. data for Indi_1) from the previously mentioned big matrix without wasting a lot of time and space (wto recopying the core part of the code again and again) for the script, and using the loop function?! in other words, I would like to detect - with loop function & the grouping variable- which values are of interest and then to plot them (e.g. data in colum 3 with data from column 4 for each individual, starting from the first to the last)?!
I hope that I described my problem clearly and hope to hear something from the expert guys :) ...
Thanks a lot in advance ..
Try the following code:
for idx=1:80
pos=find(All_Indi_Data(:,1)==idx);
eval(['Indi_' num2str(idx) '=All_Indi_Data(pos,:);']);
end
What I do is: in each iteration, I search for a value of the ID, indicated in the variable idx. Note that I do not use ´i´ as the name of a variable, because Matlab uses it and ´j´ and the imaginary unit for complex numbers and that could cause problems.
Then, using find I search for the position (or positions) of All_Indi_Data in which I can find the information of that individual. Now I have in the variable ´pos´ the indexes of the rows in which there is information for the individual of interest.
Finally, using eval I extract the data for each individual into a variable. Note that eval combined with a loop makes it easy to create lots of variables. I indicate the rows I want to extract with ´pos´ and, as I want all the columns, I use just ´:´ (you could use ´1:21´ too).
With another similar loop you can plot the information you want. For example:
for idx=1:80
eval(['x=Indi_' num2str(idx) ';']);
% Now I have in X the information for this individual
%Plot the columns of x I want
plot(x(:, 3), x(:,4));
pause; %stay here until a press a key
end
first of all, I'd like to describe my issue with the kmeans in Matlab.
I select a point via mouse and use it for cluster initialization. This works fine.
After the segmentation of the data, I reshape the data back into proper style, because I need a matrix.
Now I want to select only the cluster of which the user selected the data via mouse.
Therefore I select the index of the mouse-coordinates to select the label, which I want to segmentate. Because of other extra data which is not connected or nearby the relevant data, but also gots the same label.
I want to select only connected-components in a neighbourhood of 8.
So here is my code snippet so far:
flatimg = double(reshape(croppedimg,size(croppedimg,1)*size(croppedimg,2),size(croppedimg,3)));
% kmeans
[idx, clusters] = kmeans(flatimg,2,'start',[seedpoint1(3);seedpoint2(3)]);
% form it back to a matrix
k=reshape(idx,size(croppedimg,1),size(croppedimg,2));
%convert point, which is part of the label I want to linear index
selectedobjectpoint = sub2ind(size(croppedimg),seedpoint1(2),seedpoint1(1));
hgplabel = k(selectedobjectpoint);
idx_object = find(k, hgplabel);
% also tried: idx_object = find(k == hgplabel);
I added a screenshot, which shows the direct output of kmeans:
So my aim is it here to get only the "white" OR the "black" ones.
Help or advice appreciated. If you've got any questions regarding the snippet or the goal, feel free to ask.
Thank you in advance!
I think the FIND command is throwing you off. You want something like:
logicalImage = k == hgplabel;
bwImg = bwlabel(logicalImage);
imagesc(bwImg)
FIND will output the indices where k == hgplabel. You want the matrix of zeros and ones where k takes that value (I think).
If you just want the connected components of that, the output of bwlabel will contain unique integers for each connected component, so imagesc(bwImg == 1) will show just component 1. And you can specify the connectivity
New to matlab and I need some help.
I need to create a .mat file , using matObj or save(), that has some information that will be passed from some variable. Lets say that variable x = 1,2,3,4,5
1|2|3|4|5|
Then I need to save that in test.mat
Then I need to load that file and save something like,
6|7|8|9|10|
So I get
1|2|3|4|5|
6|7|8|9|10|
and so on.
So every time I save it goes to a new row. The numbers that go inside they are not random the above numbers are just there to make things simple to see.
Can someone help me out.
You are describing two different problems here. The first is saving and loading of data.
Saving is easy:
x = 1:5;
filename = 'myFile.mat'
save(filename, 'x'); %notice that I used the string name of the variable
Likewise loading is also simple:
filename = 'myFile.mat';
data = load(filename); % loaded variables are placed in a struct to prevent overwriting workspace variables
x = data.x;
The 2nd problem can be solved using concatenation:
lets say you want to convert the vector 1 2 3 into the matrix:
1 2 3
1 2 3
You can simply call:
v = 1:3;
m = cat(1, v, v);
Likewise you can add an additional row to the existing matrix using the same command:
m = cat(1, m, v);
I'm sure any amount of googling will get you how to save a variable to a mat file - The matlab docs are absolutely spectacular, and such a simple operation will be covered along with examples showing exactly how to use the functions.
As for the second part, use the concatenation property
new = [old1 old2];
to concatenate horizontally, and
new = [old1;old2];
to concatenate vertically. Then resave the same way that you just learned via google.
Hope this helps, and in the future, i guarantee 99% of the answers to a new user's questions will be in the top two google search results if you append "matlab" to your search. The Mathworks really set the bar on documentation in my opinion. (Of course, I last used MATLAB 3 years ago)
I am a complete novice at using matlab and am trying to work out if there is a way of optimising my code. Essentially I have data from model outputs and I need to plot them using matlab. In addition I have reference data (with 95% confidence intervals) which I plot on the same graph to get a visual idea on how close the model outputs and reference data is.
In terms of the model outputs I have several thousand files (number sequentially) which I open in a loop and plot. The problem/question I have is whether I can preprocess the data and then plot later - to save time. The issue I seem to be having when I try this is that I have a legend which either does not appear or is inaccurate.
My code (apolgies if it not elegant):
fn= xlsread(['tbobserved' '.xls']);
time= fn(:,1);
totalreference=fn(:,4);
totalreferencelowerci=fn(:,6);
totalreferenceupperci=fn(:,7);
figure
plot(time,totalrefrence,'-', time, totalreferencelowerci,'--', time, totalreferenceupperci,'--');
xlabel('Year');
ylabel('Reference incidence per 100,000 population');
title ('Total');
clickableLegend('Observed reference data', 'Totalreferencelowerci', 'Totalreferenceupperci','Location','BestOutside');
xlim([1910 1970]);
hold on
start_sim=10000;
end_sim=10005;
h = zeros (1,1000);
for i=start_sim:end_sim %is there any way of doing this earlier to save time?
a=int2str(i);
incidenceFile =strcat('result_', 'Sim', '_', a, 'I_byCal_total.xls');
est_tot=importdata(incidenceFile, '\t', 1);
cal_tot=est_tot.data;
magnitude=1;
t1=cal_tot(:,1)+1750;
totalmodel=cal_tot(:,3)+cal_tot(:,5);
h(a)=plot(t1,totalmodel);
xlim([1910 1970]);
ylim([0 500]);
hold all
clickableLegend(h(a),a,'Location','BestOutside')
end
Essentially I was hoping to have a way of reading in the data and then plot later - ie. optimise the code.
I hope you might be able to help.
Thanks.
mp
Regarding your issue concerning
I have a legend which either does not
appear or is inaccurate.
have a look at the following extracts from your code.
...
h = zeros (1,1000);
...
a=int2str(i);
...
h(a)=plot(t1,totalmodel);
...
You are using a character array as index. Instead of h(a) you should use h(i). MATLAB seems to cast the character array a to double as shown in the following example with a = 10;.
>> double(int2str(10))
ans = 49 48
Instead of h(10) the plot handle will be assigned to h([49 48]) which is not your intention.