I have 360 3D-nifti files, I want to read all these files and save into one nifti file using Nifti Analyze tool that should yield a 4D file of large size. So far I have written following lines
clear all;
clc;
fileFolder=fullfile(pwd, '\functional');
files=dir(fullfile(fileFolder, '*.nii'));
fileNames={files.name};
for i=1:length(fileNames)
fname=fullfile(fileFolder,fileNames{i});
z(i)=load_nii(fname);
y=z(i).img;
temp(:,:,:,i) = make_nii(y);
save_nii(temp(:,:,:,i), 'myfile.nii')
fprintf('Iter: %d\n', i)
end
This code facilitates with a variable temp that is 4D struct and contains all the images. However, myfile.nii is just one single file its not all the images because its size is just 6mb it should be atleast one 1gb.
Can someone please have a look and let me know where I am wrong?
The way that you have it written, your loop is overwriting myfile.nii since you're calling save_nii every time through the loop with only the latest data. You'll want to instead call save_nii only once outside of the loop and save the entire temp variable at once.
for k = 1:numel(fileNames)
fname = fullfile(fileFolder, fileNames{k});
z(k) = load_nii(fname);
y(:,:,:,k) = z(k).img;
end
% Create the ND Nifti file
output = make_nii(y);
% Save it to a file
save_nii(output, 'myfile.nii')
Related
I am trying to run multiple .mat files in matlab. So far i have 3 .mat files each containing the same variables. I want to run one .mat file and then switch to the next file. They are named like this:
file2019_1.mat %day 1
file2019_2.mat %day 2
file2019_3.mat %day 3
The code i have tried to run works for the first .mat file and it then doesnt switch to the second. Ideally i am trying to run all 3 files continuously, as in the future i could have 100s.
This is the code i tried so far:
% set up folder for .mat files containing variables of interest
myFolder = ('filepath');
filePattern = fullfile(myFolder, 'file2019_*.mat');
fileList = dir(filePattern);
% set up variable data (here it is daily mean velocity value)
% hourly, m/s (one mat file one day)
number_mat = length(fileList);
for i = 1:number_mat
load(['file2019_' num2str(i) '.mat'])
%%%% run model in here
end
Any help on how i could get this to run continuously through each mat file would be great.
Thank you.
A very easy method , just select all the files (Ctrl + A) - drag and drop them into the command window (be sure to drag the first file to load them in same order).
Or You can use this
% Read files mat1.mat through mat20.mat
for k = 1 : 20 % or whatever your numbers of files
% Create a mat filename, and load it into a structure called matData.
matFileName = sprintf('mat%d.mat', k);
if isfile(matFileName)
matData = load(matFileName);
else
fprintf('File %s does not exist.\n', matFileName);
end
end
Or
% Get a list of all txt files in the current folder, or subfolders of it.
fds = fileDatastore('*.txt', 'ReadFcn', #importdata)
fullFileNames = fds.Files
numFiles = length(fullFileNames)
% Loop over all files reading them in and plotting them.
for k = 1 : numFiles
fprintf('Now reading file %s\n', fullFileNames{k});
% Now have code to read in the data using whatever function you want.
% Now put code to plot the data or process it however you want...
end
I have multiple small *.mat files, each containing 4 input images (template{1:4} and a second channel template2{1:4}) and 4 output images (region_of_interests{1:4}), a binarized ('mask') image to train a deep neural network.
I basically followed an example on Mathworks and it suggests to use a function (in this example #matreader) to read in custom file formats.
However ...
It seems impossible to load multiple images from one *.mat file using any load function as it only allows one output, and imageDatastore doen't seem to allow loading data from workspace. How could this be achieved?
Similarly, it seems impossible to load a pixelLabelDatastore from a workspace variable. As a workaround I ended up saving the contents of my *.mat file to an image (using imwrite, saving to save_dir), and re-loading it from there (in this case, the function doesn't even allow to load *.mat files.). (How) can this be achieved without re-saving the file as image?
Here my failed attempt to do so:
%main script
image_dir = pwd; %location of *.mat files
save_dir = [pwd '/a/']; %location of saved output masks
imds = imageDatastore(image_dir,'FileExtensions','.mat','ReadFcn',#matreader); %load template (input) images
pxds = pixelLabelDatastore(save_dir,{'nothing','something'},[0 255]);%load region_of_interests (output) image
%etc, etc, go on to train network
%matreader function, save as separate file
function data=matreader(filename)
in=1; %give up the 3 other images stored in template{1:4}
load(filename); %loads template and template2, containing 4x input images each
data=cat(3,template{in},template2{in}); %concatinate 2 template input images in 3rd dimension
end
%generate example data for this question, will save into a file 'example.mat' in workspace
for ind=1:4
template{ind}=rand([200,400]);
template2{ind}=rand([200,400]);
region_of_interests{ind}=rand([200,400])>.5;
end
save('example','template','template2','output')
You should be able to achieve this using the standard load and save function. Have a look at this code:
image_dir = pwd;
save_dir = pwd;
imds = imageDatastore(image_dir,'FileExtensions',{'.jpg','.tif'});
pxds = pixelLabelDatastore(save_dir,{'nothing','something'},[0 255]);
save('images.mat','imds', 'pxds')
clear
load('images.mat') % gives you the variable "imds" and "pxds" directly -> might override previous variables
tmp = load('images.mat'); % saves all variables in a struct, access it via tmp.imds and tmp.pxds
If you only want to select the variables you want to load use:
load('images.mat','imds') % loads "imds" variable
load('images.mat','pxds') % loads "pxds" variable
load('images.mat','imds','pxds') % loads both variables
EDIT
Now I get the problem, but I fear this is not how it is going to work. The Idea behind the Datastore objects is, that it is used if the data is too big to fit in memory as a whole, but every little piece is small enough to fit in memory. You can use the Datastore object than to easily process and read multiple files on a disk.
This means for you: Simply save your images not as one big *mat file but as multiple small *.mat files that only contain one image.
EDIT 2
Is it strictly necessary to use an imageDatastore for this task? If not you can use something like the following:
image_dir = pwd;
matFiles = dir([image_dir '*.mat']);
for i=1:length(matFiles)
data = load(matFiles(i).name);
img = convertMatToImage(data); % write custom function which converts the mat input to your image
% or something like this:
% for j=1:4
% img(:,:,j) = cat(3,template{j},template2{j});
% end
% process image
end
another alternative would be to create a "image" in your 'matreader' which does not only have 2 bands but to simply put all bands (all templates) on top of each other providing a "datacube" and then in an second step after iterating over all small mat files and reading them splitting the single images out of the one bigger datacube.
would look something like this:
function data=matreader(filename)
load(filename);
for in=1:4
data=cat(3,template{in},template2{in});
end
end
and in your main file, you have to simply split the data into 4 pieces.
I have never tested it but maybe it is possible to return a cell instead of a matrix?
function data=matreader(filename)
load(filename);
data = cell(1,4)
for in=1:4
data{in}=cat(3,template{in},template2{in});
end
end
Not sure if this would work.
However, the right way to go forward from here really depends on how you plan to use the images from imds and if it is really necessary to use a imageDatastore.
I am trying to put together an animation in matlab. For this i am showing pictures containing a description of whats currently happening in the animation. So i am writing out pictures of my figures and later on put these together to an avi file again using matlab. For the description parts to "show up" long enough i use a simple loop in which the current figure is saved n-times. Unfortunatelly this process, though matlab does not have to calculate anything new, is the slowest one.
As the loop i use the following (h_f being the figure handle):
for delay = 1:80
export_fig (h_f,['-r' num2str(resolution)], ['C:\Users\Folder\Name_', '_' num2str(7700+delay) '.png'])
end
I just want to ask if there is any faster way. right now it kind of feels like matlab replots the fig each time before exporting it. So is there a way of plotting the figure once and simultaneously export it n-times?
Thanks for the help :)
If they are all really identical, then you can just copy the first file into the subsequent files. Your time will be limited by the speed of your disk drive and the size of your image files.
% Define some of the flags as variables. This'll make it clearer
% what you're doing when you revisit the code in a year.
% Flag for the resolution
resFlag = sprintf('-r%u', resolutions);
% Base folder
folder = 'C:\Users\Folder\';
% First file number
startnum = 7701;
% This is the pattern all the filenames will use
nameToken = 'Name_%u.png';
% First filename
firstFile = fullfile(folder, sprintf(nameToken, startnum));
% Export the first file
export_fig(h_f, resFlag, firstFile);
numCopies = 80;
% Copy the file
for delay = 2:numCopies
% Make a new filename
currentFile = fullfile(folder, sprintf(nameToken, startnum + delay));
% Copy the first file into the current filename.
copyfile(firstFile, currentFile);
end
I have 100 data files in a folder called "Experiment1", and I need to take all of the data from them and put them into a single matrix. Each data file contains 15 columns and 40 rows of data.
The order in which the files are in the folder is arbitrary. It doesn't matter in what order they get put into the combined matrix.
I've written some code using dlmread that will do the job:
for i = 1:100
%% Read in the relevant file.
filename = ['File_' int2str(i) '.dat']
Data = dlmread(fullfile(pwd, 'Experiment1',filename));
%% Put all the data I need in a separate matrix
NeededData(1+((i-1)*40):i+((i-1)*40)-i+40,1:15) = Data(:,1:15);
end
However, there are two things I don't like about my code.
The files have random names at present, and I'd need to manually change all their names to "File_1.dat", "File_2.dat", etc.
The code is cumbersome and hard to read.
How could I do things better?
Since you've fixed the problem of defining the name of the files to be read with dir, you can improve the way you add the read data (Data) to the output matrix (NeededData).
You can sumultaneously read the input files and add the data to the output matrix by inserting the call to dlmread directly in the assignment statement:
files=dir('*.dat');
n_files=length(files)
% Initialize the output matrix as empty
NeededData_0=[]
for i=1:n_files
% Simultaneously read input file and assign data to the output matrinx
NeededData_0=[NeededData_0;dlmread(files(i).name)]
end
In case you prefer working with the inides (as in your origina approach), since you know in advance that all the files have the same (40) number of rows) you can simplify the notation as follows:
files=dir('*.dat');
n_files=length(files)
% Define the number of rows in each inout file
n_rows=40;
% Define the number of colums in each inout file
n_col=15;
NeededData_2=nan(n_rows*n_files,n_col)
% Define the sequence of rows
r_list=1:n_rows:n_rows*n_files
for i=1:3
Data=dlmread(files(i).name)
NeededData_2(r_list(i):r_list(i)+n_rows-1,:)=Data
end
Hope this helps.
Using the suggestion to use dir present in the answers I have made the following code, which is clearly an improvement on my earlier effort. I would welcome further improvements, or suggestions for alternative approaches.
files = dir('*.dat');
for i = 1:length({files.name})
%% Read in the relevant file.
Data = dlmread(files(i).name);
%% Put all the data I need in a separate matrix
NeededData(1+((i-1)*40):i+((i-1)*40)-i+40,1:15) = Data(:,1:15);
end
I am trying to write a program where i have to read a wav file, extract some features from it and save them and then go and pick the next file repeat the same procedure. the number of wave files to be picked are more than 100. Can someone help me how to read wavfiles one after another. (say the files are named e1.wav,e2.wav and so on). someone please help me
The dir command is quite helpful here. It either displays the whole content of a directory but you can also specify a glob to just return a sub-set of files, e.g. dir('*.wav'). This returns an struct-array containing file information such as name, date, bytes, isdir and so on.
To get started, try the following:
filelist = dir('*.wav');
for file = filelist
fprintf('Processing %s\n', file.name);
fid = fopen(file.name);
% Do something here with your file.
fclose(fid);
end
Edit 1: Change the double-quotes to single-quotes (thx to user1540393).
Edit 2 (Suggested by amro): If a processing result has to be stored per file,
I often use the following pattern. I usually pre-allocate an array, a struct array or
a cell array of the same size as the filelist. Then I use an integer index to iterate
over the file list, which I can also use to write the output. If the information to be
stored is homogeneous (e.g. one scalar per file), use an array or a struct array.
However, if the information differs from file to file (e.g. vectors or matrices of different size) use a cell array instead.
An example using an ordinary array:
filelist = dir('*.wav');
% Pre-allocate an array to store some per-file information.
result = zeros(size(filelist));
for index = 1 : length(filelist)
fprintf('Processing %s\n', filelist(index).name);
% Read the sample rate Fs and store it.
[y, Fs] = wavread(filelist(index).name);
result(index) = Fs;
end
% result(1) .. result(N) contain the sample rates of each file.
An example using a cell array:
filelist = dir('*.wav');
% Pre-allocate a cell array to store some per-file information.
result = cell(size(filelist));
for index = 1 : length(filelist)
fprintf('Processing %s\n', filelist(index).name);
% Read the data of the WAV file and store it.
y = wavread(filelist(index).name);
result{index} = y;
end
% result{1} .. result{N} contain the data of the WAV files.