I am trying to edit 100 .mat files in a folder with no pattern in their names. Each file contains a matrix of size 100-by-10, and I want to convert them to 10-by-10-by-10. How do I go about this?
Provided you have a single matrix in each file, and want to overwrite the original matrix:
listing = dir('*.mat'); % finds all .mat files in your pwd
for ii = 1:numel(listing)
tmp = listing(ii).name;
s = load(tmp); % load a file
Fname = fieldnames(s); % get matrix name
out = reshape(s.(Fname{1}),[10 10 10]); % reshape
save(tmp,'out') % Save, overwriting original
end
Related
This function reads the data from multiple mat files and save them in multiple txt files. But the data (each value) are saved one value in one column and so on. I want to save the data in a form of three columns (coordinates) in the text files, so each row has three values separated by space. Reshape the data before i save them in a text file doesn't work. I know that dlmwrite should be modified in away to make newline after three values but how?
mat = dir('*.mat');
for q = 1:length(mat)
load(mat(q).name);
[~, testName, ~] = fileparts(mat(q).name);
testVar = eval(testName);
pos(q,:,:) = testVar.Bodies.Positions(1,:,:);
%pos=reshape(pos,2,3,2000);
filename = sprintf('data%d.txt', q);
dlmwrite(filename , pos(q,:,:), 'delimiter','\t','newline','pc')
end
My data structure:
These data should be extracted from each mat file and stored in the corresponding text files like this:
332.68 42.76 42.663 3.0737
332.69 42.746 42.655 3.0739
332.69 42.75 42.665 3.074
A TheMathWorks-trainer once told me that there is almost never a good reason nor a need to use eval. Here's a snippet of code that should solve your writing problem using writematrix since dlmwrite is considered to be deprecated.
It further puts the file-handling/loading on a more resilient base. One can access structs dynamically with the .(FILENAME) notation. This is quite convenient if you know your fields. With who one can list variables in the workspace but also in .mat-files!
Have a look:
% path to folder
pFldr = pwd;
% get a list of all mat-files (returns an array of structs)
Lst = dir( fullfile(pFldr,'*.mat') );
% loop over files
for Fl = Lst.'
% create path to file
pFl = fullfile( Fl.folder, Fl.name );
% variable to load
[~, var2load, ~] = fileparts(Fl.name);
% get names of variables inside the file
varInfo = who('-file',pFl);
% check if it contains the desired variables
if ~all( ismember(var2load,varInfo) )
% display some kind of warning/info
disp(strcat("the file ",Fl.name," does not contain all required varibales and is therefore skipped."))
% skip / continue with loop
continue
end
% load | NO NEED TO USE eval()
Dat = load(pFl, var2load);
% DO WHATEVER YOU WANT TO DO
pos = squeeze( Dat.(var2load)(1,:,1:2000) );
% create file name for text file
pFl2save = fullfile( Fl.folder, strrep(Fl.name,'.mat','.txt') );
writematrix(pos,pFl2save,'Delimiter','\t')
end
To get your 3D-matrix data into a 2D matrix that you can write nicely to a file, use the function squeeze. It gets rid of empty dimensions (in your case, the first dimension) and squeezes the data into a lower-dimensional matrix
Why don't you use writematrix() function?
mat = dir('*.mat');
for q = 1:length(mat)
load(mat(q).name);
[~, testName, ~] = fileparts(mat(q).name);
testVar = eval(testName);
pos(q,:,:) = testVar(1,:,1:2000);
filename = sprintf('data%d.txt', q);
writematrix(pos(q,:,:),filename,'Delimiter','space');
end
More insight you can find here:
https://www.mathworks.com/help/matlab/ref/writematrix.html
I have a .mtx file which contains a vector which I am suppose to use for matrix vector multiplication. I tried to open the file using
fopen('filename') but this does not work, it returns a single number. I have also tried using readmtx but this gives me the following error: File size does not match inputs. Expected a file size of 232316 bytes. Instead the file size is
365 bytes. Could you please advise how I can open and work with this type of file in MATLAB.
fopen('filename') outputs only the fileID, which is typically an integer >3. This fileID can be used with e.g. fscanf(fileID) to get the content of the file.
For the .mtx format, where each line contains [row-number column-number matrix-entry], you could also do something like:
%% file
filename = 'my_matrix.mtx';
%% read Matrix
Mat = read_mtx(filename);
%% function
function Mat = read_mtx(filename)
% open file
fID = fopen(filename,'r');
M = fscanf(fID, '%f');
% reshape M vector into Nx3 matrix
M = reshape(M, [3, length(M)/3])';
% assemble final matrix
Mat = zeros(M(end,1),M(end,1));
for ii = 1:size(M,1)
Mat(M(ii,1),M(ii,2)) = M(ii,3);
end
end
I have been working on making a database which contains images and their preset values and other important parameters. But unfortunately, I'm not being able to save the initial data of say 10 images in one .csv file. I have made the code that runs fine with creating .csv file but saving the last value and overwriting all the previous values. I gave also once modified that is comment down in the code using sprintf but it make .csv file for every iteration separately. But i want to make one .csv file containing 7 column with all the respective values.
My code is below and output of my code is attached Output.
Please someone guide me how to make single .csv file with 10 values for instance (could be increased to hundreds in final database) to save in 1 .csv file.
clc
clear all
myFolder = 'C:\Users\USER\Desktop\PixROIDirectory\PixelLabelData_1';
filePattern = fullfile(myFolder, '*.png'); % Change to whatever pattern you need
theFiles = dir(filePattern);
load('gTruthPIXDATA.mat','gTruth')
gTruth.LabelDefinitions;
for i=1:10
%gTruth.LabelData{i,1};
baseFileName = theFiles(i).name;
fullFileName = fullfile(myFolder, baseFileName);
fprintf(1, 'Now reading %s\n', fullFileName);
imageArray = imread(fullFileName);
oUt = regionprops(imageArray,'BoundingBox');
Y = floor(oUt.BoundingBox);
X_axis = Y(1);
Y_axis = Y(2);
Width = Y(3);
Height = Y(4);
CLASS = gTruth.LabelDefinitions{1,1};
JPG = gTruth.DataSource.Source{i,1};
PNG = gTruth.LabelData{i,1};
OUTPUT = [JPG X_axis Y_axis Width Height CLASS PNG]
% myFile = sprintf('value%d.csv',i);
% csvwrite(myFile,OUTPUT);
end
Try fprintf (https://www.mathworks.com/help/matlab/ref/fprintf.html).
You will need to open your output file to be written, then you can append lines to it through each iteration
Simple example:
A = [1:10]; % made up a matrix of numbers
fid = fopen('test.csv','w'); % open a blank csv and set as writable
for i = 1:length(A) % loop through the matrix
fprintf(fid,'%i\n',A(i)); % print each integer, then a line break \n
end
fclose(fid); % close the file for writing
How can I loop through .dbl and .txt files in a folder, find .txt files with a specific number and condition (e.g. 'laser on') and then do things to the associated .dbl file (if the names are similar)?
I don't really have much and I can't seem to access the file names I want to look through using getfield(files, 'name') so I'm really stuck. Here is what I have so far so as to give some more structure to my question.
% specify folder with the load function to manipulate .dbl files
folder = 'some folder';
% specify folder that has the data
folder2 = 'some other folder';
cd(folder);
addpath(folder2);
% specify parameters implemented in data collection program
start_delay = 0; % in ps
step_size = 20; % in ps
n_steps = 30;
% loop through folders
files = dir(folder2);
for i = 1:size(files,1)
if i == '*.txt
% find string 'ON'
% find a number in .txt file
% for .txt files with string 'ON', look for .txt files for delay =0, then 20, then 40, etc.
% find associated .dbl file
% manipulate .dbl file
end
end
The things you are looking for are the *.xxx comand for dir and strfind, take a look at this example:
txtList=dir('*.txt');
sblList=dir('*.dbl');
for ii=1:length(txtList)
fid=fopen(txtList(ii).name);
C= textscan(fid,'%s'); %depends on your formating
C=C{1}{1}; %supposing you .txt is really just one string
fclose(fid);
if (sum(strfind(C,'ON'))) %for .txt files with string 'ON'...
Equals0=strfind(C,'0'); % ... look for =0,...
Equals20=strfind(C,'20'); %then =20
%... etc
end
%you get the idea...
%do whatever you want with dblList
end
If there are the following files in the folder C:\test\:
file1.TIF, file2.TIF .... file100.TIF
Can MatLab automatically rename them to:
file_0001.TIF, file_0002.TIF, .... file_0100.TIF?
No-loop approach -
directory = 'C:\test\'; %//' Directory where TIFF images are present
filePattern = fullfile(directory, 'file*.tif'); %//' files pattern with absolute paths
old_filename = cellstr(ls(filePattern)) %// Get the filenames
file_ID = strrep(strrep(old_filename,'file',''),'.TIF','') %// Get numbers associated with each file
str_zeros = arrayfun(#(t) repmat('0',1,t), 5-cellfun(#numel,file_ID),'uni',0) %// Get zeros string to be pre-appended to each filename
new_filename = strcat('file_',str_zeros,file_ID,'.TIF') %// Generate new filenames
cellfun(#(m1,m2) movefile(m1,m2),fullfile(directory,old_filename),fullfile(directory,new_filename)) %// Finally rename files with the absolute paths
Edit 1:
For a case when you have the filenames as file27.TIF, file28.TIF, file29.TIF and so on and you would like to rename them as file0001.TIF, file0002.TIF, file0003.TIF and so on respectively, try this -
directory = 'C:\test\'; %//' Directory where TIFF images are present
filePattern = fullfile(directory, 'file*.tif'); %//' files pattern with absolute paths
old_filename = cellstr(ls(filePattern)) %// Get the filenames
file_ID = strrep(strrep(old_filename,'file',''),'.TIF','') %// Get numbers associated with each file
file_ID_doublearr = str2double(file_ID)
file_ID_doublearr = file_ID_doublearr - min(file_ID_doublearr)+1
file_ID = strtrim(cellstr(num2str(file_ID_doublearr)))
str_zeros = arrayfun(#(t) repmat('0',1,t), 4-cellfun(#numel,file_ID),'uni',0) %// Get zeros string to be pre-appended to each filename
new_filename = strcat('file',str_zeros,file_ID,'.TIF') %// Generate new filenames
cellfun(#(m1,m2) movefile(m1,m2),fullfile(directory,old_filename),fullfile(directory,new_filename)) %// Finally rename files with the absolute paths
A slightly more robust method:
dirlist = dir(fullfile(mypath,'*.TIF'));
fullnames = {dirlist.name}; % Get rid of one layer of cell array-ness
[~,fnames,~] = cellfun(#fileparts,fullnames,'UniformOutput',false); % Create cell array of the file names from the output of dir()
fnums = cellfun(#str2double,regexprep(fnames,'[^0-9]','')); % Delete any character that isn't a number, returns it as a vector of doubles
fnames = regexprep(fnames,'[0-9]',''); % Delete any character that is a number
for ii = 1:length(dirlist)
newname = sprintf('%s_%04d.TIF',fnames{ii},fnums(ii)); % Create new file name
oldfile = fullfile(mypath,dirlist(ii).name); % Generate full path to old file
newfile = fullfile(mypath,newname); % Generate full path to new file
movefile(oldfile, newfile); % Rename the files
end
Though this will accomodate filenames of any length, it does assume that there are no numbers in the filename other than the counter at the end. MATLAB likes to throw things into nested cell arrays, so I incorporated cellfun in a couple places to bring things into more manageable formats. It also allows us to vectorize some of the code.