Probably a really simple question - but I can't seem to figure it out for Matlab. I would like to import data from a list of files, and save the resulting matrices with a name derived from the original file name. There's quite a few files, so I would like to use a for loop.
In BASH I would write something like:
For sample in apple orange guava jackfruit;
do
"$sample"_matrix = someimportfunction("$sample".txt);
done
I can import the files one at a time with dlmread, I just can't figure out how to loop over the names, sort of the matlab equivelent of $.
Many thanks for any suggestions!
I think the code snippet below may do exactly what you want.
Of course, you need the files apple.txt etcetera, with numbers in them
for sample = {'apple', 'orange', 'guava', 'jackfruit'}
matrix.(sample{1}) = load([sample{1},'.txt']);
end
matrix = matrix
I get the following output:
matrix =
scalar structure containing the fields:
apple = 1 2 3
orange =
1 2
4 5
guava =
1 1 1
0 0 0
jackfruit = 17
Let's say your files are in the folder "sfolder".
Files = dir('sfolder');
num_files = length(Files);
for i=1:num_files
fid = fopen(Files(i).name); %do whatever you want now
end
This will help you go through each file in a particular directory.
Related
I'm new to MATLAB, and I can't manage to make my function work in order to save my data into a .mat file.
The input:
A structure, with 5 fields:
data: 3D matrix of 19x1000x143
labels: 1x143 matrix with 1 or -1 in it
subject_number: an integer
sampling_rate: an integer, 500 Hz
channel_names: 1x19 matrix with text in it
name: a string for the name of the file
clean: a matrix 1x143 with 1 or 0 in it.
The idea is to save only the clean data, marked as 1 in the clean matrix.
If clean(i) is equal to 1:
save data(:,:,i) and labels(:,i)
This is the code I've tried to implement in the saving.m file:
function saving(EEG_struct, clean, name)
subject_number = EEG_struct.subject_number;
fs = EEG_struct.sampling_rate;
chan_names = EEG_struct.channel_names;
nb_epoch = size(EEG_struct.data, 3);
for j=1:nb_epoch
if clean(j) == 1
% Keep the epoch and label
data = cat(3, data, EEG_struct.data(:,:,j));
labels = cat(2, labels, EEG_struct.labels(:,j));
end
end
save(name, data, labels, subject_number, fs, chan_names)
As you can see, I would like to save the data as a structure with the same shape as the EEG_struct input.
Moreover, I would like to use a parfor instead of a for, but it raised me an error I didn't quite get:
An UndefinedFunction error was thrown on the workers for 'data'. This might be because the file containing 'data' is not accessible on the workers. Use addAttachedFiles(pool, files) to specify the required files to be attached. See the documentation for 'parallel.Pool/addAttachedFiles' for more details. Caused by: Undefined function or variable 'data'.
Thanks for the help !
You can use your clean variable as a logical index and parse out your data and labels at once. So there is no need for a loop.
Also the save command needs the "names" of the vars to save not the variables themselves. So I just put ' ' around each one.
function saving(EEG_struct, clean, name)
subject_number = EEG_struct.subject_number;
fs = EEG_struct.sampling_rate;
chan_names = EEG_struct.channel_names;
nb_epoch = size(EEG_struct.data, 3);
%No need for a loop at all
data = EEG_struct.data(:,:,logical(clean));
labels = EEG_struct.labels(logical(clean)); %This is a 1xN so I removed the extra colon operator
save(name, 'data', 'labels', 'subject_number', 'fs', 'chan_names');
EDIT:
Per you comment if you want to just leave everything in the structure. I gave you 2 options for how to save it.
function saving(EEG_struct, clean, name)
%Crop out ~clead data
EEG_struct.data = EEG_struct.data(:,:,logical(clean));
EEG_struct.labels = EEG_struct.labels(logical(clean)); %This is a 1xN so I removed the extra colon operator
% Option 1
save(name, 'EEG_struct');
% Option2
save(name, '-struct', 'EEG_struct');
Option 1 will directly save the struct to the MAT file. So if you were to load the data back like this:
test = load(name);
test =
EEG_struct: [1x1 struct]
You would get your structure placed inside another structure ... which might not be ideal or require an extra line to de-nest it. On the other hand just loading the MAT file with no outputs load(name) would put EEG_struct into your current workspace. But if in a function then it sort of springs into existence without every being declared which makes code a bit harder to follow.
Option 2 uses the '-struct' option which breaks out each field automatically into separate vars in the MAT file. So loading like this:
EEG_struct = load(name);
Will put all the fields back together again. To me at least this looks cleaner when done within a function but is probably just my preference
So comment out which ever you prefer. Also, not I did not include clean in the save. You could either append it to the MAT or add it to your structure.
To get a structure the same as EEG_struct but with only the data/labels corresponding with the clean variable, you can simply make a copy of the existing structure and remove the rows where clean=0
function saving(EEG_struct, clean, name)
newstruct = EEG_struct;
newstruct.data(:,:,logical(~clean)) = '';
newstruct.labels(logical(~clean)) = '';
save(name,'newstruct');
the function dir returns an array like
.
..
Folder1
Folder2
and every time I have to get rid of the first 2 items, with methods like :
for i=1:numel(folders)
foldername = folders(i).name;
if foldername(1) == '.' % do nothing
continue;
end
do_something(foldername)
end
and with nested loops it can result in a lot of repeated code.
So can I avoid these "folders" by an easier way?
Thanks for any help!
Edit:
Lately I have been dealing with this issue more simply, like this :
for i=3:numel(folders)
do_something(folders(i).name)
end
simply disregarding the first two items.
BUT, pay attention to #Jubobs' answer. Be careful for folder names that start with a nasty character that have a smaller ASCII value than .. Then the second method will fail. Also, if it starts with a ., then the first method will fail :)
So either make sure you have nice folder names and use one of my simple solutions, or use #Jubobs' solution to make sure.
A loop-less solution:
d=dir;
d=d(~ismember({d.name},{'.','..'}));
TL; DR
Scroll to the bottom of my answer for a function that lists directory contents except . and ...
Detailed answer
The . and .. entries correspond to the current folder and the parent folder, respectively. In *nix shells, you can use commands like ls -lA to list everything but . and ... Sadly, MATLAB's dir doesn't offer this functionality.
However, all is not lost. The elements of the output struct array returned by the dir function are actually ordered in lexicographical order based on the name field. This means that, if your current MATLAB folder contains files/folders that start by any character of ASCII code point smaller than that of the full stop (46, in decimal), then . and .. willl not correspond to the first two elements of that struct array.
Here is an illustrative example: if your current MATLAB folder has the following structure (!hello and 'world being either files or folders),
.
├── !hello
└── 'world
then you get this
>> f = dir;
>> for k = 1 : length(f), disp(f(k).name), end
!hello
'world
.
..
Why are . and .. not the first two entries, here? Because both the exclamation point and the single quote have smaller code points (33 and 39, in decimal, resp.) than that of the full stop (46, in decimal).
I refer you to this ASCII table for an exhaustive list of the visible characters that have an ASCII code point smaller than that of the full stop; note that not all of them are necessarily legal filename characters, though.
A custom dir function that does not list . and ..
Right after invoking dir, you can always get rid of the two offending entries from the struct array before manipulating it. Moreover, for convenience, if you want to save yourself some mental overhead, you can always write a custom dir function that does what you want:
function listing = dir2(varargin)
if nargin == 0
name = '.';
elseif nargin == 1
name = varargin{1};
else
error('Too many input arguments.')
end
listing = dir(name);
inds = [];
n = 0;
k = 1;
while n < 2 && k <= length(listing)
if any(strcmp(listing(k).name, {'.', '..'}))
inds(end + 1) = k;
n = n + 1;
end
k = k + 1;
end
listing(inds) = [];
Test
Assuming the same directory structure as before, you get the following:
>> f = dir2;
>> for k = 1 : length(f), disp(f(k).name), end
!hello
'world
a similar solution from the one suggested by Tal is:
listing = dir(directoryname);
listing(1:2)=[]; % here you erase these . and .. items from listing
It has the advantage to use a very common trick in Matlab, but assumes that you know that the first two items of listing are . and .. (which you do in this case). Whereas the solution provided by Tal (which I did not try though) seems to find the . and .. items even if they are not placed at the first two positions within listing.
Hope that helps ;)
If you're just using dir to get a list of files and and directories, you can use Matlab's ls function instead. On UNIX systems, this just returns the output of the shell's ls command, which may be faster than calling dir. The . and .. directories won't be displayed (unless your shell is set up to do so). Also, note that the behavior of this function is different between UNIX and Windows systems.
If you still want to use dir, and you test each file name explicitly, as in your example, it's a good idea to use strcmp (or one of its relations) instead of == to compare strings. The following would skip all hidden files and folder on UNIX systems:
listing = dir;
for i = 1:length(listing)
if ~strcmp(listing(i).name(1),'.')
% Do something
...
end
end
You may also wanna exclude any other files besides removing dots
d = dir('/path/to/parent/folder')
d(1:2)=[]; % removing dots
d = d([d.isdir]) % [d.isdir] returns a logical array of 1s representing folders and 0s for other entries
I used: a = dir(folderPath);
Then used two short code that return struct:
my_isdir = a([a.isdir]) Get a struct which only has folder info
my_notdir = a(~[a.isdir]) Get a struct which only has non-folder info
Combining #jubobs and #Tal solutions:
function d = dir2(folderPath)
% DIR2 lists the files in folderPath ignoring the '.' and '..' paths.
if nargin<1; folderPath = '.'; elseif nargin == 1
d = dir(folderPath);
d = d(~ismember({d.name},{'.','..'}));
end
None of the above puts together the elements as I see the question having being asked - obtain a list only of directories, while excluding the parents.
Just combining the elements, I would go with:
function d = dirsonly(folderPath)
% dirsonly lists the unhidden directories in folderPath ignoring '.' and '..'
% creating a simple cell array without the rest of the dir struct information
if nargin<1; folderPath = '.'; elseif nargin == 1
d = dir(folderPath);
d = {d([d.isdir] & [~ismember({d.name},{'.','..'})]).name}.';
end
if hidden folders in general aren't wanted the ismember line could be replaced with:
d = {d([d.isdir] & [~strncmp({d.name},'.',1)]).name}.';
if there were very very large numbers of interfering non-directory files it might be more efficient to separate the steps:
d = d([d.isdir]);
d = {d([~strncmp({d.name},'.',1)]).name}.';
We can use the function startsWith
folders = dir("folderPath");
folders = string({folders.name});
folders = folders(~startsWith(folders,"."))
Potential Solution - just remove the fields
Files = dir;
FilesNew = Files(3:end);
You can just remove them as they are the first two "files" in the structure
Or if you are actually looking for specific file types:
Files = dir('*.mat');
I have a folder called BasePics within a folder called Images. Inside BasePics there are 30 JPEG images. I'm wondering if the following is possible: Can a script be written that reads all of these images using the imread() command. The names of the images are somewhat sequential: C1A_Base.jpg, C1B_Base.jpg, C1C_Base.jpg, C2A_Base.jpg, C2B_Base.jpg, C2C_Base.jpg, etc.... all the way up to C10C_Base.jpg
Can a loop be used somehow:
file = dir('Images\BasePics');
NF = length(file);
for k = 1:NF
images(k) = imread(fullfile('ImagesBasePics',file(k))
imagesc(images(k))
end
This is a rough idea of what I want to do, but I'm wondering if it can be done with the current naming format I have in the Images folder. I would also like to have each image being read be its own variable with the same or similar name as it is named in the folder Images\BasePics currently, rather than have an concatenated array of 30 images all under the one variable images. I would like to have 30 separate variables, with names such as A1, A2,A3,B1,B2,B3 etc...
Also when I just ask for:
dir images\BasePics
Matlab outputs 33 files, instead of 30. There are two extra files at the beginning of the folder: '.' and '..' and one at the end: 'Thumbs.db' These do not exist when I look at the folder separately, is there a way to programically have Matlab skip over these?
Thanks!!
Since you know the names of the files in advance, you can skip the dir and go ahead and read the files:
for l = 'ABC'
for n=1:10
nm = sprintf('C%d%c_Base.jpg', n, l );
fnm = sprintf('%c%d', l, n );
imgs.(fnm) = imread( fullfile('images','BasePics', nm ) );
end
end
Now you have a struct imgs with fields A1...C10 for each image.
You are very close. I would just use dir('Images\BasePics\*.jpg') to get rid of the extraneous files.
The naming system you want will not lend itself to additional batch processing (do you really want to type all of A1, A2, etc?). I would either keep it sequential, and store a list of the filenames to match, or use a struct array, like images.C1A, etc.
dirlist = dir('Images\BasePics\*.jpg');
for k = 1:length(dirlist);
fname = dirlist(k).name;
[path,name,ext] = fileparts(fname); % separate out base name of file
images.(name) = imread(fullfile('Images\BasePics', fname));
end
I'm developing a piece of k-means fuzzy code. Now I want to save the data of each iteration that is displayed by statset('Display','iter');. Help me please.
X = [randn(20,2)+ones(20,2); randn(20,2)-ones(20,2)];
opts = statset('Display','iter');
[cidx, ctrs] = kmeans(X, 2, 'Distance','city', ...
'Replicates',5, 'Options',opts);
plot(X(cidx==1,1),X(cidx==1,2),'r.', ...
X(cidx==2,1),X(cidx==2,2),'b.', ctrs(:,1),ctrs(:,2),'kx');
A dummy solution is given by the function diary which enables the storing of the matlab console output on a file.
X = [randn(20,2)+ones(20,2); randn(20,2)-ones(20,2)];
opts = statset('Display','iter');
diary('output.txt') % # Whatever is displayed from now on is saved on 'output.txt'
[cidx, ctrs] = kmeans(X, 2, 'Distance','city', ...
'Replicates',5, 'Options',opts);
diary('off') % # logging is disabled
After the execution, output.txt will contain
iter phase num sum
1 1 40 96.442
2 1 8 79.7403
3 1 6 70.2776
...
You may want to clean the content of output.txt at every run, otherwise it will just append the new log after the previous one.
One way to achieve would be to redirect the output displayed in the MATLAB terminal to a file, say 'my_file.txt'. To do so:
Use the command edit statset.m; to open the file in the MATLAB
editor.
Open the output file you require with fid =
fopen('my_file.txt','w');.
Replace fprintf( with fprintf(fid,.
You might want to keep a backup copy of statset.m too, just to be on the safe side.
EDIT
#Acorbe's solution gives the same result without all the above hassle.
how to write a program in matlab that reads a certain number of images let's say 20 for example which are saved in a given directory (C:) such that later i can use them. suppose that the images are saved by numbers. later, i am gonna use them.
I'd have the code look something like this. Assuming cell array im holds your images.
Write out:
IMG_DIR = 'C:\';
filename_root = 'image';
IMG_EXT = '.jpg';
NUM_IMAGES = 20;
for i = 1:NUM_IMAGES
imwrite(im{i}, [IMG_DIR filename_root num2str(i) IMG_EXT]);
end
Read in:
for i = 1:NUM_IMAGES
im{i} = imread([IMG_DIR filename_root num2str(i) IMG_EXT]);
end
If you don't know how many there are, you can also use ls command (works differently in Windows vs. Linux).
If you don't know, in advance, which files will be in there, but you know that they have the string in them, 'rawImage' (like 'rawImage001.jpg' etc.) you can do something like
a = dir('c:\temp');
requiredBaseFileName = 'rawImage'; % you want them to contain the substring 'rawImage'
for i = 1:length(a),
fileName = a(i).name;
if(isempty(strfind(fileName,'.jpg')) & isempty(strfind(fileName,'.png')))
continue;
end
if(isempty(strfind(fileName,requiredBaseFileName)))
continue;
end
% do your processing here
end