I am trying to access 4k images and crop some ROI based areas (4 ROI in my case) and store them in some directory. So far everything is working okay except the loops handling of the filename.
Below is my code attached. I am accessing N 4k images, crop and resize them to my desired resolution. In the end, when I tried to save the data the images got overwritten.
N=2;
for img = 1:N
x = gTruth.LabelData.crack{img,1}
for i=1:4
Cells = x(i,1:4)
baseFileName = theFiles(img).name;
fullFileName = fullfile(myFolder, baseFileName);
fprintf(1, 'Now reading %s\n', fullFileName);
imageArray = imread(fullFileName);
CroP = imcrop(imageArray,Cells);
imshow(CroP);
B = imresize(CroP,[256 256]);
imshow(B);
imwrite(B,strcat('C:\Users\USER\Desktop\Directory\imagefile_00',num2str(i),'.png'));
end
end
My question is that after loop i runs, it saves 4 images and for img again it saves four values. Now when the code runs it saves only last 4 images and not 8. I should get a i*N number of total images, but I'm getting only 4 and rest are overwritten.
How can I adapt my program to save all files?
imwrite(B,strcat('C:\Users\USER\Desktop\Directory\imagefile_00',num2str(i),'.png'));
is where the problem is. You use num2str(i) to change the number, and i=[1,2,3,4]. Thus, you cannot create a file which is outside numbers 1 to 4. Taking you want something based on img as well, you can use e.g.
imwrite(B,strcat('C:\Users\USER\Desktop\Directory\imagefile_',num2str(img),num2str(i),'.png'));
which will create a file named imagefile_11 for the first image and first region, imagefile_12 for the first image, second region, imagefile_324 for the 32nd image, fourth region etc. Change according to your needs of course.
Example in action:
>> i=3;img=1;
>> strcat('C:\Users\USER\Desktop\Directory\imagefile_',num2str(img),num2str(i),'.png')
ans =
C:\Users\USER\Desktop\Directory\imagefile_13.png
>> i=1;img=2;
>> strcat('C:\Users\USER\Desktop\Directory\imagefile_',num2str(img),num2str(i),'.png')
ans =
C:\Users\USER\Desktop\Directory\imagefile_21.png
Free advice:
i and j are the imaginary unit. It's, in my opinion, preferable not to use them as loop indices.
Your desktop is most likely not the best place to save stuff. Make a folder in for example your Documents folder with an apt name, e.g. C:\Users\USER\Documents\ROIfrom4k\
The declarations of x and Cells would benefit from a closing semicolon on the line, so as to prevent them from outputting to the console, slowing down the program and clogging the command window. The orange wiggles MATLAB puts there are not for festivity, they present a useful warning. (Not to be confused with red wiggles, those present an serious error, because of which MATLAB cannot run at all.)
Related
I have 200 time points. For each time point, there is an image, the size of which is 40*40 double, corresponds to this time point. For example, image 1 corresponds to time point 1; image k corresponds to time point k (k = 1,2,...,200).
The time points are T = 1:200, with the images named as Image_T, thus Image_1, Image_2 etc.
I want to put all these 200 images together. The final size is 40*40*200 double. The final image looks like fMRI image (fmri_szX = 40, fmri_szY = 40 and fmri_szT = 200). How to achieve that?
Thanks!
Dynamic variables
Note that whilst this is possible, it's considered to be bad programming (see for instance here, or this blog by Loren and even the Mathworks in their documentation tell you not to do this). It would be much better to load your images directly into either a 3D array or a cell structure, avoiding dynamic variable names. I just posted this for completeness; if you ever happen to have to use this solution, you should change to a (cell-) array immediately.
The gist of the linked articles as to why eval is such a bad idea, is that MATLAB can no longer predict what the outcome of the operation will be. For instance A=3*(2:4) is recognised by MATLAB to output a double-array. If you eval stuff, MATLAB can no longer do this. MATLAB is an interpreted language, i.e. each line of code is read then ran, without compiling the entire code beforehand. This means that each time MATLAB encounters eval, it has to stop, evaluate the expression, then check the output, store that, and continue. Most of the speed-engines employed by MATLAB (JIT/MAGMA etc) can't work without predicting the outcome of statements, and will therefore shut down during the eval evaluation, rendering your code very slow.
Also there's a security aspect to the usage of eval. Consider the following:
var1 = 1;
var2 = 2;
var3 = 3;
varnames = {'var1', 'var2; disp(''GOTCHA''); %', 'var3'};
accumvar = [];
for k = 1:numel(varnames)
vname = varnames{k};
disp(['Reading from variable named ' vname]); eval(['accumvar(end+1) = ' vname ';']);
end
Now accumvar will contain the desired variable names. But if you don't set accumvar as output, you might as well not use a disp, but e.g. eval('rm -rf ~/*') which would format your entire disk without even telling you it's doing so.
Loop approach
for ii = 200:-1:1
str = sprintf('Image_%d',ii);
A(:, :, :, ii) = eval(str);
end
This creates your matrix. Note that I let the for loop run backwards, so as to initialise A in its largest size.
Semi-vectorised approach
str = strsplit(sprintf('image_%d ',1:200),' '); % Create all your names
str(end) = []; % Delete the last entry (empty)
%Problem: eval cannot handle cells, loop anyway:
for ii = 200:-1:1
A(:, :, :, ii) = eval(str{ii});
end
eval does not support arrays, so you cannot directly plug the cellarray strin.
Dynamic file names
Despite having a similar title as above, this implies having your file names structured, so in the file browser, and not MATLAB. I'm assuming .jpg files here, but you can add every supported image extension. Also, be sure to have all images in a single folder and no additional images with that extension, or you have to modify the dir() call to include only the desired images.
filenames = dir('*.jpg');
for ii = length(filenames):-1:1
A(:,:,:,ii) = imread(filenames{ii});
end
Images are usually read as m*n*3 files, where m*n is your image size in pixels and the 3 stems from the fact that they're read as RGB by imread. Therefore A is now a 4D matrix, structured as m*n*3*T, where the last index corresponds to the time of the image, and the first three are your image in RGB format.
Since you do not specify how you obtain your 40*40 double, I have left the 4D matrix. Could be you read them and then switch to using a uint16 interpretation of RGB, which is a single number, which would result in a m*n*1*T variable, which you can reduce to a 3D variable by calling A = squeeze(A(:,:,1,:));
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 have 200 time points. For each time point, there is an image, the size of which is 40*40 double, corresponds to this time point. For example, image 1 corresponds to time point 1; image k corresponds to time point k (k = 1,2,...,200).
The time points are T = 1:200, with the images named as Image_T, thus Image_1, Image_2 etc.
I want to put all these 200 images together. The final size is 40*40*200 double. The final image looks like fMRI image (fmri_szX = 40, fmri_szY = 40 and fmri_szT = 200). How to achieve that?
Thanks!
Dynamic variables
Note that whilst this is possible, it's considered to be bad programming (see for instance here, or this blog by Loren and even the Mathworks in their documentation tell you not to do this). It would be much better to load your images directly into either a 3D array or a cell structure, avoiding dynamic variable names. I just posted this for completeness; if you ever happen to have to use this solution, you should change to a (cell-) array immediately.
The gist of the linked articles as to why eval is such a bad idea, is that MATLAB can no longer predict what the outcome of the operation will be. For instance A=3*(2:4) is recognised by MATLAB to output a double-array. If you eval stuff, MATLAB can no longer do this. MATLAB is an interpreted language, i.e. each line of code is read then ran, without compiling the entire code beforehand. This means that each time MATLAB encounters eval, it has to stop, evaluate the expression, then check the output, store that, and continue. Most of the speed-engines employed by MATLAB (JIT/MAGMA etc) can't work without predicting the outcome of statements, and will therefore shut down during the eval evaluation, rendering your code very slow.
Also there's a security aspect to the usage of eval. Consider the following:
var1 = 1;
var2 = 2;
var3 = 3;
varnames = {'var1', 'var2; disp(''GOTCHA''); %', 'var3'};
accumvar = [];
for k = 1:numel(varnames)
vname = varnames{k};
disp(['Reading from variable named ' vname]); eval(['accumvar(end+1) = ' vname ';']);
end
Now accumvar will contain the desired variable names. But if you don't set accumvar as output, you might as well not use a disp, but e.g. eval('rm -rf ~/*') which would format your entire disk without even telling you it's doing so.
Loop approach
for ii = 200:-1:1
str = sprintf('Image_%d',ii);
A(:, :, :, ii) = eval(str);
end
This creates your matrix. Note that I let the for loop run backwards, so as to initialise A in its largest size.
Semi-vectorised approach
str = strsplit(sprintf('image_%d ',1:200),' '); % Create all your names
str(end) = []; % Delete the last entry (empty)
%Problem: eval cannot handle cells, loop anyway:
for ii = 200:-1:1
A(:, :, :, ii) = eval(str{ii});
end
eval does not support arrays, so you cannot directly plug the cellarray strin.
Dynamic file names
Despite having a similar title as above, this implies having your file names structured, so in the file browser, and not MATLAB. I'm assuming .jpg files here, but you can add every supported image extension. Also, be sure to have all images in a single folder and no additional images with that extension, or you have to modify the dir() call to include only the desired images.
filenames = dir('*.jpg');
for ii = length(filenames):-1:1
A(:,:,:,ii) = imread(filenames{ii});
end
Images are usually read as m*n*3 files, where m*n is your image size in pixels and the 3 stems from the fact that they're read as RGB by imread. Therefore A is now a 4D matrix, structured as m*n*3*T, where the last index corresponds to the time of the image, and the first three are your image in RGB format.
Since you do not specify how you obtain your 40*40 double, I have left the 4D matrix. Could be you read them and then switch to using a uint16 interpretation of RGB, which is a single number, which would result in a m*n*1*T variable, which you can reduce to a 3D variable by calling A = squeeze(A(:,:,1,:));
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'm trying to read in a large number of jpg files using a for loop. But for some reason, the k index is not advancing. I just get A as a 460x520x3 uint8. Am I missing something?
My goal with this code is to convert all the jpg images to the same size. Since I haven't been able to advance through the images, I can't quite tell if I'm doing it right.
nFrames = length(date); % Number of frames.
for k = 1:nFrames-1 % Number of days
% Set file under consideration
A = imread(['map_EUS_' datestr(cell2mat(date_O3(k)),'yyyy_mm_dd') '_O3_MDA8.jpg']);
% Size of existing image A.
[rowsA, colsA, numberOfColorChannelsA] = size(A);
% Read in and get size of existing image B (the next image).
B = imread(['map_EUS_' datestr(cell2mat(date_O3(k+1)),'yyyy_mm_dd') '_O3_MDA8.jpg']);
[rowsB, colsB, numberOfColorChannelsB] = size(B);
% Size of B does not match A, so resize B to match A's size.
B = imresize(B, [rowsA colsA]);
eval(['print -djpeg map_EUS_' datestr(cell2mat(date_O3(k)),'yyyy_mm_dd') '_O3_MDA8_test.jpg']);
end
end
As you use imread to read the image in, it makes sense to use imwrite to write it out, rather than print/eval (also you should always think twice about using eval in MATLAB, and then think again).
You could also speed up this code somewhat - you just want to resize all the images to the size of whichever the first one is, so you don't need to keep reading in images to measure the size of them. Use imfinfo to get the size, then read in, resize, and write out B only.