How to convert .oct file into jpeg format

I am trying to convert image obtained from optical coherence tomography (.oct file) into jpeg format. The code used is below:

% inputFolder = fileparts(which('cameraman.tif')) % Determine where demo folder is (works with all versions).
inputFolder = fullfile(pwd, 'D:\MiddleEar\Matlab');
filePattern = fullfile(inputFolder, '*.oct');
% Get list of all BMP files in input folder
octFiles = dir(filePattern);
% Create the output folder:
outputFolder = fullfile(pwd, 'D:\MiddleEar\Matlab Folder\JPEG DATA');
if ~exist(outputFolder, 'dir')
  mkdir(outputFolder);
end
figure;
% Enlarge figure to full screen.
set(gcf, 'Units', 'Normalized', 'OuterPosition', [0 0 1 1]);
% Loop over all oct files, making a jpg version 
% of them in the output folder.
for k = 1 : length(octFiles)
  % Read in .oct file
  baseFileName = octFiles(k).name;
  fullFileNameInput = fullfile(inputFolder, baseFileName);
  rgbImage = imread(fullFileNameInput);
  subplot(1, 2, 1);
  imshow(rgbImage);
  title('Original image', 'FontSize', 30);
  drawnow;
  
  % Prepare output file name
  fullFileNameOutput = fullfile(outputFolder, baseFileName);
  % Converts to JPEG and gives it the .jpg extension
  fullFileNameOutput = strrep(lower(fullFileNameOutput), '.oct', 'jpg')
  imwrite(rgbImage,fullFileNameOutput);
  % Reloads it in a JPEG format to see how bad the compression artifacts are.
  rgbImage = imread(fullFileNameOutput);
  subplot(1, 2, 2);
  imshow(rgbImage);
  title('Recalled JPG image', 'FontSize', 30);
  drawnow;
  pause(1);
end
% Open Windows Explorer to the output folder:
winopen(outputFolder);

I am getting the following error message:

Error using mkdir

The filename, directory name, or volume label syntax is incorrect.

Error in test1 (line 9)

mkdir(outputFolder);

Any help with the code would be very much appreciated. Thank you.

Answer 1

[Walter Roberson]

pwd will be a fully qualified path. When you fullfile with pwd as the first parameter and D: as the second you are concatenating the two together which will result in a file name that starts with some drive specification and then later has a second drive in it. Windows does not permit two drive specifications in a single file name.

[Warid Islam]

Hi Walter,

I tried but couldn't convert the .oct files into jpeg. It would be very helpful for me if you can give me some idea about how to solve the issue. Thank you.

Best Regards

Warid Islam

[Walter Roberson]

oct files are not supported by imread. They are a custom file format. See https://www.mathworks.com/matlabcentral/answers/242474-how-to-open-oct-file-in-matlab#answer_217904

[Warid Islam]

Hi Walter,

I tried but I am unable to solve the issue. Do you have any other tutorials or codes from where I can take some ideas on how to obtain a solution. Thank you.

Best Regads

Warid Islam

[Walter Roberson]

No, I do not have any other tutorials or codes from where you can take some ideas on how to obtain a solution.

The file format is proprietary. Bioptigen will apparently supply MATLAB code to its customers, but I am not a customer of theirs. Tom Wright implemented in Python, and you can call Python from MATLAB.

Perhaps https://www.mathworks.com/matlabcentral/fileexchange/66873-octseg-optical-coherence-tomography-segmentation-and-evaluation-gui might help.

[Warid Islam]

Hi Walter,

Thank you for the suggestion. Unfortunately, the python file that Tom wrote cannot be read in github. It is displaying an error message. May be the file is not there anymore in github.

Thank you.

Warid Islam

[Walter Roberson]

sudo git clone https://github.com/tomwright01/iowa_oct_analysis.git

worked for me.

[William Warriner]

I also was looking for something along these lines for reading Bioptigen files. Thanks for posting!

To anyone else reading this after me, use the following commands to find it in the repo after cloning.

git fetch --tags --all

git checkout tags/1.0.0

It is the file "App/readBioptigenOct.py"