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How to convert .oct file into jpeg format

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Warid Islam
Warid Islam on 25 Jun 2019
Edited: William Warriner on 10 Feb 2020
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.

Answers (1)

Walter Roberson
Walter Roberson on 25 Jun 2019
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.
  7 Comments
Walter Roberson
Walter Roberson on 1 Jul 2019
sudo git clone https://github.com/tomwright01/iowa_oct_analysis.git
worked for me.
William Warriner
William Warriner on 10 Feb 2020
Edited: William Warriner on 10 Feb 2020
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"

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