loadtiff.m

function oimg = loadtiff(path)
% Copyright (c) 2012, YoonOh Tak
% All rights reserved.
% 
% Redistribution and use in source and binary forms, with or without 
% modification, are permitted provided that the following conditions are 
% met:
% 
%     * Redistributions of source code must retain the above copyright 
%       notice, this list of conditions and the following disclaimer.
%     * Redistributions in binary form must reproduce the above copyright 
%       notice, this list of conditions and the following disclaimer in 
%       the documentation and/or other materials provided with the distribution
%     * Neither the name of the Gwangju Institute of Science and Technology (GIST), Republic of Korea nor the names 
%       of its contributors may be used to endorse or promote products derived 
%       from this software without specific prior written permission.
%       
% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
% ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE 
% LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
% CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
% SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
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tStart = tic;
warn_old = warning('off', 'all'); % To ignore unknown TIFF tag.

%% Check directory and file existence
path_parent = pwd;
[pathstr, ~, ~] = fileparts(path);
if ~isempty(pathstr) && ~exist(pathstr, 'dir')
    error 'Directory is not exist.';
end
if ~exist(path, 'file')
    error 'File is not exist.';
end

%% Open file
file_opening_error_count = 0;
while ~exist('tiff', 'var')
    try
        tiff = Tiff(path, 'r');
    catch
        file_opening_error_count = file_opening_error_count + 1;
        pause(0.1);
        if file_opening_error_count > 5 % automatically retry to open for 5 times.
            reply = input('Failed to open the file. Do you wish to retry? Y/n: ', 's');
            if isempty(reply) || any(upper(reply) == 'Y')
                file_opening_error_count = 0;
            else
                error(['Failed to open the file ''' path '''.']);
            end
        end
    end
end

%% Load image information
tfl = 0; % Total frame length
tcl = 1; % Total cell length
while true
    try
        tfl = tfl + 1; % Increase frame count
        iinfo(tfl).w       = tiff.getTag('ImageWidth');
        iinfo(tfl).h       = tiff.getTag('ImageLength');
        iinfo(tfl).spp     = tiff.getTag('SamplesPerPixel');
        iinfo(tfl).bps     = tiff.getTag('BitsPerSample');
        iinfo(tfl).color   = iinfo(tfl).spp > 2; % Grayscale: 1(real number) or 2(complex number), Color: 3(rgb), 4(rgba), 6(rgb, complex number), or 8(rgba, complex number)
        iinfo(tfl).complex = any(iinfo(tfl).spp == [2 6 8]);

        if tiff.getTag('Photometric') == Tiff.Photometric.Palette
            disp('Warning: Palette information has been removed.');
        end
    catch
        error 'Failed to load image';
    end
    
    %% Sample format
    switch tiff.getTag('SampleFormat')
        % Unsupported Matlab data type: char, logical, cell, struct, function_handle, class.
        case Tiff.SampleFormat.UInt
            switch tiff.getTag('BitsPerSample')
                case 8
                    iinfo(tfl).sf = 'uint8';
                case 16
                    iinfo(tfl).sf = 'uint16';
                case 32
                    iinfo(tfl).sf = 'uint32';
            end
        case Tiff.SampleFormat.Int
            switch tiff.getTag('BitsPerSample')
                case 8
                    iinfo(tfl).sf = 'int8';
                case 16
                    iinfo(tfl).sf = 'int16';
                case 32
                    iinfo(tfl).sf = 'int32';
            end
        case Tiff.SampleFormat.IEEEFP
            switch tiff.getTag('BitsPerSample')
                case 32
                    iinfo(tfl).sf = 'single';
                case 64
                    iinfo(tfl).sf = 'double';
            end
        otherwise
            % (Unsupported)Void, ComplexInt, ComplexIEEEFP
            error 'Unsupported Matlab data type. (char, logical, cell, struct, function_handle, class)';
    end

    if tfl > 1
        % If tag information is changed, make a new cell
        if iinfo(tfl-1).w ~= iinfo(tfl).w || ...
            iinfo(tfl-1).h ~= iinfo(tfl).h || ...
            iinfo(tfl-1).spp ~= iinfo(tfl).spp || ...
            any(iinfo(tfl-1).sf ~= iinfo(tfl).sf) || ...
            iinfo(tfl-1).color ~= iinfo(tfl).color || ...
            iinfo(tfl-1).complex ~= iinfo(tfl).complex
            tcl = tcl + 1; % Increase cell count
            iinfo(tfl).fid = 1; % First frame of this cell
        else
            iinfo(tfl).fid = iinfo(tfl-1).fid + 1;
        end
    else
        iinfo(tfl).fid = 1; % Very first frame of this file
    end
    iinfo(tfl).cid = tcl; % Cell number of this frame
    
    if tiff.lastDirectory(), break; end;
    tiff.nextDirectory();
end

%% Load image data
if tcl == 1 % simple image (no cell)
    if ~iinfo(tfl).color
       oimg = zeros(iinfo(tfl).h,iinfo(tfl).w,iinfo(tfl).fid, iinfo(tfl).sf); % Grayscale image
    else
       oimg = zeros(iinfo(tfl).h,iinfo(tfl).w,iinfo(tfl).spp,iinfo(tfl).fid, iinfo(tfl).sf); % Color image
    end
    for tfl = 1:tfl
        tiff.setDirectory(tfl);
        temp = tiff.read();
        if iinfo(tfl).complex
            temp = temp(:,:,1:2:end-1,:) + temp(:,:,2:2:end,:)*1i;
        end
        if ~iinfo(tfl).color
            oimg(:,:,iinfo(tfl).fid) = temp; % Grayscale image
        else
            oimg(:,:,:,iinfo(tfl).fid) = temp; % Color image
        end
    end
else % multiple image (multiple cell)
    oimg = cell(tcl, 1);
    for tfl = 1:tfl
        tiff.setDirectory(tfl);
        temp = tiff.read();
        if iinfo(tfl).complex
            temp = temp(:,:,1:2:end-1,:) + temp(:,:,2:2:end,:)*1i;
        end
        if ~iinfo(tfl).color
            oimg{iinfo(tfl).cid}(:,:,iinfo(tfl).fid) = temp; % Grayscale image
        else
            oimg{iinfo(tfl).cid}(:,:,:,iinfo(tfl).fid) = temp; % Color image
        end
    end
end

%% Close file
tiff.close();
cd(path_parent);
warning(warn_old);

display(sprintf('The file was loaded successfully. Elapsed time : %.3f s.', toc(tStart)));
end