function saveastiff(data, path, options)
% options.color
% : true or FALSE
% : If this is true, third dimension should be 3 and the data is saved as a color image.
% options.comp
% : 'no', 'lzw', 'jpeg' or 'adobe'.
% Compression type.
% 'no' : Uncompressed(Default)
% 'lzw' : lossless LZW
% 'jpeg' : lossy JPEG
% 'adobe' : lossless Adobe-style
% options.message
% : true or FALSE.
% If this is false, all messages are skipped.
% options.ask
% : true or FALSE. If this is false, always overwrite an existing file.
% options.append
% : true or FALSE
% If path is exist, the data is appended to an existing file.
% If path is not exist, this options is ignored.
%
% Defalut value of 'options' is
% options.color = false;
% options.comp = 'no';
% options.message = false;
% options.ask = false;
% options.append = false;
%
% Examples :
%
% [X,Y,Z] = peaks(100);
% X = single(X);
% Y = single(Y);
% Z = single(Z);
% Z_index = uint8((Z - min(Z(:))) * (255 / (max(Z(:)) - min(Z(:)))));
% Z_color = uint8(ind2rgb(Z_index, hsv(256)*256));
% Z_color_multiframe = reshape([Z_color(:)*0.2 Z_color(:)*0.6 Z_color(:)], 100, 100, 3, 3);
% Z_color_noisy = uint8(single(Z_color) + rand(100, 100, 3).*50);
%
% % 8-bit, grayscale image
% saveastiff(uint8(Z_index), 'Z_uint8.tif');
%
% % Lossless LZW compression
% options.comp = 'lzw';
% saveastiff(uint8(Z_index), 'Z_uint8_LZW.tif', options);
% options.comp = 'no';
%
% % Ask a question if the file is already exist
% options.ask = true;
% saveastiff(uint8(Z_index), 'Z_uint8_LZW.tif', options);
% options.ask = false;
%
% % Allow message printing.
% options.message = true;
% saveastiff(uint8(Z_index), 'Z_uint8_LZW.tif', options);
% options.message = false;
%
% % 16-bit, grayscale image
% saveastiff(uint16(Z_index), 'Z_uint16.tif');
%
% % 32-bit single, grayscale image
% saveastiff(Z, 'Z_single.tif');
%
% % RGB color image
% options.color = true;
% saveastiff(Z_color, 'Z_rgb.tif', options);
% options.color = false;
%
% % Save each R, G and B chanels of the color image, separately.
% saveastiff(Z_color, 'Z_rgb_channel.tif');
%
% % Save the multi-frame RGB color image
% options.color = true;
% saveastiff(Z_color_multiframe, 'Z_rgb_multiframe.tif', options);
% options.color = false;
%
% % Save the noise-added RGB color image
% options.color = true;
% saveastiff(Z_color_noisy, 'Z_rgb_noisy.tif', options);
% options.color = false;
%
% % 32-bit single, 50x50x50 volume data
% saveastiff(single(rand(50, 50, 50)), 'volume_50x50x50.tif');
%
% % Append option is ignored if path dose not exist.
% options.append = true;
% saveastiff(Z_index, 'Z_uint8_append.tif', options);
% options.append = false;
%
% % You can append any type of image to an existing tiff file.
% options.append = true;
% saveastiff(single(rand(10, 10, 3)), 'Z_uint8_append.tif', options);
% options.color = true;
% saveastiff(Z_color_multiframe, 'Z_uint8_append.tif', options);
% options.color = false;
% options.append = false;
%
% 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
% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
% CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
% ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
% POSSIBILITY OF SUCH DAMAGE.
errcode = 0;
try
if isreal(data) == false
errcode = 8; assert(0);
end
if nargin < 3
options.color = false;
options.comp = 'no';
options.message = false;
options.ask = false;
options.append = false;
end
if isfield(options, 'message') == 0
options.message = false;
end
if isfield(options, 'ask') == 0
options.ask = false;
end
if isfield(options, 'append') == 0
options.append = false;
end
if isfield(options, 'comp') == 0
options.comp = 'no';
end
if isfield(options, 'color') == 0
options.color = false;
end
if (options.color == false && ndims(data) > 3) ...
|| (options.color == true && ndims(data) > 4)
errcode = 10; assert(0);
end
pathstr = fileparts(which(path));
if ~isempty(pathstr)
if strcmpi(pathstr, pwd)
if options.append
tappend = Tiff(path, 'r+');
else
if options.ask
reply = input('File already exist, do you wish to overwrite? Y/n: ', 's');
if isempty(reply), reply = 'Y'; end
if any(upper(reply) ~= 'Y')
errcode = 0; assert(0);
end
end
end
else
if options.append
if options.ask
reply = input('File already exist but not in the current folder, do you wish to append? Y/n: ', 's');
if isempty(reply), reply = 'Y'; end
if any(upper(reply) ~= 'Y')
errcode = 0; assert(0);
end
tappend = Tiff(path, 'r+');
end
else
if options.ask
reply = input('File already exist but not in the current folder, do you wish to overwrite? Y/n: ', 's');
if isempty(reply), reply = 'Y'; end
if any(upper(reply) ~= 'Y')
errcode = 0; assert(0);
end
end
end
end
else
options.append = false;
end
if exist(pathstr, 'dir')
if ~options.append && options.ask
elseif options.append
tappend = Tiff(path, 'r+');
end
else
options.append = false;
end
if isempty(data)
errcode = 2; assert(0);
end
if ~options.color
if ndims(data) >= 4, errcode = 3; assert(0); end;
[height width depth] = size(data);
tagstruct.Photometric = Tiff.Photometric.MinIsBlack;
else
if ndims(data) >= 5, errcode = 3; assert(0); end;
[height width rgb depth] = size(data);
if rgb ~= 3, errcode = 4; assert(0); end;
if strcmp(class(data), 'uint8'), data = uint8(data); end;
tagstruct.Photometric = Tiff.Photometric.RGB;
end
tagstruct.ImageLength = height;
tagstruct.ImageWidth = width;
tagstruct.SamplesPerPixel = (options.color+1)*(options.color+2)/2;
tagstruct.RowsPerStrip = height;
tagstruct.PlanarConfiguration = Tiff.PlanarConfiguration.Chunky;
% Compresstion type : http://en.wikipedia.org/wiki/Tagged_Image_File_Format
switch lower(options.comp)
case 'no'
tagstruct.Compression = 1;
case 'lzw'
tagstruct.Compression = 5;
case 'jpeg'
tagstruct.Compression = 7;
case 'adobe'
tagstruct.Compression = 8;
otherwise
if options.ask
reply = input('Unsupported compression type : Data will not be compressed.\nDo you wish to continue? Y/n: ', 's');
if isempty(reply), reply = 'Y'; end
if any(upper(reply) ~= 'Y')
tagstruct.Compression = 1;
else
errcode = 0; assert(0);
end
else
tagstruct.Compression = 1;
end
end
switch class(data)
case {'uint8', 'uint16', 'uint32'}
tagstruct.SampleFormat = 1;
case {'int8', 'int16', 'int32'}
tagstruct.SampleFormat = 2;
if options.color == 3
errcode = 8; assert(0);
end
case {'single', 'double'}
tagstruct.SampleFormat = 3;
otherwise
errcode = 9; assert(0);
end
switch class(data)
case {'uint8', 'int8'}
tagstruct.BitsPerSample = 8;
case {'uint16', 'int16'}
tagstruct.BitsPerSample = 16;
case {'uint32', 'int32'}
tagstruct.BitsPerSample = 32;
case {'single'}
tagstruct.BitsPerSample = 32;
case {'double'}
tagstruct.BitsPerSample = 64;
otherwise
errcode = 9; assert(0);
end
tStart = tic;
if ~options.append
tempfile = '~$temporal.tif';
if exist(tempfile, 'file')
delete(tempfile);
end
t = Tiff(tempfile, 'w');
fileattrib(tempfile, '+h +w', '', 's');
for d = 1:depth
t.setTag(tagstruct);
if ~options.color
t.write(data(:, :, d));
else
t.write(data(:, :, :, d));
end
if d ~= depth
t.writeDirectory();
end
end
t.close();
fileattrib(tempfile, '-h +w');
if movefile(tempfile, path, 'f') == 0
errcode = 11; assert(0);
end
else
while ~tappend.lastDirectory();
tappend.nextDirectory();
end
tappend.writeDirectory();
for d = 1:depth
tappend.setTag(tagstruct);
if ~options.color
tappend.write(data(:, :, d));
else
tappend.write(data(:, :, :, d));
end
if d ~= depth
tappend.writeDirectory();
end
end
tappend.close();
end
tElapsed = toc(tStart);
if options.message
display(sprintf('File saved successfully. Elapsed time : %.3f s.', tElapsed));
end
catch exception
if exist('t', 'var')
t.close();
if exist('tappend', 'var'), tappend.close(); end
delete(tempfile);
end
if options.message
switch errcode
case 0
error 'Unkown error.'
case 1
error 'Invalide path.';
case 2
error '''data'' is empty.';
case 3
error 'Data dimension is too large.';
case 4
error 'Third dimesion (color depth) should be 3.';
case 6
error 'RGB color image can not have int8, int16 or int32 format.';
case 8
error 'It does not support complex numbers.';
case 9
error 'Unsupported data type.';
case 10
error 'Dimension of source data is too large.';
case 11
error 'It can not be completed because the file is open';
otherwise
rethrow(exception);
end
end
end
end
