Commit 78abb88d authored by Antonio Politi's avatar Antonio Politi
Browse files

example for single pore data analysis

parent 5a2e2377
......@@ -43,3 +43,4 @@ matlabcode/FCS/example_data/Alexa/
expdata
.Rproj.user
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Copyright (c) 2017, 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
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.
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
% 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.
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
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).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 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 || ...
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)
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
function res = 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.compress
% : 'no', 'lzw', 'jpeg' or 'adobe'.
% Compression type.
% 'no' : Uncompressed(Default)
% 'lzw' : lossless LZW
% 'jpeg' : lossy JPEG (When using JPEG compression, ImageWidth,
% ImageLength, and RowsPerStrip must be multiples of 16.)
% 'adobe' : lossless Adobe-style
% options.message
% : TRUE or false.
% If this is false, all messages are skipped.
% 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.
% options.overwrite
% : true or FALSE
% Overwrite to an existing file.
% options.big
% : true or FALSE,
% Use 64 bit addressing and allows for files > 4GB
%
% Defalut value of 'options' is
% options.color = false;
% options.compress = 'no';
% options.message = true;
% options.append = false;
% options.overwrite = false;
% options.big = false;
%
% res : Return value. It is 0 when the function is finished with no error.
% If an error is occured in the function, it will have a positive
% number (error code).
%
% 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.
tStart = tic;
errcode = 0;
try
%% Init options parameter
if nargin < 3 % Use default options
options.color = false;
options.compress = 'no';
options.message = true;
options.append = false;
options.overwrite = false;
end
if ~isfield(options, 'message'), options.message = true; end
if ~isfield(options, 'append'), options.append = false; end
if ~isfield(options, 'compress'), options.compress = 'no'; end
if ~isfield(options, 'color'), options.color = false; end
if ~isfield(options, 'overwrite'), options.overwrite = false; end
if isfield(options, 'big') == 0, options.big = false; end
if isempty(data), errcode = 1; assert(false); end
if (options.color == false && ndims(data) > 3) || ...
(options.color == true && ndims(data) > 4)
% Maximum dimension of a grayscale image is 3 of [height, width, frame]
% Maximum dimension of a color image is 4 of [height, width, color, frame]
errcode = 2; assert(false);
end
%% Get image informations
% http://www.awaresystems.be/imaging/tiff/tifftags/photometricinterpretation.html
if ~options.color
if ndims(data) >= 4, errcode = 2; assert(false); end;
[height, width, depth] = size(data);
tagstruct.Photometric = Tiff.Photometric.MinIsBlack;
% tagstruct.Photometric = Tiff.Photometric.MinIsWhite;
% tagstruct.Photometric = Tiff.Photometric.Mask;
% tagstruct.Photometric = Tiff.Photometric.Separated;
else
if ndims(data) >= 5, errcode = 2; assert(false); end;
[height, width, cc, depth] = size(data); % cc: color channels. 3: rgb, 4: rgb with alpha channel
if cc ~= 3 && cc ~= 4, errcode = 3; assert(false); end;
tagstruct.Photometric = Tiff.Photometric.RGB;
% tagstruct.Photometric = Tiff.Photometric.CIELab;
% tagstruct.Photometric = Tiff.Photometric.ICCLab;
% tagstruct.Photometric = Tiff.Photometric.ITULab;
% (Unsupported)tagstruct.Photometric = Tiff.Photometric.Palette;
% (Unsupported)tagstruct.Photometric = Tiff.Photometric.YCbCr;
end
tagstruct.ImageLength = height;
tagstruct.ImageWidth = width;
tagstruct.PlanarConfiguration = Tiff.PlanarConfiguration.Chunky; % (RGB RGB,RGB RGB,RGB RGB), http://www.awaresystems.be/imaging/tiff/tifftags/planarconfiguration.html
% (Unsupported)tagstruct.PlanarConfiguration = Tiff.PlanarConfiguration.Separate; % (RRR RRR, GGG GGG, BBB BBB), % http://www.awaresystems.be/imaging/tiff/tifftags/planarconfiguration.html
tagstruct.ImageDescription = '';
%% Complex number
% http://www.awaresystems.be/imaging/tiff/tifftags/samplesperpixel.html
if ~options.color && isreal(data) % Grayscale image with real numbers
tagstruct.SamplesPerPixel = 1;
data = reshape(data, height, width, 1, depth);
elseif ~options.color && ~isreal(data) % Grayscale image with complex numbers
tagstruct.SamplesPerPixel = 2;
data = reshape([real(data) imag(data)], height, width, 2, depth);
elseif options.color && isreal(data) % Color image with real numbers
tagstruct.SamplesPerPixel = cc;
if cc == 4
tagstruct.ExtraSamples = Tiff.ExtraSamples.AssociatedAlpha; % The forth channel is alpha channel
end
data = reshape(data, height, width, cc, depth);
elseif options.color && ~isreal(data) % Color image with complex numbers
tagstruct.SamplesPerPixel = cc * 2;
if cc == 3
tagstruct.ExtraSamples = repmat(Tiff.ExtraSamples.Unspecified, 1, 3); % 3(real)+3(imag) = 6 = 3(rgb) + 3(Extra)
else
tagstruct.ExtraSamples = repmat(Tiff.ExtraSamples.Unspecified, 1, 5); % 4(real)+4(imag) = 8 = 3(rgb) + 5(Extra)
end
data = reshape([real(data) imag(data)], height, width, cc*2, depth);
end
%% Image compression
% http://www.awaresystems.be/imaging/tiff/tifftags/compression.html
switch lower(options.compress)
case 'no'
tagstruct.Compression = Tiff.Compression.None;
case 'lzw'
tagstruct.Compression = Tiff.Compression.LZW;
case 'jpeg'
tagstruct.Compression = Tiff.Compression.JPEG;
case 'adobe'
tagstruct.Compression = Tiff.Compression.AdobeDeflate;
otherwise
% Use tag nubmer in http://www.awaresystems.be/imaging/tiff/tifftags/compression.html
tagstruct.Compression = options.compress;
end
%% Sample format
% http://www.awaresystems.be/imaging/tiff/tifftags/sampleformat.html
switch class(data)
% Unsupported Matlab data type: char, logical, cell, struct, function_handle, class.
case {'uint8', 'uint16', 'uint32'}
tagstruct.SampleFormat = Tiff.SampleFormat.UInt;
case {'int8', 'int16', 'int32'}
tagstruct.SampleFormat = Tiff.SampleFormat.Int;
if options.color
errcode = 4; assert(false);
end
case {'single', 'double', 'uint64', 'int64'}
tagstruct.SampleFormat = Tiff.SampleFormat.IEEEFP;
otherwise
% (Unsupported)Void, ComplexInt, ComplexIEEEFP
errcode = 5; assert(false);
end
%% Bits per sample
% http://www.awaresystems.be/imaging/tiff/tifftags/bitspersample.html
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', 'uint64', 'int64'}
tagstruct.BitsPerSample = 64;
otherwise
errcode = 5; assert(false);
end
%% Rows per strip
maxstripsize = 8*1024;
tagstruct.RowsPerStrip = ceil(maxstripsize/(width*(tagstruct.BitsPerSample/8)*size(data,3))); % http://www.awaresystems.be/imaging/tiff/tifftags/rowsperstrip.html
if tagstruct.Compression == Tiff.Compression.JPEG
tagstruct.RowsPerStrip = max(16,round(tagstruct.RowsPerStrip/16)*16);
end
%% Overwrite check
if exist(path, 'file') && ~options.append
if ~options.overwrite
errcode = 6; assert(false);
end
end
%% Save path configuration
path_parent = pwd;
[pathstr, fname, fext] = fileparts(path);
if ~isempty(pathstr)
if ~exist(pathstr, 'dir')
mkdir(pathstr);
end
cd(pathstr);
end
%% Write image data to a file
file_opening_error_count = 0;
while ~exist('tfile', 'var')
try
if ~options.append % Make a new file
s=whos('data');
if s.bytes > 2^32-1 || options.big
tfile = Tiff([fname, fext], 'w8'); % Big Tiff file
else
tfile = Tiff([fname, fext], 'w');
end
else
if ~exist([fname, fext], 'file') % Make a new file
s=whos('data');
if s.bytes > 2^32-1 || options.big
tfile = Tiff([fname, fext], 'w8'); % Big Tiff file
else
tfile = Tiff([fname, fext], 'w');
end
else % Append to an existing file
tfile = Tiff([fname, fext], 'r+');
while ~tfile.lastDirectory(); % Append a new image to the last directory of an exiting file
tfile.nextDirectory();
end
tfile.writeDirectory();
end
end
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
errcode = 7;
assert(false);
end
end
end
end
for d = 1:depth
tfile.setTag(tagstruct);
tfile.write(data(:, :, :, d));
if d ~= depth
tfile.writeDirectory();
end
end
tfile.close();
if exist('path_parent', 'var'), cd(path_parent); end
tElapsed = toc(tStart);
if options.message
display(sprintf('The file was saved successfully. Elapsed time : %.3f s.', tElapsed));
end
catch exception
%% Exception management
if exist('tfile', 'var'), tfile.close(); end
switch errcode
case 1
if options.message, error '''data'' is empty.'; end;
case 2
if options.message, error 'Data dimension is too large.'; end;
case 3
if options.message, error 'Third dimesion (color depth) should be 3 or 4.'; end;
case 4
if options.message, error 'Color image cannot have int8, int16 or int32 format.'; end;
case 5
if options.message, error 'Unsupported Matlab data type. (char, logical, cell, struct, function_handle, class)'; end;
case 6
if options.message, error 'File already exists.'; end;
case 7
if options.message, error(['Failed to open the file ''' path '''.']); end;
otherwise
if exist('fname', 'var') && exist('fext', 'var')
delete([fname fext]);
end
if exist('path_parent', 'var'), cd(path_parent); end
rethrow(exception);
end
if exist('path_parent', 'var'), cd(path_parent); end
end
res = errcode;
end
\ No newline at end of file
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