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tiffread.m
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function stack = tiffread(filename, indices)
% tiffread, version 2.91 Nov 1, 2010
%
% stack = tiffread;
% stack = tiffread(filename);
% stack = tiffread(filename, indices);
%
% Reads 8,16,32 bits uncompressed grayscale and (some) color tiff files,
% as well as stacks or multiple tiff images, for example those produced
% by metamorph, Zeiss LSM or NIH-image.
%
% The function can be called with a file name in the current directory,
% or without argument, in which case it pops up a file opening dialog
% to allow for a manual selection of the file.
% If the stacks contains multiples images, reading can be restricted by
% specifying the indices of the desired images (eg. 1:5), or just one index (eg. 2).
%
% The returned value 'stack' is a vector struct containing the images
% and their meta-data. The length of the vector is the number of images.
% The image pixels values are stored in a field .data, which is a simple
% matrix for gray-scale images, or a cell-array of matrices for color images.
%
% The pixels values are returned in their native (usually integer) format,
% and must be converted to be used in most matlab functions.
%
% Example:
% im = tiffread('spindle.stk');
% imshow( double(im(5).data) );
%
% Only a fraction of the TIFF standard is supported, but you may extend support
% by modifying this file. If you do so, please return your modification to us,
% such that the added functionality can be redistributed to everyone.
%
% ------------------------------------------------------------------------------
%
% If you would like to acknowledge tiffread2.m in a publication,
% please cite the article for which the macro was first written:
%
% Dynamic Concentration of Motors in Microtubule Arrays
% Francois Nedelec, Thomas Surrey and A.C. Maggs
% Physical Review Letters 86: 3192-3195; 2001.
% DOI: 10.1103/PhysRevLett.86.3192
%
% Thank you!
%
%
% Francois Nedelec
% nedelec -at- embl.de
% Cell Biology and Biophysics, EMBL; Meyerhofstrasse 1; 69117 Heidelberg; Germany
% http://www.embl.org
% http://www.cytosim.org
%
%
% ------------------------------------------------------------------------------
%
% Copyright (C) 1999-2010 Francois Nedelec,
% with contributions from:
% Kendra Burbank for the waitbar
% Hidenao Iwai for the code to read floating point images,
% Stephen Lang to be more compliant with PlanarConfiguration
% Jan-Ulrich Kreft for Zeiss LSM support
% Elias Beauchanp and David Kolin for additional Metamorph support
% Jean-Pierre Ghobril for requesting that image indices may be specified
% Urs Utzinger for the better handling of color images, and LSM meta-data
% O. Scott Sands for support of GeoTIFF tags
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, version 3 of the License.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details:
% <http://www.gnu.org/licenses/>.
%
% ------------------------------------------------------------------------------
%Optimization: join adjacent TIF strips: this results in faster reads
consolidateStrips = 1;
%without argument, we ask the user to choose a file:
if nargin < 1
[filename, pathname] = uigetfile('*.tif;*.stk;*.lsm', 'select image file');
filename = [ pathname, filename ];
end
if (nargin<=1); indices = 1:10000; end
% not all valid tiff tags have been included, as they are really a lot...
% if needed, tags can easily be added to this code
% See the official list of tags:
% http://partners.adobe.com/asn/developer/pdfs/tn/TIFF6.pdf
%
% the structure IMG is returned to the user, while TIF is not.
% so tags usefull to the user should be stored as fields in IMG, while
% those used only internally can be stored in TIF.
global TIF;
TIF = [];
%counters for the number of images read and skipped
img_skip = 0;
img_read = 1;
hWaitbar = [];
%% set defaults values :
TIF.SampleFormat = 1;
TIF.SamplesPerPixel = 1;
TIF.BOS = 'ieee-le'; %byte order string
if isempty(findstr(filename,'.'))
filename = [filename,'.tif'];
end
TIF.file = fopen(filename,'r','l');
if TIF.file == -1
stkname = strrep(filename, '.tif', '.stk');
TIF.file = fopen(stkname,'r','l');
if TIF.file == -1
error(['File "',filename,'" not found.']);
else
filename = stkname;
end
end
[s, m] = fileattrib(filename);
% obtain the full file path:
filename = m.Name;
% find the file size in bytes:
% m = dir(filename);
% filesize = m.bytes;
%% read header
% read byte order: II = little endian, MM = big endian
byte_order = fread(TIF.file, 2, '*char');
if ( strcmp(byte_order', 'II') )
TIF.BOS = 'ieee-le'; % Intel little-endian format
elseif ( strcmp(byte_order','MM') )
TIF.BOS = 'ieee-be';
else
error('This is not a TIFF file (no MM or II).');
end
%% ---- read in a number which identifies file as TIFF format
tiff_id = fread(TIF.file,1,'uint16', TIF.BOS);
if (tiff_id ~= 42)
error('This is not a TIFF file (missing 42).');
end
%% ---- read the byte offset for the first image file directory (IFD)
TIF.img_pos = fread(TIF.file, 1, 'uint32', TIF.BOS);
while TIF.img_pos ~= 0
clear IMG;
IMG.filename = filename;
% move in the file to the first IFD
status = fseek(TIF.file, TIF.img_pos, -1);
if status == -1
error('invalid file offset (error on fseek)');
end
%disp(strcat('reading img at pos :',num2str(TIF.img_pos)));
%read in the number of IFD entries
num_entries = fread(TIF.file,1,'uint16', TIF.BOS);
%disp(strcat('num_entries =', num2str(num_entries)));
%read and process each IFD entry
for i = 1:num_entries
% save the current position in the file
file_pos = ftell(TIF.file);
% read entry tag
TIF.entry_tag = fread(TIF.file, 1, 'uint16', TIF.BOS);
% read entry
entry = readIFDentry;
%disp(strcat('reading entry <',num2str(TIF.entry_tag),'>'));
switch TIF.entry_tag
case 254
TIF.NewSubfiletype = entry.val;
case 256 % image width - number of column
IMG.width = entry.val;
case 257 % image height - number of row
IMG.height = entry.val;
TIF.ImageLength = entry.val;
case 258 % BitsPerSample per sample
TIF.BitsPerSample = entry.val;
TIF.BytesPerSample = TIF.BitsPerSample / 8;
IMG.bits = TIF.BitsPerSample(1);
%fprintf('BitsPerSample %i %i %i\n', entry.val);
case 259 % compression
if ( entry.val ~= 1 )
error(['Compression format ', num2str(entry.val),' not supported.']);
end
case 262 % photometric interpretation
TIF.PhotometricInterpretation = entry.val;
if ( TIF.PhotometricInterpretation == 3 )
warning('tiffread2:LookUp', 'Ignoring TIFF look-up table');
end
case 269
IMG.document_name = entry.val;
case 270 % comments:
IMG.info = entry.val;
case 271
IMG.make = entry.val;
case 273 % strip offset
TIF.StripOffsets = entry.val;
TIF.StripNumber = entry.cnt;
%fprintf('StripNumber = %i, size(StripOffsets) = %i %i\n', TIF.StripNumber, size(TIF.StripOffsets));
case 277 % sample_per pixel
TIF.SamplesPerPixel = entry.val;
%fprintf('Color image: sample_per_pixel=%i\n', TIF.SamplesPerPixel);
case 278 % rows per strip
TIF.RowsPerStrip = entry.val;
case 279 % strip byte counts - number of bytes in each strip after any compressio
TIF.StripByteCounts= entry.val;
case 282 % X resolution
IMG.x_resolution = entry.val;
case 283 % Y resolution
IMG.y_resolution = entry.val;
case 284 %planar configuration describe the order of RGB
TIF.PlanarConfiguration = entry.val;
case 296 % resolution unit
IMG.resolution_unit= entry.val;
case 305 % software
IMG.software = entry.val;
case 306 % datetime
IMG.datetime = entry.val;
case 315
IMG.artist = entry.val;
case 317 %predictor for compression
if (entry.val ~= 1); error('unsuported predictor value'); end
case 320 % color map
IMG.cmap = entry.val;
IMG.colors = entry.cnt/3;
case 339
TIF.SampleFormat = entry.val;
case 33550 % GeoTIFF ModelPixelScaleTag
IMG.ModelPixelScaleTag = entry.val;
case 33628 %metamorph specific data
IMG.MM_private1 = entry.val;
case 33629 %this tag identify the image as a Metamorph stack!
TIF.MM_stack = entry.val;
TIF.MM_stackCnt = entry.cnt;
case 33630 %metamorph stack data: wavelength
TIF.MM_wavelength = entry.val;
case 33631 %metamorph stack data: gain/background?
TIF.MM_private2 = entry.val;
case 33922 % GeoTIFF ModelTiePointTag
IMG.ModelTiePointTag = entry.val;
case 34412 % Zeiss LSM data
LSM_info = entry.val;
case 34735 % GeoTIFF GeoKeyDirectory
IMG.GeoKeyDirTag = entry.val;
case 34737 % GeoTIFF GeoASCIIParameters
IMG.GeoASCII = entry.val;
case 42113 % GeoTIFF GDAL_NODATA
IMG.GDAL_NODATA = entry.val;
otherwise
fprintf( 'Ignored TIFF entry with tag %i (cnt %i)\n', TIF.entry_tag, entry.cnt);
end
% calculate bounding box if you've got the stuff
if isfield(IMG, 'ModelPixelScaleTag') && isfield(IMG, 'ModelTiePointTag') && isfield(IMG, 'height')&& isfield(IMG, 'width'),
IMG.North=IMG.ModelTiePointTag(5)-IMG.ModelPixelScaleTag(2)*IMG.ModelTiePointTag(2);
IMG.South=IMG.North-IMG.height*IMG.ModelPixelScaleTag(2);
IMG.West=IMG.ModelTiePointTag(4)+IMG.ModelPixelScaleTag(1)*IMG.ModelTiePointTag(1);
IMG.East=IMG.West+IMG.width*IMG.ModelPixelScaleTag(1);
end
% move to next IFD entry in the file
status = fseek(TIF.file, file_pos+12, -1);
if status == -1
error('invalid file offset (error on fseek)');
end
end
%Planar configuration is not fully supported
%Per tiff spec 6.0 PlanarConfiguration irrelevent if SamplesPerPixel==1
%Contributed by Stephen Lang
if (TIF.SamplesPerPixel ~= 1) && ( ~isfield(TIF, 'PlanarConfiguration') || TIF.PlanarConfiguration == 1 )
error('PlanarConfiguration = 1 is not supported');
end
%total number of bytes per image:
PlaneBytesCnt = IMG.width * IMG.height * TIF.BytesPerSample;
%% try to consolidate the TIFF strips if possible
if consolidateStrips
%Try to consolidate the strips into a single one to speed-up reading:
BytesCnt = TIF.StripByteCounts(1);
if BytesCnt < PlaneBytesCnt
ConsolidateCnt = 1;
%Count how many Strip are needed to produce a plane
while TIF.StripOffsets(1) + BytesCnt == TIF.StripOffsets(ConsolidateCnt+1)
ConsolidateCnt = ConsolidateCnt + 1;
BytesCnt = BytesCnt + TIF.StripByteCounts(ConsolidateCnt);
if ( BytesCnt >= PlaneBytesCnt ); break; end
end
%Consolidate the Strips
if ( BytesCnt <= PlaneBytesCnt(1) ) && ( ConsolidateCnt > 1 )
%fprintf('Consolidating %i stripes out of %i', ConsolidateCnt, TIF.StripNumber);
TIF.StripByteCounts = [BytesCnt; TIF.StripByteCounts(ConsolidateCnt+1:TIF.StripNumber ) ];
TIF.StripOffsets = TIF.StripOffsets( [1 , ConsolidateCnt+1:TIF.StripNumber] );
TIF.StripNumber = 1 + TIF.StripNumber - ConsolidateCnt;
end
end
end
%% read the next IFD address:
TIF.img_pos = fread(TIF.file, 1, 'uint32', TIF.BOS);
%if (TIF.img_pos) disp(['next ifd at', num2str(TIF.img_pos)]); end
if isfield( TIF, 'MM_stack' )
sel = ( indices <= TIF.MM_stackCnt );
indices = indices(sel);
if numel(indices) > 1
hWaitbar = waitbar(0,'Reading images...','Name','TiffRead');
end
%this loop reads metamorph stacks:
for ii = indices
TIF.StripCnt = 1;
offset = PlaneBytesCnt * (ii-1);
%read the image channels
for c = 1:TIF.SamplesPerPixel
IMG.data{c} = read_plane(offset, IMG.width, IMG.height, c);
end
% print a text timer on the main window, or update the waitbar
% fprintf('img_read %i img_skip %i\n', img_read, img_skip);
if ~isempty( hWaitbar )
waitbar(img_read/numel(indices), hWaitbar);
end
[ IMG.MM_stack, IMG.MM_wavelength, IMG.MM_private2 ] = splitMetamorph(ii);
stack(img_read) = IMG;
img_read = img_read + 1;
end
break;
else
%this part reads a normal TIFF stack:
read_img = any( img_skip+img_read == indices );
if exist('stack','var')
if IMG.width ~= stack(1).width || IMG.height ~= stack(1).height
%setting read_img=0 will skip dissimilar images:
%comment-out the line below to allow dissimilar stacks
read_img = 0;
end
end
if read_img
TIF.StripCnt = 1;
%read the image channels
for c = 1:TIF.SamplesPerPixel
IMG.data{c} = read_plane(0, IMG.width, IMG.height, c);
end
try
stack(img_read) = IMG; % = orderfields(IMG);
img_read = img_read + 1;
catch
fprintf('Tiffread skipped dissimilar image %i\n', img_read+img_skip);
img_skip = img_skip + 1;
end
if all( img_skip+img_read > indices )
break;
end
else
img_skip = img_skip + 1;
end
end
end
%% remove the cell structure if there is always only one channel
flat = 1;
for i = 1:numel(stack)
if numel(stack(i).data) ~= 1
flat = 0;
break;
end
end
if flat
for i = 1:numel(stack)
stack(i).data = stack(i).data{1};
end
end
%% distribute the MetaMorph info
if isfield(TIF, 'MM_stack') && isfield(IMG, 'info') && ~isempty(IMG.info)
MM = parseMetamorphInfo(IMG.info, TIF.MM_stackCnt);
for i = 1:numel(stack)
stack(i).MM = MM(i);
end
end
%% duplicate the LSM info
if exist('LSM_info', 'var')
for i = 1:numel(stack)
stack(i).lsm = LSM_info;
end
end
%% return
if ~ exist('stack', 'var')
stack = [];
end
%clean-up
fclose(TIF.file);
if ~isempty( hWaitbar )
delete( hWaitbar );
end
end
%% ===========================================================================
function plane = read_plane(offset, width, height, plane_nb)
global TIF;
%return an empty array if the sample format has zero bits
if ( TIF.BitsPerSample(plane_nb) == 0 )
plane=[];
return;
end
%fprintf('reading plane %i size %i %i\n', plane_nb, width, height);
%determine the type needed to store the pixel values:
switch( TIF.SampleFormat )
case 1
classname = sprintf('uint%i', TIF.BitsPerSample(plane_nb));
case 2
classname = sprintf('int%i', TIF.BitsPerSample(plane_nb));
case 3
if ( TIF.BitsPerSample(plane_nb) == 32 )
classname = 'single';
else
classname = 'double';
end
otherwise
error('unsuported TIFF sample format %i', TIF.SampleFormat);
end
% Preallocate a matrix to hold the sample data:
try
plane = zeros(width, height, classname);
catch
%compatibility with older matlab versions:
eval(['plane = ', classname, '(zeros(width, height));']);
end
% Read the strips and concatenate them:
line = 1;
while ( TIF.StripCnt <= TIF.StripNumber )
strip = read_strip(offset, width, plane_nb, TIF.StripCnt, classname);
TIF.StripCnt = TIF.StripCnt + 1;
% copy the strip onto the data
plane(:, line:(line+size(strip,2)-1)) = strip;
line = line + size(strip,2);
if ( line > height )
break;
end
end
% Extract valid part of data if needed
if ~all(size(plane) == [width height]),
plane = plane(1:width, 1:height);
warning('tiffread2:Crop','Cropping data: found more bytes than needed');
end
% transpose the image (otherwise display is rotated in matlab)
plane = plane';
end
%% ================== sub-functions to read a strip ===================
function strip = read_strip(offset, width, plane_nb, stripCnt, classname)
global TIF;
%fprintf('reading strip at position %i\n',TIF.StripOffsets(stripCnt) + offset);
StripLength = TIF.StripByteCounts(stripCnt) ./ TIF.BytesPerSample(plane_nb);
%fprintf( 'reading strip %i\n', stripCnt);
status = fseek(TIF.file, TIF.StripOffsets(stripCnt) + offset, 'bof');
if status == -1
error('invalid file offset (error on fseek)');
end
bytes = fread( TIF.file, StripLength, classname, TIF.BOS );
if any( length(bytes) ~= StripLength )
error('End of file reached unexpectedly.');
end
strip = reshape(bytes, width, StripLength / width);
end
%% ==================sub-functions that reads an IFD entry:===================
function [nbBytes, matlabType] = convertType(tiffType)
switch (tiffType)
case 1
nbBytes=1;
matlabType='uint8';
case 2
nbBytes=1;
matlabType='uchar';
case 3
nbBytes=2;
matlabType='uint16';
case 4
nbBytes=4;
matlabType='uint32';
case 5
nbBytes=8;
matlabType='uint32';
case 7
nbBytes=1;
matlabType='uchar';
case 11
nbBytes=4;
matlabType='float32';
case 12
nbBytes=8;
matlabType='float64';
otherwise
error('tiff type %i not supported', tiffType)
end
end
%% ==================sub-functions that reads an IFD entry:===================
function entry = readIFDentry()
global TIF;
entry.tiffType = fread(TIF.file, 1, 'uint16', TIF.BOS);
entry.cnt = fread(TIF.file, 1, 'uint32', TIF.BOS);
%disp(['tiffType =', num2str(entry.tiffType),', cnt = ',num2str(entry.cnt)]);
[ entry.nbBytes, entry.matlabType ] = convertType(entry.tiffType);
if entry.nbBytes * entry.cnt > 4
%next field contains an offset:
offset = fread(TIF.file, 1, 'uint32', TIF.BOS);
%disp(strcat('offset = ', num2str(offset)));
status = fseek(TIF.file, offset, -1);
if status == -1
error('invalid file offset (error on fseek)');
end
end
if TIF.entry_tag == 33629 % metamorph 'rationals'
entry.val = fread(TIF.file, 6*entry.cnt, entry.matlabType, TIF.BOS);
elseif TIF.entry_tag == 34412 %TIF_CZ_LSMINFO
entry.val = readLSMinfo;
else
if entry.tiffType == 5
entry.val = fread(TIF.file, 2*entry.cnt, entry.matlabType, TIF.BOS);
else
entry.val = fread(TIF.file, entry.cnt, entry.matlabType, TIF.BOS);
end
end
if ( entry.tiffType == 2 );
entry.val = char(entry.val');
end
end
%% =============distribute the metamorph infos to each frame:
function [MMstack, MMwavelength, MMprivate2] = splitMetamorph(imgCnt)
global TIF;
MMstack = [];
MMwavelength = [];
MMprivate2 = [];
if TIF.MM_stackCnt == 1
return;
end
left = imgCnt - 1;
if isfield( TIF, 'MM_stack' )
S = length(TIF.MM_stack) / TIF.MM_stackCnt;
MMstack = TIF.MM_stack(S*left+1:S*left+S);
end
if isfield( TIF, 'MM_wavelength' )
S = length(TIF.MM_wavelength) / TIF.MM_stackCnt;
MMwavelength = TIF.MM_wavelength(S*left+1:S*left+S);
end
if isfield( TIF, 'MM_private2' )
S = length(TIF.MM_private2) / TIF.MM_stackCnt;
MMprivate2 = TIF.MM_private2(S*left+1:S*left+S);
end
end
%% %% Parse the Metamorph camera info tag into respective fields
% EVBR 2/7/2005, FJN Dec. 2007
function mm = parseMetamorphInfo(info, cnt)
info = regexprep(info, '\r\n|\o0', '\n');
parse = textscan(info, '%s %s', 'Delimiter', ':');
tokens = parse{1};
values = parse{2};
first = char(tokens(1,1));
k = 0;
mm = struct('Exposure', zeros(cnt,1));
for i=1:size(tokens,1)
tok = char(tokens(i,1));
val = char(values(i,1));
%fprintf( '"%s" : "%s"\n', tok, val);
if strcmp(tok, first)
k = k + 1;
end
if strcmp(tok, 'Exposure')
[v, c, e, pos] = sscanf(val, '%i');
unit = val(pos:length(val));
%return the exposure in milli-seconds
switch( unit )
case 'ms'
mm(k).Exposure = v;
case 's'
mm(k).Exposure = v * 1000;
otherwise
warning('tiffread2:Unit', ['Exposure unit "',unit,'" not recognized']);
mm(k).Exposure = v;
end
else
switch tok
case 'Binning'
% Binning: 1 x 1 -> [1 1]
mm(k).Binning = sscanf(val, '%d x %d')';
case 'Region'
mm(k).Region = sscanf(val, '%d x %d, offset at (%d, %d)')';
otherwise
field = regexprep(tok, ' ', '');
if strcmp(val, 'Off')
eval(['mm(k).',field,'=0;']);
elseif strcmp(val, 'On')
eval(['mm(k).',field,'=1;']);
elseif isstrprop(val,'digit')
eval(['mm(k).',field,'=str2num(val)'';']);
else
eval(['mm(k).',field,'=val;']);
end
end
end
end
end
%% ==============partial-parse of LSM info:
function R = readLSMinfo()
% Read part of the LSM info table version 2
% this provides only very partial information, since the offset indicate that
% additional data is stored in the file
global TIF;
R.MagicNumber = sprintf('0x%09X',fread(TIF.file, 1, 'uint32', TIF.BOS));
StructureSize = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.DimensionX = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.DimensionY = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.DimensionZ = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.DimensionChannels = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.DimensionTime = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.IntensityDataType = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.ThumbnailX = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.ThumbnailY = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.VoxelSizeX = fread(TIF.file, 1, 'float64', TIF.BOS);
R.VoxelSizeY = fread(TIF.file, 1, 'float64', TIF.BOS);
R.VoxelSizeZ = fread(TIF.file, 1, 'float64', TIF.BOS);
R.OriginX = fread(TIF.file, 1, 'float64', TIF.BOS);
R.OriginY = fread(TIF.file, 1, 'float64', TIF.BOS);
R.OriginZ = fread(TIF.file, 1, 'float64', TIF.BOS);
R.ScanType = fread(TIF.file, 1, 'uint16', TIF.BOS);
R.SpectralScan = fread(TIF.file, 1, 'uint16', TIF.BOS);
R.DataType = fread(TIF.file, 1, 'uint32', TIF.BOS);
OffsetVectorOverlay = fread(TIF.file, 1, 'uint32', TIF.BOS);
OffsetInputLut = fread(TIF.file, 1, 'uint32', TIF.BOS);
OffsetOutputLut = fread(TIF.file, 1, 'uint32', TIF.BOS);
OffsetChannelColors = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.TimeInterval = fread(TIF.file, 1, 'float64', TIF.BOS);
OffsetChannelDataTypes = fread(TIF.file, 1, 'uint32', TIF.BOS);
OffsetScanInformation = fread(TIF.file, 1, 'uint32', TIF.BOS);
OffsetKsData = fread(TIF.file, 1, 'uint32', TIF.BOS);
OffsetTimeStamps = fread(TIF.file, 1, 'uint32', TIF.BOS);
OffsetEventList = fread(TIF.file, 1, 'uint32', TIF.BOS);
OffsetRoi = fread(TIF.file, 1, 'uint32', TIF.BOS);
OffsetBleachRoi = fread(TIF.file, 1, 'uint32', TIF.BOS);
OffsetNextRecording = fread(TIF.file, 1, 'uint32', TIF.BOS);
% There are more information stored in this table, which is not read here
%read real acquisition times:
if ( OffsetTimeStamps > 0 )
status = fseek(TIF.file, OffsetTimeStamps, -1);
if status == -1
error('error on fseek');
end
StructureSize = fread(TIF.file, 1, 'int32', TIF.BOS);
NumberTimeStamps = fread(TIF.file, 1, 'int32', TIF.BOS);
for i=1:NumberTimeStamps
R.TimeStamp(i) = fread(TIF.file, 1, 'float64', TIF.BOS);
end
%calculate elapsed time from first acquisition:
R.TimeOffset = R.TimeStamp - R.TimeStamp(1);
end
end
function stack = tiffread(filename, indices)
% tiffread, version 2.7 January 28, 2009
%
% stack = tiffread;
% stack = tiffread(filename);
% stack = tiffread(filename, indices);
%
% Reads 8,16,32 bits uncompressed grayscale and (some) color tiff files,
% as well as stacks or multiple tiff images, for example those produced
% by metamorph, Zeiss LSM or NIH-image.
%
% The function can be called with a file name in the current directory,
% or without argument, in which case it pops up a file opening dialog
% to allow for a manual selection of the file.
% If the stacks contains multiples images, reading can be restricted by
% specifying the indices of the images to read, or just one index.
%
% The returned value 'stack' is a vector struct containing the images
% and their meta-data. The length of the vector is the number of images.
% The image pixels values are stored in a field .data, which is a simple
% matrix for gray-scale images, or a cell-array of matrices for color images.
%
% The pixels values are returned in their native (usually integer) format,
% and must be converted to be used in most matlab functions.
%
% Example:
% im = tiffread('spindle.stk');
% imshow( double(im(5).data) );
%
% Only a fraction of the TIFF standard is supported, but you may extend support
% by modifying this file. If you do so, please return your modification to
% F. Nedelec, so that the added functionality can be distributed in the future.
%
% Francois Nedelec, EMBL, Copyright 1999-2008.
% rewriten July 7th, 2004 at Woods Hole during the physiology course.
% last modified March 7, 2008.
% With contributions from:
% Kendra Burbank for the waitbar
% Hidenao Iwai for the code to read floating point images,
% Stephen Lang to be more compliant with PlanarConfiguration
% Jan-Ulrich Kreft for Zeiss LSM support
% Elias Beauchanp and David Kolin for additional Metamorph support
% Jean-Pierre Ghobril for requesting that image indices may be specified
% Urs Utzinger for the better handling of color images, and LSM meta-data
%
% Please, send us feedback/bugs/suggestions to improve this code.
% This software is provided at no cost by a public research institution.
%
% Francois Nedelec
% nedelec (at) embl.de
% Cell Biology and Biophysics, EMBL; Meyerhofstrasse 1; 69117 Heidelberg; Germany
% http://www.embl.org
% http://www.cytosim.org
%Optimization: join adjacent TIF strips: this results in faster reads
consolidateStrips = 1;
%without argument, we ask the user to choose a file:
if nargin < 1
[filename, pathname] = uigetfile('*.tif;*.stk;*.lsm', 'select image file');
filename = [ pathname, filename ];
end
if (nargin<=1); indices = 1:10000; end
% not all valid tiff tags have been included, as they are really a lot...
% if needed, tags can easily be added to this code
% See the official list of tags:
% http://partners.adobe.com/asn/developer/pdfs/tn/TIFF6.pdf
%
% the structure IMG is returned to the user, while TIF is not.
% so tags usefull to the user should be stored as fields in IMG, while
% those used only internally can be stored in TIF.
global TIF;
TIF = [];
%counters for the number of images read and skipped
img_skip = 0;
img_read = 1;
hWaitbar = [];
%% set defaults values :
TIF.SampleFormat = 1;
TIF.SamplesPerPixel = 1;
TIF.BOS = 'ieee-le'; %byte order string
if isempty(findstr(filename,'.'))
filename = [filename,'.tif'];
end
TIF.file = fopen(filename,'r','l');
if TIF.file == -1
stkname = strrep(filename, '.tif', '.stk');
TIF.file = fopen(stkname,'r','l');
if TIF.file == -1
error(['File "',filename,'" not found.']);
else
filename = stkname;
end
end
[s, m] = fileattrib(filename);
% obtain the full file path:
filename = m.Name;
% find the file size in bytes:
% m = dir(filename);
% filesize = m.bytes;
%% read header
% read byte order: II = little endian, MM = big endian
byte_order = fread(TIF.file, 2, '*char');
if ( strcmp(byte_order', 'II') )
TIF.BOS = 'ieee-le'; % Intel little-endian format
elseif ( strcmp(byte_order','MM') )
TIF.BOS = 'ieee-be';
else
error('This is not a TIFF file (no MM or II).');
end
%% ---- read in a number which identifies file as TIFF format
tiff_id = fread(TIF.file,1,'uint16', TIF.BOS);
if (tiff_id ~= 42)
error('This is not a TIFF file (missing 42).');
end
%% ---- read the byte offset for the first image file directory (IFD)
TIF.img_pos = fread(TIF.file, 1, 'uint32', TIF.BOS);
while TIF.img_pos ~= 0
clear IMG;
IMG.filename = filename;
% move in the file to the first IFD
status = fseek(TIF.file, TIF.img_pos, -1);
if status == -1
error('invalid file offset (error on fseek)');
end
%disp(strcat('reading img at pos :',num2str(TIF.img_pos)));
%read in the number of IFD entries
num_entries = fread(TIF.file,1,'uint16', TIF.BOS);
%disp(strcat('num_entries =', num2str(num_entries)));
%read and process each IFD entry
for i = 1:num_entries
% save the current position in the file
file_pos = ftell(TIF.file);
% read entry tag
TIF.entry_tag = fread(TIF.file, 1, 'uint16', TIF.BOS);
% read entry
entry = readIFDentry;
%disp(strcat('reading entry <',num2str(TIF.entry_tag),'>'));
switch TIF.entry_tag
case 254
TIF.NewSubfiletype = entry.val;
case 256 % image width - number of column
IMG.width = entry.val;
case 257 % image height - number of row
IMG.height = entry.val;
TIF.ImageLength = entry.val;
case 258 % BitsPerSample per sample
TIF.BitsPerSample = entry.val;
TIF.BytesPerSample = TIF.BitsPerSample / 8;
IMG.bits = TIF.BitsPerSample(1);
%fprintf('BitsPerSample %i %i %i\n', entry.val);
case 259 % compression
if ( entry.val ~= 1 )
error(['Compression format ', num2str(entry.val),' not supported.']);
end
case 262 % photometric interpretation
TIF.PhotometricInterpretation = entry.val;
if ( TIF.PhotometricInterpretation == 3 )
warning('tiffread2:LookUp', 'Ignoring TIFF look-up table');
end
case 269
IMG.document_name = entry.val;
case 270 % comments:
IMG.info = entry.val;
case 271
IMG.make = entry.val;
case 273 % strip offset
TIF.StripOffsets = entry.val;
TIF.StripNumber = entry.cnt;
%fprintf('StripNumber = %i, size(StripOffsets) = %i %i\n', TIF.StripNumber, size(TIF.StripOffsets));
case 277 % sample_per pixel
TIF.SamplesPerPixel = entry.val;
%fprintf('Color image: sample_per_pixel=%i\n', TIF.SamplesPerPixel);
case 278 % rows per strip
TIF.RowsPerStrip = entry.val;
case 279 % strip byte counts - number of bytes in each strip after any compressio
TIF.StripByteCounts= entry.val;
case 282 % X resolution
IMG.x_resolution = entry.val;
case 283 % Y resolution
IMG.y_resolution = entry.val;
case 284 %planar configuration describe the order of RGB
TIF.PlanarConfiguration = entry.val;
case 296 % resolution unit
IMG.resolution_unit= entry.val;
case 305 % software
IMG.software = entry.val;
case 306 % datetime
IMG.datetime = entry.val;
case 315
IMG.artist = entry.val;
case 317 %predictor for compression
if (entry.val ~= 1); error('unsuported predictor value'); end
case 320 % color map
IMG.cmap = entry.val;