function [stack, img_read] = tiffread2(filename, img_first, img_last)
% tiffread, version 2.4
%
% [stack, nbImages] = tiffread;
% [stack, nbImages] = tiffread(filename);
% [stack, nbImages] = tiffread(filename, imageIndex);
% [stack, nbImages] = tiffread(filename, firstImageIndex, lastImageIndex);
%
% 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 or NIH-image. However, the entire TIFF standard is not
% supported (but you may extend it).
%
% The function can be called with a file name in the current directory,
% or without argument, in which case it pop up a file openning dialog
% to allow manual selection of the file.
% If the stacks contains multiples images, loading can be restricted by
% specifying the first and last images to read, or just one image to read.
%
% at return, nbimages contains the number of images read, and S is a vector
% containing the different images with some additional informations. The
% image pixels values are stored in the field .data, for gray level images,
% or in the fields .red, .green and .blue
% the pixels values are in the native (integer) format,
% and must be converted to be used in most matlab functions.
%
% Example:
% im = tiffread('spindle.stk');
% imshow( double(im(5).data), [] );
%
% Francois Nedelec, EMBL, Copyright 1999-2006.
% rewriten July 7th, 2004 at Woods Hole during the physiology course.
% last modified April 12, 2006.
% Contributions:
% Kendra Burbank suggested the waitbar
% Hidenao Iwai for the code to read floating point images,
% Stephen Lang made tiffread more compliant with PlanarConfiguration
%
% Please, help us improve this software: send us feedback/bugs/suggestions
% This software is provided at no cost by a public research institution.
% However, postcards are always welcome!
%
% 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;
%if there is no argument, we ask the user to choose a file:
if (nargin == 0)
[filename, pathname] = uigetfile('*.tif;*.stk;*.lsm', 'select image file');
filename = [ pathname, filename ];
end
if (nargin<=1); img_first = 1; img_last = 10000; end
if (nargin==2); img_last = img_first; 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 = 0;
% set defaults values :
TIF.SampleFormat = 1;
TIF.SamplesPerPixel = 1;
TIF.BOS = 'l'; %byte order string
if isempty(findstr(filename,'.'))
filename = [filename,'.tif'];
end
TIF.file = fopen(filename,'r','l');
if TIF.file == -1
filename = strrep(filename, '.tif', '.stk');
TIF.file = fopen(filename,'r','l');
if TIF.file == -1
error(['file <',filename,'> not found.']);
end
end
% 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 = 'l'; %normal PC format
elseif ( strcmp(byte_order','MM') )
TIF.BOS = 'b';
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)
ifd_pos = fread(TIF.file,1,'uint32', TIF.BOS);
while (ifd_pos ~= 0)
clear IMG;
IMG.filename = fullfile( pwd, filename );
% move in the file to the first IFD
fseek(TIF.file, ifd_pos, -1);
%disp(strcat('reading img at pos :',num2str(ifd_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);
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(1,'BitsPerSample %i %i %i\n', entry.val);
case 259 % compression
if (entry.val ~= 1); error('Compression format not supported.'); end
case 262 % photometric interpretation
TIF.PhotometricInterpretation = entry.val;
if ( TIF.PhotometricInterpretation == 3 )
fprintf(1, 'warning: ignoring the look-up table defined in the TIFF file');
end
case 269
IMG.document_name = entry.val;
case 270 % comment:
TIF.info = entry.val;
case 271
IMG.make = entry.val;
case 273 % strip offset
TIF.StripOffsets = entry.val;
TIF.StripNumber = entry.cnt;
%fprintf(1,'StripNumber = %i, size(StripOffsets) = %i %i\n', TIF.StripNumber, size(TIF.StripOffsets));
case 277 % sample_per pixel
TIF.SamplesPerPixel = entry.val;
%fprintf(1,'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 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;
if ( img_last > img_first )
waitbar_handle = waitbar(0,'Please wait...','Name',['Reading ' filename]);
end
case 33630 %metamorph stack data: wavelength
TIF.MM_wavelength = entry.val;
case 33631 %metamorph stack data: gain/background?
TIF.MM_private2 = entry.val;
otherwise
fprintf(1,'ignored TIFF entry with tag %i (cnt %i)\n', TIF.entry_tag, entry.cnt);
end
% move to next IFD entry in the file
fseek(TIF.file, file_pos+12,-1);
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) && (TIF.PlanarConfiguration == 1))
error('PlanarConfiguration = %i not supported', TIF.PlanarConfiguration);
end
%total number of bytes per image:
PlaneBytesCnt = IMG.width * IMG.height * TIF.BytesPerSample;
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(1,'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:
ifd_pos = fread(TIF.file, 1, 'uint32', TIF.BOS);
%if (ifd_pos) disp(['next ifd at', num2str(ifd_pos)]); end
if isfield( TIF, 'MM_stack' )
if ( img_last > TIF.MM_stackCnt )
img_last = TIF.MM_stackCnt;
end
%this loop is to read metamorph stacks:
for ii = img_first:img_last
TIF.StripCnt = 1;
%read the image
fileOffset = PlaneBytesCnt * ( ii - 1 );
%fileOffset = 0;
%fileOffset = ftell(TIF.file) - TIF.StripOffsets(1);
if ( TIF.SamplesPerPixel == 1 )
IMG.data = read_plane(fileOffset, IMG.width, IMG.height, 1);
else
IMG.red = read_plane(fileOffset, IMG.width, IMG.height, 1);
IMG.green = read_plane(fileOffset, IMG.width, IMG.height, 2);
IMG.blue = read_plane(fileOffset, IMG.width, IMG.height, 3);
end
% print a text timer on the main window, or update the waitbar
% fprintf(1,'img_read %i img_skip %i\n', img_read, img_skip);
if exist('waitbar_handle', 'var')
waitbar( img_read/TIF.MM_stackCnt, waitbar_handle);
end
[ IMG.info, IMG.MM_stack, IMG.MM_wavelength, IMG.MM_private2 ] = extractMetamorphData(ii);
img_read = img_read + 1;
stack( img_read ) = IMG;
end
break;
else
%this part to read a normal TIFF stack:
if ( img_skip + 1 >= img_first )
TIF.StripCnt = 1;
%read the image
if ( TIF.SamplesPerPixel == 1 )
IMG.data = read_plane(0, IMG.width, IMG.height, 1);
else
IMG.red = read_plane(0, IMG.width, IMG.height, 1);
IMG.green = read_plane(0, IMG.width, IMG.height, 2);
IMG.blue = read_plane(0, IMG.width, IMG.height, 3);
end
img_read = img_read + 1;
try
stack( img_read ) = IMG;
catch
%stack
%IMG
error('The file contains dissimilar images: you can only read them one by one');
end
else
img_skip = img_skip + 1;
end
if ( img_skip + img_read >= img_last )
break;
end
end
end
%clean-up
fclose(TIF.file);
if exist('waitbar_handle', 'var')
delete( waitbar_handle );
clear waitbar_handle;
end
drawnow;
%return empty array if nothing was read
if ~ exist( 'stack', 'var')
stack = [];
end
return;
%============================================================================
function plane = read_plane(offset, width, height, planeCnt)
global TIF;
%return an empty array if the sample format has zero bits
if ( TIF.BitsPerSample(planeCnt) == 0 )
plane=[];
return;
end
%fprintf(1,'reading plane %i size %i %i\n', planeCnt, width, height);
%determine the type needed to store the pixel values:
switch( TIF.SampleFormat )
case 1
classname = sprintf('uint%i', TIF.BitsPerSample(planeCnt));
case 2
classname = sprintf('int%i', TIF.BitsPerSample(planeCnt));
case 3
if ( TIF.BitsPerSample(planeCnt) == 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:
plane = zeros(width, height, classname);
% Read the strips and concatenate them:
line = 1;
while ( TIF.StripCnt <= TIF.StripNumber )
strip = read_strip(offset, width, planeCnt, 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);
error('Cropping data: more bytes read than needed...');
end
% transpose the image (otherwise display is rotated in matlab)
plane = plane';
return;
%=================== sub-functions to read a strip ===================
function strip = read_strip(offset, width, planeCnt, stripCnt, classname)
global TIF;
%fprintf(1,'reading strip at position %i\n',TIF.StripOffsets(stripCnt) + offset);
StripLength = TIF.StripByteCounts(stripCnt) ./ TIF.BytesPerSample(planeCnt);
%fprintf(1, 'reading strip %i\n', stripCnt);
fseek(TIF.file, TIF.StripOffsets(stripCnt) + offset, 'bof');
bytes = fread( TIF.file, StripLength, classname, TIF.BOS );
if ( length(bytes) ~= StripLength )
error('End of file reached unexpectedly.');
end
strip = reshape(bytes, width, StripLength / width);
return;
%===================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 11
nbBytes=4;
matlabType='float32';
case 12
nbBytes=8;
matlabType='float64';
otherwise
error('tiff type %i not supported', tiffType)
end
return;
%===================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)));
fseek(TIF.file, offset, -1);
end
if TIF.entry_tag == 33629 %special metamorph 'rationals'
entry.val = fread(TIF.file, 6*entry.cnt, entry.matlabType, TIF.BOS);
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
return;
%==============distribute the metamorph infos to each frame:
function [info, stack, wavelength, private2 ] = extractMetamorphData(imgCnt)
global TIF;
info = [];
stack = [];
wavelength = [];
private2 = [];
if TIF.MM_stackCnt == 1
return;
end
left = imgCnt - 1;
if isfield( TIF, 'info' )
S = length(TIF.info) / TIF.MM_stackCnt;
info = TIF.info(S*left+1:S*left+S);
end
if isfield( TIF, 'MM_stack' )
S = length(TIF.MM_stack) / TIF.MM_stackCnt;
stack = TIF.MM_stack(S*left+1:S*left+S);
end
if isfield( TIF, 'MM_wavelength' )
S = length(TIF.MM_wavelength) / TIF.MM_stackCnt;
wavelength = TIF.MM_wavelength(S*left+1:S*left+S);
end
if isfield( TIF, 'MM_private2' )
S = length(TIF.MM_private2) / TIF.MM_stackCnt;
private2 = TIF.MM_private2(S*left+1:S*left+S);
end
return;
