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jacquestiffread.m
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%% loadlsm.m
% Jacques Bothma Date shared: 01/13/11
% and Alistair Boettiger
% Levine Lab Last Modified: 01/13/11
function stack = jacquestiffread(filename)
global TIF TEMPDat
TIF = [];
TEMPDat= [];
filenameout=([filename(1:end-3) 'mat']);
%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
TEMPDat.counterr=0;
TEMPDat.pastposi=0;
TEMPDat.rat=0;
TEMPDat.std=0;
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);
%TIF.img_posList=[TIF.img_pos];
%TIF.StripOffsetsList=[];
%%%%%%%%%%%%% Main processing code %%%%%%%%%%%%%%%%
count=1;
while TIF.img_pos ~= 0
TIF.BOS;
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=>uint16', TIF.BOS);
%disp(strcat('num_entries =', num2str(num_entries)));
ENT=[];
% Read and process each IFD entry, essentially reading in the header,
% image by image. LSM data is stored only in the header of the first
% file.
for i = 1:num_entries
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=>uint16', TIF.BOS);
% read entry
ENT = [TIF.entry_tag;ENT];
entry = readIFDentry; %function that reads entry
%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;
TIF.width=[IMG.width];
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 273 % strip offset
TIF.StripOffsets = entry.val;
TIF.StripNumber = entry.cnt;
% TIF.StripOffsetsList = [TIF.StripOffsetsList;TIF.StripOffsets']
%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 279 % strip byte counts - number of bytes in each strip after any compressio
TIF.StripByteCounts= entry.val;
case 284 %planar configuration describe the order of RGB
TIF.PlanarConfiguration = entry.val;
case 34412 % Zeiss LSM data
LSM_info = entry.val;
disp('Zeiss LSM data')
otherwise
fprintf( 'Ignored TIFF entry with tag %i (cnt %i)\n', TIF.entry_tag, entry.cnt);
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
%%%%%% end of reading in individual image header %%%%%%%%
%%%%%%%%% read the position of the next IFD address:
firstimage=0;
if firstimage
TIF.img_pos=0;
else
TIF.img_pos = fread(TIF.file, 1, 'uint32', TIF.BOS);
% TIF.img_posList=[TIF.img_posList;TIF.img_pos];
if IMG.width~=128
Data.(['I' num2str(count)]).TIF=TIF;
Data.(['I' num2str(count)]).IMG=IMG;
count=count+1;
end
end
end
Data.LSM_info=LSM_info;
numberofstacks = (count-1)/Data.LSM_info.DimensionZ;
for i =1:numberofstacks
for j=1:Data.LSM_info.DimensionZ
Datas.(['Stack' num2str(i)]).(['Image' num2str(j)]).TIF=Data.(['I' num2str((i-1)*Data.LSM_info.DimensionZ +j)]).TIF;
Datas.(['Stack' num2str(i)]).(['Image' num2str(j)]).IMG=Data.(['I' num2str((i-1)*Data.LSM_info.DimensionZ +j)]).IMG;
end
end
Datas.LSM_info=LSM_info;
Datas.filename=filename;
Datas.TEMPDat = TIF.TEMPDat;
save(filenameout,'Datas');
disp('data saved');
fclose(TIF.file);
end
%%%%%%%%%%%% End of Main processing code %%%%%%%%%%%%%%%%
%% ==================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 TEMPDat;
entry.tiffType = fread(TIF.file, 1, 'uint16=>uint16', TIF.BOS);
entry.cnt = fread(TIF.file, 1, 'uint32=>double', TIF.BOS); %%%edit
%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);
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;
disp('LSMinforead')
else
if entry.tiffType == 5
entry.val = fread(TIF.file, 2*entry.cnt, entry.matlabType, TIF.BOS);
elseif TIF.entry_tag == 273
entry.val = fread(TIF.file, entry.cnt, entry.matlabType , TIF.BOS);
entryvaltemp=entry.val;
for i=1:length(entry.val)
TEMPDat.rat= [TEMPDat.rat; TEMPDat.pastposi/entry.val(i)];
TEMPDat.std= [TEMPDat.std;std(TEMPDat.rat)];
if TEMPDat.pastposi/entry.val(i)>20*std(TEMPDat.rat)
TEMPDat.counterr=TEMPDat.counterr+1;
end
entry.val(i)= entry.val(i)+TEMPDat.counterr*(2^32);
TEMPDat.pastposi=entryvaltemp(i);
end
TEMPDat.entryval = entry.val; % Added export for troubleshooting
TIF.TEMPDat=TEMPDat;
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
%% ==============Full-parse of LSM info:
function R = readLSMinfo()
% Read the LSM info
global TIF TEMPDat;
R.MagicNumber = sprintf('0x%09X',fread(TIF.file, 1, 'uint32', TIF.BOS));
R.StructureSize = fread(TIF.file, 1, 'int32', TIF.BOS);
R.DimensionX = fread(TIF.file, 1, 'int32', TIF.BOS);
R.DimensionY = fread(TIF.file, 1, 'int32', TIF.BOS);
R.DimensionZ = fread(TIF.file, 1, 'int32', TIF.BOS);
R.DimensionChannels = fread(TIF.file, 1, 'int32', TIF.BOS);
R.DimensionTime = fread(TIF.file, 1, 'int32', TIF.BOS);
R.IntensityDataType = fread(TIF.file, 1, 'int32', TIF.BOS);
R.ThumbnailX = fread(TIF.file, 1, 'int32', TIF.BOS);
R.ThumbnailY = fread(TIF.file, 1, 'int32', 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);
R.OffsetVectorOverlay = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.OffsetInputLut = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.OffsetOutputLut = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.OffsetChannelColors = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.TimeInterval = fread(TIF.file, 1, 'float64', TIF.BOS);
R.OffsetChannelDataTypes = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.OffsetScanInformation = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.OffsetKsData = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.OffsetTimeStamps = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.OffsetEventList = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.OffsetRoi = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.OffsetBleachRoi = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.OffsetNextRecording = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.DisplayAspectX = fread(TIF.file, 1, 'float64', TIF.BOS);
R.DisplayAspectY = fread(TIF.file, 1, 'float64', TIF.BOS);
R.DisplayAspectZ = fread(TIF.file, 1, 'float64', TIF.BOS);
R.OffsetMeanOfRoisOverlay = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.OffsetTopoIsolineOverlay = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.OffsetLinescanOverlay = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.ToolbarFlags = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.OffsetChannelWavelength = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.OffsetChannelFactors = fread(TIF.file, 1, 'uint32', TIF.BOS);
R.ObjectiveSphereCorrection= fread(TIF.file, 1, 'float64', TIF.BOS);
R.OffsetUnmixParameters = fread(TIF.file, 1, 'uint32', TIF.BOS);
%Read Scan information
if (R.OffsetScanInformation>0)
status = fseek(TIF.file, R.OffsetScanInformation, -1);
if status == -1
error('error on fseek');
end
count=sqrt(-1);
num=1;
while count~=0
count=real(count);
A1=sprintf('0x%09X',fread(TIF.file, 1, 'uint32', TIF.BOS));
A2=fread(TIF.file, 1, 'uint32', TIF.BOS);
A3=fread(TIF.file, 1, 'uint32', TIF.BOS);
if A2==2
A4 = fread(TIF.file, A3, '*char', TIF.BOS)';
elseif A2==4
A4 = fread(TIF.file, round(A3/4), 'int32', TIF.BOS)';
elseif A2==5
A4 = fread(TIF.file, round(A3/8), 'float64', TIF.BOS)';
else
A4 = fread(TIF.file, A3, '*char', TIF.BOS)';
end
R.AllData.(['EntryNumber' num2str(num)]).FieldTag=A1;
R.AllData.(['EntryNumber' num2str(num)]).DataType=A2;
R.AllData.(['EntryNumber' num2str(num)]).Data=A4;
if (A2+A3==0) & ~(strcmp(A1,'0x0FFFFFFFF'))
count=count+1;
elseif (A2+A3==0) & (strcmp(A1,'0x0FFFFFFFF'))
count=count-1;
else
end
num=num+1;
end
end
%Summarising pertinent scan information
R.DataSummary=[];
R.DataSummary.Fluorophores={};
R.DataSummary.ExcitationWavelength={};
for i=1:num-1,
if strcmp(R.AllData.(['EntryNumber' num2str(i)]).FieldTag,'0x010000004')
R.DataSummary.Objective=R.AllData.(['EntryNumber' num2str(i)]).Data;
elseif strcmp(R.AllData.(['EntryNumber' num2str(i)]).FieldTag,'0x010000036')
try
time = datenum('30-Dec-1899', 'dd-mmm-yyyy') + R.AllData.(['EntryNumber' num2str(i)]).Data;
R.DataSummary.Time = datestr(time, 'mmmm dd, yyyy HH:MM');
catch
R.DataSummary.Time = '';%
end
elseif strcmp(R.AllData.(['EntryNumber' num2str(i)]).FieldTag,'0x070000026')
R.DataSummary.Fluorophores(end+1,1)={R.AllData.(['EntryNumber' num2str(i)]).Data};
disp(R.AllData.(['EntryNumber' num2str(i)]).Data)
elseif strcmp(R.AllData.(['EntryNumber' num2str(i)]).FieldTag,'0x090000001')
R.DataSummary.ExcitationWavelength(end+1,1)={R.AllData.(['EntryNumber' num2str(i)]).Data};
else
end
end
end