%--------------------------------------------------------------------------
function data = OutputTiffHeader( filename )
% -------------------------------------------------------------------------
% Name: OutputTiffHeader
% Disc: function to extract header information
%
% Input: filename - image file to extract data from
%
% Output: data - image header dataj
%
% Owner: Lad Dombrowski
% Center for Live Cell Imaging
% Department of Microbiology and Immunology
% University of Michigan
% http://sitemaker.umich.edu/4dimagingcenter/center_for_live-cell_imaging_home
%
% Files needed: TiffHeader.fig, TiffHeader.m, OutputTiffHeader.m
%
%
%------------------------------------------------------------------------
%
% This software is based on the tiffread software
% 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
data(1).filename = ['filename = ' filename];
%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
% default to everything
img_first = 1;
img_last = 10000;
% 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, message] = fopen(filename,'r','l');
if TIF.file == -1
filename = strrep(filename, '.tif', '.stk');
[TIF.file, message] = fopen(filename,'r','l');
if TIF.file == -1
error(['file <',filename,'> not found.']);
end
end
% read header
% keep track of the number of images
imageIndex = 1;
% read byte order: II = little endian, MM = big endian
byte_order = setstr(fread(TIF.file, 2, 'uchar'));
if ( strcmp(byte_order', 'II') )
TIF.BOS = 'l'; %normal PC format
data(imageIndex,1).byteOrder = 'Byte Order = II';
elseif ( strcmp(byte_order','MM') )
TIF.BOS = 'b';
data(imageIndex,1).byteOrder = 'Byte Order = MM';
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
% create dummy exposures for .tifs - ljd (5-22-08)
TIF.info.Exposure = 1;
%----- 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);
data(imageIndex,1).position = ['reading img at pos : ' num2str(ifd_pos)];
%read in the number of IFD entries
num_entries = fread(TIF.file,1,'uint16', TIF.BOS);
data(imageIndex,1).numEntries = ['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);
data(imageIndex,i).filePosition = ['File Position = ' num2str(file_pos)];
% read entry tag
TIF.entry_tag = fread(TIF.file, 1, 'uint16', TIF.BOS);
entry = readIFDentry;
data(imageIndex,i).entryTag = ['Entry tag = ' num2str(TIF.entry_tag)];
%disp(strcat('reading entry <',num2str(TIF.entry_tag),'>'));
switch TIF.entry_tag
case 254
TIF.NewSubfiletype = entry.val;
data(imageIndex,i).string = ['Sub-file Type = ' num2str(entry.val)];
case 256 % image width - number of column
IMG.width = entry.val;
data(imageIndex,i).string = ['Image Width = ' num2str(entry.val)];
case 257 % image height - number of row
IMG.height = entry.val;
TIF.ImageLength = entry.val;
data(imageIndex,i).string = ['Image Height = ' num2str(entry.val)];
case 258 % BitsPerSample per sample
TIF.BitsPerSample = entry.val;
TIF.BytesPerSample = TIF.BitsPerSample / 8;
IMG.bits = TIF.BitsPerSample(1);
data(imageIndex,i).string = ['Bits per sample = ' num2str(IMG.bits)];
%fprintf(1,'BitsPerSample %i %i %i\n', entry.val);
case 259 % compression
if (entry.val ~= 1) error('Compression format not supported.'); end
data(imageIndex,i).string = ['Compression = ' num2str(entry.val)];
case 262 % photometric interpretation
TIF.PhotometricInterpretation = entry.val;
data(imageIndex,i).string = ['Photometric Interpretation = ' num2str(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;
data(imageIndex,i).string = ['Document Name = ' entry.val];
case 270 % comment:
TIF.info = parseMM_info(entry.val,i);
data(imageIndex,i).string = 'Metamorph info';
data(imageIndex,i).mmInfo = TIF.info;
case 271
IMG.make = entry.val;
data(imageIndex,i).string = ['Make = ' num2str(entry.val)];
case 273 % strip offset
TIF.StripOffsets = entry.val;
TIF.StripNumber = entry.cnt;
data(imageIndex,i).string = ['Strip Offsets/Number = ' num2str(entry.val(1)) '/' num2str(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;
data(imageIndex,i).string = ['Color image: sample per pixel = ' num2str(entry.val)];
%fprintf(1,'Color image: sample_per_pixel=%i\n', TIF.SamplesPerPixel);
case 278 % rows per strip
TIF.RowsPerStrip = entry.val;
data(imageIndex,i).string = ['Rows per strip = ' num2str(entry.val)];
case 279 % strip byte counts - number of bytes in each strip after any compressio
TIF.StripByteCounts= entry.val;
data(imageIndex,i).string = ['Strip Byte Count = ' num2str(entry.val(1))];
case 282 % X resolution
IMG.x_resolution = entry.val;
data(imageIndex,i).string = ['X resolution = ' num2str(entry.val(1)) ',' num2str(entry.val(2))];
case 283 % Y resolution
IMG.y_resolution = entry.val;
data(imageIndex,i).string = ['Y resolution = ' num2str(entry.val(1)) ',' num2str(entry.val(2))];
case 284 %planar configuration describe the order of RGB
TIF.PlanarConfiguration = entry.val;
data(imageIndex,i).string = ['Planar configuration = ' num2str(entry.val)];
case 296 % resolution unit
IMG.resolution_unit= entry.val;
data(imageIndex,i).string = ['Resolution units = ' entry.typechar];
case 305 % software
IMG.software = entry.val;
len = length(entry.val);
name = '';
for iname = 1:len
name = [name entry.val(iname)];
end
data(imageIndex,i).string = ['Software = ' name];
case 306 % datetime
IMG.datetime = entry.val;
len = length(entry.val);
filedate = '';
for idate = 1:len
filedate = [filedate entry.val(idate)];
end
data(imageIndex,i).string = ['Date-Time = ' filedate];
case 315
IMG.artist = entry.val;
data(imageIndex,i).string = ['Artist = ' entry.val];
case 317 %predictor for compression
data(imageIndex,i).string = ['Predictor for compression = ' num2str(entry.val)];
if (entry.val ~= 1) error('unsuported predictor value'); end
case 320 % color map
IMG.cmap = entry.val;
IMG.colors = entry.cnt/3;
data(imageIndex,i).string = ['Color Map/Colors = ' num2str(entry.val) '/' num2str(entry.cnt/3)];
case 339
TIF.SampleFormat = entry.val;
data(imageIndex,i).string = ['Sample Format = ' num2str(entry.val)];
if (( TIF.SampleFormat ~= 1) && (TIF.SampleFormat ~= 3))
error(sprintf('unsuported sample format = %i', TIF.SampleFormat));
end
case 33628 %metamorph specific data
IMG.MM_private1 = entry.val;
% ljd 6-4-08 added illumination setting and creation time variables
if (isfield(TIF, 'MM_illumSetting'))
IMG.MM_illumSetting = TIF.MM_illumSetting;
end
if (isfield(TIF, 'MM_ctime'))
IMG.MM_ctime = TIF.MM_ctime;
end
data(imageIndex,i).string = 'Metamorph Private Data';
case 33629 %this tag identify the image as a Metamorph stack!
TIF.MM_stack = entry.val;
TIF.MM_stackCnt = entry.cnt;
data(imageIndex,i).string = ['Metamorph Stack - count = ' num2str(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;
data(imageIndex,i).string = ['Metamorph wavelength = ' num2str(entry.val(1)) ',' num2str(entry.val(2))];
case 33631 %metamorph stack data: gain/background?
TIF.MM_private2 = entry.val;
data(imageIndex,i).string = ['Metamorph - gain/background = ' num2str(entry.val(1)) ...
',' num2str(entry.val(2)) ];
case 34412 % Zeiss LSM data (I have no idea what that represents...)
IMG.LSM = entry.val;
data(imageIndex,i).string = ['Zeiss LSM data = ' num2str(entry.val)];
otherwise
data(imageIndex,i).string = ['Unrecognized tag = ' num2str(TIF.entry_tag)];
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(sprintf('PlanarConfiguration = %i not supported', TIF.PlanarConfiguration));
end
%total number of bytes per image:
PlaneBytesCnt = IMG.width * IMG.height * TIF.BytesPerSample;
data(imageIndex,i).bytesPerImage = ['Bytes per image = ' num2str(PlaneBytesCnt)];
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 (ifd_pos)
data(imageIndex,i).ifd = ['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 );
data(imageIndex,i).mmImage(ii).planeNo = ['Reading Metamorph image # ' num2str(ii)];
data(imageIndex,i).mmImage(ii).fieldOffset = ['Field offset = ' num2str(fileOffset)];
%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') && (round(ii/10) == ii/10)
waitbar( img_read/TIF.MM_stackCnt, waitbar_handle);
end
[ IMG.info, IMG.MM_stack, IMG.MM_wavelength, IMG.MM_private2 ] = extractMetamorphData(ii);
data(imageIndex,i).mmImage(ii).wavelength = ['Metamorph wavelength = ' num2str(IMG.MM_wavelength(1)), ',', ...
num2str(IMG.MM_wavelength(2))];
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
% ljd - added Exposure to .tif images data (5-22-08)
IMG.info = TIF.info;
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
% increment image counter
imageIndex = imageIndex + 1;
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);
% Preallocate the matrix to hold the data:
%string description of the type of integer needed: int8 or int16...
typecode = sprintf('int%i', TIF.BitsPerSample(planeCnt) );
%unsigned int if SampleFormat == 1
if ( TIF.SampleFormat == 1 )
typecode = [ 'u', typecode ];
% Preallocate a matrix to hold the sample data:
plane = eval( [ typecode, '(zeros(width, height))'] );
elseif ( TIF.SampleFormat == 3 )
typecode = 'float';
plane = zeros(width, height);
end
line = 1;
while ( TIF.StripCnt <= TIF.StripNumber )
strip = read_strip(offset, width, planeCnt, TIF.StripCnt, typecode );
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
plane = plane';
return;
%=================== sub-functions to read a strip ===================
function strip = read_strip(offset, width, planeCnt, stripCnt, typecode)
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, typecode, 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, typechar] = matlab_type(tiff_typecode)
switch (tiff_typecode)
case 1
nbbytes=1;
typechar='uint8';
case 2
nbbytes=1;
typechar='uchar';
case 3
nbbytes=2;
typechar='uint16';
case 4
nbbytes=4;
typechar='uint32';
case 5
nbbytes=8;
typechar='uint32';
otherwise
error('tiff type not supported')
end
return;
%===================sub-functions that reads an IFD entry:===================
function entry = readIFDentry()
global TIF;
entry.typecode = fread(TIF.file, 1, 'uint16', TIF.BOS);
entry.cnt = fread(TIF.file, 1, 'uint32', TIF.BOS);
%disp(['typecode =', num2str(entry.typecode),', cnt = ',num2str(entry.cnt)]);
[ entry.nbbytes, entry.typechar ] = matlab_type(entry.typecode);
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.typechar, TIF.BOS);
elseif TIF.entry_tag == 33628 % MM_private1 - ljd 6-4-08 added code
%disp(strcat('offset = ', num2str(offset)));
%disp(['typecode =', num2str(entry.typecode),', cnt = ',num2str(entry.cnt)]);
entry.val = fread(TIF.file, entry.cnt, entry.typechar, TIF.BOS);
for i = 1:entry.cnt-1
switch entry.val(i)
case 49 % illumsetting, magsetting, magni, magri
offset = entry.val(i+1);
if (offset < 300)
% nothing
else
fseek(TIF.file, offset, -1);
id = fread(TIF.file, 1, 'uint16', TIF.BOS);
id = fread(TIF.file, 1, 'uint16', TIF.BOS);
id = fread(TIF.file, 1, 'uint16', TIF.BOS);
switch id
case 24334 % illumSetting
%disp('49 = ')
name = setstr(fread(TIF.file, 13, 'uint8', TIF.BOS));
TIF.MM_illumSetting = setstr(fread(TIF.file, 13, 'uint8', TIF.BOS));
case 24332 % MagSetting
name = setstr(fread(TIF.file, 23, 'uint8', TIF.BOS));
case 24327 % MagRI, MagNA
name = setstr(fread(TIF.file, 25, 'uint8', TIF.BOS));
end
% name = setstr(fread(TIF.file, 1, 'uint32', TIF.BOS));
%name
end
case 16 % creation time - since midnight in milsec
%disp('16 = ');
offset = entry.val(i+1);
fseek(TIF.file, offset, -1);
date = fread(TIF.file, 1, 'uint32', TIF.BOS);
time = fread(TIF.file, 1, 'uint32', TIF.BOS);
hour = 3600000;
hours = floor(time/hour);
time = time - hours*hour;
minutes = floor(time/60000);
time = time - minutes*60000;
sec = floor(time/1000);
milsec = time - sec*1000;
TIF.MM_ctime = strcat(num2str(hours), ':', num2str(minutes), ':',...
num2str(sec), ':',num2str(milsec));
end
end
else
if entry.typecode == 5
entry.val = fread(TIF.file, 2*entry.cnt, entry.typechar, TIF.BOS);
else
entry.val = fread(TIF.file, entry.cnt, entry.typechar, TIF.BOS);
end
end
if ( entry.typecode == 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;
infoSize = size(TIF.info);
if (infoSize(2) == 1)
info = TIF.info;
else
info = TIF.info(imgCnt);
end
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;
%%%% Parse the Metamorph camera info tag into respective fields
% EVBR 2/7/2005
function mm_infor = parseMM_info(info,p)
i=0;
propCount = 1;
cpropCount = 1;
kk=info;
kk(find(double(kk)==0)) = '';
while(length(kk))
i=i+1;
[tmp, kk] = strtok(kk, 13);
% [tmp,b] = strtok(tmp, 0);
token{i} = sscanf(tmp, '%s');
end
tok = {token{1:end-1}};
len = length(tok)/11;
k=1; % changed default to 1 - for data without exposure
if (length(tok) == 0)
% more metamorph info data - at least set exposure
mm_infor(1).Exposure = 1;
end
for i=1:length(tok)
if ~isempty(token{i})
[tkk, remk] = strtok(token{i}, 58);
% if remark is empty - say so LJD - (7-15-08)
if (isempty(remk))
remk = ' empty';
end
% removed kludge for exposure only - ljd 7-22-08
%if strcmp(tkk, 'Exposure')
% k=k+1;
%end
switch tkk
case 'Exposure'
% Exposure: 200 ms -> 200
mm_infor(k).Exposure = str2double(remk(2:strfind(remk, 'ms')-1));
data(p).mmData(i).exposure = ['Metamorph Exposure = ' num2str(mm_infor(k).Exposure)];
case 'Binning'
% Binning: 1 x 1 -> [1 1]
tmp = sscanf(remk, '%c %d %c %d')';
mm_infor(k).Binning = tmp([2,4]);
data(p).mmData(i).binning = ['Metamorph Binning = ' mm_infor(k).Binning];
case 'Region'
% Region: 1392 x 1040, offset at (0, 0) -> [1392 1040], [0 0]
[a,b] = strtok(remk, ',');
tmp = sscanf(a, '%c %d %c %d')';
mm_infor(k).Region.Size = tmp([2,4]);
[a,b] = strtok(b, ',');
mm_infor(k).Region.Offset = [str2double(a(end)), str2double(b(2))];
data(p).mmData(i).region = ['Metamorph Region = ' a(end), ',' b(2)];
case 'Subtract'
% Subtract: Off -> 0
mm_infor(k).Subtract = ~strcmp(remk(2:end),'Off');
data(p).mmData(i).subtract = ['Metamorph Subtract = ', remk(2:end)];
case 'Shading'
% Shading: Off -> 0
mm_infor(k).Shading = ~strcmp(remk(2:end),'Off');
data(p).mmData(i).shading = ['Metamorph Shading = ', remk(2:end)];
case 'Digitizer'
% Digitizer: 5MHz -> 5
mm_infor(k).Digitizer = sscanf(remk(2:end), '%d %*s');
data(p).mmData(i).digitize = ['Metamorph Digitizer = ', sscanf(remk(2:end), '%d %*s')'];
case 'Gain'
% Gain: Gain 1 (1x) -> 1
mm_infor(k).Gain = sscanf(remk(strfind(remk,'(')+1:end),...
'%d %*s %d')';
data(p).mmData(i).gain = ['Metamorph Gain = ', sscanf(remk(strfind(remk,'(')+1:end),...
'%d %*s %d')'];
case 'CameraShutter'
% Camera Shutter: Always Open -> 'AlwaysOpen'
mm_infor(k).CameraShutter = remk(2:end);
data(p).mmData(i).cameraShutter = ['Metamorph Camera Shutter = ', remk(2:end)];
case 'ClearCount'
% Clear Count: 2 -> 2
tmp = sscanf(remk, '%c %d')';
mm_infor(k).ClearCount = tmp(2);
data(p).mmData(i).clearCount = ['Metamorph Clear Count = ', num2str(tmp(2))];
case 'TriggerMode'
% Trigger Mode: Normal -> 'Normal'
mm_infor(k).TriggerMode = remk(2:end);
data(p).mmData(i).tiggerMode = ['Metamorph Trigger mode = ', remk(2:end)];
case 'Temperature'
% Temperature: 20 -> 20
tmp = sscanf(remk, '%c %d')';
mm_infor(k).Temperature = tmp(2);
data(p).mmData(i).temp = ['Metamorph Camera Shutter = ', num2str(tmp(2))];
case 'ClearMode' % ljd - added ClearMode case (5-30-08)
% Clear Mode: Normal -> 'Normal'
mm_infor(k).ClearMode = remk(2:end);
data(p).mmData(i).clearMode = ['Metamorph Clear Mode = ', remk(2:end)];
case 'FramestoAverage' % ljd - FramestoAverage (5-30-08)
% FramestoAverage: Normal -> 'Normal'
mm_infor(k).FramestoAverage = remk(2:end);
data(p).mmData(i).frames = ['Metamorph Frame to Average = ', remk(2:end)];
case 'AcquiredfromPhotometrics' % ljd - AcquiredfromPhotometrics (5-30-08)
% AcquiredfromPhotometrics: Normal -> 'Normal'
mm_infor(k).AcquiredfromPhotometrics = remk(2:end);
data(p).mmData(i).photo = ['Metamorph Photometrics = ', remk(2:end)];
case 'SensorMode' % ljd - SensorMode (5-30-08)
% SensorMode: Normal -> 'Normal'
mm_infor(k).SensorMode = remk(2:end);
data(p).mmData(i).sensorMode = ['Metamorph Sensor Mode = ', remk(2:end)];
case 'MultiplicationGain' % ljd - MultiplicationGain (5-30-08)
% MultiplicationGain: Normal -> 'Normal'
mm_infor(k).MultiplicationGain = remk(2:end);
data(p).mmData(i).mult = ['Metamorph Multiplication Gain = ', remk(2:end)];
case 'Illumination' % ljd - Illumination (5-30-08)
% Illumination: Normal -> 'Normal'
mm_infor(k).Illumination = remk(2:end);
data(p).mmData(i).illumination = ['Metamorph Illumination = ', remk(2:end)];
case '[IntensityMapping]' % ljd - IntensityMapping (7-23-09)
% IntensityMapping: Normal -> 'MapCh0'
p = 1;
index = i+1;
[tkk, remk] = strtok(token{index}, 58);
while (strcmpi(tkk,'[IntensityMappingEnd]') == 0)
mm_infor(k).IntensityMapping{p} = tkk;
index = index+1;
[tkk, remk] = strtok(token{index}, 58);
p = p+1;
end
data(p).mmData(i).intensity = mm_infor(k).IntensityMapping;
case '[DisplaySettings]' % ljd - DisplaySettings (7-23-09)
% DisplaySettings: Normal -> 'Gamma0=1,DisplayMode=545,DisplayZoom=1'
p = 1;
index = i+1;
[tkk, remk] = strtok(token{index}, 58);
while (strcmpi(tkk,'[DisplaySettingsEnd]') == 0)
mm_infor(k).displaySettings{p} = tkk;
index = index+1;
[tkk, remk] = strtok(token{index}, 58);
p = p+1;
end
data(p).mmData(i).display = mm_infor(k).displaySettings;
case '[AcquisitionParameters]' % ljd - AquisitionParameters (7-23-09)
% MultiplicationGain: Normal -> 'Normal'
p = 1;
index = i+1;
[tkk, remk] = strtok(token{index}, 58);
while (strcmpi(tkk,'[AcquisitionParametersEnd]') == 0)
mm_infor(k).acquisition{p} = tkk;
index = index+1;
[tkk, remk] = strtok(token{index}, 58);
p = p+1;
end
data(p).mmData(i).acquisition = mm_infor(k).acquisition;
case '[Description]' % ljd - Description (7-23-09)
% Description: Normal -> 'Normal'
p = 1;
index = i+1;
[tkk, remk] = strtok(token{index}, 58);
while (strcmpi(tkk,'[DescriptionEnd]') == 0)
mm_infor(k).description{p} = tkk;
index = index+1;
[tkk, remk] = strtok(token{index}, 58);
p = p+1;
end
data(p).mmData(i).description = mm_infor(k).description;
case '[Physiology]' % ljd - Physiology (7-23-09)
% Physiology: Normal -> 'Normal'
p = 1;
index = i+1;
[tkk, remk] = strtok(token{index}, 58);
while (strcmpi(tkk,'[PhysiologyEnd]') == 0)
mm_infor(k).physiology{p} = tkk;
index = index+1;
[tkk, remk] = strtok(token{index}, 58);
p = p+1;
end
data(p).mmData(i).physiology = mm_infor(k).physiology;
case '[LUTCh0]' % ljd - LUTCh0 (7-23-09)
% LUTCh0: Normal -> 'Normal'
p = 1;
index = i+1;
[tkk, remk] = strtok(token{index}, 58);
while (strcmpi(tkk,'[LUTCh0End]') == 0)
mm_infor(k).LUTCh0{p} = tkk;
index = index+1;
[tkk, remk] = strtok(token{index}, 58);
p = p+1;
end
data(p).mmData(i).LUTCh0 = mm_infor(k).LUTCh0;
case '[VersionInfo]' % ljd - VersionInfo (7-23-09)
% VersionInfo: Normal -> 'Normal'
p = 1;
index = i+1;
[tkk, remk] = strtok(token{index}, 58);
while (strcmpi(tkk,'[VersionInfoEnd]') == 0)
mm_infor(k).versionInfo{p} = tkk;
index = index+1;
[tkk, remk] = strtok(token{index}, 58);
p = p+1;
end
data(p).mmData(i).version = mm_infor(k).versionInfo;
case '<MetaData>' % ljd - multitif metadata (8-28-09)
index = i+1;
[tkk, remk] = strtok(token{index}, 13);
% extract the metaData fields
tmpInfo = decodeTkk(tkk);
if (isfield(tmpInfo,'Exposure'))
mm_infor(k).Exposure = tmpInfo.Exposure;
data(p).mmData(i).exposure = ['Metamorph Exposure = ' ...
num2str(mm_infor(k).Exposure)];
end
if (isfield(tmpInfo,'Binning'))
mm_infor(k).Binning = tmpInfo.Binning;
data(p).mmData(i).binning = ['Metamorph Binning = ' ...
'[' num2str(mm_infor(k).Binning(1)) ' x ' ...
num2str(mm_infor(k).Binning(2)) ']'];
end
if (isfield(tmpInfo,'Region'))
mm_infor(k).Region = tmpInfo.Region;
sizeString = [' Size(' num2str(tmpInfo.Region.Size(1)) ',' ...
num2str(tmpInfo.Region.Size(2)) ') '];
offString = [' Offset at(' num2str(tmpInfo.Region.Offset(1)) ...
',' num2str(tmpInfo.Region.Offset(2)) ') '];
data(p).mmData(i).region = ['Metamorph Region = '...
sizeString offString];
end
if (isfield(tmpInfo,'Subtract'))
mm_infor(k).Subtract = tmpInfo.Subtract;
if (tmpInfo.Subtract)
data(p).mmData(i).subtract = ['Metamorph Subtract = On'];
else
data(p).mmData(i).subtract = ['Metamorph Subtract = Off'];
end
end
if (isfield(tmpInfo,'Shading'))
mm_infor(k).Shading = tmpInfo.Shading;
if (tmpInfo.Shading)
data(p).mmData(i).shading = ['Metamorph Shading = On'];
else
data(p).mmData(i).shading = ['Metamorph Shading = Off'];
end
end
if (isfield(tmpInfo,'Digitizer'))
mm_infor(k).Digitizer = tmpInfo.Digitizer;
data(p).mmData(i).digitize = ['Metamorph Digitizer = ' ...
mm_infor(k).Digitizer];
end
if (isfield(tmpInfo,'Gain'))
mm_infor(k).Gain = tmpInfo.Gain;
data(p).mmData(i).gain = ['Metamorph Gain = ' ...
num2str(tmpInfo.Gain(1)) '(' num2str(tmpInfo.Gain(2)) 'x)'];
end
if (isfield(tmpInfo,'CameraShutter'))
mm_infor(k).CameraShutter = tmpInfo.CameraShutter;
data(p).mmData(i).temp = ['Metamorph Camera Shutter = ' ...
mm_infor(k).CameraShutter];
end
if (isfield(tmpInfo,'ClearCount'))
mm_infor(k).ClearCount = tmpInfo.ClearCount;
data(p).mmData(i).clearCount = ['Metamorph Clear Count = ' ...
num2str(mm_infor(k).ClearCount)];
end
if (isfield(tmpInfo,'ClearMode'))
mm_infor(k).ClearMode = tmpInfo.ClearMode;
data(p).mmData(i).clearMode = ['Metamorph Clear Mode = ' ...
mm_infor(k).ClearMode];
end
if (isfield(tmpInfo,'FramestoAverage'))
mm_infor(k).FramestoAverage = tmpInfo.FramestoAverage;
data(p).mmData(i).frames = ['Metamorph Frame to Average = ' ...
num2str(mm_infor(k).FramestoAverage)];
end
if (isfield(tmpInfo,'TriggerMode'))
mm_infor(k).TriggerMode = tmpInfo.TriggerMode;
data(p).mmData(i).tiggerMode = ['Metamorph Trigger mode = ' ...
mm_infor(k).TriggerMode];
end
if (isfield(tmpInfo,'Temperature'))
mm_infor(k).Temperature = tmpInfo.Temperature;
data(p).mmData(i).temperature = ['Metamorph Temperature mode = '...
num2str(mm_infor(k).Temperature)];
end
% &&& to see what's in mm data - uncomment these two lines
%data(p).mmData(i)
%mm_infor(k)
case '<PlaneInfo>' % ljd - multitif metadata - plane info (8-28-09)
index = i+1;
[tkk, remk] = strtok(token{index}, 13);
equPos = findstr('=',tkk);
subTkk = tkk(equPos(3)+2:end-2);
mm_infor(k).planeInfo = subTkk;
data(p).mmData(i).planeInfo = mm_infor(k).planeInfo;
case '</prop>' % ljd - multitif metadata (9-9-09)
% ignore
case '</custom-prop>' % ljd - multitif metadata (9-9-09)
% ignore
case '</PlaneInfo>' % ljd - multitif metadata (9-9-09)
% ignore
otherwise
% check for <prop and <custom_prop
if (strncmp(tkk,'<prop',5))
% found <prop - extract data
[id, type, value] = decompose(tkk(6:end-1));
mm_infor(k).propid(propCount).id = id;
mm_infor(k).propid(propCount).type = type;
mm_infor(k).propid(propCount).value = value;
data(p).mmData(i).propid(propCount).id = mm_infor(k).propid(propCount).id;
data(p).mmData(i).propid(propCount).type = mm_infor(k).propid(propCount).type;
data(p).mmData(i).propid(propCount).value = mm_infor(k).propid(propCount).value;
propCount = propCount + 1;
elseif (strncmp(tkk,'<custom-prop',12))
% found <custom-prop - extract data
[id, type, value] = decompose(tkk(13:end-1));
mm_infor(k).cpropid(cpropCount).id = id;
mm_infor(k).cpropid(cpropCount).type = type;
mm_infor(k).cpropid(cpropCount).value = value;
data(p).mmData(i).cpropid(cpropCount).id = mm_infor(k).cpropid(cpropCount).id;
data(p).mmData(i).cpropid(cpropCount).type = mm_infor(k).cpropid(cpropCount).type;
data(p).mmData(i).cpropid(cpropCount).value = mm_infor(k).cpropid(cpropCount).value;
cpropCount = cpropCount + 1;
else
% unknown html tag
data(p).mmData(i).unknownStrings = tkk;
end
end
end
end
function info = decodeTkk(tkk)
% function to decode metatdata string
% go to 'Value" section
equPos = findstr('=',tkk);
% extract everything after 'Value'
subTkk = tkk(equPos(3)+2:end-2);
% find number of entries
ampPos = findstr('&#13;&#10;',subTkk);
dims = size(ampPos);
loc = 1;
for i = 1:dims(2)
% pull out metadata entries
mmString = subTkk(loc:ampPos(i)-1);
% output{i} = mmString;
mmProp = mmString(1:strfind(mmString,':')-1);
switch mmProp
case 'Exposure'
info.Exposure = str2double(mmString(10:end-2));
case 'Binning'
tempk = mmString(9:end);
tmp = sscanf(tempk, '%d %c %d')';
info.Binning = tmp([1,3]);
case 'Region'
% Region: 1392 x 1040, offset at (0, 0) -> [1392 1040], [0 0]
[a,b] = strtok(mmString(8:end), ',');
tmp = sscanf(a, '%d %c %d')';
info.Region.Size = tmp([1,3]);
[a,b] = strtok(b, ',');
info.Region.Offset = [str2double(a(end)), str2double(b(2))];
case 'Subtract'
% Subtract: Off -> 0
info.Subtract = ~strcmp(mmString(10:end),'Off');
case 'Digitizer'
% Digitizer: 5MHz -> 5
info.Digitizer = sscanf(mmString(11:end), '%d %*s');
case 'Shading'
% Shading: Off -> 0
info.Shading = ~strcmp(mmString(9:end),'Off');
case 'Gain'
% Gain: Gain 1 (1x) -> 1j
tempk = mmString(strfind(mmString,'(')-1:end);
tmp = sscanf(tempk, '%d %c %d')';
info.Gain = tmp([1,3]);
case 'CameraShutter'
% Camera Shutter: Always Open -> 'AlwaysOpen'
info.CameraShutter = mmString(15:end);
case 'ClearCount'
% Clear Count: 2 -> 2
info.ClearCount = str2num(mmString(12:end));
case 'ClearMode'
% Clear Mode: Normal -> 'Normal'
info.ClearMode = mmString(11:end);
case 'FramestoAverage'
% FramestoAverage: Normal -> 'Normal'
info.FramestoAverage = str2num(mmString(17:end));
case 'TriggerMode'
% Trigger Mode: Normal -> 'Normal'
info.TriggerMode = mmString(13:end);
case 'Temperature'
% Temperature: 20 -> 20
info.Temperature = str2num(mmString(13:end));
otherwise
mmProp;
end
loc = ampPos(i)+18;
end
function [id, type, value] = decompose(propString)
% propString has format id="xxx"type="xxxx"value="xxxx"
typePos = 1;
typePos = findstr('type=',propString);
valuePos = 1;
valuePos = findstr('value=',propString);
id = propString(5:typePos-2);
type = propString(typePos+6:valuePos-2);
value = propString(valuePos+7:end-1);
