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Commit 7de5fffc authored by Florian Vollrath's avatar Florian Vollrath
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cleaned mybfopenOnlyMetaData and added original authors

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bfmatlab/mybfopenOnlyMetaData.m
+ 86
− 158
View file @ 7de5fffc
function [metadatastruct] = mybfopenOnlyMetaData( fileName, varargin )
function [metadatastruct] = mybfopenOnlyMetaData( fileName)
% Extracts Meta Data from files
% 27.05.2013 (Version 1.0)
% Authors:
% Andre Zeug (zeug.andre@mh-hannover.de)
% Malte Butzlaff (Butzlaff.Malte@mh-hannover.de)
%
% This software is for non-commercial use only.
%% parsing imput parameters
p = inputParser;
p.StructExpand = true; % if we allow parameter structure expanding
%p.CaseSensitivity = false; % enables or disables case-sensitivity when matching entries in the argument list with argument names in the schema. Default, case-sensitive matching is disabled (false).
p.KeepUnmatched = true; % controls whether MATLAB throws an error (false) or not (true) when the function being called is passed an argument that has not been defined in the inputParser schema for this file.
% p.FunctionName = ['mybfopen v.' mybfopen_version ' (' mybfopen_date ')']; % stores a function name that is to be included in error messages that might be thrown in the process of validating input arguments to the function.
p.addParameter('verbose' , true , @(x)(islogical(x) || any(x==[0 1 2])));
p.addParameter('gui' , true , @(x)(islogical(x) || any(x==[0 1 2 3])));
p.addParameter('timestamp' , false , @(x)(isnumeric(x)));
%p.addParamValue('img_first' , false , @(x)(islogical(x) || (isscalar(x) && x>=0 && mod(x,1)==0)));
%p.addParamValue('img_last' , false , @(x)(islogical(x) || (isscalar(x) && x>=0 && mod(x,1)==0)));
p.parse(varargin{:});
par = p.Results;
% setting clock
if par.verbose
if ~par.timestamp
par.timestamp = tic;
end
t1 = toc(par.timestamp); % starts timer for verbose
end
% fprintf('\n')
% if par.verbose; t1 = output(sprintf('mybfopen: Start mybfopen v. %s (%s)!',...
% mybfopen_version ,mybfopen_date), whos, toc(par.timestamp), t1); end
% add unmached structure elements
s = fieldnames(p.Unmatched);
for n=1:length(s)
......@@ -40,22 +30,20 @@ if (nargin == 0)
else
par.fname = fileName; %[pwd '\' fileName]; % require to replace since receive error when fileName contains full path
end
% if par.verbose; t1 = output(sprintf('mybfopen: read file ''%s''',fileName), whos, toc(par.timestamp), t1); end
jPath = javaclasspath('-all');
isLociTools = cellfun(@(x) ~isempty(regexp(x, '.*bioformats_package.jar$', 'once')),jPath);
if ~any(isLociTools);
if ~any(isLociTools)
locipath = which('bioformats_package.jar');
if isempty(locipath)
locipath = fullfile(fileparts(mfilename('fullpath')), 'bioformats_package.jar');
end
assert(exist(locipath, 'file') == 2, 'Cannot automatically locate bioformats_package.jar');
% Add loci_tools to dynamic Java class path
javaaddpath(locipath);
% if par.verbose; t1 = output('mybfopen: added ''bioformats_package.jar'' to java path', whos, toc(par.timestamp), t1); end
% if par.verbose; t1 = output('mybfopen: added ''bioformats_package.jar'' to java path', whos, toc(par.timestamp), t1); end
end
% if par.verbose; t1 = output('mybfopen: generate loci class object', whos, toc(par.timestamp), t1); end
% Create a loci.formats.ReaderWrapper object
r = javaObject('loci.formats.ChannelSeparator', ...
......@@ -64,7 +52,6 @@ r = javaObject('loci.formats.ChannelSeparator', ...
OMEXMLService = javaObject('loci.formats.services.OMEXMLServiceImpl');
r.setMetadataStore(OMEXMLService.createOMEXMLMetadata());
r.setId(par.fname);
% if par.verbose; t1 = output('mybfopen: file opened', whos, toc(par.timestamp), t1); end
% extract metadata table for this series
metadataOME = r.getMetadataStore();
......@@ -75,147 +62,89 @@ iDZ = metadataOME.getPixelsSizeZ(0).getValue();
iDT = metadataOME.getPixelsSizeT(0).getValue();
imageDims = [iDY iDX iDZ iDC iDT];
numImages = r.getImageCount();
% if par.verbose; t1 = output('mybfopen: main parameter read, start data reading', whos, toc(par.timestamp), t1); end
% Get pixel information (type, etc.)
pixelType = r.getPixelType();
bpp = javaMethod('getBytesPerPixel', 'loci.formats.FormatTools', pixelType);
fp = javaMethod('isFloatingPoint', 'loci.formats.FormatTools', pixelType);
sgn = javaMethod('isSigned', 'loci.formats.FormatTools', pixelType);
if sgn
stopHere
end
little = r.isLittleEndian();
% set data format according to bit depth
switch bpp
case 1; classstr = 'uint8';
case 2; classstr = 'uint16';
case 4; classstr = 'uint32';
case 8; classstr = 'uint64';
end
% allocating memory for data
% data = zeros(imageDims, classstr);
% calc bytes per image plane
% imb = bpp*iDX*iDY/1024/1024;
% generate progress bar
% if par.gui,
% h = waitbar(0,'Please wait...','Name','mybfopen: Wait for data reading!');
% iiw = 0; iio = 0; tw = toc(par.timestamp); tr1 = tw;
% end;
% data import loop
% for ii = 1:numImages
% % update waitbar (in steps of 1%)
% if par.gui && 100*ii/numImages>iiw,
% tr = toc(par.timestamp) - tw;
% tre = tr/ii*numImages;
% waitbar(ii/numImages,h,...
% {sprintf('Import frame: %d / %d (%0.0f%%)',ii,numImages,100*ii/numImages);...
% sprintf('data read: % 8.2f MB/s, Time: %02d:%02d / %02d:%02d min',imb*(ii-iio)/(tr-tr1),floor(tr/60),floor(60*(tr/60 - floor(tr/60))),floor(tre/60),floor(60*(tre/60 - floor(tre/60))))});
% iiw = iiw + 1; iio = ii; tr1 = tr;
% end;
% get image
% plane = r.openBytes(ii - 1, 0, 0, iDX, iDY);
% arr = javaMethod('makeDataArray', 'loci.common.DataTools', plane, bpp, fp, little);
% zct = r.getZCTCoords(ii - 1) + 1;
% % store image in matrix
% data(:,:,zct(1),zct(2),zct(3)) = reshape(typecast(arr, classstr),[iDX iDY])';
% end
% if par.gui, delete(h); drawnow; end;
% if par.verbose; t1 = output('mybfopen: data reading finished', whos, toc(par.timestamp), t1); end
%data = reshape(data, imageDims);
%% transfer output
nout = max(nargout,1)-1;
if 1>0,
tt = par.fname;
tte=regexpi(tt,'/|\');
ttp=regexpi(tt,'\.');
if ~isempty(tte)
if any(ttp>tte(end))
tt = tt(tte(end)+1:ttp(end)-1);
else
tt = tt(tte(end)+1:end);
end
end
% if par.verbose; t1 = output('mybfopen: start list metadata reading', whos, toc(par.timestamp), t1); end
%% metadataList
metadataList = r.getGlobalMetadata();
metadataKeys = metadataList.keySet().iterator();
if metadataList.size()>0
% LA files contain no metadatalist
% but Andor iQ and Zeiss ZEN do
iic = 0;
for ii=1:metadataList.size()
iic = iic + 1;
try
key = metadataKeys.nextElement();
info.list{iic,1} = strrep(key,[tt ' '],'');
info.list{iic,2} = metadataList.get(key);
catch
info.list(iic,:)=[];
iic = iic - 1;
end
end
[~,ind] = sort(info.list(:,1));
info.list = info.list(ind,:);
% if par.verbose; t1 = output('mybfopen: metadata list sorted, generate structure', whos, toc(par.timestamp), t1); end
% generate structure out of list info
str = [];
for ii =1:size(info.list,1)
str = getStruckt(str, regexprep(regexprep(regexprep(info.list{ii,1},'\|',' '),'((?!\s)\W)',''),'\s*',' '), info.list{ii,2});
% (?!test)expr => Match expr and do not match test.
% \s: any whitespace character
% \W: Any character that is not alphabetic, numeric, or underscore. (equivalent to [^a-zA-Z_0-9])
end
info.liststr = str;
% if par.verbose; t1 = output('mybfopen: metadata list structure generate, read OME timestamp', whos, toc(par.timestamp), t1); end
tt = par.fname;
tte=regexpi(tt,'/|\');
ttp=regexpi(tt,'\.');
if ~isempty(tte)
if any(ttp>tte(end))
tt = tt(tte(end)+1:ttp(end)-1);
else
info.list{1,1} = 'no key';
info.list{1,2} = 'no value';
info.liststr = 'Empty';
tt = tt(tte(end)+1:end);
end
%% metadataOME
% read timestamp from OME data
Ts = zeros(numImages,1);
try
for nn=1:numImages;
Ts(nn) = metadataOME.getPlaneDeltaT(0,nn-1).value(); %remove .value() when using older versions of bioformats
end
info.Ts = reshape(Ts,[imageDims(3:end)]);
info.TimeStamp = squeeze(info.Ts(1,1,:));%-info.Ts(1,1,1)); % time in seconds
info.TStxt = 'TimeStamp for each frame';
catch
if nn>1
switch nn-1
case iDT
info.Ts = Ts(1:nn-1);
info.TimeStamp = squeeze(info.Ts);
info.TStxt = 'TimeStamp for each timepoint';
case iDT*iDZ
info.Ts = reshape(Ts(1:nn-1),[iDZ iDT]);
info.TimeStamp = squeeze(info.Ts(1,:));%-info.Ts(1,1,1)); % time in seconds
info.TStxt = 'TimeStamp for each z-section and timepoint';
case iDT*iDZ*iDC
info.Ts = reshape(Ts(1:nn-1),[iDC iDZ iDT]);
info.TimeStamp = squeeze(info.Ts(1,1,:));%-info.Ts(1,1,1)); % time in seconds
info.TStxt = 'TimeStamp for each channel, z-section and timepoint';
end
else
info.Ts = 0;
info.TimeStamp = 0;
info.TStxt = 'No TimeStamp found.';
warning('File contains no time information')
end
%% metadataList
metadataList = r.getGlobalMetadata();
metadataKeys = metadataList.keySet().iterator();
if metadataList.size()>0
% LA files contain no metadatalist
% but Andor iQ and Zeiss ZEN do
iic = 0;
for ii=1:metadataList.size()
iic = iic + 1;
try
key = metadataKeys.nextElement();
info.list{iic,1} = strrep(key,[tt ' '],'');
info.list{iic,2} = metadataList.get(key);
catch
info.list(iic,:)=[];
iic = iic - 1;
end
end
info.OME = metadataOME;
varargout(1) = {info};
metadatastruct=info
% if par.verbose; t1 = output('mybfopen: 2nd output transfered', whos, toc(par.timestamp), t1); end
[~,ind] = sort(info.list(:,1));
info.list = info.list(ind,:);
% generate structure out of list info
str = [];
for ii =1:size(info.list,1)
str = getStruckt(str, regexprep(regexprep(regexprep(info.list{ii,1},'\|',' '),'((?!\s)\W)',''),'\s*',' '), info.list{ii,2});
% (?!test)expr => Match expr and do not match test.
% \s: any whitespace character
% \W: Any character that is not alphabetic, numeric, or underscore. (equivalent to [^a-zA-Z_0-9])
end
info.liststr = str;
else
info.list{1,1} = 'no key';
info.list{1,2} = 'no value';
info.liststr = 'Empty';
end
if nout>1,
% parameter list output
varargout(2) = {par};
% if par.verbose; t1 = output('mybfopen: 3rd output transfered', whos, toc(par.timestamp), t1); end
%% metadataOME
% read timestamp from OME data
Ts = zeros(numImages,1);
try
for nn=1:numImages
Ts(nn) = metadataOME.getPlaneDeltaT(0,nn-1).value(); %remove .value() when using older versions of bioformats
end
info.Ts = reshape(Ts,[imageDims(3:end)]);
info.TimeStamp = squeeze(info.Ts(1,1,:));%-info.Ts(1,1,1)); % time in seconds
info.TStxt = 'TimeStamp for each frame';
catch
if nn>1
switch nn-1
case iDT
info.Ts = Ts(1:nn-1);
info.TimeStamp = squeeze(info.Ts);
info.TStxt = 'TimeStamp for each timepoint';
case iDT*iDZ
info.Ts = reshape(Ts(1:nn-1),[iDZ iDT]);
info.TimeStamp = squeeze(info.Ts(1,:));%-info.Ts(1,1,1)); % time in seconds
info.TStxt = 'TimeStamp for each z-section and timepoint';
case iDT*iDZ*iDC
info.Ts = reshape(Ts(1:nn-1),[iDC iDZ iDT]);
info.TimeStamp = squeeze(info.Ts(1,1,:));%-info.Ts(1,1,1)); % time in seconds
info.TStxt = 'TimeStamp for each channel, z-section and timepoint';
end
else
info.Ts = 0;
info.TimeStamp = 0;
info.TStxt = 'No TimeStamp found.';
warning('File contains no time information')
end
end
info.OME = metadataOME;
metadatastruct=info;
% close file
r.close();
% inline function for structure generation from metadatalist
......@@ -236,7 +165,6 @@ r.close();
end
else
if regexp(tt(1:tt_pos(1)-1),'^\d*$') % checks if tt is numerical
%str.(['no' tt(1:tt_pos(1)-1)]) = getStruckt(str, tt(tt_pos(1)+1:end), content);
ttn = ['no' tt(1:tt_pos(1)-1)];
else
ttn = tt(1:tt_pos(1)-1);
......
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