cleaned mybfopenOnlyMetaData and added original authors

bfmatlab/mybfopenOnlyMetaData.m

-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)
@@ -40,11 +30,10 @@ 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');
@@ -55,7 +44,6 @@ if ~any(isLociTools);
     javaaddpath(locipath);
     %     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();
@@ -75,57 +62,8 @@ 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,'\.');
@@ -136,7 +74,7 @@ if 1>0,
         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();
@@ -157,7 +95,6 @@ if 1>0,
     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)
@@ -167,7 +104,6 @@ if 1>0,
         % \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
 else
     info.list{1,1} = 'no key';
     info.list{1,2} = 'no value';
@@ -177,7 +113,7 @@ if 1>0,
 % read timestamp from OME data
 Ts = zeros(numImages,1);
 try
-        for nn=1:numImages;
+    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)]);
@@ -206,16 +142,9 @@ if 1>0,
         warning('File contains no time information')
     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
-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
-end
+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);