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fca_readfcs.m
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fca_readfcs.m
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function [fcsdat, fcshdr, fcsdatscaled] = fca_readfcs(filename)
% [fcsdat, fcshdr, fcsdatscaled] = fca_readfcs(filename);
%
% Read FCS 2.0 and FCS 3.0 type flow cytometry data file and put the list mode
% parameters to the fcsdat array with size of [NumOfPar TotalEvents].
% Some important header data are stored in the fcshdr structure:
% TotalEvents, NumOfPar, starttime, stoptime and specific info for parameters
% as name, range, bitdepth, logscale(yes-no) and number of decades.
%
% [fcsdat, fcshdr] = fca_readfcs;
% Without filename input the user can select the desired file
% using the standard open file dialog box.
%
% [fcsdat, fcshdr, fcsdatscaled] = fca_readfcs(filename);
% Supplying the third output the fcsdatscaled array contains the scaled
% parameters. It might be useful for logscaled parameters, but no effect
% in the case of linear parameters. The log scaling is the following
% operation for the "ith" parameter:
% fcsdatscaled(:,i) = ...
% 10.^(fcsdat(:,i)/fcshdr.par(i).range*fcshdr.par(i).decade;);
% Ver 2.5
% 2006-2009 / University of Debrecen, Institute of Nuclear Medicine
% Laszlo Balkay
% balkay@pet.dote.hu
%
% 14/08/2006 I made some changes in the code by the suggestion of
% Brian Harms <brianharms@hotmail.com> and Ivan Cao-Berg <icaoberg@cmu.edu>
% (given at the user reviews area of Mathwork File exchage) The program should work
% in the case of Becton EPics DLM FCS2.0, CyAn Summit FCS3.0 and FACSDiva type
% list mode files.
%
% 29/01/2008 Updated to read the BD LSR II file format and including the comments of
% Allan Moser (Cira Discovery Sciences, Inc.)
%
% 24/01/2009 Updated to read the Partec CyFlow format file. Thanks for
% Gavin A Price
%
% if noarg was supplied
if nargin == 0
[FileName, FilePath] = uigetfile('*.*','Select fcs2.0 file');
filename = [FilePath,FileName];
if FileName == 0;
fcsdat = []; fcshdr = [];
return;
end
else
filecheck = dir(filename);
if size(filecheck,1) == 0
hm = msgbox([filename,': The file does not exist!'], ...
'FcAnalysis info','warn');
fcsdat = []; fcshdr = [];
return;
end
end
% if filename arg. only contain PATH, set the default dir to this
% before issuing the uigetfile command. This is an option for the "fca"
% tool
[FilePath, FileNameMain, fext] = fileparts(filename);
FilePath = [FilePath filesep];
FileName = [FileNameMain, fext];
if isempty(FileNameMain)
currend_dir = cd;
cd(FilePath);
[FileName, FilePath] = uigetfile('*.*','Select FCS file');
filename = [FilePath,FileName];
if FileName == 0;
fcsdat = []; fcshdr = [];
return;
end
cd(currend_dir);
end
%fid = fopen(filename,'r','ieee-be');
fid = fopen(filename,'r','b');
fcsheader_1stline = fread(fid,64,'char');
fcsheader_type = char(fcsheader_1stline(1:6)');
%
%reading the header
%
if strcmp(fcsheader_type,'FCS1.0')
hm = msgbox('FCS 1.0 file type is not supported!','FcAnalysis info','warn');
fcsdat = []; fcshdr = [];
fclose(fid);
return;
elseif strcmp(fcsheader_type,'FCS2.0') || strcmp(fcsheader_type,'FCS3.0') % FCS2.0 or FCS3.0 types
fcshdr.fcstype = fcsheader_type;
%Original version does not read position correctly
% FcsHeaderStartPos = str2num(char(fcsheader_1stline(16:18)'));
% FcsHeaderStopPos = str2num(char(fcsheader_1stline(23:26)'));
% FcsDataStartPos = str2num(char(fcsheader_1stline(31:34)'));
% %BEGIN GC: correct the position
empty_space = find(fcsheader_1stline == 32);
I = find(empty_space(2:end) - empty_space(1:end-1) ~= 1);
empty_start = empty_space([1; I+1]);
empty_end = empty_space([I; length(empty_space)]);
FcsHeaderStartPos = str2num(char(fcsheader_1stline(empty_end(1)+1:empty_start(2)-1)'));
FcsHeaderStopPos = str2num(char(fcsheader_1stline(empty_end(2)+1:empty_start(3)-1)'));
FcsDataStartPos = str2num(char(fcsheader_1stline(empty_end(3)+1:empty_start(4)-1)'));
% % END GC
status = fseek(fid,FcsHeaderStartPos,'bof');
fcsheader_main = fread(fid,FcsHeaderStopPos-FcsHeaderStartPos+1,'char');%read the main header
warning off MATLAB:nonIntegerTruncatedInConversionToChar;
fcshdr.filename = FileName;
fcshdr.filepath = FilePath;
% "The first character of the primary TEXT segment contains the
% delimiter" (FCS standard)
if fcsheader_main(1) == 12
mnemonic_separator = 'FF';
else
mnemonic_separator = char(fcsheader_main(1));
end
if mnemonic_separator == '@';% WinMDI
hm = msgbox([FileName,': The file can not be read (Unsupported FCS type: WinMDI histogram file)'],'FcAnalysis info','warn');
fcsdat = []; fcshdr = [];
fclose(fid);
return;
end
fcshdr.TotalEvents = str2num(get_mnemonic_value('$TOT',fcsheader_main, mnemonic_separator));
fcshdr.NumOfPar = str2num(get_mnemonic_value('$PAR',fcsheader_main, mnemonic_separator));
fcshdr.Creator = get_mnemonic_value('CREATOR',fcsheader_main, mnemonic_separator);
for i=1:fcshdr.NumOfPar
i
fcshdr.par(i).name = get_mnemonic_value(['$P',num2str(i),'N'],fcsheader_main, mnemonic_separator);
fcshdr.par(i).name2 = get_mnemonic_value(['$P',num2str(i),'S'],fcsheader_main, mnemonic_separator);
fcshdr.par(i).range = str2num(get_mnemonic_value(['$P',num2str(i),'R'],fcsheader_main, mnemonic_separator));
fcshdr.par(i).bit = str2num(get_mnemonic_value(['$P',num2str(i),'B'],fcsheader_main, mnemonic_separator));
%============== Changed way that amplification type is treated --- ARM ==================
par_exponent_str= (get_mnemonic_value(['$P',num2str(i),'E'],fcsheader_main, mnemonic_separator));
if isempty(par_exponent_str)
% There is no "$PiE" mnemonic in the Lysys format
% in that case the PiDISPLAY mnem. shows the LOG or LIN definition
islogpar = get_mnemonic_value(['P',num2str(i),'DISPLAY'],fcsheader_main, mnemonic_separator);
if length(islogpar)==3 && isequal(islogpar, 'LOG') % islogpar == 'LOG'
par_exponent_str = '5,1';
else % islogpar = LIN case
par_exponent_str = '0,0';
end
end
% fcshdr.par(i).decade = str2num(par_exponent(1));
% if fcshdr.par(i).decade == 0
% fcshdr.par(i).log = 0;
% fcshdr.par(i).logzero = 0;
% else
% fcshdr.par(i).log = 1;
% if (str2num(par_exponent(3)) == 0)
% fcshdr.par(i).logzero = 1;
% else
% fcshdr.par(i).logzero = str2num(par_exponent(3));
% end
% end
par_exponent= str2num(par_exponent_str);
fcshdr.par(i).decade = par_exponent(1);
if fcshdr.par(i).decade == 0
fcshdr.par(i).log = 0;
fcshdr.par(i).logzero = 0;
else
fcshdr.par(i).log = 1;
if (par_exponent(2) == 0)
fcshdr.par(i).logzero = 1;
else
fcshdr.par(i).logzero = par_exponent(2);
end
end
%============================================================================================
end
fcshdr.starttime = get_mnemonic_value('$BTIM',fcsheader_main, mnemonic_separator);
fcshdr.stoptime = get_mnemonic_value('$ETIM',fcsheader_main, mnemonic_separator);
fcshdr.cytometry = get_mnemonic_value('$CYT',fcsheader_main, mnemonic_separator);
fcshdr.date = get_mnemonic_value('$DATE',fcsheader_main, mnemonic_separator);
fcshdr.byteorder = get_mnemonic_value('$BYTEORD',fcsheader_main, mnemonic_separator);
fcshdr.datatype = get_mnemonic_value('$DATATYPE',fcsheader_main, mnemonic_separator);
fcshdr.system = get_mnemonic_value('$SYS',fcsheader_main, mnemonic_separator);
fcshdr.project = get_mnemonic_value('$PROJ',fcsheader_main, mnemonic_separator);
fcshdr.experiment = get_mnemonic_value('$EXP',fcsheader_main, mnemonic_separator);
fcshdr.cells = get_mnemonic_value('$Cells',fcsheader_main, mnemonic_separator);
fcshdr.creator = get_mnemonic_value('CREATOR',fcsheader_main, mnemonic_separator);
else
hm = msgbox([FileName,': The file can not be read (Unsupported FCS type)'],'FcAnalysis info','warn');
fcsdat = []; fcshdr = [];
fclose(fid);
return;
end
%
%reading the events
%
status = fseek(fid,FcsDataStartPos,'bof');
if strcmp(fcsheader_type,'FCS2.0')
if strcmp(mnemonic_separator,'\') || strcmp(mnemonic_separator,'FF')... %ordinary or FacsDIVA FCS2.0
|| strcmp(mnemonic_separator,'/') % added by GAP 1/22/09
if fcshdr.par(1).bit == 16
fcsdat = uint16(fread(fid,[fcshdr.NumOfPar fcshdr.TotalEvents],'uint16')');
if strcmp(fcshdr.byteorder,'1,2')...% this is the Cytomics data
|| strcmp(fcshdr.byteorder, '1,2,3,4') %added by GAP 1/22/09
fcsdat = bitor(bitshift(fcsdat,-8),bitshift(fcsdat,8));
end
elseif fcshdr.par(1).bit == 32
if fcshdr.datatype ~= 'F'
fcsdat = (fread(fid,[fcshdr.NumOfPar fcshdr.TotalEvents],'uint32')');
else % 'LYSYS' case
fcsdat = (fread(fid,[fcshdr.NumOfPar fcshdr.TotalEvents],'float32')');
end
else
bittype = ['ubit',num2str(fcshdr.par(1).bit)];
fcsdat = fread(fid,[fcshdr.NumOfPar fcshdr.TotalEvents],bittype, 'ieee-le')';
end
elseif strcmp(mnemonic_separator,'!');% Becton EPics DLM FCS2.0
fcsdat_ = fread(fid,[fcshdr.NumOfPar fcshdr.TotalEvents],'uint16', 'ieee-le')';
fcsdat = zeros(fcshdr.TotalEvents,fcshdr.NumOfPar);
for i=1:fcshdr.NumOfPar
bintmp = dec2bin(fcsdat_(:,i));
fcsdat(:,i) = bin2dec(bintmp(:,7:16)); % only the first 10bit is valid for the parameter
end
end
fclose(fid);
elseif strcmp(fcsheader_type,'FCS3.0')
if strcmp(mnemonic_separator,'|') % CyAn Summit FCS3.0
fcsdat_ = (fread(fid,[fcshdr.NumOfPar fcshdr.TotalEvents],'uint16','ieee-le')');
fcsdat = zeros(size(fcsdat_));
new_xrange = 1024;
for i=1:fcshdr.NumOfPar
fcsdat(:,i) = fcsdat_(:,i)*new_xrange/fcshdr.par(i).range;
fcshdr.par(i).range = new_xrange;
end
else % ordinary FCS 3.0
fcsdat = fread(fid,[fcshdr.NumOfPar fcshdr.TotalEvents],'float32')';
end
fclose(fid);
end
%
%calculate the scaled events (for log scales)
%
fcsdatscaled = zeros(size(fcsdat));
for i = 1 : fcshdr.NumOfPar
Xlogdecade = fcshdr.par(i).decade;
XChannelMax = fcshdr.par(i).range;
Xlogvalatzero = fcshdr.par(i).logzero;
if ~fcshdr.par(i).log
fcsdatscaled(:,i) = fcsdat(:,i);
else
fcsdatscaled(:,i) = Xlogvalatzero*10.^(double(fcsdat(:,i))/XChannelMax*Xlogdecade);
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function mneval = get_mnemonic_value(mnemonic_name,fcsheader,mnemonic_separator)
if strcmp(mnemonic_separator,'\') || strcmp(mnemonic_separator,'!') ...
|| strcmp(mnemonic_separator,'|') || strcmp(mnemonic_separator,'@')...
|| strcmp(mnemonic_separator, '/') % added by GAP 1/22/08
mnemonic_startpos = findstr(char(fcsheader'),mnemonic_name);
if isempty(mnemonic_startpos)
mneval = [];
return;
end
mnemonic_length = length(mnemonic_name);
mnemonic_stoppos = mnemonic_startpos + mnemonic_length;
next_slashes = findstr(char(fcsheader(mnemonic_stoppos+1:end)'),mnemonic_separator);
next_slash = next_slashes(1) + mnemonic_stoppos;
mneval = char(fcsheader(mnemonic_stoppos+1:next_slash-1)');
elseif strcmp(mnemonic_separator,'FF')
mnemonic_startpos = findstr(char(fcsheader'),mnemonic_name);
if isempty(mnemonic_startpos)
mneval = [];
return;
end
mnemonic_length = length(mnemonic_name);
mnemonic_stoppos = mnemonic_startpos + mnemonic_length ;
next_formfeeds = find( fcsheader(mnemonic_stoppos+1:end) == 12);
next_formfeed = next_formfeeds(1) + mnemonic_stoppos;
mneval = char(fcsheader(mnemonic_stoppos + 1 : next_formfeed-1)');
end