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fca_readfcs.m
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function [fcsdat, fcshdr, fcsdatscaled, fcsdatcomp] = fca_readfcs(filename)
% [fcsdat, fcshdr, fcsdatscaled, fcsdat_comp] = 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 the 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;);
%
%
%[fcsdat, fcshdr, fcsdatscaled, fcsdat_comp] = fca_readfcs(filename);
% In that case the script will calculate the compensated fluorescence
% intensities (fcsdat_comp) if spillover data exist in the header
%
% Ver May/24/2014
% 2006-2014 / University of Debrecen, Institute of Nuclear Medicine
% Laszlo Balkay
%
% History
% 14/08/2006 I made some changes in the code by the suggestion of
% Brian Harms <[email protected]> and Ivan Cao-Berg <[email protected]>
% (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 (GAP)
%
% 20/09/2010 Updated to read the Accuri C6 format file. Thanks for
% Rob Egbert, University of Washington
%
% 07/11/2011 Updated to read Luminex 100 data file. Thanks for
% Ofir Goldberger, Stanford University
%
% 11/05/2013 The fluorescence compensation is implemeted into the code.
% Thanks for Rick Stanton, J. Craig Venter Institute, La Jolla, San Diego
%
% 12/02/2013
% MOre accurate compensation correction and amplification gain scaling is added.
% Thanks for Rachel Finck(RLF); Garry Nolan's lab at Stanford University
% Appropriate byte offset for the data segment is included for large
% file size (100Mbyte>).
% Thanks for Andrea Pagnani(AP) /Politecnico Torino, Human Genetics Foundation
% and RLF
%
% 16/05/2014
% The FCS 3.0 standard enables the mixture of word lengths in the data, this
% upgrade modified the code according to. The linefeed (ASCII code 10) as
% the mnemonic separator was also added.
% Thanks for William Peria /Fred Hutchinson Cancer Research Center
% if noarg was supplied
if nargin == 0
[FileName, FilePath] = uigetfile('*.*','Select fcs2.0 or 3.0 file');
filename = [FilePath,FileName];
if FileName == 0;
fcsdat = []; fcshdr = []; fcsdatscaled= []; fcsdat_comp= [];
return;
end
else
filecheck = dir(filename);
if size(filecheck,1) == 0
hm = msgbox([filename,': The file does not exist!'], ...
'FcAnalysis info','warn');
fcsdat = []; fcshdr = []; fcsdatscaled= []; fcsdat_comp= [];
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 = []; fcsdatscaled= []; fcsdat_comp= [];
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 = []; fcsdatscaled= []; fcsdat_comp= [];
fclose(fid);
return;
elseif strcmp(fcsheader_type,'FCS2.0') || strcmp(fcsheader_type,'FCS3.0') % FCS2.0 or FCS3.0 types
fcshdr.fcstype = fcsheader_type;
FcsHeaderStartPos = str2num(char(fcsheader_1stline(11:18)'));
FcsHeaderStopPos = str2num(char(fcsheader_1stline(19:26)'));
FcsDataStartPos = str2num(char(fcsheader_1stline(27:34)'));
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';
elseif fcsheader_main(1) == 9 % added by RLF August 2010
mnemonic_separator = 'TAB';
elseif fcsheader_main(1) == 10
mnemonic_separator = 'LF';
else
mnemonic_separator = char(fcsheader_main(1));
end
%
% if the file size larger than ~100Mbyte the previously defined
% FcsDataStartPos = 0. In that case the $BEGINDATA parameter stores the correct value
% This option was suggested by AP and RLF
%
if ~FcsDataStartPos
FcsDataStartPos = str2num(get_mnemonic_value('$BEGINDATA',fcsheader_main, mnemonic_separator));
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 = [];fcsdatscaled= []; fcsdat_comp= [];
fclose(fid);
return;
end
fcshdr.TotalEvents = str2num(get_mnemonic_value('$TOT',fcsheader_main, mnemonic_separator));
if fcshdr.TotalEvents == 0
fcsdat = 0;
fcsdatscaled = 0;
return
end
fcshdr.NumOfPar = str2num(get_mnemonic_value('$PAR',fcsheader_main, mnemonic_separator));
% if strcmp(mnemonic_separator,'LF')
% fcshdr.NumOfPar = fcshdr.NumOfPar + 1;
% end
%
fcshdr.Creator = get_mnemonic_value('CREATOR',fcsheader_main, mnemonic_separator);
%%%%%%comp matrix reader added by RLF 12_15_10
comp = get_mnemonic_value('SPILL',fcsheader_main,mnemonic_separator);
if ~isempty(comp)
%%%
compcell=regexp(comp,',','split');
nc=str2double(compcell{1});
fcshdr.CompLabels=compcell(2:nc+1);
fcshdr.CompMat=reshape(str2double(compcell(nc+2:end)'),[nc nc])';
else
fcshdr.CompLabels=[];
fcshdr.CompMat=[];
end
plate = get_mnemonic_value('PLATE NAME',fcsheader_main,mnemonic_separator);
if ~isempty(plate)
fcshdr.plate=plate;
end
%%%%%%%%%%%% RLF
for i=1:fcshdr.NumOfPar
fcshdr.par(i).name = get_mnemonic_value(['$P',num2str(i),'N'],fcsheader_main, mnemonic_separator);
fcshdr.par(i).range = str2num(get_mnemonic_value(['$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 "$PiE" mnemonic in the Lysys format
% in that case the PiDISPLAY mnem. shows the LOG or LIN definition
islogpar = get_mnemonic_value(['P',num2str(i),'DISPLAY'],fcsheader_main, mnemonic_separator);
if strcmp(islogpar,'LOG')
par_exponent_str = '5,1';
else % islogpar = LIN case
par_exponent_str = '0,0';
end
end
par_exponent= str2num(par_exponent_str);
fcshdr.par(i).decade = par_exponent(1);
if fcshdr.par(i).decade == 0
fcshdr.par(i).log = 0;
fcshdr.par(i).logzero = 0;
else
fcshdr.par(i).log = 1;
if (par_exponent(2) == 0)
fcshdr.par(i).logzero = 1;
else
fcshdr.par(i).logzero = par_exponent(2);
end
end
gain_str = get_mnemonic_value(['$P',num2str(i),'G'],fcsheader_main, mnemonic_separator); % added by RLF
if ~isempty(gain_str) % added by RLF
fcshdr.par(i).gain=str2double(gain_str);
else
fcshdr.par(i).gain=1;
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('$BYTEORD',fcsheader_main, mnemonic_separator);
if strcmp(fcshdr.byteorder, '1,2,3,4')
machineformat = 'ieee-le';
elseif strcmp(fcshdr.byteorder, '4,3,2,1')
machineformat = 'ieee-be';
end
fcshdr.datatype = get_mnemonic_value('$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 = []; fcsdatscaled= []; fcsdat_comp= [];
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,'/') || strcmp(mnemonic_separator,'TAB') % added by GAP 1/22/09 %added by RLF 09/02/10
if fcshdr.par(1).bit == 16
fcsdat = (fread(fid,[fcshdr.NumOfPar fcshdr.TotalEvents],'uint16',machineformat)');
fcsdat_orig = uint16(fcsdat);%//
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
new_xrange = 1024;
for i=1:fcshdr.NumOfPar
if fcshdr.par(i).range > 4096
fcsdat(:,i) = fcsdat(:,i)*new_xrange/fcshdr.par(i).range;
fcshdr.par(i).range = new_xrange;
end
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,'|') && strcmp(fcshdr.datatype,'I') % CyAn Summit FCS3.0
fcsdat_ = (fread(fid,[fcshdr.NumOfPar fcshdr.TotalEvents],'uint16',machineformat)');
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
elseif strcmp(mnemonic_separator,'/')
if findstr(lower(fcshdr.cytometry),'accuri') % Accuri C6, this condition added by Rob Egbert, University of Washington 9/17/2010
fcsdat = (fread(fid,[fcshdr.NumOfPar fcshdr.TotalEvents],'int32',machineformat)');
elseif findstr(lower(fcshdr.cytometry),'partec')%this block added by GAP 6/1/09 for Partec, copy/paste from above
fcsdat = uint16(fread(fid,[fcshdr.NumOfPar fcshdr.TotalEvents],'uint16',machineformat)');
%fcsdat = bitor(bitshift(fcsdat,-8),bitshift(fcsdat,8));
elseif findstr(lower(fcshdr.cytometry),'lx') % Luminex data
fcsdat = fread(fid,[fcshdr.NumOfPar fcshdr.TotalEvents],'int32',machineformat)';
fcsdat = mod(fcsdat,1024);
end
else % ordinary FCS 3.0
if strcmp(fcshdr.datatype,'D')
fcsdat = fread(fid,[fcshdr.NumOfPar fcshdr.TotalEvents],'double',machineformat)';
elseif strcmp(fcshdr.datatype,'F')
fcsdat = fread(fid,[fcshdr.NumOfPar fcshdr.TotalEvents],'float32',machineformat)';
elseif strcmp(fcshdr.datatype,'I')
fcsdat = fread(fid,[sum([fcshdr.par.bit]/16) fcshdr.TotalEvents],'uint16',machineformat)'; % sum: William Peria, 16/05/2014
end
end
fclose(fid);
end
%% this is for Ricardo Khouri converting Partec to FacsDIVA_FCS20 format
%% 28/01/2013
save_FacsDIVA_FCS20 = 0;
if strcmp(fcshdr.cytometry ,'partec PAS') && save_FacsDIVA_FCS20
fcsheader_main2 = fcsheader_main;
sep_place = strfind(char(fcsheader_main'),'/');
fcsheader_main2(sep_place) = 12;
fcsheader_1stline2 = fcsheader_1stline;
fcsheader_1stline2(31:34) = double(num2str(FcsHeaderStopPos+1));
fcsheader_1stline2(43:50) = double(' 0');
fcsheader_1stline2(51:58) = double(' 0');
FileSize = length(fcsheader_main2(:))+ length(fcsheader_1stline2(1:FcsHeaderStartPos))+ 2*length(fcsdat_orig(:));
space_char(1:8-length(num2str(FileSize)))= ' ';
fcsheader_1stline2(35:42) = double([space_char,num2str(FileSize)]);
fid2 = fopen([FilePath, FileNameMain,'_', fext],'w','b');
fwrite(fid2,[fcsheader_1stline2(1:FcsHeaderStartPos)],'char');
fwrite(fid2,fcsheader_main2,'char');
fwrite(fid2,fcsdat_orig','uint16');
fclose(fid2);
end
%calculate the scaled events (for log scales)
%RLF added gain division
if nargout>2
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).gain~=1
fcsdatscaled(:,i) = double(fcsdat(:,i))./fcshdr.par(i).gain;
elseif fcshdr.par(i).log
fcsdatscaled(:,i) = Xlogvalatzero*10.^(double(fcsdat(:,i))/XChannelMax*Xlogdecade);
else fcsdatscaled(:,i) = fcsdat(:,i);
end
end
end
if nargout>3 && ~isempty(fcshdr.CompLabels) %RLF. applied to fcsdatscaled rather than fcsdat.
compcols=zeros(1,nc);
colLabels={fcshdr.par.name};
for i=1:nc
compcols(i)=find(strcmp(fcshdr.CompLabels{i},colLabels));
end
fcsdatcomp = fcsdatscaled;
fcsdatcomp(:,compcols) = fcsdatcomp(:,compcols)/fcshdr.CompMat;
else fcsdatcomp=[];
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, '/')
mnemonic_startpos = findstr(char(fcsheader'),[mnemonic_name,mnemonic_separator]);
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)');
elseif strcmp(mnemonic_separator,'TAB') %added by RLF August 2010
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) == 9);
next_formfeed = next_formfeeds(1) + mnemonic_stoppos;
mneval = char(fcsheader(mnemonic_stoppos + 1 : next_formfeed-1)');
elseif strcmp(mnemonic_separator, 'LF') % William Peria, 16/05/2014
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_linefeeds = find( fcsheader(mnemonic_stoppos+1:end) == 10);
next_linefeed = next_linefeeds(1) + mnemonic_stoppos;
mneval = char(fcsheader(mnemonic_stoppos + 1 : next_linefeed-1)');
end