function varargout=rdann(varargin) % % [ann,anntype,subtype,chan,num,comments]=rdann(recordName, annotator, C, N, N0, AT) % % Wrapper to WFDB RDANN: % http://www.physionet.org/physiotools/wag/rdann-1.htm % % NOTE: The WFDB Toolbox uses 0 based index, and MATLAB uses 1 based index. % Due to this difference annotation values ('ann') are shifted inside % this function in order to be compatible with the WFDB native % library. The MATLAB user should leave the indexing conversion to % the WFDB Toolbox. % % Reads a WFDB annotation and returns: % % % ann % Nx1 integer vector of the annotation locations in samples % with respect to the beginning of the record. % To convert this vector to a string of time stamps see WFDBTIME. % % anntype % Nx1 character vector describing the annotation types. % For a list of standard annotation codes used by PhyioNet, see: % http://www.physionet.org/physiobank/annotations.shtml % % subtype % Nx1 integer vector describing annotation subtype. % % chan % Nx1 integer vector describing annotation channel. % % num % Nx1 integer vector describing annotation NUM. % % comments % Nx1 cell of strings describing annotation comments. % % % Required Parameters: % % recorName % String specifying the name of the record in the WFDB path or % in the current directory. % % annotator % String specifying the name of the annotation file in the WFDB path or % in the current directory. % % Optional Parameters are: % % C % An integer scalar. Return only the annotations with chan = C. % N % An integer specifying the sample number at which to stop reading the % record file. Default read all. % N0 % A 1x1 integer specifying the sample number at which to start reading the % annotion file. Default = 1, begining of the record. % % AT % The anntype character. Return only annotations with subtype = S. % Default is empty, which returns all annotations. % % % % **OPTIMIZATION NOTE: This function has been optimized for cases in which % only the annotation sample vector is required, ie for function calls of % the type: % % ann=rdann(recordName, annotator, C, N, N0, AT); % % For these cases, no string parsing is required and the formatting is % done at the Java level, increasing substantially the processing speed. % % % % Written by Ikaro Silva, 2013 % Last Modified: January 4, 2017 % Version 2.1 % Since 0.0.1 % % %Example 1- Read a signal and annotation from PhysioNet's Remote server: %[signal,Fs,tm]=rdsamp('challenge/2013/set-a/a01'); %[ann]=rdann('challenge/2013/set-a/a01','fqrs'); %plot(tm,signal(:,1));hold on;grid on %plot(tm(ann),signal(ann,1),'ro','MarkerSize',4) % %%Example 2- Read annotation from the first 500 samples only % ann=rdann('mitdb/100','atr',[],500); % % %%Example 3- Read annotations with anntype = 'V' only. % annV=rdann('mitdb/100', 'atr', [],[],[],'V'); % % % See also wfdbtime, wrann %endOfHelp persistent javaWfdbExec config if(isempty(javaWfdbExec)) javaWfdbExec=getWfdbClass('rdann'); [~,config]=wfdbloadlib; end %Set default pararamter values % [ann, anntype, subtype, chan, num, comments] = rdann(recordName, annotator, C, N, N0, AT) inputs={'recordName','annotator','C','N','N0','AT'}; outputs={'ann','anntype','subtype','chan','num','comments'}; N=[]; N0=[]; C=[]; AT=[]; for n=1:nargin if(~isempty(varargin{n})) eval([inputs{n} '=varargin{n};']) end end %Remove file extension if present if(length(recordName)>4 && strcmp(recordName(end-3:end),'.dat')) recordName=recordName(1:end-4); end wfdb_argument={'-r',recordName,'-a',annotator}; if(~isempty(N0) && N0>1) %-1 is necessary because WFDB is 0 based indexed. %RDANN expects timestamp, so convert from sample to timestamp start_time=wfdbtime(recordName,N0-1); if(~isempty(start_time{end})) wfdb_argument{end+1}='-f'; wfdb_argument{end+1}=[start_time{1}]; else error(['Could not get record header information to find start time.']) end end if(~isempty(N)) %-1 is necessary because WFDB is 0 based indexed. %RDANN expects timestamp, so convert from sample to timestamp end_time=wfdbtime(recordName,N-1); if(~isempty(end_time{end})) wfdb_argument{end+1}='-t'; wfdb_argument{end+1}=[end_time{1}]; else error(['Could not get record header information to find stop time.']) end end if(~isempty(AT)) wfdb_argument{end+1}='-p'; %-1 is necessary because WFDB is 0 based indexed. wfdb_argument{end+1}=AT; end if(~isempty(C)) wfdb_argument{end+1}='-c '; %-1 is necessary because WFDB is 0 based indexed. wfdb_argument{end+1}=[num2str(C-1)]; end if(nargout ==1) %Optmize the parsing for cases in which we are interested only in the sample number %annotation values wfdb_argument{end+1}='-e'; % Ensure first column is just elapsed time so it can be skipped. ann=javaWfdbExec.execToDoubleArray(wfdb_argument); if(config.inOctave) ann=java2mat(ann); end else %TODO: Improve the parsing of data. To avoid doing this at the ML wrapper %level! The parsing assumes each line starts with a "[" and that not "[" %occurs at the comment. %outputs={ann,anntype,subtype,chan,num,comments}; dataJava=javaWfdbExec.execToStringList(wfdb_argument); data=dataJava.toArray(); N=length(data); ann=zeros(N,1); anntype=[]; % Size to be defined at runtime subtype=zeros(N,1); chan=zeros(N,1); num=zeros(N,1); comments=cell(N,1); str=char(data(1)); if(~isempty(strfind(str,'init: can''t open header for record'))) error(str) end if(~isempty(str) && strcmp(str(1),'[')) % Absolute time stamp. Also possibly a date stamp % right after the timestamp such as: % [00:11:30.628 09/11/1989] 157 N 0 1 0 % but not always. The following case is also possible: % [00:11:30.628] 157 N 0 1 0 % % So we remove the everything between [ * ] prior to parsing for n=1:N str=char(data(n)); if(~isempty(str)) del_str=findstr(str,']'); str(1:del_str)=[]; C=textscan(str,'%d %s %d %d %d',1); ann(n)=C{1}; if(isempty(anntype)) T=size(C{2},2); anntype=zeros(N,T); end CN=length(char(C{2})); anntype(n,1:CN)=char(C{2}); subtype(n)=C{3}; chan(n)=C{4}+1;%Convert to MATLAB indexing if(~isempty(C{5})) num(n)=C{5}; end tabpos=findstr(str,char(9)); if(tabpos) comments{n}=str(tabpos(1)+1:end); end end end else %In this case there is only a relative timestamp such as: % 0:00.355 355 N 0 0 0 str=data(1); if(~isempty(strfind(str,['annopen: can''t read annotator']))) error(str) end for n=1:N str=char(data(n)); if(~isempty(str)) C=textscan(str,'%s %d %s %d %d %d',1); ann(n)=C{2}; if(isempty(anntype)) T=size(C{3}{:},2); anntype=zeros(N,T); end CN=length(C{3}{:}); anntype(n,1:CN)=C{3}{:}; subtype(n)=C{4}; chan(n)=C{5}+1;%Convert to MATLAB indexing if(~isempty(C{6})) num(n)=C{6}; end tabpos=findstr(str,char(9)); if(tabpos) comments{n}=str(tabpos(1)+1:end); end end end end anntype=char(anntype); end ann=ann+1; %Convert to MATLAB indexing for n=1:nargout eval(['varargout{n}=' outputs{n} ';']) end