function varargout=rdmimic2wave(varargin)
%
% [tm,signal,Fs,recList,sigInfo]=rdmimic2wave(subjectID,clinicalTimeStamp,dataType,beginMinute,endMinute)
%
%
%
% Output Parameters:
%
% tm
% Nx1 vector of doubles representing time in minutes if a match is
% found, otherwise tm is empty. The time of the first index is an offset
% from beginMinute. So that the total duration in minutes is:
%
% tm(end) - tm(1) = endMinute - beginMinute
%
% And the time of the clinical event (clinicalTimeStamp) in the waveform signal is given by
% (to the closest minute):
%
% timeStamp = tm(1) + beginMinute
%
%
% signal
% NxM vector of doubles representing the signals from dataType that
% match the timeStamp. If no match is found an empty matrix is
% returned.
%
% Optional Ouput:
%
% Fs
% A 1x1 double representing the sampling frequency (in Hz).
%
%recList
% A Lx1 double specifying a list of valid subjectIDs or matched record. You can use this
% field to find which IDs are in the matched waveform list (see below). If the
% subjectID is defined in the function signature, recList will be
% equal to the first found matched record if it exists.
%
%
%sigInfo
% A Mx1 structure containing meta information about the waverforms in the 'signal' output.
%
%
% Input Parameters:
%
% subjectID
% A 1x1 Double specifying a valid MIMIC II subject ID. For a list
% of valid subjectID with matched waveform use this to query:
%
% [~,~,~,recList]=rdmimic2wave([],[],dataType);
%
% Once you have a valid subjectID and pass it to RDMIMI2WAVE, recList
% will return the string name of the first matched record if any (empty otherwise).
%
%
% clinicalTimeStamp
% String specifying the clinical time of the event. This string
% should have the following format (as described in
% http://www.physionet.org/physiobank/database/mimic2wdb/matched/) :
%
% 'YYYY-MM-DD-hh-mm'
%
% Where:
% YYYY = surrogate year
% MM = month (01-12)
% DD = day (01-31)
% hh = real hour (00-23)
% mm = minute (00-59)
%
% dataType (Optional)
% String specifying what time of high resolution waveform to fetch.
% Options are: 'numerics' and 'waveform'. Default is 'numerics'.
%
%
% beginMinute (Optional)
% 1x1 Double specifying time in minutes of
% how much of the signal to get before clinicalTimeStamp occured.
% Default is 60 minutes.
%
% endMinute (Optional)
% 1x1 Double specifying time in minutes of
% how much of the signal to get after clinicalTimeStamp occured.
% Default is 60 minutes.
%
%
%
% % Example:
%[tm,signal,Fs,recList,sigInfo]=rdmimic2wave(32805,'2986-12-15-10-00',[],0,2);
%plot(tm,signal(:,2))
%title(['Found data in record: ' recList])
%legend(sigInfo(2).Description)
%
% Written by Ikaro Silva, 2013
% Last Modified: December 1, 2014
%
% Version 1.1
%
% Since 0.9.0
%
%
%
% See also rdsamp, wfdbdesc
%endOfHelp
inputs={'subjectID','clinicalTimeStamp','dataType','beginWindow','endWindow'};
outputs={'tm','signal','Fs','recList','sigInfo'};
subjectID=[];
beginWindow=60; %beginWindow in minutes!
endWindow=60; %endWindow in minutes!
dataType='numerics';
dBName='mimic2wdb/matched/';
tm=[];
signal=[];
Fs=[];
sigInfo=[];
recList=[];
for n=1:nargin
if(~isempty(varargin{n}))
eval([inputs{n} '=varargin{n};']);
end
end
persistent cachedDataType matched_id matched
if(~strcmp(cachedDataType,dataType))
switch (dataType)
case 'numerics'
matched=urlread('http://www.physionet.org/physiobank/database/mimic2wdb/matched/RECORDS-numerics');
%case 'all'
% Dont want to mess around with mixed sample rates yet...
%%matched=urlread('http://www.physionet.org/physiobank/database/mimic2wdb/matched/RECORDS');
case 'waveform'
matched=urlread('http://www.physionet.org/physiobank/database/mimic2wdb/matched/RECORDS-waveforms');
otherwise
error(['Unknow dataType. Options are: ''numerics'', ''all'', or ''waveform''']);
end
cachedDataType=dataType;
%Get patient ID list
matched_id=regexprep(regexp(matched,'(\<s\d\d\d\d\d)','match'),'s','');
for n=1:length(matched_id)
matched_id{n}=str2num(matched_id{n});
end
matched_id=unique(cell2mat(matched_id));
recList=matched_id;
end
if(isempty(subjectID))
%In this case the user is just querying for a list of matched
%records
recList=matched_id;
for n=1:nargout
eval(['varargout{n}=' outputs{n} '']);
end
return
end
%Convert timestam to serial data (in days)
dateFormat='yyyy-mm-dd-HH-MM';
clinicalDateNum=datenum(clinicalTimeStamp,dateFormat);
%Window to include before and after the measurement (in days)
beginTime=clinicalDateNum - (beginWindow/(60*24));
endTime=clinicalDateNum + (endWindow/(60*24));
%If id exists loop through the files to see if any file is within the
%specific time range of the clinial event
matched_pid=find(matched_id==subjectID,1);
if(~isempty(matched_pid))
%Get all records that match the patient and search for a record
%that includes the clinical time
strSubjectID=sprintf('%05d',subjectID);
eval(['recs=regexp(regexp(matched,''(\<s' strSubjectID '.*)'',''match''),''\n'',''split'');']);
recs=recs{:};
N=length(recs);
for n=1:N
recName=recs(n); %File name
thisTimeStamp=regexp(recName,'/s\d\d\d\d\d-','end');
if(isempty(recName{1}))
%Empty name, keep moving...
continue;
end
thisTimeStamp=recName{1,1}(1,thisTimeStamp{1}+1:end);
if(strcmp(thisTimeStamp(end),'n'))
thisTimeStamp(end)=[];
end
%Convert to datenum
thisDateNum=datenum(thisTimeStamp,dateFormat);
%Continue if this record started at or before beginTime
if(thisDateNum <= beginTime)
%Get record length and check its duration
recList=[dBName recName{:}];
sigInfo=wfdbdesc(recList);
Fs=sigInfo(1).SamplingFrequency;
waveLengthSamples=sigInfo(1).LengthSamples;
%Get the starting/ending offsets in samples wrt the beginning of
%the waveform
start_offset=round(Fs*(beginTime-thisDateNum)*24*60*60) + 1;
end_offset=round(Fs*(endTime-thisDateNum)*24*60*60) + 1;
if(end_offset <= waveLengthSamples)
%Found a match. Get the waveform and exit the the search
%Get signal and exit
[signal,Fs,tm]=rdsamp(recList,[],end_offset,start_offset);
break;
end
end %of thisDateNum< beginTime
end %of matched record sublit
end
for n=1:nargout
eval(['varargout{n}=' outputs{n} ';']);
end