function [ fio2_held ] = pnFiO2(data)
%PNFIO2 Extract FiO2 at time points associated with a PaO2 or PaCO2
%measurement
% [ fio2 ] = pnFiO2(data) extracts the FiO2 at the time points present in
% the data set. Additionally, it uses sample-and-hold to interpolate the
% FiO2 value at time points associated with PaO2 or PaCO2 measurements in
% the data. The interpolation used the following rules:
% If the patient was never on a mv then FiO2 was always = 1.
% If the patient was on a mechanical ventilation:
% If the first FiO2 when vented was missing then it was set = 1.
% If a subsequent FiO2 was missing, then the value before it was
% carried forward.
%
% Inputs:
% data - Cell array of data inputs in standard format:
% Column 1 - Subject IDs
% Column 2 - Time stamp vectors for each subject
% Column 3 - Feature name vectors for each subject
% Column 4 - Data value vectors for each subject
% Empty cells indicate no available measurements (missing data).
%
% Outputs:
% fio2 - Cell array of only fio2 data in standard format:
% Column 1 - Subject IDs
% Column 2 - Time stamp vectors for each subject
% Column 3 - Feature name vectors for each subject (only contains
% 'FiO2')
% Column 4 - Data value vectors for each subject
% Empty cells indicate no available measurements (missing data).
%
% Example
% %=== Load data in
% load('data_processed_cell.mat');
%
% %=== Calculate score
% [ fio2 ] = pnFiO2(data);
%
% See also PNEXTRACTFIELD PNLOADTEXTFILESCELL PNIANDREW PNMAIN
% References:
% Physionet Challenge 2012
% http://physionet.org/challenge/2012/
% Copyright 2012 Alistair Johnson
% $LastChangedBy: alistair $
% $LastChangedDate: 2012-04-24 22:39:24 +0100 (Tue, 24 Apr 2012) $
% $Revision: 342 $
% Originally written on GLNXA64 by Alistair Johnson, 24-Apr-2012 16:57:08
% Contact: alistairewj@gmail.com
%=== Extract fields of interest
pao2 = pnExtractField(data,'PaO2');
pco2 = pnExtractField(data,'PaCO2');
fio2 = pnExtractField(data,'FiO2');
mv = pnExtractField(data,'MechVent');
fio2_held = fio2;
%=== Loop through each patient
N = size(pao2,1);
for k=1:N
%=== If PaO2 and PaCO2 are empty, no need to do anything
if isempty(pao2{k,2}) && isempty(pco2{k,2})
continue; % Both missing, no imputation
else
t1 = pao2{k,2}; t2 = pco2{k,2};
t = unique([t1;t2]);
%=== Check MechVent - if empty, FiO2 is 1 always
if isempty(mv{k,2})
% Impute 1 for all PaO2 and PaCO2 entries
fio2_held{k,2} = t;
fio2_held{k,3} = repmat({'FiO2'},numel(t),1);
fio2_held{k,4} = ones(numel(t),1);
elseif isempty(fio2{k,2})
% Impute 1 for all PaO2 and PaCO2 entries
fio2_held{k,2} = t;
fio2_held{k,3} = repmat({'FiO2'},numel(t),1);
fio2_held{k,4} = ones(numel(t),1);
else
%=== Carry forward existing fio2 values
t_held = [fio2{k,2};t];
d_held = [fio2{k,4};zeros(numel(t),1)];
[t_held,idxSort] = unique(t_held,'first');
d_held = d_held(idxSort);
%=== If the first time measurement point is 0, we must impute
%an FiO2 of 1, as it was not measured
% fprintf('Record %g - Imputing FiO2 value of 1 as earliest PaO2/PaCO2 measurement is before FiO2 measurement.\n',k);
if d_held(1)==0
d_held(1) = 1;
end
%=== Sample and hold values
valind = find(d_held); % non-zero values
d_held(valind(2:end)) = diff(d_held(valind));
d_held = cumsum(d_held);
%=== Push to new cell
fio2_held{k,2} = t_held;
fio2_held{k,3} = repmat({'FiO2'},numel(t_held),1);
fio2_held{k,4} = d_held;
end
end
% %=== Print percent completion
% checkpoint = mod(k,ceil(N*0.20));
% if checkpoint==0
% fprintf('%2.0f%% complete.\n',floor(k/N*100));
% end
end
end