Reservoir analysis for BPplus files
License: GNU General Public License v3.0
My research interests include haemodynamics, blood pressure and cardiometabolic health.
I mostly write code for Stata and Matlab.
[ ] Extend scope of calculated variables so they match key Sphygmocor variables. [in progress]
[x ] Improve detection of end of systole
[x] Fix bug in Wf1 and Wf2 peak identification
[ ] better identification of problems with fits
[x] Improve error traps
[x] Fix bugs in figures and cut number of figures to one per dataset
[x] Improve setting default folder (rather than hard coding it) using a json as configuration file
[ ] Minor bug fixes and tidy code including converting script components to function [in progress]
[ ] SBP2 definition
[ ] SV estimation (possible beta 6 feature)
[ ] EF1 analog (possible beta 6 feature)
I have updated to 2024a version of MATLAB.
I now get the following warning
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In kreservoir_v14 (line 152)
In BPfitres_v1 (line 38)
%find crossover point
Nd=length(pd);
np=[2:Nd Nd];
prend=pr(nn:end);
k=find((prend-prd).*(prend(np)-prd(np))<=0);
%% k = 3 15 40 82
%% nn = 55
prr=pr;
prr(nn+k:end)=prd(k+1:end); %% <- this is line 152.
Would you be ok if I extract the code that reads BP+ XML files into a function?
Separation of concerns reduces the effort to maintain code by improving reuse and testability. I have created MATLAB code for comparing BP+ results to invasive recordings for a new validation paper against pressure tip cath recordings. I think it is helpful sharing code that overlaps.
For ease of use, I think it require a "rename" of variables where _ is replaced with . to group variables by the source waveforms.
ss_ai becomes ss.ai, etc. for other supra-systolic variables and waveformsba_sbp becomes ba.sbp, ba_p_all becomes ba.p_all, etc. for intra-arterial brachial variables and waveformsaosbp becomes ao.sbp, ao_p_all becomes ao.p_all, etc. for intra-arterial aortic variables and waveformssamplerate becomes metadata.samplerate, snr becomes metadata.snr etc for other measurement parameters that are not measured.i.e. we end up with a function along the lines of the following that works for both XML formats.
I wanted to ask for your thoughts on this before doing the work and proposing a PR for you repository.
function [data, metadata, ss, ba, ao]=read_BPplus(folder_name, filename)
if not (isfile([folder_name filename]))
return;
end
[data] = xml2struct([folder_name filename]);
% do we extract the measurement ID number?
metadata.id = filename;
%% Read Data from CardioScope legacy xml
if sum(strcmp(fieldnames(data), 'CardioScope')) == 1
% meta data
metadata.algo=data.CardioScope.Results.Result.Attributes.algorithm_revision; % Software algorithm
metadata.samplerate=str2double(data.CardioScope.MeasDataLogger.SampleRate.Text); % sample rate, Hz
metadata.datestring=data.CardioScope.MeasDataLogger.Attributes.datetime; % Date as text string
metadata.guid = data.CardioScope.MeasDataLogger.Attributes.guid;
metadata.snr=str2double(data.CardioScope.Results.Result.SNR.Text); % Signal to noise ratio, dB
metadata.patinet_id = '';
metadata.notes = '';
metadata.RawSuprasystolicPressure=data.CardioScope.MeasDataLogger.SSBuff.Text; % raw base 64 data
% start of pulses.
metadata.baTransitTime = 0.18;
if (contains(data.CardioScope.MeasDataLogger.Attributes.software_version,"038"))
metadata.baTransitTime = 0.06;
end
% extract CardioScope values
% nibp brachial measurement
ba.sbp=str2double(data.CardioScope.MeasDataLogger.Sys.Text); % brachial systolic BP, mmHg
ba.dbp=str2double(data.CardioScope.MeasDataLogger.Dia.Text); % diastolic BP, mmHg
ba.pp=ba.sbp-ba.dbp; % brachial pulse pressure, mmHg
ba.map=str2double(data.CardioScope.MeasDataLogger.Mean.Text); % mean arterial pressure, mmHg
ba.hr=str2double(data.CardioScope.MeasDataLogger.Hr.Text); % heart rate, bpm
% calculated aortic measurements
ao.sbp=str2double(data.CardioScope.Results.Result.aoSys.Text); % cSBP calculated by BP+, mmHg
ao.dbp=str2double(data.CardioScope.Results.Result.aoDia.Text); % cDBP calculated by BP+, mmHg
ao.map=str2double(data.CardioScope.Results.Result.aoMap.Text); % cMAP calculated by BP+, mmHg
ao.pp=ao.sbp-ao.dbp; % cPP calculated by BP+, mmHg
ao.ed = -1; % TODO Calcualte ED
ss.prv=str2double(data.CardioScope.Results.Result.RMSSD.Text); % RMSSD from suprasystolic signal
ss.ai=str2double(data.CardioScope.Results.Result.ssAI.Text); % AI from suprasystolic signal
ss.dpdt=str2double(data.CardioScope.Results.Result.ssDpDtMax.Text); % dp/dt from suprasystolic signal in uncorrected units
ss.harm=str2double(data.CardioScope.Results.Result.ssHARM.Text); % Normalized sAI
ss.pp=str2double(data.CardioScope.Results.Result.ssPP.Text); % Suprasystolic Pulse Pressure
ss.ppv=str2double(data.CardioScope.Results.Result.ssPPV.Text); % Suprasystolic Pulse Pressure Variation, %
ss.RWTTFoot=str2double(data.CardioScope.Results.Result.ssRWTTFoot.Text); % reflected wave transit time from foot of suprasystolic signal
ss.RWTTPeak=str2double(data.CardioScope.Results.Result.ssRWTTPeak.Text); % reflected wave transit time from peak of suprasystolic signal
ss.sep=str2double(data.CardioScope.Results.Result.ssSEP.Text); % Systolic ejection period, s
ss.Tn=split(data.CardioScope.Results.Result.ssAverageBeatPointsIdxs.Text,','); % Times of characteristic points?
%% brachial rhythm
ba.p_all=str2double(split(data.CardioScope.Results.Result.baEstimate.Text,','));
%% suprasystolic rhythm, average beat & start of pulses.
ss.p_all=[]; % not scaled to arterial mmHg
ss.pulseStartIndexes=str2double(split(data.CardioScope.Results.Result.ssBeatStartIdxs.Text,','));
ss.p_av = str2double(split(data.CardioScope.Results.Result.ssAverageBeat.Text,',')); % not scaled to arterial mmHg
ss.averagePulsePointsIndexes=str2double(split(data.CardioScope.Results.Result.ssAverageBeatPointsIdxs.Text,','));
%% aortic rhythm, average beat & start of pulses.
ao.p_all=str2double(split(data.CardioScope.Results.Result.aoEstimate.Text,','));
ao.pulseStartIndexes=str2double(split(data.CardioScope.Results.Result.cPulseStartIndexes.Text,','));
ao.p_av = str2double(split(data.CardioScope.Results.Result.aoAverageBeat.Text,','));
ao.averagePulsePointsIndexes=str2double(split(data.CardioScope.Results.Result.cAveragePulsePointsIndexes.Text,','));
%% aortic average beat, ao_p_av
a0=str2double(split(data.CardioScope.Results.Result.aoAverageBeat.Text,','));
% create a double beat' to deal with the errors in definition of dbp
a=[a0; a0];
plot(a);
% identify start and end of beat as minima
[~, locmin1]=min(a);
[~, locmin2]=min(a(locmin1+50:end));
locmin2=locmin2+locmin1+50;
%plot(a(locmin1:locmin2));
% filter derivative of new beat with SG to get rid of kinks at or around join
aa = sgolayfilt(diff(a),Npoly,Frame); % filter the derivative - order and framelen defined above
a1=cumsum(aa)-min(cumsum(aa))+min(a); % reconstruct
ao.p_av =a1(locmin1:locmin2-1)'; % crop to cycle
clear a0 a aa a1 locmin1 locmin2;
ao.offset = round(baTransitTime * metadata.samplerate);
ss.beatStartIdxs=str2double(split(data.CardioScope.Results.Result.ssBeatStartIdxs.Text,','));
ao.pulseStartIndexes = ss.beatStartIdxs - ao.offset;
for i = 1:length(ao.pulseStartIndexes)
if ao.pulseStartIndexes(i)<0
ao.pulseStartIndexes(i)=0;
end
end
else
%% Read Data from BPplus xml
metadata.algo=data.BPplus.Results.Result.Attributes.algorithm_revision; % Software algorithm
metadata.samplerate=str2double(data.BPplus.MeasDataLogger.SampleRate.Text); % sample rate, Hz
metadata.datestring=data.BPplus.MeasDataLogger.Attributes.datetime; % Date as text string
metadata.guid = data.BPplus.MeasDataLogger.Attributes.guid;
metadata.snr=str2double(data.BPplus.Results.Result.SNR.Text); % Signal to noise ratio, dB
metadata.RawSuprasystolicPressure=data.BPplus.MeasDataLogger.RawSuprasystolicPressure.Text; % raw base 64 data
% extract BPplus values
ba.sbp=str2double(data.BPplus.MeasDataLogger.Sys.Text); % brachial systolic BP, mmHg
ba.dbp=str2double(data.BPplus.MeasDataLogger.Dia.Text); % diastolic BP, mmHg
ba.pp=ba.sbp-ba.dbp; % brachial pulse pressure, mmHg
ba.map=str2double(data.BPplus.MeasDataLogger.Map.Text); % mean arterial pressure, mmHg
ba.hr=str2double(data.BPplus.MeasDataLogger.Pr.Text); % heart rate, bpm
ao.sbp=str2double(data.BPplus.Results.Result.cSys.Text); % cSBP calculated by BP+, mmHg
ao.dbp=str2double(data.BPplus.Results.Result.cDia.Text); % cDBP calculated by BP+, mmHg
ao.map=str2double(data.BPplus.Results.Result.cMap.Text); % cDBP calculated by BP+, mmHg
ao.pp=ao.sbp-ao.dbp; % cPP calculated by BP+, mmHg
ao.ed=str2double(data.BPplus.Results.Result.cST.Text)/1000; % cST calculated by BP+, ms, duration of systole
ss.prv=str2double(data.BPplus.Results.Result.sPRV.Text); % RMSSD from suprasystolic signal
ss.ai=str2double(data.BPplus.Results.Result.sAI.Text); % AI from suprasystolic signal
ss.dpdt=str2double(data.BPplus.Results.Result.sDpDtMax.Text); % dp/dt from suprasystolic signal in uncorrected units
%ssHARM= Can be calculated from sAI if needed
ss.pp=str2double(data.BPplus.Results.Result.sPP.Text); % Suprasystolic Pulse Pressure in the Cuff, mmHg (PP in cuff is small)
ss.ppv=str2double(data.BPplus.Results.Result.sPPV.Text); % Pulse pressure variation, % [?]
ss.RWTTFoot=str2double(data.BPplus.Results.Result.sRWTTFoot.Text); % reflected wave transit time from foot of suprasystolic signal
ss.RWTTPeak=str2double(data.BPplus.Results.Result.sRWTTPeak.Text); % reflected wave transit time from peak of suprasystolic signal
ss.sep=str2double(data.BPplus.Results.Result.sSEP.Text)/1000; % Systolic ejection period, s
ss.Tn=split(data.BPplus.Results.Result.sAveragePulsePointsIndexes.Text,','); % Times of characteristic points?
%% brachial rhythm
ba.p_all=str2double(split(data.BPplus.Results.Result.baEstimate.Text,','));
%% suprasystolic rhythm and average beat
ss.p_all=str2double(split(data.BPplus.Results.Result.sBaseLined.Text,',')); % not scaled to arterial mmHg
ss.pulseStartIndexes=str2double(split(data.BPplus.Results.Result.sPulseStartIndexes.Text,','));
ss.SelectedPulseIndexes=str2double(split(data.BPplus.Results.Result.sSelectedPulseIndexes.Text,','));
ss.p_av = split(data.BPplus.Results.Result.sAveragePulse.Text,','); % not scaled to arterial mmHg
ss.averagePulsePointsIndexes=str2double(split(data.BPplus.Results.Result.sAveragePulsePointsIndexes.Text,','));
%% aortic rhythm, average beat & start of pulses.
ao.p_all=str2double(split(data.BPplus.Results.Result.cEstimate.Text,','));
ao.pulseStartIndexes=str2double(split(data.BPplus.Results.Result.cPulseStartIndexes.Text,','));
ao.p_av=str2double(split(data.BPplus.Results.Result.cAveragePulse.Text,','))';
ao.averagePulsePointsIndexes=str2double(split(data.BPplus.Results.Result.cAveragePulsePointsIndexes.Text,','));
end
%% categorise quality based on SNR
if metadata.snr>=12
metadata.quality='Excellent';
elseif metadata.snr>=9
metadata.quality='Good';
elseif metadata.snr>=6
metadata.quality='Acceptable';
elseif metadata.snr>0
metadata.quality='Poor';
else
metadata.quality='Unacceptable';
end
end
Version 1 (Beta 4)
Updated documentation to reflect changes in beta 5 - in progress
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