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added rtMSSD
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v0.08: Replaced root median square of successive differences by root  truncated mean of successive differences (rtMSSD), because the low sampling frequency caused the median to jump.
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@raytut
raytut committed Sep 14, 2020
1 parent 1076ff6 commit 5363536
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107 changes: 83 additions & 24 deletions hera.m
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
%----------------------------------------------------------------
%HERA: Heart Rate Analysis v0.06 beta Feb 2018
%HERA: Heart Rate Analysis v0.07 beta April 2020
%
%(c) 2008-2018 Erno Hermans & Thijs vd Laar
%(c) 2008-2020 Erno Hermans & Thijs vd Laar
%----------------------------------------------------------------

%v0.02: fixed check for wavelet manager
Expand All @@ -14,6 +14,12 @@
% at the center of the figure, and does so much faster.
%v0.06: Added transparency to the red rectangles that indicate
% the rejection period.
%v0.07: Added root median square of successive differences (rMedSSD) as a
% potentially more robust measure of HRV. Updated "collect for output
% to work also with incomplete data.
%v0.08: Replaced root median square of successive differences by root
% truncated mean of successive differences (rtMSSD), because the low sampling
% frequency caused the median to jump.

function varargout = hera(varargin)
% HERA M-file for hera.fig
Expand All @@ -39,7 +45,7 @@

% Edit the above text to modify the response to help hera

% Last Modified by GUIDE v2.5 10-Mar-2013 22:53:12
% Last Modified by GUIDE v2.5 02-Jun-2020 19:27:34

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
Expand Down Expand Up @@ -329,6 +335,7 @@ function hera_save_Callback(hObject, eventdata, handles)
set(handles.hera_upperboundHF, 'String',handles.currentfile.matfile.settings.upperboundHF);
set(handles.hera_preBPM, 'String',handles.currentfile.matfile.outmeasures.preBPM);
set(handles.hera_prerMSSD, 'String',handles.currentfile.matfile.outmeasures.rMSSD);
set(handles.hera_prertMSSD, 'String',handles.currentfile.matfile.outmeasures.rtMSSD);
set(handles.hera_postBPM, 'String',handles.currentfile.matfile.outmeasures.postBPM);
set(handles.hera_LFHFrat, 'String',handles.currentfile.matfile.outmeasures.LFHFratio);
set(handles.hera_LFpower, 'String',handles.currentfile.matfile.outmeasures.LFPower);
Expand Down Expand Up @@ -660,6 +667,7 @@ function hera_clearmatfile_Callback(hObject, eventdata, handles)
handles.currentfile.matfile.upperboundHFIndex = [];
handles.currentfile.matfile.outmeasures.preBPM = [];
handles.currentfile.matfile.outmeasures.rMSSD = [];
handles.currentfile.matfile.outmeasures.rtMSSD = [];
handles.currentfile.matfile.outmeasures.LFPower = [];
handles.currentfile.matfile.outmeasures.HFPower = [];
handles.currentfile.matfile.outmeasures.LFHFratio = [];
Expand Down Expand Up @@ -1638,6 +1646,7 @@ function hera_prereject_Callback(hObject, eventdata, handles)
handles = CalcPreOutMeasures(handles);
set(handles.hera_preBPM, 'String',handles.currentfile.matfile.outmeasures.preBPM);
set(handles.hera_prerMSSD, 'String',handles.currentfile.matfile.outmeasures.rMSSD);
set(handles.hera_prertMSSD, 'String',handles.currentfile.matfile.outmeasures.rtMSSD);

%handles = drawgui(handles);
guidata(hObject, handles);
Expand Down Expand Up @@ -1708,6 +1717,7 @@ function hera_clearprereject_Callback(hObject, eventdata, handles)
handles = CalcPreOutMeasures(handles);
set(handles.hera_preBPM, 'String',handles.currentfile.matfile.outmeasures.preBPM);
set(handles.hera_prerMSSD, 'String',handles.currentfile.matfile.outmeasures.rMSSD);
set(handles.hera_prertMSSD, 'String',handles.currentfile.matfile.outmeasures.rtMSSD);

%Finish
guidata(hObject, handles);
Expand Down Expand Up @@ -1770,6 +1780,13 @@ function hera_clearprereject_Callback(hObject, eventdata, handles)
%Now Calculate rMSSD from SDs
handles.currentfile.matfile.outmeasures.rMSSD = sqrt(mean(SDs.^2));

%20200602: Now also calculate rtMSSD from SDs, using truncated means
%This uses trimmean with 20% of data removed, ie it removes the upper and
%lower 10% of the distribution.
SSDs=SDs.^2;
tMSSDs=trimmean(SSDs,20);
rtMSSD=sqrt(tMSSDs);
handles.currentfile.matfile.outmeasures.rtMSSD = rtMSSD;


%----------------------------------------------------------------
Expand Down Expand Up @@ -1864,6 +1881,7 @@ function hera_insertpeak_Callback(hObject, eventdata, handles)
handles = CalcPreOutMeasures(handles);
set(handles.hera_preBPM, 'String',handles.currentfile.matfile.outmeasures.preBPM);
set(handles.hera_prerMSSD, 'String',handles.currentfile.matfile.outmeasures.rMSSD);
set(handles.hera_prertMSSD, 'String',handles.currentfile.matfile.outmeasures.rtMSSD);

%handles = drawgui(handles);
guidata(hObject, handles);
Expand Down Expand Up @@ -1933,6 +1951,7 @@ function hera_removepeak_Callback(hObject, eventdata, handles)
handles = CalcPreOutMeasures(handles);
set(handles.hera_preBPM, 'String',handles.currentfile.matfile.outmeasures.preBPM);
set(handles.hera_prerMSSD, 'String',handles.currentfile.matfile.outmeasures.rMSSD);
set(handles.hera_prertMSSD, 'String',handles.currentfile.matfile.outmeasures.rtMSSD);

%handles = drawgui(handles);
guidata(hObject, handles);
Expand Down Expand Up @@ -2015,7 +2034,7 @@ function hera_collectoutput_Callback(hObject, eventdata, handles)
end

%Create top line with variable names
outascii = [double('filepath'),9,double('filename'),9,double('IBI_BPM'),9,double('rMSSD'),9,double('wavBPM'),9,double('LFpower'),9,double('HFpower'),9,double('LFHFratio'),13,10];
outascii = [double('filepath'),9,double('filename'),9,double('IBI_BPM'),9,double('rMSSD'),9,double('rtMSSD'),9,double('wavBPM'),9,double('LFpower'),9,double('HFpower'),9,double('LFHFratio'),13,10];
%Load all files and collect the output data
for i=1:size(ffiles,1)

Expand All @@ -2027,28 +2046,45 @@ function hera_collectoutput_Callback(hObject, eventdata, handles)
return
else
cmatfilecontent = load(cmatfile);
if numel(cmatfilecontent.matfile.outmeasures.preBPM == 1) & ...
numel(cmatfilecontent.matfile.outmeasures.rMSSD == 1) & ...
numel(cmatfilecontent.matfile.outmeasures.postBPM == 1) & ...
numel(cmatfilecontent.matfile.outmeasures.LFPower == 1) & ...
numel(cmatfilecontent.matfile.outmeasures.HFPower == 1) & ...
numel(cmatfilecontent.matfile.outmeasures.LFHFratio == 1);
[cpath,cfile,cext]=fileparts(cmatfile);
outascii = [outascii, double(cpath), 9,double(cfile),9];
outascii = [outascii, double(num2str(cmatfilecontent.matfile.outmeasures.preBPM)), 9];
outascii = [outascii, double(num2str(cmatfilecontent.matfile.outmeasures.rMSSD)), 9];
outascii = [outascii, double(num2str(cmatfilecontent.matfile.outmeasures.postBPM)), 9];
outascii = [outascii, double(num2str(cmatfilecontent.matfile.outmeasures.LFPower)), 9];
outascii = [outascii, double(num2str(cmatfilecontent.matfile.outmeasures.HFPower)), 9];
outascii = [outascii, double(num2str(cmatfilecontent.matfile.outmeasures.LFHFratio)), 13, 10];

clear cmatfilecontent

else

msgbox(['The file: ',cfile,' has not been fully processed. Finish processing this file first before collecting output.']);
return
%Update 20200415: make sure collect for output works with missing
%fields, including rtMSSD
%For each field, check if it exists and if not make an empty one
if ~isfield(cmatfilecontent.matfile.outmeasures,'preBPM')
cmatfilecontent.matfile.outmeasures.preBPM=[];
end
if ~isfield(cmatfilecontent.matfile.outmeasures,'rMSSD')
cmatfilecontent.matfile.outmeasures.rMSSD=[];
end
if ~isfield(cmatfilecontent.matfile.outmeasures,'rtMSSD')
cmatfilecontent.matfile.outmeasures.rtMSSD=[];
end
if ~isfield(cmatfilecontent.matfile.outmeasures,'postBPM')
cmatfilecontent.matfile.outmeasures.postBPM=[];
end
if ~isfield(cmatfilecontent.matfile.outmeasures,'LFPower')
cmatfilecontent.matfile.outmeasures.LFPower=[];
end
if ~isfield(cmatfilecontent.matfile.outmeasures,'HFPower')
cmatfilecontent.matfile.outmeasures.HFPower=[];
end
if ~isfield(cmatfilecontent.matfile.outmeasures,'LFHFratio')
cmatfilecontent.matfile.outmeasures.LFHFratio=[];
end

[cpath,cfile,cext]=fileparts(cmatfile);

%Copy the data into the file, and leave empty values empty
outascii = [outascii, double(cpath), 9,double(cfile),9];
outascii = [outascii, double(num2str(cmatfilecontent.matfile.outmeasures.preBPM)), 9];
outascii = [outascii, double(num2str(cmatfilecontent.matfile.outmeasures.rMSSD)), 9];
outascii = [outascii, double(num2str(cmatfilecontent.matfile.outmeasures.rtMSSD)), 9];
outascii = [outascii, double(num2str(cmatfilecontent.matfile.outmeasures.postBPM)), 9];
outascii = [outascii, double(num2str(cmatfilecontent.matfile.outmeasures.LFPower)), 9];
outascii = [outascii, double(num2str(cmatfilecontent.matfile.outmeasures.HFPower)), 9];
outascii = [outascii, double(num2str(cmatfilecontent.matfile.outmeasures.LFHFratio)), 13, 10];

clear cmatfilecontent
end
end

Expand Down Expand Up @@ -2213,3 +2249,26 @@ function hera_exportIBIs_Callback(hObject, eventdata, handles)
function outdata = nanmean_selfmade(indata)

outdata = mean(indata(~isnan(indata)));



function hera_prertMSSD_Callback(hObject, eventdata, handles)
% hObject handle to hera_prertMSSD (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of hera_prertMSSD as text
% str2double(get(hObject,'String')) returns contents of hera_prertMSSD as a double


% --- Executes during object creation, after setting all properties.
function hera_prertMSSD_CreateFcn(hObject, eventdata, handles)
% hObject handle to hera_prertMSSD (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end

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