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NPanalysis.m
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NPanalysis.m
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% Perform non parametric analysis
% generates 5 Excel spreadsheets, one for whole recordings, one for weekdays
% one for weekends, one for work days and one for days off
% modified 9/26/18 to account for possible missing rest column
% modified 11/14/18 to correct bugs relative to weekday/weekend and rest and wear column reading
% modified 5/17/20 corrected a typo line 105
% Copyright © The Brigham and Women's Hospital, Inc. THE BRIGHAM AND
% WOMEN'S HOSPITAL, INC. AND ITS AGENTS RETAIN ALL RIGHTS TO THIS SOFTWARE
% AND ARE MAKING THE SOFTWARE AVAILABLE ONLY FOR SCIENTIFIC RESEARCH
% PURPOSES. THE SOFTWARE SHALL NOT BE USED FOR ANY OTHER PURPOSES, AND IS
% BEING MADE AVAILABLE WITHOUT WARRANTY OF ANY KIND, EXPRESSED OR IMPLIED,
% INCLUDING BUT NOT LIMITED TO IMPLIED WARRANTIES OF MERCHANTABILITY AND
% FITNESS FOR A PARTICULAR PURPOSE. THE BRIGHAM AND WOMEN'S HOSPITAL, INC.
% AND ITS AGENTS SHALL NOT BE LIABLE FOR ANY CLAIMS, LIABILITIES, OR LOSSES
% RELATING TO OR ARISING FROM ANY USE OF THIS SOFTWARE.
% please report bugs and malfunctionings to [email protected]
clc
close all
clear all
warning('off')
scrsz = get(0,'ScreenSize');
PathName = uigetdir(pwd,'Select the folder containing your data files');
PathName2 = uigetdir(pwd,'Select the folder where you want to save your results');
addpath(PathName, PathName2)
datafiles=dir([PathName '\*.xlsx']);
titles=[{'Subject'};{'Numdays'};{'Amplitude (log counts)'};{'RA'};{'L5 midpoint (dec hours)'}; ...
{'M10 midpoint (dec hours)'}; {'L5 (counts)'}; {'M10 (counts)'};...
{'IS1'};{'IS2'};{'IS3'};{'IS4'};{'IS5'};{'IS6'};{'IS8'};{'IS9'}; ...
{'IS10'};{'IS12'};{'IS15'};{'IS16'};{'IS18'};{'IS20'};{'IS24'};{'IS30'};...
{'IS32'};{'IS36'};{'IS40'};{'IS45'};{'IS48'};{'IS60'};{'IV1'};{'IV2'};...
{'IV3'};{'IV4'};{'IV5'};{'IV6'};{'IV8'};{'IV9'};{'IV10'};{'IV12'};...
{'IV15'};{'IV16'};{'IV18'};{'IV20'};{'IV24'};{'IV30'};{'IV32'};{'IV36'};...
{'IV40'};{'IV45'};{'IV48'};{'IV60'};{'Valid Days'};{'TST (min)'};{'TIB (min)'};{'SE (%)'}];
xlswrite ([PathName2 '\Results.xlsx'],titles');
xlswrite ([PathName2 '\ResultsW.xlsx'],titles');
xlswrite ([PathName2 '\ResultsO.xlsx'],titles');
xlswrite ([PathName2 '\ResultsWD.xlsx'],titles');
xlswrite ([PathName2 '\ResultsWE.xlsx'],titles');
names=cell(length(datafiles),1);
data=NaN+zeros(length(datafiles),length(titles)-5); %here I store the results for all the days
dataW=NaN+zeros(length(datafiles),length(titles)-5); %here I store the results for workdays only
dataO=NaN+zeros(length(datafiles),length(titles)-5); %here I store the results for days off only
dataWD=NaN+zeros(length(datafiles),length(titles)-5); %here I store the results for work days only
dataWE=NaN+zeros(length(datafiles),length(titles)-5); %here I store the results for weekends only
D={};
TST={};
TIB={};
SE={};
tic
%%
for j=1:length(datafiles)
xlsxFn=datafiles(j).name;
name=xlsxFn;
display(name);
names{j}=name;
[~,~,tab]=xlsread([PathName '\' xlsxFn]);
% there is an header in the Excel file: if it changes size, change this value
numlineshea=1;
tab(1:numlineshea,:)=[];
% wear column could be 1/0 or w/nw
wearvec=tab(:,11);
if ischar(wearvec{1})
wear=ones(size(wearvec));
for jj=1:length(wearvec)
if ~isempty(strfind(wearvec{jj},'n'))|| ...
~isempty(strfind(wearvec{jj},'N'))
wear(jj)=0;
end
end
else
wear=cell2mat(wearvec);
end
% HANDLE NON-WEAR TIME (PART1)
% eliminate non-wear times at beginning and end
w=1;
while wear(w)==0
w=w+1;
end
ww=length(wear);
while wear(ww)==0
ww=ww-1;
end
tab=tab(w:ww,:);
wear=wear(w:ww,:);
numEntries = size(tab,1);
% assign columns to variables
try
date=datevec(cell2mat(tab(:,2)));
catch
date=datevec(tab(:,2));
end
try
time=datevec(cell2mat(tab(:,3)));
catch
time=datevec(tab(:,3));
end
actigraphy = cell2mat(tab(:,4)); % I am using axis 1
sleepvec=cell2mat(tab(:,10));
weekdayvec=tab(:,12);
work=[];
% sleep column could be 0/1 or W/S
if ischar(sleepvec(1))
sleep=zeros(size(sleepvec));
sleep(strfind(sleepvec','s'))=1;
sleep(strfind(sleepvec','S'))=1;
else
sleep=sleepvec;
end
restexist=0;
if size(tab,2)==14 % we have the rest column
restexist=1;
% I need the rest vector to combine with the sleep/wake vector
restvec=tab(:,14);
rest=ones(size(restvec));
for jj=1:length(restvec)
if ~isempty(strfind(restvec{jj},'n'))|| ...
~isempty(strfind(restvec{jj},'N'))
rest(jj)=0;
end
end
sleep=sleep.*rest;
% REST IS WEAR
wear(rest>0)=1;
end
% weekday/weekend could be 1/0 or day of the week
if ischar(weekdayvec{1})
weekday=ones(size(weekdayvec));
for jj=1:length(weekdayvec)
if ~isempty(strfind(weekdayvec{jj},'Sun')) || ~isempty(strfind(weekdayvec{jj},'Sat')) ...
|| ~isempty(strfind(weekdayvec{jj},'SUN')) || ~isempty(strfind(weekdayvec{jj},'SAT')) ...
|| ~isempty(strfind(weekdayvec{jj},'sun')) || ~isempty(strfind(weekdayvec{jj},'sat'))
weekday(jj)=0;
end
end
else
weekday=cell2mat(weekdayvec);
end
% HANDLE NON-WEAR TIME (PART2)
% replace non-wear with NaN
actigraphy(wear==0)=NaN;
timeInHours=zeros(numEntries,1);
% COMPUTE TIME IN HOURS
date=date(:,1:3);
time=time(:,4:6);
d=date(:,3);
m=date(:,2);
y=date(:,1);
dy=365; %default
dm=30; %default
if numel(unique(m))>1 %we are recording between months
% check if February
if m(1)==2
dm=28;
% check if leap year
if mod(y(1),4)==0
dm=29;
end
elseif any(m(1)==[1,3,5,7,8,10,12])
dm=31;
end
d(find(m==m(end)))=d(find(m==m(end)))+dm;
end
y=y-y(1);
m=m-m(1);
d=d-d(1);
timeInHours=d*24+time(:,1)+time(:,2)/60+time(:,3)/3600;
timeInMinutes=timeInHours*60;
% check that it makes sense
if any(diff(round(timeInMinutes*1000))~=1000)
error('Something wrong in the time/sampling')
break
end
%figure('Name', name, 'Position',...
%[0.05*scrsz(3) 0.05*scrsz(4) 0.7*scrsz(3) 0.7*scrsz(4)],...
%'Color',[1 1 1]);
% SELECT DAYS I WANT TO USE
% whole file
display('Analysis for the whole file')
%ax(1)=subplot(2,3,1);
if restexist==0
rest=NaN(size(sleep));
end
[IS, IV, L5, M10, L5mid, M10mid,RA,Amp,numdays,days,nightsleep,nightrest]=mainNParametricMatlab(timeInHours,actigraphy,sleep,rest);
if restexist==1
TIB{j,1}=num2str(nightrest);
SE{j,1}=num2str(nightsleep./nightrest*100);
else
TIB{j,1}=NaN;
SE{j,1}=NaN;
end
%title('Whole recording')
data(j,1)=numdays;
data(j,2)=Amp;
data(j,3)=RA;
data(j,4)=L5mid;
data(j,5)=M10mid;
data(j,6)=L5;
data(j,7)=M10;
data(j,8:29)=IS;
data(j,30:end)=IV;
clear ('IS', 'IV', 'L5', 'M10', 'L5mid', 'M10mid','RA','Amp','numdays')
D{j,1}=num2str(find(days));
TST{j,1}=num2str(nightsleep);
timeOfDay=mod(timeInHours,24);
% weekdays/weekends
% weekdays
display('Analysis for the weekdays')
inWE=find(weekday==0 & timeOfDay>=7); %weekend
actigraphyWD=actigraphy;
actigraphyWD(inWE)=NaN;
%ax(2)=subplot(2,3,2);
[IS, IV, L5, M10, L5mid, M10mid,RA,Amp,numdays]=mainNParametricMatlab(timeInHours,actigraphyWD,sleep,rest);
%title('Weekdays')
dataWD(j,1)=numdays;
dataWD(j,2)=Amp;
dataWD(j,3)=RA;
dataWD(j,4)=L5mid;
dataWD(j,5)=M10mid;
dataWD(j,6)=L5;
dataWD(j,7)=M10;
dataWD(j,8:29)=IS;
dataWD(j,30:end)=IV;
clear ('IS', 'IV', 'L5', 'M10', 'L5mid', 'M10mid','RA','Amp','numdays')
% weekends
display('Analysis for the weekends')
inWD=find(weekday==1 & timeOfDay>=7); %weekday
actigraphyWE=actigraphy;
actigraphyWE(inWD)=NaN;
%ax(3)=subplot(2,3,3);
[IS, IV, L5, M10, L5mid, M10mid,RA,Amp,numdays]=mainNParametricMatlab(timeInHours,actigraphyWE,sleep,rest);
%title('Weekends')
dataWE(j,1)=numdays;
dataWE(j,2)=Amp;
dataWE(j,3)=RA;
dataWE(j,4)=L5mid;
dataWE(j,5)=M10mid;
dataWE(j,6)=L5;
dataWE(j,7)=M10;
dataWE(j,8:29)=IS;
dataWE(j,30:end)=IV;
clear ('IS', 'IV', 'L5', 'M10', 'L5mid', 'M10mid','RA','Amp','numdays')
% work/off
if isempty(work)
display('No record of workdays and days off present: I will skip this analysis')
dataW(j,:)=NaN;
else
% workdays
display('Analysis for the workdays')
inO=find(work==0); %days off
actigraphyW=actigraphy;
actigraphyW(inO)=NaN;
ax(4)=subplot(2,3,4);
[IS, IV, L5, M10, L5mid, M10mid,RA,Amp,numdays]=mainNParametricMatlab(timeInHours,actigraphyW,sleep);
title('Work Days')
dataW(j,1)=numdays;
dataW(j,2)=Amp;
dataW(j,3)=RA;
dataW(j,4)=L5mid;
dataW(j,5)=M10mid;
dataW(j,6)=L5;
dataW(j,7)=M10;
dataW(j,8:29)=IS;
dataW(j,30:end)=IV;
clear ('IS', 'IV', 'L5', 'M10', 'L5mid', 'M10mid','RA','Amp','numdays')
% days off
display('Analysis for the days off')
inW=find(work); %workdays
actigraphyO=actigraphy;
actigraphyO(inW)=NaN;
ax(5)=subplot(2,3,5);
[IS, IV, L5, M10, L5mid, M10mid,RA,Amp,numdays]=mainNParametricMatlab(timeInHours,actigraphyO,sleep);
title('Days Off')
dataO(j,1)=numdays;
dataO(j,2)=Amp;
dataO(j,3)=RA;
dataO(j,4)=L5mid;
dataO(j,5)=M10mid;
dataO(j,6)=L5;
dataO(j,7)=M10;
dataO(j,8:29)=IS;
dataO(j,30:end)=IV;
clear ('IS', 'IV', 'L5', 'M10', 'L5mid', 'M10mid','RA','Amp','numdays')
%save paramfile.mat names data dataWD dataWE dataW dataO
end
end
xlswrite ([PathName2 '\Results.xlsx'],names,['A2:A', num2str(length(names)+1)]);
xlswrite ([PathName2 '\Results.xlsx'],data,['B2:AZ', num2str(length(names)+1)]);
xlswrite ([PathName2 '\Results.xlsx'],D,['BA2:BA', num2str(length(names)+1)]);
xlswrite ([PathName2 '\Results.xlsx'],TST,['BB2:BB', num2str(length(names)+1)]);
xlswrite ([PathName2 '\Results.xlsx'],TIB,['BC2:BC', num2str(length(names)+1)]);
xlswrite ([PathName2 '\Results.xlsx'],SE,['BD2:BD', num2str(length(names)+1)]);
xlswrite ([PathName2 '\ResultsWD.xlsx'],names,['A2:A', num2str(length(names)+1)]);
xlswrite ([PathName2 '\ResultsWD.xlsx'],dataWD,['B2:AZ', num2str(length(names)+1)]);
xlswrite ([PathName2 '\ResultsWE.xlsx'],names,['A2:A', num2str(length(names)+1)]);
xlswrite ([PathName2 '\ResultsWE.xlsx'],dataWE,['B2:AZ', num2str(length(names)+1)]);
xlswrite ([PathName2 '\ResultsW.xlsx'],names,['A2:A', num2str(length(names)+1)]);
xlswrite ([PathName2 '\ResultsW.xlsx'],dataW,['B2:AZ', num2str(length(names)+1)]);
xlswrite ([PathName2 '\ResultsO.xlsx'],names,['A2:A', num2str(length(names)+1)]);
xlswrite ([PathName2 '\ResultsO.xlsx'],dataO,['B2:AZ', num2str(length(names)+1)]);
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