Skip to content

Commit

Permalink
Initial commit
Browse files Browse the repository at this point in the history
  • Loading branch information
Pasan Hettiarachchi committed Mar 2, 2023
0 parents commit ce53524
Show file tree
Hide file tree
Showing 23 changed files with 2,970 additions and 0 deletions.
Binary file added Extra/ActiPASS-Diary-example.xlsx
Binary file not shown.
Binary file added Extra/ActiPASS_Variable-definitions_NewFormat_ActiPASS_Version_1.43.xlsx
Binary file not shown.
Binary file added Extra/ActiPASS_Variable-definitions_NewFormat_ActiPASS_version_1.42.xlsx
Binary file not shown.
20 changes: 20 additions & 0 deletions Extra/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
### Files which are part of ActiPASS documentation

### License

Unless otherwise specified in an individual source file, all source code in this repositery are release under **BSD 3-Clause license**. This means if a different license is included in a source file, that license supersedes the BSD 3-Clause license.

**BSD 3-Clause license**

Copyright (c) 2022, Pasan Hettiarachchi & Peter Johansson.
All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
36 changes: 36 additions & 0 deletions LICENSE.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,36 @@
# Source license

Unless otherwise specified in an individual source file, all source code in this repositery are release under **BSD 3-Clause license**. This means if a different license is included in a source file, that license supersedes **BSD 3-Clause license**.

**BSD 3-Clause License**

Copyright (c) 2023, Pasan Hettiarachchi and Peter Johansson

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

# Binary release license

Read the [License agreement to use for ActiPASS compiled binary releases](https://github.com/Ergo-Tools/ActiPASS/wiki/License-agreement#license-and-usage-agreement)
38 changes: 38 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,38 @@
# ActiPASS
[**About**](#about-actipass)

[**ActiPASS References**](https://github.com/Ergo-Tools/ActiPASS/wiki/ActiPASS-References)

[**Documentation**](https://github.com/Ergo-Tools/ActiPASS/wiki)

[**Open source contributions**](https://github.com/Ergo-Tools/ActiPASS/wiki/Open-source-software-used-by-ActiPASS)

[**Acknowledgements**](https://github.com/Ergo-Tools/ActiPASS/wiki/acknowledgements#actipass-acknowledgements)

[**End-User License Agreement (for compiled binary releases)**](https://github.com/Ergo-Tools/ActiPASS/wiki/License-agreement#license-and-usage-agreement)

[**Source code license**](https://github.com/Ergo-Tools/ActiPASS/blob/main/LICENSE.md)

<figure>
<img src="https://user-images.githubusercontent.com/26480941/170997299-6eda1630-b788-41fc-b83d-005bb2e96335.PNG"
alt="ActiPASS GUI">
<figcaption>ActiPASS - a user friendly tool to process thigh-worn accelerometer data</figcaption>
</figure>


### About ActiPASS
![ActiPASS logo blue](https://user-images.githubusercontent.com/26480941/170669286-19ad73a9-df25-4903-ad07-29746b6ca0c8.PNG)


ActiPASS is developed by: [Pasan Hettiarachchi](mailto:pasan.hettiarachchi@medsci.uu.se) and [Peter J. Johansson](mailto:peter.johansson@medsci.uu.se)
at Occupational and Environmental Medicine, Department of Medical Sciences, Uppsala University. [[Magnus Svartengren](mailto:magnus.svartengren@medsci.uu.se)]

ActiPASS is based on: Acti4 thigh accelerometer activity detection algorithm developed by Jørgen Skotte
at the National Research Centre for the Working Environment (NFA), Copenhagen, Denmark. [[Andreas Holtermann](mailto:aho@nfa.dk)]

The development of ActiPASS has partly been funded by [ProPASS Consortium](https://www.propassconsortium.org)

ActiPASS may not be used for any commercial purposes without written permission from the developers.
Please acknowledge the Developers and NFA as the source of the Software in any publications by referring to [relevant publications](https://github.com/Ergo-Tools/ActiPASS/wiki/ActiPASS-References) about Acti4 /ActiPASS.

ActiPASS is made possible by [these open source software](https://github.com/Ergo-Tools/ActiPASS/wiki/Open-source-software-used-by-ActiPASS) and developers [acknowledge](https://github.com/Ergo-Tools/ActiPASS/wiki/acknowledgements) all who contributed in various means.
20 changes: 20 additions & 0 deletions algorithms/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
## Various classifications algorithms used by ActiPASS software

### License

Unless otherwise specified in an individual source file, all source code in this repositery are release under **BSD 3-Clause license**. This means if a different license is included in a source file, that license supersedes the BSD 3-Clause license.

**BSD 3-Clause license**

Copyright (c) 2022, Pasan Hettiarachchi & Peter Johansson.
All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
257 changes: 257 additions & 0 deletions algorithms/calcBedLgc.m
Original file line number Diff line number Diff line change
@@ -0,0 +1,257 @@
% CALCBEDLGC Calculate bedtime logic using by filtering the activities
%
% %% Inputs %%%%%%%%%%%%%%%%%
% aktFull [double-n] - Full Activity vector given at 1s epoch for all days
% timeFull [datetime-n] - Full time vector given at 1s epochs
% lenAktFilt - upright events shorter than this time will be filtered out (also used for connecting ajacent SitLie bouts)
% lenLieFilt - The bedtime should at least be this amount long (also used for considering long Sit bouts for bedtime)
% VLongSitBt - very long sit bouts to consider for bedtime filtering (4*3600 default)
%
% %% Outputs%%%%%%%%%%%%%%%%%%%%
% bedLgc [double-n] - A logical vector given at 1s epoch representing bedtime status
%
% Copyright (c) 2021, Pasan Hettiarachchi .
% All rights reserved.
%
% Redistribution and use in source and binary forms, with or without
% modification, are permitted provided that the following conditions are met:
% 1. Redistributions of source code must retain the above copyright notice,
% this list of conditions and the following disclaimer.
% 2. Redistributions in binary form must reproduce the above copyright notice,
% this list of conditions and the following disclaimer in the documentation
% and/or other materials provided with the distribution.
% 3. Neither the name of the copyright holder nor the names of its contributors
% may be used to endorse or promote products derived from this software without
% specific prior written permission.
%
% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
% ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
% LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
% CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
% SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
% CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
% ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
% POSSIBILITY OF SUCH DAMAGE.


function [bedLgc,bedFlags]=calcBedLgc(aktFull,timeFull,lenAktFilt,lenLieFilt,VLongSitBt)


MinLieBt=3600; % minimum lying bout to consider for bedtime expanding
MinSitBt=7200; % try to connect sit bouts longer than this to adjacent lying or very-long sit bouts

dayStartMx=hours(9); % how late a measurement can start (for finding primary bedtimes)
dayEndMin=hours(7); % how early a measurement can end (for finding primary bedtimes)
validDay=12; % minimum valid hours criteria for detecting bedtimes (

deltaT=60; % to remove very short gaps between SitLie bouts
% find the bout-runs by running run-length-encoding
runLs=rle(aktFull);

%first filter out very small gaps between large SitLie bouts

indsRunSitLie=find((runLs{1}==1 | runLs{1}==2) & runLs{2}>MinLieBt);

for itr=1:(length(indsRunSitLie)-1)
indsGap=(indsRunSitLie(itr)+1):(indsRunSitLie(itr+1)-1);
gapL=runLs{2}(indsGap); % lengths of the bouts within the gap
gapL(ismember(runLs{1}(indsGap),[1,2]))=0; % do not consider sit/lie in the gap (consider only upright)
gapLAll=sum(gapL); % the total upright time of the gap
gapLAct=sum(gapL.*ismember(runLs{1}(indsGap),[5,6,7,8,9])); % the total walking/stair/run/other,bicycling time
if gapLAll<deltaT || (gapLAll<5*deltaT && gapLAct<deltaT) % if either the total gap length less than 1minute or gap length less than 5min & active time less than 1min

% after removing the short gap, if a sit bout is adjacent to a lie bout, mark both as lie
if runLs{1}(indsRunSitLie(itr))~=runLs{1}(indsRunSitLie(itr+1)) % after removing the short gap, if a sit bout is adjacent to a lie bout, mark both as lie
runLs{1}(indsRunSitLie(itr))=1;
runLs{1}(indsRunSitLie(itr+1))=1;
runLs{1}(indsGap)=1;
else
runLs{1}(indsGap)=runLs{1}(indsRunSitLie(itr)); %mark the gaps with same either sit or lie
end
end

end

%readjust run length encoding
if any(diff(runLs{1})==0)
runLs=rle(rle(runLs));
end

%Then expand Lie bouts and very large Sit bouts to adjacent large-sit or lie bouts by allowing a cumulative upright time of lenAktFilt
% we consider Lie bouts which are bigger than MinLieBt and Sitbouts which are bigger than VLongSitBt
indsRunSitLie=find((runLs{1}==1 & runLs{2}>MinLieBt) | (runLs{1}==2 & runLs{2}>max(VLongSitBt,lenLieFilt)));
% iterate through
for itr=1:length(indsRunSitLie)

% find how far back we can search until hitting another SitLie bout
if itr==1
goBackStart=1;
else
goBackStart=indsRunSitLie(itr-1)+1;
end
goBackEnd=indsRunSitLie(itr)-1;

% find how far forward we can search until hitting another SitLie bout
goFwdStart=indsRunSitLie(itr)+1;
if itr==length(indsRunSitLie)
goFwdEnd=length(runLs{1});
else
goFwdEnd=indsRunSitLie(itr+1)-1;
end

%find the forward and backward bouts range
goBackI=goBackEnd:-1:goBackStart;
goFwdI=goFwdStart:goFwdEnd;
% find all bout-runs for backwards and forward search (also flip the backward search bouts-runs)
runL_BK=runLs{2}(goBackI);
runL_FD=runLs{2}(goFwdI);

% do not count NW bouts shorter than lenAktFilt (make the run-length zero)
zeroBK=runLs{1}(goBackI)==0 & runL_BK<lenAktFilt;
zeroFD=runLs{1}(goFwdI)==0 & runL_FD<lenAktFilt;

% do not count sit bouts larger than MinSitBt
zeroBK=zeroBK | (runLs{1}(goBackI)==2 & runL_BK>MinSitBt);
zeroFD=zeroFD | (runLs{1}(goFwdI)==2 & runL_FD>MinSitBt);

% also need to consider sit bouts larger than MinLieBt and also close to alie bout. How to do this?

% do not count all lie bouts in forward or backward search
zeroBK=zeroBK | runLs{1}(goBackI)==1;
zeroFD=zeroFD | runLs{1}(goFwdI)==1;

% make the effectiverun lengths of ignored bouts (Nw, sit and Lie) to zero
runL_BK(zeroBK)=0;
runL_FD(zeroFD)=0;

% find the cumulative bout-runs of forward and backward search
cumSum_BK=cumsum(runL_BK);
cumSum_FD=cumsum(runL_FD);

% stop the search when sum of upright, short-sit or short-NW time reach lenAktFilt and stop at sit, lie only
numBts_BK=find(cumSum_BK<lenAktFilt & runL_BK==0,1,'last');
numBts_FD=find(cumSum_FD<lenAktFilt & runL_FD==0,1,'last');

% % find the edge of forward and backward searches (can only be a Lie bout or a large-sit or NW bout)
% numBts_BK=find(runL_BK(1:numBts_BK)==0,1,'last');
% numBts_FD=find(runL_FD(1:numBts_FD)==0,1,'last');

%mark forward and backward bout-runs as 1 (ie.e. Lie). This is just a marker of Bedtime real Activities are not changed
runLs{1}(goBackI(1:numBts_BK))=1; % mark forward adjacent sit bouts as 1
runLs{1}(goFwdI(1:numBts_FD))=1; % mark backward adjacent sit bouts as 1

% also mark the current bout as 1 (Lie). This is because we consider long sit bouts for bedtime
runLs{1}(indsRunSitLie(itr))=1;
end

% recalculate bout-runs by re-running run-length-encoding (in other words run-length-decoding)
tmpAkt=rle(runLs);

% filtering out short upright bouts
% bedLgc=~bwareaopen(tmpAkt~=1,lenAktFilt);
runLsUR=rle(tmpAkt~=1); % run length encoding of upright bouts
runLsUR{1}(runLsUR{1}==1 & runLsUR{2} < lenAktFilt)=0; % remove short upright bout from encoding (set to zero)
bedLgc=~rle(runLsUR); % inverse RLE the encoding and invert to find a logical vector of filtered sit/lie

% filter out one last time by and and considering a minimum of lenLieFilt and VLongSitBt for bedtime
runLsBL=rle(bedLgc);

for itr=1:length(runLsBL{1})
if runLsBL{1}(itr)==1
if aktFull(runLsBL{3}(itr))==1 && aktFull(runLsBL{4}(itr))==1 % if this sit/lie bout starts and ends with lying
% do-not consider this lying bout because if it's too short
if runLsBL{2}(itr)<lenLieFilt
runLsBL{1}(itr)=0;
end
else % else if this sit/lie bout does not both starts and ends with lying
if runLsBL{2}(itr)<max(VLongSitBt,lenLieFilt)
runLsBL{1}(itr)=0; % do-not consider this lying bout because it's too short
end
end

end
end


%do a run-length-decoding and return the betime logical vector
bedLgc=rle(runLsBL);

%% scan through the full days to select primary bedtimes.
runLsBL=rle(bedLgc); % re-do the run-length-encoding (because we changed the encoding above)

startDay=dateshift(timeFull(1),'start','day'); % if the day starts dayStartMx hours or later starting day is next day, otherwise start day is today
endDay=dateshift(timeFull(end),'start','day'); % if the day ends dayEndMin or earlier last day is last-calander day, otherwise last-day is previous day

selDays=startDay:endDay;

% only consider bedtimes falling within the startDay:endDay
selBedtms=find(runLsBL{1}==1);
bdLengths=runLsBL{2}(selBedtms);
bedStarts=timeFull(runLsBL{3}(selBedtms));
bedEnds=timeFull(runLsBL{4}(selBedtms));
bedMidpts=bedStarts+(bedEnds-bedStarts)/2;
tod_MidPts=timeofday(bedMidpts); % the timeofday of the midpoints as a duration vector
numChcks=3; % the number of different scoring checks

% create a scoring matrix to iterate through days and try to flag bedtimes for selection
selScore=zeros(length(selBedtms),numChcks); % a column vector to hold priority-score of each bedtime

%score based on the length of the bedtime
selScore(:,1)=bdLengths/max(bdLengths);

% score based on whether midpoints of bedtimes falls within 22:00 - 08:00 or 08:00 to 22:00
nightMidPts=tod_MidPts>=hours(22) | tod_MidPts<hours(8);
selScore(nightMidPts,2)=1;
selScore(~nightMidPts,2)=0.5;



% score by iterating through each bedtime
for itr=1:length(selBedtms)
%score based on percentage of lying time within each bedtime
selScore(itr,3)=sum(aktFull(runLsBL{3}(selBedtms(itr)):runLsBL{4}(selBedtms(itr)))==1)/runLsBL{2}(selBedtms(itr));
end

% iterate through each day and score based on number of bedtime-midpoints falling on 16:00 to 16:00 periods
% 2. Mark primary/secondary bedtimes based on a 48h window

bedFlags=zeros(length(selBedtms),1); % the primary/secondary bedtime marker intialised as zeros

% iterate through each day and find primary/secondary bedtimes based on a 48h window
for itrDay=1:length(selDays)
% find bedtimes embedded in a period of 04:00 to 04:00 of the selected day and proportion of inclusion (using midpoint)
startT48h=max(selDays(itrDay)-hours(8),timeFull(1)); endT48h=min(selDays(itrDay)+hours(40),timeFull(end)); % start end times of current 24h window

% find the total valid time within the 48h window (use data from previous iteration when available)

validHrs48h=sum(aktFull(timeFull>=startT48h & timeFull<endT48h)~=0)/3600;

% find how many bedtimes we should look for
numBeds48h=round(validHrs48h/24);

% find bedtimes where it's midpoint is within selected time window
embdBed48h=find(bedMidpts>=startT48h & bedMidpts<endT48h);

if length(embdBed48h)<=numBeds48h
bedFlags(embdBed48h)=1;
else
bedFlags(embdBed48h)=-1;
selScr48h=prod(selScore(embdBed48h,:),2);
[~,indKp]=maxk(selScr48h,numBeds48h);
bedFlags(embdBed48h(indKp))=1;
end
end

bedFlags=[bedFlags,selScore,prod(selScore,2)];

% remove low scoring bedtimes from run-length-encoding
% runLsBL{1}(selBedtms(indDel))=0;

% finaly do a run-length-decoding to derive bedtimes
% bedLgc=rle(runLsBL);
% bedLgc=bwareaopen(bedLgc,lenLieFilt);

end
Loading

0 comments on commit ce53524

Please sign in to comment.