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### Files which are part of ActiPASS documentation
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### License
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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.
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**BSD 3-Clause license**
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Copyright (c) 2022, Pasan Hettiarachchi & Peter Johansson.
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All rights reserved.
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Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
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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.
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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.
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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.
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**.
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**BSD 3-Clause License**
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Copyright (c) 2023, Pasan Hettiarachchi and Peter Johansson
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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3. Neither the name of the copyright holder nor the names of its
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contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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# Binary release license
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Read the [License agreement to use for ActiPASS compiled binary releases](https://github.com/Ergo-Tools/ActiPASS/wiki/License-agreement#license-and-usage-agreement)
<figcaption>ActiPASS - a user friendly tool to process thigh-worn accelerometer data</figcaption>
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</figure>
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### About ActiPASS
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ActiPASS is developed by: [Pasan Hettiarachchi](mailto:pasan.hettiarachchi@medsci.uu.se) and [Peter J. Johansson](mailto:peter.johansson@medsci.uu.se)
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at Occupational and Environmental Medicine, Department of Medical Sciences, Uppsala University. [[Magnus Svartengren](mailto:magnus.svartengren@medsci.uu.se)]
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ActiPASS is based on: Acti4 thigh accelerometer activity detection algorithm developed by Jørgen Skotte
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at the National Research Centre for the Working Environment (NFA), Copenhagen, Denmark. [[Andreas Holtermann](mailto:aho@nfa.dk)]
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The development of ActiPASS has partly been funded by [ProPASS Consortium](https://www.propassconsortium.org)
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ActiPASS may not be used for any commercial purposes without written permission from the developers.
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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.
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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.
## Various classifications algorithms used by ActiPASS software
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### License
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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.
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**BSD 3-Clause license**
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Copyright (c) 2022, Pasan Hettiarachchi & Peter Johansson.
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All rights reserved.
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Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
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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.
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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.
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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.
gapL=runLs{2}(indsGap); % lengths of the bouts within the gap
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gapL(ismember(runLs{1}(indsGap),[1,2]))=0; % do not consider sit/lie in the gap (consider only upright)
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gapLAll=sum(gapL); % the total upright time of the gap
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gapLAct=sum(gapL.*ismember(runLs{1}(indsGap),[5,6,7,8,9])); % the total walking/stair/run/other,bicycling time
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ifgapLAll<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
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% after removing the short gap, if a sit bout is adjacent to a lie bout, mark both as lie
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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
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runLs{1}(indsRunSitLie(itr))=1;
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runLs{1}(indsRunSitLie(itr+1))=1;
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runLs{1}(indsGap)=1;
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else
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runLs{1}(indsGap)=runLs{1}(indsRunSitLie(itr)); %mark the gaps with same either sit or lie
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end
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end
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end
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%readjust run length encoding
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if any(diff(runLs{1})==0)
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runLs=rle(rle(runLs));
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end
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%Then expand Lie bouts and very large Sit bouts to adjacent large-sit or lie bouts by allowing a cumulative upright time of lenAktFilt
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% we consider Lie bouts which are bigger than MinLieBt and Sitbouts which are bigger than VLongSitBt
%mark forward and backward bout-runs as 1 (ie.e. Lie). This is just a marker of Bedtime real Activities are not changed
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runLs{1}(goBackI(1:numBts_BK))=1; % mark forward adjacent sit bouts as 1
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runLs{1}(goFwdI(1:numBts_FD))=1; % mark backward adjacent sit bouts as 1
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% also mark the current bout as 1 (Lie). This is because we consider long sit bouts for bedtime
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runLs{1}(indsRunSitLie(itr))=1;
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end
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% recalculate bout-runs by re-running run-length-encoding (in other words run-length-decoding)
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tmpAkt=rle(runLs);
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% filtering out short upright bouts
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% bedLgc=~bwareaopen(tmpAkt~=1,lenAktFilt);
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runLsUR=rle(tmpAkt~=1); % run length encoding of upright bouts
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runLsUR{1}(runLsUR{1}==1& runLsUR{2} <lenAktFilt)=0; % remove short upright bout from encoding (set to zero)
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bedLgc=~rle(runLsUR); % inverse RLE the encoding and invert to find a logical vector of filtered sit/lie
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% filter out one last time by and and considering a minimum of lenLieFilt and VLongSitBt for bedtime
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runLsBL=rle(bedLgc);
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for itr=1:length(runLsBL{1})
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if runLsBL{1}(itr)==1
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if aktFull(runLsBL{3}(itr))==1&& aktFull(runLsBL{4}(itr))==1% if this sit/lie bout starts and ends with lying
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% do-not consider this lying bout because if it's too short
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if runLsBL{2}(itr)<lenLieFilt
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runLsBL{1}(itr)=0;
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end
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else% else if this sit/lie bout does not both starts and ends with lying
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if runLsBL{2}(itr)<max(VLongSitBt,lenLieFilt)
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runLsBL{1}(itr)=0; % do-not consider this lying bout because it's too short
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end
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end
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end
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end
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%do a run-length-decoding and return the betime logical vector
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bedLgc=rle(runLsBL);
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%%scan through the full days to select primary bedtimes.
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runLsBL=rle(bedLgc); % re-do the run-length-encoding (because we changed the encoding above)
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startDay=dateshift(timeFull(1),'start','day'); % if the day starts dayStartMx hours or later starting day is next day, otherwise start day is today
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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
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selDays=startDay:endDay;
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% only consider bedtimes falling within the startDay:endDay
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selBedtms=find(runLsBL{1}==1);
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bdLengths=runLsBL{2}(selBedtms);
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bedStarts=timeFull(runLsBL{3}(selBedtms));
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bedEnds=timeFull(runLsBL{4}(selBedtms));
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bedMidpts=bedStarts+(bedEnds-bedStarts)/2;
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tod_MidPts=timeofday(bedMidpts); % the timeofday of the midpoints as a duration vector
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numChcks=3; % the number of different scoring checks
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% create a scoring matrix to iterate through days and try to flag bedtimes for selection
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selScore=zeros(length(selBedtms),numChcks); % a column vector to hold priority-score of each bedtime
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%score based on the length of the bedtime
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selScore(:,1)=bdLengths/max(bdLengths);
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% score based on whether midpoints of bedtimes falls within 22:00 - 08:00 or 08:00 to 22:00
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