Tracking Data Post Processing Software

for manuscript Social network plasticity decreases disease transmission in a eusocial insect 65;6003;1c

Information:

The repository https://github.com/laurentkeller/anttrackingUNIL contains tools for the processing and analysis of automated tracking data.

Pipeline installation instructions (linux only)

The project contains a cmake build system. Preferably cmake is used, because it allows to install the header files, so the trk-vid-overlay project (which also contains a cmake build system) can be compiled very easily as well. The minimum cmake version required is 3.10, but it might be possible to use an older version. In that case, the first line in the file anttrackingUNIL/CMakeLists.txt needs to be changed accordingly. cmake can be downloaded here: cmake.org or on ubuntu via "sudo apt install cmake". Instructions for compilation without cmake are given below.

With cmake

1. Navigate to the project folder

cd anttrackingUNIL

2. Make and enter build folder

mkdir build
cd build

3. Generate

cmake ..

4. Compile

make

5. Optionally, but recommended if trk-vid-overlay needs to be compiled later on, install the headers and atrkutil library

sudo make install

6. The executables can be found in anttrackingUNIL/build/bin, for usage instructions type for example:

./change_tagid

Without cmake:

1. Download and unzip or clone the repository content (anttrackingUNIL-master.zip file)
2. Create a folder which will hold all executables files (the full path to that folder is later referred to as build)
3. Open a command window and navigate to the anttrackingUNIL-master folder

Installation of main analysis programs

4. Run the following commands:

cd src
mkdir build

g++ -o build/change_tagid change_tagid.cpp exception.cpp utils.cpp datfile.cpp tags3.cpp -I ../inc;
g++ -o build/controldat controldat.cpp datfile.cpp tags3.cpp exception.cpp -I ../inc;
g++ -o build/define_death define_death.cpp exception.cpp datfile.cpp tags3.cpp utils.cpp -I ../inc
g++ -o build/filter_interactions_cut_immobile filter_interactions_cut_immobile.cpp exception.cpp tags3.cpp utils.cpp -I ../inc;
g++ -o build/filter_interactions_no_cut filter_interactions_no_cut.cpp exception.cpp tags3.cpp utils.cpp -I ../inc;
g++ -o build/heatmap3_tofile heatmap3_tofile.cpp datfile.cpp exception.cpp tags3.cpp histogram.cpp statistics.cpp utils.cpp -I ../inc;
g++ -o build/interaction_all_close_contacts interaction_all_close_contacts.cpp exception.cpp tags3.cpp utils.cpp -I ../inc;
g++ -o build/interaction_any_overlap interaction_any_overlap.cpp exception.cpp tags3.cpp utils.cpp -I ../inc;
g++ -o build/interaction_close_front_contacts interaction_close_front_contacts.cpp exception.cpp tags3.cpp utils.cpp -I ../inc;
g++ -o build/time_investment time_investment.cpp exception.cpp utils.cpp plume.cpp datfile.cpp tags3.cpp -I ../inc;
g++ -o build/trackconverter trackconverter_modular.cpp exception.cpp tags3.cpp utils.cpp trackconverter_functions.cpp -I ../inc;
g++ -o build/trajectory trajectory.cpp datfile.cpp exception.cpp tags3.cpp -I ../inc;
g++ -o build/zone_converter zone_converter.cpp exception.cpp utils.cpp plume.cpp datfile.cpp -I ../inc;

5. The executables are then built in the folder anttrackingUNIL/src/build/, for usage instructions type for example:

./change_tagid

Installation of Antorient (linux)

AntOrient is the fruit of a collaboration with Alessandro Crespi and the original sources are hosted on https://github.com/daniellemersch/AntOrient .

Please note, since there are no license for AntOrient yet, the license in this repository (GPLv3) does not apply to AntOrient. It means that you need to ask permission to both copyright holders to use AntOrient.

1. Preliminaries: wxWidgets

You need to install wxWidgets 3.0.0 beforehand. On Ubuntu/Debian, you can do as described here: https://wiki.codelite.org/pmwiki.php/Main/WxWidgets30Binaries#toc2

2. Download the AntOrient sources.

AntOrient sources are accessible thorugh a git submodule.

git submodule update --init

Sources will be downloaded in a new AntOrient subdirectory.

3. Compilation of AntOrient

In the command window, navigate to the Antorient folder, and run the following commands:

cd AntOrient
make clean
make

4. Last step

Copy the executable file named 'datcorr', which was produced within the Antorient folder during step 7, into the build folder

Installation of Plume (windows only)

1. Download the Plume folder on your computer
2. Double-click on the Plume.exe executable