Installation

It is recommended to install fort-myrmidon, py-fort-myrmidon via pip and to install fort-studio using flatpak.

fort-studio through flatpak

Simply adds the following remotes to install fort studio through its appstream identifier io.github.formicidae_tracker.Studio

`bash flatpak remote-add --if-not-exists --user flathub https://dl.flathub.org/repo/flathub.flatpakrepo flatpak remote-add --if-not-exists --user tuleu.science https://packages.tuleu.science/tuleu.science.flatpakrepo flatpak install org.freedesktop.Platform.ffmpeg-full//23.08 flatpak install io.github.formicidae_tracker.Studio `

Warning

If videos fails to load in fort-studio, please make sure that the full ffmpeg version is installed with flatpak install org.freedesktop.Platform.ffmpeg-full//23.08. Unfortunately flatpak does not allow automatic install of extensions.

Note

fort-studio used to be distribued via a snap. This is not maintained anymore.

fort-myrmidon and python bindings

The bindings with it C++ backend can be installed through a wheel.

`bash pip install formicidae-tracker-myrmidon `

Note

Only recent linux distribution are supported at the moment (manylinux_2_28).

Note

fort-myrmidon used to be distribued with conda. This is not supported anymore since version v0.9.0

Installation from source

Dependencies

fort-myrmidon and fort-studio depends on the following libraries:

  • eigen3

  • protobuf

  • tbb >= 2

  • libasio

  • libavutil

  • libavcodec

  • libavformat

  • libswscale

  • GLog ( fort-studio only )

  • Qt 5 ( fort-studio only )

  • libqtcharts ( fort-studio only )

  • pybind11-dev ( Python bindings only )

  • python3-pandas ( Python bindings only )

  • python3-tqdm ( Python bindings only )

  • python3-opencv ( Python bindings only )

Under debian, you can install them with the following command.

`bash sudo apt install libeigen3-dev libprotobuf-dev protobuf-compiler libtbb-dev libasio-dev libavutil-dev libavcodec-dev libavformat-dev libswscale-dev qt6-base-dev libgoogle-glog-dev qt5-qmake libqt5charts5-dev pybind11-dev python3-tqdm python3-pandas python3-opencv `

Including fort-studio to your project

Python

After installing the formicidae-tracker-myrmidon package in an environment, the fort_myrmidon module is available to python in that environment.

Note

The examples in this documentation assumes this module to be included as :

import fort_myrmidon as fm

R

After installing the r-fort-myrmidon package in an environment, the FortMyrmidon package is available to the R version packaged with this environment. The system packaged R will not be able to see nor to use without crashing the FortMyrmidon package.

C++

After installing the libfort-myrmidon package, libraries and header files for fort-myrmidon will be available to the targeted conda environment. The recommanded way is to use CMake to build your project and link with fort-myrmidon.
G

find_package(FortMyrmidon REQUIRED) include_directories(FORT_MYRMIDON_INCLUDE_DIRS) # fort-myrmidon requires at least the c++17 standard set(CMAKE_CXX_STANDARD 17)

# once my-target is created target_link_libraries(my-target ${FORT_MYRMIDON_LIBRARIES})

A pkg-config configuration file is also available, but it is not nicely integrated with conda. Its utilisation should be avoided.

Using rstudio with conda

If you are an rstudio user, you will remark that it will always use the system’s R version instead of the one you installed with conda, which means that it will never be able to find r-fort-myrmidon. Indeed, rstudio will use the first R version found in the PATH, and if you launch it from the system’s menu, it cannot find the version you installed as a user (it is not conda-aware), and defaults to the system’s one. There are two means to circumvent that:

  1. Runs rstudio from a terminal within the right environment (recommended). One can simply use the following commands to activate my-env and run rstudio within it:

    conda activate my-env-name
rstudio

  2. Installs and runs rstudio from conda. It is not recommended as it is a more heavy solution and will make your environments much more complex and time-consuming to solve.