Installation instructions
=========================

Dependencies
------------

BIP depends on a number of specific external libraries for running:

- LibTIFF - TIFF Library and Utilities (https://libtiff.gitlab.io/libtiff/)

- FFTW - Fastest Fourier Transform in the West (https://fftw.org/)

- HDF5 - High-performance data management and storage suite (https://www.hdfgroup.org/solutions/hdf5/)

- yaml-cpp - A YAML parser and emitter in C++ (https://github.com/jbeder/yaml-cpp)

If you plan to run PlantSeg training and prediction operators through BIP, you must install Miniconda and PlantSeg. Please refer to PlantSeg installation instructions.

Linux installation: Ubuntu 22.04
--------------------------------

Installing the dependencies
~~~~~~~~~~~~~~~~~~~~~~~~~~~

You need super-user rights to install the required dependencies. We assume here you are under the Ubuntu linux distribution, and that you are listed in the sudo-ers.

Install LibTIFF:

::

   sudo apt install libtiff5

Install FFTW:

::

   sudo apt install libfftw3-dev

Install HDF5:

::

   sudo apt install libhdf5-103-1 libhdf5-cpp-103-1

Install yaml-cpp:

::

   sudo apt install libyaml-cpp0.7

Copying the executable at the right place
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Download the distributed BIP executable from the website. Save the file in a directory, typically ``$HOME/bin``. We recommend to use a directory that is included in your ``$PATH`` environment variable. This way, you can access BIP from any location on your system without having to type the full access path to the executable file.

The ``$HOME/bin`` directory is generally already listed in the ``$PATH`` environment variable. If not, you can add the following lines to your ``$HOME/.profile`` hidden file:

::

   # set PATH so it includes user's private bin if it exists
   if [ -d "$HOME/bin" ] ; then
     PATH="$HOME/bin:$PATH"
   fi

Simplifying the executable filename
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

You can remove the date from the executable filename (this is strongly recommended, unless you have some specific reasons not to do so). This can be done through the graphical user interface of the file navigator, or from a terminal, from example:

::

       cd ~/bin
       mv bip-2025.09.05 bip

Checking and setting execution rights
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Check that you have executable permissions on the BIP file. This can be done from the file navigator, by right-clicking on the file and then going into the Permissions tab, clicking "Allow execution" (under Ubuntu). Alternatively, this can be done by opening a terminal, going into the directory where BIP is installed, and entering the command:

::

   chmod a+x bip

To check that the installation is correct, open a terminal and simply enter:

::

   bip

The command should display BIP usage and the list of available operators.

Linux installation: Ubuntu 24.04
--------------------------------

The procedure is the same as above, except you have to replace ``libtiff5`` by ``libtiff6``, and ``libyaml-cpp0.7`` by ``libyaml-cpp0.8``.

Windows installation
--------------------

Download the distributed archive for Windows from BIP website. Extract the folder contained in this archive to the desired location on your system, typically in ``Program Files``. Add the extracted folder to your ``Path`` environment variable.

To check that the installation is correct, open a command-line interpreter (``cmd.exe``) or command-line shell (``PowerShell`` or ``MSYS2`` shell) and enter:

::

   bip

The command should display BIP usage and the list of available operators.