Overview
ilastik Basics
Installation
ilastik FIJI plugin
Startup screen
Data Selection
Data Navigation
Layers
Exporting Output
Batch Processing
Headless Operation
FAQ / Common Problems
Performance tips
ilastik Workflows
Neural Network Classification
Pixel Classification
Trainable Domain Adaptation (beta)
Voxel Segmentation Workflow (beta)
Autocontext
Object Classification
Boundary-based Segmentation with Multicut
Tracking
Density Counting
Carving
IIBoost Synapse Detection
Use Cases
Animal Tracking

Legacy Installation Instructions

Commercial Solver Installation

CPLEX Installation and Setup

Applies to ilastik versions 1.3.0 (cplex 1260), 1.3.2 (cplex 1280), and 1.3.3 (cplex 1290),

Application for Academic License at IBM

IBM CPLEX is a commercial solver which is free for academic use. Details on the application for an academic license, may be found on the IBM Academic Initiative website. Please note that it might take some days until the application gets approved by IBM.

Download IBM CPLEX

Once the license has been approved by IBM, instructions for download will be provided.

The current version of ilastik works with IBM ILOG CPLEX Optimization Studio V12.9. After choosing the appropriate platform, you have to agree with the IBM license. Finally, CPLEX may be downloaded and is ready to install.

Important note: It is not sufficient to download the Trial version of CPLEX since its solver can only handle very small problem sizes. Please make sure, the correct version is downloaded as described here.

The following sections contain platform-specific instructions for CPLEX installation on Windows as well as on Linux and Mac.

Setup on Windows

Run the installer by double clicking the executable that you’ve downloaded.

On Windows, there are typically no further modifications needed after installing CPLEX. After a successful installation, learning the weights in the Tracking with Learning Workflow will be enabled. If it isn’t, something went wrong with the CPLEX installation. To track down the problem, proceed like this:

Make sure that the environment variable CPLEX_STUDIO_DIR129 is set and points to the proper location. You can check this by typing echo %CPLEX_STUDIO_DIR129% at the DOS command prompt. The output should be something like C:\Program Files\IBM\ILOG\CPLEX_Studio129.
Make sure that cplex is in the PATH. Type where cplex at a DOS prompt. It should produce something like C:\Program Files\ibm\ILOG\CPLEX_Studio129\cplex\bin\x64_win64\cplex.exe (the path prefix should match the contents of the CPLEX_STUDIO_DIR129 variable).
Make sure that the directory containing cplex.exe also contains cplex129.dll, ILOG.CPLEX.dll, and ILOG.Concert.dll.

Learning the weights in the Tracking with Learning Workflow should now be enabled. If it isn’t, you may copy the files cplex129.dll, ILOG.CPLEX.dll, and ILOG.Concert.dll (if you can locate them somewhere) to the binary folder of the ilastik installation, usually located at C:\Program Files\ilastik\bin. If it still doesn’t work, please contact us.

Setup on Linux and Mac

On Linux and Mac, the CPLEX installer comes as a commandline executable (cplex-someversion.sh on Linux and cplex-someversion.bin on Mac). To install it, open a terminal and run bash /path/to/your/cplex-someversion.sh (or bash /path/to/your/cplex-someversion.bin on Mac).

Hint: on Mac and most Linux distributions you can drag and drop the installer file into the terminal to get the full path appended to your command line.

CPLEX packages for Linux and Mac do not provide shared versions of all required libraries, but only static variants. In order to enable CPLEX with ilastik, the static libraries have to be converted. Before you can convert your static CPLEX libraries into shared library versions, you need to have a compiler installed on your machine. You can check whether you already have a compiler installed by running the following command in a terminal (open the Terminal app!).

gcc --version

If no compiler is installed, choose what to do depending on your OS version:

For Linux, use your OS package manager (e.g. apt-get) to install the gcc package.
For all OSX < 10.9, so up to Mountain Lion, you need to install XCode from the AppStore. Then you need to go to XCode’s Preferences, to the Downloads tab, and install the command line tools.
For OSX 10.9 Mavericks it suffices to install the command line tools using the following command without installing XCode.
```
xcode-select --install
```
Then you need to accept the XCode licence by running “sudo gcc” once.

Now you can run a script, that will convert your CPLEX static libraries into shared libraries, and install them into the appropriate directory of your ilastik directory. Starting with ilastik-1.1.7, this script can be found in ilastik-1.*.*/ilastik-meta/ilastik/scripts. Prior to that version the script needs to be downloaded manually in the terminal:

wget https://raw.githubusercontent.com/ilastik/ilastik/master/scripts/install-cplex-shared-libs.sh

Navigate to the directory containing the script and execute it:

# navigate to the script location, e.g. /path/to/ilastik-1.*-Linux/ilastik-meta/ilastik/scripts
cd /path/to/script
# Linux:
bash install-cplex-shared-libs.sh /path/to/your/cplex-root-dir /path/to/ilastik-1.*-Linux
# Mac:
bash install-cplex-shared-libs.sh /path/to/your/cplex-root-dir /path/to/ilastik-1.*-OSX.app

In the command above, /path/to/your/cplex-root-dir is the location of your cplex studio installation. It should contain directories named concert and cplex, among others.

Note: The above script installs CPLEX directly into your ilastik installation. Once you’ve done that, you should not distribute your copy of ilastik to others, unless you have a license to distribute CPLEX.

After a successful installation, learning the weights in the Tracking with Learning Workflow will be enabled.