ilastik-build

ilastik-build downloads and compiles all dependencies needed by ilastik (and a few additional ones that are frequently needed for experimentation, such as ipython and matplotlib) and ilastik itself. It builds upon BuildEM, Janelia Farm's build system for the FlyEM project (see there for a description of the underlying philosophy).

It is currently able to do 32-bit and 64-bit builds on Windows 7 or 8 using Microsoft Visual Studio 2010 or 2012.

Usage

Preliminaries:

• Install MS Visual Studio 2010 or 2012 (MSVC Express will not work), git, cmake, and ActiveState perl. perl is not part of ilastik, but needed to compile Qt.
• If you want to build scipy and scikit-learn, MinGW and MSYS are needed to compile Fortran sources. MinGW is also needed for packages that do not support Visual Studio (e.g. libiconv). You must install the MinGW 64-bit (e.g. from http://sourceforge.net/projects/mingwbuilds/files/host-windows/releases/, choose the version 'threads-win32' and exception handling 'sjlj') or 32-bit (e.g. from http://sourceforge.net/projects/mingw/files/Installer/mingw-get-inst/) compiler suite and the MSYS tools (e.g. from http://sourceforge.net/projects/mingw-w64/files/External%20binary%20packages%20%28Win64%20hosted%29/MSYS%20%2832-bit%29/). When the MinGW download is compressed with 7-zip, you need this program for decompression as well. Make sure that MINGW/bin contains gfortran.exe and gendef.exe (64-bit build only), and MSYS/bin contains make.exe, wget.exe, patch.exe, and grep.exe.
• If you want to create an .exe installer, also install NSIS.
• Remove possibly interfering software from your PATH variable (e.g. an existing Python or Qt installation, the MinGW gcc compiler).

Configuration:

• Open Visual Studio's 32-bit or 64-bit DOS command shell. It can usually be found in the Start menu under "Programs->Microsoft Visual Studio 2010->Visual Studio Tools->Visual Studio x64 Win64 Command Prompt" or similar. The choice of shell determines if you create a 32-bit or 64-bit installation. Simply adding cl.exe to your PATH does NOT work because additional settings are required to ensure VisualStudio works properly (for the curious: the VS installation contains a script vcvarsall.bat that is executed at the start of the VisualStudio shell to take care of this).
• Create a directory for the cmake-created build scripts (e.g. ilastik-build/build) and goto this directory:

    % mkdir <build-directory>
    % cd <build-directory>

• Configure the build system (use the generator -G "Visual Studio 11 Win64" if you have Visual Studio 2012, and drop Win64 for a 32-bit build):

    % cmake -G "Visual Studio 10 Win64" -DILASTIK_DEPENDENCY_DIR=<prefix>  <path-to-build-system>

• You have to specify additional command line parameters if you want to include optional packages, see below.

This will create a file ilastik.sln in the <build-directory> that can be opened with Visual Studio. In the above cmake call, <path-to-build-system> is the directory where ilastik-build has been checked out (typically just .. when we are in ilastik-build/build), and <prefix> is the desired path where the dependencies will be installed. The actual installations will be located in the subdirectories <prefix>\bin, <prefix>\lib, <prefix>\include, <prefix>\python, and <prefix>\Qt4. The sources (including cached tar archives and intermediate files) go into <prefix>\src. The ilastik Python modules will be installed into <prefix>\ilastik.

VTK

To include VTK into the build, use:

    % cmake -G "Visual Studio 10 Win64" -DILASTIK_DEPENDENCY_DIR=<prefix> -DWITH_VTK=1  <path-to-build-system>

SciPy

If you want to compile scipy as well, use :

    % cmake -G "Visual Studio 10 Win64" -DILASTIK_DEPENDENCY_DIR=<prefix> -DWITH_SCIPY=1 \
      -DMSYS_PATH=<path-to-msys-binaries> -DMINGW_PATH=<path-to-mingw-binaries>  <path-to-build-system>

The MINGW_PATH cmake variable must point to the MinGW binary directory (for example -DMINGW_PATH=C:\mingw-builds\x64-4.8.1-posix-seh-rev5\mingw64\bin) and the MSYS_PATH should point to the MSYS binary directory (for example -DMSYS_PATH=C:\msys\1.0\bin).

pgmLink

pgmLink depends on the proprietary software IBM ILOG CPLEX. If you are an academic you can obtain a free license from the IBM Academic Initiative. As of CPLEX version 12.5.1, pgmLink can be compiled with both Visual Studio 2010 and 2012. Only 64-bit builds of pgmlink are currently supported.

Install cplex and use:

    % cmake -G "Visual Studio 10 Win64" -DILASTIK_DEPENDENCY_DIR=<prefix> -DWITH_PGMLINK=1 <path-to-build-system>

Cplex will not be part of the ilastik installation bundle. You have to copy your cplex dll (for instance "cplex1251.dll") to the bin\ directory manually or put the CPLEX binary directory in your PATH variable.

The different options can also be combined. The cmake generator should be changed as approriate.

Compilation and Installation:

• Open ilastik.sln, switch to "Release" mode and build the project ilastik. In theory, this should build and install everything in one go. In practice, it sometimes stops with an error message like "Cannot extract sources". If this happens, just build ilastik again (this doesn't rebuild already installed dependencies). Due to unknown reasons, Visual Studio always believes that the compilation of numpy failed, although everything was actually ok. In this case, open "numpy-1.6.2->CMakeRules", right-click on numpy-1.6.2-download.rule and remove this rule. Do likewise with numpy-1.6.2-patch.rule. Then build ilastik again.
• Do not build the targets ALL_BUILD and INSTALL.
• Add the following directories to your PATH variable:

    % <prefix>\bin
    % <prefix>\Qt4\bin
    % <prefix>\python
    % <prefix>\python\Scripts   # optional

Create an .exe Installer:

• Open ilastik.sln, and build the project PACKAGE. The installer will be named something like ilastik-1.0.0-win64.exe in the directory where ilastik.sln resides.

Using ilastik:

• To use the installed ilastik version, call ilastik.bat in the installation's root directory. It automatically sets PATH and PYTHONPATH appropriately.
• To use another ilastik version together with the installed dependencies, set the environment variable ILASTIK_DIR to the root of your ilastik installation before calling ilastik.bat. The specified directory must have subdirectories lazyflow, volumina, and ilastik, holding the respective sources or modules. Example:

    % set ILASTIK_DIR=c:\Users\ukoethe\ilastik
    % c:\ilastik\ilastik.bat