View source for SimpleITK/GettingStarted/Visual guide to building on Linux

This guide gives detailed instructions for building SimpleITK on Linux. It is written for beginners getting started with SimpleITK.  There are examples of how to develop and execute simple programs in C Sharp and Lua.

== Why Linux? ==
* Linux is freely available
* It has all the required tools
* Did I mention it's free?

== Step 1: Get Linux ==
The first step is to install a Linux distribution. Some popular ones are:
* [http://www.ubuntu.com/download Ubuntu]
* [http://www.linuxmint.com/download.php Linux Mint]
* [http://www.debian.org/ Debian]

And here is a [http://www.makeuseof.com/tag/debian-ubuntu-linux-mint-distribution/ comparison of those distributions].

There are many online tutorials explaining how to install your chosen Linux distribution:
*Ubuntu
** [https://help.ubuntu.com/community/Installation Ubuntu Installation guide]
** [http://www.youtube.com/watch?v=GhnLk3gviWY Learn How to Install Ubuntu Linux in 5 Minutes (youtube)]
** [https://seogadget.co.uk/the-ubuntu-installation-guide The Ubuntu Installation Guide (with pictures)]
*Mint
** [http://www.linuxmint.com/documentation/user-guide/english_15.0.pdf Linux Mint User Guide (English)]
** [http://www.howtogeek.com/howto/20079/install-linux-mint-on-your-windows-computer-or-netbook/ Install Linux Mint on your Windows computer (howtogeek)]
** [http://www.youtube.com/watch?v=7IK35nZuTlk How to Install Linux Mint (youtube)]
*Debian
** [https://www.youtube.com/watch?v=TIuOFqQ-XTk Debian 7 Installation (youtube)]
** [http://www.wikihow.com/Install-Debian Install Debian]

If you are a Windows user, you may consider running Linux on a virtual machine. Some popular virtual machine environments are:
* [https://www.virtualbox.org/ VirtualBox]
* [http://www.vmware.com/ VMWare]

If you are a Mac OS X user, you can also run Linux in a virtual machine.  Two virtual machine environments for OS X are:
* [http://www.parallels.com/products/desktop/ Parallels]
* [http://www.vmware.com/products/fusion/ VMWare Fusion]

Again, there are heaps of tutorials:
* [http://www.psychocats.net/ubuntu/virtualbox Installing Ubuntu inside Windows using VirtualBox]
* [http://www.wikihow.com/Install-Ubuntu-on-VirtualBox How to Install Ubuntu on VirtualBox]
* [http://www.zealfortechnology.com/2014/03/install-linux-mint-16-on-virtualbox.html Install Mint 16 on VirtualBox]
* [http://www.youtube.com/watch?v=D-NYWSoiaTg How to Install Linux Mint in Virtualbox (youtube)]

This guide uses Debian 7, but the steps are very similar for other Linux distributions.

== Step 2: Install build tools ==
{| valign="top"
|- valign="top" 
| The next step is to install the required build tools.

Open a terminal window (Application Menu > Terminal Emulator) and run the following command:
 sudo apt-get install cmake cmake-curses-gui gcc g++ git

Confirm that you want to install the packages (press "y"), then wait for the installation to complete.

Alternatively, you could manually select each software package from the [http://www.nongnu.org/synaptic/ Synaptic Package Manager] (Application Menu > Settings > Synaptic Package Manager).

By default building SimpleITK produces the SimpleITK [http://en.wikipedia.org/wiki/C%2B%2B C++] libraries and the SimpleITK [http://en.wikipedia.org/wiki/Lua_(programming_language) Lua] interpreter.  It also supports bindings for other languages.  To build this support, additional packages need to be installed.  The following table shows the supported language bindings and the corresponding command to install the additional packages required for each language.

{| border=1
|-
! Programming Language
! Command to install the build tools
|-
| [http://en.wikipedia.org/wiki/C_Sharp_(programming_language) C#]
| sudo apt-get install monodevelop
|-
| [http://en.wikipedia.org/wiki/Java_(programming_language) Java]
| sudo apt-get install eclipse
|-
| [http://en.wikipedia.org/wiki/R_programming_language R]
| sudo apt-get install r-base r-base-dev
|-
| [http://en.wikipedia.org/wiki/Ruby_(programming_language) Ruby]
| sudo apt-get install ruby
|-
| [http://en.wikipedia.org/wiki/Python_(programming_language) Python]
| sudo apt-get install python python-dev
|-
| [http://en.wikipedia.org/wiki/Tcl Tcl]
| sudo apt-get install tcl tcl-dev tk tk-dev
|-
| All languages
| sudo apt-get install monodevelop eclipse r-base r-base-dev ruby python python-dev tcl tcl-dev tk tk-dev
|}

|[[File:SimpleITK_visual_guide_step02_01.png|200px|thumb|Install the build tools by opening the terminal]]
[[File:SimpleITK_visual_guide_step02_02.png|200px|thumb|In the terminal, use apt-get to install the build tools]]
[[File:SimpleITK_visual_guide_step02_03.png|200px|thumb|Build tools could also be installed using the software manager]]
|}

== Step 3: Get SimpleITK source code ==
{|
|
The next step is to get the SimpleITK source code using git.

Decide where you want to put the source code. I'm putting mine in my home directory:
 cd ~

Now download the SimpleITK source code, by entering the following command in the Terminal:
 git clone --recursive  http://itk.org/SimpleITK.git

Now change to the SimpleITK directory:
 cd SimpleITK
| [[File:SimpleITK_visual_guide_step03_02.png|200px|thumb|Get the SimpleITK source code using <code>git</code>]]
|}

== Step 4: Build SimpleITK ==
The next step is to start building.

The recommended way to build is via the so-called "super build".  The build directory should not be inside the source tree.  I put the build directory in the same directory as the source tree.
 cd ~
 mkdir SimpleITK-build
 cd SimpleITK-build
 cmake ../SimpleITK/SuperBuild

The SuperBuild generates make files which takes care of downloading and building ITK, SWIG, and Lua, as well as SimpleITK.

To start the (long) build process, type:
 make

On my test system, a 4 core virtual machine with 16 GB of RAM, the build took just over an hour.

After the build is finished, you need to add SimpleITK to your <code>LD_LIBRARY_PATH</code>:
 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:~/SimpleITK-build/lib

You can now (optionally) check whether the build was successful:
 cd ~/SimpleITK-build
 ctest

All (or at least most) of the tests should pass.

== Step 5: Use SimpleITK ==

SimpleITK is available to a variety of languages.  In this section we give simple example programs demonstrating the SimpleITK API in C Sharp and Lua.

=== A simple C# program ===
[[File:SimpleITK_visual_guide_step05_CSharp_01.png|200px|thumb|Open MonoDevelop]]
This sub-section will describe how to create a simple C# application using SimpleITK from MonoDevelop.

Open MonoDevelop (Application Menu > Development > MonoDevelop).

[[File:SimpleITK_visual_guide_step05_CSharp_02.png|200px|thumb|Create Console Project]]
Select File > New > Solution.

Select C# > Console Project. Enter a suitable name e.g. "sitk" and uncheck "Create directory for directory". Select "Forward" and then "OK".

[[File:SimpleITK_visual_guide_step05_CSharp_03.png|200px|thumb|Edit References]]
In the Solution explorer, right-click "Selection" and select "Edit References...".

[[File:SimpleITK_visual_guide_step05_CSharp_04.png|200px|thumb|Add SimpleITKCSharpManaged.dll]]
Select the ".Net Assembly" tab, navigate to "~/SimpleITK-build/SimpleITK-build/Wrapping/CSharpBinaries", select "SimpleITKCSharpManaged.dll", click "Add", and then close the window by selecting "OK". This will copy "SimpleITKCSharpManaged.dll" to your build directory e.g. "bin/Debug" or "bin/Release". You must also '''manually copy''' "libSimpleITKCSharpNative.so" to your build directories:
 mkdir ~/sitk/bin/Debug
 mkdir ~/sitk/bin/Release
 cp ~/SimpleITK-build/SimpleITK-build/Wrapping/CSharpBinaries/libSimpleITKCSharpNative.so ~/sitk/bin/Debug
 cp ~/SimpleITK-build/SimpleITK-build/Wrapping/CSharpBinaries/libSimpleITKCSharpNative.so ~/sitk/bin/Release

SimpleITK has now been added as a project reference.

[[File:SimpleITK_visual_guide_step05_CSharp_05.png|200px|thumb|A simple C# program]]
The following short program creates an image of a Gaussian blob, generates a derivative image from the Gaussian, scales and windows the derivative's intensities, converts the result to 8-bit unsigned ints, and writes out a PNG file:

 using System;
 using sitk = itk.simple.SimpleITK;
 
 namespace itk.simple
 {
     class MainClass
     {
         public static void Main (string[] args)
         {
             var size = new VectorUInt32 (new uint[] { 128, 128 });
             var sigma = new VectorDouble (new Double[] { 32.0, 32.0 });
             var center = new VectorDouble (new Double[] { 64.0, 64.0 });
 
             var gauss = sitk.GaussianSource (PixelIDValueEnum.sitkFloat32, size, sigma, center);
 
             var deriv = sitk.Cast (128.0 + 24.0 * sitk.Derivative (gauss), PixelIDValueEnum.sitkUInt8);
 
             sitk.WriteImage (deriv, "gauss-deriv-test.png");
         }
     }
 }

Note that in the example, the derivative image's intensities are scaled mathematically to illustrate SimpleITK's overloading of the mathematically operators.  The image intensities could also be scaled using SimpleITK's RescaleIntesity function.

To build the project press "F8" or select Build > Build All from the menu.

To debug the project, add a breakpoint at a desired location and press "F5".

[[File:SimpleITK_visual_guide_step05_CSharp_06.png|200px|thumb|Gaussian Derivative image]]
The Gaussian Derivative image to the right shows the results of the C# example program.

=== Using Lua ===
[http://www.lua.org/about.html Lua] is a fast, portable, lightweight scripting language that is included with the SimpleITK source code.  Because the entire source code for Lua is less than 600kb, it takes very little space relative to large projects such as SimpleITK.  That makes Lua very popular as an embedded scripting language.

In this SimpleITK/Lua example we show how to use a text editor to produce a SimpleITK example in Lua and execute the program.

[[File:SimpleITK_visual_guide_step05_Lua01.png|200px|thumb|Open Mousepad]]

By default, Debian with the Xfce user interface, comes with '''Mousepad''' (Application Menu > Accessories > Mousepad), a simple text editor.  Other possible editors include '''gedit''' with Gnome or '''kedit''' with KDE.


[[File:SimpleITK_visual_guide_step05_Lua_02.png|200px|thumb|Simple Lua Program]]
The following is a simple Lua example similar to the C# example in the previous section.  This program creates an image of a Gaussian blob, computes a derivative image of the Gaussian, rescales the floating point image to 0-255, casts it to a unsigned char image, and writes the result to a PNG file.

 local sitk = {}
 sitk = SimpleITK
 
 size = sitk.VectorUInt32();
 size:push_back(128);
 size:push_back(128);
 
 sigma = sitk.VectorDouble();
 sigma:push_back(32.0);
 sigma:push_back(32.0);
 
 center = sitk.VectorDouble();
 center:push_back(64.0);
 center:push_back(64.0);
 
 gauss = sitk.GaussianSource (sitk.sitkFloat32, size, sigma, center);
 
 deriv = sitk.Derivative(gauss);
 
 result = sitk.RescaleIntensity(deriv, 0, 255.0)
 
 result = sitk.Cast(result, sitk.sitkUInt8)
 
 sitk.WriteImage(result, "sitk-lua-test.png");

The script is slightly different than the C# example in that the RescaleIntensity filter is used.  In C# mathematical operators are overloaded for SimpleITK images.  This is not the case for Lua, so mathematical operations on SimpleITK images are a bit more complicated.  Therefore I chose to use a built in filter.

To try out the program, copy the code and paste it into Mousepad.  Then Save it as "DerivativeExample.lua" and enter the following command in a Terminal window.

 ~/SimpleITK-build/SimpleITK-build/bin/SimpleITKLua DerivativeExample.lua

[[File:SimpleITK_visual_guide_step05_lua_03.png|200px|thumb|Lua Derivative image]]
The Lua Derivative image on the right shows the output of the our SimpleITK Lua example.  The result is similar to, although not the same as the C Sharp produced image.  They are different because the image intensities are not scaled in the same manner.