Difference between revisions of "SimpleITK/GettingStarted"

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{{SimpleITKMigrationHeader}}
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[[Image: SimpleITK-SquareTransparentLogo.png|center]]
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SimpleITK provides a simplified interface to ITK in a variety of languages.  You can either download binaries, if they are available for your platform and prefered language, or you can build SimpleITK yourself.
 
SimpleITK provides a simplified interface to ITK in a variety of languages.  You can either download binaries, if they are available for your platform and prefered language, or you can build SimpleITK yourself.
  
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After you have installed SimpleITK, please look to the [[ITK_Release_4/Outreach/Conferences/MICCAI 2011/SimpleITK|Tutorial]]  or the [http://www.itk.org/SimpleITKDoxygen/html/ Doxygen] pages for more information.
 
After you have installed SimpleITK, please look to the [[ITK_Release_4/Outreach/Conferences/MICCAI 2011/SimpleITK|Tutorial]]  or the [http://www.itk.org/SimpleITKDoxygen/html/ Doxygen] pages for more information.
  
=Binaries=
+
=Downloading the binaries=
  
 
One of the great advantages of SimpleITK is that (typically) you do not have to build it — you can simply download the binaries and get started right away!
 
One of the great advantages of SimpleITK is that (typically) you do not have to build it — you can simply download the binaries and get started right away!
  
Currently, the following systems have binaries which you can easily download: python. We are currently (Feb 2012) working on creating binaries for the following systems: C#, Java. We are also working towards R packaging as well.
+
Currently, '''Python''' binaries are available on Microsoft Windows, GNU Linux and Apple OS X. '''C# and Java''' binaries are available for Windows. We are also working towards supporting '''R''' packaging.
  
 
==Python binary files==
 
==Python binary files==
  
The list of the binary python packages available is maintained [http://www.itk.org/SimpleITKDoxygen/html/PyDownload.html here].
+
There are currently two Python binary package choices: Python Wheels,  and Anaconda packages for the Anaconda Python distribution.
 +
 
 +
==== Use a Virtual Environment ====
 +
 
 +
Before you install SimpleITK we <b>highly recommend</b> that you create a virtual environment into which you install the package. Note that different Python versions and distributions have different programs for creating and managing virtual environments.
 +
 
 +
The use of a virtual environment allows you to elegantly deal with package compatability issues, to quote [http://docs.python-guide.org/en/latest/ The Hitchhiker’s Guide to Python!]:
 +
<blockquote>A Virtual Environment is a tool to keep the dependencies required by different projects in separate places, by creating virtual Python environments for them. It solves the “Project X depends on version 1.x but, Project Y needs 4.x” dilemma, and keeps your global site-packages directory clean and manageable.</blockquote>
 +
 
 +
Programs for creating virtual environments include [https://packaging.python.org/en/latest/installing/#creating-virtual-environments virtualenv and pyvenv] for generic Python distributions, [http://conda.pydata.org/docs/using/envs.html conda] for the anaconda distribution, and [http://docs.enthought.com/canopy/configure/canopy-cli.html canopy_cli] for the canopy distribution.
 +
 
 +
=== Wheels for Generic Python Distribution ===
  
Both your version of python and operating system must be available to be able to use the binary distribution. The package does not need to be downloaded from above, as SimpleITK is registered on the [http://pypi.python.org/pypi/SimpleITK/ Python Packaging Index]. The binary built packages are distributed as python eggs. They can be installed with the "easy_install" utility from the setuptools python package.
+
If you are working with the [https://www.python.org/ generic Python distribution] you can install a Wheel with the lasted version of pip (>=9.0).
 
If your system does not already have easy_install you will need to install this python package. Please go to the setuptools  [http://pypi.python.org/pypi/setuptools setuptools home page] for detailed instructions.
 
  
Once you have installed setuptools and easy_install is in your path then run the following command as root to install the package in system's site-packages:
+
First thing you should do is create a virtual environment (virtualenv or pyvenv tools) and activate it.
$ sudo easy_install SimpleITK
 
  
This command will check the available packages, and choose the one that is most recent and matches your system.
+
<u>Note</u>: you can always manually download the wheels for your operating system and Python version directly from [http://sourceforge.net/projects/simpleitk/files/SimpleITK/ sourceforge].
  
For advanced users you may be able to install SimpleITK in a [http://pypi.python.org/pypi/virtualenv virtual python environment], so that it does not modify the global python environment.
+
 
 +
From the command line use the [https://pip.pypa.io/en/latest/index.html pip program] to install:
 +
 
 +
$ pip install SimpleITK
 +
 
 +
The pip package manager should automatically find the correct package for Microsoft Windows, Apple OS X and GNU Linux if your version and architecture are supported. If no binary package is found, then a source distribution will be downloaded and attempted to be compiled and you should look into [[#Build_It_Yourself]].
 +
 
 +
:: If your pip version in the virtual environment is stale (<9.0) you need to update it (pip install -U pip).
 +
 
 +
=== Anaconda Distribution ===
 +
 
 +
First thing you should do is create a virtual environment ([https://conda.pydata.org/docs/using/envs.html conda] tool) and activate it.
 +
 
 +
Currently there are compiled binaries on [https://conda.anaconda.org/simpleitk Anaconda Cloud], easily installed with:
 +
 
 +
$ conda install -c <nowiki>https://conda.anaconda.org/simpleitk</nowiki> SimpleITK
 +
 
 +
Beta and release candidate packages are also available on Anaconda cloud under the dev label:
 +
 
 +
$conda install -c <nowiki>https://conda.anaconda.org/simpleitk/label/dev</nowiki> SimpleITK
 +
 
 +
=== Enthought Canopy Distribution ===
 +
 
 +
First thing you should do is create a virtual environment (canopy_cli tool) and activate it.
 +
 
 +
Currently there are no binaries supported with this distribution. You will need to compile SimpleITK yourself. (Using pip installation may work.)
  
 
==C# binary files==
 
==C# binary files==
  
Binaries for select C# platform can be found on [http://sourceforge.net/projects/simpleitk/files/SimpleITK/0.4.0/CSharp/ SimpleITK's SourceForge page]. Installation of library should involve only importing the unzip files into you C# environment.
+
'''Binaries for select C# platform''' can be found on [https://sourceforge.net/projects/simpleitk/files/SimpleITK/1.0.0/CSharp/ SimpleITK's SourceForge page]. Installing the library should only involve importing the unzipped files into you C# environment. The files have the following naming convention:
 +
SimpleITK-version-CSharp-buildplatform-targetplatform.zip
 +
eg.
 +
SimpleITK-1.0.0-CSharp-win32-x86.zip
 +
SimpleITK-1.0.0-CSharp-win64-x64.zip
  
More information about getting started with a sample C# program can be found in [[ITK/Release_4/SimpleITK/GettingStarted/Visual_guide_to_building_on_Linux#A_simple_C.23_program| A visual guide to building SimpleITK on Linux]]
+
Details about how to set up a C# Visual Studio project with SimpleITK can be found in the [[SimpleITK/GettingStarted/A_visual_guide_to_SimpleITK_with_CSharp|Visual Guide to SimpleITK with CSharp]].
 +
 
 +
More information about getting started with a sample C# program can be found in [[SimpleITK/GettingStarted/Visual_guide_to_building_on_Linux#A_simple_C.23_program| A visual guide to building SimpleITK on Linux]]
  
 
==Java binary files==
 
==Java binary files==
  
Binaries for select Java platforms can be found on [http://sourceforge.net/projects/simpleitk/files/SimpleITK/0.4.0/Java/ SimpleITK's SourceForge page]. Installation instructions are at [[a visual guide to SimpleITK in Java]].
+
'''Binaries for select Java platforms''' can be found on [https://sourceforge.net/projects/simpleitk/files/SimpleITK/1.0.0/Java/ SimpleITK's SourceForge page]. Installation instructions are available at [[SimpleITK/GettingStarted/A visual guide to SimpleITK in Java|a visual guide to SimpleITK in Java]].
 +
 
 +
==Nightly binaries==
 +
 
 +
The '''latest binaries''' for the current development version of SimpleITK are also generally available. Binary packages are built as part of the nightly regression testing system. The download links are available from the [https://open.cdash.org/index.php?project=SimpleITK '''CDash'''] '''dashboard''' in the "Nightly Packages" section.
 +
 
 +
Each row on the dashboard is a SimpleITK build on a particular system, and if the build was successful there will be a '''package icon''': https://open.cdash.org/img/package.png which links to the packages build by the system. A user may directly download the built package from such a link.
  
 
=Build It Yourself=
 
=Build It Yourself=
  
In many cases it is not required to build SimpleITK. The easiest way is to use the pre-compiled binary files (see [[ITK_Release_4/SimpleITK/GettingStarted#Binaries|here]]). Some reasons why you might want to build SimpleITK from source are:
+
In many cases a user does not need to build SimpleITK because of the pre-built binaries available (see [[SimpleITK/GettingStarted#Binaries|above]]). However there are several reasons a user might prefer to '''build SimpleITK from source''':
 
* The binary files for your programming language of choice are not (yet) distributed
 
* The binary files for your programming language of choice are not (yet) distributed
 
* You want the live on the bleeding edge by using the latest-and-greatest version of SimpleITK
 
* You want the live on the bleeding edge by using the latest-and-greatest version of SimpleITK
 
* You want to wrap your own filters using the SimpleITK infrastructure
 
* You want to wrap your own filters using the SimpleITK infrastructure
 
* You want to contribute to the development of SimpleITK
 
* You want to contribute to the development of SimpleITK
 +
* To use the SimpleITK's C++ interface and/or use ITK directly
  
 +
=== Prerequisites ===
 
To build SimpleITK you need:
 
To build SimpleITK you need:
* A recent version of [http://www.cmake.org/ cmake].
+
* A recent version of [http://www.cmake.org/ CMake] >= 3.3 with SSL support for https.
* A supported [http://www.vtk.org/Wiki/ITK_Release_4/SimpleITK/FAQ#Is_my_compiler_supported.3F compiler].
+
* A supported [[SimpleITK/FAQ#Is_my_compiler_supported.3F|compiler]]
* Source code
+
* To use the latest developmental version, source code can be downloaded with [http://git-scm.com/ git] >= 1.65
** Released source code can be found on SimpleITK's [http://sourceforge.net/projects/simpleitk/ SourceForge Page]
+
** Git is required if building SimpleITK using "SuperBuild" (see below) to automatically download the matching version of ITK, SWIG, etc...
** Alternatively, the latest developmental version can be download with git.
+
** Windows users may prefer [http://msysgit.github.com/ msysGit]
  git clone --recursive  http://itk.org/SimpleITK.git
+
* It is recommended to have numpy installed when testing Python bindings
 +
 
 +
=== Recipes / Formulas / Short Cuts ===
 +
 
 +
For some environments we have short cuts, scripts, for automated building of SimpleITK (see their repository for more details):
 +
 
 +
* For '''Python''': The [https://github.com/scikit-build/scikit-build scikit-build] based distutils based [https://github.com/scikit-build/scikit-build setup.py frontend] can be used to build, install, and package SimpleITK for Python.
 +
 
 +
* For the '''Anaconda Python''' distribution: The recipe and instructions for the SimpleITK build are in [https://github.com/SimpleITK/SimpleITKCondaRecipe this GitHub repository].  
 +
 
 +
* For the '''R language''': A devtools installer and instructions are available from [https://github.com/SimpleITK/SimpleITKRInstaller this GitHub repository].
 +
 
 +
* '''On the Mac''', with the [http://brew.sh/ Homebrew package manager], a SimpleITK formula is available: https://github.com/Homebrew/homebrew-science/blob/master/simpleitk.rb for multiple language wrappings.
 +
 
 +
* For the '''Lua language''' with the Luarocks module deployment system, a SimpleITK rockspec is available form [https://github.com/SimpleITK/SimpleITKLuaRock this GitHub repository].
 +
 
 +
=== Source code ===
 +
 
 +
If one of the above language specific front-ends are not used then SimpleITK must be build directly.
 +
 
 +
There are two options to obtain the SimpleITK source code:
 +
# Download a released version from the SimpleITK [https://sourceforge.net/projects/simpleitk/ SourceForge] page
 +
# Download the latest development version using git
 +
  git clone http://itk.org/SimpleITK.git
  
After SimpleITK's souce code is obtained it is '''STRONGLY''' recommended to run cmake on the SuperBuild subdirectory of SimpleITK:
+
=== Building using SuperBuild ===
 +
After downloading SimpleITK's source code we '''STRONGLY''' recommend to run cmake on the SuperBuild subdirectory of SimpleITK.  Execute the following commands in the parent of the SimpleITK source directory to configure the SuperBuild:
 
  mkdir SimpleITK-build
 
  mkdir SimpleITK-build
 
  cd SimpleITK-build
 
  cd SimpleITK-build
 
  cmake ../SimpleITK/SuperBuild
 
  cmake ../SimpleITK/SuperBuild
  
The SuperBuild will automatically download and build the matching version of ITK and SWIG needed to compile SimpleITK. This is the recommended way to build SimpleITK and is easiest.
+
The SuperBuild will automatically download and build the matching version of ITK and SWIG needed to compile SimpleITK. Additionally, it will set recommended compilation flags to minimize the size of the library and enable support for large libraries. This is the recommended way to build SimpleITK and is easiest.
  
 
If you get an error message saying that ITK_DIR is not set then, you did not correctly point cmake to the SuperBuild sub-directory. Please erase your binary directory, and point cmake to the SimpleITK/SuperBuild sub-directory.
 
If you get an error message saying that ITK_DIR is not set then, you did not correctly point cmake to the SuperBuild sub-directory. Please erase your binary directory, and point cmake to the SimpleITK/SuperBuild sub-directory.
  
The cmake configuration process should automatically find supported languages and enable SimpleITK wrapping for them. To manually enable a language toggle the appropriate WRAP_LANGUAGE cmake variable to ON.  Verify and/or correct the advanced cmake variables to the language specific executable, libraries and include directories.
+
The cmake configuration process should automatically find supported languages and enable SimpleITK wrapping for them. To manually enable a language toggle the appropriate WRAP_LANGUAGE cmake variable to ON.  Verify and/or correct the advanced cmake variables to the language specific executable, libraries and include directories. For example if you have multiple Python installations ensure that all related Python variable refer to the same versions.
  
Then use your make utility or your cmake choosen build utility to build SimpleITK.  After completion, add the SimpleITK-build/lib directory to you LD_LIBRARY_PATH (Linux) or DYLD_LIBRARY_PATH (Mac) environment.
+
Then use your make utility or your cmake chosen build utility to build SimpleITK.
  
 
SimpleITK takes a while to build. Some tips and tricks to speed up development time are listed [http://www.itk.org/SimpleITKDoxygen/html/Developer.html#TandT here].
 
SimpleITK takes a while to build. Some tips and tricks to speed up development time are listed [http://www.itk.org/SimpleITKDoxygen/html/Developer.html#TandT here].
 +
 +
=== Building Manually ===
 +
This is '''not''' the recommended way of building SimpleITK, but it can be useful if you want to use a system version of ITK, etc. , or if you do not want to (or can not) use git.
 +
 +
# Setup the prerequisites as described above (i.e. CMake and supported compiler)
 +
# Install the matching version of [http://www.swig.org/ SWIG] >= 3.0.11
 +
#* e.g. Windows users may install [http://prdownloads.sourceforge.net/swig/swigwin-3.0.11.zip swigwin-3.0.11]
 +
# Download the SimpleITK source code from the [https://sourceforge.net/projects/simpleitk/files/SimpleITK/ SourceForge] page
 +
# Download the matching version of ITK, found by examining the `SuperBuild/External_ITK.cmake` file.
 +
# Configure ITK using CMake
 +
#* e.g. BUILD_EXAMPLES=OFF, BUILD_TESTING=OFF, BUILD_SHARED_LIBS=OFF, '''ITK_USE_REVIEW=ON'''
 +
# Build ITK
 +
#* Be sure to note the build settings e.g. Release x64
 +
# Configure SimpleITK using CMake
 +
#* Set ITK_DIR to the location of the ITK build location from the previous steps
 +
# Build SimpleITK
 +
#* Be sure to configure the build settings exactly the same as ITK e.g. Release x64 and CXX_FLAGS
 +
 +
=== Advanced Build Options ===
 +
 +
SimpleITK is aware of the enabled and disabled ITK Modules. It is possible to customize SimpleITK by disabling unneeded ITK modules or to extend SimpleITK by writing custom json file dependent an ITK Remote Modules being enabled.
 +
 +
Additionally, each of the Examples directory, and each of the Wrapping subdirectories can be configured as independent CMake project dependent on an installed SimpleITK.
 +
 +
===[[SimpleITK/GettingStarted/Visual_guide_to_building_on_Linux|A visual guide to building SimpleITK on Linux]]===
  
 
==Testing==
 
==Testing==
 +
 +
After compilation the prudent thing to due is to test SimpleITK to ensure your build is stable and suitable for installation and use. The following commands execute the SimpleITK tests.
 +
 
  cd SimpleITK-build/SimpleITK-build
 
  cd SimpleITK-build/SimpleITK-build
 
  ctest
 
  ctest
  
If all tests fail, verify that you have the testing data in your source tree (the reason for the "--recursive" flag in the git command) AND that you've added the correct path to your *_LIBRARY_PATH.
+
On Windows you will need to specify configuration.  Typically that would be the Release configuration, as such:
 +
cd SimpleITK-build/SimpleITK-build
 +
ctest -C Release
  
 
==Python installation==
 
==Python installation==
  
To install a built python package, as root:
+
To install a built python package into the system Python, as root run:
   cd SimpleITK-build/Wrapping
+
   cd SimpleITK-build/Wrapping/Python
   python PythonPackage/setup.py install
+
   python Packaging/setup.py install
  
==A visual guide to building SimpleITK on Linux==
+
Alternatively, a Python virtual environment can be created and the distribution installed there.
  
[[ITK/Release_4/SimpleITK/GettingStarted/Visual_guide_to_building_on_Linux|A visual guide to building SimpleITK on Linux]]
+
A Python Wheel file (.whl)  can be created in the "Wrapping/Python/dist" directory, by building the "dist" target. If you have used the Superbuild with the "make" generator then issue the following command:
 +
  make -C SimpleITK-build dist
 +
 
 +
==R installation==
 +
 
 +
To install a built R package:
 +
 
 +
  cd SimpleITK-build/Wrapping/R/Packaging
 +
  R CMD INSTALL SimpleITK
 +
 
 +
This will install the R package "SimpleITK" in /usr/local as root or your local R installation directory.
 +
 
 +
 
 +
If you are working in a multi-user environment, and are considerate of your fellow users you can install the package in a local directory:
 +
 
 +
<ol> <li> Create a local directory where you will install your R packages</li></ol>
 +
  mkdir my_R_libs
 +
<ol start="2"> <li> Add an environment variable to your .bashrc</li></ol>
 +
  export R_LIBS="/path_to/my_R_libs"
 +
<ol start="3"> <li> source your .bashrc and check the R library path, in an R shell >.libPaths()</li></ol>
 +
<ol start="4"> <li>install </li></ol>
 +
 
 +
  cd SimpleITK-build/Wrapping/R/Packaging
 +
  R CMD INSTALL -l /path_to/my_R_libs  SimpleITK
  
 
=Recommended Software=
 
=Recommended Software=
  
To enable the "sitk::Show" function to work we recommend downloading a recent version of [http://rsbweb.nih.gov/ij/download.html ImageJ]. The recent versions come with support for the Nifti ( *.nii ) file format which SimpleITK uses to display.
+
== Fiji (Fiji is Just ImageJ) ==
 +
 
 +
SimpleITK has a built in function, [https://itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#ac8416e6e7f02dedfe8373b83dbea411d  '''"itk::simple::Show()"'''], which can be used for viewing images in an interactive session. Currently, this function by default Show invokes [https://fiji.sc '''Fiji'''] then [http://rsbweb.nih.gov/ij/ '''ImageJ'''] to display images.  ImageJ was chosen because it can handle all the image types that SimpleITK supports, even 3D vector images with n components.
 +
 
 +
The Show function first searches the "PATH" environment variable, then additional standard locations are examined, if problems are encountered the correct path can be added to this environment variable and the '''"debugOn'''" option to '''"Show'''" flag set.
 +
 
 +
====ImageJ====
 +
 
 +
If ImageJ is used then we recommend downloading a recent version of [http://rsbweb.nih.gov/ij/download.html ImageJ] from the official home page. Recent versions come with support for the [http://nifti.nimh.nih.gov/nifti-1/ Nifti] ( *.nii ) file format, which SimpleITK uses to export to ImageJ.
 +
 
 +
'''Note:''' '''Linux installation''' requires an additional step. The '''"Show'''" function searches for an executable named ImageJ or imagej, however the default tarball does not come with this file. Instead it comes with a file names [http://imagej.nih.gov/ij/download/linux/unix-script.txt script]. This file contains the installation instructions. In short the file should be renamed to "imagej" and the site specific variables for the installation location, and java must be set. Also consider the "newwindow" variable... Do you really want a new instance of ImageJ launched each time you use Show? Lastly, as the installation instructions indicate, the imagej wrapper should be in your path.
 +
 
 +
==iPython and Jupyter==
 +
 
 +
If you are using python, [http://ipython.org/ '''ipython'''] with [http://jupyter.org Jupyter] is terrific environment to perform interactive computing for image processing. With the addition of numpy and scipy, you'll have a powerful interactive environment.
  
If you are using python, [http://ipython.org/ ipython] is great environment to perform interactive commands for image processing.
+
We have instructional [http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/ SimpleITK Jupyter Notebooks] which can help you get started.

Latest revision as of 13:57, 19 June 2017

NOTICE
This page is being migrated to Read The Docs!

For the up to date version please see this page!

SimpleITK-SquareTransparentLogo.png

SimpleITK provides a simplified interface to ITK in a variety of languages. You can either download binaries, if they are available for your platform and prefered language, or you can build SimpleITK yourself.

Additionally, there are several recommended third-party software packages.

After you have installed SimpleITK, please look to the Tutorial or the Doxygen pages for more information.

Downloading the binaries

One of the great advantages of SimpleITK is that (typically) you do not have to build it — you can simply download the binaries and get started right away!

Currently, Python binaries are available on Microsoft Windows, GNU Linux and Apple OS X. C# and Java binaries are available for Windows. We are also working towards supporting R packaging.

Python binary files

There are currently two Python binary package choices: Python Wheels, and Anaconda packages for the Anaconda Python distribution.

Use a Virtual Environment

Before you install SimpleITK we highly recommend that you create a virtual environment into which you install the package. Note that different Python versions and distributions have different programs for creating and managing virtual environments.

The use of a virtual environment allows you to elegantly deal with package compatability issues, to quote The Hitchhiker’s Guide to Python!:

A Virtual Environment is a tool to keep the dependencies required by different projects in separate places, by creating virtual Python environments for them. It solves the “Project X depends on version 1.x but, Project Y needs 4.x” dilemma, and keeps your global site-packages directory clean and manageable.

Programs for creating virtual environments include virtualenv and pyvenv for generic Python distributions, conda for the anaconda distribution, and canopy_cli for the canopy distribution.

Wheels for Generic Python Distribution

If you are working with the generic Python distribution you can install a Wheel with the lasted version of pip (>=9.0).

First thing you should do is create a virtual environment (virtualenv or pyvenv tools) and activate it.

Note: you can always manually download the wheels for your operating system and Python version directly from sourceforge.


From the command line use the pip program to install:

$ pip install SimpleITK

The pip package manager should automatically find the correct package for Microsoft Windows, Apple OS X and GNU Linux if your version and architecture are supported. If no binary package is found, then a source distribution will be downloaded and attempted to be compiled and you should look into #Build_It_Yourself.

If your pip version in the virtual environment is stale (<9.0) you need to update it (pip install -U pip).

Anaconda Distribution

First thing you should do is create a virtual environment (conda tool) and activate it.

Currently there are compiled binaries on Anaconda Cloud, easily installed with:

$ conda install -c https://conda.anaconda.org/simpleitk SimpleITK

Beta and release candidate packages are also available on Anaconda cloud under the dev label:

$conda install -c https://conda.anaconda.org/simpleitk/label/dev SimpleITK

Enthought Canopy Distribution

First thing you should do is create a virtual environment (canopy_cli tool) and activate it.

Currently there are no binaries supported with this distribution. You will need to compile SimpleITK yourself. (Using pip installation may work.)

C# binary files

Binaries for select C# platform can be found on SimpleITK's SourceForge page. Installing the library should only involve importing the unzipped files into you C# environment. The files have the following naming convention:

SimpleITK-version-CSharp-buildplatform-targetplatform.zip

eg.

SimpleITK-1.0.0-CSharp-win32-x86.zip
SimpleITK-1.0.0-CSharp-win64-x64.zip

Details about how to set up a C# Visual Studio project with SimpleITK can be found in the Visual Guide to SimpleITK with CSharp.

More information about getting started with a sample C# program can be found in A visual guide to building SimpleITK on Linux

Java binary files

Binaries for select Java platforms can be found on SimpleITK's SourceForge page. Installation instructions are available at a visual guide to SimpleITK in Java.

Nightly binaries

The latest binaries for the current development version of SimpleITK are also generally available. Binary packages are built as part of the nightly regression testing system. The download links are available from the CDash dashboard in the "Nightly Packages" section.

Each row on the dashboard is a SimpleITK build on a particular system, and if the build was successful there will be a package icon: package.png which links to the packages build by the system. A user may directly download the built package from such a link.

Build It Yourself

In many cases a user does not need to build SimpleITK because of the pre-built binaries available (see above). However there are several reasons a user might prefer to build SimpleITK from source:

  • The binary files for your programming language of choice are not (yet) distributed
  • You want the live on the bleeding edge by using the latest-and-greatest version of SimpleITK
  • You want to wrap your own filters using the SimpleITK infrastructure
  • You want to contribute to the development of SimpleITK
  • To use the SimpleITK's C++ interface and/or use ITK directly

Prerequisites

To build SimpleITK you need:

  • A recent version of CMake >= 3.3 with SSL support for https.
  • A supported compiler
  • To use the latest developmental version, source code can be downloaded with git >= 1.65
    • Git is required if building SimpleITK using "SuperBuild" (see below) to automatically download the matching version of ITK, SWIG, etc...
    • Windows users may prefer msysGit
  • It is recommended to have numpy installed when testing Python bindings

Recipes / Formulas / Short Cuts

For some environments we have short cuts, scripts, for automated building of SimpleITK (see their repository for more details):

  • For the Anaconda Python distribution: The recipe and instructions for the SimpleITK build are in this GitHub repository.
  • For the Lua language with the Luarocks module deployment system, a SimpleITK rockspec is available form this GitHub repository.

Source code

If one of the above language specific front-ends are not used then SimpleITK must be build directly.

There are two options to obtain the SimpleITK source code:

  1. Download a released version from the SimpleITK SourceForge page
  2. Download the latest development version using git
git clone http://itk.org/SimpleITK.git

Building using SuperBuild

After downloading SimpleITK's source code we STRONGLY recommend to run cmake on the SuperBuild subdirectory of SimpleITK. Execute the following commands in the parent of the SimpleITK source directory to configure the SuperBuild:

mkdir SimpleITK-build
cd SimpleITK-build
cmake ../SimpleITK/SuperBuild

The SuperBuild will automatically download and build the matching version of ITK and SWIG needed to compile SimpleITK. Additionally, it will set recommended compilation flags to minimize the size of the library and enable support for large libraries. This is the recommended way to build SimpleITK and is easiest.

If you get an error message saying that ITK_DIR is not set then, you did not correctly point cmake to the SuperBuild sub-directory. Please erase your binary directory, and point cmake to the SimpleITK/SuperBuild sub-directory.

The cmake configuration process should automatically find supported languages and enable SimpleITK wrapping for them. To manually enable a language toggle the appropriate WRAP_LANGUAGE cmake variable to ON. Verify and/or correct the advanced cmake variables to the language specific executable, libraries and include directories. For example if you have multiple Python installations ensure that all related Python variable refer to the same versions.

Then use your make utility or your cmake chosen build utility to build SimpleITK.

SimpleITK takes a while to build. Some tips and tricks to speed up development time are listed here.

Building Manually

This is not the recommended way of building SimpleITK, but it can be useful if you want to use a system version of ITK, etc. , or if you do not want to (or can not) use git.

  1. Setup the prerequisites as described above (i.e. CMake and supported compiler)
  2. Install the matching version of SWIG >= 3.0.11
  3. Download the SimpleITK source code from the SourceForge page
  4. Download the matching version of ITK, found by examining the `SuperBuild/External_ITK.cmake` file.
  5. Configure ITK using CMake
    • e.g. BUILD_EXAMPLES=OFF, BUILD_TESTING=OFF, BUILD_SHARED_LIBS=OFF, ITK_USE_REVIEW=ON
  6. Build ITK
    • Be sure to note the build settings e.g. Release x64
  7. Configure SimpleITK using CMake
    • Set ITK_DIR to the location of the ITK build location from the previous steps
  8. Build SimpleITK
    • Be sure to configure the build settings exactly the same as ITK e.g. Release x64 and CXX_FLAGS

Advanced Build Options

SimpleITK is aware of the enabled and disabled ITK Modules. It is possible to customize SimpleITK by disabling unneeded ITK modules or to extend SimpleITK by writing custom json file dependent an ITK Remote Modules being enabled.

Additionally, each of the Examples directory, and each of the Wrapping subdirectories can be configured as independent CMake project dependent on an installed SimpleITK.

A visual guide to building SimpleITK on Linux

Testing

After compilation the prudent thing to due is to test SimpleITK to ensure your build is stable and suitable for installation and use. The following commands execute the SimpleITK tests.

cd SimpleITK-build/SimpleITK-build
ctest

On Windows you will need to specify configuration. Typically that would be the Release configuration, as such:

cd SimpleITK-build/SimpleITK-build
ctest -C Release

Python installation

To install a built python package into the system Python, as root run:

 cd SimpleITK-build/Wrapping/Python
 python Packaging/setup.py install

Alternatively, a Python virtual environment can be created and the distribution installed there.

A Python Wheel file (.whl) can be created in the "Wrapping/Python/dist" directory, by building the "dist" target. If you have used the Superbuild with the "make" generator then issue the following command:

 make -C SimpleITK-build dist

R installation

To install a built R package:

 cd SimpleITK-build/Wrapping/R/Packaging
 R CMD INSTALL SimpleITK

This will install the R package "SimpleITK" in /usr/local as root or your local R installation directory.


If you are working in a multi-user environment, and are considerate of your fellow users you can install the package in a local directory:

  1. Create a local directory where you will install your R packages
 mkdir my_R_libs
  1. Add an environment variable to your .bashrc
 export R_LIBS="/path_to/my_R_libs"
  1. source your .bashrc and check the R library path, in an R shell >.libPaths()
  1. install
 cd SimpleITK-build/Wrapping/R/Packaging
 R CMD INSTALL -l /path_to/my_R_libs  SimpleITK

Recommended Software

Fiji (Fiji is Just ImageJ)

SimpleITK has a built in function, "itk::simple::Show()", which can be used for viewing images in an interactive session. Currently, this function by default Show invokes Fiji then ImageJ to display images. ImageJ was chosen because it can handle all the image types that SimpleITK supports, even 3D vector images with n components.

The Show function first searches the "PATH" environment variable, then additional standard locations are examined, if problems are encountered the correct path can be added to this environment variable and the "debugOn" option to "Show" flag set.

ImageJ

If ImageJ is used then we recommend downloading a recent version of ImageJ from the official home page. Recent versions come with support for the Nifti ( *.nii ) file format, which SimpleITK uses to export to ImageJ.

Note: Linux installation requires an additional step. The "Show" function searches for an executable named ImageJ or imagej, however the default tarball does not come with this file. Instead it comes with a file names script. This file contains the installation instructions. In short the file should be renamed to "imagej" and the site specific variables for the installation location, and java must be set. Also consider the "newwindow" variable... Do you really want a new instance of ImageJ launched each time you use Show? Lastly, as the installation instructions indicate, the imagej wrapper should be in your path.

iPython and Jupyter

If you are using python, ipython with Jupyter is terrific environment to perform interactive computing for image processing. With the addition of numpy and scipy, you'll have a powerful interactive environment.

We have instructional SimpleITK Jupyter Notebooks which can help you get started.