Difference between revisions of "SimpleITK/FAQ"
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Latest revision as of 12:57, 15 June 2017
|This page is being migrated to Read The Docs!
For the up to date version please see this page!
This page hosts frequently asked questions about SimpleITK, and their answers.
- 1 Installation
- 2 How to Use
- 2.1 What filters are currently available in SimpleITK?
- 2.2 What image file formats can SimpleITK read?
- 2.3 How do I read a RAW image into SimpleITK?
- 2.4 Can I use another image file viewer beside ImageJ?
- 2.5 How can I use 3D Slicer to view my images?
- 2.6 How can I use a newer Java with ImageJ on Mac OS X?
- 3 Wrapping
- 4 Compilation
- 4.1 Is my compiler supported?
- 4.2 Why am I getting a compilation error on OSX Mavericks?
- 4.3 Why does the Superbuild fail compiling PCRE on Mac OS X?
- 4.4 Do I need to download an option package for TR1 support?
- 4.5 Do I need to download an optional package for C99?
- 4.6 How do I build with Visual Studio 2008?
- 4.7 What Configurations on Windows are Supported For Building?
- 4.8 Why are all of the configurations not supported on Windows?
- 4.9 Where is the Test Data?
- 4.10 Why is CMake unable to download ExternalData?
Why do I get an error about a missing Dynamic Library when running SimpleITK with Python on windows?
This error has been resolved with SimpleITK version 0.5.1 and should no longer occur. Upgrading to the latest SimpleITK is encouraged.
This error occurs after you have downloaded the Windows SimpleITK binaries when you are running python and try to import SimpleITK. There is an error about a missing DLL on Windows when you don't have Visual Studio 10 and no other application has installed certain libraries before. You will need to download the Visual Studio 10 redistribution libraries. The libraries are available for download here.
I am using the binary distribution of SimpleITK for Anaconda, why do I get an error about libpng?
ImportError: dlopen(./_SimpleITK.so, 2): Library not loaded: @rpath/libpng15.15.dylib Referenced from: .../lib/python2.7/site-packages/SimpleITK/_SimpleITK.so Reason: image not found
This can be resolved by installing the version of libpng that SimpleITK 0.9 was built against:
conda create -n sitkpy anaconda libpng=1.5 unix/mac: source activate sitkpy
win: activate sitkpy conda install -c https://conda.binstar.org/simpleitk/channel/main SimpleITK conda install libpng=1.5
This set of commands:
- creates the virtual environment with our choice of libpng version, all other anaconda packages will be compatible with this version.
- activate the virtual environment.
- installs SimpleITK into the virtual environment (unfortunately this will automatically upgrade you to libpng 1.6).
- downgrades to libpng 1.5 so that library versions are compatible.
We are currently investigating why the anaconda build system is not expressing version dependency for shared libraries. We how this will not be an issue with the next binary package.
How to Use
What filters are currently available in SimpleITK?
As of March 2014 we have approximately 260 ITK image filters wrapped for SimpleITK. The filter coverage table shows the current set of ITK filters in SimpleITK. Additionally the Doxygen can be looked at to determine if a filter is available.
What image file formats can SimpleITK read?
How do I read a RAW image into SimpleITK?
In general raw image files are missing information. They do not contain the nessesary header information to describe the basic size and type for the data, so this format is intrinsically deficient. The RawImageIO class is not available in SimpleITK so there is no direct way to programmatically hard code this header information. The suggested way is to create a Meta image header file (*.mhd) which references the raw data file and describes the size and type of the data. The documentation on how to write a Meta image header can be found here.
The following is a sample Meta image header file, perhaps of name sample.mhd:
ObjectType = Image NDims = 3 DimSize = 256 256 64 ElementType = MET_USHORT ElementDataFile = image.raw (this tag must be last in a MetaImageHeader)
Can I use another image file viewer beside ImageJ?
By default when the Show function is called, SimpleITK writes out a temporary image in Nifti format then launches ImageJ. The user can override the file format of the temporary file and/or the application used to handle that file.
The temporary file format can be specified via the SITK_SHOW_EXTENSION environment variable. For example, if the user wanted to export a PNG file, on Linux it might look like this:
SITK_SHOW_EXTENSION=".png" export SITK_SHOW_EXTENSION
Use of an extension unsupported by ITK results in an error message. For the supported image formats, here is the ITK Image IO Filters.
The default display application for all image types is ImageJ. To override ImageJ with some other application, use the SITK_SHOW_COMMAND environment variable. For instance, on Unix systems, using GNOME's image viewer eog would be:
SITK_SHOW_EXTENSION=".png" export SITK_SHOW_EXTENSION SITK_SHOW_COMMAND="eog" export SITK_SHOW_COMMAND
To override the default display applications for only color or 3d images, there are the SITK_SHOW_COLOR_COMMAND and SITK_SHOW_3D_COMMAND environment variables.
More details on the Show function, including use of the "%a" and "%f" tokens, is at the Show function Doxygen page.
How can I use 3D Slicer to view my images?
3D Slicer is a very powerful and popular application for visualization and medical image computing. The SITK_SHOW_COMMAND environment variable may be used to display images in Slicer instead of SimpleITK's default viewer, ImageJ. The following are examples of what settings for SITK_SHOW_COMMAND might look like for Mac OS X, Linux and Windows to use Slicer.
Mac OS X
set SITK_SHOW_COMMAND=:"c:\Program Files\Slicer 4.2.2-1\Slicer"
The value of SITK_SHOW_COMMAND should be modified to point to wherever Slicer is installed. If you only want to use Slicer for volumetric 3D images, use the SITK_SHOW_3D_COMMAND environment variable instead of SITK_SHOW_COMMAND.
How can I use a newer Java with ImageJ on Mac OS X?
By default on Mac OS X, the ImageJ application expects Java 6, which is old and unsupported. The latest supported version of Java (currently version 8u25) can be downloaded from Oracle's Java Development kit page. The following bash commands will set up the SITK_SHOW_COMMAND and SITK_SHOW_COLOR_COMMAND to invoke ImageJ's jar file using the Java compiler.
ij="/Applications/ImageJ/" ijcmd="java -Dplugins.dir=$ij/plugins -jar $ij/ImageJ.app/Contents/Resources/Java/ij.jar" export SITK_SHOW_COMMAND="$ijcmd -eval 'open( \"%f\" );'" export SITK_SHOW_COLOR_COMMAND="$ijcmd -eval 'open( \"%f\" ); run(\"Make Composite\", \"display=Composite\");'"
The first lines set a variable pointing to the standard location for the ImageJ directory. If ImageJ is installed somewhere else, the line should be modified. The second line provides the command to launch ImageJ using the Java compiler. It includes flags that point to ImageJ's plugiin directory and ImageJ's ij.jar file.
The SITK_SHOW_COMMAND tells SimpleITK.Show() to launch Java with ij.jar and then execute the open macro with an image file. The SITK_SHOW_COLOR_COMMAND does these same things and then executes the ImageJ "Make Composite" command to treat a multichannel image as a composite color image.
Is my compiler supported?
SimpleITK uses advanced C++ meta-programming to instantiate ITK's Images and Filters. Addtionally, we use some headers which are included in the C99 and C++ TR1 extension. Therefore SimpleITK places additional requirements on the compiler beyond what is required for ITK. In principle we require C++x03 with C99's "stdint.h" and TR1's "functional". If your compiler has those features it is likely able to be supported.
The additional requirement for a supported compiler is that it is on the nightly dashboard. With this regard, the list of supported compilers is on the SimpleITK SimpleITK dashboard. We welcome user contributions to the nightly dashboard to expand the list of supported compilers.
Committed to Support
- GCC 4.2-4.7
- Visual Studio 2008 with Service Pack 1 (VS9)
- Visual Studio 2012 (VS10) ( including Express )
- Visual Studio 2012 (VS11)
- Compiling on a MS Windows 32-bit OS with static libraries is not supported due to lack of memory.
- With SimpleITK release 0.4.0, Visual Studio 2008 was not compiling. This problem has since been remedied in the development branch on April 18th, 2012.
- With SimpleITK release 0.7.0, Visual Studio 2008 is not able to compile all wrapped languages at the same time, it's recommenced to choose one at a time.
Why am I getting a compilation error on OSX Mavericks?
With SimpleITK <=0.7 the following error occurred during compilation on Apple OSX 10.9 Mavericks with clang 5.0:
SimpleITK/Code/Common/include/sitkMemberFunctionFactoryBase.h:106:16: error: no member named 'tr1' in namespace 'std' typedef std::tr1::function< MemberFunctionResultType ( ) > FunctionObjectType; ~~~~~^
With Xcode 5.0, Apple's distributed version of clang (5.0) changed which implementation of the C++ Standard Library it uses by default. Previous versions of clang (4.2 and earlier) used GNU's libstdc++ , while clang 5.0 now uses LLVM's libc++. SimpleITK 0.7 and earlier require certain features from C++ tr1 which are not implemented in LLVM's libc++ but are available in GNU's libstdc++.
To build SimpleITK <=0.7 with clang 5.0, you can configure the compiler to use GNU's stdlibc++. This change must be done at the initial configuration:
cmake "-DCMAKE_CXX_FLAGS:STRING=-stdlib=libstdc++" ../SimpleITK/SuperBuild
NOTE: If you already have a build directory which has been partially configured the contents must be deleted. The above line needs to be done for an initial configuration in an empty build directory. NOTE: This work around does not work when with the CMake "Xcode" generator. It is recommended to just use the default "Unix Makefiles" generator, to build SimpleITK, and get using SimpleITK, not building it.
The following is a compatibility table for clang 5.0. It shows that the default of libc++ does not work with SimpleITK, while the other options do. The choice of which standard library to use and which C++ language standard to use are independent.
|Clang 5.0 compatibility||-stdlib=libc++||-stdlib=libstdc++|
For SimpleITK >=0.8, support for the tr1 features migrated to C++11 has been improved with better feature detection, and the necessary flags are now automatically added. LLVM's libc++ will now work if compiling with the C++11 standard by adding the flag "-std=c++11" in the initial configuration.
To further complicate dependencies and interactions, some downloadable languages such as Java, or R, may be compiled against GNU's libstdc++. This may cause a conflict in the types used in the interface resulting in compilation errors while wrapping the language.
Why does the Superbuild fail compiling PCRE on Mac OS X?
If the Xcode command line tools are not properly set up on OS X, PCRE could fail to build in the Superbuild process with messages such as:
checking whether we are cross compiling... configure: error: in `/your/build/path/SimpleITK/PCRE-prefix/src/PCRE-build': configure: error: cannot run C compiled programs. If you meant to cross compile, use `--host'. See `config.log' for more details [10/13] Performing build step for 'PCRE'
To install the command line developer tools enter the following: xcode-select --install
To reset the default command line tools path: xcode-select --reset
Do I need to download an option package for TR1 support?
Visual Studio 2008 requires an additional download for TR1 support. This support is best provided with the Service Pack 1. There is a separate TR1 feature pack which can be downloaded, but it is no longer recommended since Service Pack 1 includes TR1 and numerous bug and performance improvements.
Do I need to download an optional package for C99?
SimpleITK will proved a "stdint.h" header if missing on the system.
How do I build with Visual Studio 2008?
Visual Studio 2008 is the oldest supported Microsoft development environment that SimpleITK supports. To build SimpleITK, certain features of C++TR1 are required. These features are best provided by the "Microsoft Visual Studio 2008 Service Pack 1" (or try this link ). Alternatively just the Visual C++ 2008 Feature Pack Release can be installed. Please note that all our dashboard machines now use SP1.
Older versions of SimpleITK (<0.7.0) requires a also required a separately downloaded stdint.h for this compiler. This is not automatically provided if needed. If it's still needed the file can be downloaded here. For 64-bit Microsoft Windows it should be dragged with the GUI into the appropriate include path for the architecture.
What Configurations on Windows are Supported For Building?
There are quite a large number of configuration options available for the Windows platform. The following table is a guide line of what is regularly tested and confirmed to work or fail.
|Architecture||Library Type||Visual Studio 2008 SP1 (VS9 )||Visual Studio 2010 ( VS10 )||Visual Studio 2012 ( VS11 )||Visual Studio 2013 ( VS13 )|
|32-bit Window OS||Only Intel 32-bit||Static||FAIL||FAIL||FAIL||FAIL|
|64-bit Window OS||Intel 32-bit||Static||Nightly||Nightly||Nightly||Nightly|
|Nightly||This combination of options is nightly tested, and known to work.|
|This combinations has been manually tested, and is expected to work.|
|It is not known if this combinations of options will work.|
|This combination likely has problems, and is not recommended.|
|FAIL||These options are known not to work.|
This table has been updated for the release branch, master, as of February 15th 2013.
Why are all of the configurations not supported on Windows?
One of the following errors frequently occur when the set of configuration options fail:
LINK : fatal error LNK1102: out of memory
LINK : fatal error LNK1248: image size (80000010) exceeds maximum allowable size (80000000)
These errors occur because of limitations in the compiler's linker or the operating system. For 64-bit architectures the linker is still only 32-bits on some Visual Studios. In certain configurations the linker can run out of memory. Also the Windows operating systems have a hard limit of 2GB for the size of libraries. For Debug mode configurations this limit can be encounted.
In general building in Debug mode should not be necessary, unless you are trying to debug SimpleITK or ITK. This configuration produces libraries that are very large because the compiler must maintain symbols for all instantiated ITK classes and member functions for each template parameters that a class is instantiating.
Where is the Test Data?
The testing data is not stored in the SimpleITK repository or as part of the source code. It is mirrored on several data repositories on the web.
If you have obtained the source code from the git repository, it should be downloaded as part of the build process via the CMake ExternalData module.
If you have downloaded a tar-ball of the source code there should be an accompanying "SimpleITKData" tar-ball available, which contains the external data. It should populate the .ExternalData subdirectory of the SimpleITK source code directory when extracted.
Why is CMake unable to download ExternalData?
When compiling SimpleITK you may get and error like the following:
Object MD5=2e115fe26e435e33b0d5c022e4490567 not found at: https://placid.nlm.nih.gov/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported protocol") https://simpleitk.github.io/SimpleITKExternalData/MD5/2e115fe26e435e33b0d5c022e4490567 ("Unsupported protocol") https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported protocol") https://insightsoftwareconsortium.github.io/ITKTestingData/MD5/2e115fe26e435e33b0d5c022e4490567 ("Unsupported protocol") https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567 ("Unsupported protocol")
This indicates that CMake was not compiles with SSL support. The "Unsupported protocol" message indicate that CMake can not communicate via "https".
The solution is to use a compiled version of CMake which supports SSL. If you compile CMake yourself, simply reconfigure CMake with the "CMAKE_USE_OPENSSL option enabled.