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1 Extensions

Extensions

What is an extension ?

An extension could be seen as a delivery package bundling together one or more Slicer modules. After installing an extension, the associated modules will be presented to the user as built-in ones

The Slicer community maintains a website referred to as the Slicer Extensions Catalog to support finding, downloading and installing of extensions. Access to this website is integral to Slicer and facilitated by the Extensions Manager functionality built into the distributed program.

The Catalog classifies extensions into three levels of compliance:

Category 1: Fully compliant Slicer Extensions: Slicer license, open source, maintained.
Category 2: Open source, contact exists.
Category 3: All other extensions (work in progress, beta, closed source etc).

To publish extensions, developers should consider reading the following pages:

What is the extensions catalog ?

The extensions catalog provides Slicer users with a convenient way to access the extensions previously uploaded on the extensions server:

from within Slicer with the help of the extensions manager
from the web: http://slicer.kitware.com/midas3/slicerappstore

Why there are no windows 32-bit extensions available ?

Win 32 has a very limited amount of memory available to an application.
Many registration and segmentation algorithms fail on that platform because they run out of memory, when used with state of large data.
Some of these failures are just that, some can crash slicer. Even though the "real" failure is caused by overextending the capabilities of the hardware (in a way the users fault), it appears to the user that Slicer does not work.
If you search the archives of slicer-users there are several such complaints until we started to discourage people to use 32 bit.

Discussion: http://massmail.spl.harvard.edu/public-archives/slicer-users/2013/006703.html

Should I install the nightly version to access to last extension updates ?

If the extension developers contributed updates for the current stable release, you don't have to install the nightly version of Slicer. You can simply update the extension. Consider reading How to update an already installed extension ?.

On the other hand, if the extension developers stopped to maintain the version of their extension built against the stable release (so that we can use the latest feature that will be in the next Slicer release), downloading the nightly is the only way to get the latest version of the extension.

How to update an already installed extension?

Assuming updates extensions are available for your version of Slicer, extensions can either be updated manually or automatically.

See Updating installed extensions

How to manually download an extension package?

1) Get revision associated with your install or built Slicer (Menu -> Help -> About). The revision is a number preceded by r character, for example: if the complete version string is 4.3.1-2014-09-14 r23677 the revision is 23677

2) Open the extension catalog (app store). The default Slicer extension catalog is available at: http://slicer.kitware.com/midas3/slicerappstore

3) Select operating system, bitness and enter revision in the empty textbox between the bitness selector and the searchbox. If no revision is entered then the No extensions found message will be displayed.

4) Click Download button of the selected extension to download the extension package.

How to manually install an extension?

1) Get the extension package matching your Slicer version.

2.a) Either install the extension package using the Slicer extension called "DeveloperToolsForExtensions"

2.b.i) Or extract the archive (zip or tar.gz) in a folder. You should then have a folder like:

/path/to/<slicer_revision>-<os>-<bitness>-<extension_name>-<extension_scm><extension_revision>-YYYY-MM-DD

containing one or more of the following folders:

lib/Slicer-X.Y/cli-modules
lib/Slicer-X.Y/qt-loadable-modules
lib/Slicer-X.Y/qt-scripted-modules

For more details: Documentation/4.5/Developers/DirectoryStructure

2.b.ii) There are two options:

2.b.ii.a) In the Module settings (Menu -> Edit -> Settings), add all existing paths ending with:

lib/Slicer-X.Y/cli-modules
lib/Slicer-X.Y/qt-loadable-modules
lib/Slicer-X.Y/qt-scripted-modules

2.b.ii.b) Start Slicer specifying the option --additional-module-paths with all existing paths listed in 4.a.

How to create a custom Slicer version with selected extensions pre-installed?

1) Download and install Slicer

2) Install all necessary extensions manually (as described above) in <slicer_install_dir>/lib/Slicer-X.Y/...

3) If all the files in <slicer_install_dir> are copied to any other folder/computer/USB drive/portable storage device then Slicer can be launched by running the Slicer executable in the main directory. No installation or administrative access rights are necessary. Slicer can even be launched directly from a USB drive, without copying files to the computer.

What is an extension description file ?

See Description file description

Can an extension contain different types of modules ?

Yes. Extensions are used to package together all types of Slicer modules.

Should the name of the source repository match the name of the extension ?

Assuming your extension is named AwesomeFilter, generally, we suggest to name the extension repository either SlicerAwesomeFilter, Slicer-AwesomeFilter, Slicer_AwesomeFilter, SlicerExtension-AwesomeFilter, SlicerExtension_AwesomeFilter.

Doing so will minimize confusion by clearly stating that the code base is associated with Slicer.

What is the Extensions Index ?

Think of the ExtensionsIndex as a repository containing a list of extension description files *.s4ext used by the Slicer extensions build system to build, test, package and upload extensions on the extensions server.

Once uploaded on an extensions server, within Slicer, extensions can be installed using the extensions manager.

The extensions catalog provides Slicer users with a convenient way to access the extensions previously uploaded.

There are multiple branches on the ExtensionsIndex:

master: This branch contain description files of extensions that will be built against Slicer nightly.
[...]
4.10: This branch contain description files of extensions that will be built against latest Slicer 4.10 available patch release.

The reasoning behind this approach is that since both the Slicer API and ABI associated with Slicer base libraries are changing often, compatibility of the extensions available for download is guaranteed by building extensions against every Slicer revisions.

It means that developer willing to have their extensions available on the different versions of Slicer will have to submit pull requests for each version.

What is an API Key ?

See http://en.wikipedia.org/wiki/Application_programming_interface_key

How to obtain an API key to submit on the extension server ?

In order to upload extensions on the slicer extensions server, it is required to:

Create an account on the extension server: http://slicer.kitware.com by clicking on the Register link in the top right corner

This image shows the top portion of http://slicer.kitware.com after it has been expanded by clicking the Register button.

Go to NA-MIC community and click on Join community
Retrieve your API key looking at your account details:
1. Go to http://slicer.kitware.com. If needed, signin by clicking on Login in the top right corner.
2. Click on your name in the top right corner.
3. Click on My account.
4. Click on API tab.
5. Copy the API Key associated with Default application.
  1. There is currently a bug preventing api key containing non alpanumeric characters from being used.
    If your Default api key contain for example a /, try to delete the api key and regenerate one that is not containing "/" and is named Default.
    We are working on the issue to update the build system so that it properly escape "/" and also get in touch with Midas team so that api key containing just number and letter are generated.

How to cache API credentials ?

There is now a new feature that allow you to "cache" your credential [1]. If you set the two environment variables, MIDAS_PACKAGE_EMAIL and MIDAS_PACKAGE_API_KEY, you would simply need to configure your extension using:

cd MyExtension-build
cmake -DCMAKE_BUILD_TYPE:STRING=Release -DSlicer_DIR:PATH=/path/to/Slicer-Superbuild/Slicer-build ../MyExtension
make ExperimentalUpload

[1] http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=22457

Where can I find the extension templates ?

The module and extension templates are available in the Slicer source tree: https://github.com/Slicer/Slicer/tree/master/Utilities/Templates/

Using the Extension Wizard, you could easily create a new extension without having to copy, rename and update manually every files.

How to build an extension ?

Assuming that the source code of your extension is located in folder MyExtension, this could be achieved doing:

Makefile	Visual Studio
$ mkdir MyExtension-build $ cd MyExtension-build $ cmake -DCMAKE_BUILD_TYPE:STRING=Release -DSlicer_DIR:PATH=/path/to/Slicer-Superbuild/Slicer-build ../MyExtension $ make	Start CMake, select source and build directory Add `Slicer_DIR` entry to the cache Click on `Configure`, select generator, then click on `Generate` button. Open `MyExtension.sln`, select `Release` configuration, then menu `Project -> Build Solution`.

How to package an extension ?

Assuming your extension has been built into folder MyExtension-build, this could be achieved doing:

Makefile	Visual Studio
$ make package	Open `MyExtension.sln` Select `PACKAGES` project, then right click and select `Build`

How are Superbuild extension packaged ?

Extensions using the Superbuild mechanism build projects in two steps:

First, the project dependencies are built in an outer-build directory.
Then, the project itself is built in an inner-build directory

Extensions can use the Superbuild mechanism. However, developers have to be careful that the packaging macros clean the project before reconfiguring it. This means that if ones uses the Slicer extension packaging macros inside the inner-build directory, when packaging and uploading the extension package, the project will be reconfigured, and variables passed from the outer-build directory will be lost. If the project only depends on libraries that Slicer builds, this is not an issue. If the project has specific dependencies that Slicer does not compile on its own, the developer should be careful to instantiate the Slicer extension packaging macros only in the outer-build directory. This only means that in the latter case, tests should be instantiated in the outer-build directory to allow the Slicer extension building process to test the extension before uploading the extension and the tests results.

How to upload an extension ?

If not already done, send an email on the slicer developers list asking to be granted write permission on the experimental folder.

To: slicer-devel@bwh.harvard.edu
Subject: Extension NAME-OF-YOUR-EXTENSION - Asking permission to write to the Experimental folder
Hi, 

This extension will allow to [...]

Could you grant user YourUserName write access to the Experimental folder ?

Assuming your extension has been built and packaged into folder MyExtension-build, this could be achieved by first re-configuring the project providing your midas credentials and then building the ExperimentalUploadOnly target:

Makefile	Visual Studio
$ cmake -DMIDAS_PACKAGE_EMAIL:STRING=<YOUR-MIDAS-LOGIN> -DMIDAS_PACKAGE_API_KEY:STRING=<YOUR-MIDAS-APIKEY> . $ make ExperimentalUploadOnly	Start CMake, select source and build directory Add `MIDAS_PACKAGE_EMAIL` and `MIDAS_PACKAGE_API_KEY` entries to the cache Open `MyExtension.sln` Select `Release` configuration Select `ExperimentalUploadOnly` project, then right click and select `Build`

Can an extension depend on other extensions ?

Yes. An ExtensionFoo can depend on ExtensionBar

The dependency should be specified as a list by setting the variable EXTENSION_DEPENDS in the extension CMakeLists.txt.

For example, if you have ModuleA, ModuleB and ModuleC and ModuleA can be used as standalone one. You could create the following extensions:

Extension1 containing ModuleA
Extension2 containing ModuleB and ModuleC

and add the following variable to Extension2/CMakeLists.txt:

set(EXTENSION_DEPENDS Extension1)

User:

If user installs Extension2, Extension1 will automatically be installed first.

Developer:

The generated extension description file have a depends field. See here for details.
The extension framework will build the extension in order. When building Extension2, it will pass the CMake option -DExtension1_DIR:PATH=/path/to/Extension1-build.

What are the extension specific targets: ExperimentalUpload, ExperimentalUploadOnly, ... ?

Slicer extension build system provides the developer with a set of convenient targets allowing to build and upload extensions.

Target name	Description
`Experimental`	Configure, build, test the extension and publish result on CDash.
`ExperimentalUpload`	Equivalent to Experimental target followed by packaging and upload of the extension on the extension server.
`ExperimentalUploadOnly`	Only proceed to the upload of the extension on the extension server.
`test` or `BUILD_TESTS`	Locally execute the test
`package` or `PACKAGE`	Locally package the extension

Is --launch flag available for a MacOSX installed Slicer.app ?

On MacOSx, running Slicer with the --help argument does NOT list the usual launcher related options.

$ ./Slicer.app/Contents/MacOS/Slicer --help
Usage
 Slicer [options]
 
 Options
   --, --ignore-rest                     Ignores the rest of the labeled arguments following this flag. (default: false)
   -h, --help                            Display available command line arguments.
   [...]
   --version                             Displays version information and exits.

To provide some background information, when generating the package that will be distributed, an application bundle Slicer.app is created. As explained here, a bundle is a directory with a standardized hierarchical structure that holds executable code and the resources used by that code. It means that since all libraries contained within a bundle are referenced relatively to the location of either the CLI or the Slicer executable, the use of launcher does NOT make sens.

To help fixing-up the libraries, executables and plugins so that they reference each other in a relative way, CMake provides us with the BundleUtilities module.

This module is used in two situations:

Fixup of Slicer application itself. See SlicerCPack.cmake#L36-68 and SlicerCPackBundleFixup.cmake.in
Fixup of an extension package. See SlicerExtensionCPack.cmake#L126-143 and SlicerExtensionCPackBundleFixup.cmake.in

What is the difference between Documentation/Nightly/Modules and Documentation/Nightly/Extensions ?

As suggested by the namespace names:

All module documentation pages should be located under Documentation/Nightly/Modules
All extension documentation pages should be located under Documentation/Nightly/Extensions

For example, if an an extension named DoSomethingGreat bundles three modules ModuleA, ModuleB and ModuleC. The following pages should be created:

Documentation/Nightly/Extensions/DoSomethingGreat
Documentation/Nightly/Modules/ModuleA
Documentation/Nightly/Modules/ModuleB
Documentation/Nightly/Modules/ModuleC

In case your extension bundles only one module, the extension name is expected to match the module name. For example, if your extension is named DoSomethingAwesome, the associated module is expected to be named DoSomethingAwesome. The following pages will then be created:

Documentation/Nightly/Extensions/DoSomethingAwesome
Documentation/Nightly/Modules/DoSomethingAwesome

where page Extensions/DoSomethingAwesome redirect to page Modules/DoSomethingAwesome.

To setup a redirection, simply add the following text to page Extensions/DoSomethingAwesome:

#REDIRECT [[Documentation/Nightly/Modules/DoSomethingAwesome]]

For an example, see here

More details about redirection are available here: http://www.mediawiki.org/wiki/Help:Redirects

Which URL should be associated with EXTENSION_HOMEPAGE metadata ?

Extensions available through the Slicer Extensions Catalog are expected to have a page created under the Nightly documentation namespace. The corresponding URL should be associated with the EXTENSION_HOMEPAGE metadata.

For example:

set(EXTENSION_HOMEPAGE "http://slicer.org/wiki/Documentation/Nightly/Extensions/DoSomethingGreat")
set(EXTENSION_HOMEPAGE "http://slicer.org/wiki/Documentation/Nightly/Extensions/DoSomethingAwesome")

Note that this also apply for extension bundling only one module. Indeed, in this case the page will redirect to the appropriate module page. For example: http://www.slicer.org/wiki/Documentation/Nightly/Extensions/SkullStripper

How to rename an extension to add new features ?

If you created an extension to perform Task1, but later on, your module is getting more generic and you add some other tasks, the name of your extension might change. In order to rename, your extension, you should:

Remove your old extension from the ExtensionsIndex
Then, submit your extension again (including new features) with a new name
Make also sure to add redirection from the "deprecated" module documentation to the "new" pages. On the Slicer wiki, this could be using the #REDIRECT instruction.

How to check if an extension is built by Slicer Extensions build system ?

Sometimes an extension could be built either as a standalone package or as a Slicer extension.

To differenciate the two cases, the developer could check for the value of:

<ExtensionName>_BUILD_SLICER_EXTENSION

This variable will be set to ON when the extension is built by the Slicer Extensions build system.

For details: https://github.com/Slicer/Slicer/blob/ff5f5a866d8afcaa0f2e6f615cc8f8cf07361741/Extensions/CMake/SlicerBlockBuildPackageAndUploadExtension.cmake#L95

How often extensions are uploaded on the extensions server ?

Slicer extensions are built and uploaded on the extensions server every day.

To be more specific, the frequency of extensions build and upload associated with:

Slicer nightly package occurs every night and also continuously during the day.
Slicer 4.10 lastest stable release package occurs every night.

Will an extension be uploaded if associated tests are failing ?

Independently of the extension test results, if the extension could be successfully packaged, it will be uploaded on the extensions server.

How do I associate a remote with my local extension git source directory ?

1) Start a terminal (or Git Bash on Windows)

2) Get the associated SSH remote url. Need help ?

3) Associate the remote URL with your local git source tree

git remote add origin git://github.com/<username>/MyExtension

Which remote name is expected for extension git checkout ?

When packaging an extension and generating the associated description file, the system will look for a remote named origin.

In case you get the error reported below, you will have to either rename or add a remote. Need help ?

CMake Warning at /path/to/Slicer/CMake/FindGit.cmake:144 (message):
No remote origin set for git repository: /path/to/MyExtension
Call Stack (most recent call first):
/path/to/Slicer/CMake/SlicerMacroExtractRepositoryInfo.cmake:99 (GIT_WC_INFO)
/path/to/Slicer/CMake/SlicerExtensionCPack.cmake:55 (SlicerMacroExtractRepositoryInfo)
CMakeLists.txt:25 (include)

Why ExtensionWizard failed to describe extension: "script does not set 'EXTENSION_HOMEPAGE'" ?

The issue is that the your extension has a "non standard" layout and the wizard was now way of extracting the expected information.

Similar issue has been discussed and reported for the "SPHARM-PDM" or UKF extension.

First half of the solution would be to move the metadata from Common.cmake to CMakeLists.txt as it is done in [1]

Then, you could make sure there is a project() statement by following what is suggested in [2]

If you prefer not to re-organize your extension, you could still contribute extension description file. See here for details.

[1] http://www.nitrc.org/plugins/scmsvn/viewcvs.php?view=rev&root=spharm-pdm&revision=228

[2] http://www.na-mic.org/Bug/view.php?id=3737#c12081

Is project() statement allowed in extension CMakeLists.txt ?

Following Slicer r22038, the project statement is required.

Is call to "if(NOT Slicer_SOURCE_DIR)" required to protect "find_package(Slicer)" in extension CMakeLists.txt ?

Following Slicer r22063, protecting call to find_package(Slicer) with if(NOT Slicer_SOURCE_DIR) is optional and should be removed to keep code simpler and easier to maintain.

Before:

cmake_minimum_required(VERSION 2.8.9)

if(NOT Slicer_SOURCE_DIR)
  find_package(Slicer COMPONENTS ConfigurePrerequisites)
endif()

if(NOT Slicer_SOURCE_DIR)
  set(EXTENSION_NAME EmptyExtensionTemplate)
  set(EXTENSION_HOMEPAGE "http://www.slicer.org/wiki/Documentation/Nightly/Extensions/EmptyExtensionTemplate")
  set(EXTENSION_CATEGORY "Examples")
  set(EXTENSION_CONTRIBUTORS "Jean-Christophe Fillion-Robin (Kitware)")
  set(EXTENSION_DESCRIPTION "This is an example of extension bundling N module(s)")
  set(EXTENSION_ICONURL "http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Extensions/Testing/EmptyExtensionTemplate/EmptyExtensionTemplate.png?revision=21746&view=co")
  set(EXTENSION_SCREENSHOTURLS "http://wiki.slicer.org/slicerWiki/images/4/42/Slicer-r19441-EmptyExtensionTemplate-screenshot.png")
endif()

if(NOT Slicer_SOURCE_DIR)
  find_package(Slicer REQUIRED)
  include(${Slicer_USE_FILE})
endif()

add_subdirectory(ModuleA)

if(NOT Slicer_SOURCE_DIR)
  include(${Slicer_EXTENSION_CPACK})
endif()

After:

cmake_minimum_required(VERSION 2.8.9)

find_package(Slicer COMPONENTS ConfigurePrerequisites)

project(EmptyExtensionTemplate)

set(EXTENSION_HOMEPAGE "http://www.slicer.org/wiki/Documentation/Nightly/Extensions/EmptyExtensionTemplate")
set(EXTENSION_CATEGORY "Examples")
set(EXTENSION_CONTRIBUTORS "Jean-Christophe Fillion-Robin (Kitware)")
set(EXTENSION_DESCRIPTION "This is an example of empty extension")
set(EXTENSION_ICONURL "http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Extensions/Testing/EmptyExtensionTemplate/EmptyExtensionTemplate.png?revision=21746&view=co")
set(EXTENSION_SCREENSHOTURLS "http://wiki.slicer.org/slicerWiki/images/4/42/Slicer-r19441-EmptyExtensionTemplate-screenshot.png")

find_package(Slicer REQUIRED)
include(${Slicer_USE_FILE})

add_subdirectory(ModuleA)

include(${Slicer_EXTENSION_CPACK})

Why is the --contribute option is not available with the ExtensionWizard ?

Wizard contribute option is available only (1) if Slicer is built with OpenSSL support or (2) directly from the nightly.

To build Slicer with SSL support, you need to build (or download) Qt with SSL support and configure Slicer with -DSlicer_USE_PYTHONQT_WITH_OPENSSL:BOOL=ON

How dependent extensions are configured and built ?

If an ExtensionB depends on an ExtensionA, ExtensionA should be listed as dependency in the metadata of ExtensionB.

This can be done setting EXTENSION_DEPENDS in the CMakeLists.txt or by specifying depends field in the description file.

Doing so will ensure that:

(1) the extension build system configure the extensions in the right order
(2) ExtensionB is configured with option ExtensionA_DIR.

Documentation/4.5/Developers/FAQ/Extensions

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