View source for Documentation/4.4/Developers/FAQ/Extensions

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{{:Documentation/{{documentation/version}}/FAQ/Extensions}}

== What is an extension description file ? ==

See [[Documentation/{{documentation/version}}/Developers/Extensions/DescriptionFile|Description file description]]

== Can an extension contain different type of modules ? ==

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

See also [[Documentation/{{documentation/version}}/Developers/FAQ#What_is_an_extension_.3F|What_is_an_extension ?]]

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

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

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

== What is the Extensions Index ? ==

{{:Documentation/{{documentation/version}}/Developers/Extensions/Index}}

== 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 ? ==
{{:Documentation/{{documentation/version}}/Developers/Tutorials/ObtainExtensionServerApiKey}}

== 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, <code>MIDAS_PACKAGE_EMAIL</code> and <code>MIDAS_PACKAGE_API_KEY</code>, you would simply need to configure your extension using:

{{pre2|<nowiki>
cd MyExtension-build
cmake -DCMAKE_BUILD_TYPE:STRING=Release -DSlicer_DIR:PATH=/path/to/Slicer-Superbuild/Slicer-build ../MyExtension
make ExperimentalUpload
</nowiki>}}

[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 [[Documentation/{{documentation/version}}/Developers/ExtensionWizard|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 <code>MyExtension</code>, this could be achieved doing:

{|width = "100%"
! width="50%" style="border-bottom: 1px solid darkgrey;font-size: 75%;"| Makefile
! width="50%" style="border-bottom: 1px solid darkgrey;font-size: 75%;"| Visual Studio
|-
| valign="top" |
{{pre2|<nowiki>
$ mkdir MyExtension-build
$ cd MyExtension-build
$ cmake -DCMAKE_BUILD_TYPE:STRING=Release -DSlicer_DIR:PATH=/path/to/Slicer-Superbuild/Slicer-build ../MyExtension
$ make</nowiki>
}}
| valign="top" |
<ol start="1" style="list-style-type: decimal;">
<li>Start CMake, select source and build directory</li>
<li>Add <code>Slicer_DIR</code> entry to the cache</li>
<li>Click on <code>Configure</code>, select generator, then click on <code>Generate</code> button.</li>
<li>Open <code>MyExtension.sln</code>, select <code>Release</code> configuration, then menu <code>Project -> Build Solution</code>.</li>
</ol>
|}

== How to package an extension ? ==

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

{|width = "100%"
! width="50%" style="border-bottom: 1px solid darkgrey;font-size: 75%;"| Makefile
! width="50%" style="border-bottom: 1px solid darkgrey;font-size: 75%;"| Visual Studio
|-
| valign="top" |
{{pre2|<nowiki>
$ make package
</nowiki>
}}
| valign="top" |
<ol start="1" style="list-style-type: decimal;">
<li>Open <code>MyExtension.sln</code></li>
<li>Select <code>PACKAGES</code> project, then right click and select <code>Build</code></li>
</ol>
|}

== How to upload an extension ? ==

<ol style="list-style-type:none; border-left:thick solid red; padding-left:1em;">
  <li>{{:Documentation/{{documentation/version}}/Developers/Tutorials/BuildTestPackageDistributeExtensions/ExperimentalFolderAccess}}</li>
</ol>

Assuming your extension has been built and packaged into folder <code>MyExtension-build</code>, this could be achieved by first re-configuring the project providing your [[#How_to_obtain_an_API_key_to_submit_on_the_extension_server_.3F|midas credentials]] and then building the <code>ExperimentalUploadOnly</code> target:

{|width = "100%"
! width="50%" style="border-bottom: 1px solid darkgrey;font-size: 75%;"| Makefile
! width="50%" style="border-bottom: 1px solid darkgrey;font-size: 75%;"| Visual Studio
|-
| valign="top" |
{{pre2|<nowiki>
$ cmake -DMIDAS_PACKAGE_EMAIL:STRING=<YOUR-MIDAS-LOGIN> -DMIDAS_PACKAGE_API_KEY:STRING=<YOUR-MIDAS-APIKEY> .
$ make ExperimentalUploadOnly
</nowiki>
}}
| valign="top" |
<ol start="1" style="list-style-type: decimal;">
<li>Start CMake, select source and build directory</li>
<li>Add <code>MIDAS_PACKAGE_EMAIL</code> and <code>MIDAS_PACKAGE_API_KEY</code> entries to the cache</li>
<li>Open <code>MyExtension.sln</code></li>
<li>Select <code>Release</code> configuration</li>
<li>Select <code>ExperimentalUploadOnly</code> project, then right click and select <code>Build</code></li>
</ol>
|}

== Can an extension depend on other extensions ? ==

Yes. An <code>ExtensionFoo</code> can depend on <code>ExtensionBar</code>

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

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

* <code>Extension1</code> containing  <code>ModuleA</code>
* <code>Extension2</code> containing  <code>ModuleB</code> and <code>ModuleC</code>

and add the following variable to <code>Extension2/CMakeLists.txt</code>:
<pre>
set(EXTENSION_DEPENDS Extension1)
</pre>

'''User''': 
* If user installs <code>Extension2</code>, <code>Extension1</code> will automatically be installed first.

'''Developer''': 
* The generated extension description file have a <code>depends</code> field. See [[Documentation/{{documentation/version}}/Developers/Extensions/DescriptionFile|here]] for details.
* The extension framework will build the extension in order. When building <code>Extension2</code>, it will pass the CMake option <code>-DExtension1_DIR:PATH=/path/to/Extension1-build</code>.

== 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.

<table class="alternate">
  <tr>
    <th>Target name</th>
    <th>Description</th>
  </tr>
  <tr>
    <td><code>Experimental</code></td>
    <td>Configure, build, test the extension and publish result on CDash.</td>
  </tr>
  <tr>
    <td><code>ExperimentalUpload</code></td>
    <td>Equivalent to Experimental target followed by packaging and upload of the extension on the extension server.</td>
  </tr>
  <tr>
    <td><code>ExperimentalUploadOnly</code></td>
    <td>Only proceed to the upload of the extension on the extension server.</td>
  </tr>
  <tr>
    <td><code>test</code> or <code>BUILD_TESTS</code></td>
    <td>Locally execute the test</td>
  </tr>
  <tr>
    <td><code>package</code> or <code>PACKAGE</code></td>
    <td>Locally package the extension</td>
  </tr>
</table>

== 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 <code>Slicer.app</code> is created. As explained [http://developer.apple.com/library/mac/#documentation/CoreFoundation/Conceptual/CFBundles/Introduction/Introduction.html 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 [http://www.cmake.org/cmake/help/v2.8.8/cmake.html#module:BundleUtilities BundleUtilities] module.

This module is used in two situations:
# Fixup of Slicer application itself. See [https://github.com/Slicer/Slicer/blob/master/CMake/SlicerCPack.cmake#L36-68 SlicerCPack.cmake#L36-68] and [https://github.com/Slicer/Slicer/blob/master/CMake/SlicerCPackBundleFixup.cmake.in SlicerCPackBundleFixup.cmake.in]
# Fixup of an extension package. See [https://github.com/Slicer/Slicer/blob/master/CMake/SlicerExtensionCPack.cmake#L126-143 SlicerExtensionCPack.cmake#L126-143] and [https://github.com/Slicer/Slicer/blob/master/CMake/SlicerExtensionCPackBundleFixup.cmake.in 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 <code>Documentation/Nightly/Modules</code>
* All extension documentation pages should be located under <code>Documentation/Nightly/Extensions</code>


For example, if an an extension named <code>DoSomethingGreat</code> bundles three modules <code>ModuleA</code>, <code>ModuleB</code> and <code>ModuleC</code>. The following pages should be created:
* <code>Documentation/Nightly/Extensions/DoSomethingGreat</code>
* <code>Documentation/Nightly/Modules/ModuleA</code>
* <code>Documentation/Nightly/Modules/ModuleB</code>
* <code>Documentation/Nightly/Modules/ModuleC</code>


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 <code>DoSomethingAwesome</code>, the associated module is expected to be named <code>DoSomethingAwesome</code>. The following pages will then be created:
* <code>Documentation/Nightly/Extensions/DoSomethingAwesome</code>
* <code>Documentation/Nightly/Modules/DoSomethingAwesome</code>
where page <code>Extensions/DoSomethingAwesome</code> redirect to page <code>Modules/DoSomethingAwesome</code>.


To setup a redirection, simply add the following text to page <code>Extensions/DoSomethingAwesome</code>:
<pre>
#REDIRECT [[Documentation/Nightly/Modules/DoSomethingAwesome]]
</pre>
For an example, see [http://www.slicer.org/wiki?title=Documentation/Nightly/Extensions/SkullStripper&action=edit 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 <code>Nightly</code> documentation namespace. The corresponding URL should be associated with the <code>EXTENSION_HOMEPAGE</code> metadata.

For example:
* <code><nowiki>set(EXTENSION_HOMEPAGE "http://slicer.org/wiki/Documentation/Nightly/Extensions/DoSomethingGreat")</nowiki></code>
* <code><nowiki>set(EXTENSION_HOMEPAGE "http://slicer.org/wiki/Documentation/Nightly/Extensions/DoSomethingAwesome")</nowiki></code>

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 [http://www.mediawiki.org/wiki/Help:Redirects #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:
<pre>
<ExtensionName>_BUILD_SLICER_EXTENSION
</pre>

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 [[Documentation/{{documentation/version}}/Developers/Extensions/Server|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 {{documentation/currentversion}} 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 [[Documentation/{{documentation/version}}/Developers/Extensions/Server|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. [https://help.github.com/articles/which-remote-url-should-i-use#cloning-with-ssh Need help ?]

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

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

== Which remote name is expected for extension git checkout ? ==

When packaging an extension and generating the associated [[Documentation/{{documentation/version}}/Developers/Extensions/DescriptionFile|description file]], the system will look for a remote named <code>origin</code>.

In case you get the error reported below, you will have to either rename or add a remote. [http://git-scm.com/book/en/Git-Basics-Working-with-Remotes Need help ?]

<pre>
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)
</pre>

== 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 [[Documentation/{{documentation/version}}/Developers/Tutorials/Contribute_Extension_Description_File|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 [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=22038 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 [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=22063 r22063], protecting call to <code>find_package(Slicer)</code> with <code>if(NOT Slicer_SOURCE_DIR)</code>
is optional and should be removed to keep code simpler and easier to maintain.

Before:

{{pre2|<nowiki>
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://www.slicer.org/w/img_auth.php/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()
</nowiki>}}

After:

{{pre2|<nowiki>
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://www.slicer.org/w/img_auth.php/4/42/Slicer-r19441-EmptyExtensionTemplate-screenshot.png")

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

add_subdirectory(ModuleA)

include(${Slicer_EXTENSION_CPACK})
</nowiki>}}

== 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 <code>-DSlicer_USE_PYTHONQT_WITH_OPENSSL:BOOL=ON</code>

== 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 <code>EXTENSION_DEPENDS</code> in the <code>CMakeLists.txt</code> or by specifying <code>depends</code> field in the [[Documentation/{{documentation/version}}/Developers/Extensions/DescriptionFile|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 <code>ExtensionA_DIR</code>.