Slicer Wiki - User contributions [en]

Documentation/Nightly/Developers/FAQ/Extensions

2017-03-13T13:37:10Z

Mholden8: /* How to run extension tests ? */

<noinclude>{{documentation/versioncheck}}</noinclude>
<noinclude>__TOC__
={{#titleparts: {{PAGENAME}} | | -1 }}=</noinclude><includeonly>
='''Developer FAQ: {{{1}}}'''=
</includeonly>

{{: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 types of modules ? ==

Yes. Extensions are used to package together all types 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%;"| Linux or MacOSX (Makefile)
! width="50%" style="border-bottom: 1px solid darkgrey;font-size: 75%;"| Windows (Visual Studio)
|-
| valign="top" |

Start a terminal.
{{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>
}}

'''MaxOSX''': Extension '''must be configured''' specifying <code>CMAKE_OSX_*</code> variables matching the one used to configure Slicer:
* <code>-DCMAKE_OSX_ARCHITECTURES:STRING=x86_64</code>
* <code>-DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=/same/as/Slicer</code>
* <code>-DCMAKE_OSX_SYSROOT:PATH=SameAsSlicer</code>

| valign="top" |

Run ''CMake (cmake-gui)'' from the Windows Start menu.
<ol start="1" style="list-style-type: decimal;">
<li>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>
</ol>

Start Windows Explorer. [http://www.wikihow.com/Open-Windows-Explorer Need help?]
<ol>
<li>Open <code>MyExtension.sln</code> in Visual Studio</li>
<li>Select '''Release''' build configuration.</li>
<li>Select menu <code>Project -> Build Solution</code></li>
</ol>
|}

== Is there a way to automatically set CMAKE_OSX_* variables ? ==

Within your extension, including the <code>ConfigurePrerequisites</code> component before the project statement should ensure it uses the same CMAKE_OSX_* variables as Slicer:

<pre>
find_package(Slicer COMPONENTS ConfigurePrerequisites REQUIRED)

project(Foo)

[...]

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

[...]
</pre>

Note: The <code>ConfigurePrerequisites</code> component should be considered experimental and could change without notice.

For more details, see [https://github.com/Slicer/Slicer/blob/75fc96bf05e65659eb5204f47b5205442cc6fd8e/CMake/SlicerConfig.cmake.in#L10-L38 here].

== How to run extension tests ? ==

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%;"| Linux or MacOSX (Makefile)
! width="50%" style="border-bottom: 1px solid darkgrey;font-size: 75%;"| Windows (Visual Studio)
|-
| valign="top" |

Start a terminal.
{{pre2|<nowiki>
$ ctest -j<NUMBEROFCORES>
</nowiki>
}}

| valign="top" |

To run all tests, start Windows Explorer. [http://www.wikihow.com/Open-Windows-Explorer Need help?]
<ol start="1" style="list-style-type: decimal;">
<li>Open <code>MyExtension.sln</code> in Visual Studio</li>
<li>Select <code>RUN_TESTS</code> project, then right click and select <code>Build</code></li>
</ol>
 

To run test individually, open Command Line Prompt. [http://windows.microsoft.com/en-us/windows/command-prompt-faq Need help?]
{{pre2|<nowiki>
> cd C:\path\to\MyExtension-build
> ctest -R NameOfTest -V
</nowiki>
}}
 

To debug individual tests.
<ol start="1" style="list-style-type: decimal;">
<li>Launch Visual Studio from the Command Line Prompt: <code>C:\path\to\Slicer-build\Slicer.exe --VisualStudio --launcher-no-splash --launcher-additional-settings C:\path\to\MyExtension-build\AdditionalLauncherSettings.ini C:\path\to\MyExtension-build\MyExtension.sln</code></li>
<li>Find the project of the test you want to debug (e.g. ''qSlicerMODULE_NAMEModuleGenericCxxTests'').</li>
<li>Go to the project debugging properties (right-click -> Properties, then Configuration Properties / Debugging).</li>
<li>In ''Command Arguments'', type the name of the test you want to run (e.g. ''qSlicerMODULE_NAMEModuleGenericTest'').</li>
<li>If the test takes arguments, enter the arguments after the test name in ''Command Arguments''.</li>
<li>Set the project as the StartUp Project (right-click -> Set As StartUp Project).</li>
<li>Start debugging (F5).</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%;"| Linux or MacOSX (Makefile)
! width="50%" style="border-bottom: 1px solid darkgrey;font-size: 75%;"| Windows (Visual Studio)
|-
| valign="top" |

Start a terminal.
{{pre2|<nowiki>
$ make package
</nowiki>
}}

| valign="top" |

Start Windows Explorer. [http://www.wikihow.com/Open-Windows-Explorer Need help?]
<ol start="1" style="list-style-type: decimal;">
<li>Open <code>MyExtension.sln</code></li> in Visual Studio
<li>Select <code>PACKAGES</code> project, then right click and select <code>Build</code></li>
</ol>
|}

== 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 ? ==

{{remark|red|{{:Documentation/{{documentation/version}}/Developers/Tutorials/BuildTestPackageDistributeExtensions/ExperimentalFolderAccess}} }}

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%;"| Linux or MacOSX (Makefile)
! width="50%" style="border-bottom: 1px solid darkgrey;font-size: 75%;"| Windows (Visual Studio)
|-
| valign="top" |

Start a terminal.
{{pre2|<nowiki>
$ cmake -DMIDAS_PACKAGE_EMAIL:STRING=<YOUR-MIDAS-LOGIN> -DMIDAS_PACKAGE_API_KEY:STRING=<YOUR-MIDAS-APIKEY> .
$ make ExperimentalUploadOnly
</nowiki>
}}

| valign="top" |

Run ''CMake (cmake-gui)'' from the Windows Start menu.
<ol start="1" style="list-style-type: decimal;">
<li>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>
</ol>

Start Windows Explorer. [http://www.wikihow.com/Open-Windows-Explorer Need help?]
<ol>
<li>Open <code>MyExtension.sln</code></li> in Visual Studio
<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/slicerWiki/index.php?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/slicerWiki/index.php/Documentation/Nightly/Extensions/DoSomethingGreat")</nowiki></code>
* <code><nowiki>set(EXTENSION_HOMEPAGE "http://slicer.org/slicerWiki/index.php/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/slicerWiki/index.php/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/slicerWiki/index.php/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()
</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/slicerWiki/index.php/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})
</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>.

== How to package third party libraries ? ==

Extensions integrating third party libraries should follow the [https://github.com/Slicer/Slicer/tree/master/Utilities/Templates/Extensions/SuperBuild SuperBuild extension template].

Each third party libraries will be configured and built using a dedicated <code>External_MyLib.cmake</code> file, the install location of binaries and libraries should be set to <code>Slicer_INSTALL_BIN_DIR</code> and <code>Slicer_INSTALL_LIB_DIR</code>.

These relative paths are the one that the extensions manager will consider when generating the launcher and application settings for a given extension.

== Can I use C++11/14/17 language features ? ==

Since Slicer is not built with these features (it used c++98/c++03), you should not use C++11/14/17 language features in your extensions.

If your extension can be compiled as a standalone project where you would like to use newer feature, you could rely on CMake detecting compile features. See [https://cmake.org/cmake/help/v3.5/manual/cmake-compile-features.7.html cmake-compile-features] for more details.

== How do I publish a paper about my extension ? ==

Consider publishing a paper describing your extension. This link contains a list of journals that publish papers about software:

[http://www.software.ac.uk/resources/guides/which-journals-should-i-publish-my-software http://www.software.ac.uk/resources/guides/which-journals-should-i-publish-my-software]

== How to force a different Slicer revision for downloading different extension ? ==

Since extensions available from the [[Documentation/{{documentation/currentversion}}/SlicerApplication/ExtensionsManager|Extensions Manager]] are associated with a particular slicer revision, for testing purpose it is practical to override the current revision. This can be done by explicitly setting a revision number.

<pre>
>>> extensionManagerModel = slicer.app.extensionsManagerModel()
>>> extensionManagerModel.slicerRevision = "25742"
</pre>

Documentation/4.3/Announcements

2013-09-13T16:09:26Z

Mholden8:

<noinclude>{{documentation/versioncheck}}</noinclude>
__NOTOC__

{|width="100%"
|align="center"|
[[image:Slicer4Announcement-HiRes.png|center|'''{{documentation/version}}''']]
|}

{|align="center" border="1" style="text-align:center; font-size:120%; border-spacing: 0; padding: 0px;" cellpadding="10"
|[[#Summary|Summary ]]
|[[#What is 3D Slicer|What is 3D Slicer]]
|[[#Slicer {{documentation/version}} Highlights|Slicer {{documentation/version}} Highlights]]
|[[#Slicer Extensions|Slicer Extensions]]
|[[#Other Improvements, Additions & Documentation| Other Improvements, Additions & Documentation]]
|}
=Summary=

The [http://www.slicer.org/pages/Acknowledgments community] of Slicer developers is proud to announce the release of '''Slicer {{documentation/version}}'''.

*Slicer {{documentation/version}} introduces
** a new App store, called the extension manager, for adding capabilities to Slicer. Close to 40 plug-ins are currently available.
** close to 500 feature improvements and bug fixes lead to improved performance and stability.
** augmentation of many modules.
** improved workflows in registration and dMRI
** the multivolume explorer allows interaction with time series and DCE data.
** major improvements to the DICOM module
** a new Markups module to streamline the use of fiducial lists

*Click here to [http://download.slicer.org/ download] Slicer {{documentation/version}} for different platforms and find pointers to the source code, mailing lists and bug tracker.
*Please note that Slicer continues to be a research package and is not intended for clinical use. Testing of functionality is an ongoing activity with high priority, however, some features of Slicer are not fully tested.
*The [[Documentation/{{documentation/version}}/Training|Slicer Training]] page provides a series of courses for learning how to use Slicer. The portfolio contains self-guided presentation and sample data sets.

The main [http://www.slicer.org slicer.org] pages provide a guided tour to the application, training materials, and the development community. New users should start there because we try to keep the pages organized and up to date.

Find out more about Slicer {{documentation/version}} in the webinar held on [...]:

[[Image:Webinar-Slicer-4.1.png|link=http://vimeo.com/41096643|400px|center]]

=What is 3D Slicer=
Slicer is a community platform created for the purpose of subject specific image analysis and visualization.

* Multi-modality imaging including, MRI, CT, US, nuclear medicine, and microscopy
* Multi organ from head to toe
* Bidirectional interface for devices
* Expandable and interfaced to multiple toolkits

There is no restriction on use, but permissions and compliance with rules are responsibility of users. For details on the license see [http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl here]

=Slicer {{documentation/version}} Highlights=
<gallery caption="New and Improved Toolkits and Modules" widths="250px" heights="150px" perrow="3">
Image:ITK_logo.png|Moved from ITKv3 to ITKv4
Image:SimpleITK_Logo.png|Added SimpleITK
Image:CLIAutoRun.png|Added AutoRun mode for CLI modules to interactively search in parameter space and to create pipelines of filters. Watch the [https://vimeo.com/64813350 demo]!
Image:Markups-GUI-Collapsed.png|The [[Documentation/{{documentation/version}}/Modules/Markups|Markups]] module replaces Annotation fiducials.
</gallery>

= Slicer Extensions =

<gallery caption="New and Improved Extensions" widths="250px" heights="150px" perrow="4">
Image:AirwaySegmentation-ICON.png|[[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|Airway Segmentation]] to segment the airway from chest CT images.{{new}}
Image:CMRTK-logo.png|[[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] to analyze cardiac LGE-MRI images. {{new}}
Image:ChangeTracker logo.png|[[Documentation/{{documentation/version}}/Extensions/ChangeTracker| Change Tracker]] for quantification of the subtle changes in pathology.{{new}}
Image:DiceSimilarityCoefficient.png|[[Documentation/{{documentation/version}}/Extensions/DiceComputation|Dice Computation]] to calculate the Dice Similarity Coefficient (DSC) between multiple label map images.{{new}}
Image:DTIAtlasBuilder.jpeg|[[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTI Atlas Builder]] to create an Atlas image as an average of several DTI images that will be registered.{{updated}}
Image:DTIPrep.png|[[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTI Prep]].{{updated}}
Image:DTIProcess-mj.png|[[Documentation/{{documentation/version}}/Extensions/DTIProcess| DTI Process]].{{updated}}
Image:ErodeDilateLabelIcon.png|[[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|Erode/Dilate Label]] to perform binary erosion and dilation on a specified label.{{new}}
Image:FacetedVisualizer.png|[[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|Faceted Visualizer]] to create flexible visualizations using Slicer by combining a 3D digital atlas and 3D scene models with an ontology.{{updated}}
Image:FiberViewerLight.png|[[Documentation/{{documentation/version}}/Extensions/FiberViewerLight| Fiber Viewer Light]] to create fiber clusters based on methods such as Length, Gravity, Hausdorff, or Mean Distribution and Normalized Cut.{{updated}}
Image:IASEM.png|[[Documentation/{{documentation/version}}/Extensions/IASEM| IASEM]] to segmentation and process of IASEM Electron Microscopy images.{{new}}
Image:QuickToolsLogo.png|[[Documentation/{{documentation/version}}/Extensions/ImageMaker|Image Maker]] to create volumes from scratch. {{new}}
Image:LAScarSegmenter.png|[[Documentation/{{documentation/version}}/Extensions/LAScarSegmenter|LA Scar Segmenter]] to perform segmentation of the left atrial scarring tissue from MR images. {{new}}
Image:LASegmenter.png|[[Documentation/{{documentation/version}}/Extensions/LASegmenter|LA Segmenter]] to perform segmentation of the left atrium from MR images.{{new}}
Image:LongitudinalPETCTLogo.png|[[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT| Longitudinal PET/CT]] to provide a user friendly Slicer interface for quantification of DICOM PET/CT image data.{{updated}
Image:MatlabBridgeLogo.png|[[Documentation/{{documentation/version}}/Extensions/MatlabBridge| Matlab Bridge]] to allow running Matlab functions directly in 3D Slicer.{{new}}
Image:ModelClipIcon.png|[[Documentation/{{documentation/version}}/Extensions/ModelClip| Model Clip]] to set osteotomy trajectory with multiple planes, and clip the model with just one click.{{new}}
Image:PathPlannerIcon.png|[[Documentation/{{documentation/version}}/Extensions/PathPlanner| Path Planner]]to facilitate the creation of trajectory.{{new}}
Image:PkModeling.png|[[Documentation/{{documentation/version}}/Extensions/PkModeling| Pk Modeling]] to calculate quantitative parameters from Dynamic Contrast Enhanced DCE-MRI images.{{new}}
Image:PlusRemoteLogo.png|[[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] to send commands through OpenIGTLink Remote to PLUS.{{new}}
Image:Portplacement_icon.png|[[Documentation/{{documentation/version}}/Extensions/PortPlacement| Port Placement]]to assists in the planning of surgical port placement in laparoscopic procedures.{{new}}
Image:ReportingLogo.png|[[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] to create image annotations/markup that are stored in a structured form.{{updated}}
Image:SkullStripper.png|[[Documentation/{{documentation/version}}/Extensions/SkullStripper|Skull Stripper]] to register an atlas image to the patient data.{{updated}}
Image:SlicerIGTLogo.png|[[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] to use all the advanced features of 3D Slicer for real-time navigation.{{new}}
Image:SlicerRT Logo 2.0 128x128.png|[[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] is a tool for powerful radiotherapy research. {{updated}}
Image:SlicerToKiwiExporterLogo.png|[[Documentation/{{documentation/version}}/Extensions/SlicerToKiwiExporter|Slicer To Kiwi Exporter]] to provide an easy way to export [[Documentation/{{documentation/version}}/Modules/Models|models]] into a [http://www.kiwiviewer.org/ KiwiViewer].{{new}}
Image:SobolevSegmenter.png|[[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|Sobolev Segmenter]] implements Sobolev inner product based active contour, using the Chan-Vese energy functional.{{updated}}
Image:SwissSkullStripper.png|[[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|Swiss Skull Stripper]] to register an atlas image to the patient data.{{new}}
Image:TrackerStabilizer.png|[[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|Tracker Stabilizer]] to output a filtered transform node based on an tracker input (transform node).{{new}}
Image:TransformVisualizerLogo.png|[[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] to visualize any transform (linear transform, B-spline deformable transform, any other non-linear transform) or vector volume.{{new}}
Image:TubeTK-scaled.png|[[Documentation/{{documentation/version}}/Extensions/TubeTK| TubeTK]] is an open-source toolkit for the segmentation, registration, and analysis of tubes and surfaces in images.{{updated}}
Image:UKFTractography.png|[[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKF Tractography]] a framework which uses an unscented Kalman filter for performing tractography.{{updated}}
Image:VisuaLine.png|[[Documentation/{{documentation/version}}/Extensions/VisuaLine|VisuaLine]] to display lines in Slicer.{{updated}}
Image:WindowLevelEffectLogo.png|[[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|Window/Level Effect]] to adjust window/level for volumes using mouse and/or region of interest.{{new}}
Image:XNATSlicerIcon.jpg|[[Documentation/{{documentation/version}}/Extensions/XNATSlicer| XNAT Slicer]] Secure GUI-based IO with any XNAT server.{{new}}
Image:PerkTutorLogo.png|[[Documentation/{{documentation/version}}/Extensions/PerkTutor|PerkTutor]] for training in image-guided needle interventions.{{new}}

<!-- You could user either {{new}} or {{updated}} macros.

</gallery>

= Other Improvements, Additions & Documentation =
<gallery caption="" widths="250px" heights="150px" perrow="3">
Image:SlicerModels-Large.svg|Added advanced controls for the [[Documentation/{{documentation/version}}/Modules/Models|model display representation]]
Image:SlicerModels-Large.svg|Depth peeling option for translucent surface models in [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D views]]

Image:Fiber select.PNG|Added [[Documentation/{{documentation/version}}/Modules/FiberBundleLabelSelect|fiber selection based on label map module]]

Image:Fiber select.PNG|Added individual fiber editing option in [[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Tractography Display module]]

Image:SlicerVolume-Large.svg|Added read/write support for [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat|MRC files]]
Image:ctkDoubleSpinBox.gif|Improved support for image precision.
Image:QSlicerDarkStyle.png|Slicer theme for low intensity environment.
</gallery>

= For Developers: Looking at the Code Changes =

From a git checkout you can easily see the all the commits since the time of the 4.4.2 release:

git log --since="Sat Dec 8 03:32:53 2012"

To see a summary of your own commits, you could use something like:

git log --since="Sat Dec 8 03:32:53 2012" --oneline --author=pieper

see [https://www.kernel.org/pub/software/scm/git/docs/git-log.html the git log man page] for more options.

[[Release_Details#Slicer_{{documentation/version}}.0|Commit stats and full changelog]]

= Related Projects =
<gallery caption="" widths="250px" heights="150px" perrow="3">
</gallery>

Documentation/4.3/Modules/WorkflowSegmentation

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Documentation/4.3/Extensions

2013-09-13T16:02:33Z

Mholden8:

<noinclude>{{documentation/versioncheck}}</noinclude>
<noinclude>
__TOC__
</noinclude>= Extensions by Category =

==Cat 1==

==Cat 2==
* [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)
* [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|SwissSkullStripper]] (Bill Lorensen)
* [[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Steve Pieper)
** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]
** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]
** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]
** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]
** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]
** [[Documentation/{{documentation/version}}/Modules/PatientHierarchy|Patient hierarchy]]
** [[Documentation/{{documentation/version}}/Modules/DeformationFieldVisualizer|Transform visualizer (moved to separate extension)]]
** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)
*** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTImport|Plastimatch DICOM-RT import]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTExport|Plastimatch DICOM-RT export]] [[image:UnderConstruction.png|tumb|10px]]
*** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]
*** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)
** [[Documentation/{{documentation/version}}/Modules/CollectFiducials|CollectFiducials]] (Tamas Ungi)
** [[Documentation/{{documentation/version}}/Modules/CreateModels|CreateModels]] (Tamas Ungi, Matthew Holden)
** [[Documentation/{{documentation/version}}/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (Tamas Ungi, Andras Lasso)
** [[Documentation/{{documentation/version}}/Modules/UltrasoundSnapshots|UltrasoundSnapshots]] (Tamas Ungi, Franklin King)
** [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|Matlab Bridge]] (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)
* [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)
* [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)
* [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)
* [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)
* [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)
* [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|SobolevSegmenter]] (Arie Nakhmani)
* [[Documentation/{{documentation/version}}/Extensions/QuickTools|QuickTools]] (Julien Finet)
** [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]]
* [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]]
* [[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|ErodeDilateLabel]] (Junichi)
* [[Documentation/{{documentation/version}}/Extensions/ThingiverseBrowser|ThingiverseBrowser]] (Nigel Goh)
* [[Documentation/{{documentation/version}}/Extensions/PathPlanner|PathPlanner]] (Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/VisuaLine|VisuaLine]] (Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/VirtualFractureReconstruction|Virtual Fracture Reconstruction]] (Karl Fritscher, Peter Karasev)
* [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]] (Pietro Nardelli)
* [[Documentation/{{documentation/version}}/Extensions/ModelClip|ModelClip]] (Jun Lin, Xiaojun Chen)
* [[Documentation/{{documentation/version}}/Extensions/SurfaceMirror|SurfaceMirror]] (Jiaxi Luo, Ruqing Ye, Xiaojun Chen)
* [[Documentation/{{documentation/version}}/Extensions/Scoliosis|Scoliosis]] (Franklin King, Tamas Ungi)
**[[Documentation/{{documentation/version}}/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (Franklin King, Tamas Ungi)
* [[Documentation/{{documentation/version}}/Extensions/PortPlacement|Port Placement]] (Andinet Enquobahrie, Luis G. Torres)
* [[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] (Franklin King, Tamas Ungi)
* [[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] (Franklin King, Andras Lasso, Csaba Pinter)
* [[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|WindowLevelEffect]] (Andrey Fedorov, Steve Pieper)
* [[Documentation/{{documentation/version}}/Extensions/PerkTutor|PerkTutor]] (Tamas Ungi, Matthew Holden)
** [[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]
** [[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]
** [[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]

==Cat 3==
* [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation->TrainModel]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation->PredictLesions]] (Mark Scully)
* [[Documentation/{{documentation/version}}/Extensions/IASEM|IASEM]] (Bradley Lowekamp)
<noinclude>
{{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}
</noinclude>

Documentation/Nightly/Modules/WorkflowSegmentation

2013-09-12T23:33:12Z

Mholden8: Created page with '<noinclude>{{documentation/versioncheck}}</noinclude>  {{documentation/{{documentation/version}}/module-header}} <!-- -----------------------…'

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Author: Tamas Ungi (Queen's University), Matthew Holden (Queen's University) 
Contact: Tamas Ungi, <email>ungi@cs.queesnu.ca</email> 
Website: http://perktutor.org/ 
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
{|
[[Image:PerkTutorLogo.png]]
|
The Workflow Segmentation module is part of the [http://perktutor.org/ Perk Tutor] extension. The purpose of the Workflow Segmentation module is to provide real-time instruction to medical trainees performing needle-based interventions by analyzing the procedural workflow.

Please visit the Workflow Segmentation wiki for more information: https://github.com/PerkTutor/WorkflowSegmentation/wiki.
|
|}


{{documentation/{{documentation/version}}/module-section|Use Cases}}
N/A


{{documentation/{{documentation/version}}/module-section|Tutorials}}
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{{documentation/{{documentation/version}}/module-section|Panels and their use}}
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{{documentation/{{documentation/version}}/module-section|Similar Modules}}
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{{documentation/{{documentation/version}}/module-section|References}}
N/A


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/TransformRecorder

2013-09-12T23:30:08Z

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Author: Tamas Ungi (Queen's University), Matthew Holden (Queen's University) 
Contact: Tamas Ungi, <email>ungi@cs.queesnu.ca</email> 
Website: http://perktutor.org/ 
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
{|
[[Image:PerkTutorLogo.png]]
|
The Transform Recorder module is part of the [http://perktutor.org/ Perk Tutor] extension. The purpose of the Transform Recorder module is to record and save tool trajectories associated with needle-based interventions.

Please visit the Transform Recorder wiki for more information: https://github.com/PerkTutor/TransformRecorder/wiki.
|
|}


{{documentation/{{documentation/version}}/module-section|Use Cases}}
N/A


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
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{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


{{documentation/{{documentation/version}}/module-section|References}}
N/A


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/PerkEvaluator

2013-09-12T23:28:09Z

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Author: Tamas Ungi (Queen's University), Matthew Holden (Queen's University) 
Contact: Tamas Ungi, <email>ungi@cs.queesnu.ca</email> 
Website: http://perktutor.org/ 
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
{|
[[Image:PerkTutorLogo.png]]
|
The Perk Evaluator module is part of the [http://perktutor.org/ Perk Tutor] extension. The purpose of the Perk Evaluator module is to review previously recorded procedures, and calculate motion efficiency metrics.

Please visit the Perk Evaluator wiki for more information: https://github.com/PerkTutor/PerkEvaluator/wiki.
|
|}


{{documentation/{{documentation/version}}/module-section|Use Cases}}
N/A


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
N/A



{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


{{documentation/{{documentation/version}}/module-section|References}}
N/A


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Extensions

2013-09-09T19:57:42Z

Mholden8:

<noinclude>{{documentation/versioncheck}}</noinclude>
<noinclude>
__TOC__
</noinclude>= Extensions by Category =

==Cat 1==

==Cat 2==
* [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)
* [[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Steve Pieper)
** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]
** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]
** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]
** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]
** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]
** [[Documentation/{{documentation/version}}/Modules/PatientHierarchy|Patient hierarchy]]
** [[Documentation/{{documentation/version}}/Modules/DeformationFieldVisualizer|Transform visualizer (moved to separate extension)]]
** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)
*** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTImport|Plastimatch DICOM-RT import]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTExport|Plastimatch DICOM-RT export]] [[image:UnderConstruction.png|tumb|10px]]
*** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]
*** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)
** [[Documentation/{{documentation/version}}/Modules/CollectFiducials|CollectFiducials]] (Tamas Ungi)
** [[Documentation/{{documentation/version}}/Modules/CreateModels|CreateModels]] (Tamas Ungi, Matthew Holden)
** [[Documentation/{{documentation/version}}/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (Tamas Ungi, Andras Lasso)
** [[Documentation/{{documentation/version}}/Modules/UltrasoundSnapshots|UltrasoundSnapshots]] (Tamas Ungi, Franklin King)
** [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|Matlab Bridge]] (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)
* [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)
* [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)
* [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)
* [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)
* [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)
* [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|SobolevSegmenter]] (Arie Nakhmani)
* [[Documentation/{{documentation/version}}/Extensions/QuickTools|QuickTools]] (Julien Finet)
** [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]]
* [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]]
* [[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|ErodeDilateLabel]] (Junichi)
* [[Documentation/{{documentation/version}}/Extensions/ThingiverseBrowser|ThingiverseBrowser]] (Nigel Goh)
* [[Documentation/{{documentation/version}}/Extensions/PathPlanner|PathPlanner]] (Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/VisuaLine|VisuaLine]] (Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/VirtualFractureReconstruction|Virtual Fracture Reconstruction]] (Karl Fritscher, Peter Karasev)
* [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]] (Pietro Nardelli)
* [[Documentation/{{documentation/version}}/Extensions/ModelClip|ModelClip]] (Jun Lin, Xiaojun Chen)
* [[Documentation/{{documentation/version}}/Extensions/SurfaceMirror|SurfaceMirror]] (Jiaxi Luo, Ruqing Ye, Xiaojun Chen)
* [[Documentation/{{documentation/version}}/Extensions/Scoliosis|Scoliosis]] (Franklin King, Tamas Ungi)
**[[Documentation/{{documentation/version}}/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (Franklin King, Tamas Ungi)
* [[Documentation/{{documentation/version}}/Extensions/PortPlacement|Port Placement]] (Andinet Enquobahrie, Luis G. Torres)
* [[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] (Franklin King, Tamas Ungi)
* [[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] (Franklin King, Andras Lasso, Csaba Pinter)
* [[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|WindowLevelEffect]] (Andrey Fedorov, Steve Pieper)
* [[Documentation/{{documentation/version}}/Extensions/PerkTutor|PerkTutor]] (Tamas Ungi, Matthew Holden)
** [[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]
** [[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]
** [[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]

==Cat 3==
* [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation->TrainModel]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation->PredictLesions]] (Mark Scully)
* [[Documentation/{{documentation/version}}/Extensions/IASEM|IASEM]] (Bradley Lowekamp)
<noinclude>
{{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}
</noinclude>

Documentation/Nightly/Extensions/PerkTutor

2013-09-09T19:53:01Z

Mholden8:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Authors: Tamas Ungi (Queen's University), Matthew S. Holden (Queen's University) 
Contact: Tamas Ungi, <email>ungi@cs.queensu.ca</email> 
Website: http://perktutor.org/ 
License: [http://www.slicer.org/pages/LicenseText Slicer license]


{{documentation/{{documentation/version}}/extension-section|Extension Description}}
{|
[[Image:PerkTutorLogo.png]]
|
Perk Tutor is an extension of 3D Slicer, a free, open source software for visualization and image analysis. Perk Tutor can be installed from the 3D Slicer Extension Manager on Windows, Mac, and Linux to use all the advanced features of 3D Slicer for real-time navigation. Perk Tutor contains modules for training in image-guided needle interventions.

Please visit the PerkTutor website for more information: http://perktutor.org/.
|
|}


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]
*[[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]
*[[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}


{{documentation/{{documentation/version}}/extension-section|Tutorials}}


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|References}}


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
{{documentation/{{documentation/version}}/extension-developerinfo}}


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions/PerkTutor

2013-09-09T19:52:32Z

Mholden8:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Authors: Tamas Ungi (Queen's University), Matthew S. Holden (Queen's University) 
Contact: Tamas Ungi, <email>ungi@cs.queensu.ca</email> 
Website: http://perktutor.org/ 
License: [http://www.slicer.org/pages/LicenseText Slicer license]


{{documentation/{{documentation/version}}/extension-section|Extension Description}}
{|
[[Image:PerkTutorLogo.png]]
|
Perk Tutor is an extension of 3D Slicer, a free, open source software for visualization and image analysis. Perk Tutor can be installed from the 3D Slicer Extension Manager on Windows, Mac, and Linux to use all the advanced features of 3D Slicer for real-time navigation. Perk Tutor contains modules for training in image-guided needle interventions.

Please visit the PerkTutor website for more information: http://perktutor.org/.
|
|}


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]
*[[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]
*[[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}


{{documentation/{{documentation/version}}/extension-section|Tutorials}}


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|References}}


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
{{documentation/{{documentation/version}}/extension-developerinfo}}


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions/PerkTutor

2013-09-09T19:52:05Z

Mholden8:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
This work is part of the National Alliance for Medical Image Computing (NAMIC). 
Authors: Tamas Ungi (Queen's University), Matthew S. Holden (Queen's University) 
Contact: Tamas Ungi, <email>ungi@cs.queensu.ca</email> 
Website: http://perktutor.org/ 
License: [http://www.slicer.org/pages/LicenseText Slicer license]


{{documentation/{{documentation/version}}/extension-section|Extension Description}}
{|
[[Image:PerkTutorLogo.png]]
|
Perk Tutor is an extension of 3D Slicer, a free, open source software for visualization and image analysis. Perk Tutor can be installed from the 3D Slicer Extension Manager on Windows, Mac, and Linux to use all the advanced features of 3D Slicer for real-time navigation. Perk Tutor contains modules for training in image-guided needle interventions.

Please visit the PerkTutor website for more information: http://perktutor.org/.
|
|}


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]
*[[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]
*[[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}


{{documentation/{{documentation/version}}/extension-section|Tutorials}}


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|References}}


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
{{documentation/{{documentation/version}}/extension-developerinfo}}


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions/PerkTutor

2013-09-09T19:49:45Z

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
This work is part of the National Alliance for Medical Image Computing (NAMIC). 
Authors: Tamas Ungi (Queen's University), Matthew S. Holden (Queen's University) 
Contact: Tamas Ungi, <email>ungi@cs.queensu.ca</email> 
Website: http://perktutor.org/ 
License: [http://www.slicer.org/pages/LicenseText Slicer license]


{{documentation/{{documentation/version}}/extension-section|Extension Description}}
{|
[[PerkTutorLogo.png]]
|
Perk Tutor is an extension of 3D Slicer, a free, open source software for visualization and image analysis. Perk Tutor can be installed from the 3D Slicer Extension Manager on Windows, Mac, and Linux to use all the advanced features of 3D Slicer for real-time navigation. Perk Tutor contains modules for training in image-guided needle interventions.

Please visit the PerkTutor website for more information: http://perktutor.org/.
|
|}


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]
*[[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]
*[[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}


{{documentation/{{documentation/version}}/extension-section|Tutorials}}


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|References}}


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
{{documentation/{{documentation/version}}/extension-developerinfo}}


{{documentation/{{documentation/version}}/extension-footer}}