TubeTK/Slicer: Difference between revisions

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'''[[TubeTK|Home]]'''
*[[TubeTK/About|About]]
*[[TubeTK/Images|Image Gallery]]
*[[TubeTK/Data|Data and Publications]]
<br>
<br>
<b>[http://public.kitware.com/Wiki/TubeTK Home]</b>
----
*[[TubeTK/About | About]]
*[[TubeTK/Events | Events]]
*[[TubeTK/Images | Image Gallery]]
*[[TubeTK/Data | Data and Publications]]
<br>
<br>
<hr>
'''For Users'''
* [[TubeTK/Installation|Installation]]
* [[TubeTK/Documentation|Methods & Apps]]
* [[TubeTK/Slicer|TubeTK with 3D Slicer]]
* [[TubeTK/OsiriX|TubeTK with OsiriX]]
<br>
<br>
<b>For Users</b>
----
* [[TubeTK/Installation | Installation]]
* [[TubeTK/Documentation | Methods & Apps]]
* [[TubeTK/Slicer | TubeTK with Slicer]]
* [[TubeTK/ImageJ | TubeTK with ImageJ]]
<br>
<br>
<hr>
'''For Developers'''
* [[TubeTK/Development|Development Docs]]
<br>
<br>
<b>For Developers</b>
----
* [[TubeTK/Development | Development Docs]]
<br>
<br>
<hr>
'''[https://github.com/TubeTK/TubeTK/issues Report Bugs<br>Request Features]'''
<br>
<br>
<b>[[TubeTK/Team | Contact Us]]</b>
<br>
----
<br>
'''[[TubeTK/Contact|Contact Us]]'''


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= TubeTK in 3D Slicer =
= TubeTK in 3D Slicer =


* Please use [http://www.slicer.org/slicerWiki/index.php/Slicer4 Slicer4]
== Overview ==
* Note that there are different instructions for '''users''' and '''developers'''
** For now, TubeTK must be built from source:  [[TubeTK/Development | See the TubeTK developers page for instructions to build and extend TubeTK]]
** '''Users''': Download a pre-compiled version of Slicer
** '''Developers''': Build Slicer from source


== Users ==
Slicer 3D is the recommended platform for using TubeTK.  Using TubeTK stand-alone from the command-line is also well supported.


=== Download 3D Slicer ===
You must first install Slicer, and then build TubeTK using that installed version of Slicer to provide the dependencies for TubeTK (e.g., ITK, VTK, CTK).
* Download from http://www.slicer.org/pages/Special:SlicerDownloads
* Select "Type of Download": Snapshots
* Choose your operating system: Windows, Mac OS X, Linux or Solaris
* File to download = the latest version of Slicer4, e.g., "Slicer-4.0.beta..."


=== Add TubeTK's Command Line Modules ===
== Details ==
* Copy the TubeTK plugins to Slicer's plugins directory.  TubeTK plugins include the substring 'tube':
cp '''<YourTubeTKBuildDirectory>'''/TubeTK-Build/lib/TubeTK/Plugins/*tube*
      '''<YourSlicerDirectory>'''/lib/Slicer3/Plugins


=== Run 3D Slicer ===
=== Get CMake ===
cd '''<YourSlicerDirectory>'''
./Slicer


* The TubeTK modules will now be in the list of modules
Install the current stable release of CMake
* Download binaries from http://www.cmake.org


== Developers ==
=== Get 3D Slicer ===
Install the current stable release of Slicer
* '''Download 3D Slicer Binaries:''' from http://download.slicer.org/
* '''Or, build 3D Slicer from source:''' [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers/Build_Instructions Slicer4 Build Instructions]
** Configuration recommendations:
*** In CMake, turn-on advanced options and change BUILD_TYPE to Release
*** In CMake, change Slicer_USE_PYTHONQT_WITH_TCL to OFF


=== Build 3D Slicer ===
=== Get Boost (optional) ===
* Build Slicer4 according to the [http://www.slicer.org/slicerWiki/index.php/Slicer4_Build_instructions Slicer4 Build Instructions]
Boost is used by select TubeTK applications.
* Boost must be built from source to resolve linking errors on 64 bit machines on current binaries for Boost
* Version 1.54 or later is needed
* Download from http://www.boost.org/


=== Add TubeTK's Command Line Modules ===
=== Build TubeTK using Slicer ===
* Copy the TubeTK plugins to Slicer's plugins directory. TubeTK plugins include the substring 'tube':
TubeTK will use Slicer's ITK, VTK, and other libraries during its build process, to ensure compatibility with Slicer.
cp '''<YourTubeTKBuildDirectory>'''/TubeTK-Build/lib/TubeTK/Plugins/*tube*  
* In CMake, set the following options
    '''<YourSlicerBuildDirectory>'''/Slicer-build/lib/Slicer3/Plugins
** BUILD_TYPE = Release
** USE_SLICER_MODULES = True


=== Add TubeTK's Slicer python modules ===
=== Configure Slicer to load TubeTK's modules ===
* Copy all of TubeTK's slicer python modules to Slicer's QTScriptableModules directory:
Run Slicer
cp '''<YourTubeTKSourceDirectory>'''/Applications/SlicerModules/*.py
* Edit -> Application Settings -> Modules -> Additional module paths (click >> to the right of the box, then the Add button)
    '''<YourSlicerSourceDirectory>'''/QTScriptedModules/Scripts
* Select '''<YourTubeTKBuildDirectory>'''/TubeTK-Build/lib/TubeTK/Plugins/
* Add TubeTK's slicer python modules to the list in '''<YourSlicerSourceDirectory>'''/QTScriptedModules/Scripts/CMakeLists.txt
* Restart Slicer
* Re-build Slicer


=== Run 3D Slicer ===
=== Restart 3D Slicer ===
  cd '''<YourSlicerBuildDirectory>'''/Slicer-build
* On restart, the TubeTK modules will now be in the list of modules. All TubeTK module names end with (TubeTK)
./Slicer


* The TubeTK modules will now be in the list of modules
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[[Category:TubeTK|Slicer]]

Latest revision as of 14:20, 6 January 2015

__NOTITLE__


TubeTK Header.jpg

Home




For Users




For Developers




Report Bugs
Request Features




Contact Us

TubeTK in 3D Slicer

Overview

Slicer 3D is the recommended platform for using TubeTK. Using TubeTK stand-alone from the command-line is also well supported.

You must first install Slicer, and then build TubeTK using that installed version of Slicer to provide the dependencies for TubeTK (e.g., ITK, VTK, CTK).

Details

Get CMake

Install the current stable release of CMake

Get 3D Slicer

Install the current stable release of Slicer

  • Download 3D Slicer Binaries: from http://download.slicer.org/
  • Or, build 3D Slicer from source: Slicer4 Build Instructions
    • Configuration recommendations:
      • In CMake, turn-on advanced options and change BUILD_TYPE to Release
      • In CMake, change Slicer_USE_PYTHONQT_WITH_TCL to OFF

Get Boost (optional)

Boost is used by select TubeTK applications.

  • Boost must be built from source to resolve linking errors on 64 bit machines on current binaries for Boost
  • Version 1.54 or later is needed
  • Download from http://www.boost.org/

Build TubeTK using Slicer

TubeTK will use Slicer's ITK, VTK, and other libraries during its build process, to ensure compatibility with Slicer.

  • In CMake, set the following options
    • BUILD_TYPE = Release
    • USE_SLICER_MODULES = True

Configure Slicer to load TubeTK's modules

Run Slicer

  • Edit -> Application Settings -> Modules -> Additional module paths (click >> to the right of the box, then the Add button)
  • Select <YourTubeTKBuildDirectory>/TubeTK-Build/lib/TubeTK/Plugins/
  • Restart Slicer

Restart 3D Slicer

  • On restart, the TubeTK modules will now be in the list of modules. All TubeTK module names end with (TubeTK)