Documentation/4.3/ScriptRepository - Revision history

Lasso: Moved FillRoi.py module to an official extension: VolumeClip (Volume clip with ROI)

2014-10-25T19:05:56Z

Moved FillRoi.py module to an official extension: VolumeClip (Volume clip with ROI)

Fedorov at 20:37, 25 April 2014

2014-04-25T20:37:26Z

Fedorov: /* Launching Slicer */

2014-02-28T21:57:14Z

Launching Slicer

Fedorov: /* Launching Slicer */

2014-02-28T21:57:02Z

Launching Slicer

Fedorov: /* Launching Slicer */

2014-02-28T21:56:48Z

Launching Slicer

Fedorov: /* Community-contributed examples */

2014-02-28T21:56:31Z

Community-contributed examples

Fedorov: /* Community-contributed examples */

2014-02-28T21:17:10Z

Community-contributed examples

UpdateBot: Nightly -> 4.3

2013-09-05T03:41:35Z

Nightly -> 4.3

New page

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

=Community-contributed modules=

Usage: save the .py file to a directory, add the directory to the additional module paths in the Slicer application settings.

==Segmentation==
* [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/sandbox/FillRoiModule/FillRoi.py FillRoi.py]: Fill a region of interest in a labelmap volume with a constant value. This can be used after an automatic segmentation for removing certain regions of a volume.

==Filters==
* [https://raw.github.com/pieper/VolumeMasker/master/VolumeMasker.py VolumeMasker.py]: Update a target volume with the results of setting all input volume voxels to 0 except for those that correspond to a selected label value in an input label map (Used for example in the volume rendering in [https://www.youtube.com/watch?v=dfu2gugHLHs this video).

==DICOM==
* [https://gist.github.com/pieper/6186477 dicom header browser] to easily scroll through dicom files using dcmdump.

=Community-contributed examples=

Usage: Copy-paste the shown code lines or linked .py file contents into Python console in Slicer.

==Capture==
* Get a MRML node in the scene based on the node name and call methods of that object. For the MRHead sample data:
vol=slicer.util.getNode('MR*')
vol.GetImageData().GetDimensions()
* Capture the full Slicer screen and save it into a file
img = qt.QPixmap.grabWidget(slicer.util.mainWindow()).toImage()
img.save('c:/tmp/test.png')
* [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/sandbox/CaptureRotationVideo/CaptureRotationVideo.py CaptureRotationVideo.py]: Capture a video of the scene rotating in the 3D view

==Launching Slicer==
* How to open an .mrb file with Slicer at the command line?
Slicer.exe --python-code "slicer.util.loadScene( 'f:/2013-08-23-Scene.mrb' )"
* How to run a script in the Slicer environment in batch mode (without showing any graphical user interface)?
Slicer.exe --python-code "doSomething; doSomethingElse; etc." --testing --no-splash --no-main-window

← Older revision		Revision as of 19:05, 25 October 2014
Line 6:		Line 6:

	Usage: save the .py file to a directory, add the directory to the additional module paths in the Slicer application settings.		Usage: save the .py file to a directory, add the directory to the additional module paths in the Slicer application settings.
−
−	~~==Segmentation==~~
−	* [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/sandbox/FillRoiModule/FillRoi.py FillRoi.py]: Fill a region of interest in a labelmap volume with a constant value. This can be used after an automatic segmentation for removing certain regions of a volume.

	==Filters==		==Filters==

@@ Line 38: / Line 38: @@
 * To create an animated gif of the saved frames, you can use the following tools:
 ** [https://developer.apple.com/library/mac/documentation/Darwin/Reference/ManPages/man1/sips.1.html sips] (Mac only) to convert single frame to GIF format (cannot save as .gif with QImage)
-** [http://www.lcdf.org/gifsicle/ gifsicle]] to combine individual frames into a single animated gif (gifsicle is a command line tool, so you can batch it!)
+** [http://www.lcdf.org/gifsicle/ gifsicle] to combine individual frames into a single animated gif (gifsicle is a command line tool, so you can batch it!)

@@ Line 37: / Line 37: @@
    Slicer.exe --python-code "doSomething; doSomethingElse; etc." --testing --no-splash --no-main-window
 * To create an animated gif of the saved frames, you can use the following tools:
-** [[https://developer.apple.com/library/mac/documentation/Darwin/Reference/ManPages/man1/sips.1.html sips] (Mac only) to convert single frame to GIF format (cannot save as .gif with QImage)
+** [https://developer.apple.com/library/mac/documentation/Darwin/Reference/ManPages/man1/sips.1.html sips] (Mac only) to convert single frame to GIF format (cannot save as .gif with QImage)
-** [[http://www.lcdf.org/gifsicle/ gifsicle]] to combine individual frames into a single animated gif (gifsicle is a command line tool, so you can batch it!)
+** [http://www.lcdf.org/gifsicle/ gifsicle]] to combine individual frames into a single animated gif (gifsicle is a command line tool, so you can batch it!)

@@ Line 36: / Line 36: @@
 * How to run a script in the Slicer environment in batch mode (without showing any graphical user interface)?
    Slicer.exe --python-code "doSomething; doSomethingElse; etc." --testing --no-splash --no-main-window
-* To create an animated gifs of the saved frames, you can use the following tools:
+* To create an animated gif of the saved frames, you can use the following tools:
 ** [[https://developer.apple.com/library/mac/documentation/Darwin/Reference/ManPages/man1/sips.1.html sips] (Mac only) to convert single frame to GIF format (cannot save as .gif with QImage)
 ** [[http://www.lcdf.org/gifsicle/ gifsicle]] to combine individual frames into a single animated gif (gifsicle is a command line tool, so you can batch it!)

← Older revision		Revision as of 21:56, 28 February 2014
Line 36:		Line 36:
	* How to run a script in the Slicer environment in batch mode (without showing any graphical user interface)?		* How to run a script in the Slicer environment in batch mode (without showing any graphical user interface)?
	Slicer.exe --python-code "doSomething; doSomethingElse; etc." --testing --no-splash --no-main-window		Slicer.exe --python-code "doSomething; doSomethingElse; etc." --testing --no-splash --no-main-window
		+	* To create an animated gifs of the saved frames, you can use the following tools:
		+	** [[https://developer.apple.com/library/mac/documentation/Darwin/Reference/ManPages/man1/sips.1.html sips] (Mac only) to convert single frame to GIF format (cannot save as .gif with QImage)
		+	** [[http://www.lcdf.org/gifsicle/ gifsicle]] to combine individual frames into a single animated gif (gifsicle is a command line tool, so you can batch it!)

@@ Line 31: / Line 31: @@
    img = qt.QPixmap.grabWidget(slicer.app.layoutManager().sliceWidget(viewNames[0]))
 * [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/sandbox/CaptureRotationVideo/CaptureRotationVideo.py CaptureRotationVideo.py]: Capture a video of the scene rotating in the 3D view
 ==Launching Slicer==
 * How to open an .mrb file with Slicer at the command line?
@@ Line 36: / Line 40: @@
 * How to run a script in the Slicer environment in batch mode (without showing any graphical user interface)?
    Slicer.exe --python-code "doSomething; doSomethingElse; etc." --testing --no-splash --no-main-window