Difference between revisions of "Documentation/Nightly/Modules/SlicerToKiwiExporter"

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'''Extension:''' [[Documentation/{{documentation/version}}/Extensions/SlicerToKiwiExporter|SlicerToKiwiExporter]]<br>
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'''Acknowledgments:'''
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This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.<br>
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'''Author:''' Jean-Christophe Fillion-Robin ({{collaborator|name|kitware}})<br>
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'''Contributor1:''' Pat Marion ({{collaborator|name|kitware}})<br>
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'''Contributor2:''' Steve Pieper ({{collaborator|name|isomics}})<br>
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'''Contributor3:''' Atsushi Yamada (Shiga University of Medical Science)<br>
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'''Contact:''' Jean-Christophe Fillion-Robin, <email>jchris.fillionr@kitware.com</email><br>
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Extension: [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]]<br>
 
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Acknowledgments:
 
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This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.<br>
 
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Implementation of the Fuzzy Classification was contributed by Dr. Ming-Ching Chang from GE Research.<br>
 
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[http://www.oasis-brains.org/ OASIS datasets] were used to generate images on this page.<br>
 
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Author: Xiaodong Tao ({{collaborator|name|ge}})<br>
 
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Contributor1: Jean-Christophe Fillion-Robin ({{collaborator|name|kitware}})<br>
 
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Contact: Xiaodong Tao, <email>taox@research.ge.com</email><br>
 
  
 
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The SlicerToKiwiExporter module provides Slicer user with any easy way to export [[Documentation/{{documentation/version}}/Modules/Models|models]] into a [http://www.kiwiviewer.org/ KiwiViewer] scene file.
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[http://www.kiwiviewer.org/ KiwiViewer] is a free, open-source visualization app for exploring scientific and medical datasets that runs on Android and iOS mobile devices with multi-touch interaction. [http://www.kiwiviewer.org/ KiwiViewer] supports a variety of file formats, including obj, stl, ply, and vtk. Datasets may be loaded into [http://www.kiwiviewer.org/ KiwiViewer] from the SD card, email attachments, or Midas, or DropBox, or downloaded from a URL.
  
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The following tutorials will provide steo-by-step instructions to:
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* [[#Saving_a_MRML_scene_as_KiwiViewer_scene_file|Export a Slicer MRML scene into KiwiViewer scene file]]
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* [[#Uploading_KiwiViewer_Scene_file_to_Midas|Upload the exported file onto a shared data source]]
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* [[#Loading_KiwiViewer_Scene_file_from_Midas|Load the exported file into KiwiViewer]]
  
 
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Interactively show an audience models created using slicer on an iPad.
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|[[Image:SkullStripperOutput-3-6.png|thumb|340px|Brain mask as contour]]
 
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|[[Image:SkullStripperSurface-3-6.png|thumb|375px|Brain surface]]
 
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== Saving a MRML scene as KiwiViewer scene file ==
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<gallery widths=450px perrow=2>
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File:SlicerToKiwiExporter-Slicer-install.png|Install extension named "SlicerToKiwiExporter". [[Documentation/{{documentation/version}}/SlicerApplication/ExtensionsManager#Installing_an_extension|Need help?]]
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File:SlicerToKiwiExporter SaveDialog Select-file-format 1.png| (1) Open save dialog and (2) select <code>KiwiViewer File (*.kiwi.zip)</code> file format.
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File:SlicerToKiwiExporter SaveDialog Select-dest-directory 2.png| (3 & 4) Choose destination directory
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File:SlicerToKiwiExporter SaveDialog ClickSave 3.png| (5) Click on "Save" to export the MRML scene.
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File:SlicerToKiwiExporter_CheckLog_4.png| Open error dialog (View -> Error Log) and check log.
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In this example, we can confirm that the MRML scene has been exported to <code>/home/jchris/Desktop/MyKiwiFiles/nac-hncma-atlas2013-Slicer4Version.kiwi.zip</code>
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</gallery>
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== Uploading KiwiViewer Scene file to Midas ==
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<ol start="1" style="list-style-type: decimal;">
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{{:Documentation/{{documentation/version}}/Developers/Tutorials/CreateMidasAccount/steps}}
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<li><p>If not already done, send an email on the [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-user slicer users list] asking to be granted write permission on the [http://slicer.kitware.com/midas3/folder/1682 KiwiViewer folder].</p>
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<pre>
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To: slicer-user@bwh.harvard.edu
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Subject: Asking permission to write to the KiwiViewer folder
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Hi,
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I am user KiwiView application to [...]
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Could you grant user YourUserName write access to the KiwiViewer folder ?
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</pre></li>
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<li><p>Go to http://slicer.kitware.com, click on Communities (1) and select "NA-MIC" (2)</p>
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[[File:SlicerToKiwiExporter-UploadMidas SelectNAMIC Community.png|450px]]
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<li><p>Browse, select the destination folder "Kiwiviewer" (3) and click on "Upload here" (4)</p>
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[[File:SlicerToKiwiExporter-UploadMidas Upload.png|450px]]
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</li>
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<li><p>Select one or more files (5) and click "Upload" button (6)</p>
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[[File:SlicerToKiwiExporter-UploadMidas SelectFile-and-upload.png|450px]]
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</li>
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<li><p>Upload is complete</p>
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[[File:SlicerToKiwiExporter-UploadMidas complete.png|450px]]
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</li>
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</ol>
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== Loading KiwiViewer Scene file from Midas ==
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<gallery widths=265px heights=350px perrow=4>
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File:SlicerToKiwiExporter Kiwiviewer 1.PNG|Tap on "Info" (1) and enter "http://slicer.kitware.com/midas3" for "Midas Host"
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File:SlicerToKiwiExporter Kiwiviewer 2.PNG|Tap on "Documents", then tap on "Midas" in the available Network Data Sources
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File:SlicerToKiwiExporter Kiwiviewer 3.PNG|Tap on "NA-MIC"
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File:SlicerToKiwiExporter Kiwiviewer 4.PNG|Tap on "Public"
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File:SlicerToKiwiExporter Kiwiviewer 5.PNG|Tap on "KiwiViewer"
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File:SlicerToKiwiExporter Kiwiviewer 6.PNG|Tap on KiwiViewer scene file to download and visualize.
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File:SlicerToKiwiExporter Kiwiviewer 7.PNG|Download in progress ...
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File:SlicerToKiwiExporter Kiwiviewer 8.PNG|Downloaded file is automatically loaded
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File:SlicerToKiwiExporter Kiwiviewer 9.PNG|Tap on "Settings" icon to see data properties
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</gallery>
  
 
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* Xiaodong Tao, Ming-ching Chang, “A Skull Stripping Method Using Deformable Surface and Tissue Classification”, SPIE Medical Imaging, San Diego, CA, 2010.
 
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* Ming-ching Chang, Xiaodong Tao “Subvoxel Segmentation and Representation of Brain Cortex Using Fuzzy Clustering and Gradient Vector Diffusion”, SPIE Medical Imaging, San Diego, CA, 2010.
 
  
  
 
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{{documentation/{{documentation/version}}/module-section|Information for Developers}}
 
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Source: https://github.com/jcfr/SlicerToKiwiExporter
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{{documentation/{{documentation/version}}/module-developerinfo}}
 
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Latest revision as of 00:57, 2 April 2015

Home < Documentation < Nightly < Modules < SlicerToKiwiExporter


For the latest Slicer documentation, visit the read-the-docs.


Introduction and Acknowledgements

Extension: SlicerToKiwiExporter
Acknowledgments: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Author: Jean-Christophe Fillion-Robin (Kitware)
Contributor1: Pat Marion (Kitware)
Contributor2: Steve Pieper (Isomics, Inc.)
Contributor3: Atsushi Yamada (Shiga University of Medical Science)
Contact: Jean-Christophe Fillion-Robin, <email>jchris.fillionr@kitware.com</email>

Kitware, Inc.  
Isomics, Inc.  
Shiga University of Medical Science  

Module Description

The SlicerToKiwiExporter module provides Slicer user with any easy way to export models into a KiwiViewer scene file.

KiwiViewer is a free, open-source visualization app for exploring scientific and medical datasets that runs on Android and iOS mobile devices with multi-touch interaction. KiwiViewer supports a variety of file formats, including obj, stl, ply, and vtk. Datasets may be loaded into KiwiViewer from the SD card, email attachments, or Midas, or DropBox, or downloaded from a URL.

The following tutorials will provide steo-by-step instructions to:

Use Cases

Interactively show an audience models created using slicer on an iPad.

Tutorials

Saving a MRML scene as KiwiViewer scene file

  • Install extension named "SlicerToKiwiExporter". Need help?

  • (1) Open save dialog and (2) select KiwiViewer File (*.kiwi.zip) file format.

  • (3 & 4) Choose destination directory

  • (5) Click on "Save" to export the MRML scene.

  • Open error dialog (View -> Error Log) and check log.

Uploading KiwiViewer Scene file to Midas

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

    2. Slicer-midas-extensions-server-registration.png

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

  2. Go to NA-MIC community and click on Join community

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

    To: slicer-user@bwh.harvard.edu
Subject: Asking permission to write to the KiwiViewer folder
Hi, 

I am user KiwiView application to [...]

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

  4. Go to http://slicer.kitware.com, click on Communities (1) and select "NA-MIC" (2)

    SlicerToKiwiExporter-UploadMidas SelectNAMIC Community.png

  5. Browse, select the destination folder "Kiwiviewer" (3) and click on "Upload here" (4)

    SlicerToKiwiExporter-UploadMidas Upload.png

  6. Select one or more files (5) and click "Upload" button (6)

    SlicerToKiwiExporter-UploadMidas SelectFile-and-upload.png

  7. Upload is complete

    SlicerToKiwiExporter-UploadMidas complete.png

Loading KiwiViewer Scene file from Midas

  • Tap on "Info" (1) and enter "http://slicer.kitware.com/midas3" for "Midas Host"

  • Tap on "Documents", then tap on "Midas" in the available Network Data Sources

  • Tap on "NA-MIC"

  • Tap on "Public"

  • Tap on "KiwiViewer"

  • Tap on KiwiViewer scene file to download and visualize.

  • Download in progress ...

  • Downloaded file is automatically loaded

  • Tap on "Settings" icon to see data properties

Panels and their use

Similar Modules

References

Information for Developers

Source: https://github.com/jcfr/SlicerToKiwiExporter

Work in progress
 Section under construction.
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