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* Thijs van der Hulst, <email>J.M.van.der.Hulst@astro.rug.nl</email>
 
* Thijs van der Hulst, <email>J.M.van.der.Hulst@astro.rug.nl</email>
 
* Jos Roerdink <email>j.b.t.m.roerdink@rug.nl</email>
 
* Jos Roerdink <email>j.b.t.m.roerdink@rug.nl</email>
[http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerAstro Back to SlicerAstro home]
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[[Documentation/Nightly/Extensions/SlicerAstro|Back to SlicerAstro home]]
 
{{documentation/{{documentation/version}}/module-introduction-end}}
 
{{documentation/{{documentation/version}}/module-introduction-end}}
  
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<br>
 
<br>
 
<h4>Handling the loading and writing of FITS files</h4><br>
 
<h4>Handling the loading and writing of FITS files</h4><br>
[[File:AstroLoading.png|1000 px]]
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[[File:AstroLoading.png|750 px]]
  
 
<br>
 
<br>
<h4> The display of the Astronomical World Coordinate (WCS) and Data Probing for 2D views </h4><br>
 
  
[[File:Astro2Daxes.png|1000 px]]
+
<h4> MRML nodes that store the data-cube and the FITS keywords in the 3DSlicer object-tree (Data module) </h4><br>
  
 +
[[File:AstroData.png|500 px]]
  
 
<br>
 
<br>
 
<h4>The control of the display coordinates</h4><br>
 
<h4>The control of the display coordinates</h4><br>
 
[[File:AstroVolumeInformation.png|1000 px]]
 
[[File:AstroVolumeInformation.png|1000 px]]
 +
 +
<br>
 +
<h4> The display of Beam information in the XY view </h4><br>
 +
 +
[[File:AstroHistogram.png|1000 px]]
  
 
<br>
 
<br>
 
<h4>The control of the 2D color transfer function</h4><br>
 
<h4>The control of the 2D color transfer function</h4><br>
[[File:AstroDisplay.png|1000 px]]
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[[File:Astro2DColorFunction1.png|1000 px]]
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[[File:Astro2DColorFunction2.png|1000 px]]
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[[File:Astro2DColorFunction3.png|1000 px]]
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[[File:Astro2DColorFunction4.png|1000 px]]
 +
 
 +
<br>
 +
<h4> The display of the Astronomical World Coordinate (WCS) and Data Probing for 2D views </h4><br>
 +
 
 +
[[File:Astro2DAxes1.png|1000 px]]
 +
 
 +
<br>
 +
<h4> The display of Beam information in the XY view </h4><br>
 +
 
 +
[[File:AstroBeam.png|1000 px]]
  
 
<br>
 
<br>
 
<h4>The control of the 3D color transfer function</h4><br>
 
<h4>The control of the 3D color transfer function</h4><br>
[[File:AstroRendering.png|1000 px]]
+
[[File:Astro3DColorFunction.png|1000 px]]
  
 
<br>
 
<br>
 
<h4>Tools to convert mask from FITS files (e.g., generated by SoFiA) into segmentations objects and viceversa</h4><br>
 
<h4>Tools to convert mask from FITS files (e.g., generated by SoFiA) into segmentations objects and viceversa</h4><br>
 
[[File:AstroMask2.png|1000 px]]
 
[[File:AstroMask2.png|1000 px]]
 +
[[File:AstroMask6.png|1000 px]]
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
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<br>
 
<br>
<h4>This editor effect can create multiple segmentation (3D contours) of the input volume.</h4><br>
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<h4>AstroCloudLasso Effect</h4><br>
[[File:AstroContourEffect.png|1000 px]]
+
The AstroCloudLasso segmentation editor effect is a tool to interactively perform a 3D selection.
 +
This 3D selection (the segmentation) can be used either for:
  
<b>Contour Levels info</b>:
+
1. changing an imported mask generated by automated algorithms (e.g., source finders);<br>
 +
2. providing an input mask to a variety of tools in SlicerAstro (e.g., MomentMaps module and Modeling module).<br>
  
The Levels can be specified as a list (e.g., 'VALUE1;VALUE2;VALUE3')
+
[[File:AstroMask3.png|1000 px]]
or in the following format 'FISRT:LAST:SPACING'.
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[[File:AstroMask4.png|1000 px]]
In the case of a list, it is possible also to specify for each Contour both the MIN and MAX intensity values of the level (e.g., 'CONTOUR1MIN,CONTOUR1MAX;CONTOUR2MIN,CONTOUR2MAX').                                         
 
If the string is preceded by 'RMS', the levels are evaluated in units of RMS of the datacube.  
 
  
The contours in SlicerAstro are a full 3D segmentation. Therefore it can be computationally heavy
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<!-- ---------------------------- -->
to segment (marching cubes algorithm) and visualize around the noise range [-2, 2] RMS for large datacubes.
+
{{documentation/{{documentation/version}}/module-section|References}}
 +
<pre>
 +
@ARTICLE{2017A&C....19...45P,
 +
  author = {{Punzo}, D. and {van der Hulst}, J.~M. and {Roerdink}, J.~B.~T.~M. and  
 +
{Fillion-Robin}, J.~C. and {Yu}, L.},
 +
    title = "{SlicerAstro: A 3-D interactive visual analytics tool for HI data}",
 +
  journal = {Astronomy and Computing},
 +
archivePrefix = "arXiv",
 +
  eprint = {1703.06651},
 +
primaryClass = "astro-ph.IM",
 +
keywords = {Radio lines: galaxies, Scientific visualization, Visual analytics, Agile software development, Object oriented development, Empirical software validation},
 +
    year = 2017,
 +
    month = apr,
 +
  volume = 19,
 +
    pages = {45-59},
 +
      doi = {10.1016/j.ascom.2017.03.004},
 +
}
 +
</pre>
 +
 
 +
<!-- ---------------------------- -->
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/module-footer}}
 
{{documentation/{{documentation/version}}/module-footer}}
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->

Latest revision as of 03:36, 27 November 2019

Home < Documentation < Nightly < Modules < AstroVolume

For the stable Slicer documentation, visit the 4.10 page.

European Research Council Kapteyn Astronomical Institute

Introduction and Acknowledgements

Authors:
Davide Punzo (Kapteyn Astronomical Institute, University of Groningen)
Thijs van der Hulst (Kapteyn Astronomical Institute, University of Groningen)
Jos Roerdink (Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen)

Contributors:
Jean-Christophe Fillion-Robin (Kitware)
Steve Pieper (Isomics)
Andras Lasso (PerkLab, Queen's)

Acknowledgements:
This work was supported by the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement nr. 291-531.

Contacts:

  • Davide Punzo, <email>punzodavide@hotmail.it</email>; <email>D.Punzo@astro.rug.nl</email>
  • Thijs van der Hulst, <email>J.M.van.der.Hulst@astro.rug.nl</email>
  • Jos Roerdink <email>j.b.t.m.roerdink@rug.nl</email>

Back to SlicerAstro home

Module Description

The AstroVolume can read/write FITS file (astronomical data format) and handle the color function and display of Astro Volumes.


Panels and their use


Handling the loading and writing of FITS files


AstroLoading.png


MRML nodes that store the data-cube and the FITS keywords in the 3DSlicer object-tree (Data module)


AstroData.png


The control of the display coordinates


AstroVolumeInformation.png


The display of Beam information in the XY view


AstroHistogram.png


The control of the 2D color transfer function


Astro2DColorFunction1.png Astro2DColorFunction2.png Astro2DColorFunction3.png Astro2DColorFunction4.png


The display of the Astronomical World Coordinate (WCS) and Data Probing for 2D views


Astro2DAxes1.png


The display of Beam information in the XY view


AstroBeam.png


The control of the 3D color transfer function


Astro3DColorFunction.png


Tools to convert mask from FITS files (e.g., generated by SoFiA) into segmentations objects and viceversa


AstroMask2.png AstroMask6.png


Astro segmentation editor effect


AstroCloudLasso Effect


The AstroCloudLasso segmentation editor effect is a tool to interactively perform a 3D selection. This 3D selection (the segmentation) can be used either for:

1. changing an imported mask generated by automated algorithms (e.g., source finders);
2. providing an input mask to a variety of tools in SlicerAstro (e.g., MomentMaps module and Modeling module).

AstroMask3.png AstroMask4.png

References

@ARTICLE{2017A&C....19...45P,
   author = {{Punzo}, D. and {van der Hulst}, J.~M. and {Roerdink}, J.~B.~T.~M. and 
	{Fillion-Robin}, J.~C. and {Yu}, L.},
    title = "{SlicerAstro: A 3-D interactive visual analytics tool for HI data}",
  journal = {Astronomy and Computing},
archivePrefix = "arXiv",
   eprint = {1703.06651},
 primaryClass = "astro-ph.IM",
 keywords = {Radio lines: galaxies, Scientific visualization, Visual analytics, Agile software development, Object oriented development, Empirical software validation},
     year = 2017,
    month = apr,
   volume = 19,
    pages = {45-59},
      doi = {10.1016/j.ascom.2017.03.004},
}