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

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<h4> The display of the Astronomical World Coordinate (WCS) and Data Probing for 2D views </h4><br>
<h4> The display of the Astronomical World Coordinate (WCS) and Data Probing for 2D views </h4><br>
[[File:Astro2Daxes.png|1000 px]]

Revision as of 16:08, 23 February 2018

Home < Documentation < Nightly < Modules < AstroVolume

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

European Research Council Kapteyn Astronomical Institute

Introduction and Acknowledgements

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)

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

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.


  • 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


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


The control of the display coordinates


The display of Beam information in the XY view


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


The display of Beam information in the XY view


The control of the 3D color transfer function


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

AstroContours Effect

This editor effect can create multiple segmentation (3D contours) of the input volume.


The Contour Levels can be specified using the following format:

'FISRT:LAST+SPACING' for linear spacing or 'FISRT:LAST*SPACING' for non linear spacing.

The levels can also be specified as a list (e.g., 'VALUE1;VALUE2;VALUE3'). 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 '3DDisplayThreshold', the levels are evaluated in units of the value of 3DDisplayThreshold of the dataset.

If the Histogram is active in the plot view and a selection is made, by typing the string 'Histogram' will create a segmentation around the selection.

The contours in SlicerAstro are a full 3D segmentation. Therefore it can be computationally heavy to segment (marching cubes algorithm) and visualize around the noise range [-2, 2] RMS for large datacubes.

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


   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},