GAIA version 3: Displaying cubes and extracting spectra

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In release version 3 the cube handling toolbox has been considerably enhanced. It is now much faster at moving between slices, handles FITS cubes as well as NDFs, and now features an all new, built-in, real-time interactive spectral extraction display, which provides point and region extraction.

It also has new controls for creating channel map images and selecting ranges for baseline subtraction. On 64bit platforms cubes greater than 2Gb can be handled.

As part of these cube handling updates, all the image analysis toolboxes now also work on cube slices and spectral analysis features are provided by communication with SPLAT-VO, which works outside of GAIA.

Displaying slices from cubes

In this image you can see the new style cube handling toolbox. Movement through the cube planes can be done by dragging the Index of plane: control. The world coordinate of the plane is displayed in the Coordinate of plane: label and its units in the Coordinate type: label.

You can also view the cube from the perspective of other sides by selecting a new Axis:. By default the third axis is assumed to be the spectral one.

Spectral extraction

To extract a spectrum from a cube you just click on the image plane. To move around the cube just drag over the image. Note that to change the displayed range you need to click again as during dragging the range is fixed to that of the first spectrum extracted.

In this image you can see a spectrum extracted from the cube at the position indicated by the blue cross. The coordinate of the currently extracted plane is indicated in the spectral plot by the vertical red line. You can drag on the red line to move image planes.

Spectra can also be extracted over regions. To create a region just press one of the shape buttons and drag out the region on the image. The region can be selected, resized and moved. In this image a circular region is being used.

Spectral comparison

It is possible to compare one spectrum with another.

To do this extract a spectrum and then press the Set button in the Reference: line. Now extract another spectrum and the previous one will be shown in green (you will not see this until you extract a new spectrum). In the image above two regions have been used, one to define the reference and one the extraction. To get rid of the reference spectrum press the Clear button.

Changing the spectral coordinates

It is possible to change between many different types of spectral coordinate system (in fact most of those defined in FITS paper III), provided your cube has a calibration. To do this just select the required system in one of the Coords: menus. If you have a rest frequency defined then you can move to velocities from frequency or wavelength.

Animating through a range of slices

Using the control in the Animate tab you can automatically step through a range of image planes. At the end of the range you can choose to either stop, continuously start again from the beginning, or continuously reverse direction (Rock 'n Roll).

Integrated intensity images

You can integrate the planes of a cube in various ways to produce images. This is all done using the Collapse tab. It's called Collapse as it's really just a front end to the KAPPA application COLLAPSE, that you can run from the command-line (/shells).

This image shows the integrated intensity of the whole cube. It's possible to select a range to collapse. Other combination methods are:

  • Mean - Mean value
  • WMean - Weighted mean in which each data value is weighted by the reciprocal of the associated variance.
  • Mode - Modal value
  • Median - Median value. Note that this is extremely memory and CPU intensive for large datasets; use with care!
  • Absdev - Mean absolute deviation from the unweighted mean.
  • Comax - Co-ordinate of the maximum value.
  • Comin - Co-ordinate of the minimum value.
  • Integ - Integrated value, being the sum of the products of the value and pixel width in world co-ordinates.
  • Iwc - Intensity-weighted co-ordinate, being the sum of each value times its co-ordinate, all divided by the integrated value (see the Integ option).
  • Iwd - Intensity-weighted dispersion of the co-ordinate, normalised like Iwc by the integrated value.
  • Max - Maximum value.
  • Min - Minimum value.
  • Rms - Root-mean-square value.
  • Sigma - Standard deviation about the unweighted mean.
  • Sum - The total value.

Channel maps

Using the Chanmap controls you can create a "Channel map" image of the cube. A channel map image is like a collapsed one, except that the spectral dimension is divided into a number of ranges and each of these is collapsed images is added to the result in a grid arrangement.

The image above shows a cube that has been collapsed into four ranges. So each channel map is representative of a range of spectral values. As you can see a channel map can have a special grid overlaid (see the Image-Analysis->Overlay axes grid... toolbox) and when you click on one pane the corresponding positions in the other panes is identified and the mean spectral coordinate used in that pane is displayed in the Selected coord: label.

Baseline subtraction

These controls run the KAPPA application MFITTREND to fit and subtract baselines from each spectrum in the cube. The baseline is estimated as a polynomial fit, of the selected order. Each spectrum is fitted independently and the data selected for each fit can include up to four ranges along the spectral axis.

Analysing spectra

GAIA doesn't provide any analysis functions. It concentrates on inspection. So to analyse spectra you can save them to disk file (see the File menu item in a spectral plot), or more conveniently you can send them to the SPLAT-VO application by pressing the Send button in the SPLAT-VO: controls. It is also possible to send spectra to other PLASTIC-enabled applications.

Operations supported on image slices

The image slices can be analysed by any of the usual toolboxes, such as regions statistics and aperture photometry. The only restriction is that the slices are temporary files so will be deleted when GAIA exits (or sooner).

Data formats and efficiency

The toolbox should handle both NDF and FITS data cubes with more-or-less equal efficiency, except for the Collapse, Chanmap and Baseline operations. In this case the FITS cube will be converted into an NDF first, so clearly it would be better to convert to NDF format first.

Normally the cube file is memory mapped to access the data. Usually this gives a good compromise between startup speed and access speed. However, for very large cubes (2Gb and up) the access speed can suffer as the data is only read incrementally on demand. This is particularly noticeable when plotting spectra (which are usually accessed sparsely in the third dimension), typically this manifests itself as a very slow response, which suddenly becomes much faster after clicking on the cube many times. To avoid this behaviour you can choose to read the cube into core memory (but make sure you have sufficient first), in one chunk. To do this select the Memory map cube data option in the Options menu (and wait a while).

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Copyright © 2006 Particle Physics and Astronomy Research Council
Copyright © 2008-2009 Science and Technlogy Facilities Council
Copyright © 2009-2013 Peter W. Draper
Last modified: 02-Jun-2016
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