## Chapter 10Using GAIA

### 10.1 Removing a baseline with GAIA

(1)
Select the spectrum you want to use as your template for the entire cube.
(2)
Select the Baseline tab in the "Display image sections of a cube" window.
(3)
Select the order of the baseline you want to fit and remove.
(4)
Check the Show limits on plot button to interactively draw your baseline windows. You can click and drag the edges of these limit lines in the "Spectral plot" window.
(5)
Check Enable for each new baseline window you want to define.
(6)
Click Run.

### 10.2 Creating channel maps with GAIA

You can display channel maps in Gaia by selecting the region of a spectrum you wish to collapse over. You can use a spectrum from any of the pixels in the cube and the region selected will be applied to the whole map.

(1)
Select the spectrum you want to use as your template for the entire cube.
(2)
Select the Chanmap tab in the "Display image sections of a cube" window.
(3)
Check the Show limits on plot box to interactively draw the range over which to collapse your cube. You can click and drag the end-bars of the limit lines in the "Spectral plot" window.
(4)
Select the collapse method (Max is chosen in the example).

(5)
Use the slider bars to select the total number of channels you want to generate and the number of x-axis channels. The x-axis channel number sets the aspect ratio for the resulting display grid.
(6)
Click Run. The result is shown in the figure below.

### 10.3 Contouring with GAIA

(1)
Open the map you wish to contour over.
(2)
Select Image-Analysis$>$Contouring from the menu bar across the top of the main window.
(3)
Select the file you wish to contour in the "Contouring" window.
(4)
Generate your contours in the Generate tab found on the left-hand side of the "Contouring" window. The example below defines linearly spaced contours starting at 900K. Clicking the Generate button will return you to the Levels tab.

You can also input or edit the contour levels manually in the Levels tab.

(5)
Customise the look of your contours under the Options menu. You can experiment with the other tabs (Region and Key) for options concerning contour area and legend.

(6)
Click the Draw Contours button to make the contours appear over your map in the main window. If you are contouring over a cube you can scroll through the velocity axis whilst the contours remain fixed on top.

(7)
To add a second set of contours select File$>$New window in the top menu of the "Contouring" window. Here you can define a second image to be contoured and specify new levels and appearance. Open as many new contouring windows as necessary.

To save the graphic, there is a File $>$ Print, but some people prefer a tool with a capture facility such as xv.

### 10.4 Overlaying clumps and catalogues with GAIA

Gaia can display two- or three-dimensional clump catalogues that have been generated by the Cupid routine findclumps (see Section 9.5). Clump catalogues in this format are also available for download from the JCMT Science Archive.

(1)
Open your cube for three-dimensional clump finding or your integrated map for two-dimensional clump finding.
(2)
Select Image-Analysis$>$Positions$>$Import CUPID catalogue from the menu bar across the top of the main window. Note that for two-dimensional catalogues an alternative route is to select Data-Servers$>$Local catalogs. In this case you can skip Step 3.

(3)
In the "Import CUPID catalogue" window, select a file with the Choose file... button. For polygon shapes tick the STC shape box. You can change the RA/Dec co-ordinates from Cen1/Cen2, which give the central position of the clumps, to Peak1/Peak2 which give the position of the peak within them.
(4)
A catalogue window for your FITS file will appear listing all the sources and their positions and extents.

(5)
Outlines of your clumps, or symbols at the peak positions, will be automatically overlaid on your map. If this does not happen, click the Plot button on the catalogue window. When you click on a clump from the catalogue list the outline of that clump will appear in bold on your map.

(6)
If you are displaying a three-dimensional catalogue over a cube, it will only display clumps which include data from the current slice. The clumps shown will update as you move through the cube.

### 10.5 Displaying average spectrum with GAIA

(1)
Select the Spectrum tab in the "Display image sections of a cube" window.
(2)
Define the shape of your region by selecting one of the Define region buttons (a circle is chosen in the example below).
(3)
Select the combination method (Mean is chosen in the example below).

(4)
Draw the shape on your map by clicking and dragging the mouse. The "Spectral plot" window will automatically update to show your combined spectrum. You can re-position and resize your shape at any time. You can see from Figure 10.12 that the averaged spectrum gives a much clearer profile of the source.

### 10.6 Collapsing your cube with GAIA

(1)
Select the axis you want to collapse you to collapse over by selecting from the Axis drop-down list in the "Display image sections of a cube" window.
(2)
Select the spectrum you want to use as a template for your cube.
(3)
Select the Collapse tab in the "Display image sections of a cube" window.
(4)
Check the Show limits on plot button to interactively select your collapse region. You can click and drag the edges of these limit lines in the "Spectral plot" window. Position these around the region you wish to collapse over.
(5)
Select the collapse method via the Combination method drop-down list (Integ is selected in the example below).
(6)
Click Run. The main window will automatically update to show your collapse image.

### 10.7 Three-dimensional visualisation with GAIA

(1)
Select View$>$3D Visualisation$>$Iso surfaces.../Volume rendering in the "Display image sections of a cube" window.

(2)
Click and drag the image display to change the orientation in the "Volume render" window.

(3)
Include axes labelling, the image plane and other features using the check boxes on the side bar.

### 10.8 Sending spectra to SPLAT

Gaia has very limited analysis functionality for spectra. Whereas Splat is a sophisticated graphical spectral-analysis tool. Any spectrum displayed in Gaia (a single-position spectrum or a spectrum averaged over some region 10.5) can be sent (via a protocol called SAMP) to Splat for more-detailed spectral analysis.

Splat offers the ability to further process, fit, or identify spectral lines. You can also plot different spectra in the same window and make publishable files. The full Splat documentation can be found here in SUN/243.

Here are some instructions on how to do this.

(1)
Start Splat, if it is not already running.
% splat &
(2)
Click on the Interop menu item in Splat. If the SAMP control icon has a red circle, it means that the SAMP communication hub is running. If, however, the icon has a white circle, you need to start a hub. To do this press the Register with HUB button at the bottom of the window, and then press the Start internal hub button in the window that pops up.
(3)
If you had Gaia already running before the hub was active, then in Gaia select the Interop$>$Register to register your GAIA with the hub.
(4)
Select the spectrum you wish to send from Gaia.
(5)
Click on SPLAT-VO Send: replace or Send: add button near the bottom of the "Display image sections of a cube" window. The spectrum should appear in a Splat window.

SAMP can also transmit images and catalogues between compliant applications. For example, you might have a selected catalogue of sources observed elsewhere in Topcat and want to plot the locations over your HARP maps in Gaia.