3. Quick Start Guide

CUBISM has two major functions: building cubes from IRS Spectral Mapping data sets, and analyzing those cubes. Building cubes from collections of mapping data sets is in principle a simple process: the correct ‘BCDs’ are collected together in a project, the cube build parameters are adjusted, and the cube is built. Further refinement of the cube includes identifying bad pixels to exclude from the cube build, selecting and creating the appropriate background frames, configuring the calibration details and cube build options, etc. Although straightforward, this process can take a good deal of time. Users should expect to spend between one-half and one hour per IRS slit, building and cleaning their cubes (flagging and removing bad pixels, etc.).

With the assembled cube, you can perform a variety of types of analysis, including extracting 1D spectra in specific regions and building 2D spectral maps. There are many details which can affect the cube assembly process, and impact the quality of the final assembled product. Here we will quickly go through the basic steps required to build a cube, extract a spectrum, and build a spectral map, leaving all of the (important) details aside for now. These details are covered later in this manual.

An important note before we begin concerns the scope of a CUBISM project. Each CUBISM project pertains to a single IRS slit, e.g. Long-Low order 1 (LL1), Short-Low order 2 (SL2) or Short-High (SH). Each of the low-res slits are a single spectral order, but the high-res slits have 10 orders, each. Just as a reminder, there are four IRS modules (SL, LL, SH, and LH), with each low-res module containing two slits and each high-res module containing one slit. For data sets with mapping observations in all four low-resolution orders (SL1, SL2, LL1 and LL2), four individual cubes will be built, and analyzed as a set. A full low-res and high-res IRS map will therefore produce six spectral cubes (the four for low-res and two additional for SH and LH) and there will be six CUBISM project (‘.cpj’) files.

3.1 Example Data Set

We have assembled a small example data set, using data from the SINGS IRS Short-Low order 1 (SL1) spectral mapping observations of nearby galaxy NGC 3049. The example data set should be available where you obtained this manual. Unpack it, and follow along. The set includes the following:

‘data/’

A directory containing all of the data files.

‘ngc3048_irac_8um.fits’

A 8 micron IRAC image of the galaxy.

‘ngc3049_sl1.bgl’

The background record list.

‘ngc3049_sl1.bpl’

The bad pixel list.

‘ngc3049_SL1.cpj’

The pre-built cube project.

‘ngc3049_SL1_cube.fits’

The pre-built cube as a 3D FITS image.

‘ngc3049_SL1_cube_unc.fits’

The pre-built cube uncertainties as a 3D FITS image.

3.2 Building Your First Cube

Here we take you through the process of assembling a cube with the pre-packaged data set.

To get going, start Cubism (see section Running):

IDL> cubism

You can either Create New Cube Project to build it from scratch, or skip directly to the “answer key”, choosing the pre-built cube project file ‘ngc3049_SL1.cpj’ bundled in the example, moving ahead to the next section.

Once you have chosen to create a new cube project, give it a useful name when prompted, like ‘NGC3049 SL1’. You'll be presented with a blank CUBISM Project window. Read in the full example data set by clicking on the Import AOR button at the bottom. Select the ‘data’ directory. CUBISM will search for all IRS data files at or beneath that directory, and group all discovered data files by object and mapping AOR, allowing you to select among them. In this case, only two AORs are found, one for SL1, and one for SL2. Select them both to load data from both mapped orders, and all the relevant files will then be loaded into the project. When you are warned that no calibration set has been loaded, and that the latest is being used, simply acknowledge the warning.

Normally, you would now choose background records among the record set (see section Backgrounds), and select bad pixels (see section Bad Pixels). In this case, we have pre-built the background record list and bad pixel list for you. Specify the background ‘BCD’ records to be used by choosing ‘Background->Load Background Recs...’, and loading ‘ngc3049_sl1.bgl’, choosing Average + Min/Max Trim when prompted. Similarly, load the prepared bad pixels using BadPix->Load Bad Pixels..., choosing ‘ngc3049_sl1.bpl’.

Choose Edit->Select All and then Record->View Record Stack... to pop-up a viewer displaying an average stack of all the records. In the viewer, choose Tools->Scale Image with Histogram, and draw a scaling box on the dark part of the image at left by clicking and dragging from top-left to bottom right. You should see two spectral orders appear with an obvious spectrum in the center. Move the scaling box around by click and drag to highlight different features.

Back in the main CUBISM Project window, hit the Build Cube button, and watch the build progress. You should see the cube build feedback in a window which opens. Click the Save button and save the project to disk as a ‘.cpj’ file. Congratulations, you have completed your first spectral cube.

3.3 Visualizing the AORs

Before you move on to examine the cube, visualize the spectral mapping AOR by choosing Record->Visualize AORs.... Select the ‘ngc3048_irac_8um.fits’ file, and the viewer should fill with an image and some yellow outlines of the AOR regions. Click on the histogram scaling tool button (second from left) and drag to create a histogram scaling box to bring the galaxy into view. Click on the zoom tool (leftmost), and draw a box around these record outlines to zoom in and examine the records overlaid on the 8 micron image.

3.4 Navigating the Cube

Now that the cube is built, hit the View Cube button to display the cube in the same viewer window. In this window, click on the Extract button (a cube with a line through it), or select Tools->Extract Spectra and Stack Cubes. Click and drag a rectangular extraction region, from upper left to lower right, on the cube, and the CubeSpec window will appear showing you the extracted spectrum. Center the purple box on the galaxy seen in the right hand side of the cube.

In the CubeSpec window, click Map and then choose ‘Region: Peak’. Click and release at 11 micron and then 11.8 micron to define a peak region highlighting the 11.3 micron PAH feature. This will then be highlighted in red on the spectrum, and the image in the CubeView window will change showing a map of NGC 3049 averaged over the wavelength region you have selected.

Congratulations, you have just created your first spectral map with CUBISM. By choosing ‘Region: Continuum’, and setting continuum regions on either side of your peak region, you could now create a continuum-subtracted spectral map. Read on to learn more about the detailed steps for cube assembly and analysis.

This document was generated by JD Smith on July, 14 2009 using texi2html 1.78.