Monday, August 24, 2009

Measuring Spectral Lines

From reader Fred:

When you've got spectral lines in emission, what's the best way of actually reliably measuring them in AIPS? Half the time, when JMFIT is run on a line, the peak and integrated fluxes come out identical (which makes me suspicious!).

my (small amount of) insight below the fold...

I don't usually measure spectral lines in AIPS, and am much more likely to do it in say, IDL, so I don't have any direct insight for you. I'm guessing that JMFIT is not a good way to measure lines, though. I have used JMFIT a lot for measuring continuum point sources, and I can tell you that when the peak and the integrated flux come out to be about equal, this usually means that the source is unresolved. I'm guessing that your spectral lines aren't all actually unresolved (<1 channel in width?), so perhaps JMFIT just doesn't really know what to do with spectral lines. The problem might be that it expects everything to be in terms of mJy/beam, and it usually knows what the beam is in RA/Dec coordinates, and so it is all set up to fit a gaussian to a source and figure out how many beams it covers and how many mJy it emits. This whole set-up doesn't makes much sense when you are talking about one of the coordinates being mJy/channel...

So, I'm skeptical of using JMFIT, but it might be possible. Unfortunately I don't have other suggestions in AIPS, but I bet other people do?

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Monday, August 17, 2009

Multiple contours on one plot

From reader Carl:

Hey I'm bumping this because I have a question regarding contour plots. I'd like to overlay 3 separate contour plots onto each other. The AIPS documentation indicates that it can display plots from multiple images, but is a little ambiguous as to whether it can display the contour plots of both images, or just the contour of one and the greyscale of another. Reading the AIPS help file and playing with the task seem to hint that the latter is the case. I'm just wondering if anyone knows for sure whether this can be done in AIPS, and if so, how. Thanks!

Thanks for the question Carl. See below for my response.

I don't know for sure because I've never tried it, but I'm pretty sure that you can only have one set of contours in KNTR. AIPS plotting is not the most flexible.

Some solutions that might not be great:

1) Use a programming language (Python, IDL, perl, C, fortran, etc) and a fits library to read in your files and then plot them exactly like you want.

2) Make three different contour plots of exactly the same area and overlay them in Illustrator.

Anybody else have some solutions?

I'm wishing that for my latest paper, I'd done custom plots instead of AIPS plots. My hope is that the plotting situation will improve with CASA since it's all plugged into Python and the plotting libraries there.

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Friday, August 7, 2009

Flip frequency axis in UV data?

Hey, does anyone know an equivalent of 'TRANS' in the UV domain? I have two datasets that I need to DBCON, but they are in reverse order (i.e. CDELT > 0 for one, and CDELT < 0 for the other). Is there a task to flip the UV sideband?

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Thursday, August 6, 2009

Amplitude Self-Calibration and Flux Levels

If you want to get really high dynamic range, self-calibration is a necessary. (See this post for the basics of self-calibrating in AIPS.) However, getting the fluxes right (especially for weak extended emission) is tough. See below for more details.

Usually you start off with a phase calibration boxing more and more sources as you improve the model. I usually start boxing fairly conservatively and then box more freely in later phase self-calibration interations. The amplitude self-calibration, however, is slightly different in that you need to include all the emission that's real and none that's not, i.e., you need to make the best possible image of your source. If you don't include all the emission (say the diffuse stuff), then you are essentially saying that there's zero flux in that part of the image and the fluxes in the resulting image will be forced downward closer to that value.

There are a couple things to check to see how well you're doing with the flux estimates. One is to plot the visibility amplitudes vs. uv distance. They should be more or less the same. If you have amplitudes in the amplitude self-calibration data that are significantly below that in the unself-calibrated data you've got problems. Another thing to check is how much total flux you're recovering. The total clean components you use (given in the output of IMAGR) should be close to the total flux in the image and the fluxes of sources shouldn't go down after amplitude self-calibration.

Thanks to Crystal Brogan and Bill Cotton for their help with this issue.

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