Collected Shreds of AIPS Wisdom

Remote login to AIPS

2011-11-08T02:39:00.000-06:00

So, you're away from your computer (say it's in Wisconsin and you're in South Africa), but need to log in to AIPS remotely to get some (simple) work done. Since I do this about once every six months and have to relearn how to do it every time, here's the solution.
ssh into your machine, then instead of just typing at the terminal:

> aips

> aips da=<computer name=>

both of which give me errors or repeatedly ask for me to retype my password, try:

> aips notv da=<computer name>

Eh, voila! I can use AIPS without complaint.
True, you can't use the tv to view your data, but that would be a pain to do remotely anyway. When I make an image, I output an .PS file and rsync it to my local machine. rsync is nifty and worth learning, if you don't know it already.

Gridding with SDIMG

2010-07-15T09:43:00.004-05:00

I am trying to use SDIMG to grid some GBT data to 25 arcmin. The gridding parameters are set like in IMAGR, with XTYPE, YTYPE, XPARM, YPARM. Does anyone know how to make sense of the gridding parameters? Right now I use mysterious parameters given to me by Jay Lockman, which are idealized to the 9 arcmin L-band beam. I can't figure out what they mean to change them. The AIPS help files are just as mysterious to me.

Inconsistencies between UVPLT and TVFLG?

2010-07-05T14:11:00.003-05:00

Here's a question from Anonymous:

I am re-reducing 1667 MHz OH spectral line data from project AC319 (JUN-92, polarizations RR, LL, RL, LR). I chose one spectral channel from one day, and I plotted the visibility amplitudes with both TVFLG and UVPLT. The data are split, and they are for the program source W22.

I plotted the visibility amplitudes in UVPLT (stokes 'rr'), and I don't see any amplitudes over 20 Jy for baseline lengths 4 - 9 kilolambda. However, when I plot the same data in TVFLG (stokes 'rr', sorted by length), I see a number of amplitudes higher than 20 Jy in the same baseline range.

Why would the higher amplitudes be displayed by TVFLG but not by UVPLT? In both cases, I chose flagver =-1, so no flagging should have been applied when I ran either task.

I'm not sure of the exact answer to your question, but there are lots of ways for TVFLG and UVPLT to give slightly different pictures of your data:

--Is XINC set in UVPLT?
--Are you sure your looking at the same channel in each case, and not averaging channels in either case?
--TVFLG may be secretly time averaging your visibilities. To make sure that it's not time averaging, find out what your integration time is and input this as DPARM(6). Then, once the data are actually loaded, look at the AVG parameter stated in the bottom left of the tv screen. If it is set to a number greater than 1, than time averaging is occurring. To change this averaging time, click on 'enter smooth time'.

Excluding single-channel flux peaks

2010-06-07T14:36:00.002-05:00

Reader Linda asks

I'm trying to use the AIPS task BLANK to blank an HI data cube. I am using the method where you blank a convolved version of your cube to exclude flux < 2-3*noise and then use that convolved cube as a filter to blank your original image. With the help of other kind folks, I've got this part worked out. But I would also like to exclude single-channel flux peaks. Does anyone know of a way to ask AIPS to only keep pixels with signal that is above a set level in a specified number of consecutive channels? It seems like using OPCODE = 'FLTW' might be helpful, but my attempts at using this haven't produced anything useful.

I'd really appreciate any help!

Any suggestions?

BPLOT is a really cool task

2010-03-26T17:10:00.007-05:00

I recently learned about a task in AIPS which is very good for assessing bandpass stability---BPLOT. If you have multiple bandpass solutions, it will plot each one, stacking them one on top of each other as a time sequence. To the left is an example plot from BPLOT. Try it, you'll like it!

Getting rid of distracting black lines in TVFLG/SPFLG

2010-03-26T15:21:00.003-05:00

Have you ever loaded your data into TVFLG or SPFLG and seen what looks like lots of blank times (manifested as horizontal black lines cutting through your data)?

This is because TVFLG/SPFLG is trying to load your data with a time bin that is not a multiple of your integration time. So---the solution is to set DPARM(6)! Set DPARM(6) to your integration time in seconds; e.g., for GMRT data:


DPARM(6) = 16.7

(or, if you have time averaged your data, set it equal to your averaging time).

Watch out for the STOKES parameter when plotting (even if you don't care about polarization)

2010-03-23T17:29:00.005-05:00

When using the many plotting/flagging programs in AIPS, make sure to check the value of the STOKES parameter before plotting (try help stokes to see the options and select the one appropriate for that data set). Different tasks have different STOKES defaults, so sometimes displaying data in one program results in a totally different plot than in another program because one is including some polarizations the other is not. This particularly can be a problem if you have cross-polarization values you don't care about (yet).

CVEL bug

2010-03-03T13:20:00.006-06:00

I received an email yesterday informing people of a bug in CVEL - that is, if you run CVEL on a data set after SPLIT with an NX table, you are affected! I wanted to post it here in case you're not on the Midnight Job (MNJ) list (which I wasn't). Essentially, CVEL will only shift the first scan to the new velocity axis, while the other scans are not shifted. This bug is explained here. I think the possible fixes are to either run CVEL before SPLIT or to run the midnight job to update your AIPS version and then rerun the new CVEL version on your data.

CASA guides

2010-02-17T18:44:00.003-06:00

Hey! If you're learning CASA, check out this new collection of tips and tutorials that I've been contributing to:
http://casaguides.nrao.edu/

And let me know if you see obvious holes in the documentation there (which is, clearly, still under development).

Error in PCAL

2010-02-17T18:40:00.002-06:00

Here's a question from Akshaya Rane:

I am doing polarization calibration and while trying to run 'pcal', I have encountered the following error. Does this has to do something with qualifiers?

PCAL 3: TOTAL INTENSITIES MUST BE PROVIDED
PCAL 3: Purports to die of UNNATURAL causes

Any thoughts?

I should add that Eric Greisen says that if you spend an hour trying to figure out something in AIPS, and you can't, you should feel free to email him and ask his help.

AIPS to CASA cheat sheet

2010-02-04T23:15:00.050-06:00

So, i've been spending the last couple days learning CASA, and I think the most intuitive way to think about it is in terms of what I would be doing in AIPS. Hence the below table. Most tasks in AIPS have a parallel in CASA, although it's not always a one-to-one transfer.

Update: New and improved as of March 5, 2010:

AIPS	CASA	Purpose
APROPOS	taskhelp	List tasks with a short description of their purposes
BLCAL	blcal	Calculate a baseline-based gain calibration solution
BLCHN	blcal	Calculate a baseline-based bandpass calibration solution
BPASS	bandpass	Calibrate bandpasses
CALIB	gaincal	Calibrate gains (amplitudes and phases)
CLCAL	applycal	Apply calibration to data
COMB	immath	Combine images
CPASS	cpass	Calibrate bandpasses by polynomial fitting
DBCON	concat	Concatenate ''u-v'' datasets
DEFAULT	default	Load a task with default parameters
FILLM	importvla	Import old-format VLA data
FITLD	importuvfits	Import a ''u-v'' dataset which is in FITS format
FITLD	importfits	Import an image which is in FITS format
FITTP	exportuvfits	Write a ''u-v'' dataset to FITS format
FITTP	exportfits	Write an image to FITS format
FRING	---	Calibrate group delays and phase rates.
GETJY	fluxscale	Determine flux densities for other cals
GO	go	Run a task
HELP	help	Display the help page for a task
IMAGR	clean	Image and deconvolve
IMFIT	imfit	Fit gaussian components to an image
IMHEAD	vishead	View header for ''u-v'' data
IMHEAD	imhead	View header for an image
IMLIN	imcontsub	Subtract continuum in image plane
IMLOD	importfits	Import a FITS image
IMSTAT	imstat	Measure statistics on an image
INP	inp	View task parameters
JMFIT	imfit	Fit gaussian components to an image
LISTR	listobs	Print basic data
MCAT	ls	List image data files
MOMNT	immoments	Compute moments from an image
OHGEO	imregrid	Regrids an image onto another image's geometry
PBCOR	immath	Correct an image for the primary beam
PCAL	polcal	Calibrate polarization
POSSM	plotcal	Plot bandpass calibration tables
POSSM	plotms	Plot spectra
PRTAN	listobs	Print antenna locations
PRTAN	plotants	Plot antenna locations
QUACK	flagdata	Remove first integrations from scans
RENAME	mv	Rename an image or dataset
SETJY	setjy	Set flux densities for flux cals
SMOTH	imsmooth	Smooth an image
SNPLT	plotcal	Plot gain calibration tables
SPFLG	viewer	Flag raster image of time v. channel
SPLIT	split	Write out ''u-v'' files for individual sources
TASK	inp	Load a task with current parameters
TGET	tget	Load a task with parameters last used for that task
TVALL	viewer	Display image
TVFLG	viewer	Flag raster image of time v. baseline
UCAT	ls	List ''u-v'' data files
UVFIX	fixvis	Compute ''u'', ''v'', and ''w'' coordinates
UVFLG	flagdata	Flag data
UVLIN	uvcontsub	Subtract continuum from ''u-v'' data
UVLSF	uvcontsub	Subtract continuum from ''u-v'' data
UVPLT	plotms	Plot ''u-v'' data
UVSUB	uvsub	Subtracts model ''u-v'' data from corrected ''u-v'' data
WIPER	plotms	Plot and flag ''u-v'' data
ZAP	rmtables	Delete data files

Do you have a favorite AIPS-to-CASA pair? Disagree with any of the above? Let me know in the comments! I'm still learning.

p.s. I'm supposed to be writing CASA documentation for the beginner (e.g., myself), so I doubt this is the last time I will be seeking feedback.

p.p.s. ~~Why is blogger putting this horrific space before my table? I can't get rid of it and it looks fine in the preview. quack.~~ This tip seemed to get rid of it.

Plot labels and tick marks

2010-02-04T22:42:00.002-06:00

Reader René would like to know about some aesthetic issues in plotting:

I have a question regarding labeling. The LTYPE-parameter (eg. in task 'greys') lets you plot "Label in arcsec or other units from reference pixel". This is just what I need, but it stupidly plots it in degrees instead of arcminutes. Is there a way to change this? (Except transforming the coordinates of the whole image I mean ...)

Also is there a way to adjust the number of ticks to plot? (Add minor and major ticks?)

Joining Spectral Line Data with Multiple IFs

2010-01-25T12:50:00.013-06:00

Occasionally I've encountered line data that are taken in 4-IF mode - that is, where you have 2 IFs, each tuned to different frequencies, that overlap on their edges. I found these to be a pain to combine the last time I worked with them (in my first Astronomy research project ever!), and they have resurfaced again now.. but I've discovered a much easier solution: UJOIN!

UJOIN takes a data set with 2 IFs tuned to different frequencies (as from 4-IF mode at the VLA), and joined them together. It even deals with re-weighting the overlap regions because now there's more data there! You will want to use UJOIN on data that has already been calibrated (gain AND bandpass).

Here are the inputs:


AIPS 1: UJOIN     Converts IFs to additional spectral channels
AIPS 1: Adverbs     Values                 Comments
AIPS 1: ----------------------------------------------------------------
AIPS 1: INNAME     ' '                     Input UV file name (name)
AIPS 1: INCLASS    ' '                     Input UV file name (class)
AIPS 1: INSEQ         0                    Input UV file name (seq. #)
AIPS 1: INDISK        0                    Input UV file disk unit #
AIPS 1: OUTNAME    ' '                     Output UV file name (name)
AIPS 1: OUTCLASS   ' '                     Output UV file name (class)
AIPS 1: OUTSEQ        0                    Output UV file name (seq. #)
AIPS 1: OUTDISK       1                    Output UV file disk unit #.
AIPS 1: CHANSEL    *all 0                  Begin, end input channels,
AIPS 1:                                    begin output channel each IF
AIPS 1: OPCODE     ' '                     'DIFF' to output the vis
AIPS 1:                                    difference in the overlap
AIPS 1: DOWEIGHT      1                    0 => delete spectrum if any
AIPS 1:                                    IF or channel is flagged
AIPS 1:                                    < -0.5 => keep data even if
AIPS 1:                                    one of the IFs is flagged
AIPS 1:                                    > 0.5 => delete channel if
AIPS 1:                                    one of the IFs is flagged

The main thing to set is CHANSEL. This is a 6-element array:


chansel(1) - first channel to use from IF 1
chansel(2) - last channel to use from IF 1
chansel(3) - output channel that corresponds to 1st input channel from IF 1 (ugh)
chansel(4) - first channel to use from IF 2
chansel(5) - last channel to use from IF 2
chansel(6) - output channel that corresponds to 1st input channel from IF 2 (ugh again)

The AIPS help file on UJOIN has some helpful information on how to set these values properly, but I will reproduce what I did to set these - it's not completely straightforward.

Using UJOIN on your own data
First, you should apply all your calibrations in SPLIT. Make sure that when you SPLIT off your science source, you keep BIF and EIF set to 0 - this will create a single source file with both IFs.

Then, you will need to figure out the frequency and reference pixel of each of your observations (f_1, p_1, f_2, p_2). I did this by SPLITting each IF off separately from the LINE data and then running IMHEAD on each. You should also record delta_f (from IMHEAD again - this should be the same for each IF). In my case, f_2 was bigger than f_1 - if this is different for you, you'll have some sign differences somewhere and CHANSEL will be in a different order.

Next, figure out if any of the channels in your IFs are on the edges of the bandpass. You will not want to keep these channels as they will add noise into the final, combined UV data. Typically, look at the region where the bandpass is flat-ish, and use that. To find these, you will want to use POSSM to take a quick look at your bandpass solutions for each antenna:


default possm
aparm = 0, 1, 0.7, 1.3, -180, 180, 0, 2, 0, 0
source [bpass calibrator]
solint -1
nplots 9
dotv 1
bpver 0

Find the first and last channels of the flat-ish region for each IF (n_first,1; n_last,1; n_first,2; n_last,2).

Now you can start setting CHANSEL with the first and last channels for IF 1:


chansel(1) = n_first,1      # first channel from flat-ish part of bpass, if 1
chansel(2) = n_last,1       # last channel from flat-ish part of bpass, if 1
chansel(3) = 1              # ichansel(1) goes into output channel 1
chansel(4) = n_first,2      # first channel from flat-ish part of bpass, if 2
chansel(5) = n_last,2       # last channel from flat-ish part of bpass, if 2

Now we move on to chansel(6), which is not nearly as easy as the above part was. Here you have to figure out which output channel corresponds to chansel(4). You'll have to take into consideration all the other ichansel values. Here is the equation I came up with for ichansel(6):

You can find the derivation at the end of this post if you're interested or getting incorrect answers. (As Martha Haynes once said, "You get what you pay for and this is free!")

As a reminder, here's what all of the variables stand for:


        n = this is the value for ichansel(6)
    f_1,0 = reference frequency of IF 1
    f_2,0 = reference frequency of IF 2
  delta_f = frequency steps between channels
n_first,1 = first channel of IF 1 used in output
n_first,2 = first channel of IF 2 used in output
      p_1 = reference channel of IF 1
      p_2 = reference channel of IF 2

Testing that UJOIN did the right thing
You'll probably want to check that this actually worked correctly. The UJOIN help recommends that you use POSSM to check that the spectrum of the phase calibrator is flat.

- First, SPLIT off the phase calibrator separately.

- Next, run UJOIN on this phase calibrator file with the same inputs as for the galaxy.

- Check that the spectrum of the UJOIN data is flat in POSSM:


default possm
aparm 0
solint 0
nplots 0
source [phase calibrator]

This should plot the phase calibrator spectrum with data from all antennas averaged together.

My derivation of the ichansel(6) equation:
To figure this out, I wrote some equations to find the frequency at a given channel (f1, f2):

These tell you the frequency (f_1, f_2) at an arbitrary channel (n_1, n_2) for each IF. f_1,0 tells you the frequency at reference pixel p_1 for IF 1. f_2,0 tells you the frequency at reference pixel p_2, for IF 2. delta_f is the frequency steps between each channel.

Now we can write an equation to for the frequency of the output channels:

We can sub in for f_out,0 because we know what channel we're setting as the first output channel (ichansel 1!), and we know its frequency from the above equation for f_1 (n_1) for IF 1:

Now we want to know what output channel (n) corresponds to the first channel of IF 2 (n_first,2). Where does this occur in f_out?

Now just rearrange that for n!

TV suddenly red?

2010-01-19T10:57:00.003-06:00

Is your TV suddenly mis-behaving and showing everything in red rather than in black and white? Make sure that TVCHAN=1.

IBLED error (related to the TV?)

2010-01-08T10:53:00.004-06:00

Reader Ruta asks:

hi, i have come across an error message copied below while running task 'ibled' on a single source datafile. whats happening and why am i getting this error..? thanks in advance.
localh> IBLED1: Loading data for baseline 1 - 2
localh> IBLED1: Loading data from ***/12:00:53 to ***/11:54:54
localh> IBLED1: There are 25 valid vis. points on this baseline
localh> IBLED1: Loading AMPLITUDE
localh> IBLED1: with Stokes I chs 1- 1 IFs 1- 1
localh> IBLED1: Displaying pixels 1 to 35
localh> IBLED1: Data range 1.092369E+04 1.093816E+04
localh> IBLED1: VISLAB: ERROR 2 RETURNED FROM IMVECT
localh> IBLED1: IBFOAD: ERROR 2 FROM VISLAB
localh> IBLED1: LOADING ERROR 2 FROM IBFOAD
localh> IBLED1: TELEVISION I/O ERROR 2 FROM SETFRM
localh> IBLED1: Temporary master file to be destroyed
localh> IBLED1: Destroyed 1 extension files of type FC
localh> IBLED1: Destroyed UV image file: catno= 540 disk= 3
localh> IBLED1: Purports to die of UNNATURAL causes
localh> IBLED1: voodoo 31DEC09 TST: Cpu= 1.8 Real= 3 IO= 17

Does anyone have any ideas other than double-checking the parameters to make sure that they are correct?

Heads Up! Inverted Axes for EVLA-VLA data..

2009-11-10T13:25:00.015-06:00

I recently encountered an issue with one spectral line data set observed during the EVLA-VLA transition (like all my other data sets). So far, only this data set in particular is affected, but it could possibly apply to others if you notice this behavior. If you notice rotation that should not be there compared to other images, this may affect you!

Here are the weird things about this data set:

The velocity axis appears to be backwards, but the header seems normal (is, the cdelt3 value in the header is not of the opposite sign).
Compared to other observations of the same galaxy taken in different configurations, the map is rotated by 180 degrees on the plane of the sky, but again, the header seems normal (cdelt1/2 are both normal).

I spent a lot of time trying to figure out the cause of this and originally chalked it up to user error - i.e., something went wrong in the calibration, which gave the phases the opposite sign. Or so I thought.

Well! Turns out it was a bona fide problem with the EVLA transition, which inverted the velocity axis and gave the phase an incorrect sign. This has mostly been corrected in the archive, but is apparently still present in a few, lingering data sets. The fix for this is to use the task "FLOPM" on the data (after SPLIT) with opcode "VLAE".

Voila! Problem solved. Now if I could only get back the three weeks I spent banging my head against the proverbial AIPS wall.

IMERG SECRETS

2009-11-10T07:00:00.009-06:00

IMERG is a program that combines single dish and interferometer data (see Stanimirovic (2002) for details on the algorithm). In short, this algorithm (also referred to as "feathering") fourier transforms both the single dish and the interferometer data, uses the overlap region in uv space between the interferometer and single dish data to determine a scaling factor for the single dish data, adds the interferometer image and the scaled single dish image in fourier space, and then fourier transforms it back.

IMERG has a couple of extra caveats that the user should be aware of before running:

Both images need to be square and the dimensions a power of two.
Make very sure there are no blanks in either image. Use REMAG to replace any blanks with zero. Note that OHGEO will blank any region in the transformed image that is outside the boundaries of the original image. One of the signs that you may have some blanks in your image is really small scaling factors (~1e-8).
Make sure that the single dish image is big enough, i.e., make sure the galaxy is much smaller than the entire image.

Edit (11/13/09): As far as I can tell, IMERG does absolutely no checking that the two images have the same axes, so beware and double check that both images are the same. Also the beam that gets put in the resulting image is the single dish beam, not the interferometer beam. Use ADDBEAM to change.

Multi-frequency synthesis in AIPS?

2009-11-06T16:54:00.013-06:00

(Edited based on re-reading the documentation this morning.)

Does any one here have experience with multi-frequency synthesis in AIPS? I've got a WSRT data set with 8 continuous IFs each with 64 channels. I'm currently setting


bif=1; eif=8
bchan=2; echan=50; nchav=49

in IMAGR.

I was going to run it through self-calibration as usual.(See the following post for details.) Is there anything else I need to do?

[Edited 11/11/09: See Michael Rupen's comment on this post for the answer.]

"Air Mass Chart" for Radio Observations?

2009-09-25T23:35:00.003-05:00

A question that has plagued me for quite some time, as I prepare my EVLA proposal:
Do you all know of a tool to find the rise/set times and elevations of radio sources? My favorite tool for seeing the trajectory of an object through the sky is 'airchart' in IRAF, but unfortunately IRAF assumes you are an optical astronomer and only tracks your sources through the nighttime. Anyone know of something similar for all 24 hours? (the GMRT has one, but it assumes the GMRT's latitude, which is rather different than the VLA's).

Combining VLA Spectral Line Data with Different Channel Spacings: a Solution!

2009-09-14T15:11:00.016-05:00

I remember thinking about this briefly in a post further down, and neither Amanda nor I could come to a good solution without resorting to Miriad. After running into the problem myself and spending a lot of time dealing with AIPS, I think I've come to a solution.

Caveat: this is only valid for combining VLA data with other VLA data. I don't think it will work with ATNF/GMRT + VLA data, but I haven't tried.

I managed to fix this problem in the case of VLA data with a combination of UVCOP, SPECR, and CVEL. Basically, it works because the VLA correlator setup is all multiples of two. In general, if you have a data set with twice as many channels, it has half the channel spacing. This is not always true due to an observer's ability to set up IFs in different ways, but the channel spacings should always differ by some power of two.

Now for the solution(s).

For example, imagine you have spectral line data set A with 127 channels and spacing of 6.1 kHz, and data set B with 255 channels and spacing of 3.05 kHz. (The extra channel from each needed to make a power of two is the Channel 0 data set. So you really only have 127 instead of 128 and 255 instead of 256 channels.) Effectively, you will have to either double the channel spacing of data set B, or half the channel size of data set A.

In order to DBCON, you will need to jump through many AIPS hoops in order to make sure that both data sets have:
- the same number of channels
- the same spectral resolution
- the same frequencies assigned to the same channels

To degrade the high-resolution data:
- First, you will need to use UVCOP to chop off one channel in data set B, so an integer number of channels in SPECR will give you the correct velocity resolution. It shouldn't matter if you chop one off from the beginning or from the end, as these are generally line free.

- Next, use SPECR to regrid data set B to the proper channel spacing. In this case, you will want a channel spacing of 6.1 kHz. This means that you need to tell SPECR to regrid to half as many channels. Each new channel has twice the original channel spacing. In this case, you will tell SPECR to use npoints 127, which is conveniently half of 254.

- Now run CVEL on both data sets. The correct inputs are described at the bottom of this guide. The main APARM values to set are:


aparm(1) = [velocity in m/s to be assigned to..]
aparm(2) = [..this channel number]

Essentially, you have regridded both of your data sets to a system where the given velocity is assigned to the given channel. It may spit out a lot of errors saying that it is shifting the channels by many km/s, but as long as the same channels in both data sets correspond to the same velocities, you're set.

- Run UVCOP to chop off additional channels if necessary. In this case, the data sets should be the same, but depending on correlator settings, you may have to chop off additional channels. This time, always chop them off from the end, because you have regridded your data so that the first channels in the set line up with the first channels in the other data set.

- Run DBCON to combine both data sets. DBCON will shift RA and Dec as long as the pointing centers aren't vastly different.

To oversample the low-resolution data:

- Use SPECR to regrid data set A to 254 (NOT 255) channels. This will effectively chop your channel width in half, so it matches data set B. You will deal with the fact that both data sets have a different number of channels in a few steps, so don't worry.

- Use CVEL to assign the same frequency to the same channel for both observations. This will shift each spectrum in frequency/channel, but will not resize the channel spacing. More instructions for using CVEL are at the bottom of the guide. The important inputs are:


aparm(1) = [velocity in m/s to be assigned to..]
aparm(2) = [..this channel number]

Essentially, you have regridded both of your data sets to a system where the given velocity is assigned to the given channel. CVEL may spit out a LOT of errors telling you that you are shifting your channels by a lot, but as long as your galaxy shows up in the same channels in both datasets, you should be okay.

- use UVCOP to chop off additional channels. Data set A (after SPECR) has 1 fewer channel than data set B. Fix this by chopping off the last channel of data set B using UVCOP. Set BCHAN 0 and ECHAN 254.

- Use DBCON to combine data set A (after SPECR + CVEL) and data set B (after CVEL + UVCOP). It should shift the RA and Dec of the one of the data sets unless they have vastly different pointing centers.

Now for something completely different (aka additional notes):

Occasionally you will have to chop off more channels from data set A, depending on your correlator set up for both observations. The key point is to make sure that both data sets have the same number of channels with the same channel spacing and the same velocity definition (e.g., channel 52 = -50 km/s).

And now some info on running CVEL. In some of our observations, we did not use Doppler tracking (Oh, EVLA, you'll be awesome one day), so we also had to tell CVEL the rest frequency of our HI line so it could calculate gas velocity. You may not need all of these inputs, but here's how I had to set the APARM values, which is really the meat of CVEL:

aparm -50000 52 1 0 1.420e09 5752 1 0

What does this mean? Well!


aparm(1) = -50000
aparm(2) = 52

Together these two values shift the spectrum so that a velocity of -50000 m/s lines up with channel 52. This will be different for each galaxy - in our case, it's a galaxy with a systemic velocity of -50000 m/s (NGC 404 in fact).


aparm(3) = 1
aparm(4) = 0

These set the velocity definition. The first sets the reference to heliocentric velocity, and the second tells AIPS to use the optical definition.


aparm(5) = 1.420e09
aparm(6) = 5752

This sets the rest frequency of your line in GHz. AIPS does not have enough precision for all the significant figures, so you have to use two APARM values. If you're working with something other than HI, I recommend reading the help file to figure out how to input your frequency.


aparm(7) = 1

This is set to 1 for VLA data.

Measuring Spectral Lines

2009-08-24T23:17:00.007-05:00

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?

Multiple contours on one plot

2009-08-17T16:44:00.005-05:00

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.

Flip frequency axis in UV data?

2009-08-07T09:28:00.008-05:00

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?

Amplitude Self-Calibration and Flux Levels

2009-08-06T02:12:00.005-05:00

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.

Mulit-Resolution Clean Tutorial?

2009-06-22T11:01:00.007-05:00

Here is a very reasonable request from an anonymous reader:

Can someone write about multi-resolution clean(MRC)..basically the steps involved and the way self cal should be carried out while using MRC ? thanks in advance.

which I can not fulfill, as I have never successfully pulled off a MRC. You might try looking at the EXPLAIN file for IMAGR in the section called "Extended Source Options".

If anyone knows better resources for learning about how to implement multi-resolution clean, please let us know!

FreqID tolerance

2009-06-22T10:53:00.001-05:00

And another question from reader Korinne:

With data all observed looking for a particular spectral line over a few objects, should you use different frequency ids for the objects or can you use the same frequency id? I've been using a suggested value of a 2 MHz frequency tolerance in the manual which means they all end up with the same frequency id, but I do not know if it's right.

Thoughts?

Combining Data with Different Pointings

2009-06-22T10:42:00.005-05:00

Here is a question from reader Korinne:

I have data from three VLA pointings in L band at the same frequency (with the same channel width) but with different pointing centres which cover an area of an object and partially overlap, unintentionally as the pointings don't overlap at the other frequency we observed that the observations were mostly set up for.

What is the best way to combine this data? I initially imaged and cleaned and then combined with flatn, but it seems like there might be some way to do it at the uv level, but from my readings of the cookbook I can't figure out how I would go about that, particularly in slightly more detail.

My answer below the fold...

I think you want DBCON, which can concatenate data in UV space. Try reading this post. The answer is basically that it depends on just how different your different data pointing are.

If you are actually talking about mosaicing a source, where your various pointings are offset by significant fractions of the primary beam, then FLATN might be your best bet. A bit more discussion of mosaicing here.

Combining Spectral Line UV Data (with slightly different channel setups)

2009-06-14T11:40:00.008-05:00

Update: See this lovely post by Adrienne

This is a very good question from reader SillyWolf. I know several of us have been wondering how to concatenate spectral line data sets that have approx. the same wavelength coverage, but different channel setups (different widths, different centers). So any advice would be greatly appreciated by many people!

There are two VLA archive data which were observed in spectral line mode.
These two archive data cover very similar frequency range.
The point is that:
not only they have different pointing center (about 1 arcmin away from each other), but also their reference frequencies do not match each other, so their frequencies don't match channel by channel !!
I want to combine these two data together. can I use DBCON to combine them in UV domain, or I have to resample one of these datacubes in image domain and combine them together?

Averaging Image Channels

2009-06-12T11:20:00.006-05:00

Here is a good question from Sanch:

I am trying to average spectral channels in an image cube. Can anyone suggest what's the best way
to do it in AIPS?
I don't want to go back to the UV data and re-reduce it to get the image, as the data I am
working on is huge (VLBI data).

And some more details:

She wants to average together channels in a channel map. In other words, she has a channel map with, say, 100 channels and she wants to turn it into a map with 50 channels. Channels 1 and 2 would be averaged together and become the new "Channel 1," channels 3 and 4 would be averaged together and become the new "Channel 2," and so on.

Thoughts, AIPS gurus?

Channels and CALIB

2009-05-23T17:05:00.008-05:00

When one is self-calibrating a multi-channel data set, and one gives CALIB a BCHAN and ECHAN value, what is CALIB doing with the channels? Is it averaging them all before it calibrates?

If it is doing that, then why bother making a Channel 0 data set to calibrate off of? Simply because CALIB runs much faster if it doesn't have to deal with multiple channels? Is there something wrong with using a multi-channel data set to do the initial calibration (on the phase cal + flux cal sources?)

A Coarse Course on 3-D imaging

2009-05-13T10:51:00.014-05:00

An anonymous reader requests:
can someone help me out by writing the detail process of 3d imaging/cleaning after split file is created? I am new to AIPS and any kind of help is welcomed. thanks in advance..

I would recommend that you look at Joe Lazio's write-up, starting right about here:

http://lwa.nrl.navy.mil/tutorial/node31.html

He discusses using SETFC and IMAGR to image with multiple facets.

Some supplementary personal opinions of mine below the break...

So, what I would do is run SETFC as he instructs-- SETFC parameters look like:


AIPS 2: SETFC:  Task to make a BOXFILE for input to IMAGR
AIPS 2: Adverbs     Values                 Comments
AIPS 2: ----------------------------------------------------------------
AIPS 2: INNAME     'NGC3631'               UV dataset name (name)
AIPS 2: INCLASS    'AVSPC'                 UV dataset name (class)
AIPS 2: INSEQ         1                    UV dataset name (seq. #)
AIPS 2: INDISK        5                    Disk drive #
AIPS 2: SOURCES    *all ' '                Source selected
AIPS 2: BCOUNT        1                    First field number to use
AIPS 2: BOXFILE    'N3631_610.BOX'
AIPS 2:                                    disk file to write to (the
AIPS 2:                                    input BOXFILE for IMAGR)
AIPS 2: CELLSIZE      0.8         0.8      (X,Y) size of grid in asec
AIPS 2: IMSIZE     2048        2048        field size
AIPS 2: SHIFT         0           0        Position shift (RA,Dec) asec
AIPS 2:                                    for all fields
AIPS 2: FLUX          0                    Minimum component flux =
AIPS 2:                                    (source * beam)
AIPS 2: BPARM         0.35       10        (1) Inner region radius (deg)
AIPS 2:               0           1.5      (2) Field overlap (pixels)
AIPS 2:               0.1       512        (3) Factor to scale NVSS
AIPS 2:             512        *rest 0         fluxes, 0 -> 1
AIPS 2:                                    (4) Radius NVSS search (deg)
AIPS 2:                                    (5) Flux limit in NVSS (Jy)
AIPS 2:                                    (6) IMSIZE for NVSS fields
AIPS 2:                                    (7) IMSIZE for Sun fields
AIPS 2:                                    (8) Write Clean boxes for
AIPS 2:                                        NVSS fields
AIPS 2:                                    (9) Maximum allowed phase
AIPS 2:                                        error in imaging
AIPS 2:                                    (10) Points per beaam
AIPS 2: PBPARM     *all 0                  Beam parameters:
AIPS 2:                                    (1) Cutoff; (2) Use (3)-(7)
AIPS 2:                                    (3)-(7) Beam shape parms
AIPS 2: INFILE     ' '
AIPS 2:                                    NVSS input file name
AIPS 2:                                    ' ' => AIPS provided.

But I'd also make sure your CELLSIZE is small enough to thoroughly sample point sources. What i would do is run SETFC once with CELLSIZE= 0 and IMSIZE = 0, and then decrease the CELLSIZE by a factor of 2 or 3, add that to the SETFC parameters, and rerun SETFC. You can let it suggest an IMSIZE to you, given the new CELLSIZE. The max IMSIZE i like to use is 2048, because much bigger than that and IMAGR will average large number of pixels together to show you the field.

Oftentimes I will tile the central portion of the image (out to ~1 primary beam, or to where bandwidth smearing really bites you, depending on the data; set by BPARM(1)) with bigger fields (IMSIZE=2048) and then let SETFC search for NVSS sources out to a radius ~2 times that of the primary beam (Radius set by BPARM(4)). I put smaller fields on these NVSS sources-- say 512 pixels (Set by BPARM(6)).

So, then you will have a list of boxes saved in a file (labelled by BOXFILE). It's now time to image. My IMAGR parameters look like this:


AIPS 2: IMAGR: Wide field imaging/Clean task
AIPS 2: Adverbs     Values                 Comments
AIPS 2: ----------------------------------------------------------------
AIPS 2: INNAME     'NGC3631'               Input UV data (name)
AIPS 2: INCLASS    'UVCOP'                 Input UV data (class)
AIPS 2: INSEQ         2                    Input UV data (seq. #)
AIPS 2: INDISK        5                    Input UV data disk drive #
AIPS 2: SOURCES    *all ' '                Source name
AIPS 2: QUAL         -1                    Calibrator qualifier -1=>all
AIPS 2: CALCODE    ' '                     Calibrator code '    '=>all
AIPS 2: TIMERANG   *all 0                  Time range to use
AIPS 2: SELBAND      -1                    Bandwidth to select (kHz)
AIPS 2: SELFREQ      -1                    Frequency to select (MHz)
AIPS 2: FREQID       -1                    Freq. ID to select.
AIPS 2: SUBARRAY      0                    Sub-array, 0=>all
AIPS 2: ANTENNAS   *all 0                  Antennas to plot
AIPS 2: BASELINE   *all 0                  Baselines with ANTENNAS
AIPS 2: DOCALIB      -1                    > 0 calibrate data & weights
AIPS 2:                                    > 99 do NOT calibrate weights
AIPS 2: GAINUSE       0                    CL (or SN) table to apply
AIPS 2: DOPOL        -1                    If >0.5 correct polarization.
AIPS 2: BLVER        -1                    BL table to apply.
AIPS 2: FLAGVER       0                    Flag table version
AIPS 2: DOBAND       -1                    If >0.5 apply bandpass cal.
AIPS 2:                                    Method used depends on value
AIPS 2:                                    of DOBAND (see HELP file).
AIPS 2: BPVER        -1                    Bandpass table version
AIPS 2: SMOOTH     *all 0                  Smoothing function. See
AIPS 2:                                    HELP SMOOTH for details.
AIPS 2: STOKES     ' '                     Stokes parameters (see HELP)
AIPS 2: BCHAN         1                    Low freq. channel 0 for cont.
AIPS 2: ECHAN        56                    Highest freq channel
AIPS 2: CHANNEL       0                    Restart channel number
AIPS 2: NCHAV        56                    Number of chan. to average.
AIPS 2: CHINC         1                    Channel incr. between maps.
AIPS 2: BIF           0                    First IF in average.
AIPS 2: EIF           0                    Last IF in average.
AIPS 2: OUTNAME    'N3631_6'               Output image name (name)
AIPS 2: OUTDISK       5                    Output image disk drive #
AIPS 2: OUTSEQ        0                    Output seq. no.
AIPS 2: OUTVER        0                    CC ver. no (Continuum only)
AIPS 2:                                    *** SET OUTVER ON RESTARTS
AIPS 2: IN2NAME    ' '                     UV work file name
AIPS 2: IN2CLASS   ' '                     UV work file class
AIPS 2: IN2SEQ        0                    UV work file seq
AIPS 2:                                    *** SET TO KEEP WORK FILE
AIPS 2: IN2DISK       0                    UV work file disk
AIPS 2: CELLSIZE      0.8         0.8      (X,Y) size of grid in asec
AIPS 2: IMSIZE      512         512        Minimum image size
AIPS 2: NFIELD       21                    Number of fields (max 4096)
AIPS 2: DO3DIMAG      1                    > 0 => use different tangent
AIPS 2:                                    points for each field
AIPS 2: FLDSIZE    *all 0                  Clean size of each field.
AIPS 2: RASHIFT    *all 0                  RA shift per field (asec)
AIPS 2: DECSHIFT   *all 0                  DEC shift per field (asec)
AIPS 2: UVTAPER       0           0        (U,V) Gaussian taper
AIPS 2:                                      units are kilo-lambda
AIPS 2: UVRANGE       0           0        Min & max baseline (klambda)
AIPS 2: GUARD         0           0        x,y guard band fractional
AIPS 2:                                    radius
AIPS 2: ROTATE        0                    Rotate image CCW from N by
AIPS 2:                                    ROTATE degrees
AIPS 2: ZEROSP     *all 0                  0-spacing fluxes and weights
AIPS 2:                                    SEE HELP!!
AIPS 2: UVWTFN     ' '                     UV dist. weight function
AIPS 2: UVSIZE        0           0        Array size for doing uniform
AIPS 2:                                    weights.  0 -> actual field
AIPS 2:                                    size.
AIPS 2: ROBUST        0                    Robustness power: -5 -> pure
AIPS 2:                                    uniform weights, 5 => natural
AIPS 2: UVBOX         0                    Additional rows and columns
AIPS 2:                                    used in weighting.
AIPS 2: UVBXFN        1                    Box function type when UVBOX
AIPS 2:                                    > 0.  0 -> 1 round pill box.
AIPS 2: XTYPE         5                    Conv. function type in x
AIPS 2:                                      default spheroidal
AIPS 2: YTYPE         5                    Conv. function type in y
AIPS 2:                                      default spheroidal
AIPS 2: XPARM      *all 0                  Conv. function parms for x
AIPS 2: YPARM      *all 0                  Conv. function parms for y
AIPS 2: NITER      130000                  Maximum # of Clean components
AIPS 2: BCOMP      *all 0                  Begin at BCOMP component
AIPS 2:                                    Specify for each field.
AIPS 2: ALLOKAY       0                    For restart: > 0 => beams
AIPS 2:                                    okay, > 1 => work file too
AIPS 2: NBOXES        0                    Number of boxes for Clean
AIPS 2:                                    NB: field 1 only.
AIPS 2: CLBOX      *all 0                  Four coordinates for each box
AIPS 2: BOXFILE    'N3631_610.BOX'         Input file of field params
AIPS 2:                                    and Clean boxes; ' ' => use
AIPS 2:                                    FLDSIZE, RASHIFT, DECSHIFT,
AIPS 2:                                    NBOXES, CLBOX only.
AIPS 2: OBOXFILE   'N3631_610.BOX'         Output file for final Clean
AIPS 2:                                    boxes
AIPS 2: GAIN          0.1                  Clean loop gain
AIPS 2: FLUX          0                    Minimum Clean component (Jy)
AIPS 2: MINPATCH    121                    Min. BEAM half-width in AP.
AIPS 2: BMAJ          0                    FWHM(asec) major axis Clean
AIPS 2:                                    restoring beam.
AIPS 2: BMIN          0                    FWHM(asec) minor axis Clean
AIPS 2:                                    restoring beam.
AIPS 2: BPA           0                    Clean beam position angle
AIPS 2: OVERLAP       2                    1 => restore components to
AIPS 2:                                    overlapped fields, >=2=>
AIPS 2:                                    expect overlaps in Cleaning
AIPS 2: PHAT          0                    Prussian hat height.
AIPS 2: FACTOR        0                    Speedup factor see HELP
AIPS 2: CMETHOD    ' '                     Modeling method:
AIPS 2:                                    'DFT','GRID','    '
AIPS 2: IMAGRPRM   *all 0                  Task enrichment parameters
AIPS 2:                                    (1) Antenna diameter (m)
AIPS 2:                                    (2) Source Spectral index
AIPS 2:                                    (3) Frequency scaling factor
AIPS 2:                                    (4) > 0 -> SDI Clean factor
AIPS 2:                                    (5) >0 => scale residuals
AIPS 2:                                    (6) Half-width in x of box
AIPS 2:                                    (7) Half-width in y of box
AIPS 2:                                    (8) Filter components whose
AIPS 2:                                    neighborhood is weaker than
AIPS 2:                                    IMAGRPRM(8) Jy.  0 -> don't
AIPS 2:                                    (9) Radius in pixels for the
AIPS 2:                                    IMAGRPRM(8) test.
AIPS 2:                                    (10) multiplier of image size
AIPS 2:                                    to get beam size: 0 => 2;
AIPS 2:                                    2, 1, 0.5 0.25 supported
AIPS 2:                                    (11-16) Multi-resolution
AIPS 2:                                    added controls
AIPS 2:                                    (17) spectral index radius
AIPS 2:                                         0 -> no correction
AIPS 2:                                    (19) Dynamic range limit
AIPS 2:                                    (20) Retry factor (see help)
AIPS 2: NGAUSS        0                    Number of resolutions to use
AIPS 2: WGAUSS     *all 0                  Resolutions in arc sec >= 0
AIPS 2: FGAUSS     *all 0                  Minimum flux for each resol.
AIPS 2: MAXPIXEL      0                    Maximum pixels searched in
AIPS 2:                                    each major cycle.
AIPS 2: IN3NAME    ' '                     Spectral index image name
AIPS 2: IN3CLASS   ' '                     Spectral index image class
AIPS 2: IN3SEQ        0                    Spectral index image sequence
AIPS 2:                                    number
AIPS 2: IN3DISK       0                    Spectral index image disk
AIPS 2: IN4NAME    ' '                     Spectral curvature name
AIPS 2: IN4CLASS   ' '                     Spectral curvature class
AIPS 2: IN4SEQ        0                    Spectral curvature sequence
AIPS 2:                                    number
AIPS 2: IN4DISK       0                    Spectral curvature disk
AIPS 2: FQTOL        -1                    Frequency tolerance in kHz
AIPS 2:                                    (primary beam & spec index)
AIPS 2: DOTV          1                    Display residuals on TV ?
AIPS 2:                                    Start with field = DOTV
AIPS 2: GRCHAN        0                    Graphics channel of boundary
AIPS 2: BADDISK    *all 0                  Disks to avoid for scratch.

You're going to want to set CELLSIZE to the same value you used with SETFC. IMSIZE should be the size of the smallest field you are using-- so in this case, 512. Don't worry, IMAGR is smart enough to know that some of the fields are bigger than this. NFIELD should be set to the number of fields output by SETFC. Set DO3D = 1 whenever you use facets. Set BOXFILE and OBOXFILE to the name of the file outputted from SETFC. Finally, set OVERLAP=2 and DOTV=1. See Joe Lazio's write-up for more detail on other parameters.

Don't be surprised that imaging with multiple facets can be realllly slooow...especially if you also have multiple channels. You're going to want to watch IMAGR run on the TV and set clean boxes around your sources, which can sometimes swallow up an entire afternoon or more. On the bright side, now that you have set OBOXFILE, all the clean boxes will be saved to it, so you might not have to watch IMAGR run on the TV next time (unless you say, have self-caled and a bunch of new sources have popped up which now need to be boxed).

The rough general idea is that IMAGR is going to try to find the facet with the brightest flux peak in it, and it will present this facet to you for cleaning. Put boxes around the sources in the facet with TVBOX/REBOX, and then click on CONTINUE CLEAN. IMAGR will now clean some flux out of these boxes, and search again for the facet with the brightest peak. Just keep boxing and continuing to clean until it seems like you've cleaned pretty deeply. There's a good chance some of the facets don't have any sources in them, in which case you can just not box anything at all and then tell IMAGR to CONTINUE CLEAN. If there are no boxes, it will not clean anything.

When you finally STOP CLEANING, IMAGR will restore all the clean components and present you with NFIELD images. You can then use these images to self calibrate, if you like.

If I am planning on doing several self cal iterations, I will often go through the facets and eliminate those with no sources. I just edit the BOX file to remove the facets with no sources, and then decrease the NFIELD parameter in IMAGR appropriately.

When you're happy with your imaging, you can use FLATN to turn the many facets into one single big image. See the Lazio instructions here:

http://lwa.nrl.navy.mil/tutorial/node36.html

Super Resolution

2009-05-12T12:02:00.004-05:00

When people say they have 'super-resolved' their source-- say, by having a 0.75" beam for VLA 20 cm A config observations-- what do they mean? Did they just ask CLEAN to give them a 0.75" restoring beam? This makes me feel very nervous. What do you guys think? Is it a good idea in some cases?

AIPS Scripting Example Sans Commentary

2009-04-15T15:24:00.005-05:00

For your viewing pleasure, here's an example AIPS script. What the script does is calibrate a VLA continuum data set (including polarization). Note that this script is NOT guaranteed to work for YOUR data! DO NOT USE THIS SCRIPT BLINDLY. I am posting this as an example of AIPS scripting, not as an example of how to reduce data.

See below the cut for the code.



*
* REDUCE.099
*
* Purpose: a set of routines designed to aid in the calibration process. Note that
*          these procedures use stuff in VLAPROCS. RUN VLAPROCS before running 
*          routines in this file.
*
* NOTES on Run Files with AIPS: 
*
*         AIPS is stupid, so indenting stuff with tab characters causes AIPS to 
*         barf on a run file.
*
*         To run a RUNFILE, create an environment variable in your shell with the 
*         directory where the runfile is. Name the runfile with something short 
*         ending in .099 (user number in hex; use EHEX in AIPS to find). In AIPS, 
*         change your version to version='myvlar080705'. Caution: you don't want 
*         any of your routine names or values to be the same as something already 
*         in AIPS. For example, naming a routine CLCAL will cause AIPS to use your
*         CLCAL routine rather than the actual CLCAL routine. You read in your 
*         runfile with 'RUN reduce.099'. Changed the file and need to run again? 
*         Then just do RUN reduce.099 again. Note that AIPS doesn't get rid of 
*         the first instance of RUN reduce.099 in memory, so you need to use 
*         COMPRESS periodically to get rid of old reduce.099 stuff. COMPRESS also 
*         helps when you have issues after redefining variables etc. To nuke a 
*         procedure from the procedures list (help procs to see), use scratch. 
*         The procedure still takes up memory however until you run a compress. I 
*         haven't figured out how to get rid of old adverbs. 
*     
*         Getting errors that say 'AIPS: SYMBOL?' means that POPS (the scripting 
*         language) doesn't recognize the command. Try help popsym to get a list 
*         of the commands available to you.
* 
*         'TXTMAT: NO MEMBER NAME GIVEN' means that you should make sure there's
*          procedure in the memory of AIPS.
*
*         Note that the read command expects single quotes about whatever you 
*         enter on the keyboard. Respond 'Y' rather than Y to any prompts.
*      
*         Make sure that the last line of the file is empty otherwise the last 
*         line of the program will not be read.
*       
*
* Date              Programmer             Description of Changes
* ----------------------------------------------------------------------
* 3/21/06           A.A. Kepley            Original Code
* 3/23/06           A.A. Kepley            Modified for new 12/05/05 dataset
* 9/12/06     A.A. Kepley            Modified for use with AM694 dataset
* 2/09/06           A.A. Kepley            Modified for use with AM643 dataset
* ======================================================================
*
proc dreduceme
*
* Purpose: dummy procedure to create variables used later
*
* Inputs: none
*
* Outputs: none
* 
* Method: none
* 
* Date              Programmer             Description of Changes
* ----------------------------------------------------------------------
* 3/21/06           A.A. Kepley            Original Code
* 3/23/06           A.A. Kepley            Modified for new 12/05/05 dataset
*
     string*8 pri_cal                         $ name of primary calibrator.
     string*8 sec_cal                         $ name of secondary calibrator. Also
                                              $ used to calibrate the instrumental
                                              $ polarization response.
     string*8 obj_name(15)                    $ name of object (maybe more than 1). 
     scalar   nobj                            $ number of objects
     string*50 myoutname                      $ name of output file for various 
                                              $ tasks.
     string*15 dataprefix                     $ what data set I'm reducing.
     scalar   myrefant                        $ reference antenna (1-29).
     string*8 myprompt                        $ prompt value.
     scalar   polangle                        $ polarization angle
     array   pri_uvr(2)                   $ set uvrange for primary calibrator
     array   sec_uvr(2)                   $ set uvrange for secondary calibrators
     scalar  mysolint                          $ set my solution interval
     scalar  mypsolint    $ set my solution interval for my polarization
*
return;finish
*
* ======================================================================
*
proc reduceme
*
* Purpose: Main calibration routine. This routine pretty thoroughly clobbers
*          your AIPS environment you might want to do a save at the command 
*          line so you can go back to the way things were (using get) 
* 
* Inputs:  The user needs to change the values for INNAME, INCLASS, INSEQ, 
*          INDISK, PRI_CAL, SEC_CAL, OBJ_NAME, DATAPREFIX, and MYREFANT for
*          each data set.             .
*
* Outputs: calibrated data set with final calibration table in CL 3 and 
*          gain and phase calibration table in CL 2. This task also produces a 
*          number of files in order to check on the calibration in your main home
*          directory. If you run reduceme several times, the information from the 
*          later runs will be appended to the files. The files also include the
*          task input parameters used to run the tasks. The files are named with 
*          the data set you are reducing, the object name, and the task which was 
*          run.
*          
* Method:  This calibration routine is for single channel continuum calibration 
*          including polarization calibration. It follows the procedures in 
*          Chapter 4 of the 31DEC05 version of the AIPS Cookbook closely.
*          It uses the old method of calibrating the primary flux calibrator 
*          uv limits rather than a model of the source.
* 
*          REMEMBER TO CHECK ALL OUTPUT TO MAKE SURE THE REDUCTION WENT WELL AND
*          THAT THE ROUTINE IS DOING WHAT YOU THINK IT SHOULD BE DOING. 
* 
* Date              Programmer             Description of Changes
* ----------------------------------------------------------------------
* 3/21/06           A.A. Kepley            Original Code
* 3/23/06           A.A. Kepley            Modified for new 12/05/05 dataset
* 9/12/06           A.A. Kepley            Modified for AM694_1 dataset
* 2/09/07           A.A. Kepley            Modified for AM643_1 dataset

* cleaning things up.
     clrmsg
     dowait true
     default getjy
     default setjy
     default calib
     default clcal
     default listr
     default pcal
     default rldif
     default clcor

* input file to calibrate 
     INNAME     'AM643_1     '          $ Input image name (name)
     INCLASS    'X BAND'                $ Input image name (class)
     INSEQ         1                    $ Input image name (seq. #)
     INDISK        1                    $ Input image disk unit #

* primary, secondary calibrator, and object to calibrate
     pri_cal = '0521+166'
     sec_cal = '0244+624'
     obj_name = 'N1569',''
     
* Other defaults for calibration
     nobj = 1
     dataprefix = 'AM643_1.'
     myrefant = 5
     flagver 1
     pri_uvr = 0,45            $ since the data are all less than 20 klamdba 
     sec_uvr = 0,0             $ this isn't too important
     polangle = -20
     mysolint = 0.0
     mypsolint = 1.0

* Run setjy to find the flux value for the primary calibrator
     prtask 'SETJY'                     $ clearing out the results
     clrmsg                             $ of previous runs of setjy.
     task 'SETJY'
     sources pri_cal,''
     optype 'calc'
     calcode ''
     freqid 1
     aparm 0
     go
* Save the results of the setjy run
     myoutname dataprefix !! pri_cal !! '.SETJY'
     docrt false
     outprint myoutname  
     prtask 'AIPS'
     clrmsg
     inputs setjy                       $ printing out the setjy inputs
     prtmsg
     prtask 'setjy'                     $ printing out the setjy results
     prtmsg

* Run VLACALIB on the primary calibrator
*     calsour pri_cal,''
*     calcode ''
*     uvrange pri_uvr
*     refant myrefant
*     snver 1
*     minamper 10
*     minphser 10
*     docalib false 
*     gainuse 0
*     doprint 1
*     myoutname dataprefix !! pri_cal !! '.CALIB'
*     outprint myoutname
*     vlacalib

* Run VLACALIB on the secondary calibrator
*     calsour sec_cal,''
*     calcode ''
*     uvrange sec_uvr
*     refant myrefant
*     snver 1
*     minamper 10
*     minphser 10
*     doprint 1
*     myoutname dataprefix !! sec_cal !! '.CALIB'
*     outprint myoutname
*     vlacalib

* Run CALIB on the primary calibrator
     prtask 'CALIB'
     clrmsg
     task 'CALIB'
     calsour pri_cal,''
     calcode ''
     bchan 1
     echan 0
     antennas 0
     uvrange pri_uvr
     weightit 0
     snver 1
     minamper 10
     minphser 10
     docalib false 
     clr2name
     clroname
     refant myrefant
     gainuse 0
     dopol false
     doband false
     solint mysolint
     solsub 0
     solmin 0
     soltype ''
     aparm  4,0
     aparm(6) 2
     solmode 'A&P'
     cparm 0, 0, minamper/10, minphser/10, 1, 0    
     go
* Save results of CALIB run
     myoutname dataprefix !! pri_cal !! '.CALIB'     
     docrt false
     outprint myoutname
     prtask 'AIPS'
     clrmsg
     inputs calib
     prtmsg
     prtask 'calib'
     prtmsg

* Run CALIB on the secondary calibrator
     prtask 'CALIB'
     clrmsg
     task 'CALIB'
     calsour sec_cal,''
     calcode ''
     bchan 1
     echan 0
     antennas 0
     uvrange sec_uvr
     weightit 0
     snver 1
     minamper 10
     minphser 10
     docalib false 
     clr2name
     clroname
     refant myrefant
     gainuse 0
     dopol false
     doband false
     solint mysolint
     solsub 0
     solmin 0
     soltype ''
     aparm  4,0
     aparm(6) 2
     solmode 'A&P'
     cparm 0, 0, minamper/10, minphser/10, 1, 0    
     go
* Save results of CALIB run
     myoutname dataprefix !! sec_cal !! '.CALIB'     
     docrt false
     outprint myoutname
     prtask 'AIPS'
     clrmsg
     inputs calib
     prtmsg
     prtask 'calib'
     prtmsg

* Transfering the flux density scale determined by the primary calibrator 
* to the secondary calibrator and the polarization angle calibrator
     prtask 'getjy'
     clrmsg
     task 'getjy'
     sources sec_cal,''
     soucode ''
     calsour pri_cal,''
     calcode ''
     bif 1; eif 2
     freqid 1
     snver 1
     go
* Save the results of the setjy run
     myoutname dataprefix !! sec_cal !! '.GETJY'
     docrt false
     outprint myoutname
     prtask 'aips'
     clrmsg
     inputs getjy
     prtmsg
     prtask 'getjy'
     prtmsg

* Applying the gain and phase solutions from the secondary calibrator to the data
     prtask 'clcal'
     clrmsg
     task 'clcal'
     sources sec_cal, obj_name, ''
     soucode ''
     calsour sec_cal,''
     calcode ''
     opcode 'cali'
     interpol '2pt'
     doblank 1
     dobtween 0
     snver 1
     gainver 1
     gainuse 2
     refant myrefant
     go
* Save the results of the calib run
     myoutname dataprefix !! sec_cal !! '.CLCAL'
     docrt false
     outprint myoutname
     prtask 'aips'
     clrmsg
     inputs clcal
     prtmsg
     prtask 'clcal'
     prtmsg

* Applying the gain and phase solutions from the primary calibrator to the 
* primary calibrator 
     prtask 'clcal'
     clrmsg
     task 'clcal'
     sources pri_cal,''
     soucode ''
     calsour pri_cal,''
     calcode ''
     opcode 'cali'
     interpol '2pt'
     doblank 1
     dobtween 0
     snver 1
     gainver 1
     gainuse 2
     refant myrefant
     go
* Save the results of the calib run
     myoutname dataprefix !! pri_cal !! '.CLCAL'
     docrt false
     outprint myoutname
     prtask 'aips'
     clrmsg
     inputs clcal
     prtmsg
     prtask 'clcal'
     prtmsg

* looking at the results of the gain and phase calibration
     task 'listr'
     optype 'matx'
     sources pri_cal,''
     uvrange pri_uvr
     calcode ''
     stokes ''
     freqid 1
     bif 1; eif 1
     docalib 2
     gainuse 2
     dparm 5, 1, 0                $ plot scalar averaged amp+phase
     docrt false
     myoutname dataprefix !! pri_cal !! '.GPCALRES'
     outprint myoutname
     go
     bif 2; eif 2
     go

     task 'listr'
     optype 'matx'
     sources sec_cal,''
     uvrange sec_uvr
     calcode ''
     stokes ''
     freqid 1
     bif 1; eif 1
     docalib 2
     gainuse 2
     dparm 5, 1, 0                $ plot scalar averaged amp+phase
     docrt false
     myoutname dataprefix !! sec_cal !! '.GPCALRES'
     outprint myoutname
     go
     bif 2; eif 2
     go

     bif 1; eif 2

* prompting to see if I want to do polarization calibration
     print 'Do polarization calibration (Y/N)?'
     read myprompt
     if myprompt = 'N' then 
         return
     end

* Calibrating the instrumental polarization 
     prtask 'pcal'
     clrmsg
     task 'pcal'
     calsour sec_cal,''
     docalib 2
     gainuse 2
     solint mypsolint
     soltype 'appr'
     prtlev 1
     bparm 0
     cparm 0
     go
* Save the results of the pcal run
     myoutname dataprefix !! sec_cal !! '.PCAL'
     docrt false
     outprint myoutname
     prtask 'aips'
     clrmsg
     inputs pcal
     prtmsg
     prtask 'pcal'
     prtmsg

* calibrate the absolute phase angle using either 3C286 (1331+305) or 
* 3C138 (0521+166)
    prtask 'rldif'
    clrmsg
    task 'rldif'
    sources pri_cal,''
    uvrange pri_uvr
    docalib 2
    gainuse 2
    dopol true
    docrt false
    myoutname dataprefix !! pri_cal !! '.RLDIF'
    outprint myoutname
    go

* changing RLdif output to a phase offset correction    
* I've changed the following (9/12/06) so that the polarization angle is set 
* earlier in the program depending on what polarization angle source is used.
    for i = 1:2
         clcorprm(i) = polangle - clcorprm(i)
    end

    print 'finish clcorprm'

* applying the polarization corrections to the data
    prtask 'clcor'
    clrmsg
    task 'clcor'
    sources ''
    stokes 'L'
    gainver 2
    gainuse 3
    opcode 'polr'
    go
* saving the results of the clcor run
    myoutname dataprefix !! obj_name(1) !! '.CLCOR'
    docrt false
    outprint myoutname
    prtask 'aips'
    clrmsg
    inputs clcor
    prtmsg
    prtask 'clcor'
    prtmsg

* checking the polarization calibration
    task 'rldif'
    sources pri_cal, sec_cal,''
    uvrange pri_uvr
    freqid 1
    bif 1; eif 2
    docalib 2
    gainuse 3
    dopol 1
    docrt false
    myoutname dataprefix !! pri_cal !! '.PCALRES'
    outprint myoutname
    go

return;finish
*
* ======================================================================
*
proc killcal
*
* Purpose: clean up old calibration to run new calibration.
*
* Inputs: none
*
* Outputs: deletes all CL tables except CL 1 and all SN tables.
*
* Method: none
* 
* Date              Programmer             Description of Changes
* ----------------------------------------------------------------------
* 3/21/06           A.A. Kepley            Original Code
*
*
    vlareset
    inext 'sn'
    invers -1
    extdest

return; finish
*
* ======================================================================
*
proc test
* 
* Purpose: test stuff
* 
     print 'Y or N'
     read myprompt
     print myprompt
     if myprompt = 'Y' then 
          print 'Yay for Yes!'
          return
     else 
          print 'Boo for no!'
     end

     print 'hello world'

return; finish
* 
* ====================================================================== 
*

AIPS Scripting: Progress Update

2009-04-15T15:14:00.005-05:00

From reader Bruce:

This scripting stuff is very useful, but I can't find scripting AIPS #3 and etc. Is it out there?

I have lots of files to input, run sdgrid on, then write out. I have no idea how I could go about making sure stuff gets in the right slot to work for any given task.

The short answer is that I haven't gotten around to writing it yet. (thesis) I'll put it on my to-do list for my observing run next month. It's a good task for 2 in the morning. I'll post an example script without commentary, in case some one would find it useful.

The slightly longer answer is that you don't need to worry about catalog slots. Instead of dealing with stuff through the getn mechanism, i.e., getn 209, you want to use the actual name of the file (INNAME, INCLASS, INSEQ, INDISK, etc.). That way you know you have the file you want, and don't have to depend on the catalog number always being the same.

More Missing Flux Cals

2009-03-07T12:16:00.005-06:00

I'm reducing archival data, and a flux calibrator was unfortunately not taken at the beginning and the end of the observation. It was only taken at the beginning, and when I read the data in with FILLM, FILLM says that the antennas moved between my flux cal and my phase cal/data. FILLM then puts the flux cal in a different UV file from the data/phase cal.

I'm thinking the antennas couldn't have moved THAT much over 15 minutes (and all i want is a flux anyway), so I'd still like to use the flux cal (also there are no appropriate recent fluxes for the phase cal in any of the NRAO databases that Claudia suggested.) Is there a way to
a) apply a flux calibration solution from another uv file?
or
b) relax FILLM's requirements so that it will not be so sensitive to moving antennas and put everything in one file?
or
c) append a source to another UV file? I know uvglu appends in frequency, but i don't think it appends sources.

Thanks!

WBR Step 7C: Apply Your Calibration

2009-03-05T21:11:00.003-06:00

After you have calibrated your calibrators, you are going to want to apply this calibration to your source data-- the object you actually care about imaging.

First, you need to make a CL table that interpolates the amplitude/phase solutions found every ~30 minutes for the phase calibrator to your source data. You can use CLCAL or VLACLCAL to do this. Let's say your sources are "PHS_CAL' and 'COOL_GAL', and you have a lovely SN table for 'PHS_CAL' which you determined using the steps in Section 6. Then your inputs to CLCAL will look like this:


AIPS 1: CLCAL     Task to manage SN and CL calibration tables
AIPS 1: Adverbs     Values                 Comments
AIPS 1: ----------------------------------------------------------------
AIPS 1: INNAME     'NICE_DATA'            Input UV file name (name)
AIPS 1: INCLASS    'L BAND'                Input UV file name (class)
AIPS 1: INSEQ         2                    Input UV file name (seq. #)
AIPS 1: INDISK        1                    Input UV file disk unit #
AIPS 1: SOURCES    'PHS_CAL'              Source list to calibrate
AIPS 1:            'COOL_GAL'  *rest ' '
AIPS 1: SOUCODE    ' '                     Source "Cal codes"
AIPS 1: CALSOUR    'PHS_CAL'              Cal sources for calibration
AIPS 1:            *rest ' '
AIPS 1: QUAL         -1                    Source qualifier -1=>all
AIPS 1: CALCODE    ' '                     Calibrator code '    '=>all
AIPS 1: TIMERANG   *all 0                  Time range to calibrate
AIPS 1: SUBARRAY      0                    Subarray, 0=>all,
AIPS 1: ANTENNAS   *all 0                  Antennas selected, 0=> all
AIPS 1: SELBAND      -1                    Bandwidth to select (kHz)
AIPS 1: SELFREQ      -1                    Frequency to select (MHz)
AIPS 1: FREQID       -1                    Freq. ID to select.
AIPS 1: OPCODE     ' '                     Operation 'MERG','CALI',
AIPS 1:                                    'CALP'; ' ' => 'CALI'
AIPS 1: INTERPOL   '2PT'                   Interpolation function,
AIPS 1:                                    choices are: '2PT','SIMP',
AIPS 1:                                    'AMBG','CUBE','SELF','POLY',
AIPS 1:                                    'SELN'; see HELP for details
AIPS 1: CUTOFF        0                    Interpolation limit in
AIPS 1:                                    time (min); 0=> no limit.
AIPS 1: SAMPTYPE   ' '                     Smoothing function
AIPS 1: BPARM      *all 0                  Smoothing parameters
AIPS 1: ICUT          0.1                  Cutoff for functional forms
AIPS 1: DOBLANK       0                    Blanked value interpolation
AIPS 1: DOBTWEEN      0                    > 0 -> smooth all sources
AIPS 1:                                    together; else separate them
AIPS 1: SMOTYPE    ' '                     Data to smooth
AIPS 1: SNVER         0                    Input SN table, 0=>all.
AIPS 1: INVERS        0                    Upper SN table vers in a
AIPS 1:                                    range.  0=>SNVER
AIPS 1: GAINVER       1                    Input Cal table 0=>high
AIPS 1: GAINUSE       2                    Output CAL table 0=>high+1
AIPS 1: REFANT        8                    Reference antenna 0=>pick.
AIPS 1: BADDISK    *all 0                  Disks to avoid for scratch

Now CL table #2 has all the info you need to calibrate your data!

Next, you want to apply this calibration and split your 'COOL_GAL' data off into a single source file. For this, use SPLIT.


AIPS 1: SPLIT     Task to split multi-source uv data to single source
AIPS 1: Adverbs     Values                 Comments
AIPS 1: ----------------------------------------------------------------
AIPS 1:                                    also works on single files.
AIPS 1: INNAME     'NICE_DATA'            Input UV file name (name)
AIPS 1: INCLASS    'L BAND'                Input UV file name (class)
AIPS 1: INSEQ         2                    Input UV file name (seq. #)
AIPS 1: INDISK        1                    Input UV file disk unit #
AIPS 1: SOURCES    'COOL_GAL'             Source list
AIPS 1:            *rest ' '
AIPS 1: QUAL         -1                    Source qualifier -1=>all
AIPS 1: CALCODE    ' '                     Calibrator code '    '=>all
AIPS 1: TIMERANG   *all 0                  Time range to copy
AIPS 1: STOKES     ' '                     Stokes type to pass.
AIPS 1: SELBAND      -1                    Bandwidth to select (kHz)
AIPS 1: SELFREQ      -1                    Frequency to select (MHz)
AIPS 1: FREQID       -1                    Freq. ID to select.
AIPS 1: BIF           0                    Lowest IF number 0=>all
AIPS 1: EIF           0                    Highest IF number 0=>all
AIPS 1: BCHAN         0                    Lowest channel number 0=>all
AIPS 1: ECHAN         0                    Highest channel number
AIPS 1: SUBARRAY      0                    Subarray, 0=>all
AIPS 1: DOCALIB       2                    > 0 calibrate data & weights
AIPS 1:                                    > 99 do NOT calibrate weights
AIPS 1: GAINUSE       2                    CL (or SN) table to apply
AIPS 1: DOPOL        -1                    If >0 correct polarization.
AIPS 1: BLVER         -1                    BL table to apply.
AIPS 1: FLAGVER       0                    Flag table version
AIPS 1: DOBAND       -1                    If >0 apply bandpass cal.
AIPS 1:                                    Method used depends on value
AIPS 1:                                    of DOBAND (see HELP file).
AIPS 1: BPVER         1                    Bandpass table version
AIPS 1: SMOOTH     *all 0                  Smoothing function. See
AIPS 1:                                    HELP SMOOTH for details.
AIPS 1: OUTCLASS   'SPLIT'                 Output UV file name (class)
AIPS 1: OUTSEQ        0                    Output UV file name (seq. #)
AIPS 1: OUTDISK       0                    Output UV file disk unit #.
AIPS 1: DOUVCOMP     -1                    1 (T) => compressed data
AIPS 1: APARM      *all 0                  Control information:
AIPS 1:                                      1 = 1 => avg. freq. in IF
AIPS 1:                                               multi-channel out
AIPS 1:                                        = 2 => avg. freq. in IF
AIPS 1:                                               single channel out
AIPS 1:                                        = 3 => avg IF's also
AIPS 1:                                      2 = Input avg. time (sec)
AIPS 1:                                      3 > 0 => Drop subarrays
AIPS 1:                                      4 > 0 => calibrate weights
AIPS 1:                                      5 = 0 pass only xc data
AIPS 1:                                        = 1 pass xc and ac data
AIPS 1:                                        = 2 pass only ac data
AIPS 1:                                      6 > 0 add full source name
AIPS 1:                                            to header
AIPS 1: NCHAV         0                    Number of chan. to average.
AIPS 1:                                    (used if APARM(1) = 1)
AIPS 1:                                    <= 0 -> ALL
AIPS 1: CHINC         0                    Channel incr. between output
AIPS 1:                                    channels (used if APARM(1)=1)
AIPS 1: ICHANSEL   *all 0                  Array of channel start, stop,
AIPS 1:                                    and increment numbers and IF
AIPS 1:                                    number to be used when
AIPS 1:                                    averaging in frequency.
AIPS 1:                                    (used if APARM(1) = 2, 3)
AIPS 1: BADDISK    *all 0                  Disks to avoid for scratch

The most important things to have set here are DOCAL = 2 and GAINUSE=2. If you have done other fancy things like a baseline-dependent calibration or a bandpass calibration, you can also apply those here.

SPLIT will make a file with just the calibrated data for your source of interest. You'll need to flag this single-source file, and then you'll be ready to image!

Imaging with AIPS

2009-03-05T09:09:00.005-06:00

Reader Elena has a question:

Could some of you indicate me a tutorial for imaging with AIPS ?
I would need something with examples, and possibly considering both point-like and extended sources.
So far I found this :
http://www-astro.physics.ox.ac.uk/~hrk/AIPS_TUTORIAL/HRK_AIPS_1.html#24.
It's not focused on imaging, but there are some useful images as examples. Besides, it doesn't consider the case when one can not self-calibrate (e.g. looking for all Stokes parameters), that would be very interesting for me.

My response is below.

Elena, I would suggest that you read the AIPS COOKBOOK section on imaging and check out the synthesis imaging summer school book on imaging as well. I also encourage you to play around with IMAGR and see how changing the different parameters changes the image.

Why is imaging quick sometimes and slloooow others?

2009-03-04T20:52:00.005-06:00

I have 6 sources, each with 2-3 hours of continuum L-band data on them. For five of them, imaging and self-calibration are really quite quick, but one of the sources takes a factor of 5-6 longer to image/calibrate than the others! Its correlator setup is not different, it was taken only one day previous to the other sources, and it has a similar amount of time on source. Any ideas about why imagr seems to choke for this source? Thanks!

Casa and high frequency data

2009-02-27T09:05:00.004-06:00

A question from reader Adam:

Do you folks do any work with high frequency (K and Q band) data? Do you use CASA at all? I've been trying to do both.

My (Amanda) response is below. Feel free to add yours in the comments.

I've just started playing with CASA, but not with high frequency data. My impressions are that the core utilities are there and that they're making great progress debugging everything and adding functionality. That being said, be extremely careful using CASA for production data reduction and make sure you double-check everything.

I've heard from other people that there are performance issues associated with large data sets on 32-bit computers.

This error paves the road to madness

2009-02-25T18:06:00.005-06:00

Not to be melodramatic or anything.
But this error:


SCREAT: FAILED TO CREATE REQUESTED SCRATCH FILE
CALCOP: ERROR     5 CREATING SCRATCH FILE

has started popping up all over the place ever since i updated to 31Dec08 version of aips. The relevant task always crashes after giving me this error.

It often pops up when I'm just doing an innocent UVPLT-- and sometimes if I load my data up in TVFLG and wiggle my mouse around and push a few buttons, when i quit out and try UVPLT, the error will be gone. But sometimes it won't.

And i was just trying to run BLCAL and got the error for that script too! I've checked to make sure my uv data is not being read or written. I don't understand what it means. Any thoughts?

CVEL and DBCON with ATCA Data

2009-02-10T11:12:00.007-06:00

I'm reducing some archival, multi-configuration HI data from the ATCA and am having trouble getting the velocity axis quite right. I've put the correct velocity definition in the header using CVEL and then am combining the individual data sets using DBCON with DOPOS=1,1 so it checks the position and frequency information in the header. However, when I make the image and compare to the originally published image the velocities for various features are way off (~40 to 100 km/s). Any words of wisdom from the peanut gallery on using CVEL and DBCON together?

I've mostly been following The Analysis of ATCA data with AIPS, but it's a little light on detail on this issue.

Watch out for those FreqIDs!

2009-02-09T13:28:00.003-06:00

If you're a continuum observer (especially if you use the single-channel, 50 MHz correlator setting at the VLA), it's important to remember when reducing line data that each different set of frequencies in line data is given its own FreqID number. Some tasks work fine with datasets with multiple FreqIDs (e.g., LISTR), but other tasks (e.g., TVFLG or SPFLG) need to be told what FREQID to use or they won't find the data. You can control how the FREQIDs are assigned in FILLM.

Clean Boxes from SETFC

2009-01-28T18:36:00.004-06:00

Here is a question from an anonymous reader:

I'm new to AIPS, and noticed that using SETFC automatically sets clean boxes for every facet, the same size as every facet. When I've been wide field imaging, I've just been adding smaller clean boxes around sources on top of these. Is this ok, or is it better to delete these automatic boxes, and just manually add ones around obvious sources? Thanks.

I think I know the answer to this, if you click to read on...

You definitely want to delete the big clean box. By and large, you don't want clean boxes to overlap, and you do not want to clean your entire field (which is what you're doing if you leave that big clean box). Someone at NRAO once really stressed to me that you want your clean boxes placed as tightly around the real flux in your sources as possible. So get rid of those big boxes.

Bad Gain Exponents

2009-01-16T10:04:00.011-06:00

I'm trying to calibrate some archival VLA HI data from 1989 and FILLM keeps giving me scary messages about BAD GAIN EXPONENTS, e.g.,


MCCHED:  0/02:34:45.0 12 x 12  BAD GAIN EXPONENT      26

AIPS seems to really not like this. ~~The source table of the resulting data file only contains the first source observed, which is not right.~~ I'm was going to be more aggressive about the FILLM selection parameters to avoid the bad times, but was wondering if anyone else has encountered this?

EDIT: After playing with the TIMERANG keyword for FILLM, it seems like this is a problem with how AIPS is reading in the file. Everytime I change the TIMERANG keyword, the data with the BAD GAIN EXPONENTS changes to the earliest data in the file. Weird.

Importing Miriad files into AIPS

2008-12-15T23:01:00.004-06:00

A question from Danny:

Hello AIPS ninjas.

Is there any way to import miriad *.uv files -the kind that are whole directories full of binary files- into AIPS?

~Danny

Kvis & AIPS awesomeness!

2008-12-10T19:48:00.008-06:00

You can use kvis to view your AIPS images directly! See below for more details. Thanks to Bryan Gaensler for this awesome tip.

The program kvis is an image viewer that is part of the karma image analysis package. An undocumented, but cool feature of this program is that if you navigate to your AIPS data directory (typically somewhere like $AIPS_ROOT/DATA/LOCALHOST_1) in the kvis file selector you will see each AIPS image file with its correct name (instead of crytic filenames like FQD001001.099;) and be able to click on them and view them. Once you've got then in kvis, you can even save to FITS.

Missing Scans!

2008-12-05T15:27:00.007-06:00

I'm reducing some EVLA-VLA data, and I discovered that one of the calibrator scans was missing in the data. It was listed in the "scan list" on the archive and the observe files were (to the best of our knowledge) correct. After emailing the analysts, we figured out that the scan was flagged by the online flagger. You can read in the data without applying these online flags using CPARM(3) = 16.

I'm still trying to figure out why it was flagged, and I'm assuming that this information is stored in the "OF Table" extension. However, I haven't been able to find any information on that table using google (googling "aips 'OF table'" doesn't really work because you get a lot of pages with properties of tables, not info about the OF table).

I'll post what I learn about this (if anything), but it's something to keep in mind if you find yourself missing scans..

Multi-scale clean vs. regular clean

2008-10-20T10:07:00.004-05:00

Those of you clean afficiandos should check out this recent astro-ph article:
Multi-Scale CLEAN: A comparison of its performance against classical CLEAN in galaxies using THINGS

SUBIM question

2008-10-20T10:06:00.002-05:00

A question from reader Jenny:

I'm trying to combine two optical images using AIPS (don't ask why!) but the FITS images I have are not centred on the sources I want to combine. I want to use SUBIM to create images centred on my targets but is there a way to get the task to create the image using the ra and dec of the target rather than TRC and BLC?

Mystery Error: TASK HAS NOT BEGUN IN 15.1 SECONDS

2008-10-20T09:24:00.005-05:00

A question from Tony:

Has anyone start getting the following error message:

AIPS 1: TASK HAS NOT BEGUN IN 15.1 SECONDS
AIPS 1: Begin check for any 'standard' scratch files
AIPS 1: Scratch files -- destroyed: 0 still active: 0
AIPS 1: Resumes

A few people across the department have receive the same error message, and I think it is a problem related to 31DEC08.

But why 15.1 seconds?!

Imaging GMRT Data

2008-10-14T12:20:00.004-05:00

A plea for advice from an anonymous reader:

Off topic, & quite possibly a stupid question from an AIPS newbie, but I'd really appreciate any help. I'm currently processing some GMRT data (30mins, 610MHz, 38 facets, each imsize 512, cellsize 1.5), & IMAGR seems to take a very long time to run, ~2hrs for 1000 iterations. I'm wondering if this is normal, or if something has gone wrong during the SPLAT process, where I split off the source from the multi source dataset, and averaged every 7 channels between channels 1 & 105.

IMAGR, with NCHAV=15,when running, appears to process channels 1-15, then 2-16,3-17 etc, is this normal for data that has been averaged as above?
Thanks.

Importing AIPS images into IRAF

2008-09-15T17:25:00.010-05:00

Here is a question from reader donkeypuncher:

I'd like to use IRAF to do some analysis on images produced in AIPS. Alas, I am unable to open in IRAF the FITS files output by AIPS (task FITTP). I get this simple, non-informative message when I attempt to use the IRAF task display:

ERROR: Cannot open image (IMAGE.FITS)

I'm guessing it's a format issue, because I have no problem loading in ds9. Any ideas?

BTW, I like the site, thanks for your contributions!

My guess at an answer can be found if you click below..

I think that IRAF needs and expects the '.fits' suffix to be in all small letters. Try changing your image name to 'image.fits' and see if that helps.
Also-- something else I've noticed is that optical software often freaks out at the small pixel values in AIPS images (For example, are your pixel values on the order 10^-3 to 10^-6?). Once you get your image into IRAF, you might want to try multiplying your entire image by some large constant, say a million, using imarith. This could potentially save you headaches.

Flux calibration scales at the VLA?

2008-09-15T10:53:00.005-05:00

I've run into what looks like a systematic offset between flux scales of earlier observations and my observations. I'm using the 1999.2 coefficients to set my flux scale and it looks like the earlier observations are using the coefficients from Baars et al. (1977). Any ideas on what the differences are between these two systems? 5%? 10%? 20%? I've tried searching the VLA calibration documentation for the information, but didn't find anything useful (although maybe I missed something).

Clearing AIPS Variables?

2008-08-21T11:56:00.003-05:00

During my recent forays into AIPS scripting, I have often wanted to change how a variable is defined...say by changing an array from dimensions of 50 to 200. When I try to do this, AIPS tells me that the variable is 'ALREADY DF' (or defined, i'm guessing). Is there some way to clear a variable?

Well, I just thought to do a 'RESTORE 0', which seems to clear everything. So maybe that it is the best solution?

MSGSRV Aesthetics

2008-08-17T17:54:00.005-05:00

I've been wanting a scrollbar in my MSGSRV for as long as I can remember, and I finally got one! This is how I did it (on my Mac, running X11)...

I made a .Xdefaults file in my home directory with these lines:


AIPSmsg*scrollBar: True
AIPSmsg*saveLines: 500

I quit out of AIPS and in the xterm where I was running aips, I typed:


xrdb -load ~/.Xdefaults

to make my computer register the .Xdefaults file.

When I started up AIPS again, I had a scroll bar! This page gave me this hint, plus tells you how to change other MSGSRV settings, like colors.

Reading ASCII Tables into AIPS?

2008-08-14T18:43:00.004-05:00

I'm trying to write a script where I repeat some steps on lots of different objects, and therefore I want to read a list of coordinates into AIPS. I currently have an ASCII list of x and y values. Can i read it into AIPS as two arrays so that my script can access them? Or do I have to do something hideous like manually fill the arrays within my script?

AIPS system temperatures.. in miriad?

2008-08-14T13:40:00.003-05:00

So we're trying to reduce our data in AIPS and then image in it miriad. Sounds familiar. Anyway, we want to use options=systemp when inverting the uv data. However, I've noticed that miriad doesn't appear to correctly import the system temperatuers from AIPS when using "fits" to read in the fits file that I wrote with AIPS using FITTP. In fact, it sets all the system temperatures to 60K, exactly.

There is an option in fits (varwt) to use the reciprocal of the noise variance on a visibility as its weight, but the system temperatures are still set to 60K.

Ideas?

Mosaicing: AIPS/Miriad/whatever works!

2008-08-11T14:48:00.004-05:00

Is anyone familiar with mosacing techniques in AIPS, Miriad, or both? I have 21cm VLA spectral line data, taken mosaic-style, and am having a heck of a time trying to stitch the pointings together. Here's what I have done so far:

Reduced in the standard manner with AIPS up until the 'SPLIT' step
Wrote out each pointing with FITTP
Loaded into Miriad
In Miriad, 'invert', 'mossdi', and 'restor', mostly with the defaults for parameters

The best way I can describe the results is like a bad patchwork quilt...does anyone know of a good cookbook or guide for putting together pointings into a mosaic? I know AIPS has some tasks for this (VTESS/UTESS/LTESS) but I haven't had success with them. Thanks!

Katie

How does CALIB make use of clean components?

2008-07-22T10:22:00.005-05:00

A question from Sam Tun....
I've been working on some self-cal programs for the Owens Valley Solar Array, and I am having similar problems as these. I would want a self-caled map that gives me a good approximation to my CLEAN map fluxes, but no go on that. So, my question is, does anyone know what is done to the clean components to get them to return appropriate visibilities to feed into self-cal? I believe that in AIPS you feed the CLEAN map as a model into calib, but does anyone know the details of what goes on in there (or where to find them)? Gracias.

Total Flux in an Image Region?

2008-07-22T10:14:00.005-05:00

A question from an anonymous reader...
But I have this issue: How to find the total flux in a given region? tvstat can make regions, but it shows only mean and rms. Is there any task that will show total flux under a selection?

How does DBCON deal with flagging?

2008-07-16T20:22:00.006-05:00

Does anybody out there understand how DBCON flags your data? The help file is being less than transparent. DBCON seems to copy over all the FG tables from the first image you give it to the DBCON'd file, but does not appear to copy FG tables from the second image.

There is this note in the help file:
"Also, any CL, FG, TY, WX, IM, MC, PC, AT, CT, OB, or GC tables with version=1 will have their source numbers translated and appended to the end of the corresponding table (if any) from the first file."
So, let's say I have 13 flag tables for Image1 and 6 flag tables for Image2 (which happens a lot with the new crazy FG table creation scheme). Does this mean FG #1 for Image2 gets appended to FG tables 1-13 from Image1? And then in the futere, I will be apply a combination of FG#1 to Image1 and FG #13 to Image2? That's kinda dumb...

How to Know When You Can Self-Cal and What Solint To Use

2008-07-09T16:51:00.006-05:00

Have you ever done a self-calibration run to find out the self cal is actually making your images worse, not better? Have you ever guessed at what SOLINT to use while self calibrating? I know I have!

People always say you should evaluate the signal-to-noise of your data before self-calibrating, but I never understood what this meant until today! There is a simple equation to find out if you can self-cal and if the SOLINT you are considering might be too short....

First image your data and clean it pretty good. Afterwards you can look in the image header and not the total cleaned flux. This is your 'Signal'.

Second of all, you want to calculate the noise in your data, per baseline per SOLINT. First, measure the rms noise in your image, in Jy/beam (sig_image). Next, calculate the number of baselines in your data (N_base where N_base = ((N_ant * N_ant-1) / 2) and N_ant is the number of operational antennae). Finally, figure out how much time-on-source went into making your image, in minutes (TOS). The noise of your data per baseline for a given SOLINT (in minutes) is then:
Noise = sig_image * sqrt(N_base) * sqrt(TOS/SOLINT)

Now, compare the 'Signal' with the 'Noise'. For 'P' self cal, you want the Signal to be at least 5 times greater than the Noise. If it's not, then increase your SOLINT. For A&P self cal, you probably want a signal-to-noise of 10-20, at least.

Note: If you are doing multi-facet imaging (at lower frequencies), you want to use the total flux in your data-- that is the sum from all facets, The image headers tell you this as 'CCTOTAL'.

Self Calibration and DBCON

2008-07-09T16:41:00.006-05:00

Let's say you have two data sets that you want to DBCON together. Should you self calibrate them individually? or after DBCONing?

The tip I got is you should self-cal each data set individually as best you can, then DBCON. However, after DBCONing, there might be some small gain offsets between the two data sets. Do a final A&P self cal on the DBCONed data set with a really long SOLINT, so that you basically have one SN solution per data set. This will ensure the original data sets are as consistent with one another as possible.

Two More Ways to Identify Bad Data

2008-07-09T16:30:00.006-05:00

Crystal also said a good way to identify RFI is to look at Stokes V, either in TVFLG or UVPLT or whatever. RFI is usually polarized and will pop out as unusually high baselines/channels/times.

Stokes V will usually mimic your amplitude structure (as a function of baseline length). So, for example, if your source has high amplitudes at short baselines, Stokes V should also be a bit higher on these short baselines (so don't get confused and flag them).

And another way to find that bad data-- Data weights. Plot your data in UVPLT with BPARM = 0 13. The weights for all the data should cluster-- if there are any points that are anomalously low or high, flag them! Crystal says she likes to use WIPER. Obviously, be more concerned about data with really high weights that really low weights-- because this data will affect your overall data set more, as it is up-weighted!

Don't Clip Your Data!

2008-07-09T16:22:00.004-05:00

I'm at the GBT, and just had a nice long chat with Crystal Brogan (who was very helpful when she reeally didn't need to be). I'm gonna list a few tips she suggests.

Here's one: DON'T CLIP!! She said that if you clip your data based on amplitude (or phase), what you're really doing is masking the lower-level bad data. A baseline is probably all bad if it has quite a few high points, and you don't want to just flag the really high stuff, you want to flag it all. If you clip the high stuff, it will be very hard to ever identify that whole baseline as bad. You'll essentially be 'losing' bad data. I know CLIPing is sometimes tempting, especially at the GMRT, but I can see that it's an especially bad idea in this case.

Need Larger Fonts on Plots

2008-06-30T14:57:00.005-05:00

I'm trying to get the labels for my plots in AIPS to be much larger than the default. LWPLA has an option to specify the font size, dparm(8), but after playing with it, it seems like 24pt is the maximum font size. I would really like to use something bigger than this. I can modify the labels manually in Illustrator, but that requires repositioning all the labels, which is way too time intensive. Any other ideas?

UPDATE: Solution using ASPMM parameter in LWPLA detailed in comments.

Bins in UVPLT

2008-06-28T15:06:00.004-05:00

You know what is a great easy way to visualize your data that I often forget about? Bin your data in UVPLT! For example, if you are making a UV distance vs. Amplitude plot, then you can actually see the amplitude structure instead of just seeing tons of points ranging all the way down to an amplitude of zero.

All you have to do is set BPARM(8) = 50 or the number of bins you want.

I think it also plots up faster this way then plotting lots of individual points!
Of course, if what you care about is a handful of really pathelogical points, than this is not the right strategy. But if you are, say, trying to identify a bad baseline or something, this works great!

Calibrating Data without a Flux Calibrator

2008-06-17T18:21:00.003-05:00

Sometimes when I get data from the archive, it appears that the observers have not observed a flux calibrator. There is a phase calibrator. Is it possible to use this data? Is the data really only good for imaging and getting the morphology of an object, but you can not trust it for absolute fluxes? I feel like I should be able to do something clever to get fluxes...

Flagging After A&P Self Calibration?

2008-06-08T11:50:00.003-05:00

I've been wondering lately-- when you run an Amplitude & Phase Self-Cal run, often times this can make certain parts of your data look anomalously high or low. Usually it's pretty mild, but a couple of times, it has been rather dramatic. A bit distressing, as I don't really understand why CALIB chose to make my amplitudes worse...

But anyway, does anyone out there have opinions on whether you should flag your data again after an A&P self cal? If you do flag, do you then copy the flag table over to the un-A&P-self-calibrated data set, and the re-self-calibrate using this new flag table? And iterate so on till no more "bad" data pops up on the A&P self cal?

DBCONing Data Sets From Different Epochs

2008-06-06T15:59:00.005-05:00

If you are an archive monger like me, you might find yourself reducing one J2000. data set and one B1950. data set, and then wanting to concatenate them together. If you try to do this, DBCON will yell at you. So...

You will have to run EPOSWTCH on the 1950 data set to bring it into epoch 2000. However, if you try to run DBCON now, DBCON will still yell at you and say:


tsingt> DBCON1: DEC      AXIS HAS UNEQUAL ATTRIBUTES
tsingt> DBCON1: Purports to die of UNNATURAL causes

As explained by Eric Greisen here , this is because the image you EPOSWTCHed now has a Declination axis with a rotation imposed upon it. For example:


AIPS 1: Image=NGC1569   (UV)         Filename=N1569_3B    .SC_P1 .   1
AIPS 1: Telescope=VLA                Receiver=VLA
AIPS 1: Observer=AA116               User #=   53
AIPS 1: Observ. date=21-AUG-1990     Map date=06-JUN-2008
AIPS 1: # visibilities    135940     Sort order  TB
AIPS 1: Rand axes: UU-L-SIN  VV-L-SIN  WW-L-SIN  BASELINE  TIME1
AIPS 1:            WEIGHT  SCALE
AIPS 1: ----------------------------------------------------------------
AIPS 1: Type    Pixels   Coord value     at Pixel     Coord incr   Rotat
AIPS 1: COMPLEX      1   1.0000000E+00       1.00  1.0000000E+00    0.00
AIPS 1: STOKES       4  -1.0000000E+00       1.00 -1.0000000E+00    0.00
AIPS 1: FREQ         1   8.4149000E+09       1.00  5.0000000E+07    0.00
AIPS 1: IF           2   1.0000000E+00       1.00  1.0000000E+00    0.00
AIPS 1: RA           1    04 30 49.498       1.00       3600.000    0.00
AIPS 1: DEC          1    64 50 59.587       1.00       3600.000   -0.60
AIPS 1: ----------------------------------------------------------------
AIPS 1: Coordinate equinox 2000.00
AIPS 1: Rest freq      0.000         Vel type: OPTICAL wrt YOU
AIPS 1: Alt ref. value  0.00000E+00  wrt pixel    1.00
AIPS 1: Maximum version number of extension files of type FQ is   1
AIPS 1: Maximum version number of extension files of type HI is   1
AIPS 1: Maximum version number of extension files of type AN is   1
AIPS 1: Maximum version number of extension files of type WX is   1
AIPS 1: Maximum version number of extension files of type FG is   1

You can get rid of this rotation using UVSRT:


AIPS 1: UVSRT:  Task which sorts UV data
AIPS 1: Adverbs     Values                 Comments
AIPS 1: ----------------------------------------------------------------
AIPS 1: INNAME     'N1569_3B'              Input UV file name (name)
AIPS 1: INCLASS    'SC_P1'                 Input UV file name (class)
AIPS 1: INSEQ         1                    Input UV file name (seq. #)
AIPS 1: INDISK        1                    Disk unit # of input UV data
AIPS 1: OUTNAME    ' '                     Sorted UV file name (name)
AIPS 1: OUTCLASS   'ROTAT'                 Sorted UV file name (class)
AIPS 1: OUTSEQ        0                    Sorted UV file name (seq. #)
AIPS 1: OUTDISK       0                    Disk unit # of sorted UV data
AIPS 1:                                      0 => highest with space
AIPS 1:                                    If outfile spec. equals the
AIPS 1:                                    infile spec., output will
AIPS 1:                                    overwrite the input
AIPS 1: BADDISK    *all 0                  Disk drive #'s to avoid
AIPS 1: SORT       ' '                     Two char. sort order, eg.'XY'
AIPS 1:                                    blank => 'XY'
AIPS 1: ROTATE        0.6                  Angle thru which to rotate.
AIPS 1:                                    positive rotates CCW
AIPS 1: DEFER         0                    Defer output file creation?

Note that the ROTATE parameter is the negative of the rotation noted in the header. Now you should be able to DBCON the EPOSWTCHed data with the other J2000 data set!

(You may have to UVSRT the DBCONed data so that it is in TB order again.)

Calibrating One Calibrator with Two UVranges

2008-06-02T17:53:00.004-05:00

The VLA calibrator manual recommends that if you are using 3c286 as your flux calibrator at 20 cm in A configuration, you should use the uvrange 0-18 AND 90-180 (for the latter, decrease flux by 6%). This makes me wonder how on earth one would do this. First of all, I do not know how to calibrate on two separate uvranges and then merge that information. Second of all, I do not know how to reduce a flux by 6%. Anyone? Anyone?

Help Miriad Selfcal Tip

2008-03-07T17:17:00.004-06:00

IGNORE THE FOLLOWING POST. If Miriad is rescaling to large values during the self-calibration process, this is a sign that something is wrong with your self-calibration and you need to increase the self-calibration interval or need more clean components.

This is a bit off the beaten path, but I'd thought I'd post it anyway. If you're self-calibrating in Miriad, it helps to set the noscale option.

The noscale option prevents Miriad from rescaling the gains during amplitude+phase self-calibrating so that the rms gain is 1.0. If you have a lot of outliers, not setting this option can play havoc with the derived amplitudes. A sign that this may be a problem for your data would be unrealistically large amplitudes (much greater than 1.0) after amplitude+phase self-calibration.

Bandpass calibration trauma

2008-02-04T15:29:00.001-06:00

I've been working on bandpass calibrating some WSRT data. Usually this is a pretty simple process, but for some reason I can't get it to work out here. When I calibrate the data I'm getting large closure errors that seem to be baseline and polarization dependent. Before bandpass calibration, I went through the data and flagged anything that looked like it had an amplitude that was off. After flagging I thought the data looked pretty good in SPFLG. Changing the reference antenna or the calibration source doesn't fix the problem. What had partially fixed the problem for the LL feed at least was going from the default SOLTYPE to SOLTYPE='L1R', which uses a more robust method of fitting the bandpass that is less sensitive to variations in the input data.

Any ideas? I've put my inputs to BPASS and some sample output below.

Update (2/4/08): It looks like using bpassprm(5) = -1 instead of bpassprm(5) = 0 works. bpassprm(5) = -1 is only supposed to be used in cases of decent phase stability. It averages over time and then averages the ichansel channels rather than averaging the ichansel channels on a record-by-record base as does bpassprm(5)=0. Therefore, bpassprm(5)=-1 gives me a bit more signal enabling better bandpass calibration. The phase stability of my observations is pretty good, so I think I'm safe using this parameter.]

AIPS 1: BPASS     Task to generate a "Bandpass" (BP) table.
AIPS 1: Adverbs     Values                 Comments
AIPS 1: ----------------------------------------------------------------
AIPS 1: USERID        0                    User number
AIPS 1: INNAME     'POLANG'                Input UV file name (name)
AIPS 1: INCLASS    '13CM'                  Input UV file name (class)
AIPS 1: INSEQ         3                    Input UV file name (seq. #)
AIPS 1: INDISK        2                    Input UV file disk unit #
AIPS 1:
AIPS 1:                                    Data Selection
AIPS 1: CALSOUR    '3C286'                 Bandpass calibrator sources.
AIPS 1:            *rest ' '
AIPS 1: QUAL         -1                    Calibrator qualifier -1=>all
AIPS 1: CALCODE    ' '                     Calibrator code '    '=>all
AIPS 1: UVRANG        0           0        UV range to select
AIPS 1: TIMERANG   *all 0                  Time range to select
AIPS 1: SELBAND      -1                    Bandwidth to select (kHz)
AIPS 1: SELFREQ      -1                    Frequency to select (MHz)
AIPS 1: FREQID        1                    Freq. ID to select.
AIPS 1: BIF           0                    Lowest IF number 0=>all
AIPS 1: EIF           0                    Highest IF number 0=>all
AIPS 1: SUBARRAY      0                    Subarray, 0=>all
AIPS 1: ANTENNAS   *all 0                  Antennas to select
AIPS 1:
AIPS 1:                                    CLEAN map (optional)
AIPS 1: IN2NAME    ' '                     Cleaned map name (name)
AIPS 1: IN2CLASS   ' '                     Cleaned map name (class)
AIPS 1: IN2SEQ        0                    Cleaned map name (seq. #)
AIPS 1: IN2DISK       0                    Cleaned map disk unit #
AIPS 1: INVERS       -1                    CC file version #.
AIPS 1: NCOMP      *all 0                  # comps to use for model.
AIPS 1:                                    1 value per field
AIPS 1: FLUX          0                    Lowest CC component used.
AIPS 1: NMAPS         0                    No. Clean map files
AIPS 1: CMETHOD    ' '                     Modeling method:
AIPS 1:                                    'DFT','GRID','    '
AIPS 1: SMODEL     *all 0                  Source model, 1=flux,2=x,3=y
AIPS 1:                                    See HELP SMODEL for details.
AIPS 1:
AIPS 1:                                    Control options
AIPS 1: DOCALIB       1                    > 0 calibrate data & weights
AIPS 1:                                    > 99 do NOT calibrate weights
AIPS 1: GAINUSE       2                    CL table to apply (SN table
AIPS 1:                                    to apply to single-source)
AIPS 1: DOPOL        -1                    If >0 correct polarization.
AIPS 1: BLVER        -1                    BL table to apply.
AIPS 1: FLAGVER       1                    Flag table version
AIPS 1: DOBAND       -1                    If >0 apply bandpass cal.
AIPS 1:                                    Method used depends on value
AIPS 1:                                    of DOBAND (see HELP file).
AIPS 1: BPVER         0                    Bandpass table version
AIPS 1: SOLINT        0                    Solution interval (mins)
AIPS 1:                                    -1 => do whole time range
AIPS 1: SOLTYPE    'L1R'                   Soln type,'  ','L1','GCON',
AIPS 1: REFANT        5                    Reference antenna
AIPS 1: OUTVERS       0                    Output BP table version
AIPS 1:                                    0 => a new table to be
AIPS 1:                                         generated.
AIPS 1: SMOOTH     *all 0                  Smoothing function.
AIPS 1:                                    BE VERY CAREFUL HERE.
AIPS 1: ANTWT      *all 0                  Ant. wts (0 => 1.)
AIPS 1: WEIGHTIT      0                    Modify data weights function
AIPS 1: MINAMPER     10                    Amplitude closure error
AIPS 1:                                    regarded as excessive in %
AIPS 1: MINPHSER     10                    Phase closure error regarded
AIPS 1:                                    as excessive in degrees
AIPS 1: BPASSPRM      0           2        Control information:
AIPS 1:               0           0        1: if > 0 use only the
AIPS 1:               0          10           autocorrelation data.
AIPS 1:              10           1        2: print level - see help
AIPS 1:               1           3        3: If > 0 do not divide data
AIPS 1:               0                       by source model
AIPS 1:                                    4: If > 0 store phases only
AIPS 1:                                       in the BP table.
AIPS 1:                                    5: Divide by 'channel 0'
AIPS 1:                                       **** SEE HELP - NEW ****
AIPS 1:                                    6: amp closure error limit -
AIPS 1:                                       print channels averaging
AIPS 1:                                       over this if (2) > 0
AIPS 1:                                    7: phase closure error limit
AIPS 1:                                       print channels averaging
AIPS 1:                                       over this if (2) > 0
AIPS 1:                                    8: > 0 => scalar average
AIPS 1:                                    9: > 0 => interpolate over
AIPS 1:                                       flagged channels if poss.
AIPS 1:                                    10:1 => normalize amplitudes
AIPS 1:                                         using all channels
AIPS 1:                                       2 => normalize amplitudes
AIPS 1:                                         using ICHANSEL channels
AIPS 1:                                       3 => normalize amplitudes
AIPS 1:                                         and zero average phase
AIPS 1:                                         using ICHANSEL channels
AIPS 1:                                       4 => normalize amplitudes
AIPS 1:                                         and zero average phase
AIPS 1:                                         using all channels
AIPS 1:                                       0 => no deliberate norm.
AIPS 1:                                    11: > 0 solution weights are
AIPS 1:                                       independent of channel
AIPS 1:                                       = -1 weights scaled
AIPS 1:                                         by amplitude**2
AIPS 1:                                       < -1.5 weights scaled by
AIPS 1:                                         1 / amplitude**2
AIPS 1: ICHANSEL      5          50        Array of start and stop chan
AIPS 1:               1           1        numbers, plus a channel
AIPS 1:               5          50        increment and IF to be used
AIPS 1:               1           2        to select channels to sum to
AIPS 1:               5          50        find a 'channel 0'.  If all
AIPS 1:               1           3        0, range set to inner 75% of
AIPS 1:               5          50        observing band.
AIPS 1:               1           4           5          50
AIPS 1:               1           5           5          50
AIPS 1:               1           6           5          50
AIPS 1:               1           7           5          50
AIPS 1:               1           8        *rest 0
AIPS 1: SPECINDX      0                    Spectral index to correct
AIPS 1:                                    'Channel 0' uv-data
AIPS 1: IN3NAME    ' '                     Channel 0 uv name (name)
AIPS 1:                                    must be '' to suppress option
AIPS 1: IN3CLASS   ' '                     Channel 0 uv name (class)
AIPS 1:                                    must be '' to suppress option
AIPS 1: IN3SEQ        0                    Channel 0 uv name (seq. #)
AIPS 1: IN3DISK       0                    Channel 0 uv disk unit #
AIPS 1: BADDISK    *all 0                  Disks to avoid for scratch

localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7   1  Rpol
localh> BPASS1:     1-  2   25%    0d    1- 10  123%    0d    1- 13   44%    1d
localh> BPASS1:     1- 14   32%    1d    2-  4   34%    1d    2-  6   73%  178d
localh> BPASS1:     2-  7   25%    2d    2-  8  133%    0d    2-  9  238%  180d
localh> BPASS1:     2- 10  917%  178d    2- 11  662%    2d    2- 12  298%  178d
localh> BPASS1:     2- 13   80%    0d    2- 14  118%    1d    3-  8   53%    0d
localh> BPASS1:     3- 10   13%    1d    3- 13   20%    0d    3- 14   27%    0d
localh> BPASS1:     4-  6   74%    0d    4-  8   20%    2d    4-  9   63%    1d
localh> BPASS1:     4- 10  120%  178d    4- 11   31%    0d    4- 12   52%    0d
localh> BPASS1:     4- 13   35%    1d    4- 14   52%    1d    5-  8   63%    1d
localh> BPASS1:     5- 13   19%    0d    5- 14   28%    0d    6-  7   28%    1d
localh> BPASS1:     6-  9  111%    1d    6- 10  906%    0d    6- 11   84%    1d
localh> BPASS1:     6- 12  126%    1d    6- 14   24%    2d    7-  8  243%    2d
localh> BPASS1:     7-  9   26%    0d    7- 10  167%    0d    8- 11  140%  176d
localh> BPASS1:     8- 12   19%  178d    8- 13   32%    2d    8- 14   51%    2d
localh> BPASS1:     9- 10  801%    0d    9- 11   72%    0d    9- 12  107%    1d
localh> BPASS1:     9- 14   18%    2d   10- 11  586%    1d   10- 12  864%    0d
localh> BPASS1:    10- 13  205%    0d   10- 14   60%  176d   11- 12   64%    1d
localh> BPASS1:    12- 13   11%    0d   12- 14   28%    0d
localh> BPASS1: Closure error statistics: IF  7 correlator  1
localh> BPASS1: Channel   Mean amp &  amp**2    Mean phase & phase**2    Excess
localh> BPASS1:     1       52.84    104.74         16.72      53.59        53
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7   2  Rpol
localh> BPASS1:     1- 13   13%    0d    2-  8   19%    2d    2- 13   13%    7d
localh> BPASS1:     2- 14   21%    5d    4-  8   11%    1d    4- 13   11%    2d
localh> BPASS1:     4- 14   16%    0d    5- 14   10%    1d    6- 12   12%    0d
localh> BPASS1:     7- 10   11%    1d    8- 12    1%   11d    9- 12   12%    1d
localh> BPASS1:    10- 12   12%    3d   10- 14   13%    1d
localh> BPASS1:     2        4.90      6.60          2.13       3.30        14
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7   3  Rpol
localh> BPASS1:     6- 10   13%    0d    6- 14   11%    1d    9- 10   13%    1d
localh> BPASS1:     3        2.66      4.15          0.58       0.78         3
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7   4  Rpol
localh> BPASS1:     6- 10   11%    0d    6- 14   11%    1d    9- 14   10%    2d
localh> BPASS1:    10- 13   12%    1d
localh> BPASS1:     4        2.66      4.08          0.57       0.76         4
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7   5  Rpol
localh> BPASS1:     6- 10   11%    0d    6- 14   10%    1d   10- 13   12%    1d
localh> BPASS1:     5        2.60      3.99          0.53       0.69         3
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7   6  Rpol
localh> BPASS1:     6-  7   10%    0d    6- 10   11%    0d    6- 14   12%    1d
localh> BPASS1:     9- 14   11%    2d   10- 13   12%    1d
localh> BPASS1:     6        2.65      4.10          0.55       0.73         5
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7   7  Rpol
localh> BPASS1:     6-  7   10%    1d    6- 14   12%    1d   10- 13   12%    1d
localh> BPASS1:     7        2.58      3.92          0.51       0.69         3
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7   8  Rpol
localh> BPASS1:    10- 13   10%    1d
localh> BPASS1:     8        2.20      3.30          0.55       0.73         1
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7   9  Rpol
localh> BPASS1:     6-  7   11%    1d   10- 13   11%    1d
localh> BPASS1:     9        2.24      3.37          0.51       0.68         2
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7  35  Rpol
localh> BPASS1:     6- 14   11%    1d
localh> BPASS1:    35        2.27      3.37          0.56       0.75         1
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7  36  Rpol
localh> BPASS1:     6- 14   11%    1d
localh> BPASS1:    36        2.23      3.38          0.55       0.74         1
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7  37  Rpol
localh> BPASS1:     6- 14   12%    1d
localh> BPASS1:    37        2.28      3.46          0.52       0.71         1
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7  38  Rpol
localh> BPASS1:     6-  7   11%    0d    6- 14   12%    1d
localh> BPASS1:    38        2.32      3.58          0.54       0.73         2
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7  39  Rpol
localh> BPASS1:     6-  7   10%    1d    6- 14   11%    1d
localh> BPASS1:    39        2.31      3.52          0.54       0.73         2
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7  40  Rpol
localh> BPASS1:     6-  7   11%    0d    6- 14   11%    1d
localh> BPASS1:    40        2.28      3.49          0.54       0.73         2
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7  41  Rpol
localh> BPASS1:     6-  7   11%    1d    6- 14   11%    1d    9- 10   10%    0d
localh> BPASS1:    10- 13   12%    1d
localh> BPASS1:    41        2.47      3.78          0.52       0.70         4
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7  42  Rpol
localh> BPASS1:     6- 10   11%    0d    6- 14   10%    1d    7- 14   13%    1d
localh> BPASS1:    10- 13   12%    1d
localh> BPASS1:    42        2.79      4.24          0.54       0.73         4
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7  43  Rpol
localh> BPASS1:     6-  7   10%    1d    7- 10   15%    0d    7- 14   13%    1d
localh> BPASS1:     9- 10   11%    1d   10- 13   10%    1d
localh> BPASS1:    43        2.85      4.38          0.55       0.75         5
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7  44  Rpol
localh> BPASS1:     6- 14   10%    1d    7- 14   13%    1d    9- 10   10%    1d
localh> BPASS1:    10- 13   10%    1d
localh> BPASS1:    44        2.57      3.94          0.56       0.76         4
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7  45  Rpol
localh> BPASS1:     6-  7   11%    1d    6- 14   11%    1d    7- 14   12%    1d
localh> BPASS1:     9- 10   10%    0d    9- 14   10%    2d   10- 13   10%    1d
localh> BPASS1:    45        2.57      3.97          0.54       0.74         6
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7  46  Rpol
localh> BPASS1:     6-  7   10%    1d    6- 14   11%    1d    7- 14   12%    1d
localh> LOGFILE FOR USER  333 GETTING LARGE: USE PRTMSG AND CLRMSG NOW!         
localh> BPASS1:    46        2.52      3.87          0.56       0.77         3
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7  47  Rpol
localh> BPASS1:     6- 14   11%    1d    7- 14   13%    1d    9- 10   10%    0d
localh> BPASS1:    47        2.67      4.04          0.58       0.76         3
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7  48  Rpol
localh> BPASS1:     6- 14   11%    1d   10- 13   11%    1d
localh> BPASS1:    48        2.58      3.86          0.57       0.76         2
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7  49  Rpol
localh> BPASS1:     6- 14   10%    1d   10- 13   12%    1d
localh> BPASS1:    49        2.59      3.87          0.55       0.72         2
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7  50  Rpol
localh> BPASS1:     6- 14   11%    1d    9- 10   10%    0d   10- 13   12%    1d
localh> BPASS1:    50        2.59      3.88          0.56       0.73         3
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7  51  Rpol
localh> BPASS1:     9- 10   10%    0d
localh> BPASS1:    51        2.27      3.41          0.52       0.70         1
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7  52  Rpol
localh> BPASS1:     9- 10   10%    0d    9- 14   10%    2d
localh> BPASS1:    52        2.07      3.11          0.52       0.69         2
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7  62  Rpol
localh> BPASS1:     8- 11   11%    0d    8- 14   12%    1d    9- 14   10%    0d
localh> BPASS1:    10- 13   14%    2d
localh> BPASS1:    62        2.98      4.31          0.88       1.11         4
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7  63  Rpol
localh> BPASS1:     1- 12   11%    3d    2-  4   15%    4d    2- 12   10%    8d
localh> BPASS1:     3-  7   13%    1d    4-  7    7%   12d    4-  8   19%   10d
localh> BPASS1:     4- 11   14%    5d    5- 11   10%    3d    5- 12   11%    1d
localh> BPASS1:     7- 11   11%    7d    7- 12   16%    4d    8- 12   16%    3d
localh> BPASS1:     8- 13   14%    4d    8- 14   18%    2d   10- 13   13%    5d
localh> BPASS1:    10- 14   13%    6d   11- 13   12%    3d   11- 14   12%    1d
localh> BPASS1:    63        6.02      7.44          3.66       4.36        18
localh> BPASS1: Closure errors at  3/  2 47 50. IF/Chn no.    7  64  Rpol
localh> BPASS1:     1-  7   23%    2d    1-  8   35%   12d    1- 11    2%   12d
localh> BPASS1:     1- 12   17%    8d    1- 13    2%   11d    1- 14    2%   15d
localh> BPASS1:     2-  3   14%    5d    2-  4   63%    8d    2-  6   16%   12d
localh> BPASS1:     2-  7  203%   27d    2-  8  156%   14d    2- 10   15%    7d
localh> BPASS1:     2- 11    4%   55d    2- 12  107%   48d    2- 13   34%   45d
localh> BPASS1:     2- 14    3%   56d    3-  7   28%    4d    3-  8   41%   12d
localh> BPASS1:     3- 11    6%   12d    3- 12    9%   13d    3- 14    4%   13d
localh> BPASS1:     4-  7   73%   35d    4-  8   68%   28d    4- 10    5%   10d
localh> BPASS1:     4- 11   53%   23d    4- 12    5%   46d    4- 13   64%    2d
localh> BPASS1:     4- 14   66%   20d    5-  6   10%    2d    5-  7   11%   17d
localh> BPASS1:     5-  8    2%   21d    5- 11   27%    4d    5- 12   30%    1d
localh> BPASS1:     5- 13   16%    9d    5- 14   30%    8d    6-  7    6%   19d
localh> BPASS1:     6-  8   27%   26d    6- 11   19%    9d    6- 12   34%    7d
localh> BPASS1:     6- 14   27%    6d    7-  8  178%   15d    7-  9   15%   16d
localh> BPASS1:     7- 10   12%   11d    7- 11  125%   45d    7- 12  257%   31d
localh> BPASS1:     7- 13   50%   47d    7- 14   88%   43d    8-  9   11%   22d
localh> BPASS1:     8- 10   22%   21d    8- 11   55%   55d    8- 12  164%   42d
localh> BPASS1:     8- 13   17%   56d    8- 14    9%   53d    9- 11    5%   12d
localh> BPASS1:     9- 12   27%    3d    9- 13    4%   13d    9- 14    3%   15d
localh> BPASS1:    10- 11   10%   14d   10- 12   20%    9d   10- 13   12%    9d
localh> BPASS1:    10- 14   20%   13d   11- 12  128%   20d   11- 13   72%    6d
localh> BPASS1:    11- 14   90%    1d   12- 13   96%   23d   12- 14  106%   16d
localh> BPASS1:    13- 14   47%    6d
localh> BPASS1:    64       27.85     45.82         15.40      21.64        67
localh> BPASS1: Antenna  1  IF  7  corr 1  had        12 excess closure errors
localh> BPASS1: Antenna  2  IF  7  corr 1  had        26 excess closure errors
localh> BPASS1: Antenna  3  IF  7  corr 1  had        11 excess closure errors
localh> BPASS1: Antenna  4  IF  7  corr 1  had        24 excess closure errors
localh> BPASS1: Antenna  5  IF  7  corr 1  had        13 excess closure errors
localh> BPASS1: Antenna  6  IF  7  corr 1  had        51 excess closure errors
localh> BPASS1: Antenna  7  IF  7  corr 1  had        40 excess closure errors
localh> BPASS1: Antenna  8  IF  7  corr 1  had        31 excess closure errors
localh> BPASS1: Antenna  9  IF  7  corr 1  had        29 excess closure errors
localh> BPASS1: Antenna 10  IF  7  corr 1  had        54 excess closure errors
localh> BPASS1: Antenna 11  IF  7  corr 1  had        26 excess closure errors
localh> BPASS1: Antenna 12  IF  7  corr 1  had        31 excess closure errors
localh> BPASS1: Antenna 13  IF  7  corr 1  had        40 excess closure errors
localh> BPASS1: Antenna 14  IF  7  corr 1  had        62 excess closure errors

Double Sources-- and not the AGN kind

2008-01-04T02:47:00.002-06:00

I'm having this problem with some archival data from 1990. I have two nights of data on a galaxy, spaced a few nights apart from one another. I calibrate the nights separately, and image them separately. It rapidly becomes obvious that the images from the two nights are shifted relative to one another, but not in any simple way. The galaxy center, at the image center, is at the same position in both, but as you go out radially, the first night's sources are further out, radially. It's as if the image is stretched one night, relative to the other.

AIPS thinks that both images have the same pixel scale, so that means a source will have different R.A. and Dec (by about an arcminute, pretty bad!) between the two nights' images. If I DBCON the two nights, I get lots of double sources.

The observational setup claims to be exactly the same between the two nights-- same pointing center, same correlator set-up.

Anyone have any idea what might be causing this? I think I've had a similar problem with GMRT data before, and gave up temporarily and went on to a different project. I'm guessing it's a calibration issue?

Setting up New Data Disks

2007-12-03T13:14:00.000-06:00

My latest organizational scheme for AIPS is to give each project a new AIPS data disk. I just spent some time adding a new data disk to my AIPS installation on my laptop. Here's what I did to get it. (BTW, I've got a MacBook, but that shouldn't matter for this.)

In $AIPS_ROOT, cd to DA00. Save a copy of the DADEVS.LIST file as DADEVS.LIST.old. Then edit the DADEVS.LIST. I just copied the first uncommented line (set up by AIPS) and incremented the data disk number by 1, i.e., LOCALHOST_2. Now save a copy of the NETSP file in the same directory to NETSP.old. Again, edit the file by copying the first uncommented line and incrementing the data disk number by 1. Finally, cd to $AIPS_ROOT/DATA, mkdir LOCALHOST_2 (or whatever your new data disk is named), cd to LOCALHOST_2, and create a file named SPACE (touch SPACE). Now when you start up AIPS you should have additional data disks available.

Most of this tip was taken from the AIPS Manager FAQ (see "How do I configure new AIPS data areas?").

Your friend, the tilde

2007-10-04T21:03:00.000-05:00

Ever had to enter a lot of numbers into an array in an AIPS script and run out of room (like in this post)? Trying to figure out the mysteries of plcolor without typing 5 million numbers? In your time of need, the handy tilde will help you out. See below the fold for more details.

The popsym help file (type help popsym to access) gives you this handy tidbit of information on the tilde


A(i) ~ 1,2,3  Store values in A(i),A(i+1)... (change only as many as on RHS)

Now here's an example,


filename = '10208722.UVF','10208724.UVF','10208726.UVF','10208727.UVF'
filename(5) ~ '10208733.UVF','10303423.UVF','10303424.UVF','10303461.UVF'

Tah-Dah!! That's all there really is to it. Use the tilde, Luke -- your fingers will thank you.

Beam Squint and Self Calibration (relevant even if you don't care about polarization!)

2007-09-21T15:45:00.000-05:00

Here's another tip from Juan Uson about a self-cal trick to get the very best dynamic range in your images.

The VLA has beam squint in Stokes V. What this means is that away from the center of your field, the RR and LL polarizations separate a bit (I don't really understand the details of this). This leads to an image artifact-- if you have a bright source off the center of your field, it'll seem like you can't clean it very well. Even if you've done your very best job at self calibration and cleaned very deeply, there will still remain rings around the source (which of course drives up your noise).

One easy fix for this problem is to do a normal Phase self calibration, but when it's time for your A&P self calibration, average your RR and LL. I believe the relevant parameter for this in CALIB is APARM(3) > 1. This should give you a self cal that is not affected by the beam squint, and models your bright sources better!

Clean Components and Self Calibration

2007-09-21T15:34:00.000-05:00

Well, I just talked to Juan Uson from NRAO-Charlottesville, and he delivered some useful information for us burgeoning self-cal experts.

He says that you should ALWAYS use all your clean components for self calibration. Don't cut at the first negative! He says that when they were first learning about self cal, they were very timid and therefore advised people to cut at the first negative, but now they know better. You want to use your very best clean component model for self cal, which includes all components!

Here are some reasons why--

a bright source that is centered on the edge between two pixels will actually take an infinite number of clean components to model, because basically the clean algorithm keeps exchanging flux back and forth between the surrounding pixels. so, to model such a source, there are lots of negative clean components required.

if a source has any complex structure at all, you can't really effectively model it without using some negative components.

I told him that occasionally, the word on the street is "Just self cal off of one bright source that you know the structure of, and leave the rest of the flux alone." When I tried to do that once, the self cal created fictional ghost sources in my data and it scared me! Juan was not surprised; he said its a terrible idea to self cal on only a select few sources. Basically what self cal does is divide your real fluxes by your model fluxes, and try to make the residuals look like noise. If there is still real flux in your residuals (because your clean model is based off only a select few sources), then it will try to turn that real flux into noise and crazy things will happen.

So, clean out all your flux, and use all your clean components!

Filling data that includes midnight

2007-09-19T10:35:00.002-05:00

When you get your data from the archive, it's normally in several files. For me, each file is usually a day's worth of data, so I fill and calibrate each data file separately. However, if you have observations that go from say 20:00 on 17-Feb to 6:00 on 18-Feb, the archive creates a separate files for the observations on the 17th and for the observations on the 18th. You need to read in both files to calibrate that series of observations.

Complications with Shamelessly Raiding the Archive

2007-09-17T15:19:00.003-05:00

Amanda and I are spending the week in Socorro, so hopefully we will be learning little new AIPS facts every day! Here's my first one:

Sometimes I have dreams about raiding the VLA archive and combining like 6 different data sets. However, often times the data sets will have slightly different centers-- in my case, often one observer centers on the galaxy's center, while another observer center on a supernova that goes off in the outskirts of the galaxy, some 5 arcminutes away. I was wondering, can you just DBCON these two data sets together, and AIPS can handle it?

The answer is...

DBCON can adjust the phases, so yes, it can image data from two pointings with significantly different centers. What Miller Goss said you have to be wary of is that DBCON doesn't adjust amplitudes. So, if there are two different pointing centers, the center of your galaxy is going to fall in different locations of the primary beam in the different observations. If you are combining two observations separated by 5 arcminutes at 20cm, where the primary beam is 30 arcminutes, this shouldn't be a big issue...probably the primary beam sensitivity of the two pointings will only vary by a few percent. However, if the separation of your pointings starts approaching the size of the primary beam, then you can no longer use DBCON and need to think of some other way to combine the data.

AIPS Binary Downloads

2007-08-10T00:18:00.000-05:00

Oh my god. Installing software on my new mac makes me feel like a complete idiot.

There are all these detailed websites about how to install aips on your mac, but NONE (not one!) of them link to the actualy binaries! Many of them mention that said binaries exist. I think they are available by ftp. Ftp to what, though, i ask you? Does anybody know how to download the aips binaries so i can get on with this installation nightmare?

Multiple output files

2007-07-26T10:18:00.002-05:00

If one wants to write out multiple fits files at a time which have same inname and inclass just different inseq no. how does one do that?

limited line length in runfiles

2007-07-25T09:38:00.000-05:00

in runfiles you can't have lines longer than ~70 characters (i'm not sure what the actual limit is). i've only had a problem with this once when i was defining a large array of filenames for the multiple pointings in a mosaic. the only way to get the whole array defined was to fill in the last three entries manually. i've posted the code i used below.


     string*8 obj_name(15)
     obj_name = 'GH40-1','GH40-2','GH40-3','GH40-4','GH40-5','GH40-6'
     obj_name(7) = 'GH40-7'
     obj_name(8) = 'GH40-8'
     obj_name(9) = 'GH40-9'

Note added by Amanda on 10/05/07: It's actually easier to use the tilde. See this post.

SMOTH and and regridding

2007-07-05T12:58:00.001-05:00

Can anyone suggest an AIPS task that can help me with the following? I'm looking at emission lines in a diffuse source. I needed to try and increase my S/N levels, but could not smooth the line because it has some complicated structure (multiple velocity components, etc) that I want to fit. So, I smoothed spatially using SMOTH.

Since my beam is now almost twice the size that it used to be (6'' instead of 4'') I think the pixel size of the original image may be oversampling the beam. Can I regrid the smoothed image to have 1'' pixels instead of 0.5'' pixels? How?

Thanks,
Katie

Gaussian Fitting

2007-07-04T17:33:00.002-05:00

Here is a request from an anonymous reader; any advice, anyone?

Can you please help me with the following? I have an image with 5 substructures in it. The peaks inthe image decrease in size from left to right, the leftmost two are the brightest. All of them are close to each other. With AIPS jmfit I can fit not more than 4 gaussians. I played around a bit and noticed that dividing the whole image into two parts and fitting 2 gaussians and 3 gaussians respectively in the two parts does not work properly and gives a bad fit. So I came up with this idea. I can first fit four gaussians to first four peaks, and then from the whole image subtract the brightest two. To the residual image now I fit 3 gaussians. I checked whether this technique gives me a good fit to a slice of data (Wrote my own fortran programs for that). It seems to work but my problem is how to do it in aips.

So my problem is the following. I want to fit 4 gaussians to a selected range of data. Then subtract only the brightest two gaussian from the whole image. Then fit other three gaussians to another restricted part of the data. Could anyone please help me on this?

self-calibration subtleties : 2 questions

2007-06-30T10:39:00.000-05:00

i have a dataset which shows significantly different structure depending on the weighting (robust value) used when i image it. should i self-cal using maps with a natural weighting that show the diffuse emission or maps with a more uniform weighting which emphasize the point sources? i'm inclined to use a robust value around 0 because i feel like the point sources are more reliable self-cal targets (and contribute more flux) even though what i really care about is the diffuse stuff and the maps i make for the analysis will use a robust > 0.

do i always need to self-cal using clean components from the entire primary beam even if the source i care about is only in the inner 15%? since it does seem true that "the best self-cal model is the one that contains the most flux" i think i am obligated to image the entire primary beam during self-calibration.

Reference Frequencies (Center v. Edge?)

2007-06-20T16:49:00.000-05:00

I've come to the conclusion that for 1-channel continuum data coming from the VLA, the frequency that you see in the header and in your LISTR 'scans' ouput is the center of your bandwidth (not the beginning).

I come to this conclusion mostly because the L-band observing guide on the VLA web page says that "The two recommended center frequencies are 1365 and 1435 MHz." I used the defaults when I made my observe files, and now my LISTR output lists these two frequencies.

EDIT: June 21 2007
And these words from Eric Greisen

In FITS coordinates, the stated coordinate is at the center of each
voxel.  It may be moved by having a non-integer reference pixel.  In
normal VLA data we do not do that, so these frequencies are nominally
at the center of your band.  I say nominally, because if the bandshape
is not symmetric about the center, then the effective frequency will
diverge from the one stated.  True astrometry should never be done
with wide, asymmetric bandshapes (and the VLA at 50 MHz is
asymmetric).

Where did R go?

2007-06-19T15:55:00.001-05:00

Ok, this is kind of a strange thing. I'm working with Pband data. I've gone through initial flagging, and then I run CALIB. But for some reason it's not finding my R data... so I get 1/2 good solutions and 1/2 failed solutions (because it finds the L just fine). But I look at the data (and when I flagged it too) and it's *there*. Has anyone encountered this? What's going on and how to I fix it? I'm using pretty standard inputs...

Reference Frequencies (AIPS v. Miriad)

2007-06-14T11:41:00.002-05:00

I went back and reviewed my early post; this is an update, with a few more details.

I've been working with GMRT data reduced in AIPS, and ATCA data reduced in MIRIAD.
It turns out that (at least for GMRT observations) AIPS gives the reference frequency (in imhead or prtan) as the frequency in the middle of the first channel, whereas Miriad gives the reference frequency (in prthd or uvlist, options=spectral) as that measured at the end of the first channel. But don't freak out yet--the channels still contain the same data, they are just identified differently in AIPS vs Miriad. See "read more" for details.

It's relatively easy to see from reading the headers, so I'm not sure why this caused me trouble when I first posted it (notice the "at Pixel" in the AIPS header):

From AIPS:

AIPS 1: Image=NGC2997 (UV) Filename=15JAN .UVLIN . 1
AIPS 1: Telescope=GMRT Receiver=GMRT
AIPS 1: Observer=PISANO User #= 43
AIPS 1: Observ. date=14-JAN-2007 Map date=18-APR-2007
AIPS 1: # visibilities 325734 Sort order TB
AIPS 1: Rand axes: UU-L-SIN VV-L-SIN WW-L-SIN BASELINE TIME1
AIPS 1: WEIGHT SCALE
AIPS 1: ----------------------------------------------------------------
AIPS 1: Type Pixels Coord value at Pixel Coord incr Rotat
AIPS 1: COMPLEX 1 1.0000000E+00 1.00 1.0000000E+00 0.00
AIPS 1: STOKES 2 -1.0000000E+00 1.00 -1.0000000E+00 0.00
AIPS 1: FREQ 128 1.4129999E+09 0.50 3.1250000E+04 0.00
AIPS 1: IF 1 1.0000000E+00 1.00 1.0000000E+00 0.00
AIPS 1: RA 1 09 45 38.811 1.00 3600.000 0.00
AIPS 1: DEC 1 -31 09 27.768 1.00 3600.000 0.00
AIPS 1: ----------------------------------------------------------------
AIPS 1: Coordinate equinox 2000.00
AIPS 1: Rest freq 0.000 Vel type: RADIO wrt YOU
AIPS 1: Alt ref. value 0.00000E+00 wrt pixel 1.00
AIPS 1: Max version number of extension files type HI is 1
AIPS 1: Max version number of extension files type FQ is 1
AIPS 1: Max version number of extension files type AN is 1

From MIRIAD:

****************************************************************
Filename: 15jan.uvlin/
Telescope: GMRT
Object: ngc2997 Observer: PISANO
First time: 07JAN15:18:31:06.8
Number of antennae: 30
Polarisations Present: RR,LL
Type of correlations present: crosscorrelation
----------------------------------------------------------------
Spectral Correlations:
Spectrum Channels Freq(chan=1) Increment Restfreq
1 128 1.41302 0.000031 1.42041 GHz
Total number of correlations: 83387904
Correlations are stored in 16-bit form
----------------------------------------------------------------
J2000 Source RA: 9:45:38.811 Dec: -31:09:27.76
Apparent Source RA: 9:45:58.554 Dec: -31:11:18.61

As a side note, when checking the reference freq in AIPS check the outputs of both imhead and prtan--an AIPS bug is that occassionally they don't match!
From Chapter 8 of the AIPS cookbook:
"Another, more serious, problem is that two locations in the FITS file give the "reference frequency" -- the header and the antenna table. In principle these should agree. However there are instances when they will differ. Task FITS will issue a warning when this happens, and will use the antenna table reference frequency as the true reference frequency. In some cases this will be the correct frequency. In others it will not."...pg 8-7

**Note, this is now consistent with one of Laura's later posts (Edited by KMH 9/6/07).

Tricky, Tricky FOR Loops

2007-06-12T14:43:00.000-05:00

I was just trying to write a FOR loop which would run UVCOP many times. When I ran

for i = 1 to 10; bchan i; echan i; go uvcop; end

AIPS would set bchan and echan to 1, then it would run UVCOP once, then it would set bchan and echan to 2, and end the FOR loop. I really didn't know what the problem was-- this loop should work. Then Eric told me this trick: put WAIT before the END, so that now your loop looks like this:

for i = 1 to 10; bchan i; echan i; go uvcop; wait; end

I guess what was happening was that the loop was continuing on before uvcop had finished running, and the loop was getting all confused. It worked with a WAIT!

XYZ

2007-06-11T10:48:00.000-05:00

What does AIPS consider the x, y, and z axes? For example, XSMTH smoothes your data along the x axis. What on earth does this mean? I would think the z axis would be velocity.

Tarballs?

2007-06-11T10:41:00.003-05:00

Is there a way to read out a whole bunch of files from AIPS at once? My hard drive on my laptop is getting full, so I wanted to tar up all the files from a reduction of one of my galaxies, read it out to a fits file, and scp it over to my work computer. Is there a way to do this, or do i have to run FITTP on each file individually?

File Sizes

2007-06-08T18:28:00.000-05:00

Anybody know how to figure out how much hard drive space each aips file is taking up? I can look in the DATA directory, but all the names are written in code there. It would be so much nice if there was an actual aips command.

WBR Step 6L: Calibration

2007-06-04T23:57:00.002-05:00

Calibration is usually a somewhat iterative process. I will lightly flag my calibrator, then calibrate the calibrator, then see if any new funky looking data points have appeared. If they have, I will flag again and calibrate again. Wash, rinse, repeat until no funky data points show up.

So how do you calibrate your data anyway?

Assuming you've lightly flagged your phase and flux calibrators, according to Step 5, now we're ready to run SETJY. SETJY basically just writes to your data the most accurate flux for your flux calibrator. Important parameters to consider here:
--SOURCES '1331+305', '0137+331', or '0542+498' (whichever one you used. sometimes you will have two different flux calibrators, and you can enter them both here.
--OPTYPE 'CALC'


AIPS 1: SETJY     Task to enter source info into source (SU) table.
AIPS 1: Adverbs     Values                 Comments
AIPS 1: ----------------------------------------------------------------
AIPS 1: INNAME     'AC825_FQ1'             Input image name (name)
AIPS 1: INCLASS    'CH 0'                  Input image name (class)
AIPS 1: INSEQ         1                    Input image name (seq. #)
AIPS 1: INDISK        1                    Input image disk unit #
AIPS 1: SOURCES    '1331+305'              Sources to modify.
AIPS 1:            *rest ' '
AIPS 1: QUAL         -1                    Source qualifier -1=>all
AIPS 1: BIF           0                    Low IF # for flux density
AIPS 1: EIF           0                    High IF # for flux density
AIPS 1: ZEROSP     *all 0                  I,Q,U,V flux density (Jy)
AIPS 1: OPTYPE     'CALC'                  '    ' => use other adverbs
AIPS 1:                                    for required operation
AIPS 1:                                    'CALC' => determine
AIPS 1:                                    3C286/3C48/1934 fluxes from
AIPS 1:                                    standard formulae
AIPS 1:                                    'REJY' => reset source
AIPS 1:                                    fluxes to zero.
AIPS 1:                                    'REVL' => reset velocity
AIPS 1:                                    to zero
AIPS 1:                                    'RESE' => reset fluxes &
AIPS 1:                                    velocities to zero.
AIPS 1: CALCODE    ' '                     New calibrator code:
AIPS 1:                                      '----' => change to blank
AIPS 1: SYSVEL        0                    Velocity of source (km/s)
AIPS 1: RESTFREQ      0           0        Line rest frequency (Hz)
AIPS 1: VELTYP     ' '                     Velocity type 'LSR,'HELIO'
AIPS 1: VELDEF     ' '                     Velocity definition 'RADIO',
AIPS 1:                                    'OPTICAL'
AIPS 1: FREQID        0                    FQ table entry to use for
AIPS 1:                                    velocity information and
AIPS 1:                                    'CALC' option
AIPS 1: APARM      *all 0                  (1): Pixel to which SYSVEL
AIPS 1:                                         refers ( 0=>1)
AIPS 1:                                    (2): Only for 'CALC' option:
AIPS 1:                                      <= 0 => use latest VLA
AIPS 1:                                          values (1999.2) or,
AIPS 1:                                          for 1934-638, the
AIPS 1:                                          ATCA value of 30Jul94.
AIPS 1:                                         1 => use Baars values
AIPS 1:                                          or old ATCA/PKS values
AIPS 1:                                          for 1934-638
AIPS 1:                                         2 => use VLA 1995.2
AIPS 1:                                          values or for 1934-638
AIPS 1:                                          the ATCA value of
AIPS 1:                                          30Jul94.
AIPS 1:                                      >= 3 => use oldest VLA
AIPS 1:                                          values (1990) or,
AIPS 1:                                          for 1934-638, the
AIPS 1:                                          ATCA value of 30Jul94.
AIPS 1:                                    (3): Only for 'CALC' option:
AIPS 1:                                         multiply the calculated
AIPS 1:                                         fluxes by APARM(3) with
AIPS 1:                                         0 -> 1

Now it's time to run calib!
(I wouldn't use VLACALIB (like the AIPS cookbook tells you too) because some parts of VLACALIB are a bit of a black box, and can set certain parameters quite mysteriously (I've had it use SOLINT = 400 before, for no good reason).

Run calib on your flux calibrator first. Here are some parameters you should definitely worry about and set:
CALSOUR '1331+305' (name of flux calibrator)
UVRANGE (find this in the VLA calibrator manual. the best calibrators are ones where you don't have to set this.)
DOCALIB 2 (apply weights)
REFANT 6 (you chose a refant in step 3, use it!)
SOLINT 1 (this is how often to solve for a calibration solution. 1 seems to work well often.)
SOLMODE 'A&P' (calibrate amplitudes and phases)


AIPS 1: CALIB:  Task to determine calibration for data.
AIPS 1: Adverbs     Values                 Comments
AIPS 1: ----------------------------------------------------------------
AIPS 1:                                    Input uv data.
AIPS 1: INNAME     'AC825_FQ1'                UV file name (name)
AIPS 1: INCLASS    'CH 0'                     UV file name (class)
AIPS 1: INSEQ         1                       UV file name (seq. #)
AIPS 1: INDISK        1                       UV file disk drive #
AIPS 1:                                    Data selection (multisource):
AIPS 1: CALSOUR    '1331+305'              Calibrator sources
AIPS 1:            *rest ' '
AIPS 1: QUAL         -1                    Calibrator qualifier -1=>all
AIPS 1: CALCODE    ' '                     Calibrator code '    '=>all
AIPS 1: SELBAND      -1                    Bandwidth to select (kHz)
AIPS 1: SELFREQ      -1                    Frequency to select (MHz)
AIPS 1: FREQID        1                    Freq. ID to select.
AIPS 1: TIMERANG   *all 0                  Time range to use.
AIPS 1: BCHAN         0                    Lowest channel number 0=>all
AIPS 1: ECHAN         0                    Highest channel number
AIPS 1: ANTENNAS   *all 0                  Antennas to select. 0=all
AIPS 1: DOFIT      *all 0                  Subset of ANTENNAS list for
AIPS 1:                                    which solns are desired.
AIPS 1: ANTUSE     *all 0                  Mean gain is calculated
AIPS 1:                                    (CPARM(2)>0) using only the
AIPS 1:                                    listed antennas. See explain.
AIPS 1: SUBARRAY      0                    Subarray, 0=>all
AIPS 1: UVRANGE       0           0        Range of uv distance for full
AIPS 1:                                    weight
AIPS 1: WTUV          0                    Weight outside UVRANGE 0=0.
AIPS 1: WEIGHTIT      0                    Modify data weights function
AIPS 1:                                    Cal. info for input:
AIPS 1: DOCALIB       2                    If >0 calibrate data
AIPS 1:                                    = 2 calibrate weights
AIPS 1: GAINUSE       0                    CL table to apply.
AIPS 1: DOPOL        -1                    If >0 correct polarization.
AIPS 1: BLVER        -1                    BL table to apply.
AIPS 1: FLAGVER       1                    Flag table version
AIPS 1: DOBAND       -1                    If >0 apply bandpass cal.
AIPS 1:                                    Method used depends on value
AIPS 1:                                    of DOBAND (see HELP file).
AIPS 1: BPVER         1                    Bandpass table version
AIPS 1: SMOOTH     *all 0                  Smoothing function. See
AIPS 1:                                    HELP SMOOTH for details.
AIPS 1:
AIPS 1:                                    CLEAN map. See HELP.
AIPS 1: IN2NAME    ' '                        Cleaned map name (name)
AIPS 1: IN2CLASS   ' '                        Cleaned map name (class)
AIPS 1: IN2SEQ        0                       Cleaned map name (seq. #)
AIPS 1: IN2DISK       0                       Cleaned map disk unit #
AIPS 1: INVERS        0                    CC file version #.
AIPS 1: NCOMP      *all 0                  # comps to use for model.
AIPS 1:                                    1 value per field
AIPS 1: FLUX          0                    Lowest CC component used.
AIPS 1: NMAPS         0                    No. Clean map files
AIPS 1: CMETHOD    ' '                     Modeling method:
AIPS 1:                                    'DFT','GRID','    '
AIPS 1: CMODEL     ' '                     Model type: 'COMP','IMAG'
AIPS 1: SMODEL     *all 0                  Source model, 1=flux,2=x,3=y
AIPS 1:                                    See HELP SMODEL for models.
AIPS 1:
AIPS 1:                                    Output uv data file.
AIPS 1: OUTNAME    ' '                        UV file name (name)
AIPS 1: OUTCLASS   ' '                        UV file name (class)
AIPS 1: OUTSEQ        0                       UV file name (seq. #)
AIPS 1: OUTDISK       0                       UV file disk drive #
AIPS 1:
AIPS 1:                                    Solution control adverbs:
AIPS 1: REFANT        6                    Reference antenna
AIPS 1: SOLINT        1                    Solution interval (min)
AIPS 1: SOLSUB        0                    Solution subinterval
AIPS 1: SOLMIN        0                    Min solution interval
AIPS 1: APARM      *all 0                  General parameters
AIPS 1:                                       1=min. no. antennas
AIPS 1:                                       2 > 0 => data divided
AIPS 1:                                       3 > 0 => avg. RR,LL
AIPS 1:                                       5 > 0 => avg. IFs.
AIPS 1:                                       6=print level, 1=good,
AIPS 1:                                         2 closure, 3 SNR
AIPS 1:                                       7=SNR cutoff (0=>5)
AIPS 1:                                       8=max. ant. # (no AN)
AIPS 1:                                       9 > 0 => pass failed soln
AIPS 1:                                    Phase-amplitude Parameters:
AIPS 1: DOFLAG        0                    Flag on closure error?
AIPS 1: SOLTYPE    ' '                     Soln type,'  ','L1','GCON',
AIPS 1:                                       'R', 'L1R', 'GCOR'
AIPS 1: SOLMODE    'A&P'                   Soln. mode: 'A&P','P','P!A',
AIPS 1:                                    'GCON',
AIPS 1: SOLCON        0                    Gain constraint factor.
AIPS 1: MINAMPER      0                    Amplitude closure error
AIPS 1:                                    regarded as excessive in %
AIPS 1: MINPHSER      0                    Phase closure error regarded
AIPS 1:                                    as excessive in degrees
AIPS 1: CPARM      *all 0                  Phase-amp. parameters
AIPS 1:                                       1 = Min el for gain
AIPS 1:                                            normalization (deg)
AIPS 1:                                       2 >0 => normalize gain
AIPS 1:                                       3 avg. amp. closure err
AIPS 1:                                       4 avg. ph. closure err
AIPS 1:                                       5 >0 => scalar average
AIPS 1:                                       6 limit clipping in robust
AIPS 1: SNVER         0                    Output SN table, 0=>new table
AIPS 1: ANTWT      *all 0                  Ant. weights (0=>1.0)
AIPS 1: GAINERR    *all 0                  Std. Dev. of antenna gains.
AIPS 1: BADDISK    *all 0                  Disk no. not to use for
AIPS 1:                                       scratch files.

You will get some output that looks like this:


localh> CALIB1: Writing SN table    1
localh> CALIB1: RPOL, IF= 1 The average gain over these antennas is  3.080E+00
localh> CALIB1: RPOL, IF= 2 The average gain over these antennas is  3.088E+00
localh> CALIB1: LPOL, IF= 1 The average gain over these antennas is  3.033E+00
localh> CALIB1: LPOL, IF= 2 The average gain over these antennas is  3.086E+00
localh> CALIB1: Found         2321 good solutions
localh> CALIB1: Failed on        7 solutions

Some ways to tell if your data is really acting up is if you have tons of bad solutions (if you do, you might want to consider increasing your solint). Additionally, for some telescopes (not really for the VLA), if you have lots of bad solutions, you might have to tell CALIB to accept points of lower quality.
aparm(1) = 4 (CALIB default is a minimum of 6 antennas for a good solution, you could decrease it to 4.)
aparm(7) = 3 (CALIB default is a signal-to-noise in your solutions of 5. This is a bit high for some telescopes, and can reasonably be decreased to 3.)
soltype = 'L1' (this should be a more robust method for finding solutions (robust against outlying points). However, AIPS wants you to know that you will "lose some statistical efficiency". You could try other robust soltypes, too, but be warned they might be slow.)

Additionally, in my experience, it's a good thing that those 4 numbers (one for each polarization and IF) are all about the same (around 3.08). If one is really different than the others, than it might imply that their is bad data in that if/polarization.

All CALIB does is spit out a 'SN' table. The way we have it right now (SNVER = 0), every time you run CALIB it will spit out a new SN table. If you set SNVER = 1, every time you run CALIB, it would just append new information to this table.

Let's see if this calibration brought up any new bad data that needs to be flagged. If we want to apply calibration to our data in tasks like UVPLT and TVFLG, the calibration needs to be in a 'CL' table, not a "SN' table (yeah, stupid AIPS rule). To copy our 'SN' table to a 'CL' table, use VLACLCAL. First, you will need to type:


run vlaprocs

to load up the task VLACLCAL. Then set three important parameters. In this case, we'll use:
SOURCES = '1331+305' (the name of your flux cal)
CALSOUR = '1331+305' (the name of your flux cal)
REFANT = 6 (your reference antenna)


AIPS 1: VLACLCAL  Procedure to run CLCAL and LISTR for VLA data.
AIPS 1: Adverbs     Values                 Comments
AIPS 1: ----------------------------------------------------------------
AIPS 1:                                    Use RUN VLAPROCS first
AIPS 1: INNAME     'AC825_FQ1'             Input UV file name (name)
AIPS 1: INCLASS    'CH 0'                  Input UV file name (class)
AIPS 1: INSEQ         1                    Input UV file name (seq. #)
AIPS 1: INDISK        1                    Input UV file disk unit #
AIPS 1: SOURCES    '1331+305'              Source list to calibrate
AIPS 1:            *rest ' '
AIPS 1: SOUCODE    ' '                     Source "Cal codes"
AIPS 1: CALSOUR    '1331+305'              Cal sources for calibration
AIPS 1:            *rest ' '
AIPS 1: QUAL         -1                    Source qualifier -1=>all
AIPS 1: CALCODE    ' '                     Calibrator code '    '=>all
AIPS 1: FREQID        1                    Unique frequency code
AIPS 1: TIMERANG   *all 0                  Time range to calibrate
AIPS 1: SUBARRAY      0                    Subarray, 0=>all
AIPS 1: INTERPOL   ' '                     Interpolation function
AIPS 1: SAMPTYPE   ' '                     Smoothing function
AIPS 1: DOBLANK       0                    Blanked value interpolation
AIPS 1: DOBTWEEN      1                    > 0 -> smooth all sources
AIPS 1:                                    together; else separate them
AIPS 1: SMOTYPE    ' '                     Data to smooth
AIPS 1: BPARM      *all 0                  Smoothing parameters
AIPS 1: ICUT           .1                  Cutoff for functional forms
AIPS 1: GAINVER       0                    Input Cal table 0=>1
AIPS 1: GAINUSE       0                    Output CAL table 0=>2
AIPS 1: REFANT        6                    Reference antenna 0=>pick.
AIPS 1: DOPRINT       1                    >0 Print messages to a file
AIPS 1:                                    or to the printer.
AIPS 1: OUTPRINT   *all ' '                Printer disk file to save
AIPS 1: BADDISK    *all 0                  Disks to avoid for scratch

This should write out a CL table 2. If you want to apply this caibration in, say, TVFLG, you would just use
DOCAL = 2
GAINUSE = 2
and that applies the CL table 2.

At this point, I also like to flag on phase. I've had a few data sets where amplitudes looks ok for the calibrators, but there are still some quite aberrant points in phase. In general, any points with phases > +/-10 degrees are probably bad (for your calibrators, which are point sources!!! unfortunately, you won't be able to flag on phase at all for your target source, because your target source will not be a point source and will therefore have phases running the whole gamut from -180 to +180 degrees.)

If you want to 'undo' the calibration (let's say because you flagged some data, and now you want to do a new and improved calibration and no longer need your old one), just delete your SN tables, and all CL tables which are greater than 1. BUT DON'T DELETE CL TABLE 1!!! This has important basic information in it.

When you think you have the very best calibration for your flux calibrator, I like to then repeat this same process for my phase calibrator. Iterate by running CALIB and VLACLCAL on your phase calibrator, and then flagging it until in uvplt there are very no aberrant points left in amplitude or phase. (Make sure you check each IF and each polarization!)

Now, when you trust your calibration/flagging for both your calibrators, Delete your SN tables and CL table #2. Let's do final runs of CALIB. At this point I set SNVER = 1 so that CALIB will write out solutions for both calibrators to the same SN table.
--Run CALIB on your flux calibrator.
--Run CALIB on your phase calibrator.

Now, run GETJY to get a flux for your phase calibrator. Parametrs to set:
SOURCES = your phase calibrator
CALSOUR = your flux calibrator


AIPS 1: GETJY     Task to determine source flux densities.
AIPS 1: Adverbs     Values                 Comments
AIPS 1: ----------------------------------------------------------------
AIPS 1: INNAME     'AC825'                 Input UV file name (name)
AIPS 1: INCLASS    'CH 0'                  Input UV file name (class)
AIPS 1: INSEQ         1                    Input UV file name (seq. #)
AIPS 1: INDISK        1                    Input UV file disk unit #
AIPS 1: SOURCES    '1033+395'              Source list to find fluxes
AIPS 1:            *rest ' '
AIPS 1: SOUCODE    ' '                     Source "Cal codes"
AIPS 1: CALSOUR    '1331+305'              Cal sources for calibration
AIPS 1:            *rest ' '
AIPS 1: QUAL         -1                    Source qualifier -1=>all
AIPS 1: CALCODE    ' '                     Calibrator code '    '=>all
AIPS 1: BIF           0                    Lowest IF number 0=1
AIPS 1: EIF           0                    Highest IF number
AIPS 1: TIMERANG   *all 0                  Time range of solutions.
AIPS 1: ANTENNAS   *all 0                  Antennas to use
AIPS 1: SUBARRAY      0                    Subarray, 0=>all
AIPS 1: SELBAND      -1                    Bandwidth to select (kHz)
AIPS 1: SELFREQ      -1                    Frequency to select (MHz)
AIPS 1: FREQID        2                    Freq. ID to select.
AIPS 1: SNVER         2                    Input SN table, 0=>all.

You will get some output that looks like this:


localh> GETJY1: Task GETJY  (release of 31DEC05) begins
localh> GETJY1:    Source:Qual      CALCODE IF  Flux (Jy)
localh> GETJY1: 1033+395        :  0   A     1     .40437 +/-    .00091
localh> GETJY1:                              2     .39109 +/-    .00074
localh> GETJY1: Appears to have ended successfully
localh> GETJY1: localhost    31DEC05 TST: Cpu=        .0  Real=       0

At this point, what you want to worry about is the errors in the fluxes determined for your phase cal. If they are big, something has gone awry. What you do NOT need to worry about is if the fluxes are significantly different from those in the VLA calibrator manual. Remember that these calibrators are AGN-- they vary in flux!! Flux calibrators have been chosen because their fluxes are hopefully quite steady, but phase calibrators have only been chosen to be pointy. Their fluxes may vary. That's why you are comparing them with the flux calibrator, to get the best flux determination for them at the time of your observations!

A fun exercise is to look up your phase calibrator using this Java applet. It will show you how the flux of your calibrator has changed over time (their are only data points here when someone has actually used your phase calibrator for their VLA observations).

Finally, do final runs of VLACLCAL.
Do one run with
SOURCES = your phase cal, your target sources
CALSOUR = your phase cal
Do one more run with
SOURCES = your flux cal
CALSOUR = your flux cal
The defaults on VLACLCAL are smart enough to always output to CL table #2 (even if it already exists).

A good way to do a final check of your calibration (although it should be quite good if you have done it the iterative way I suggest!) is to run LISTR in 'MATX' mode.
OPTYPE = 'MATX'
SOURCES = your phase cal
DOCAL = 2
GAINUSE = 2
DPARM(1) = 5
DOCRT = -1
OUTPRINT = a file name


AIPS 1: LISTR:  Task to print UV data and calibration tables.
AIPS 1: Adverbs     Values                 Comments
AIPS 1: ----------------------------------------------------------------
AIPS 1: USERID        0                    User number.
AIPS 1: INNAME     'AC825'                 UV data (name).
AIPS 1: INCLASS    'CH 0'                  UV data (class).
AIPS 1: INSEQ         1                    UV data (seq. #).  0 => high
AIPS 1: INDISK        1                    Disk unit #.       0 => any
AIPS 1: OPTYPE     'MATX'                  List type:
AIPS 1:                                     'MATX','LIST','GAIN','SCAN'
AIPS 1: INEXT      'CL'                    CL, SN or TY table for 'GAIN'
AIPS 1: INVER         0                    CL, Sn or TY table version
AIPS 1: SOURCES    '1033+395'              Source list
AIPS 1:            *rest ' '
AIPS 1: CALCODE    ' '                     Calibrator code '    '=>all
AIPS 1: TIMERANG   *all 0                  Time range to list
AIPS 1: STOKES     ' '                     Stokes type to list.
AIPS 1: SELBAND      -1                    Bandwidth to select (kHz)
AIPS 1: SELFREQ      -1                    Frequency to select (MHz)
AIPS 1: FREQID        0                   Freq. ID to select.
AIPS 1:                                    None selected => 1.
AIPS 1: BIF           1                    Lowest IF number 0=1
AIPS 1: EIF           1                    Highest IF number
AIPS 1: BCHAN         1                    Low channel number 0=>1
AIPS 1: ECHAN         0                    High channel number
AIPS 1: ANTENNAS   *all 0                  Antennas to list
AIPS 1: BASELINE   *all 0                  Baselines with ANTENNAS
AIPS 1: UVRANGE     0           0        UV range in kilolambda
AIPS 1: SUBARRAY      0                    Subarray, 0=>1
AIPS 1:                                    Cal. info for input:
AIPS 1: DOCALIB       2                    If >0 calibrate data
AIPS 1:                                    = 2 calibrate weights
AIPS 1: GAINUSE       2                   CAL (CL or SN) table to apply
AIPS 1: DOPOL        -1                    If >0 correct polarization.
AIPS 1: BLVER        -1                    BL table to apply.
AIPS 1: FLAGVER       0                    Flag table version
AIPS 1: DOBAND       -1                    If >0 apply bandpass cal.
AIPS 1:                                    Method used depends on value
AIPS 1:                                    of DOBAND (see HELP file).
AIPS 1: BPVER        -1                    Bandpass table version
AIPS 1: SMOOTH     *all 0                  Smoothing function. See
AIPS 1:                                    HELP SMOOTH for details.
AIPS 1: DPARM         5           1        Control info:
AIPS 1:            *rest 0                 (1) 0=amp, 1=phase, 2=rms
AIPS 1:                                        3=amp+rms, 4=phase+rms
AIPS 1:                                        5=amp+phase, 6=delay,
AIPS 1:                                        7=rate, 8=SNR, 9=par. ang
AIPS 1:                                        10 = Tsys, 11=elev,
AIPS 1:                                        12 = multiband delay
AIPS 1:                                        13 = Tant  14 = weights
AIPS 1:                                        N.B. Options 3 and 4 only
AIPS 1:                                        valid for OPTYPE = 'MATX'
AIPS 1:                                    (2) 0=vec avg, 1=scalar
AIPS 1:                                    (3) No. col (4-10) def=4.
AIPS 1:                                    (4) avg. time min (MATX,LIST)
AIPS 1:                                        *** significant
AIPS 1:                                    (5) Type of gain listings:
AIPS 1:                                        0 => all with same scale
AIPS 1:                                        like DEC-10 listings;
AIPS 1:                                        1 => scan/source info at
AIPS 1:                                        source/scan boundaries.
AIPS 1:                                    (6) Matrix scaling control:
AIPS 1:                                        0 => plot amp & rms
AIPS 1:                                        matrices with same scale;
AIPS 1:                                        1 => self-scale each
AIPS 1:                                        separately.
AIPS 1:                                    (7) > 0 self-scale phase
AIPS 1:                                        displays, else degrees.
AIPS 1: DOACOR       -1                    > 0 include autocorrelations
AIPS 1: FACTOR        0                    When DPARM(5)=0 Multiply
AIPS 1:                                    gain listings by FACTOR,
AIPS 1:                                    0=> use scale factor from
AIPS 1:                                    first record printed.
AIPS 1: DOCRT        -1                    > 0 -> use the terminal,
AIPS 1:                                    else use the line printer
AIPS 1:                                    > 72 => terminal width
AIPS 1: OUTPRINT   'MATX_CAL1'
AIPS 1:                                    Printer disk file to save
AIPS 1: BADDISK    *all 0                  Disk to avoid for scratch.

When you look at this list of numbers, amplitudes should be near constant between baselines and in time. Phases should be around zero. Lots of 0's and 1's are good! Teens and 20's are bad! If you have nice phases that are mostly small numbers, then...

Congratulations! You have calibrated your data!!!

WBR Step 5L: Flag Your Calibrators

2007-06-04T15:20:00.000-05:00

Ok, 'L' stands for Line data. Most of the steps for reducing line data can also be found in Appendix B of the AIPS cookbook. What we have to do first is flag the Channel 0 data for our calibrators.

First, you should know that flagging is really a matter of personal taste. This is the way I like to do it, but you might find something that you like a whole lot more.

Secondly, don't be surprised when flagging is by far the most time consuming aspect of interferometric data reduction. Especially if you're screwing around with data from the VLA as it is transitioning to the EVLA.

Thirdly, at least at this stage, only flag on amplitude. After some calibration, you might consider flagging on phase, but not yet.

A good place to start flagging is QUACK. QUACK flags the beginning of each scan of data, because often times the first little bit of time on an object is bad. QUACK from the 31Dec05 release of AIPS was really quite transparent, with parameters looking like this:


AIPS 1: QUACK     Flags specified portion of scans of UV data
AIPS 1: Adverbs     Values                 Comments
AIPS 1: ----------------------------------------------------------------
AIPS 1: INNAME     'AC825_FQ1'             Input UV file name (name)
AIPS 1: INCLASS    'CH 0'                  Input UV file name (class)
AIPS 1: INSEQ         1                    Input UV file name (seq. #)
AIPS 1: INDISK        1                    Input UV file disk unit #
AIPS 1: SOURCES    *all ' '                Sources selected/deselected
AIPS 1: SUBARRAY      0                    Subarray number 0=>all.
AIPS 1: SELBAND      -1                    Bandwidth to flag (kHz)
AIPS 1: SELFREQ      -1                    Frequency to flag (MHz)
AIPS 1: FREQID        1                    Freq. ID to flag. -1=>all.
AIPS 1:                                    0=> first Freq. ID.
AIPS 1: TIMERANG   *all 0                  Time: start day,hr,min,sec
AIPS 1:                                          stop day,hr,min,sec.
AIPS 1: ANTENNAS   *all 0                  Antennas to flag
AIPS 1: FLAGVER       0                    Flag table version number
AIPS 1: OPCODE     'ENDB'                  'END ', 'BEG ', 'ENDB'
AIPS 1:                                    'TAIL';   ' ' => 'BEG '
AIPS 1: REASON     *all ' '                Reason (24 char.)
AIPS 1: APARM         0            .33     (1) => Cutting time (min)
AIPS 1:            *rest 0                 from end (ENDG) 0 => 2
AIPS 1:                                    (2) => Cutting time (min)
AIPS 1:                                    from beg/end (BEGB/ENDB)
AIPS 1:                                    0 => 0.1
AIPS 1:                                    (3) Back start of flagging
AIPS 1:                                     <0 => no padding (0 seconds)
AIPS 1:                                      0 => 5 seconds [default]
AIPS 1:                                     >0 => APARM(3) seconds

In this case, I'm flagging the last third of a minute in each scan. If you wanted to flag the first part of a scan, you would set
OPCODE = 'BEG'. The Dec07 version of QUACK is really different and I don't understand it yet. Maybe someone can write in with pointers about it?

Good. Next, I like to look at my data in TVFLG and give it a quick flag. Here are some important parameters to consider before your run TVFLG.
SOURCES-- only look at one calibrator at a time in TVFLG. Otherwise your scale will be all messed up and you'll be confused.
TIMERANG-- You really really want all of your data to be able to fit with a smooth time of 10 seconds. What will happen is that if there is too much time spent on your source, AIPS will force you to average your data for multiples of 10s, and this is bad. Because you will flag your data, and think you got rid of the really bright points, but then you will look at all the visibilities in UVPLT and still see lots of bright points. You will be in for far fewer nasty surprises if you make sure smooth time is 10s (In the TVFLG window, it should say AVG 1). Therefore, if you're getting AVG > 1, you should probably break your data up and view it several times in TVFLG with different timeranges. You probably won't know if you need to set a timerange until you load up TVFLG once, and see how much data there is.
DOCAL = 2-- apply weights to your data before you view them in TVFLG.


AIPS 1: TVFLG:  Task to edit UV data using the TV display and cursor
AIPS 1: Adverbs     Values                 Comments
AIPS 1: ----------------------------------------------------------------
AIPS 1: USERID        0                    User number.
AIPS 1: INNAME     'AC825_FQ1'             UV data (name).
AIPS 1: INCLASS    'CH 0'                  UV data (class).
AIPS 1: INSEQ         1                    UV data (seq. #).  0 => high
AIPS 1: INDISK        1                    Disk unit #.       0 => any
AIPS 1: DOCAT         0                    Catalog work file ?
AIPS 1: IN2SEQ        1                    Sequence number of work file
AIPS 1: IN2DISK       1                    Disk number of work file
AIPS 1: DOHIST       -1                    Record flags in history file
AIPS 1: SOURCES    '1331+305'              Source list
AIPS 1:            *rest ' '
AIPS 1: CALCODE    ' '                     Calibrator code '    '=>all
AIPS 1: TIMERANG   *all 0                  Time range to include
AIPS 1: STOKES     ' '                     Stokes type to display
AIPS 1: SELBAND      -1                    Bandwidth to select (kHz)
AIPS 1: SELFREQ      -1                    Frequency to select (MHz)
AIPS 1: FREQID        0                    Freq. ID to select.
AIPS 1: BIF           0                    Lowest IF number 0=1
AIPS 1: EIF           0                    Highest IF number
AIPS 1: BCHAN         0                    Lowest channel number 0=>1
AIPS 1: ECHAN         0                    Highest channel number
AIPS 1: ANTENNAS   *all 0                  Antennas to include
AIPS 1: BASELINE   *all 0                  Baselines with ANTENNAS
AIPS 1: UVRANGE       0           0        UV range in kilolambda
AIPS 1: SUBARRAY      0                    Subarray, 0 => all, but the
AIPS 1:                                    task is more efficient doing
AIPS 1:                                    one at a time
AIPS 1:                                    Cal. info for input:
AIPS 1: DOCALIB       2                    If >0 calibrate data
AIPS 1:                                    = 2 calibrate weights
AIPS 1: GAINUSE       1                    CAL (CL or SN) table to apply
AIPS 1: DOPOL        -1                    If >0 correct polarization.
AIPS 1: BLVER        -1                    BL table to apply.
AIPS 1: FLAGVER       1                    Flag table version 0 => high
AIPS 1:                                       < 0 no flagging on input
AIPS 1:                                       Used w single-source too
AIPS 1: DOBAND       -1                    If >0 apply bandpass cal.
AIPS 1:                                    Method used depends on value
AIPS 1:                                    of DOBAND (see HELP file).
AIPS 1: BPVER         0                    Bandpass table version
AIPS 1: SMOOTH     *all 0                  Smoothing function. See
AIPS 1:                                    HELP SMOOTH for details.
AIPS 1: DPARM         0           0        Control info:
AIPS 1:               0           0        (1) 0=amp, 1=phase, 2=rms,
AIPS 1:              10          10            3=rms/mean for initial
AIPS 1:            *rest 0                     display, can choose any
AIPS 1:                                        interactively later
AIPS 1:                                    (2) > 0 include autocorr data
AIPS 1:                                    (3) >0 = baseline as ant pair
AIPS 1:                                        for B as x-axis only
AIPS 1:                                    (4) >0 => divide by source
AIPS 1:                                        IPOL flux
AIPS 1:                                    (5) Expand time ranges by
AIPS 1:                                        DPARM(5) in sec
AIPS 1:                                    (6) y-axis interval: give the
AIPS 1:                                        sample time in seconds.
AIPS 1:                                        default = 10 seconds.
AIPS 1:                                    (7) initial IF displayed, 0
AIPS 1:                                        => BIF, can choose BIF -
AIPS 1:                                        EIF interactively
AIPS 1:                                    (8) initial channel displayed
AIPS 1:                                        0 => BCHAN, can choose
AIPS 1:                                        BCHAN - ECHAN later
AIPS 1:                                        interactively
AIPS 1:                                    (9,10) pixrange for initial
AIPS 1:                                        TV load - can reset later
AIPS 1:                                        interactively
AIPS 1: BADDISK    *all 0                  Disks to avoid for scratch
AIPS 1:                                    and for master grid file.

Make sure that you look at all your channels, polarizations, and IFs. I like the 'clip interactively' command a lot for getting rid of high or low points.

I recently (finally!) figured out how to invert the scale in TVFLG, so that low points appear bright. Use the 'tvtransf' option, type an 'a' to get an option to change the contrast/brightness of the image. A little square will pop up. Type 'c' now to invert the image, and then move your mouse around with the button held down to get an image stretch you like. Tah Dah!

One useful note: You have to set the Stokes Flag in terms of 0's and 1's, and this is what the binary code means:
1000-- flag only right polarization
0100--flag only left polarization
1111--flag both polarizations

NOTE: TVFLG can take a long time to load if you have lots of channels or data. It's usually pretty fast for the calibrators, because you don't usually spend much time on them. But while TVFLG is loading up your target data (no, we're not there yet), you might want to go eat lunch. Depending on the data set.

Finally, double check everything in UVPLT. Beware, UVPLT likes to plot data in terms of Stokes I, which is quite confusing. Choose to plot STOKES = 'RR' or 'LL' for more clarity. BPARM is the important set of parameters which mostly determine what you're plotting. BPARM = 0 is a good place to start, as this plots amplitude against the length of your baselines.

WBR Step 5C. Flag Your Calibrators

2007-05-27T05:31:00.001-05:00

Ok, 'C' stands for continuum. There are slightly different calibration steps for deep continuum data; I'm going to follow the tips for L-Band data reduction given at this VLA website. That means we won't be using the CH 0 data, we'll be making our own Channel 0 after we bandpass-calibrate the line data. But I'm getting ahead of myself. What we have to do first is flag our calibrators. I like to only flag the calibrators very lightly, then calibrate them, and then flag more heavily on the calibrated data.

First, you should know that flagging is really a matter of personal taste. This is the way I like to do it, but you might find something that you like a whole lot more.

Secondly, don't be surprised when flagging is by far the most time consuming aspect of interferometric data reduction. Especially if you're screwing around with data from the VLA as it is transitioning to the EVLA.

Thirdly, at least at this stage, only flag on amplitude. After some calibration, you might consider flagging on phase, but not yet.

Fourthly, before you calibrate, I recommend you only flag on dramatically bad looking amplitudes. Don't get too selective yet.

So, as I mentioned above, let's run all of the below commands on the line data. This is more work for you, as you have to look at each channel, but it seems to be the more meticulous way of doing it. If you prefer, I guess you could flag on your CH 0 data, then just copy over the flag (FG) table (using TACOP) to the LINE data set. That might be faster. But you still should probable do a brief run through each channel to make sure there's nothing really glaring that you missed, when you averaged all the channels together.

A good place to start flagging is QUACK. QUACK flags the beginning of each scan of data, because often times the first little bit of time on an object is bad. QUACK from the 31Dec05 release of AIPS was really quite transparent, with parameters looking like this:


AIPS 1: QUACK     Flags specified portion of scans of UV data
AIPS 1: Adverbs     Values                 Comments
AIPS 1: ----------------------------------------------------------------
AIPS 1: INNAME     'AC825_FQ1'             Input UV file name (name)
AIPS 1: INCLASS    'LINE'                  Input UV file name (class)
AIPS 1: INSEQ         1                    Input UV file name (seq. #)
AIPS 1: INDISK        1                    Input UV file disk unit #
AIPS 1: SOURCES    *all ' '                Sources selected/deselected
AIPS 1: SUBARRAY      0                    Subarray number 0=>all.
AIPS 1: SELBAND      -1                    Bandwidth to flag (kHz)
AIPS 1: SELFREQ      -1                    Frequency to flag (MHz)
AIPS 1: FREQID        1                    Freq. ID to flag. -1=>all.
AIPS 1:                                    0=> first Freq. ID.
AIPS 1: TIMERANG   *all 0                  Time: start day,hr,min,sec
AIPS 1:                                          stop day,hr,min,sec.
AIPS 1: ANTENNAS   *all 0                  Antennas to flag
AIPS 1: FLAGVER       0                    Flag table version number
AIPS 1: OPCODE     'ENDB'                  'END ', 'BEG ', 'ENDB'
AIPS 1:                                    'TAIL';   ' ' => 'BEG '
AIPS 1: REASON     *all ' '                Reason (24 char.)
AIPS 1: APARM         0            .33     (1) => Cutting time (min)
AIPS 1:            *rest 0                 from end (ENDG) 0 => 2
AIPS 1:                                    (2) => Cutting time (min)
AIPS 1:                                    from beg/end (BEGB/ENDB)
AIPS 1:                                    0 => 0.1
AIPS 1:                                    (3) Back start of flagging
AIPS 1:                                     <0 => no padding (0 seconds)
AIPS 1:                                      0 => 5 seconds [default]
AIPS 1:                                     >0 => APARM(3) seconds


AIPS 1: TVFLG:  Task to edit UV data using the TV display and cursor
AIPS 1: Adverbs     Values                 Comments
AIPS 1: ----------------------------------------------------------------
AIPS 1: USERID        0                    User number.
AIPS 1: INNAME     'AC825_FQ1'             UV data (name).
AIPS 1: INCLASS    'CH 0'                  UV data (class).
AIPS 1: INSEQ         1                    UV data (seq. #).  0 => high
AIPS 1: INDISK        1                    Disk unit #.       0 => any
AIPS 1: DOCAT         0                    Catalog work file ?
AIPS 1: IN2SEQ        1                    Sequence number of work file
AIPS 1: IN2DISK       1                    Disk number of work file
AIPS 1: DOHIST       -1                    Record flags in history file
AIPS 1: SOURCES    '1331+305'              Source list
AIPS 1:            *rest ' '
AIPS 1: CALCODE    ' '                     Calibrator code '    '=>all
AIPS 1: TIMERANG   *all 0                  Time range to include
AIPS 1: STOKES     ' '                     Stokes type to display
AIPS 1: SELBAND      -1                    Bandwidth to select (kHz)
AIPS 1: SELFREQ      -1                    Frequency to select (MHz)
AIPS 1: FREQID        0                    Freq. ID to select.
AIPS 1: BIF           0                    Lowest IF number 0=1
AIPS 1: EIF           0                    Highest IF number
AIPS 1: BCHAN         0                    Lowest channel number 0=>1
AIPS 1: ECHAN         0                    Highest channel number
AIPS 1: ANTENNAS   *all 0                  Antennas to include
AIPS 1: BASELINE   *all 0                  Baselines with ANTENNAS
AIPS 1: UVRANGE       0           0        UV range in kilolambda
AIPS 1: SUBARRAY      0                    Subarray, 0 => all, but the
AIPS 1:                                    task is more efficient doing
AIPS 1:                                    one at a time
AIPS 1:                                    Cal. info for input:
AIPS 1: DOCALIB       2                    If >0 calibrate data
AIPS 1:                                    = 2 calibrate weights
AIPS 1: GAINUSE       1                    CAL (CL or SN) table to apply
AIPS 1: DOPOL        -1                    If >0 correct polarization.
AIPS 1: BLVER        -1                    BL table to apply.
AIPS 1: FLAGVER       1                    Flag table version 0 => high
AIPS 1:                                       < 0 no flagging on input
AIPS 1:                                       Used w single-source too
AIPS 1: DOBAND       -1                    If >0 apply bandpass cal.
AIPS 1:                                    Method used depends on value
AIPS 1:                                    of DOBAND (see HELP file).
AIPS 1: BPVER         0                    Bandpass table version
AIPS 1: SMOOTH     *all 0                  Smoothing function. See
AIPS 1:                                    HELP SMOOTH for details.
AIPS 1: DPARM         0           0        Control info:
AIPS 1:               0           0        (1) 0=amp, 1=phase, 2=rms,
AIPS 1:              10          10            3=rms/mean for initial
AIPS 1:            *rest 0                     display, can choose any
AIPS 1:                                        interactively later
AIPS 1:                                    (2) > 0 include autocorr data
AIPS 1:                                    (3) >0 = baseline as ant pair
AIPS 1:                                        for B as x-axis only
AIPS 1:                                    (4) >0 => divide by source
AIPS 1:                                        IPOL flux
AIPS 1:                                    (5) Expand time ranges by
AIPS 1:                                        DPARM(5) in sec
AIPS 1:                                    (6) y-axis interval: give the
AIPS 1:                                        sample time in seconds.
AIPS 1:                                        default = 10 seconds.
AIPS 1:                                    (7) initial IF displayed, 0
AIPS 1:                                        => BIF, can choose BIF -
AIPS 1:                                        EIF interactively
AIPS 1:                                    (8) initial channel displayed
AIPS 1:                                        0 => BCHAN, can choose
AIPS 1:                                        BCHAN - ECHAN later
AIPS 1:                                        interactively
AIPS 1:                                    (9,10) pixrange for initial
AIPS 1:                                        TV load - can reset later
AIPS 1:                                        interactively
AIPS 1: BADDISK    *all 0                  Disks to avoid for scratch
AIPS 1:                                    and for master grid file.

WBR Step 4. One File per Each Day of Observations

2007-05-27T05:00:00.000-05:00

Sometimes, your data is taken over multiple days. You want to calibrate each day separately. You can do this by setting 'timerang' in calib, but that scares me a little bit and has lots of room for mistakes. What I prefer to do is SPLIT off each day of observing, so that you'll have a UV file for each day of data. After you've calibrated each file individually, you can combine all the data back together using DBCON.

So how do you split your data according to observation day?

Using SPLIT!
Well, first of all, check in that scan list you got from LISTR to see what days you observed on.
Then run split with 'timerang' set to only include one of those days. For example, only include data taken on day 1:
timerang = 1 0 0 0 1 23 0 0
will include all data take on day 1 between 0 hr and 23 hr.

Everything else in SPLIT you will probably want to leave as default. Except for maybe 'outclass', which you could change to something like, say, 'line_1' (so that you remenber this is the line data from day 1).

SPLIT will generate a new UV file. You need to run INDXR on it to generate a new NX table. The defaults of INDXR are just fine for these purposes.

Unfortunately, you are going to have to do each of the following flagging/calibration steps for each file individually. Sorry, dudes.

I want a $%ing beam on my image

2007-05-23T11:37:00.001-05:00

This should be easy, but I've totally forgotten how to do it. How do I get the beam displayed on the TV when I'm looking at my image?

On a non-aips note, we had a small earthquake in Socorro last night-- 3.3 mag! It was my first one and I'm very excited about it.

CPARM(2) and Self Cal

2007-05-22T15:38:00.002-05:00

Emily read in the GMRT documentation that, when doing A&P self calibration, you should set CPARM(2) = 1, which means you would 'normalize gains'. However, we didn't really understand what this meant, and didn't understand why we were doing it. Today I asked Miller Goss, who's visiting UW from NRAO, and he said...

You should set CPARM(2) = 1 only if you don't trust your amplitudes initially! If you think your original amplitude calibration is not so good, say in the case of VLBA data or certain frequencies at the GMRT, you might want to set it.

However, at the VLA, you should set CPARM(2) = 0 because your original amplitude calibration was really quite decent. (At least at L and C band, not sure about crazy other frequencies!)

UVRANGEs contradict Calibrator Quality Ratings

2007-05-21T19:39:00.000-05:00

What does it mean if your calibrator has a good ("P") rating in the calibrator manual for your array configuration whose longest baseline is ~50 kilolambda--- but then there's a uvrange limitation on it with a uvmin of 100 kilolambda? I'm trying to use calibrator 0841+708 at C band in C array.

5/23/07:
Resolution: After talking to Miller Goss, I think that this must be a typo in the manual. The amplitudes look fine, for the most part, and there is no obvious confusing source in the field. So, I guess this is just a word of caution about the manual, that it can make mistakes some times!

5/24/07:
More Resolution: Rick Perley had this to say about the current state of the VLA calibrator manual:

  Right you are!  The 'P' in that column/row should be an 'S', I think.  It's one of the 'core-dominated' source
types that make good high frequency, high resolution calibrators. 
   Nobody is keeping up the manual these days (Greg Taylor used to do this, but he's now gone to UNM).  We'll
certainly get back on this after the EVLA settles in, and we'll be able to utilize far more sources as calibrators.
In the meantime, I'll make a note in my copy.