ADMIT tricks and advanced script usage

In this section we describe some more advanced usages of ADMIT, particularly in the use of the Unix command line.

Input FITS files: listfitsa

The script listfitsa helps to quickly summarizing cube size, source name, ra/dec/freq and filesize of your FITS files. The script will accept the usual wild card style arguments. E.g.:

$ listfitsa *.fits

concat.spw17.image.fits [118, 118, 4096, 1] Serpens_Main 277.491666667 1.22916666667 244.867618746 0.212
concat.spw19.image.fits [116, 116, 4096, 1] Serpens_Main 277.491666667 1.22916666667 240.948346249 0.205
concat.spw21.image.fits [108, 108, 4096, 1] Serpens_Main 277.491666667 1.22916666667 225.785304399 0.178
concat.spw23.image.fits [110, 110, 4080, 1] Serpens_Main 277.491666667 1.22916666667 229.146014394 0.184
concat.spw33.image.fits [138, 138, 4096, 1] Serpens_Main 277.491666667 1.22916666667 342.937829665 0.291
concat.spw35.image.fits [138, 138, 4080, 1] Serpens_Main 277.491666667 1.22916666667 341.196253808 0.289
concat.spw37.image.fits [144, 144, 4096, 1] Serpens_Main 277.491666667 1.22916666667 354.435171299 0.316
concat.spw39.image.fits [142, 142, 4096, 1] Serpens_Main 277.491666667 1.22916666667 351.698458419 0.308

The optional -v option can be used for a verbose listing of the FITS header.

Output FITS files: image2fits

If you are in an ADMIT developer environment, your unix shell has direct access to a number of CASA commands. In particular the

$ image2fits in=test0.admit/x.csm out=test0.mom0.fits

(make sure you have a proper 4-element $CASAPATH, otherwise this command will fail).

An alternative is the ADMIT script casa2fits, which handles multiple casa images and appends the fits extension:

$ casa2fits

Running ADMIT recipes

We already discussed ADMIT recipes earlier, but list them here for completeness. You run them in the shell as follows:

$ admit_recipe Line_Moment test0.fits

and just typing the command admit_recipe will list the currently available recipes.

Export ADMIT projects

If you want to share a project with a collaborator, or have a developer look at certain types of problems, you can turn your ADMIT project into a tar file. The script admit_export makes this a little easier, and also have an option to make a more lightweight version of the project if your recipient does not need the actual cubes. This is actually the default of the script,

$ admit_export test0.admit
Writing brief test0.admit.tar.gz

$ admit_export -a test0.admit -b test00.admit
Writing all in test0.admit.tar.gz
Writing brief test00.admit.tar.gz

You can export as many projects as you want, and whenever the -a or -b arguments are mentioned, subsequent projects are in their respective modes.

Native File Browser

The aopen script is an alternative to the web based review (and re-run) of an ADMIT project. It will use whatever your native OS has available to resolve how to display a file given the file extension of magic marker. It will accept a directory name, with no arguments it will open the current directory.

Line Fitting

In each ADMIT directory where LineID has run you can currently find ascii tables that represent the different spectra that feed into LineID, albeit via their respective BDP’s.

  1. (make sure multiple points come out right now)

The tables have two columns, the observed frequency and the “spectrum”. Technically we call each of them a spectrum, as they represent some response where we expect a signal where the transition is. See below. Of course, within ADMIT these tables are really properly stored within a BDP (an XML file). For example, the file is probably in a file x.csp.bdp

Doppler Recession

Optical, Radio and Relativistic conventions exist. CASA has conversion routines, so does astropy, and we have a version in admit.util. Would be good to reference that here. Add some reminder math as well?

apar files

Some of the ADMIT scripts can use an apar file to help you set script parameters. These are ascii files, actually meant to be executable python code (the first line should contain a magic ** -- python -- ** marker for emacs zealots)

Scripts will typically support looking at certain default names, in the following order:

  1. <scriptname>.apar for global parameters (for example admit1.apar)
  2. <fitsname>.apar for specific files (for example test0.fits.apar)
  3. <aparname>.apar for personal use (for example test123.apar, if your script supported the –apar test123.apar command line option; does).

An example to use executable code is in $ADMIT/etc/data/test253_spw3.fits.apar

runa1 and

The runa1 script is a very simple front-end to the more complex script, which is the current (and still evolving) model how to run ADMIT on the pipeline. It contains some decision making which depends on running an admit project at critical times.

You would only pass the name of a fits file to the script, and the script tries to figure out what type of ALMA (or non-ALMA) fits file you have and call appropriately. The flow of the script can be controlled by a number of admit parameters (apar, see below), that match certain AT keywords. You can store these in an apar file, but it has to be python executable code.

If you want to use runa1, here’s a sample workflow and strategy:

  1. Run the script “listfitsa” on the fits file to get the object name for vlsr

    $ listfitsa uid___A001_X12b_X231.NGC_1068_sci.spw17.cube.I.pbcor.fits
    -> [1000, 1000, 3839, 1] NGC_1068 40.6696170833 -0.0133133333333 14.301

    This is a 1000 x 1000 x 3839 cube, source name is NGC_1068, RA,DEC are 40.6696170833 -0.0133133333333 and the datasize is 14.3 GB

    If that does not resolve the source name, use “listfitsa -v” and debug the full header to find the sourcename (e.g. OBJECT vs. FIELD issue? use of quotes?)

  2. Enter the appropriate VLSR into ADMIT; there are several ways to do this:

    1. enter it into $ADMIT/etc/, but this requires you to be able to write there and there is the issue what happens if ADMIT gets updated
    2. enter it into a private apar file:
      1. admit1.apar , which is used for all fits files in the working directory if you use admit1 (other recipes should support this as well)n
      2. test0.fits.apar, which would only be used for that fits file

    You can use NED or SIMBAD, but be sure to get the VLSRK, since that’s the official ALMA frame of reference

    and stuff this into admit1.apar so each fits file will. We have this code in, could add a python commandline interface

    If the ALMA source name has spaces, you must use quotes. Otherwise not needed.

  3. PB correction is currently very slow in ADMIT (CASA) for large cubes. Especially if your imaging area has a large portion outside of the 50% you could use a straight ADMIT on the pbcor file, since the inner portion is not affected. To confirm you can do this, run with maxlines=0 in admit1.apar and inspect the cubesum (CSM) map how much smaller you can make your map. e.g.

    $ runa1 uid___A001_X12b_X231.NGC_1068_sci.spw17.cube.I.pbcor.fits

    Assuming all your spw’s have the same imaging area, add these into admit1.apar via the inbox= (and optionally inedge=) keywords for

    inbox  = [xmin,ymin,xmax,ymax]
    inedge = [2,2]

    and use the full fits name:

    runa1 uid___A001_X12b_X231.NGC_1068_sci.spw17.cube.I.pbcor.fits

    If you must go the slow way, the runa1 script needs the shorter name to deal with the pbcor.fits and pb.fits file, as follows:

    runa1 uid___A001_X12b_X231.NGC_1068_sci.spw17.cube.I
    Example: just Ingest_AT takes 53 mins on this 14GB cube, but in just

    pbcor.fits mode it was barely 4 mins.

    full:   real/user/sys     100m25.976s / 60m50.785s / 22m35.384s   DIED IN LINEID
    pbcor:  real/user/sys      27m9.151s  / 17m50.085s /  4m10.644s   OK
                pbcor(")     full(")
    ingest        223        3205
    cubestats     552         602
    cubesum        47          47
    pvslice       479         574
    lineid         19           -
    linecube       90           -
  4. If you have a large (>1?) set of fits cubes with the ALMA naming and directory (project/SOUS/MOUS/GOUS/products) convention, there’s a script do_aap in ADMIT that can help you processing all data in a clean directory. Alternatively you can run admit (e.g. runa1) inside of each of the (project/SOUS/MOUS/GOUS/products) directories.

    Essentially, the do_aap script creates symlinks into those trees but processes in local admit directories, outside of the ALMA tree structure. See documentation in script, and more examples to come here.

    A version of do_aap exists that works from working/ instead of product/, and looks for the “*.cont.residual” files, which are the continuum subtracted cubes.

admit1 apar parameters

The ADMIT apar parameters can be placed in up to three files, processed in the following order

  1. admit1.apar : if present, this apar file will be first parsed
  2. fitsfilename.apar : if present, this apar file will be parsed next
  3. aparname.apar : if present as argument to the –apar command line argument to, this will be read last.

They normally contain python variables, used by admit1, but can also contain python code, if you parameters need a minor computation.

useMask  = False       # Ingest_AT(mask=)

This uses a mask where fits data == 0.0. Normally not needed, as ALMA fits cubes are properly masked where needed.

vlsr     = None        # Ingest_AT(vlsr=) and LineID_AT(vlsr=)

Somewhat peculiar. Normally is a float, so you would use vlsr=236.0, but by setting it to the None python value, we tell the AT to try it figure it out from the RESTFREQ, if present. If no value found, 0.0 will be used and most likely LineID will not do a great job. Look at the output for Ingest_AT, where it lists the VLSRc value.

maxpos   = []          # CubeSpectrum_AT(pos=)

Paired positions, e.g. maxpos=[10,10,64,64,128,128], for the probes for a spectrum through the cube with CubeSpectrum_AT that will also normally serve as input for LineID_AT. You can also use CASA’s RA-DEC position: maxpos=[‘00h47m33.041s’,’-25d17m26.61s’]

robust   = ['hin',1.5]  # CubeStats_AT(robust=)

Robust noise, as an alternative to the default MAD scheme.

contsub  = [None]           # ContinuumSub_AT(contsub=)

By default no continuum is subtracted. You can set this to either a blank list ([]), in which case the LineSegment_AT() will be used to block out potential lines and determine the continuum, or a specific number of tuples can be given where the continuum should be fitted, for example [(0,99), (900,999)]

insmooth = []               # smooth inside of Ingest_AT, in pixels
inbox    = []               # box to cut in Ingest_AT  [x0,y0,x1,y1] or [x0,y0,z0,x1,y1,z1]
inedge   = []               # edges to cut in Ingest_AT [zleft,zright]
                            # [0] and [1] are spatial
                            # [2] is frequency:    1=>Hanning  >1 Boxcar
smooth   = []               # if set, smooth the cube right after ingest (list of 2 or 3 can be given)
usePeak  = True             # LineCubeSpectra through peak of a Moment0 map? (else pos[] or SpwCube Peak)
useCSM   = False            # if usePeak, should CubeSum (CSM) be used (instead of mom0 from LineCube)
pvslice  = []               # PV Slice (x0,y0,x1,y1)
pvslit   = []               # PV Slice (xc,yc,len,pa)  if none given, it will try and find out
pvwidth  = 5                # width of a slit in PV (>1 will decrease the noise in PV)
usePV    = True             # make a PVSlice?
usePPP   = True             # create and use PeakPointPlot?
useMOM   = True             # if no lines are found, do a MOM0,1,2 anyways ?
minOI    = 0                # If at least minOI linecubes present, use them in an OverlapIntegral; 0 turns off OI
pvSmooth = [10,10]          # smooth the PVslice ?   Pos or Pos,Vel pixel numbers
maxlines = -1               # limit the # linecubes? (set to 0 if you want to exit after LineID_AT)
linebdp  = [True, True, False]    #  use of [CSP,CST,PVC] for LineID?
contbdp  = [True, True]           #  use of [CSP,CST] for LineSegment
cspbdp   = [True, True, True]     #  use of [CST,CSM, SL] for initial CubeSpectrum
lineUID  = False                  # if True, this would run LineID(identifylines=False) [old relic]
lineSEG  = True                   # if True, it also runs LineSegment (aiding in automated ContinuumSub)
linepar  = ()                     # if set, (numsigma,minchan,maxgap); both LineSegment and LineID
iterate  = True                   # iterate to find narrower higher S/N peaks
online   = False                  # use splatalogue online?
reflist  = 'etc/co_lines.list'    # pick one from $ADMIT/etc
llsmooth = []                     # if set, apply this smoothing to the inputs for LineSegment and LineId

Here is a different descriptive explanation about how guide you through the darkness of running admit1, with comments for future expansion of this script. Again,the parameters listed are the APAR parameters, which are close to (but not necessarely identical to) the AT keywords.

A FITS cube (file=) is selected for ingestion into the ADMIT flow. This needs to be a noise flat data cube. If you get a primary beam corrected cube (where the noise increases near the edges of the field), it will need to be multiplied by the primary beam, in order to get noise flat images. This is a current limitation of ADMIT, it works best if the image has more-or-less constant RMS accross the field, although we do allow it to very per channel. The pb= keyword is meant to pass a primary beam into the flow, you can leave it blank if you don’t need it.

An optional continuum map (cont=) can be added to the flow. This will be used to find one or more continuum sources, which can then be used as probes for a spectrum, but more on that below.

At the ingest stage, there are a few procedures worth mentioning:

  1. A subregion can be given using inbox=. This can be very useful if you are certain the source is limited spatially and/or spectrally. This can save a huge amount of processing.
  2. If no box was given, you can also specify taking out a number of edge channels using inedge=.
  3. Smoothing can be applied to the cube using insmooth=. Although there is a separate Smooth_AT available to do this as a separate step in the flow, this will take up extra disk space. need to confirm if flux is conserved in this step

The cube can now be smoothed, potentially to help in the line detection. Once the line detection has succeeded, you can opt to continue with the original higher resolution cube. You trigger a smoothing operation with smooth=.

Although Ingest_AT will report some global stastics of the cube (a min,max,RMS), these are not what we call robust statistics (an attempt to ignore the signal and compute the statistics on the remainder).

Thus the first step after the data has been ingested (and smoothed) is a thorough analysis of the statistics. This is currently done on a plane by plane basis, since they can differ. Different methods to reject the signal and attempt to get a robust statistics is available wiht the robust= keyword.

If the RMS(channel) plot shows suspicious “lines” where lines are also present, this could be the result of:

  1. Missing short spacings where there is source structure in a line. You would also expect to see the minval to show that line structure
  2. Extended emission where even the robust noise detection failed. You can try different methods or robust=, in particular the half-fit should be less sensitive.
  3. Continuum emission had not been (properly) subtracted.

More on CubeSum, CubeSpectrum now. Then go into LineSegment_AT

After the continuum has been subtracted based on the LineSegment’s, a good strategy to check on its correctness would be to take the new continuum free cube, and extract a new CubeSum of the line based on the segments, as well as a sum of all the emission that was not deemed part of the lines (x-test_line.csm), to check if no remaining line or continuum emission was left. It should be a pure noise map, and we need a cubestats and histogram for this. Should find the noise to be sigma/sqrt(nchan). This map is x-test_cont.csm.

We now have new CST and CSP and perhaps a PVC. They can be fed into LineID_AT for line identification.

runa2 and

This is a special version of admit1 for just continuum maps. The flow will only call CubeStats_AT and SFind2D_AT and present a list of found sources and fluxes. The –cont option in admit1 can be used to pass a continuum map and use the brightest continuum source position as probe for CubeSpectrum_AT in that flow.

runa4 and

The runa4 script is a simple front-end for, which allows you to take an ASCII spectrum (frequency in column 1, in GHz, spectrum value in column 2, arbitrary units). For example, from the Unix command line

$ runa4 test0.admit/

would import this table into a CubeSpectrum_BDP and rerun the LineSegment_AT and LineId_AT tasks and allow you to experiment with LineID_AT. Parameters can be placed in admit4.apar or in this specific case.

admit4 apar parameters

vlsr     = 0.0              # LineID_AT(vlsr=)

Set the VLSR (remember to use the VLSK frame of reference for ALMA data) for LineID

loglevel = 10               # 10=DEBUG, 15=TIMING 20=INFO 30=WARNING 40=ERROR 50=FATAL

The default ADMIT loglevel is 20, and some verbose feedback from the work done in LineSegment and LineID needs loglevel=10.

lineUID  = False            # LineID_AT(identifylines=True)

This would limit the LineID run to only identifying line segments, and it’s output should be identical to LineSegment. By default lines will be identified.

linepar  = ()               # LineID_AT(numsigma=,minchan=,maxgap=) and LineSegment_AT(...)

A convenience

llsmooth = []               # LineID_AT(smooth=) and LineSegment_AT(...)
iterate  = True             # LineID_AT(iterate=)
csub     = None             # LineID_AT(csub=) and LineSegment_AT(...)

Since only one spectrum is read, only the CubeSpectrum csub parameter (normally a list) has to be set as an integer here.

online   = False            # LineID_AT(online=)

By default the CASA internal slsearch() is used to query a smaller version of Splatalogue, but with online=True the web interface can be used, at the cost of some latency.

reflist  = 'etc/co_lines.list'    # LineID(references=)

Pick a references list, a table of names/frequencies (in GHz), to be overplotted on the LineID plots for comparison. Some example references list files are in $ADMIT/etc/*_lines.list)