First Look at Image Analysis CASA 6.5.4

This guide is written for CASA 6.5.4 and uses Python 3.

The first few tutorials provided us with a spectral line data cube and a continuum image. Next we'd like to understand some of the properties of the images that we have produced.

In case you don't have the images from the first tutorials handy, let's start by copying the image files from the working directory in the full data package to our current directory (after untarring them, if you haven't already):

# In CASA
os.system('rm -rf twhya_cont.image')
os.system('cp -r ../working/twhya_cont.image .')
os.system('rm -rf twhya_n2hp.image')
os.system('cp -r ../working/twhya_n2hp.image .')

If you do have images from the prior tutorials, you'll want fifth_image.image (our best continuum image) from the self-cal tutorial, which you will substitute for twhya_cont.image, and twhya_n2hp.image from the spectral line tutorial.

Recall that we orient ourselves with measurement sets (UV data) using the listobs task. For images, an analogous way to get basic header information is to use the imhead task.

# In CASA
imhead('twhya_cont.image')
imhead('twhya_n2hp.image')

CASA prints the image header information to the logger:

imhead::::casa  ##########################################
imhead::::casa  ##### Begin Task: imhead             #####
imhead::::casa  imhead( imagename='twhya_cont.image', mode='summary', hdkey='', hdvalue='', verbose=False )
ImageMetaData::summary
ImageMetaData::summary+ Image name       : twhya_cont.image
ImageMetaData::summary+ Object name      : TW Hya
ImageMetaData::summary+ Image type       : PagedImage
ImageMetaData::summary+ Image quantity   : Intensity
ImageMetaData::summary+ Pixel mask(s)    : mask0
ImageMetaData::summary+ Region(s)        : None
ImageMetaData::summary+ Image units      : Jy/beam
ImageMetaData::summary+ Restoring Beam   : 0.609236 arcsec, 0.452453 arcsec, -51.5786 deg
ImageMetaData::summary
ImageMetaData::summary+ Direction reference : J2000
ImageMetaData::summary+ Spectral  reference : LSRK
ImageMetaData::summary+ Velocity  type      : RADIO
ImageMetaData::summary+ Rest frequency      : 3.72637e+11 Hz
ImageMetaData::summary+ Pointing center     :  11:01:51.796000  -34.42.17.366000
ImageMetaData::summary+ Telescope           : ALMA
ImageMetaData::summary+ Observer            : cqi
ImageMetaData::summary+ Date observation    : 2012/11/19/07:56:26.544000
ImageMetaData::summary+ Telescope position: [2.22514e+06m, -5.44031e+06m, -2.48103e+06m] (ITRF)
ImageMetaData::summary+
ImageMetaData::summary+ Axis Coord Type      Name             Proj Shape Tile   Coord value at pixel        Coord incr Units
ImageMetaData::summary+ ----------------------------------------------------------------------------------------------------
ImageMetaData::summary+ 0    0     Direction Right Ascension   SIN   250  250  11:01:51.796   125.00     -1.000000e-01 arcsec
ImageMetaData::summary+ 1    0     Direction Declination       SIN   250  250 -34.42.17.366   125.00      1.000000e-01 arcsec
ImageMetaData::summary+ 2    1     Stokes    Stokes                    1    1             I
ImageMetaData::summary+ 3    2     Spectral  Frequency                 1    1   3.72637e+11     0.00 2.34445114878e+08 Hz
ImageMetaData::summary+                      Velocity                                     0     0.00     -1.886149e+02 km/s
imhead::::casa  Task imhead complete. Start time: 2023-10-06 14:07:35.341678 End time: 2023-10-06 14:07:38.267440
imhead::::casa  ##### End Task: imhead               #####
imhead::::casa  ##########################################

imhead::::casa  ##########################################
imhead::::casa  ##### Begin Task: imhead             #####
imhead::::casa  imhead( imagename='twhya_n2hp.image', mode='summary', hdkey='', hdvalue='', verbose=False )
ImageMetaData::summary
ImageMetaData::summary+ Image name       : twhya_n2hp.image
ImageMetaData::summary+ Object name      : TW Hya
ImageMetaData::summary+ Image type       : PagedImage
ImageMetaData::summary+ Image quantity   : Intensity
ImageMetaData::summary+ Pixel mask(s)    : mask0
ImageMetaData::summary+ Region(s)        : None
ImageMetaData::summary+ Image units      : Jy/beam
ImageMetaData::summary+ Restoring Beam   : 0.614894 arcsec, 0.453196 arcsec, -52.3802 deg
ImageMetaData::summary
ImageMetaData::summary+ Direction reference : J2000
ImageMetaData::summary+ Spectral  reference : LSRK
ImageMetaData::summary+ Velocity  type      : RADIO
ImageMetaData::summary+ Rest frequency      : 3.72672e+11 Hz
ImageMetaData::summary+ Pointing center     :  11:01:51.796000  -34.42.17.366000
ImageMetaData::summary+ Telescope           : ALMA
ImageMetaData::summary+ Observer            : cqi
ImageMetaData::summary+ Date observation    : 2012/11/19/07:56:26.544000
ImageMetaData::summary+ Telescope position: [2.22514e+06m, -5.44031e+06m, -2.48103e+06m] (ITRF)
ImageMetaData::summary+
ImageMetaData::summary+ Axis Coord Type      Name             Proj Shape Tile   Coord value at pixel      Coord incr Units
ImageMetaData::summary+ --------------------------------------------------------------------------------------------------
ImageMetaData::summary+ 0    0     Direction Right Ascension   SIN   250  125  11:01:51.796   125.00   -1.000000e-01 arcsec
ImageMetaData::summary+ 1    0     Direction Declination       SIN   250   50 -34.42.17.366   125.00    1.000000e-01 arcsec
ImageMetaData::summary+ 2    1     Stokes    Stokes                    1    1             I
ImageMetaData::summary+ 3    2     Spectral  Frequency                15    5  3.726725e+11     0.00 -6.21550810e+05 Hz
ImageMetaData::summary+                      Velocity                                     0     0.00    5.000000e-01 km/s
imhead::::casa  Task imhead complete. Start time: 2023-10-06 14:07:38.461741 End time: 2023-10-06 14:07:38.501495
imhead::::casa  ##### End Task: imhead               #####
imhead::::casa  ##########################################

Statistics

Often we'd like to measure basic image statistics and fluxes. Recall you can do these operations pretty easily in CARTA. You can also get statistics using the imstat task.

# In CASA
my_stats = imstat('twhya_n2hp.image', chans='0~4')

The imstat task returns a python dictionary, and you can examine the contents as follows:

# In CASA
print(my_stats)
print(my_stats['rms'])

It's useful to see that the RMS is about 26 mJy/beam in the line cube.

You can also just print the dictionary to the terminal screen:

# In CASA
imstat("twhya_n2hp.image", chans="0~4")

This task is useful for measuring basic source characteristics. For example, calculate the statistics for a box encompassing the disk - you see that the integrated flux is about 1.8 Jy.

# In CASA
imstat("sis14_twhya_cont.image", box="100,100,150,150")
my_stats = imstat("sis14_twhya_cont.image", box="100,100,150,150")
print(my_stats['flux'])

Alternatively, a box defined off the disk will give image noise statistics.

# In CASA
imstat("sis14_twhya_cont.image", box="25,150,225,200")

Moments

For the spectral line cube, it's very useful to "collapse" the cube in various ways to analyze the emission. The immoments task lets you do this.

The first few "moments" are defined as follows:

 moments = -1 : mean value of the spectral coordinate
 moments =  0 : integrated value of the spectral coordinate
 moments =  1 : intensity weighted coordinate; traditionally used to get 'velocity fields'
 moments =  2 : intensity weighted dispersion of the coordinate; traditionally used to get "velocity dispersion"

A more complete description of image moments is given here in the CASA reference manual.

Figure 1: The zero moment of the N2H+ image.

Let's make a moment 0 image clipped at ~1 sigma:

# In CASA
os.system("rm -rf sis14_twhya_n2hp.mom0")
immoments("twhya_n2hp.image",
          outfile="sis14_twhya_n2hp.mom0",
          includepix=[20e-3,100],
          chans="4~12",
          moments=0)

Make a moment 1 image clipped at ~2 sigma:

# In CASA
os.system("rm -rf sis14_twhya_n2hp.mom1")
immoments("twhya_n2hp.image",
          outfile="sis14_twhya_n2hp.mom1",
          includepix=[40e-3,100],
          chans="4~12",
          moments=1)

At this point we have a few really neat things to see: first the line shows a hole in the middle. Overlay it on the dust (continuum) disk using the viewer and you can notice that they align but with the N2H+ existing only outside a certain radius - in this case the "snow line". Also have a look at the velocity field to see the rotation of the disk.

The imview task has some command-line scripting capability. For example, here we show how to overlay the line moment 0 (as a contour plot) on the continuum.

Figure 2: The N2H+ moment zero map as contours, overlaid on the continuum emission of TW Hydra. The plot demonstrates the "show line".

# In CASA
imview(raster={'file': 'sis14_twhya_cont.image',
'range': [-0.01,0.5]},
contour={'file': 'sis14_twhya_n2hp.mom0',
'levels': [0.5,0.6,0.7,0.8] })

Here, we are not using the primary beam corrected images and cubes when creating our moment maps. Remember that it's often very convenient to work in images before primary beam correction because the noise is the same across the field (e.g., this is a clean data set to search for signal) but it's very important to remember to apply this correction before calculating fluxes or intensities for science.

Export FITS images

CASA is great (of course) but you will ultimately want to export your data to a common format to analyze in other programs, share with other astronomers, or archive. It's easy to export images from CASA's image format to FITS images via the exportfits command.

# In CASA
exportfits(imagename="sis14_twhya_cont.image",
           fitsimage="twhya_cont.fits",
           overwrite=True)

For the cube we want to specify additionally that the frequency axis will be written out as velocity.

# In CASA
exportfits(imagename="twhya_n2hp.image",
           fitsimage="twhya_n2hp.fits",
           velocity=True,
           overwrite=True)