Difference between revisions of "Antennae Band7 - Imaging for CASA 3.3"

From CASA Guides
Jump to navigationJump to search
Line 259: Line 259:
 
Figure 13 shows a comparison plot betwee the moment 0 maps of ALMA and SMA data using the {{viewer}}. The fluxes, peak locations and large scale structure are consistent. Both southern and northern components have been combined.
 
Figure 13 shows a comparison plot betwee the moment 0 maps of ALMA and SMA data using the {{viewer}}. The fluxes, peak locations and large scale structure are consistent. Both southern and northern components have been combined.
  
[[File:Antennae_CO3-2.png||Fig. 13. The CO(3-2) total intensity map (moment 0)  comparison with SMA data. Colour image is ALMA data, combining southern and northern mosaics. contours show SMA data (Ueda, Iono, Petitpas et al., in preparation, to be submitted to ApJ).]]
+
[[File:Antennae_CO3-2.png|center| Fig. 13. The CO(3-2) total intensity map (moment 0)  comparison with SMA data. Colour image is ALMA data, combining southern and northern mosaics. contours show SMA data (Ueda, Iono, Petitpas et al., in preparation, to be submitted to ApJ).]]
  
 
====Exporting Fits Images====
 
====Exporting Fits Images====

Revision as of 12:47, 27 July 2011


Overview

This section of the AntennaeBand7 CASA Guide cover the imaging of the continuum and spectral line data. It begins where the Antennae Band7 - Calibration section left off. If you completed the Calibration section of the guide, then you may want to continue with the calibrated data sets. If you did not complete the Calibration section, then you can download the calibrated uv-data from the region closest to your location:

North America Europe East Asia

Then download the file 'Antennae_Band7_CalibratedData.tgz' to obtain the calibrated uvdata. Once the download has finished, unpack the file using 'tar -xvzf Antennae_Band7_CalibratedData.tgz' and change directory (cd) to Antennae_Band7_CalibratedData. You should have Antennae_South.ms and Antennae_North.ms in your working directory. Then start CASA with the 'casapy' command.

Continuum map

We will make 345 GHz continuum images for the two regions covered by the mosaics. We use the task clean over the channels that are free of the line emission. The line-free channels are found by plotting the average spectrum. We find the CO(3-2) line from channels 50 to 100 in the southern mosaic, and from 70 to 100 in the northern mosaic.

Fig. 1. Southern mosaic: Amplitude vs. channel. The CO(3-2) line is seen from 50 to 100
Fig. 2. Northern mosaic: Amplitude vs. channel. The CO(3-2) line is seen from 70 to 100
# In CASA
plotms(vis='Antennae_South.cal.ms',xaxis='channel',yaxis='amp',
      avgtime='1e8',avgscan=T)
plotms(vis='Antennae_North.cal.ms',xaxis='channel',yaxis='amp',
      avgtime='1e8',avgscan=T)

The avgtime is set to a large value so that it averages over all the integrations, and avgscan is set to allow averaging of the different scans.

Next we create the continuum emission map. We use the default non-interactive mode and niter=0 as a first step to see if there is any continuum emission. The resolution in Band 7 for the extended configuration is approximately 1 arcsec. We therefore choose a cell size of 0.2 arcsec to oversample the beam sufficiently (at least three times). Note that we need to delete any previous clean output images before proceeding with the clean command, otherwise CASA will clean the data further instead of producing new output images.

For the northern mosaic:

Fig. 3. 345 GHz continuum image of the northern mosaic
Fig. 4. 345 GHz continuum image of the southern mosaic
# In CASA
os.system('rm -rf Antennae_North.Cont.Clean*')

clean(vis='Antennae_North.cal.ms',imagename='Antennae_North.Cont.Clean',
     field='',phasecenter='12',
     mode='mfs',restfreq='345.79599GHz',
     spw='0:0~50,0:120~164',
     imagermode='mosaic',
     imsize=500,cell='0.2arcsec',
     interactive=F,
     niter=1000, threshold='0.5mJy')

The input parameters include:

  • vis='Antennae_North.cal.ms': The calibrated dataset on the science target
  • imagename='Antennae_North.Cont.Clean': The base name of the output images
  • phasecenter='12': the source id of the mosaic.
  • spw='0:0~50,0:120~164': To specify only the line-free channels
  • mode='mfs': Multi-Frequency Synthesis: The default mode, which produces one image from all the specified data combined
  • niter=1000: Maximum number of clean iterations
  • theshold='0.5mJy': Stop cleaning if the maximum residual is below this value (~1.5 times the rms noise)
  • imsize=500, cell='0.2arcsec': Image size in pixels, chosen to cover the mosaic, and the cell size per pixel in arcsec to properly sample the synthesized beam (at least three times).

For the southern mosaic we modify the phase center and the line-free channels:

# In CASA
os.system('rm -rf Antennae_South.Cont.Clean*')

clean(vis='Antennae_South.cal.ms',imagename='Antennae_South.Cont.Clean',
     field='',phasecenter='15',
     mode='mfs',restfreq='345.79599GHz',
     spw='0:0~30,0:120~164',
     imagermode='mosaic',
     imsize=500,cell='0.2arcsec',
     interactive=F,
     niter=1000, threshold='0.5mJy')

The Half Power Beam Width (HPBW) of the elliptical synthesized beam is:

  • Northern mosaic: 1.28" times 0.66", with a position angle (PA) equal to 86 deg.
  • Southern mosaic: 1.15" times 0.66", and PA equal to 68 deg.


We will determine some statistics for the images using the task imstat:

# In CASA
imstat('Antennae_North.Cont.Clean.image')
imstat('Antennae_South.Cont.Clean.image')

The peak flux densities of the images are ~4.4 and 2.9 mJy for the southern and northern mosaics, and both have a similar rms ~ 0.3 mJy, thus the obtained dynamic ranges are larger or equal than 10.

CO(3-2) map

Continuum subtraction

Such continuum emission is too small to have any significant effect on the line. However, it is educative to subtract the continuum emission in the uv-domain using the task uvcontsub.

# In CASA

uvcontsub(vis = 'Antennae_North.cal.ms',
	  fitspw='0:5~50,0:120~164', solint ='inf', 
	  fitorder = 1, fitmode = 'subtract')

uvcontsub(vis = 'Antennae_South.cal.ms',
	  fitspw='0:5~30,0:120~164', solint ='inf', 
	  fitorder = 1, fitmode = 'subtract')

where:

  • fitspw='0:5~50,0:120~164': Correspond to the line-free channels
  • fitorder = 1: We substract just a first-order polynomial
  • fitmode = 'subtract': Subtract the continuum from all channels. Note that the result is stored in the CORRECTED_DATA column

Clean CO(3-2) line

Next, we clean the CO(3-2) line emission. We obtain the dirty map first with clean and niter=0:

Fig. 5. Cleaning of northern mosaic. The plot shows one of the channels in the interactive cleaning showing CO(3-2) emission. The white region indicates the clean mask considered for this specific channel.
# In CASA
os.system('rm -rf Antennae_North.Line,Antennae_South.Line*')
clean(vis='Antennae_North.cal.ms',
     imagename='Antennae_North.Line.Clean',
     spw='0',field='',phasecenter='12',
     mode='velocity',outframe='LSRK',restfreq='345.79599GHz',
     nchan=60,start='1300km/s',width='10km/s',
     imagermode='mosaic',
     imsize=500,cell='0.2arcsec',
     interactive=T,
     niter=0)

clean(vis='Antennae_South.cal.ms',
     imagename='Antennae_South.Line.Clean',
     spw='0',field='',phasecenter='15',
     mode='velocity',outframe='LSRK',restfreq='345.79599GHz',
     nchan=60,start='1300km/s',width='10km/s',
     imagermode='mosaic',
     imsize=500,cell='0.2arcsec',
     interactive=T,
     niter=0)


Notable parameters include:

  • mode='velocity',outframe='LSRK',restfreq='345.79599GHz',nchan=60,start='1300km/s',width='10km/s': To produce a data cube specified by the number of channels("nchan"=60), and "start" and "width" local standard of rest velocities (starting at 1300 km/s and with velocity widths of 10 km/s). The rest frequency of the CO line is used.
  • start='', nchan=31, width='': To include all 31 channels specified by spw, with no channel averaging
  • niter=0: Maximum number of clean iterations.

The (line-free) channel rms for the northern and southern mosaics are 2.7 mJy/beam and 2.4 mJy/beam, respectively, for 2.3 and 3.8 hours times on source approximately. The ALMA sensitivity calculator gives an on-source observing time of ~3-4 hours to reach a noise level of 2.5 mJy using 12 antennas for an angular resolution of 1 arcsec. Note that the fields are overlapping by 0.5 the size of the primary beam.

We modify the following keywords to clean the mosaics:

# In CASA
minpb=0.2
interactive=T: To do interactive cleaning with the viewer GUI 

#For the Northern mosaic
threshold='4.0mJy'

#For the Southern mosaic
threshold='3.5mJy',
imsize=1000

*minpb=0.2
*interactive=T: To do interactive cleaning with the viewer GUI (read more about this below)
*threshold='5 mJy': Stop cleaning if the maximum residual is below this value.

The threshold is ~ 1.5 the rms of the line-free channel for each dataset. We double the imsize of the southern mosaic to increase the dirty beam, as the emission is quite extended along the mosaic. Using interactive=T the viewer will open when it is ready to start an interactive clean. Step through to the channels to see how extended the emission is. Then either use "All Channels" to define the same clean mask for all channels, or select "This Channel" to select different masks for each channel. Once you have defined a polygon region, you need to double click inside it to save the mask region. You can use the "tape deck" to step through the channels again and check that the emission in all channels fits within the mask(s) you have created. Note that the mask we defined above does not include all emission -- you will have to change the mask interactively! To continue with clean use the "Next action" buttons in the green area on the Viewer Display GUI: The red X will stop clean where you are; the blue arrow will stop the interactive part of clean, but continue to clean non-interactively until reaching the stopping niter or threshold (whichever comes first); and the green arrow will clean until it reaches the "iterations" parameter on the left side of the green area.

When the cleaning has finished, you may want to inspect the resulting data cube

imview (raster={'file': 'Antennae_North.Line.Clean.image'})
imview (raster={'file': 'Antennae_South.Line.Clean.image'})

Moment maps

Next, we make the integrated intensity maps and velocity fields of the CO(3-2) emission using the task immoments. Note that we choose to run the immoments separately for the total intensity map and the velocity field because we want to use different flux thresholds.

For the northern mosaic the moment 0 and 1 can be calculated as follows:

Fig. 6. The CO(3-2) total intensity map (moment 0) of the northern mosaic
Fig. 7. The CO(3-2) velocity field (moment 1) of the northern mosaic
# In CASA
os.system('rm -rf Antennae_North.Line.Clean.Mom.image*') 
immoments('Antennae_North.Line.Clean.image', 
   moments=[0], axis="spec", 
 outfile='Antennae_North.Line.Clean.Mom.image.integrated')

immoments('Antennae_North.Line.Clean.image', 
   moments=[1], axis="spec", 
    mask="Antennae_North.Line.Clean.image>3.5e-2",
   outfile='Antennae_North.Line.Clean.Mom.Mask.image.weighted_coord')

And for the southern mosaic:

Fig. 8. The CO(3-2) total intensity map (moment 0) of the southern mosaic
Fig. 9. The CO(3-2) velocity field (moment 1) of the southern mosaic
# In CASA
os.system('rm -rf Antennae_South.Line.Clean.Mom.image*') 

immoments('Antennae_South.Line.Clean.image', 
   moments=[0], axis="spec",
   outfile='Antennae_South.Line.Clean.Mom.image.integrated')

immoments('Antennae_South.Line.Clean.image', 
   moments=[1], axis="spec", 
   mask="Antennae_South.Line.Clean.image>2.5e-2",
   outfile='Antennae_South.Line.Clean.Mom.Mask.image.weighted_coord')

where:

  • moments=[x]: To specify that we wish to make the xth moment map. The 0th moment map gives integrated emission and the 1st gives the intensity-weighted velocity field
  • axis='spectral': Indicates the moment axis; in this case, 'spectral'
  • mask="Antennae_North.Line.Clean.image>X" Mask applied to the image before calculating the moments. Consider pixels in Antennae_North.Line.Clean.image that are larger than X
  • outfile='result-ngc3256_CO1-0.mom0': The output image name

Finally, we visualize the different moments using imview:

# In CASA
imview (
  raster={'file': 'Antennae_North.Line.Clean.Mom.image.integrated',
  'colorwedge':T,},
  zoom=2, out='Antennae_North.Line.Clean.Mom.image.integrated.png')

imview (
   raster={'file': 'Antennae_North.Line.Clean.Mom.Mask.image.weighted_coord',
   'range': [1500,1750],'colorwedge':T},
   zoom=2, out='Antennae_North.Line.Clean.Mom.Mask.image.velfield.png')

imview (
   raster={'file': 'Antennae_South.Line.Clean.Mom.image.integrated',
   'colorwedge':T},
   zoom=2,out='Antennae_South.Line.Clean.Mom.image.integrated.png')

imview (
   raster={'file': 'Antennae_South.Line.Clean.Mom.Mask.image.weighted_coord',
   'range': [1300,1900],'colorwedge':T},
   zoom=2, out='Antennae_South.Line.Clean.Mom.Mask.image.velfield.png')

Comparison with previous SMA CO(3-2) data

We compare with SMA CO(3-2) data (Ueda, Iono, Petitpas et al., in preparation, to be submitted to ApJ). Figure 13 shows a comparison plot betwee the moment 0 maps of ALMA and SMA data using the viewer. The fluxes, peak locations and large scale structure are consistent. Both southern and northern components have been combined.

Fig. 13. The CO(3-2) total intensity map (moment 0) comparison with SMA data. Colour image is ALMA data, combining southern and northern mosaics. contours show SMA data (Ueda, Iono, Petitpas et al., in preparation, to be submitted to ApJ).

Exporting Fits Images

You can convert from CASA format to FITS if you want to analyze the data using another software package. If you have difficulty with the standard FITS output from CASA, try setting velocity=T and/or dropstokes=T.


# In CASA
exportfits(imagename='Antennae_North.Line.Clean.image',fitsimage='Antennae_North.Line.Clean.image.fits')
exportfits(imagename='Antennae_North.Line.Clean.Mom.image.integrated',fitsimage='Antennae_North.Line.Clean.Mom.image.integrated.fits')
exportfits(imagename='Antennae_North.Line.Clean.Mom.Mask.image.weighted_coord',fitsimage='Antennae_North.Line.Clean.Mom.Mask.image.weighted_coord.fits')
# In CASA
exportfits(imagename='Antennae_South.Line.Clean.image',fitsimage='Antennae_South.Line.Clean.image.fits')
exportfits(imagename='Antennae_South.Line.Clean.Mom.image.integrated',fitsimage='Antennae_South.Line.Clean.Mom.image.integrated.fits')
exportfits(imagename='Antennae_South.Line.Clean.Mom.Mask.image.weighted_coord',fitsimage='Antennae_South.Line.Clean.Mom.Mask.image.weighted_coord.fits')


Daniel Espada 12:00 UT, 21 July 2011