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| The first few tutorials provided us with a spectral line data cube and a continuum image. Next we'd like to
| | #REDIRECT [[First_Look_at_Image_Analysis_CASA_6.5.4]] |
| understand some of the properties of the images that we have produced.
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| In case you don't have the images from the first tutorials handy, let's start by copying the image files from the working_data directory to our current directory:
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| <source lang="python">
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| # In CASA
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| os.system("rm -rf sis14_twhya_cont.image")
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| os.system("cp -r ../working_data/sis14_twhya_cont.image .")
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| os.system("rm -rf sis14_twhya_n2hp.image")
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| os.system("cp -r ../working_data/sis14_twhya_n2hp.image .")
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| </source>
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| Recall that we orient ourselves with measurement sets (UV data) using the {{listobs}} task.
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| For images, an analogous way to get basic header information is to use the {{imhead}} task.
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| <source lang="python">
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| # In CASA
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| imhead("sis14_twhya_cont.image")
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| imhead("sis14_twhya_n2hp.image")
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| </source>
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| CASA prints the image header information to the logger:
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| <pre style="background-color: #fffacd;">
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| imhead ##########################################
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| imhead ##### Begin Task: imhead #####
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| imhead imhead(imagename="sis14_twhya_cont.image",mode="summary",hdkey="",hdvalue="",verbose=False)
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| ImageMetaData
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| ImageMetaData Image name : sis14_twhya_cont.image
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| ImageMetaData Object name : TW Hya
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| ImageMetaData Image type : PagedImage
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| ImageMetaData Image quantity : Intensity
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| ImageMetaData Pixel mask(s) : None
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| ImageMetaData Region(s) : None
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| ImageMetaData Image units : Jy/beam
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| ImageMetaData Restoring Beam : 0.789582 arcsec, 0.551785 arcsec, -58.4646 deg
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| ImageMetaData
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| ImageMetaData Direction reference : J2000
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| ImageMetaData Spectral reference : LSRK (-> TOPO)
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| ImageMetaData Velocity type : RADIO
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| ImageMetaData Rest frequency : 3.72637e+11 Hz
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| ImageMetaData Pointing center : 11:01:51.796000 -34.42.17.366000
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| ImageMetaData Telescope : ALMA
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| ImageMetaData Observer : cqi
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| ImageMetaData Date observation : 2012/11/19/07:37:00
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| ImageMetaData Telescope position: [2.22506e+06m, -5.44006e+06m, -2.48168e+06m] (ITRF)
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| ImageMetaData
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| ImageMetaData Axis Coord Type Name Proj Shape Tile Coord value at pixel Coord incr Units
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| ImageMetaData ----------------------------------------------------------------------------------------------------
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| ImageMetaData 0 0 Direction Right Ascension SIN 256 256 11:01:51.796 128.00 -1.000000e-01 arcsec
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| ImageMetaData 1 0 Direction Declination SIN 256 256 -34.42.17.366 128.00 1.000000e-01 arcsec
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| ImageMetaData 2 1 Stokes Stokes 1 1 I
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| ImageMetaData 3 2 Spectral Frequency 1 1 3.72637e+11 0.00 2.35055441345e+08 Hz
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| ImageMetaData Velocity 0 0.00 -1.891126e+02 km/s
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| imhead ##### End Task: imhead #####
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| imhead ##########################################
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| imhead ##########################################
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| imhead ##### Begin Task: imhead #####
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| imhead imhead(imagename="sis14_twhya_n2hp.image",mode="summary",hdkey="",hdvalue="",verbose=False)
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| ImageMetaData
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| ImageMetaData Image name : sis14_twhya_n2hp.image
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| ImageMetaData Object name : TW Hya
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| ImageMetaData Image type : PagedImage
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| ImageMetaData Image quantity : Intensity
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| ImageMetaData Pixel mask(s) : mask0
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| ImageMetaData Region(s) : None
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| ImageMetaData Image units : Jy/beam
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| ImageMetaData Restoring Beam : 0.709488 arcsec, 0.469052 arcsec, -53.779 deg
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| ImageMetaData
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| ImageMetaData Direction reference : J2000
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| ImageMetaData Spectral reference : LSRK
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| ImageMetaData Velocity type : RADIO
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| ImageMetaData Rest frequency : 3.72672e+11 Hz
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| ImageMetaData Pointing center : 11:01:51.796000 -34.42.17.366000
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| ImageMetaData Telescope : ALMA
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| ImageMetaData Observer : cqi
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| ImageMetaData Date observation : 2012/11/19/07:56:27
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| ImageMetaData Telescope position: [2.22506e+06m, -5.44006e+06m, -2.48168e+06m] (ITRF)
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| ImageMetaData
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| ImageMetaData Axis Coord Type Name Proj Shape Tile Coord value at pixel Coord incr Units
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| ImageMetaData --------------------------------------------------------------------------------------------------
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| ImageMetaData 0 0 Direction Right Ascension SIN 250 125 11:01:51.796 125.00 -8.000000e-02 arcsec
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| ImageMetaData 1 0 Direction Declination SIN 250 50 -34.42.17.366 125.00 8.000000e-02 arcsec
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| ImageMetaData 2 1 Stokes Stokes 1 1 I
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| ImageMetaData 3 2 Spectral Frequency 15 5 3.72672e+11 0.00 -6.21550826e+05 Hz
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| ImageMetaData Velocity 0 0.00 5.000000e-01 km/s
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| imhead ##### End Task: imhead #####
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| imhead ##########################################
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| </pre>
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| == Statistics ==
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| Often we'd like to measure basic image
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| statistics and fluxes. Recall you can do these operations pretty easily in the viewer, by
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| dragging out a box and then right-double clicking inside it to get statistics for that region. You can also get statistics using the {{imstat}} task.
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| <source lang="python">
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| # In CASA
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| my_stats = imstat("sis14_twhya_n2hp.image", chans="0~4")
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| </source>
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| The {{imstat}} task returns a python dictionary, and you can examine the contents as follows:
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| <source lang="python">
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| # In CASA
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| print my_stats
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| print my_stats['rms']
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| </source>
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| It's useful to see that the RMS is about 20 mJy/beam in the
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| line cube.
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| You can also just print the dictionary to the terminal screen:
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| <source lang="python">
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| # In CASA
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| imstat("sis14_twhya_n2hp.image", chans="0~4")
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| </source>
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| This task is useful for measuring basic source characteristics. For example,
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| calculate the statistics for a box encompassing the disk - you see that the
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| integrated flux is about 1.5 Jy.
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| <source lang="python">
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| # In CASA
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| imstat("sis14_twhya_cont.image", box="100,100,150,150")
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| my_stats = imstat("sis14_twhya_cont.image", box="100,100,150,150")
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| print my_stats['flux']
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| </source>
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| Alternatively, a box defined off the disk will give image noise statistics.
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| <source lang="python">
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| # In CASA
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| imstat("sis14_twhya_cont.image", box="25,150,225,200")
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| </source>
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| == Moments ==
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| For the spectral line cube, it's very useful to "collapse" the cube in
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| various ways to analyze the emission. The {{immoments}} task lets you do
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| this.
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| The first few "moments" are defined as follows:
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| <pre>
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| moments = -1 : mean value of the spectral coordinate
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| moments = 0 : integrated value of the spectral coordinate
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| moments = 1 : intensity weighted coordinate; traditionally used to get 'velocity fields'
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| moments = 2 : intensity weighted dispersion of the coordinate; traditionally used to get "velocity dispersion"
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| </pre>
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| A more complete description of image moments is given [http://casa.nrao.edu/docs/CasaRef/image.moments.html here in the CASA reference manual].
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| <figure id="Imaging-tutorial-analysis-mom0.png">
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| [[File:Imaging-tutorial-analysis-mom0.png|thumb|<caption>The zero moment of the N2H+ image.</caption>]]
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| </figure>
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| Let's make a moment 0 image clipped at ~1 sigma:
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| <source lang="python">
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| # In CASA
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| os.system("rm -rf sis14_twhya_n2hp.mom0")
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| immoments("sis14_twhya_n2hp.image",
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| outfile="sis14_twhya_n2hp.mom0",
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| includepix=[20e-3,100],
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| chans="4~12",
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| moments=0)
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| </source>
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| Make a moment 1 image clipped at ~2 sigma:
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| <source lang="python">
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| # In CASA
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| os.system("rm -rf sis14_twhya_n2hp.mom1")
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| immoments("sis14_twhya_n2hp.image",
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| outfile="sis14_twhya_n2hp.mom1",
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| includepix=[40e-3,100],
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| chans="4~12",
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| moments=1)
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| </source>
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| At this point we have a few really neat things to see: first the
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| line shows a hole in the middle. Overlay it on the dust (continuum)
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| disk using the viewer and you can notice that they align but with the N2H+
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| existing only outside a certain radius - in this case the "snow line".
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| Also have a look at the velocity field to see the rotation of the
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| disk.
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| The {{imview}} task has some command-line scripting capability. For example, here we show how to overlay the line moment
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| 0 (as a contour plot) on the continuum.
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| <figure id="Imaging-tutorial-analysis-overlay.png">
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| [[File:Imaging-tutorial-analysis-overlay.png|thumb|<caption>The N2H+ moment zero map as contours, overlaid on the continuum emission of TW Hydra. The plot demonstrates the "show line".</caption>]]
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| </figure>
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| <source lang="python">
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| # In CASA
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| imview(raster={'file': 'sis14_twhya_cont.image',
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| 'range': [-0.01,0.5]},
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| contour={'file': 'sis14_twhya_n2hp.mom0',
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| 'levels': [0.5,0.6,0.7,0.8] })
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| </source>
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| == Export FITS images ==
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| CASA is great (of course) but you will ultimately want to export
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| your data to a common format to analyze in other programs, share
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| with other astronomers, or archive. It's easy to export images from
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| CASA's image format to FITS images via the {{exportfits}} command.
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| <source lang="python">
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| # In CASA
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| exportfits(imagename="sis14_twhya_cont.image",
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| fitsimage="twhya_cont.fits",
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| overwrite=True)
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| </source>
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| For the cube we want to specify additionally that the frequency axis
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| will be written out as velocity.
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| <source lang="python">
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| # In CASA
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| exportfits(imagename="sis14_twhya_n2hp.image",
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| fitsimage="twhya_n2hp.fits",
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| velocity=True,
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| overwrite=True)
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| </source>
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