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| '''This guide is written for CASA 5.7 and uses Python 2. TFor the most recent CASA version, using python 3 see [https://casaguides.nrao.edu/index.php?title=First_Look_at_Image_Analysis_CASA_6 First Look at Image Analysis CASA 6]'''
| | #REDIRECT [[First_Look_at_Image_Analysis_CASA_6.6.1]] |
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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
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| 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/ 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/sis14_twhya_cont.image .")
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| os.system("rm -rf twhya_n2hp.image")
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| os.system("cp -r ../working/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("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) : 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 : 0.830341 arcsec, 0.683704 arcsec, -66.1199 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 : 3.72637e+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 : 2012/11/19/07:56:27
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| ImageMetaData Telescope position: [2.22514e+06m, -5.44031e+06m, -2.48103e+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 250 250 11:01:51.796 125.00 -1.000000e-01 arcsec
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| ImageMetaData 1 0 Direction Declination SIN 250 250 -34.42.17.366 125.00 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 2.34445114878e+08 Hz
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| ImageMetaData Velocity 0 0.00 -1.886149e+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="twhya_n2hp.image",mode="summary",hdkey="",hdvalue="",verbose=False)
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| ImageMetaData
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| ImageMetaData Image name : 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 : 0.750766 arcsec, 0.598023 arcsec, -59.397 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: [2.22514e+06m, -5.44031e+06m, -2.48103e+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 3.726725e+11 0.00 -6.21550810e+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("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 26 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("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 1.8 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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| [[File:Imaging-tutorial-analysis-mom0_5.7.png|thumb|<caption>The zero moment of the N2H+ image.</caption>]]
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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("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("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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| [[File:Imaging-tutorial-analysis-overlay_5.7.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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| <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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| 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.
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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="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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