Difference between revisions of "Einstein-Face (CASA 3.2)"

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{{Simulations Intro}}
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''A new version of this page exists for CASA 3.3: [[Einstein-Face (CASA 3.3)]].''
 +
 
'''Simulations using non-science images: the face of Einstein
 
'''Simulations using non-science images: the face of Einstein
 
'''
 
'''
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Simdata can be used to simulate any digitized image. These toy models can be particularly useful for examining the effects of varying uv-coverage on image fidelity if the "truth" model is a familiar object or image. In this example (which is on page 13 of the [http://almatelescope.ca/ALMA-ESPrimer.pdf ALMA Early Science Primer])we use the face of Albert Einstein.
 
Simdata can be used to simulate any digitized image. These toy models can be particularly useful for examining the effects of varying uv-coverage on image fidelity if the "truth" model is a familiar object or image. In this example (which is on page 13 of the [http://almatelescope.ca/ALMA-ESPrimer.pdf ALMA Early Science Primer])we use the face of Albert Einstein.
  
'''Step 1:''' obtain your image. Typically from the internet.
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In this example, we grabbed a JPG image of Einstein's face from the internet.  Simdata likes input images in fits format, so we used Gimp to convert the file.  (Instructions to [[Convert jpg to fits]].)  The original image is shown below. You can grab the converted fits file here from the [http://casaguides.nrao.edu/index.php?title=Sim_Inputs Simulation Inputs CASA Guide page].
  
 
[[File:Einstein.jpg]]
 
[[File:Einstein.jpg]]
  
In this case, it is a jpg file.
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'''Prepare inputs for simdata'''
 
 
'''Step 2:''' Convert your image to FITS
 
 
 
Various software programs have conversion to FITS enabled. The ([http://www.gimp.org GIMP]) was used in this case.
 
A handy list of FITS conversion programs is maintained by GSFC [http://fits.gsfc.nasa.gov/fits_viewer.html here]
 
 
 
For the GIMP, start up the software
 
 
 
>gimp &
 
 
 
and in the main window select "Open" from the "File" menu.
 
 
 
The image will open up in a new window, you can use the GIMP to modify
 
the image (adjust contrast, colormap etc).
 
 
 
Then, select "Save as" from the "File" menu in the window containing the image,
 
and hit "Select File Type" in the dialog box to bring up the file type options, and
 
select "Flexible Image Transport System". Pick a name for your file ending in .fits, e.g. einstein.fits
 
 
 
[[File:Gimp_save.jpg|300px]]
 
  
'''Step 3:''' check your file
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Start with the 10min full science observation. Inputs to simdata are given below. The integration time
 
+
is set much longer than realistic (300s, compared to 1-10s in practice) to speed the computation. The map spacing is set to ensure that only one pointing is observed. The image scale is chosen to ensure good sampling of the beam, and the observation is pointed near the Chandra Deep Field South:
Read your file into e.g. [http://hea-www.harvard.edu/RD/ds9/ ds9]to check that a valid FITS file has been produced. You can
 
also examine the pixel values to examine the scaling of the image. In this case,
 
Einstein's forehead has pixel values around 230 and the background around 40, so there
 
is plenty of contrast. You can also examine the image header in ds9. Under the "File"
 
menu, select "Display FITS Header" and examine the output. Make sure that SIMPLE = T, NAXIS=2 and
 
check BITPIX. In this case, BITPIX=8, which is not valid for reading into CASA, so we need to  
 
change that at the next step.
 
 
 
FITS header produced by GIMP:
 
 
 
SIMPLE  =                    T
 
                                               
 
BITPIX  =                    8
 
                                                 
 
NAXIS  =                    2 
 
                                               
 
NAXIS1  =                  300
 
                                               
 
NAXIS2  =                  327 
 
                                               
 
BZERO  =            0.000000 
 
                                               
 
BSCALE  =            1.000000 
 
                                               
 
DATAMIN =            0.000000 
 
                                               
 
DATAMAX =          255.000000                                                 
 
                                                                               
 
HISTORY THIS FITS FILE WAS GENERATED BY GIMP USING FITSRW                     
 
                                                                               
 
COMMENT FitsRW is (C) Peter Kirchgessner (peter@kirchgessner.net), but available
 
 
 
COMMENT under the GNU general public licence. 
 
                               
 
COMMENT For sources see http://www.kirchgessner.net                           
 
                                                                               
 
COMMENT Image type within GIMP: GIMP_GRAY_IMAGE                               
 
                                                                               
 
END                                                                           
 
 
 
'''Step 4''' Add FITS header keywords and change the format
 
 
 
At this stage, we need to perform some manipulations on the FITS file to get it readable by CASA.
 
For convenience, we are also adding a WCS at this point (though this can also be done in simdata).
 
This routine is written in IDL, using the [http://idlastro.gsfc.nasa.gov/ IDL astronomy library],
 
but similar manipulations can be carried out in IRAF, or using the python PyWCS and PyFITS libraries,
 
available from the [http://www.astropython.org/ astropython project].
 
 
 
The IDL script is in [[File:Make_2dimage.pro.txt]] (remove the .txt from the filename before using).
 
 
 
IDL>make_2dimage,'einstein.fits',0,299,27,326
 
 
 
The IDL code performs the following manipulations:
 
 
 
1) Reads in the FITS file as a 2D array, trims it to 300x300 pixels and converts it to real, 300x300x1 array
 
(the third dimension is added for generality to allow the construction of an image cube, it is
 
not actually necessary in this particular case).
 
 
 
2) Creates header keywords corresponding to the axis types (CTYPE1,2,3) values at the
 
reference pixels (CRVAL1,2,3), the reference pixel positions (CRPIX1,2,3) and the axis
 
increments (CDELT1,2,3), and the epoch (EPOCH).
 
 
 
3) Writes out the modified FITS file as "twodmodel.fits"
 
 
 
'''Step 5''' Start CASA and prepare inputs for simdata
 
 
 
Start with the 10min full science observation:
 
 
 
>casapy
 
  
 
<source lang="python">
 
<source lang="python">
  
 
default 'simdata'
 
default 'simdata'
project = 'fs_cfg8_10m'
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project = 'fs_cfg8_10m' # Full science, configuration 08, 10 minutes
modifymodel = F
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modifymodel = T
skymodel = 'twodmodel.fits'
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skymodel = 'Einstein.fits'
 +
indirection = 'J2000 03h30m00 -28d00m00'
 +
incell = '0.043arcsec'
 +
incenter = '245GHz'
 +
inwidth = '2GHz'
 
setpointings = T
 
setpointings = T
 
integration = '300s'
 
integration = '300s'
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pointingspacing = '1arcmin'
 
pointingspacing = '1arcmin'
 
predict = T
 
predict = T
 +
graphics = 'both'
 
</source>
 
</source>
  
 
Antenna configuration:  
 
Antenna configuration:  
ALMA antenna configuration files are stored in a directory that depends on your CASA installation  
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ALMA antenna configuration files are stored in a directory that depends on your CASA installation.
to be sure of finding them, identify the CASAPATH variable using the os.getenv command, and pick
+
To be sure of finding them, identify the CASAPATH variable using the os.getenv command, and pick
 
the configuration you want. Details on configuration choices are given in the  
 
the configuration you want. Details on configuration choices are given in the  
[[http://casaguides.nrao.edu/index.php?title=M51_at_z_%3D_0.1_and_z_%3D_0.3] M51 simulation guide].
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M51 simulation guide [http://casaguides.nrao.edu/index.php?title=M51_at_z_%3D_0.1_and_z_%3D_0.3].
  
  
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repodir=os.getenv("CASAPATH").split(' ')[0]
 
repodir=os.getenv("CASAPATH").split(' ')[0]
 
antennalist        =  repodir+"/data/alma/simmos/alma.out08.cfg"
 
antennalist        =  repodir+"/data/alma/simmos/alma.out08.cfg"
refdate = '2012/05/21/22:00:00'
 
 
totaltime = '600s'
 
totaltime = '600s'
 
thermalnoise = ""
 
thermalnoise = ""
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weighting = 'natural'
 
weighting = 'natural'
 
analyze=F
 
analyze=F
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overwrite=T
 
simdata
 
simdata
 
</source>
 
</source>
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<source lang="python">
 
<source lang="python">
 
tget simdata
 
tget simdata
project = 'fs_cfg8_1hr'
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project = 'fs_cfg8_1hr' # Full science, configuration 08, 1 hour
 
totaltime = '3600s'
 
totaltime = '3600s'
 
simdata
 
simdata
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Which should look something like: [[File:einstein_fs_cfg8_1hr.gif]]
 
Which should look something like: [[File:einstein_fs_cfg8_1hr.gif]]
  
Note that the image quality is noticeably better in this ~full track image, even in Full Science.
+
Finally, two Early Science simulations, using the extended configuration. One 10min simulation:
 
 
Finally, two Early Science simulations, using the 250m configuration. One 10min simulation:
 
  
 
<source lang="python">
 
<source lang="python">
 
tget simdata
 
tget simdata
project = 'es_cfg250_10m'
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project = 'es_extended_10m'
antennalist = repodir+"/data/alma/simmos/alma.early.250m.cfg"
+
antennalist = repodir+"/data/alma/simmos/alma.cycle0.extended.cfg"
 
totaltime = '600s'
 
totaltime = '600s'
 
simdata
 
simdata
 
</source>
 
</source>
  
which looks like this: [[File:einstein_es_cfg250_10min.gif]]
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which looks like this: [[File:einstein_es_extended_10min.gif]]
  
 
and a 4hr simulation:
 
and a 4hr simulation:
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<source lang="python">
 
<source lang="python">
 
tget simdata
 
tget simdata
project = 'es_cfg250_4hr'
+
project = 'es_extended_4hr'
 
totaltime = '14400s'
 
totaltime = '14400s'
 
simdata
 
simdata
 
</source>
 
</source>
  
which looks like this: [[File:einstein_es_cfg250_4hr.gif]]
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which looks like this: [[File:einstein_es_extended_4hr.gif]]
  
 
'''Further experiments:'''
 
'''Further experiments:'''
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The result is: [[File:einstein_fs_cfg16_1hr.gif]]
 
The result is: [[File:einstein_fs_cfg16_1hr.gif]]
 +
 +
{{Simulations Intro}}

Latest revision as of 15:07, 21 October 2011

Simulating Observations in CASA

A new version of this page exists for CASA 3.3: Einstein-Face (CASA 3.3).

Simulations using non-science images: the face of Einstein

Simdata can be used to simulate any digitized image. These toy models can be particularly useful for examining the effects of varying uv-coverage on image fidelity if the "truth" model is a familiar object or image. In this example (which is on page 13 of the ALMA Early Science Primer)we use the face of Albert Einstein.

In this example, we grabbed a JPG image of Einstein's face from the internet. Simdata likes input images in fits format, so we used Gimp to convert the file. (Instructions to Convert jpg to fits.) The original image is shown below. You can grab the converted fits file here from the Simulation Inputs CASA Guide page.

Einstein.jpg

Prepare inputs for simdata

Start with the 10min full science observation. Inputs to simdata are given below. The integration time is set much longer than realistic (300s, compared to 1-10s in practice) to speed the computation. The map spacing is set to ensure that only one pointing is observed. The image scale is chosen to ensure good sampling of the beam, and the observation is pointed near the Chandra Deep Field South:

default 'simdata'
project = 'fs_cfg8_10m'  # Full science, configuration 08, 10 minutes
modifymodel = T
skymodel = 'Einstein.fits'
indirection = 'J2000 03h30m00 -28d00m00'
incell = '0.043arcsec'
incenter = '245GHz'
inwidth = '2GHz'
setpointings = T
integration = '300s'
mapsize = ['1arcmin','1arcmin']
maptype = 'hexagonal'
pointingspacing = '1arcmin'
predict = T
graphics = 'both'

Antenna configuration: ALMA antenna configuration files are stored in a directory that depends on your CASA installation. To be sure of finding them, identify the CASAPATH variable using the os.getenv command, and pick the configuration you want. Details on configuration choices are given in the M51 simulation guide [1].


repodir=os.getenv("CASAPATH").split(' ')[0]
antennalist        =  repodir+"/data/alma/simmos/alma.out08.cfg"
totaltime = '600s'
thermalnoise = ""
image = T
vis = '$project.ms'
imsize = [300,300]
cell = '0.043arcsec'
niter = 2000
weighting = 'natural'
analyze=F
overwrite=T
simdata

The output image should have a synthesized beam of 0.62"x0.56" and look something like: Einstein fs cfg8 10min.gif

Now we repeat for an 1hr observation:

tget simdata
project = 'fs_cfg8_1hr'  # Full science, configuration 08, 1 hour
totaltime = '3600s'
simdata

Which should look something like: Einstein fs cfg8 1hr.gif

Finally, two Early Science simulations, using the extended configuration. One 10min simulation:

tget simdata
project = 'es_extended_10m'
antennalist = repodir+"/data/alma/simmos/alma.cycle0.extended.cfg"
totaltime = '600s'
simdata

which looks like this: Einstein es extended 10min.gif

and a 4hr simulation:

tget simdata
project = 'es_extended_4hr'
totaltime = '14400s'
simdata

which looks like this: Einstein es extended 4hr.gif

Further experiments:

Some more things to try:

An 8hr observation shows the improvement obtained by obtaining fuller uv-coverage in the full science array:

tget simdata
antennalist = repodir+"/data/alma/simmos/alma.out08.cfg"
project = 'fs_cfg8_8hr'
totaltime = '28800s'
simdata

Which should look something like: Einstein fs cfg8 8hr.gif

An attempt to make a higher resolution image shows what happens when short spacings are missing in the configuration. Configuration 16 has a 0.17x0.15 beam, still better than Nyquist sampling of the model image (which has 0.043" pixels). However, the lack of short spacings in the configuration leads to poorly sampled structure on large spatial scales. In practice, one would need to combine these observations with a set in a more compact configuration (such as 8) to sample both the large and small spatial structures.

tget simdata
antennalist = repodir+"/data/alma/simmos/alma.out16.cfg"
project = 'fs_cfg16_1hr'
totaltime = '3600s'
simdata

The result is: Einstein fs cfg16 1hr.gif

Simulating Observations in CASA