Examples of various rst directives

Here’s a cheatsheet.

Code

Example:

import parser
b = parser.Parser("myfile.xml")

def my_function():
    "just a test"
    print 8/2

end example.

Include a python file:

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#! /usr/bin/env casarun
#
#
#   admit4.py :  example flow to read in an ascii spectrum and run it through LineSegments and LineID
#                The spectrum needs freq (in GHz) in col1 and intensity (arbitrary units) in col5.
#
#   Usage:      $ADMIT/admit/test/admit4.py  [options] spectrum.tab
#
#   this will create a spectrum.admit directory with all the BDP's and associated data products inside.
#
#   Note that the current ADMIT will create files like testCubeSpectrum.tab, testCubeStats.tab and
#   testPVCorr.tab inside the .admit directory for you to run them through admit4.py
#
#   A typical run with 100 channels takes about 10" (fair amount of casa overhead,
#   even though none is used here; cpu in the 3 tasks is only little over 4")
#
#   time $ADMIT/admit/test/admit4.py --alias x testCubeSpectrum.tab > testCubeSpectrum.tab.log
#   7.584u 2.345s 0:10.15 97.7%	0+0k 0+2584io 0pf+0w
#   TIMING : Dtime: CubeSpectrum END [ 0.294537   0.4536109]
#   TIMING : Dtime: LineSegment END [ 2.14727     2.17343116]
#   TIMING : Dtime: LineID END [ 2.105823    2.14143705]
#
#   Options:
#   -a  alias          (doesn't actually work)
#   -r  apar_file
#   -o  output_dir
#   -s  stop_label
#
#   @todo  make it also understand bdp's
#
# =================================================================================================================
# python system modules
import sys, os, math
import argparse as ap

import admit

version  = '30-mar-2016'

#  ===>>> set some parameters for this run <<<=================================================================
#
#  !!! do not change these defaults, these are meant to be our desired defaults    !!!
#  !!! in an ideal universe. Instead, use the commented section below to enable    !!!
#  !!! them, or add your favorites to some new value to experiment with.           !!!


file     = ''               # the default FITS input name to be ingested (basename is used for apar file)
alias    = ''               # -a --alias : use a short alias instead of the possibly long basename?
apar     = ''               # -r --apar:   add this apar as well (file.apar is also checked for)
out      = ''               # -o --out:    alternative output admit name (instead of file.admit)
stop     = ''               # -s --stop:   early labeled bailout ('ingest', ...)

plot     = 't'              #
#
vlsr     = 0.0              # either set it below, or make get_vlsr() to work (else vlsr=0 will be used)
plotmode = admit.PlotControl.BATCH # NOPLOT, BATCH, INTERACTIVE, SHOW_AT_END
plottype = admit.PlotControl.PNG   # PNG, JPG, etc.
loglevel = 10               # 10=DEBUG, 15=TIMING 20=INFO 30=WARNING 40=ERROR 50=FATAL
#
doClean  = True
lineUID  = False            # if True, this would run LineID(identifylines=False) [old relic]
linepar  = ()               # if set, (numsigma,minchan,maxgap)
llsmooth = []               # smooothing for LineSegment and LineID
iterate  = True             #
csub     = None             # or 0,1,2,....
online   = False
tier1width = 0.0            #
#
reflist  = 'etc/co_lines.list'    # pick one from $ADMIT/etc
#-----------------------------------------------------------------------------------------------------------------------
#-------------------- command line parsing -----------------------------------------------------------------------------
#                     @todo cannot overload casa, it parses first (e.g. -c)
sys.argv = admit.utils.casa_argv(sys.argv)

parser = ap.ArgumentParser(description='Process a single FITS continuum and optional PB correction')
parser.add_argument('-a','--alias' ,nargs=1, help='Alias')
parser.add_argument('-o','--out'   ,nargs=1, help='Optional output admit directory basename, instead derived from file')
parser.add_argument('-r','--apar'  ,nargs=1, help='ADMIT parameter file (in addition to "file.apar"')
parser.add_argument('-s','--stop'  ,nargs=1, help='early bailout label')
parser.add_argument('file'         ,nargs=1, help='FITSMap (or CASA image, or MIRIAD image)')
parser.add_argument('--version', action='version', version='%(prog)s ' + version)
try:
    args = vars(parser.parse_args())
except:
    sys.exit(1)

if args['file']   != None: file   = args['file'][0]
if args['alias']  != None: alias  = args['alias'][0]
if args['apar']   != None: apar   = args['apar'][0]
if args['out']    != None: out    = args['out'][0]
if args['stop']   != None: stop   = args['stop'][0]

admit.utils.assert_files([file])                # this will halt the script if something doesn't exist

#if plot == "f": 
#    plotmode=admit.PlotControl.NONE

#-----------------------------------------------------------------------------------------------------------------------
#------------------------------------------------------- start of script -----------------------------------------------

#  announce version
print 'ADMIT4: Version ',version

#  do the work in a proper ".admit" directory
adir =  admit.utils.admit_dir(file,out)
#   dirty method, it really should check if adir is an admit directory
if doClean and adir != file:
    print "Removing previous results from ",adir
    os.system('rm -rf %s' % adir)
    create=True
else:
    create=False


# parse apar file(s) first, overwriting local apar variables
for ap1 in ['admit4.apar', file+".apar", apar]:         # loop over 3 possible apar files, set parameters
    if ap1 != "" and os.path.isfile(ap1):
        print "Found parameter file ",ap1
        execfile(ap1)
        
a = admit.Project(adir,name='Testing ADMIT4 style pipeline - version %s' % version,create=create,loglevel=loglevel)

if a.new:
    print "Starting a new ADMIT using ",file
    cmd = 'cp -a %s %s' % (sys.argv[0],adir)
    os.system(cmd)
    a.set(admit_dir=adir)
    #
    for ap in ['admit4.apar', file+".apar", apar]:         # loop over 3 possible apar files
        if ap != "" and os.path.isfile(ap):
            print "Found parameter file ",ap
            os.system('cp %s %s' % (ap,adir))
else:
    print "All done, we just read an existing admit.xml and it should do nothing"
    print "Use admit0.py to re-run inside of your admit directory"
    #
    a.fm.diagram(a.dir()+'admit.dot')
    a.show()
    a.showsetkey()
    sys.exit(0)      # doesn't work in IPython!

# Default ADMIT plotting environment
a.plotparams(plotmode,plottype)

# GenerateSpectrum
# here we use a little backdoor in GenerateSpectrum_AT that reads in
# a spectrum 
gs1 = a.addtask(admit.GenerateSpectrum_AT(file=file,seed=-1,alias=alias))
gstab1 = (gs1,0)

if stop == 'generate':  a.exit(1)

# LineSegment
ls1 = a.addtask(admit.LineSegment_AT(),[gstab1])
if len(linepar) > 0:
    a[ls1].setkey('numsigma',linepar[0])
    a[ls1].setkey('minchan', linepar[1])
    a[ls1].setkey('maxgap',  linepar[2])
a[ls1].setkey('csub',[0,csub])
a[ls1].setkey('iterate',iterate)
a[ls1].setkey('smooth',llsmooth)
lstab1 = (ls1,0)

if stop == 'segment':  a.exit(1)

# LineID
ll1 = a.addtask(admit.LineID_AT(),[gstab1])
if len(linepar) > 0:
    a[ll1].setkey('numsigma',linepar[0])
    a[ll1].setkey('minchan', linepar[1])
    a[ll1].setkey('maxgap',  linepar[2])
if lineUID:
    a[ll1].setkey('identifylines',False)
a[ll1].setkey('csub',[0,csub])
a[ll1].setkey('iterate',iterate)
a[ll1].setkey('smooth',llsmooth)
a[ll1].setkey('vlsr',vlsr)
a[ll1].setkey('references',reflist)
a[ll1].setkey('online',online)
a[ll1].setkey('tier1width',tier1width)

lltab1 = (ll1,0)

# finish off !
a.run()

a.showsetkey(adir+'/admit.apar')

end include

Math

\[(project_{out},AT_{out},BDP_{out},project_{in},AT_{in},BDP_{in})\]

Image

_images/connection.png

Figure

A figure

Example Flow.

Figure 1: The connection in this diagram connects two ATs, a1 and a2, inside a single project p0. The output BDP of a1 is an input BDP of a2, i.e., \(b1 \equiv b2\). A given output BDP may be the input to an arbitrary number of ATs, but can be the output one and only one AT. For virtual projects, the first and fourth indices in the tuple, i1 and i2, would differ.

Notes, See Also, Todo

Note

This is a note box. I have found that you have to end the note with a ”..” comment indicator on the following line or the note absorbed everything below it at the same indent level.

Normal text here.

Design Style AT1

Description

A description of purpose of this AT.

Use Case

At least one example use case that demonstrates how this AT fits in a typical flow.

Input BDPs

Description of input BDP(s), but note that the detailed contents of the BDPs are described elsewhere.

  • SomeName1_BDP - bla bla
  • SomeName2_BDP - bla bla

Input Keywords

Description of required and optional keywords.

  • key1 - bla bla
  • key2 - bla bla

Output BDPs

Description of output BDP(s), and their optional output graphics. The naming convention of output BDP(s) is also useful to add here, as they are normally automated (some AT’s allow you to set them explicitly).

  • SomeName1_BDP - bla bla
  • SomeName2_BPD - bla bla

Procedure

The procedure the AT uses to achieve its goals.

CASA Tasks Used

What CASA tasks (or tools) it uses.

  • task1 - bla bla
  • task2 - bla bla
  • tool3 - bla bla

Design Style AT2

Description

Some description.

Use Case

Some use case

Input BDPs

  • SomeName1 - bla bla
  • SomeName2 - bla bla

Input Keywords

  • key1 - bla bla
  • key2 - bla bla

Output BDPs

  • SomeName1 - bla bla
  • SomeName1 - bla bla

Procedure

The procedure

CASA Tasks Used

  • task1 - bla bla
  • task2 - bla bla

User Guide Examples

And here we will add some user guide examples.

See also

This is a see-also box.

Todo

This is a to-do box. (why is it not in a box??)