| 1 | """
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| 2 | This is the ATNF Single Dish Analysis package.
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| 3 |
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| 4 | """
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| 5 | import os,sys
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| 6 |
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| 7 | def _validate_bool(b):
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| 8 | 'Convert b to a boolean or raise'
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| 9 | bl = b.lower()
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| 10 | if bl in ('f', 'no', 'false', '0', 0): return False
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| 11 | elif bl in ('t', 'yes', 'true', '1', 1): return True
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| 12 | else:
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| 13 | raise ValueError('Could not convert "%s" to boolean' % b)
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| 14 |
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| 15 | def _validate_int(s):
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| 16 | 'convert s to int or raise'
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| 17 | try: return int(s)
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| 18 | except ValueError:
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| 19 | raise ValueError('Could not convert "%s" to int' % s)
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| 20 |
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| 21 | def _asap_fname():
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| 22 | """
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| 23 | Return the path to the rc file
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| 24 |
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| 25 | Search order:
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| 26 |
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| 27 | * current working dir
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| 28 | * environ var ASAPRC
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| 29 | * HOME/.asaprc
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| 30 |
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| 31 | """
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| 32 |
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| 33 | fname = os.path.join( os.getcwd(), '.asaprc')
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| 34 | if os.path.exists(fname): return fname
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| 35 |
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| 36 | if os.environ.has_key('ASAPRC'):
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| 37 | path = os.environ['ASAPRC']
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| 38 | if os.path.exists(path):
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| 39 | fname = os.path.join(path, '.asaprc')
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| 40 | if os.path.exists(fname):
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| 41 | return fname
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| 42 |
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| 43 | if os.environ.has_key('HOME'):
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| 44 | home = os.environ['HOME']
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| 45 | fname = os.path.join(home, '.asaprc')
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| 46 | if os.path.exists(fname):
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| 47 | return fname
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| 48 | return None
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| 49 |
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| 50 |
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| 51 | defaultParams = {
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| 52 | # general
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| 53 | 'verbose' : [True, _validate_bool],
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| 54 | 'useplotter' : [True, _validate_bool],
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| 55 | 'insitu' : [True, _validate_bool],
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| 56 |
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| 57 | # plotting
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| 58 | 'plotter.gui' : [True, _validate_bool],
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| 59 | 'plotter.stacking' : ['p', str],
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| 60 | 'plotter.panelling' : ['s', str],
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| 61 | 'plotter.colours' : ['', str],
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| 62 | 'plotter.linestyles' : ['', str],
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| 63 | 'plotter.decimate' : [False, _validate_bool],
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| 64 | 'plotter.ganged' : [True, _validate_bool],
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| 65 |
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| 66 | # scantable
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| 67 | 'scantable.save' : ['ASAP', str],
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| 68 | 'scantable.autoaverage' : [True, _validate_bool],
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| 69 | 'scantable.freqframe' : ['LSRK', str], #default frequency frame
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| 70 | 'scantable.allaxes' : [True, _validate_bool], # apply action to all axes
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| 71 | 'scantable.plotter' : [True, _validate_bool], # use internal plotter
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| 72 | 'scantable.verbosesummary' : [False, _validate_bool]
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| 73 |
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| 74 | # fitter
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| 75 | }
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| 76 |
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| 77 | def list_rcparameters():
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| 78 |
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| 79 | print """
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| 80 | # general
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| 81 | # print verbose output
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| 82 | verbose : True
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| 83 |
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| 84 | # preload a default plotter
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| 85 | useplotter : True
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| 86 |
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| 87 | # apply operations on the input scantable or return new one
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| 88 | insitu : True
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| 89 |
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| 90 | # plotting
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| 91 |
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| 92 | # do we want a GUI or plot to a file
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| 93 | plotter.gui : True
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| 94 |
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| 95 | # default mode for colour stacking
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| 96 | plotter.stacking : Pol
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| 97 |
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| 98 | # default mode for panelling
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| 99 | plotter.panelling : scan
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| 100 |
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| 101 | # push panels together, to share axislabels
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| 102 | plotter.ganged : True
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| 103 |
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| 104 | # decimate the number of points plotted bya afactor of
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| 105 | # nchan/1024
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| 106 | plotter.decimate : False
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| 107 |
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| 108 | # default colours/linestyles
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| 109 | plotter.colours :
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| 110 | plotter.linestyles :
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| 111 |
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| 112 | # scantable
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| 113 | # default ouput format when saving
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| 114 | scantable.save : ASAP
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| 115 | # auto averaging on read
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| 116 | scantable.autoaverage : True
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| 117 |
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| 118 | # default frequency frame to set when function
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| 119 | # scantable.set_freqfrmae is called
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| 120 | scantable.freqframe : LSRK
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| 121 |
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| 122 | # apply action to all axes not just the cursor location
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| 123 | scantable.allaxes : True
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| 124 |
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| 125 | # use internal plotter
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| 126 | scantable.plotter : True
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| 127 |
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| 128 | # Control the level of information printed by summary
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| 129 | scantable.verbosesummary : False
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| 130 |
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| 131 | # Fitter
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| 132 | """
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| 133 |
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| 134 | def rc_params():
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| 135 | 'Return the default params updated from the values in the rc file'
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| 136 |
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| 137 | fname = _asap_fname()
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| 138 |
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| 139 | if fname is None or not os.path.exists(fname):
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| 140 | message = 'could not find rc file; returning defaults'
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| 141 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
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| 142 | #print message
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| 143 | return ret
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| 144 |
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| 145 | cnt = 0
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| 146 | for line in file(fname):
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| 147 | cnt +=1
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| 148 | line = line.strip()
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| 149 | if not len(line): continue
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| 150 | if line.startswith('#'): continue
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| 151 | tup = line.split(':',1)
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| 152 | if len(tup) !=2:
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| 153 | print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
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| 154 | continue
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| 155 |
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| 156 | key, val = tup
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| 157 | key = key.strip()
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| 158 | if not defaultParams.has_key(key):
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| 159 | print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
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| 160 | continue
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| 161 |
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| 162 | default, converter = defaultParams[key]
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| 163 |
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| 164 | ind = val.find('#')
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| 165 | if ind>=0: val = val[:ind] # ignore trailing comments
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| 166 | val = val.strip()
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| 167 | try: cval = converter(val) # try to convert to proper type or raise
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| 168 | except Exception, msg:
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| 169 | print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
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| 170 | continue
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| 171 | else:
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| 172 | # Alles Klar, update dict
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| 173 | defaultParams[key][0] = cval
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| 174 |
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| 175 | # strip the conveter funcs and return
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| 176 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
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| 177 | print ('loaded rc file %s'%fname)
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| 178 |
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| 179 | return ret
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| 180 |
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| 181 |
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| 182 | # this is the instance used by the asap classes
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| 183 | rcParams = rc_params()
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| 184 |
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| 185 | rcParamsDefault = dict(rcParams.items()) # a copy
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| 186 |
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| 187 | def rc(group, **kwargs):
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| 188 | """
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| 189 | Set the current rc params. Group is the grouping for the rc, eg
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| 190 | for scantable.save the group is 'scantable', for plotter.stacking, the
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| 191 | group is 'plotter', and so on. kwargs is a list of attribute
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| 192 | name/value pairs, eg
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| 193 |
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| 194 | rc('scantable', save='SDFITS')
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| 195 |
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| 196 | sets the current rc params and is equivalent to
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| 197 |
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| 198 | rcParams['scantable.save'] = 'SDFITS'
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| 199 |
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| 200 | Use rcdefaults to restore the default rc params after changes.
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| 201 | """
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| 202 |
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| 203 | aliases = {}
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| 204 |
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| 205 | for k,v in kwargs.items():
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| 206 | name = aliases.get(k) or k
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| 207 | key = '%s.%s' % (group, name)
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| 208 | if not rcParams.has_key(key):
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| 209 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
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| 210 |
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| 211 | rcParams[key] = v
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| 212 |
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| 213 |
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| 214 | def rcdefaults():
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| 215 | """
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| 216 | Restore the default rc params - the ones that were created at
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| 217 | asap load time
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| 218 | """
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| 219 | rcParams.update(rcParamsDefault)
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| 220 |
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| 221 |
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| 222 | def _is_sequence_or_number(param, ptype=int):
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| 223 | if isinstance(param,tuple) or isinstance(param,list):
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| 224 | out = True
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| 225 | for p in param:
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| 226 | out &= isinstance(p,ptype)
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| 227 | return out
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| 228 | elif isinstance(param, ptype):
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| 229 | return True
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| 230 | return False
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| 231 |
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| 232 |
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| 233 | # workaround for ipython, which redirects this if banner=0 in ipythonrc
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| 234 | sys.stdout = sys.__stdout__
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| 235 | sys.stderr = sys.__stderr__
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| 236 |
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| 237 | # Logging
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| 238 | from asap._asap import Log as _asaplog
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| 239 | global asaplog
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| 240 | asaplog=_asaplog()
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| 241 | if rcParams['verbose']:
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| 242 | asaplog.enable()
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| 243 | else:
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| 244 | asaplog.disable()
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| 245 |
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| 246 | def print_log():
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| 247 | log = asaplog.pop()
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| 248 | if len(log) and rcParams['verbose']: print log
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| 249 | return
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| 250 |
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| 251 | from asapfitter import *
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| 252 | from asapreader import reader
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| 253 |
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| 254 | from asapmath import *
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| 255 | from scantable import *
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| 256 | from asaplinefind import *
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| 257 | from asapfit import *
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| 258 |
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| 259 | from numarray import logical_and as mask_and
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| 260 | from numarray import logical_or as mask_or
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| 261 | from numarray import logical_not as mask_not
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| 262 |
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| 263 | if rcParams['useplotter']:
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| 264 | from asapplotter import *
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| 265 | gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
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| 266 | plotter = asapplotter(gui)
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| 267 | del gui
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| 268 |
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| 269 | __date__ = '$Date: 2005-11-24 03:12:33 +0000 (Thu, 24 Nov 2005) $'.split()[1]
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| 270 | __version__ = '1.2'
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| 271 |
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| 272 | if rcParams['verbose']:
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| 273 | def list_scans(t = scantable):
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| 274 | import sys, types
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| 275 | globs = sys.modules['__main__'].__dict__.iteritems()
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| 276 | print "The user created scantables are:"
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| 277 | sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
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| 278 | print filter(lambda x: not x.startswith('_'), sts)
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| 279 | return
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| 280 |
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| 281 | def commands():
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| 282 | x = """
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| 283 | [The scan container]
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| 284 | scantable - a container for integrations/scans
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| 285 | (can open asap/rpfits/sdfits and ms files)
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| 286 | copy - returns a copy of a scan
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| 287 | get_scan - gets a specific scan out of a scantable
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| 288 | (by name or number)
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| 289 | summary - print info about the scantable contents
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| 290 | set_cursor - set a specific Beam/IF/Pol 'cursor' for
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| 291 | further use
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| 292 | get_cursor - print out the current cursor position
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| 293 | stats - get specified statistic of the spectra in
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| 294 | the scantable
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| 295 | stddev - get the standard deviation of the spectra
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| 296 | in the scantable
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| 297 | get_tsys - get the TSys
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| 298 | get_time - get the timestamps of the integrations
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| 299 | get_sourcename - get the source names of the scans
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| 300 | get_unit - get the currnt unit
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| 301 | set_unit - set the abcissa unit to be used from this
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| 302 | point on
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| 303 | get_abcissa - get the abcissa values and name for a given
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| 304 | row (time)
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| 305 | set_freqframe - set the frame info for the Spectral Axis
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| 306 | (e.g. 'LSRK')
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| 307 | set_doppler - set the doppler to be used from this point on
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| 308 | set_instrument - set the instrument name
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| 309 | get_fluxunit - get the brightness flux unit
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| 310 | set_fluxunit - set the brightness flux unit
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| 311 | create_mask - return an mask in the current unit
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| 312 | for the given region. The specified regions
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| 313 | are NOT masked
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| 314 | get_restfreqs - get the current list of rest frequencies
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| 315 | set_restfreqs - set a list of rest frequencies
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| 316 | lines - print list of known spectral lines
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| 317 | flag_spectrum - flag a whole Beam/IF/Pol
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| 318 | save - save the scantable to disk as either 'ASAP'
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| 319 | or 'SDFITS'
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| 320 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
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| 321 | nscan - the number of scans in the scantable
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| 322 | nrow - te number of integrations in the scantable
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| 323 | history - print the history of the scantable
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| 324 | get_fit - get a fit which has been stored witnh the data
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| 325 | average_time - return the (weighted) time average of a scan
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| 326 | or a list of scans
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| 327 | average_pol - average the polarisations together.
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| 328 | The dimension won't be reduced and
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| 329 | all polarisations will contain the
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| 330 | averaged spectrum.
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| 331 | auto_quotient - return the on/off quotient with
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| 332 | automatic detection of the on/off scans
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| 333 | (matched pairs and 1 off - n on)
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| 334 | quotient - return the on/off quotient
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| 335 | scale - return a scan scaled by a given factor
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| 336 | add - return a scan with given value added
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| 337 | bin - return a scan with binned channels
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| 338 | resample - return a scan with resampled channels
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| 339 | smooth - return the spectrally smoothed scan
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| 340 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
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| 341 | auto_poly_baseline - automatically fit a polynomial baseline
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| 342 | gain_el - apply gain-elevation correction
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| 343 | opacity - apply opacity correction
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| 344 | convert_flux - convert to and from Jy and Kelvin brightness
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| 345 | units
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| 346 | freq_align - align spectra in frequency frame
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| 347 | rotate_xyphase - rotate XY phase of cross correlation
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| 348 | rotate_linpolphase - rotate the phase of the complex
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| 349 | polarization O=Q+iU correlation
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| 350 | freq_switch - perform frequency switching on the data
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| 351 | stats - Determine the specified statistic, e.g. 'min'
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| 352 | 'max', 'rms' etc.
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| 353 | stddev - Determine the standard deviation of the current
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| 354 | beam/if/pol
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| 355 |
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| 356 | [Math] Mainly functions which operate on more than one scantable
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| 357 |
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| 358 | average_time - return the (weighted) time average
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| 359 | of a list of scans
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| 360 | quotient - return the on/off quotient
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| 361 | simple_math - simple mathematical operations on two scantables,
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| 362 | 'add', 'sub', 'mul', 'div'
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| 363 | [Fitting]
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| 364 | fitter
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| 365 | auto_fit - return a scan where the function is
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| 366 | applied to all Beams/IFs/Pols.
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| 367 | commit - return a new scan where the fits have been
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| 368 | commited.
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| 369 | fit - execute the actual fitting process
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| 370 | store_fit - store the fit paramaters in the data (scantable)
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| 371 | get_chi2 - get the Chi^2
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| 372 | set_scan - set the scantable to be fit
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| 373 | set_function - set the fitting function
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| 374 | set_parameters - set the parameters for the function(s), and
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| 375 | set if they should be held fixed during fitting
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| 376 | set_gauss_parameters - same as above but specialised for individual
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| 377 | gaussian components
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| 378 | get_parameters - get the fitted parameters
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| 379 | plot - plot the resulting fit and/or components and
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| 380 | residual
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| 381 | [Plotter]
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| 382 | asapplotter - a plotter for asap, default plotter is
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| 383 | called 'plotter'
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| 384 | plot - plot a (list of) scantable
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| 385 | save - save the plot to a file ('png' ,'ps' or 'eps')
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| 386 | set_mode - set the state of the plotter, i.e.
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| 387 | what is to be plotted 'colour stacked'
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| 388 | and what 'panelled'
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| 389 | set_cursor - only plot a selected part of the data
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| 390 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
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| 391 | set_legend - specify user labels for the legend indeces
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| 392 | set_title - specify user labels for the panel indeces
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| 393 | set_abcissa - specify a user label for the abcissa
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| 394 | set_ordinate - specify a user label for the ordinate
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| 395 | set_layout - specify the multi-panel layout (rows,cols)
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| 396 | set_colors - specify a set of colours to use
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| 397 | set_linestyles - specify a set of linestyles to use if only
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| 398 | using one color
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| 399 | set_mask - set a plotting mask for a specific polarization
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| 400 |
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| 401 | [Reading files]
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| 402 | reader - access rpfits/sdfits files
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| 403 | read - read in integrations
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| 404 | summary - list info about all integrations
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| 405 |
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| 406 | [General]
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| 407 | commands - this command
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| 408 | print - print details about a variable
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| 409 | list_scans - list all scantables created bt the user
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| 410 | del - delete the given variable from memory
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| 411 | range - create a list of values, e.g.
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| 412 | range(3) = [0,1,2], range(2,5) = [2,3,4]
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| 413 | help - print help for one of the listed functions
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| 414 | execfile - execute an asap script, e.g. execfile('myscript')
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| 415 | list_rcparameters - print out a list of possible values to be
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| 416 | put into $HOME/.asaprc
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| 417 | mask_and,mask_or,
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| 418 | mask_not - boolean operations on masks created with
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| 419 | scantable.create_mask
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| 420 |
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| 421 | Note:
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| 422 | How to use this with help:
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| 423 | # function 'summary'
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| 424 | [xxx] is just a category
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| 425 | Every 'sub-level' in this list should be replaces by a '.' Period when
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| 426 | using help
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| 427 | Example:
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| 428 | ASAP> help scantable # to get info on ths scantable
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| 429 | ASAP> help scantable.summary # to get help on the scantable's
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| 430 | ASAP> help average_time
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| 431 |
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| 432 | """
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| 433 | print x
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| 434 | return
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| 435 |
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| 436 | def welcome():
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| 437 | return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
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| 438 |
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| 439 | Please report any bugs to:
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| 440 | asap@atnf.csiro.au
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| 441 |
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| 442 | [IMPORTANT: ASAP is 0-based]
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| 443 | Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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