| [100] | 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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| [226] | 5 | import os,sys
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| 6 |
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| [513] | 7 | def _validate_bool(b):
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| [226] | 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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| [513] | 15 | def _validate_int(s):
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| [226] | 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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| [513] | 21 | def _asap_fname():
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| [226] | 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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| [274] | 29 | * HOME/.asaprc
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| [706] | 30 |
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| [226] | 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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| [706] | 50 |
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| [226] | 51 | defaultParams = {
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| 52 | # general
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| [513] | 53 | 'verbose' : [True, _validate_bool],
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| 54 | 'useplotter' : [True, _validate_bool],
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| [542] | 55 | 'insitu' : [True, _validate_bool],
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| [706] | 56 |
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| [226] | 57 | # plotting
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| [706] | 58 | 'plotter.gui' : [True, _validate_bool],
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| [226] | 59 | 'plotter.stacking' : ['p', str],
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| 60 | 'plotter.panelling' : ['s', str],
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| [700] | 61 | 'plotter.colours' : ['', str],
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| 62 | 'plotter.linestyles' : ['', str],
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| [710] | 63 | 'plotter.decimate' : [False, _validate_bool],
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| 64 | 'plotter.ganged' : [True, _validate_bool],
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| [1022] | 65 | 'plotter.histogram' : [False, _validate_bool],
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| [710] | 66 |
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| [226] | 67 | # scantable
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| 68 | 'scantable.save' : ['ASAP', str],
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| [513] | 69 | 'scantable.autoaverage' : [True, _validate_bool],
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| [226] | 70 | 'scantable.freqframe' : ['LSRK', str], #default frequency frame
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| [513] | 71 | 'scantable.verbosesummary' : [False, _validate_bool]
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| [226] | 72 |
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| 73 | # fitter
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| 74 | }
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| 75 |
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| [255] | 76 | def list_rcparameters():
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| [706] | 77 |
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| [255] | 78 | print """
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| [737] | 79 | # general
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| 80 | # print verbose output
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| 81 | verbose : True
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| [255] | 82 |
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| [737] | 83 | # preload a default plotter
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| 84 | useplotter : True
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| [255] | 85 |
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| [737] | 86 | # apply operations on the input scantable or return new one
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| 87 | insitu : True
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| [706] | 88 |
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| [737] | 89 | # plotting
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| [710] | 90 |
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| [737] | 91 | # do we want a GUI or plot to a file
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| 92 | plotter.gui : True
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| [710] | 93 |
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| [737] | 94 | # default mode for colour stacking
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| 95 | plotter.stacking : Pol
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| [255] | 96 |
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| [737] | 97 | # default mode for panelling
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| 98 | plotter.panelling : scan
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| [255] | 99 |
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| [737] | 100 | # push panels together, to share axislabels
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| 101 | plotter.ganged : True
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| [710] | 102 |
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| [737] | 103 | # decimate the number of points plotted bya afactor of
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| 104 | # nchan/1024
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| 105 | plotter.decimate : False
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| [733] | 106 |
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| [737] | 107 | # default colours/linestyles
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| 108 | plotter.colours :
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| 109 | plotter.linestyles :
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| [700] | 110 |
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| [1022] | 111 | # enable/disable histogram plotting
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| 112 | plotter.histogram : False
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| 113 |
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| [737] | 114 | # scantable
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| 115 | # default ouput format when saving
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| 116 | scantable.save : ASAP
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| 117 | # auto averaging on read
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| 118 | scantable.autoaverage : True
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| [255] | 119 |
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| [737] | 120 | # default frequency frame to set when function
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| 121 | # scantable.set_freqfrmae is called
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| 122 | scantable.freqframe : LSRK
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| [255] | 123 |
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| [737] | 124 | # Control the level of information printed by summary
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| 125 | scantable.verbosesummary : False
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| [706] | 126 |
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| [737] | 127 | # Fitter
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| 128 | """
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| [706] | 129 |
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| [226] | 130 | def rc_params():
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| 131 | 'Return the default params updated from the values in the rc file'
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| [706] | 132 |
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| [513] | 133 | fname = _asap_fname()
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| [706] | 134 |
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| [226] | 135 | if fname is None or not os.path.exists(fname):
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| 136 | message = 'could not find rc file; returning defaults'
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| 137 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
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| 138 | #print message
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| 139 | return ret
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| [706] | 140 |
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| [226] | 141 | cnt = 0
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| 142 | for line in file(fname):
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| 143 | cnt +=1
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| 144 | line = line.strip()
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| 145 | if not len(line): continue
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| 146 | if line.startswith('#'): continue
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| 147 | tup = line.split(':',1)
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| 148 | if len(tup) !=2:
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| 149 | print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
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| 150 | continue
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| [706] | 151 |
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| [226] | 152 | key, val = tup
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| 153 | key = key.strip()
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| 154 | if not defaultParams.has_key(key):
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| 155 | print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
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| 156 | continue
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| [706] | 157 |
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| [226] | 158 | default, converter = defaultParams[key]
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| 159 |
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| 160 | ind = val.find('#')
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| 161 | if ind>=0: val = val[:ind] # ignore trailing comments
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| 162 | val = val.strip()
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| 163 | try: cval = converter(val) # try to convert to proper type or raise
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| 164 | except Exception, msg:
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| 165 | 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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| 166 | continue
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| 167 | else:
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| 168 | # Alles Klar, update dict
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| 169 | defaultParams[key][0] = cval
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| 170 |
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| 171 | # strip the conveter funcs and return
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| 172 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
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| [466] | 173 | print ('loaded rc file %s'%fname)
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| [226] | 174 |
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| 175 | return ret
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| 176 |
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| 177 |
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| 178 | # this is the instance used by the asap classes
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| [706] | 179 | rcParams = rc_params()
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| [226] | 180 |
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| 181 | rcParamsDefault = dict(rcParams.items()) # a copy
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| 182 |
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| 183 | def rc(group, **kwargs):
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| 184 | """
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| 185 | Set the current rc params. Group is the grouping for the rc, eg
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| [379] | 186 | for scantable.save the group is 'scantable', for plotter.stacking, the
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| 187 | group is 'plotter', and so on. kwargs is a list of attribute
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| [226] | 188 | name/value pairs, eg
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| 189 |
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| [379] | 190 | rc('scantable', save='SDFITS')
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| [226] | 191 |
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| 192 | sets the current rc params and is equivalent to
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| [706] | 193 |
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| [379] | 194 | rcParams['scantable.save'] = 'SDFITS'
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| [226] | 195 |
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| 196 | Use rcdefaults to restore the default rc params after changes.
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| 197 | """
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| 198 |
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| [379] | 199 | aliases = {}
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| [706] | 200 |
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| [226] | 201 | for k,v in kwargs.items():
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| 202 | name = aliases.get(k) or k
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| 203 | key = '%s.%s' % (group, name)
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| 204 | if not rcParams.has_key(key):
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| 205 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
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| [706] | 206 |
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| [226] | 207 | rcParams[key] = v
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| 208 |
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| 209 |
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| 210 | def rcdefaults():
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| 211 | """
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| 212 | Restore the default rc params - the ones that were created at
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| 213 | asap load time
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| 214 | """
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| 215 | rcParams.update(rcParamsDefault)
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| 216 |
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| [513] | 217 |
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| 218 | def _is_sequence_or_number(param, ptype=int):
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| 219 | if isinstance(param,tuple) or isinstance(param,list):
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| [928] | 220 | if len(param) == 0: return True # empty list
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| [513] | 221 | out = True
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| 222 | for p in param:
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| 223 | out &= isinstance(p,ptype)
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| 224 | return out
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| 225 | elif isinstance(param, ptype):
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| 226 | return True
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| 227 | return False
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| 228 |
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| [928] | 229 | def _to_list(param, ptype=int):
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| 230 | if isinstance(param, ptype):
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| 231 | if ptype is str: return param.split()
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| 232 | else: return [param]
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| 233 | if _is_sequence_or_number(param, ptype):
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| 234 | return param
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| 235 | return None
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| [715] | 236 |
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| [944] | 237 | def unique(x):
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| [992] | 238 | """
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| 239 | Return the unique values in a list
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| 240 | Parameters:
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| 241 | x: the list to reduce
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| 242 | Examples:
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| 243 | x = [1,2,3,3,4]
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| 244 | print unique(x)
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| 245 | [1,2,3,4]
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| 246 | """
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| [944] | 247 | return dict([ (val, 1) for val in x]).keys()
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| 248 |
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| [992] | 249 | def list_files(path=".",suffix="rpf"):
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| 250 | """
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| 251 | Return a list files readable by asap, such as rpf, sdfits, mbf, asap
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| 252 | Parameters:
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| 253 | path: The directory to list (default '.')
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| 254 | suffix: The file extension (default rpf)
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| 255 | Example:
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| 256 | files = list_files("data/","sdfits")
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| 257 | print files
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| 258 | ['data/2001-09-01_0332_P363.sdfits',
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| 259 | 'data/2003-04-04_131152_t0002.sdfits',
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| 260 | 'data/Sgr_86p262_best_SPC.sdfits']
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| 261 | """
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| 262 | import os
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| 263 | if not os.path.isdir(path):
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| 264 | return None
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| 265 | valid = "rpf sdf sdfits mbf asap".split()
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| 266 | if not suffix in valid:
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| 267 | return None
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| 268 | files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
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| 269 | return filter(lambda x: x.endswith(suffix),files)
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| 270 |
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| [715] | 271 | # workaround for ipython, which redirects this if banner=0 in ipythonrc
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| 272 | sys.stdout = sys.__stdout__
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| 273 | sys.stderr = sys.__stderr__
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| 274 |
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| 275 | # Logging
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| 276 | from asap._asap import Log as _asaplog
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| 277 | global asaplog
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| [710] | 278 | asaplog=_asaplog()
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| [715] | 279 | if rcParams['verbose']:
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| 280 | asaplog.enable()
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| 281 | else:
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| 282 | asaplog.disable()
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| 283 |
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| 284 | def print_log():
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| 285 | log = asaplog.pop()
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| 286 | if len(log) and rcParams['verbose']: print log
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| 287 | return
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| 288 |
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| [113] | 289 | from asapfitter import *
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| [895] | 290 | from asapreader import reader
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| [944] | 291 | from selector import selector
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| [710] | 292 |
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| [100] | 293 | from asapmath import *
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| [880] | 294 | from scantable import *
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| 295 | from asaplinefind import *
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| [876] | 296 | #from asapfit import *
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| [285] | 297 |
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| [466] | 298 | from numarray import logical_and as mask_and
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| 299 | from numarray import logical_or as mask_or
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| 300 | from numarray import logical_not as mask_not
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| 301 |
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| [928] | 302 | if rcParams['useplotter']:
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| 303 | from asapplotter import *
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| 304 | gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
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| 305 | plotter = asapplotter(gui)
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| 306 | del gui
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| [285] | 307 |
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| [574] | 308 | __date__ = '$Date: 2006-06-06 03:19:50 +0000 (Tue, 06 Jun 2006) $'.split()[1]
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| [1059] | 309 | __version__ = '2.0.1'
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| [100] | 310 |
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| [706] | 311 | if rcParams['verbose']:
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| [1014] | 312 | def version(): print "ASAP %s(%s)"% (__version__, __date__)
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| [706] | 313 | def list_scans(t = scantable):
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| 314 | import sys, types
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| 315 | globs = sys.modules['__main__'].__dict__.iteritems()
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| 316 | print "The user created scantables are:"
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| 317 | sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
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| 318 | print filter(lambda x: not x.startswith('_'), sts)
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| 319 | return
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| [100] | 320 |
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| [715] | 321 | def commands():
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| 322 | x = """
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| [113] | 323 | [The scan container]
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| 324 | scantable - a container for integrations/scans
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| [182] | 325 | (can open asap/rpfits/sdfits and ms files)
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| [113] | 326 | copy - returns a copy of a scan
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| 327 | get_scan - gets a specific scan out of a scantable
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| [984] | 328 | (by name or number)
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| 329 | set_selection - set a new subselection of the data
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| 330 | get_selection - get the current selection object
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| [113] | 331 | summary - print info about the scantable contents
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| [182] | 332 | stats - get specified statistic of the spectra in
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| 333 | the scantable
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| 334 | stddev - get the standard deviation of the spectra
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| 335 | in the scantable
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| [113] | 336 | get_tsys - get the TSys
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| 337 | get_time - get the timestamps of the integrations
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| [733] | 338 | get_sourcename - get the source names of the scans
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| [794] | 339 | get_azimuth - get the azimuth of the scans
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| 340 | get_elevation - get the elevation of the scans
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| 341 | get_parangle - get the parallactic angle of the scans
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| [876] | 342 | get_unit - get the current unit
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| [513] | 343 | set_unit - set the abcissa unit to be used from this
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| 344 | point on
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| [255] | 345 | get_abcissa - get the abcissa values and name for a given
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| 346 | row (time)
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| [113] | 347 | set_freqframe - set the frame info for the Spectral Axis
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| 348 | (e.g. 'LSRK')
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| [276] | 349 | set_doppler - set the doppler to be used from this point on
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| [984] | 350 | set_dirframe - set the frame for the direction on the sky
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| [240] | 351 | set_instrument - set the instrument name
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| [255] | 352 | get_fluxunit - get the brightness flux unit
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| [240] | 353 | set_fluxunit - set the brightness flux unit
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| [188] | 354 | create_mask - return an mask in the current unit
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| 355 | for the given region. The specified regions
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| 356 | are NOT masked
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| [255] | 357 | get_restfreqs - get the current list of rest frequencies
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| 358 | set_restfreqs - set a list of rest frequencies
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| [1012] | 359 | flag - flag selected channels in the data
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| [116] | 360 | save - save the scantable to disk as either 'ASAP'
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| 361 | or 'SDFITS'
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| [486] | 362 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
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| [733] | 363 | nscan - the number of scans in the scantable
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| [984] | 364 | nrow - te number of spectra in the scantable
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| [486] | 365 | history - print the history of the scantable
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| [530] | 366 | get_fit - get a fit which has been stored witnh the data
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| [706] | 367 | average_time - return the (weighted) time average of a scan
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| [513] | 368 | or a list of scans
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| 369 | average_pol - average the polarisations together.
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| [113] | 370 | The dimension won't be reduced and
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| 371 | all polarisations will contain the
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| 372 | averaged spectrum.
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| [992] | 373 | convert_pol - convert to a different polarisation type
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| [690] | 374 | auto_quotient - return the on/off quotient with
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| 375 | automatic detection of the on/off scans
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| [733] | 376 | (matched pairs and 1 off - n on)
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| [1014] | 377 | scale, *, / - return a scan scaled by a given factor
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| 378 | add, +, - - return a scan with given value added
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| [513] | 379 | bin - return a scan with binned channels
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| 380 | resample - return a scan with resampled channels
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| 381 | smooth - return the spectrally smoothed scan
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| 382 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
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| [706] | 383 | auto_poly_baseline - automatically fit a polynomial baseline
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| [780] | 384 | recalc_azel - recalculate azimuth and elevation based on
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| 385 | the pointing
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| [513] | 386 | gain_el - apply gain-elevation correction
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| 387 | opacity - apply opacity correction
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| 388 | convert_flux - convert to and from Jy and Kelvin brightness
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| [255] | 389 | units
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| [513] | 390 | freq_align - align spectra in frequency frame
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| [1014] | 391 | invert_phase - Invert the phase of the cross-correlation
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| 392 | swap_linears - Swap XX and YY
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| [513] | 393 | rotate_xyphase - rotate XY phase of cross correlation
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| 394 | rotate_linpolphase - rotate the phase of the complex
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| 395 | polarization O=Q+iU correlation
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| [733] | 396 | freq_switch - perform frequency switching on the data
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| 397 | stats - Determine the specified statistic, e.g. 'min'
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| 398 | 'max', 'rms' etc.
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| 399 | stddev - Determine the standard deviation of the current
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| 400 | beam/if/pol
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| [1014] | 401 | [Selection]
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| 402 | selector - a selection object to set a subset of a scantable
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| 403 | set_scans - set (a list of) scans by index
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| 404 | set_cycles - set (a list of) cycles by index
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| 405 | set_beams - set (a list of) beamss by index
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| 406 | set_ifs - set (a list of) ifs by index
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| 407 | set_polarisations - set (a list of) polarisations by name
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| 408 | or by index
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| 409 | set_names - set a selection by name (wildcards allowed)
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| 410 | set_tsys - set a selection by tsys thresholds
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| 411 | reset - unset all selections
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| 412 | + - merge to selections
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| [733] | 413 |
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| [513] | 414 | [Math] Mainly functions which operate on more than one scantable
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| [100] | 415 |
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| [706] | 416 | average_time - return the (weighted) time average
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| [513] | 417 | of a list of scans
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| 418 | quotient - return the on/off quotient
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| 419 | simple_math - simple mathematical operations on two scantables,
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| 420 | 'add', 'sub', 'mul', 'div'
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| 421 | [Fitting]
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| [113] | 422 | fitter
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| 423 | auto_fit - return a scan where the function is
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| 424 | applied to all Beams/IFs/Pols.
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| 425 | commit - return a new scan where the fits have been
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| 426 | commited.
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| 427 | fit - execute the actual fitting process
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| [984] | 428 | store_fit - store the fit parameters in the data (scantable)
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| [113] | 429 | get_chi2 - get the Chi^2
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| 430 | set_scan - set the scantable to be fit
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| 431 | set_function - set the fitting function
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| 432 | set_parameters - set the parameters for the function(s), and
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| 433 | set if they should be held fixed during fitting
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| [513] | 434 | set_gauss_parameters - same as above but specialised for individual
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| 435 | gaussian components
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| [113] | 436 | get_parameters - get the fitted parameters
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| [513] | 437 | plot - plot the resulting fit and/or components and
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| 438 | residual
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| [210] | 439 | [Plotter]
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| 440 | asapplotter - a plotter for asap, default plotter is
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| 441 | called 'plotter'
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| [984] | 442 | plot - plot a scantable
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| [378] | 443 | save - save the plot to a file ('png' ,'ps' or 'eps')
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| [210] | 444 | set_mode - set the state of the plotter, i.e.
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| 445 | what is to be plotted 'colour stacked'
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| 446 | and what 'panelled'
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| [984] | 447 | set_selection - only plot a selected part of the data
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| [733] | 448 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
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| [255] | 449 | set_legend - specify user labels for the legend indeces
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| 450 | set_title - specify user labels for the panel indeces
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| [733] | 451 | set_abcissa - specify a user label for the abcissa
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| [255] | 452 | set_ordinate - specify a user label for the ordinate
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| [378] | 453 | set_layout - specify the multi-panel layout (rows,cols)
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|---|
| [733] | 454 | set_colors - specify a set of colours to use
|
|---|
| 455 | set_linestyles - specify a set of linestyles to use if only
|
|---|
| 456 | using one color
|
|---|
| [1054] | 457 | set_histogram - plot in historam style
|
|---|
| [733] | 458 | set_mask - set a plotting mask for a specific polarization
|
|---|
| [706] | 459 |
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| [182] | 460 | [Reading files]
|
|---|
| 461 | reader - access rpfits/sdfits files
|
|---|
| [984] | 462 | open - attach reader to a file
|
|---|
| 463 | close - detach reader from file
|
|---|
| [182] | 464 | read - read in integrations
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|---|
| 465 | summary - list info about all integrations
|
|---|
| 466 |
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|---|
| [113] | 467 | [General]
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|---|
| 468 | commands - this command
|
|---|
| 469 | print - print details about a variable
|
|---|
| 470 | list_scans - list all scantables created bt the user
|
|---|
| [992] | 471 | list_files - list all files readable by asap (default rpf)
|
|---|
| [113] | 472 | del - delete the given variable from memory
|
|---|
| 473 | range - create a list of values, e.g.
|
|---|
| 474 | range(3) = [0,1,2], range(2,5) = [2,3,4]
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|---|
| 475 | help - print help for one of the listed functions
|
|---|
| 476 | execfile - execute an asap script, e.g. execfile('myscript')
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|---|
| [255] | 477 | list_rcparameters - print out a list of possible values to be
|
|---|
| [274] | 478 | put into $HOME/.asaprc
|
|---|
| [466] | 479 | mask_and,mask_or,
|
|---|
| 480 | mask_not - boolean operations on masks created with
|
|---|
| 481 | scantable.create_mask
|
|---|
| [706] | 482 |
|
|---|
| [210] | 483 | Note:
|
|---|
| 484 | How to use this with help:
|
|---|
| 485 | # function 'summary'
|
|---|
| 486 | [xxx] is just a category
|
|---|
| 487 | Every 'sub-level' in this list should be replaces by a '.' Period when
|
|---|
| [706] | 488 | using help
|
|---|
| [210] | 489 | Example:
|
|---|
| 490 | ASAP> help scantable # to get info on ths scantable
|
|---|
| 491 | ASAP> help scantable.summary # to get help on the scantable's
|
|---|
| 492 | ASAP> help average_time
|
|---|
| 493 |
|
|---|
| [715] | 494 | """
|
|---|
| 495 | print x
|
|---|
| 496 | return
|
|---|
| [113] | 497 |
|
|---|
| [706] | 498 | def welcome():
|
|---|
| 499 | return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
|
|---|
| [100] | 500 |
|
|---|
| [1035] | 501 | Please report any bugs via:
|
|---|
| 502 | http://sourcecode.atnf.csiro.au/cgi-bin/trac_asap.cgi/newticket
|
|---|
| [100] | 503 |
|
|---|
| [378] | 504 | [IMPORTANT: ASAP is 0-based]
|
|---|
| [706] | 505 | Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
|
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