| 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,shutil, platform |
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| 6 | |
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| 7 | # Set up AIPSPATH and first time use of asap i.e. ~/.asap/* |
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| 8 | plf = None |
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| 9 | if sys.platform == "linux2": |
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| 10 | if platform.architecture()[0] == '64bit': |
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| 11 | plf = 'linux_64b' |
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| 12 | else: |
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| 13 | plf = 'linux_gnu' |
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| 14 | elif sys.platform == 'darwin': |
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| 15 | plf = 'darwin' |
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| 16 | else: |
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| 17 | # Shouldn't happen - default to linux |
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| 18 | plf = 'linux' |
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| 19 | asapdata = __path__[-1] |
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| 20 | os.environ["AIPSPATH"] = "%s %s somwhere" % ( asapdata, plf) |
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| 21 | userdir = os.environ["HOME"]+"/.asap" |
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| 22 | if not os.path.exists(userdir): |
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| 23 | print 'First time ASAP use. Setting up ~/.asap' |
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| 24 | os.mkdir(userdir) |
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| 25 | shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap") |
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| 26 | f = file(userdir+"/asapuserfuncs.py", "w") |
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| 27 | f.close() |
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| 28 | f = file(userdir+"/ipythonrc", "w") |
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| 29 | f.close() |
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| 30 | del asapdata, userdir, shutil, platform |
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| 31 | |
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| 32 | def _validate_bool(b): |
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| 33 | 'Convert b to a boolean or raise' |
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| 34 | bl = b.lower() |
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| 35 | if bl in ('f', 'no', 'false', '0', 0): return False |
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| 36 | elif bl in ('t', 'yes', 'true', '1', 1): return True |
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| 37 | else: |
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| 38 | raise ValueError('Could not convert "%s" to boolean' % b) |
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| 39 | |
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| 40 | def _validate_int(s): |
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| 41 | 'convert s to int or raise' |
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| 42 | try: return int(s) |
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| 43 | except ValueError: |
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| 44 | raise ValueError('Could not convert "%s" to int' % s) |
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| 45 | |
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| 46 | def _asap_fname(): |
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| 47 | """ |
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| 48 | Return the path to the rc file |
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| 49 | |
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| 50 | Search order: |
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| 51 | |
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| 52 | * current working dir |
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| 53 | * environ var ASAPRC |
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| 54 | * HOME/.asaprc |
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| 55 | |
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| 56 | """ |
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| 57 | |
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| 58 | fname = os.path.join( os.getcwd(), '.asaprc') |
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| 59 | if os.path.exists(fname): return fname |
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| 60 | |
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| 61 | if os.environ.has_key('ASAPRC'): |
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| 62 | path = os.environ['ASAPRC'] |
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| 63 | if os.path.exists(path): |
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| 64 | fname = os.path.join(path, '.asaprc') |
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| 65 | if os.path.exists(fname): |
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| 66 | return fname |
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| 67 | |
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| 68 | if os.environ.has_key('HOME'): |
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| 69 | home = os.environ['HOME'] |
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| 70 | fname = os.path.join(home, '.asaprc') |
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| 71 | if os.path.exists(fname): |
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| 72 | return fname |
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| 73 | return None |
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| 74 | |
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| 75 | |
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| 76 | defaultParams = { |
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| 77 | # general |
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| 78 | 'verbose' : [True, _validate_bool], |
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| 79 | 'useplotter' : [True, _validate_bool], |
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| 80 | 'insitu' : [True, _validate_bool], |
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| 81 | |
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| 82 | # plotting |
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| 83 | 'plotter.gui' : [True, _validate_bool], |
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| 84 | 'plotter.stacking' : ['p', str], |
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| 85 | 'plotter.panelling' : ['s', str], |
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| 86 | 'plotter.colours' : ['', str], |
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| 87 | 'plotter.linestyles' : ['', str], |
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| 88 | 'plotter.decimate' : [False, _validate_bool], |
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| 89 | 'plotter.ganged' : [True, _validate_bool], |
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| 90 | 'plotter.histogram' : [False, _validate_bool], |
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| 91 | |
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| 92 | # scantable |
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| 93 | 'scantable.save' : ['ASAP', str], |
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| 94 | 'scantable.autoaverage' : [True, _validate_bool], |
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| 95 | 'scantable.freqframe' : ['LSRK', str], #default frequency frame |
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| 96 | 'scantable.verbosesummary' : [False, _validate_bool], |
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| 97 | 'scantable.storage' : ['memory', str] |
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| 98 | # fitter |
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| 99 | } |
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| 100 | |
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| 101 | def list_rcparameters(): |
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| 102 | |
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| 103 | print """ |
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| 104 | # general |
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| 105 | # print verbose output |
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| 106 | verbose : True |
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| 107 | |
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| 108 | # preload a default plotter |
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| 109 | useplotter : True |
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| 110 | |
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| 111 | # apply operations on the input scantable or return new one |
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| 112 | insitu : True |
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| 113 | |
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| 114 | # plotting |
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| 115 | |
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| 116 | # do we want a GUI or plot to a file |
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| 117 | plotter.gui : True |
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| 118 | |
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| 119 | # default mode for colour stacking |
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| 120 | plotter.stacking : Pol |
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| 121 | |
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| 122 | # default mode for panelling |
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| 123 | plotter.panelling : scan |
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| 124 | |
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| 125 | # push panels together, to share axislabels |
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| 126 | plotter.ganged : True |
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| 127 | |
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| 128 | # decimate the number of points plotted bya afactor of |
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| 129 | # nchan/1024 |
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| 130 | plotter.decimate : False |
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| 131 | |
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| 132 | # default colours/linestyles |
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| 133 | plotter.colours : |
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| 134 | plotter.linestyles : |
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| 135 | |
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| 136 | # enable/disable histogram plotting |
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| 137 | plotter.histogram : False |
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| 138 | |
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| 139 | # scantable |
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| 140 | |
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| 141 | # default storage of scantable (memory/disk) |
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| 142 | scantable.storage : memory |
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| 143 | # default ouput format when saving |
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| 144 | scantable.save : ASAP |
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| 145 | # auto averaging on read |
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| 146 | scantable.autoaverage : True |
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| 147 | |
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| 148 | # default frequency frame to set when function |
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| 149 | # scantable.set_freqfrmae is called |
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| 150 | scantable.freqframe : LSRK |
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| 151 | |
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| 152 | # Control the level of information printed by summary |
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| 153 | scantable.verbosesummary : False |
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| 154 | |
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| 155 | # Fitter |
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| 156 | """ |
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| 157 | |
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| 158 | def rc_params(): |
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| 159 | 'Return the default params updated from the values in the rc file' |
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| 160 | |
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| 161 | fname = _asap_fname() |
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| 162 | |
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| 163 | if fname is None or not os.path.exists(fname): |
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| 164 | message = 'could not find rc file; returning defaults' |
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| 165 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
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| 166 | #print message |
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| 167 | return ret |
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| 168 | |
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| 169 | cnt = 0 |
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| 170 | for line in file(fname): |
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| 171 | cnt +=1 |
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| 172 | line = line.strip() |
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| 173 | if not len(line): continue |
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| 174 | if line.startswith('#'): continue |
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| 175 | tup = line.split(':',1) |
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| 176 | if len(tup) !=2: |
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| 177 | print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname)) |
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| 178 | continue |
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| 179 | |
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| 180 | key, val = tup |
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| 181 | key = key.strip() |
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| 182 | if not defaultParams.has_key(key): |
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| 183 | print ('Bad key "%s" on line %d in %s' % (key, cnt, fname)) |
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| 184 | continue |
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| 185 | |
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| 186 | default, converter = defaultParams[key] |
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| 187 | |
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| 188 | ind = val.find('#') |
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| 189 | if ind>=0: val = val[:ind] # ignore trailing comments |
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| 190 | val = val.strip() |
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| 191 | try: cval = converter(val) # try to convert to proper type or raise |
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| 192 | except ValueError, msg: |
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| 193 | 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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| 194 | continue |
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| 195 | else: |
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| 196 | # Alles Klar, update dict |
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| 197 | defaultParams[key][0] = cval |
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| 198 | |
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| 199 | # strip the conveter funcs and return |
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| 200 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
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| 201 | print ('loaded rc file %s'%fname) |
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| 202 | |
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| 203 | return ret |
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| 204 | |
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| 205 | |
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| 206 | # this is the instance used by the asap classes |
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| 207 | rcParams = rc_params() |
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| 208 | |
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| 209 | rcParamsDefault = dict(rcParams.items()) # a copy |
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| 210 | |
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| 211 | def rc(group, **kwargs): |
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| 212 | """ |
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| 213 | Set the current rc params. Group is the grouping for the rc, eg |
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| 214 | for scantable.save the group is 'scantable', for plotter.stacking, the |
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| 215 | group is 'plotter', and so on. kwargs is a list of attribute |
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| 216 | name/value pairs, eg |
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| 217 | |
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| 218 | rc('scantable', save='SDFITS') |
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| 219 | |
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| 220 | sets the current rc params and is equivalent to |
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| 221 | |
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| 222 | rcParams['scantable.save'] = 'SDFITS' |
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| 223 | |
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| 224 | Use rcdefaults to restore the default rc params after changes. |
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| 225 | """ |
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| 226 | |
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| 227 | aliases = {} |
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| 228 | |
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| 229 | for k,v in kwargs.items(): |
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| 230 | name = aliases.get(k) or k |
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| 231 | key = '%s.%s' % (group, name) |
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| 232 | if not rcParams.has_key(key): |
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| 233 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name)) |
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| 234 | |
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| 235 | rcParams[key] = v |
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| 236 | |
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| 237 | |
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| 238 | def rcdefaults(): |
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| 239 | """ |
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| 240 | Restore the default rc params - the ones that were created at |
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| 241 | asap load time |
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| 242 | """ |
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| 243 | rcParams.update(rcParamsDefault) |
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| 244 | |
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| 245 | |
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| 246 | def _is_sequence_or_number(param, ptype=int): |
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| 247 | if isinstance(param,tuple) or isinstance(param,list): |
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| 248 | if len(param) == 0: return True # empty list |
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| 249 | out = True |
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| 250 | for p in param: |
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| 251 | out &= isinstance(p,ptype) |
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| 252 | return out |
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| 253 | elif isinstance(param, ptype): |
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| 254 | return True |
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| 255 | return False |
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| 256 | |
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| 257 | def _to_list(param, ptype=int): |
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| 258 | if isinstance(param, ptype): |
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| 259 | if ptype is str: return param.split() |
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| 260 | else: return [param] |
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| 261 | if _is_sequence_or_number(param, ptype): |
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| 262 | return param |
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| 263 | return None |
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| 264 | |
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| 265 | def unique(x): |
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| 266 | """ |
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| 267 | Return the unique values in a list |
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| 268 | Parameters: |
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| 269 | x: the list to reduce |
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| 270 | Examples: |
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| 271 | x = [1,2,3,3,4] |
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| 272 | print unique(x) |
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| 273 | [1,2,3,4] |
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| 274 | """ |
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| 275 | return dict([ (val, 1) for val in x]).keys() |
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| 276 | |
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| 277 | def list_files(path=".",suffix="rpf"): |
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| 278 | """ |
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| 279 | Return a list files readable by asap, such as rpf, sdfits, mbf, asap |
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| 280 | Parameters: |
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| 281 | path: The directory to list (default '.') |
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| 282 | suffix: The file extension (default rpf) |
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| 283 | Example: |
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| 284 | files = list_files("data/","sdfits") |
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| 285 | print files |
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| 286 | ['data/2001-09-01_0332_P363.sdfits', |
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| 287 | 'data/2003-04-04_131152_t0002.sdfits', |
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| 288 | 'data/Sgr_86p262_best_SPC.sdfits'] |
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| 289 | """ |
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| 290 | import os |
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| 291 | if not os.path.isdir(path): |
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| 292 | return None |
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| 293 | valid = "rpf sdf sdfits mbf asap".split() |
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| 294 | if not suffix in valid: |
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| 295 | return None |
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| 296 | files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)] |
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| 297 | return filter(lambda x: x.endswith(suffix),files) |
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| 298 | |
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| 299 | # workaround for ipython, which redirects this if banner=0 in ipythonrc |
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| 300 | sys.stdout = sys.__stdout__ |
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| 301 | sys.stderr = sys.__stderr__ |
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| 302 | |
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| 303 | # Logging |
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| 304 | from asap._asap import Log as _asaplog |
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| 305 | global asaplog |
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| 306 | asaplog=_asaplog() |
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| 307 | if rcParams['verbose']: |
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| 308 | asaplog.enable() |
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| 309 | else: |
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| 310 | asaplog.disable() |
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| 311 | |
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| 312 | def print_log(): |
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| 313 | log = asaplog.pop() |
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| 314 | if len(log) and rcParams['verbose']: print log |
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| 315 | return |
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| 316 | |
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| 317 | from asapfitter import * |
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| 318 | from asapreader import reader |
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| 319 | from selector import selector |
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| 320 | |
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| 321 | from asapmath import * |
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| 322 | from scantable import scantable |
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| 323 | from asaplinefind import * |
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| 324 | #from asapfit import * |
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| 325 | |
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| 326 | from numarray import logical_and as mask_and |
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| 327 | from numarray import logical_or as mask_or |
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| 328 | from numarray import logical_not as mask_not |
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| 329 | |
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| 330 | if rcParams['useplotter']: |
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| 331 | from asapplotter import * |
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| 332 | gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui'] |
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| 333 | plotter = asapplotter(gui) |
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| 334 | del gui |
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| 335 | |
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| 336 | |
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| 337 | __date__ = '$Date: 2006-07-28 05:12:20 +0000 (Fri, 28 Jul 2006) $'.split()[1] |
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| 338 | __version__ = '2.1a' |
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| 339 | |
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| 340 | if rcParams['verbose']: |
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| 341 | def version(): print "ASAP %s(%s)"% (__version__, __date__) |
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| 342 | def list_scans(t = scantable): |
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| 343 | import sys, types |
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| 344 | globs = sys.modules['__main__'].__dict__.iteritems() |
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| 345 | print "The user created scantables are:" |
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| 346 | sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs)) |
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| 347 | print filter(lambda x: not x.startswith('_'), sts) |
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| 348 | return |
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| 349 | |
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| 350 | def commands(): |
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| 351 | x = """ |
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| 352 | [The scan container] |
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| 353 | scantable - a container for integrations/scans |
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| 354 | (can open asap/rpfits/sdfits and ms files) |
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| 355 | copy - returns a copy of a scan |
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| 356 | get_scan - gets a specific scan out of a scantable |
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| 357 | (by name or number) |
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| 358 | drop_scan - drops a specific scan out of a scantable |
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| 359 | (by number) |
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| 360 | set_selection - set a new subselection of the data |
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| 361 | get_selection - get the current selection object |
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| 362 | summary - print info about the scantable contents |
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| 363 | stats - get specified statistic of the spectra in |
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| 364 | the scantable |
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| 365 | stddev - get the standard deviation of the spectra |
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| 366 | in the scantable |
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| 367 | get_tsys - get the TSys |
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| 368 | get_time - get the timestamps of the integrations |
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| 369 | get_sourcename - get the source names of the scans |
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| 370 | get_azimuth - get the azimuth of the scans |
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| 371 | get_elevation - get the elevation of the scans |
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| 372 | get_parangle - get the parallactic angle of the scans |
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| 373 | get_unit - get the current unit |
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| 374 | set_unit - set the abcissa unit to be used from this |
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| 375 | point on |
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| 376 | get_abcissa - get the abcissa values and name for a given |
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| 377 | row (time) |
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| 378 | set_freqframe - set the frame info for the Spectral Axis |
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| 379 | (e.g. 'LSRK') |
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| 380 | set_doppler - set the doppler to be used from this point on |
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| 381 | set_dirframe - set the frame for the direction on the sky |
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| 382 | set_instrument - set the instrument name |
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| 383 | get_fluxunit - get the brightness flux unit |
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| 384 | set_fluxunit - set the brightness flux unit |
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| 385 | create_mask - return an mask in the current unit |
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| 386 | for the given region. The specified regions |
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| 387 | are NOT masked |
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| 388 | get_restfreqs - get the current list of rest frequencies |
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| 389 | set_restfreqs - set a list of rest frequencies |
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| 390 | flag - flag selected channels in the data |
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| 391 | save - save the scantable to disk as either 'ASAP' |
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| 392 | or 'SDFITS' |
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| 393 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans |
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| 394 | nscan - the number of scans in the scantable |
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| 395 | nrow - te number of spectra in the scantable |
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| 396 | history - print the history of the scantable |
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| 397 | get_fit - get a fit which has been stored witnh the data |
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| 398 | average_time - return the (weighted) time average of a scan |
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| 399 | or a list of scans |
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| 400 | average_channel - return the (median) average of a scantable |
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| 401 | average_pol - average the polarisations together. |
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| 402 | The dimension won't be reduced and |
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| 403 | all polarisations will contain the |
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| 404 | averaged spectrum. |
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| 405 | convert_pol - convert to a different polarisation type |
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| 406 | auto_quotient - return the on/off quotient with |
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| 407 | automatic detection of the on/off scans (closest |
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| 408 | in time off is selected) |
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| 409 | scale, *, / - return a scan scaled by a given factor |
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| 410 | add, +, - - return a scan with given value added |
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| 411 | bin - return a scan with binned channels |
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| 412 | resample - return a scan with resampled channels |
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| 413 | smooth - return the spectrally smoothed scan |
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| 414 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols |
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| 415 | auto_poly_baseline - automatically fit a polynomial baseline |
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| 416 | recalc_azel - recalculate azimuth and elevation based on |
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| 417 | the pointing |
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| 418 | gain_el - apply gain-elevation correction |
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| 419 | opacity - apply opacity correction |
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| 420 | convert_flux - convert to and from Jy and Kelvin brightness |
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| 421 | units |
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| 422 | freq_align - align spectra in frequency frame |
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| 423 | invert_phase - Invert the phase of the cross-correlation |
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| 424 | swap_linears - Swap XX and YY |
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| 425 | rotate_xyphase - rotate XY phase of cross correlation |
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| 426 | rotate_linpolphase - rotate the phase of the complex |
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| 427 | polarization O=Q+iU correlation |
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| 428 | freq_switch - perform frequency switching on the data |
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| 429 | stats - Determine the specified statistic, e.g. 'min' |
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| 430 | 'max', 'rms' etc. |
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| 431 | stddev - Determine the standard deviation of the current |
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| 432 | beam/if/pol |
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| 433 | [Selection] |
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| 434 | selector - a selection object to set a subset of a scantable |
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| 435 | set_scans - set (a list of) scans by index |
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| 436 | set_cycles - set (a list of) cycles by index |
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| 437 | set_beams - set (a list of) beamss by index |
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| 438 | set_ifs - set (a list of) ifs by index |
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| 439 | set_polarisations - set (a list of) polarisations by name |
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| 440 | or by index |
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| 441 | set_names - set a selection by name (wildcards allowed) |
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| 442 | set_tsys - set a selection by tsys thresholds |
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| 443 | reset - unset all selections |
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| 444 | + - merge to selections |
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| 445 | |
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| 446 | [Math] Mainly functions which operate on more than one scantable |
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| 447 | |
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| 448 | average_time - return the (weighted) time average |
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| 449 | of a list of scans |
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| 450 | quotient - return the on/off quotient |
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| 451 | simple_math - simple mathematical operations on two scantables, |
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| 452 | 'add', 'sub', 'mul', 'div' |
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| 453 | quotient - build quotient of the given on and off scans |
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| 454 | (matched pairs and 1 off/n on are valid) |
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| 455 | |
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| 456 | [Fitting] |
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| 457 | fitter |
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| 458 | auto_fit - return a scan where the function is |
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| 459 | applied to all Beams/IFs/Pols. |
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| 460 | commit - return a new scan where the fits have been |
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| 461 | commited. |
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| 462 | fit - execute the actual fitting process |
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| 463 | store_fit - store the fit parameters in the data (scantable) |
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| 464 | get_chi2 - get the Chi^2 |
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| 465 | set_scan - set the scantable to be fit |
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| 466 | set_function - set the fitting function |
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| 467 | set_parameters - set the parameters for the function(s), and |
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| 468 | set if they should be held fixed during fitting |
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| 469 | set_gauss_parameters - same as above but specialised for individual |
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| 470 | gaussian components |
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| 471 | get_parameters - get the fitted parameters |
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| 472 | plot - plot the resulting fit and/or components and |
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| 473 | residual |
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| 474 | [Plotter] |
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| 475 | asapplotter - a plotter for asap, default plotter is |
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| 476 | called 'plotter' |
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| 477 | plot - plot a scantable |
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| 478 | save - save the plot to a file ('png' ,'ps' or 'eps') |
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| 479 | set_mode - set the state of the plotter, i.e. |
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| 480 | what is to be plotted 'colour stacked' |
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| 481 | and what 'panelled' |
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| 482 | set_selection - only plot a selected part of the data |
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| 483 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax] |
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| 484 | set_legend - specify user labels for the legend indeces |
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| 485 | set_title - specify user labels for the panel indeces |
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| 486 | set_abcissa - specify a user label for the abcissa |
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| 487 | set_ordinate - specify a user label for the ordinate |
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| 488 | set_layout - specify the multi-panel layout (rows,cols) |
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| 489 | set_colors - specify a set of colours to use |
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| 490 | set_linestyles - specify a set of linestyles to use if only |
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| 491 | using one color |
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| 492 | set_histogram - plot in historam style |
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| 493 | set_mask - set a plotting mask for a specific polarization |
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| 494 | |
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| 495 | [Reading files] |
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| 496 | reader - access rpfits/sdfits files |
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| 497 | open - attach reader to a file |
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| 498 | close - detach reader from file |
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| 499 | read - read in integrations |
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| 500 | summary - list info about all integrations |
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| 501 | |
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| 502 | [General] |
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| 503 | commands - this command |
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| 504 | print - print details about a variable |
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| 505 | list_scans - list all scantables created bt the user |
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| 506 | list_files - list all files readable by asap (default rpf) |
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| 507 | del - delete the given variable from memory |
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| 508 | range - create a list of values, e.g. |
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| 509 | range(3) = [0,1,2], range(2,5) = [2,3,4] |
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| 510 | help - print help for one of the listed functions |
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| 511 | execfile - execute an asap script, e.g. execfile('myscript') |
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| 512 | list_rcparameters - print out a list of possible values to be |
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| 513 | put into $HOME/.asaprc |
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| 514 | mask_and,mask_or, |
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| 515 | mask_not - boolean operations on masks created with |
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| 516 | scantable.create_mask |
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| 517 | |
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| 518 | Note: |
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| 519 | How to use this with help: |
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| 520 | # function 'summary' |
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| 521 | [xxx] is just a category |
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| 522 | Every 'sub-level' in this list should be replaces by a '.' Period when |
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| 523 | using help |
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| 524 | Example: |
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| 525 | ASAP> help scantable # to get info on ths scantable |
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| 526 | ASAP> help scantable.summary # to get help on the scantable's |
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| 527 | ASAP> help average_time |
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| 528 | |
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| 529 | """ |
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| 530 | print x |
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| 531 | return |
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| 532 | |
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| 533 | def welcome(): |
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| 534 | return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package |
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| 535 | |
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| 536 | Please report any bugs via: |
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| 537 | http://sourcecode.atnf.csiro.au/cgi-bin/trac_asap.cgi/newticket |
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| 538 | |
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| 539 | [IMPORTANT: ASAP is 0-based] |
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| 540 | Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__) |
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