| 1 | """ |
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| 2 | This is the ATNF Single Dish Analysis package. |
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| 3 | |
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| 4 | """ |
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| 5 | import os,sys |
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| 6 | |
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| 7 | def _validate_bool(b): |
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| 8 | 'Convert b to a boolean or raise' |
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| 9 | bl = b.lower() |
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| 10 | if bl in ('f', 'no', 'false', '0', 0): return False |
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| 11 | elif bl in ('t', 'yes', 'true', '1', 1): return True |
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| 12 | else: |
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| 13 | raise ValueError('Could not convert "%s" to boolean' % b) |
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| 14 | |
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| 15 | def _validate_int(s): |
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| 16 | 'convert s to int or raise' |
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| 17 | try: return int(s) |
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| 18 | except ValueError: |
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| 19 | raise ValueError('Could not convert "%s" to int' % s) |
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| 20 | |
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| 21 | def _asap_fname(): |
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| 22 | """ |
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| 23 | Return the path to the rc file |
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| 24 | |
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| 25 | Search order: |
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| 26 | |
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| 27 | * current working dir |
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| 28 | * environ var ASAPRC |
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| 29 | * HOME/.asaprc |
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| 30 | |
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| 31 | """ |
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| 32 | |
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| 33 | fname = os.path.join( os.getcwd(), '.asaprc') |
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| 34 | if os.path.exists(fname): return fname |
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| 35 | |
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| 36 | if os.environ.has_key('ASAPRC'): |
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| 37 | path = os.environ['ASAPRC'] |
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| 38 | if os.path.exists(path): |
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| 39 | fname = os.path.join(path, '.asaprc') |
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| 40 | if os.path.exists(fname): |
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| 41 | return fname |
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| 42 | |
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| 43 | if os.environ.has_key('HOME'): |
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| 44 | home = os.environ['HOME'] |
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| 45 | fname = os.path.join(home, '.asaprc') |
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| 46 | if os.path.exists(fname): |
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| 47 | return fname |
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| 48 | return None |
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| 49 | |
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| 50 | |
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| 51 | defaultParams = { |
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| 52 | # general |
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| 53 | 'verbose' : [True, _validate_bool], |
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| 54 | 'useplotter' : [True, _validate_bool], |
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| 55 | 'insitu' : [False, _validate_bool], |
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| 56 | |
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| 57 | # plotting |
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| 58 | 'plotter.stacking' : ['p', str], |
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| 59 | 'plotter.panelling' : ['s', str], |
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| 60 | |
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| 61 | # scantable |
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| 62 | 'scantable.save' : ['ASAP', str], |
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| 63 | 'scantable.autoaverage' : [True, _validate_bool], |
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| 64 | 'scantable.freqframe' : ['LSRK', str], #default frequency frame |
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| 65 | 'scantable.allaxes' : [True, _validate_bool], # apply action to all axes |
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| 66 | 'scantable.plotter' : [True, _validate_bool], # use internal plotter |
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| 67 | 'scantable.verbosesummary' : [False, _validate_bool] |
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| 68 | |
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| 69 | # fitter |
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| 70 | } |
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| 71 | |
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| 72 | def list_rcparameters(): |
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| 73 | |
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| 74 | print """ |
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| 75 | # general |
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| 76 | # print verbose output |
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| 77 | verbose : True |
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| 78 | |
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| 79 | # preload a default plotter |
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| 80 | useplotter : True |
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| 81 | |
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| 82 | # apply operations on the input scantable or return new one |
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| 83 | insitu : False |
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| 84 | |
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| 85 | # plotting |
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| 86 | # default mode for colour stacking |
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| 87 | plotter.stacking : 'Pol' |
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| 88 | |
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| 89 | # default mode for panelling |
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| 90 | plotter.panelling : 'scan' |
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| 91 | |
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| 92 | # scantable |
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| 93 | # default ouput format when saving |
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| 94 | scantable.save : 'ASAP' |
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| 95 | # auto averaging on read |
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| 96 | scantable.autoaverage : True |
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| 97 | |
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| 98 | # default frequency frame to set when function |
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| 99 | # scantable.set_freqfrmae is called |
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| 100 | scantable.freqframe : 'LSRK' |
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| 101 | |
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| 102 | # apply action to all axes not just the cursor location |
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| 103 | scantable.allaxes : True |
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| 104 | |
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| 105 | # use internal plotter |
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| 106 | scantable.plotter : True |
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| 107 | |
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| 108 | # Control the level of information printed by summary |
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| 109 | scantable.verbosesummary : False |
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| 110 | |
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| 111 | # Fitter |
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| 112 | """ |
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| 113 | |
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| 114 | def rc_params(): |
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| 115 | 'Return the default params updated from the values in the rc file' |
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| 116 | |
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| 117 | fname = _asap_fname() |
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| 118 | |
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| 119 | if fname is None or not os.path.exists(fname): |
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| 120 | message = 'could not find rc file; returning defaults' |
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| 121 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
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| 122 | #print message |
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| 123 | return ret |
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| 124 | |
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| 125 | cnt = 0 |
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| 126 | for line in file(fname): |
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| 127 | cnt +=1 |
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| 128 | line = line.strip() |
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| 129 | if not len(line): continue |
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| 130 | if line.startswith('#'): continue |
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| 131 | tup = line.split(':',1) |
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| 132 | if len(tup) !=2: |
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| 133 | print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname)) |
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| 134 | continue |
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| 135 | |
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| 136 | key, val = tup |
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| 137 | key = key.strip() |
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| 138 | if not defaultParams.has_key(key): |
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| 139 | print ('Bad key "%s" on line %d in %s' % (key, cnt, fname)) |
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| 140 | continue |
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| 141 | |
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| 142 | default, converter = defaultParams[key] |
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| 143 | |
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| 144 | ind = val.find('#') |
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| 145 | if ind>=0: val = val[:ind] # ignore trailing comments |
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| 146 | val = val.strip() |
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| 147 | try: cval = converter(val) # try to convert to proper type or raise |
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| 148 | except Exception, msg: |
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| 149 | 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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| 150 | continue |
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| 151 | else: |
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| 152 | # Alles Klar, update dict |
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| 153 | defaultParams[key][0] = cval |
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| 154 | |
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| 155 | # strip the conveter funcs and return |
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| 156 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
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| 157 | print ('loaded rc file %s'%fname) |
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| 158 | |
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| 159 | return ret |
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| 160 | |
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| 161 | |
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| 162 | # this is the instance used by the asap classes |
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| 163 | rcParams = rc_params() |
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| 164 | |
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| 165 | rcParamsDefault = dict(rcParams.items()) # a copy |
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| 166 | |
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| 167 | def rc(group, **kwargs): |
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| 168 | """ |
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| 169 | Set the current rc params. Group is the grouping for the rc, eg |
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| 170 | for scantable.save the group is 'scantable', for plotter.stacking, the |
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| 171 | group is 'plotter', and so on. kwargs is a list of attribute |
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| 172 | name/value pairs, eg |
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| 173 | |
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| 174 | rc('scantable', save='SDFITS') |
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| 175 | |
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| 176 | sets the current rc params and is equivalent to |
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| 177 | |
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| 178 | rcParams['scantable.save'] = 'SDFITS' |
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| 179 | |
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| 180 | Use rcdefaults to restore the default rc params after changes. |
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| 181 | """ |
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| 182 | |
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| 183 | aliases = {} |
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| 184 | |
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| 185 | for k,v in kwargs.items(): |
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| 186 | name = aliases.get(k) or k |
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| 187 | key = '%s.%s' % (group, name) |
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| 188 | if not rcParams.has_key(key): |
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| 189 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name)) |
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| 190 | |
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| 191 | rcParams[key] = v |
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| 192 | |
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| 193 | |
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| 194 | def rcdefaults(): |
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| 195 | """ |
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| 196 | Restore the default rc params - the ones that were created at |
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| 197 | asap load time |
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| 198 | """ |
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| 199 | rcParams.update(rcParamsDefault) |
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| 200 | |
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| 201 | |
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| 202 | def _is_sequence_or_number(param, ptype=int): |
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| 203 | if isinstance(param,tuple) or isinstance(param,list): |
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| 204 | out = True |
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| 205 | for p in param: |
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| 206 | out &= isinstance(p,ptype) |
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| 207 | return out |
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| 208 | elif isinstance(param, ptype): |
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| 209 | return True |
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| 210 | return False |
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| 211 | |
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| 212 | from asapfitter import * |
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| 213 | from asapreader import reader |
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| 214 | from asapmath import * |
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| 215 | from scantable import * |
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| 216 | from asaplinefind import * |
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| 217 | from asapfit import * |
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| 218 | |
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| 219 | from numarray import logical_and as mask_and |
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| 220 | from numarray import logical_or as mask_or |
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| 221 | from numarray import logical_not as mask_not |
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| 222 | |
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| 223 | if rcParams['useplotter']: |
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| 224 | if os.environ.has_key('DISPLAY'): |
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| 225 | print "Initialising asapplotter with the name 'plotter' ..." |
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| 226 | import asapplotter |
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| 227 | plotter = asapplotter.asapplotter() |
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| 228 | else: |
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| 229 | print "No $DISPLAY set. Disabling plotter.\n" |
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| 230 | |
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| 231 | #from numarray ones,zeros |
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| 232 | |
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| 233 | |
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| 234 | __date__ = '$Date: 2005-03-01 04:12:17 +0000 (Tue, 01 Mar 2005) $' |
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| 235 | __version__ = '0.99' |
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| 236 | |
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| 237 | def list_scans(t = scantable): |
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| 238 | import sys, types |
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| 239 | #meta_t = type(t) |
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| 240 | #if meta_t == types.InstanceType: |
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| 241 | # t = t.__class__ |
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| 242 | #elif meta_t not in [types.ClassType, types.TypeType]: |
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| 243 | # t = meta_t |
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| 244 | globs = sys.modules['__main__'].__dict__.iteritems() |
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| 245 | print "The user created scantables are:" |
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| 246 | x = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs)) |
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| 247 | print x |
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| 248 | |
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| 249 | def commands(): |
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| 250 | x = """ |
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| 251 | [The scan container] |
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| 252 | scantable - a container for integrations/scans |
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| 253 | (can open asap/rpfits/sdfits and ms files) |
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| 254 | copy - returns a copy of a scan |
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| 255 | get_scan - gets a specific scan out of a scantable |
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| 256 | summary - print info about the scantable contents |
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| 257 | set_cursor - set a specific Beam/IF/Pol 'cursor' for |
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| 258 | further use |
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| 259 | get_cursor - print out the current cursor position |
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| 260 | stats - get specified statistic of the spectra in |
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| 261 | the scantable |
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| 262 | stddev - get the standard deviation of the spectra |
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| 263 | in the scantable |
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| 264 | get_tsys - get the TSys |
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| 265 | get_time - get the timestamps of the integrations |
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| 266 | get_unit - get the currnt unit |
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| 267 | set_unit - set the abcissa unit to be used from this |
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| 268 | point on |
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| 269 | get_abcissa - get the abcissa values and name for a given |
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| 270 | row (time) |
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| 271 | set_freqframe - set the frame info for the Spectral Axis |
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| 272 | (e.g. 'LSRK') |
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| 273 | set_doppler - set the doppler to be used from this point on |
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| 274 | set_instrument - set the instrument name |
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| 275 | get_fluxunit - get the brightness flux unit |
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| 276 | set_fluxunit - set the brightness flux unit |
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| 277 | create_mask - return an mask in the current unit |
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| 278 | for the given region. The specified regions |
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| 279 | are NOT masked |
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| 280 | get_restfreqs - get the current list of rest frequencies |
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| 281 | set_restfreqs - set a list of rest frequencies |
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| 282 | lines - print list of known spectral lines |
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| 283 | flag_spectrum - flag a whole Beam/IF/Pol |
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| 284 | save - save the scantable to disk as either 'ASAP' |
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| 285 | or 'SDFITS' |
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| 286 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans |
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| 287 | history - print the history of the scantable |
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| 288 | get_fit - get a fit which has been stored witnh the data |
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| 289 | average_time - return the (weighted) time average of a scan |
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| 290 | or a list of scans |
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| 291 | average_pol - average the polarisations together. |
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| 292 | The dimension won't be reduced and |
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| 293 | all polarisations will contain the |
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| 294 | averaged spectrum. |
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| 295 | quotient - return the on/off quotient |
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| 296 | scale - return a scan scaled by a given factor |
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| 297 | add - return a scan with given value added |
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| 298 | bin - return a scan with binned channels |
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| 299 | resample - return a scan with resampled channels |
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| 300 | smooth - return the spectrally smoothed scan |
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| 301 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols |
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| 302 | gain_el - apply gain-elevation correction |
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| 303 | opacity - apply opacity correction |
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| 304 | convert_flux - convert to and from Jy and Kelvin brightness |
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| 305 | units |
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| 306 | freq_align - align spectra in frequency frame |
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| 307 | rotate_xyphase - rotate XY phase of cross correlation |
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| 308 | rotate_linpolphase - rotate the phase of the complex |
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| 309 | polarization O=Q+iU correlation |
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| 310 | [Math] Mainly functions which operate on more than one scantable |
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| 311 | |
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| 312 | average_time - return the (weighted) time average |
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| 313 | of a list of scans |
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| 314 | quotient - return the on/off quotient |
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| 315 | simple_math - simple mathematical operations on two scantables, |
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| 316 | 'add', 'sub', 'mul', 'div' |
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| 317 | [Fitting] |
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| 318 | fitter |
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| 319 | auto_fit - return a scan where the function is |
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| 320 | applied to all Beams/IFs/Pols. |
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| 321 | commit - return a new scan where the fits have been |
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| 322 | commited. |
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| 323 | fit - execute the actual fitting process |
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| 324 | store_fit - store the fit paramaters in the data (scantable) |
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| 325 | get_chi2 - get the Chi^2 |
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| 326 | set_scan - set the scantable to be fit |
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| 327 | set_function - set the fitting function |
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| 328 | set_parameters - set the parameters for the function(s), and |
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| 329 | set if they should be held fixed during fitting |
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| 330 | set_gauss_parameters - same as above but specialised for individual |
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| 331 | gaussian components |
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| 332 | get_parameters - get the fitted parameters |
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| 333 | plot - plot the resulting fit and/or components and |
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| 334 | residual |
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| 335 | [Plotter] |
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| 336 | asapplotter - a plotter for asap, default plotter is |
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| 337 | called 'plotter' |
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| 338 | plot - plot a (list of) scantable |
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| 339 | save - save the plot to a file ('png' ,'ps' or 'eps') |
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| 340 | set_mode - set the state of the plotter, i.e. |
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| 341 | what is to be plotted 'colour stacked' |
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| 342 | and what 'panelled' |
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| 343 | set_cursor - only plot a selected part of the data |
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| 344 | set_range - set a 'zoom' window |
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| 345 | set_legend - specify user labels for the legend indeces |
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| 346 | set_title - specify user labels for the panel indeces |
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| 347 | set_ordinate - specify a user label for the ordinate |
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| 348 | set_abcissa - specify a user label for the abcissa |
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| 349 | set_layout - specify the multi-panel layout (rows,cols) |
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| 350 | |
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| 351 | [Reading files] |
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| 352 | reader - access rpfits/sdfits files |
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| 353 | read - read in integrations |
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| 354 | summary - list info about all integrations |
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| 355 | |
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| 356 | [General] |
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| 357 | commands - this command |
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| 358 | print - print details about a variable |
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| 359 | list_scans - list all scantables created bt the user |
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| 360 | del - delete the given variable from memory |
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| 361 | range - create a list of values, e.g. |
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| 362 | range(3) = [0,1,2], range(2,5) = [2,3,4] |
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| 363 | help - print help for one of the listed functions |
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| 364 | execfile - execute an asap script, e.g. execfile('myscript') |
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| 365 | list_rcparameters - print out a list of possible values to be |
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| 366 | put into $HOME/.asaprc |
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| 367 | mask_and,mask_or, |
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| 368 | mask_not - boolean operations on masks created with |
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| 369 | scantable.create_mask |
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| 370 | |
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| 371 | Note: |
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| 372 | How to use this with help: |
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| 373 | # function 'summary' |
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| 374 | [xxx] is just a category |
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| 375 | Every 'sub-level' in this list should be replaces by a '.' Period when |
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| 376 | using help |
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| 377 | Example: |
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| 378 | ASAP> help scantable # to get info on ths scantable |
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| 379 | ASAP> help scantable.summary # to get help on the scantable's |
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| 380 | ASAP> help average_time |
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| 381 | |
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| 382 | """ |
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| 383 | print x |
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| 384 | return |
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| 385 | |
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| 386 | print """Welcome to ASAP - the ATNF Single Dish Analysis Package |
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| 387 | This is a testing pre-release %s |
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| 388 | |
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| 389 | Please report any bugs to: |
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| 390 | Malte.Marquarding@csiro.au |
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| 391 | |
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| 392 | [IMPORTANT: ASAP is 0-based] |
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| 393 | Type commands() to get a list of all available ASAP commands. |
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| 394 | """ % (__version__) |
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