| 1 | """ |
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| 2 | This is the ATNF Single Dish Analysis package. |
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| 3 | |
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| 4 | """ |
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| 5 | import os,sys |
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| 6 | |
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| 7 | def _validate_bool(b): |
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| 8 | 'Convert b to a boolean or raise' |
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| 9 | bl = b.lower() |
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| 10 | if bl in ('f', 'no', 'false', '0', 0): return False |
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| 11 | elif bl in ('t', 'yes', 'true', '1', 1): return True |
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| 12 | else: |
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| 13 | raise ValueError('Could not convert "%s" to boolean' % b) |
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| 14 | |
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| 15 | def _validate_int(s): |
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| 16 | 'convert s to int or raise' |
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| 17 | try: return int(s) |
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| 18 | except ValueError: |
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| 19 | raise ValueError('Could not convert "%s" to int' % s) |
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| 20 | |
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| 21 | def _asap_fname(): |
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| 22 | """ |
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| 23 | Return the path to the rc file |
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| 24 | |
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| 25 | Search order: |
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| 26 | |
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| 27 | * current working dir |
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| 28 | * environ var ASAPRC |
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| 29 | * HOME/.asaprc |
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| 30 | |
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| 31 | """ |
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| 32 | |
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| 33 | fname = os.path.join( os.getcwd(), '.asaprc') |
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| 34 | if os.path.exists(fname): return fname |
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| 35 | |
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| 36 | if os.environ.has_key('ASAPRC'): |
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| 37 | path = os.environ['ASAPRC'] |
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| 38 | if os.path.exists(path): |
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| 39 | fname = os.path.join(path, '.asaprc') |
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| 40 | if os.path.exists(fname): |
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| 41 | return fname |
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| 42 | |
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| 43 | if os.environ.has_key('HOME'): |
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| 44 | home = os.environ['HOME'] |
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| 45 | fname = os.path.join(home, '.asaprc') |
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| 46 | if os.path.exists(fname): |
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| 47 | return fname |
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| 48 | return None |
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| 49 | |
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| 50 | |
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| 51 | defaultParams = { |
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| 52 | # general |
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| 53 | 'verbose' : [True, _validate_bool], |
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| 54 | 'useplotter' : [True, _validate_bool], |
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| 55 | 'insitu' : [True, _validate_bool], |
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| 56 | |
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| 57 | # plotting |
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| 58 | 'plotter.gui' : [True, _validate_bool], |
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| 59 | 'plotter.stacking' : ['p', str], |
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| 60 | 'plotter.panelling' : ['s', str], |
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| 61 | 'plotter.colours' : ['', str], |
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| 62 | 'plotter.linestyles' : ['', str], |
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| 63 | 'plotter.decimate' : [False, _validate_bool], |
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| 64 | 'plotter.ganged' : [True, _validate_bool], |
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| 65 | |
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| 66 | # scantable |
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| 67 | 'scantable.save' : ['ASAP', str], |
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| 68 | 'scantable.autoaverage' : [True, _validate_bool], |
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| 69 | 'scantable.freqframe' : ['LSRK', str], #default frequency frame |
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| 70 | 'scantable.allaxes' : [True, _validate_bool], # apply action to all axes |
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| 71 | 'scantable.plotter' : [True, _validate_bool], # use internal plotter |
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| 72 | 'scantable.verbosesummary' : [False, _validate_bool] |
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| 73 | |
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| 74 | # fitter |
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| 75 | } |
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| 76 | |
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| 77 | def list_rcparameters(): |
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| 78 | |
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| 79 | print """ |
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| 80 | # general |
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| 81 | # print verbose output |
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| 82 | verbose : True |
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| 83 | |
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| 84 | # preload a default plotter |
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| 85 | useplotter : True |
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| 86 | |
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| 87 | # apply operations on the input scantable or return new one |
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| 88 | insitu : True |
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| 89 | |
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| 90 | # plotting |
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| 91 | |
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| 92 | # do we want a GUI or plot to a file |
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| 93 | plotter.gui : True |
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| 94 | |
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| 95 | # default mode for colour stacking |
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| 96 | plotter.stacking : Pol |
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| 97 | |
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| 98 | # default mode for panelling |
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| 99 | plotter.panelling : scan |
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| 100 | |
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| 101 | # push panels together, to share axislabels |
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| 102 | plotter.ganged : True |
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| 103 | |
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| 104 | # decimate the number of points plotted bya afactor of |
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| 105 | # nchan/1024 |
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| 106 | plotter.decimate : False |
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| 107 | |
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| 108 | # default colours/linestyles |
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| 109 | plotter.colours : |
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| 110 | plotter.linestyles : |
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| 111 | |
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| 112 | # scantable |
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| 113 | # default ouput format when saving |
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| 114 | scantable.save : ASAP |
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| 115 | # auto averaging on read |
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| 116 | scantable.autoaverage : True |
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| 117 | |
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| 118 | # default frequency frame to set when function |
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| 119 | # scantable.set_freqfrmae is called |
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| 120 | scantable.freqframe : LSRK |
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| 121 | |
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| 122 | # apply action to all axes not just the cursor location |
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| 123 | scantable.allaxes : True |
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| 124 | |
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| 125 | # use internal plotter |
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| 126 | scantable.plotter : True |
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| 127 | |
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| 128 | # Control the level of information printed by summary |
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| 129 | scantable.verbosesummary : False |
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| 130 | |
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| 131 | # Fitter |
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| 132 | """ |
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| 133 | |
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| 134 | def rc_params(): |
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| 135 | 'Return the default params updated from the values in the rc file' |
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| 136 | |
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| 137 | fname = _asap_fname() |
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| 138 | |
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| 139 | if fname is None or not os.path.exists(fname): |
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| 140 | message = 'could not find rc file; returning defaults' |
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| 141 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
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| 142 | #print message |
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| 143 | return ret |
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| 144 | |
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| 145 | cnt = 0 |
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| 146 | for line in file(fname): |
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| 147 | cnt +=1 |
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| 148 | line = line.strip() |
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| 149 | if not len(line): continue |
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| 150 | if line.startswith('#'): continue |
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| 151 | tup = line.split(':',1) |
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| 152 | if len(tup) !=2: |
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| 153 | print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname)) |
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| 154 | continue |
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| 155 | |
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| 156 | key, val = tup |
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| 157 | key = key.strip() |
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| 158 | if not defaultParams.has_key(key): |
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| 159 | print ('Bad key "%s" on line %d in %s' % (key, cnt, fname)) |
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| 160 | continue |
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| 161 | |
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| 162 | default, converter = defaultParams[key] |
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| 163 | |
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| 164 | ind = val.find('#') |
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| 165 | if ind>=0: val = val[:ind] # ignore trailing comments |
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| 166 | val = val.strip() |
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| 167 | try: cval = converter(val) # try to convert to proper type or raise |
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| 168 | except Exception, msg: |
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| 169 | print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg)) |
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| 170 | continue |
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| 171 | else: |
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| 172 | # Alles Klar, update dict |
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| 173 | defaultParams[key][0] = cval |
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| 174 | |
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| 175 | # strip the conveter funcs and return |
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| 176 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
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| 177 | print ('loaded rc file %s'%fname) |
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| 178 | |
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| 179 | return ret |
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| 180 | |
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| 181 | |
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| 182 | # this is the instance used by the asap classes |
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| 183 | rcParams = rc_params() |
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| 184 | |
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| 185 | rcParamsDefault = dict(rcParams.items()) # a copy |
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| 186 | |
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| 187 | def rc(group, **kwargs): |
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| 188 | """ |
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| 189 | Set the current rc params. Group is the grouping for the rc, eg |
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| 190 | for scantable.save the group is 'scantable', for plotter.stacking, the |
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| 191 | group is 'plotter', and so on. kwargs is a list of attribute |
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| 192 | name/value pairs, eg |
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| 193 | |
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| 194 | rc('scantable', save='SDFITS') |
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| 195 | |
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| 196 | sets the current rc params and is equivalent to |
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| 197 | |
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| 198 | rcParams['scantable.save'] = 'SDFITS' |
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| 199 | |
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| 200 | Use rcdefaults to restore the default rc params after changes. |
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| 201 | """ |
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| 202 | |
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| 203 | aliases = {} |
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| 204 | |
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| 205 | for k,v in kwargs.items(): |
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| 206 | name = aliases.get(k) or k |
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| 207 | key = '%s.%s' % (group, name) |
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| 208 | if not rcParams.has_key(key): |
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| 209 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name)) |
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| 210 | |
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| 211 | rcParams[key] = v |
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| 212 | |
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| 213 | |
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| 214 | def rcdefaults(): |
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| 215 | """ |
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| 216 | Restore the default rc params - the ones that were created at |
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| 217 | asap load time |
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| 218 | """ |
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| 219 | rcParams.update(rcParamsDefault) |
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| 220 | |
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| 221 | |
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| 222 | def _is_sequence_or_number(param, ptype=int): |
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| 223 | if isinstance(param,tuple) or isinstance(param,list): |
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| 224 | out = True |
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| 225 | for p in param: |
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| 226 | out &= isinstance(p,ptype) |
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| 227 | return out |
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| 228 | elif isinstance(param, ptype): |
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| 229 | return True |
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| 230 | return False |
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| 231 | |
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| 232 | |
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| 233 | # workaround for ipython, which redirects this if banner=0 in ipythonrc |
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| 234 | sys.stdout = sys.__stdout__ |
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| 235 | sys.stderr = sys.__stderr__ |
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| 236 | |
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| 237 | # Logging |
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| 238 | from asap._asap import Log as _asaplog |
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| 239 | global asaplog |
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| 240 | asaplog=_asaplog() |
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| 241 | if rcParams['verbose']: |
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| 242 | asaplog.enable() |
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| 243 | else: |
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| 244 | asaplog.disable() |
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| 245 | |
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| 246 | def print_log(): |
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| 247 | log = asaplog.pop() |
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| 248 | if len(log) and rcParams['verbose']: print log |
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| 249 | return |
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| 250 | |
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| 251 | from asapfitter import * |
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| 252 | from asapreader import reader |
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| 253 | |
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| 254 | from asapmath import * |
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| 255 | from scantable import * |
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| 256 | from asaplinefind import * |
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| 257 | from asapfit import * |
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| 258 | |
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| 259 | from numarray import logical_and as mask_and |
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| 260 | from numarray import logical_or as mask_or |
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| 261 | from numarray import logical_not as mask_not |
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| 262 | |
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| 263 | if rcParams['useplotter']: |
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| 264 | from asapplotter import * |
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| 265 | gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui'] |
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| 266 | plotter = asapplotter(gui) |
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| 267 | del gui |
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| 268 | |
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| 269 | __date__ = '$Date: 2005-12-07 03:18:09 +0000 (Wed, 07 Dec 2005) $'.split()[1] |
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| 270 | __version__ = '1.2.1' |
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| 271 | |
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| 272 | if rcParams['verbose']: |
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| 273 | def list_scans(t = scantable): |
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| 274 | import sys, types |
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| 275 | globs = sys.modules['__main__'].__dict__.iteritems() |
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| 276 | print "The user created scantables are:" |
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| 277 | sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs)) |
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| 278 | print filter(lambda x: not x.startswith('_'), sts) |
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| 279 | return |
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| 280 | |
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| 281 | def commands(): |
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| 282 | x = """ |
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| 283 | [The scan container] |
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| 284 | scantable - a container for integrations/scans |
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| 285 | (can open asap/rpfits/sdfits and ms files) |
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| 286 | copy - returns a copy of a scan |
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| 287 | get_scan - gets a specific scan out of a scantable |
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| 288 | (by name or number) |
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| 289 | summary - print info about the scantable contents |
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| 290 | set_cursor - set a specific Beam/IF/Pol 'cursor' for |
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| 291 | further use |
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| 292 | get_cursor - print out the current cursor position |
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| 293 | stats - get specified statistic of the spectra in |
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| 294 | the scantable |
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| 295 | stddev - get the standard deviation of the spectra |
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| 296 | in the scantable |
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| 297 | get_tsys - get the TSys |
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| 298 | get_time - get the timestamps of the integrations |
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| 299 | get_sourcename - get the source names of the scans |
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| 300 | get_unit - get the currnt unit |
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| 301 | set_unit - set the abcissa unit to be used from this |
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| 302 | point on |
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| 303 | get_abcissa - get the abcissa values and name for a given |
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| 304 | row (time) |
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| 305 | set_freqframe - set the frame info for the Spectral Axis |
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| 306 | (e.g. 'LSRK') |
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| 307 | set_doppler - set the doppler to be used from this point on |
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| 308 | set_instrument - set the instrument name |
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| 309 | get_fluxunit - get the brightness flux unit |
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| 310 | set_fluxunit - set the brightness flux unit |
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| 311 | create_mask - return an mask in the current unit |
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| 312 | for the given region. The specified regions |
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| 313 | are NOT masked |
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| 314 | get_restfreqs - get the current list of rest frequencies |
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| 315 | set_restfreqs - set a list of rest frequencies |
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| 316 | lines - print list of known spectral lines |
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| 317 | flag_spectrum - flag a whole Beam/IF/Pol |
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| 318 | save - save the scantable to disk as either 'ASAP' |
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| 319 | or 'SDFITS' |
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| 320 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans |
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| 321 | nscan - the number of scans in the scantable |
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| 322 | nrow - te number of integrations in the scantable |
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| 323 | history - print the history of the scantable |
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| 324 | get_fit - get a fit which has been stored witnh the data |
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| 325 | average_time - return the (weighted) time average of a scan |
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| 326 | or a list of scans |
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| 327 | average_pol - average the polarisations together. |
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| 328 | The dimension won't be reduced and |
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| 329 | all polarisations will contain the |
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| 330 | averaged spectrum. |
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| 331 | auto_quotient - return the on/off quotient with |
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| 332 | automatic detection of the on/off scans |
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| 333 | (matched pairs and 1 off - n on) |
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| 334 | quotient - return the on/off quotient |
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| 335 | scale - return a scan scaled by a given factor |
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| 336 | add - return a scan with given value added |
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| 337 | bin - return a scan with binned channels |
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| 338 | resample - return a scan with resampled channels |
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| 339 | smooth - return the spectrally smoothed scan |
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| 340 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols |
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| 341 | auto_poly_baseline - automatically fit a polynomial baseline |
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| 342 | recalc_azel - recalculate azimuth and elevation based on |
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| 343 | the pointing |
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| 344 | gain_el - apply gain-elevation correction |
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| 345 | opacity - apply opacity correction |
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| 346 | convert_flux - convert to and from Jy and Kelvin brightness |
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| 347 | units |
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| 348 | freq_align - align spectra in frequency frame |
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| 349 | rotate_xyphase - rotate XY phase of cross correlation |
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| 350 | rotate_linpolphase - rotate the phase of the complex |
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| 351 | polarization O=Q+iU correlation |
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| 352 | freq_switch - perform frequency switching on the data |
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| 353 | stats - Determine the specified statistic, e.g. 'min' |
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| 354 | 'max', 'rms' etc. |
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| 355 | stddev - Determine the standard deviation of the current |
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| 356 | beam/if/pol |
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| 357 | |
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| 358 | [Math] Mainly functions which operate on more than one scantable |
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| 359 | |
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| 360 | average_time - return the (weighted) time average |
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| 361 | of a list of scans |
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| 362 | quotient - return the on/off quotient |
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| 363 | simple_math - simple mathematical operations on two scantables, |
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| 364 | 'add', 'sub', 'mul', 'div' |
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| 365 | [Fitting] |
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| 366 | fitter |
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| 367 | auto_fit - return a scan where the function is |
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| 368 | applied to all Beams/IFs/Pols. |
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| 369 | commit - return a new scan where the fits have been |
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| 370 | commited. |
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| 371 | fit - execute the actual fitting process |
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| 372 | store_fit - store the fit paramaters in the data (scantable) |
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| 373 | get_chi2 - get the Chi^2 |
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| 374 | set_scan - set the scantable to be fit |
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| 375 | set_function - set the fitting function |
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| 376 | set_parameters - set the parameters for the function(s), and |
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| 377 | set if they should be held fixed during fitting |
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| 378 | set_gauss_parameters - same as above but specialised for individual |
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| 379 | gaussian components |
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| 380 | get_parameters - get the fitted parameters |
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| 381 | plot - plot the resulting fit and/or components and |
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| 382 | residual |
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| 383 | [Plotter] |
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| 384 | asapplotter - a plotter for asap, default plotter is |
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| 385 | called 'plotter' |
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| 386 | plot - plot a (list of) scantable |
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| 387 | save - save the plot to a file ('png' ,'ps' or 'eps') |
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| 388 | set_mode - set the state of the plotter, i.e. |
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| 389 | what is to be plotted 'colour stacked' |
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| 390 | and what 'panelled' |
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| 391 | set_cursor - only plot a selected part of the data |
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| 392 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax] |
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| 393 | set_legend - specify user labels for the legend indeces |
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| 394 | set_title - specify user labels for the panel indeces |
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| 395 | set_abcissa - specify a user label for the abcissa |
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| 396 | set_ordinate - specify a user label for the ordinate |
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| 397 | set_layout - specify the multi-panel layout (rows,cols) |
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| 398 | set_colors - specify a set of colours to use |
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| 399 | set_linestyles - specify a set of linestyles to use if only |
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| 400 | using one color |
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| 401 | set_mask - set a plotting mask for a specific polarization |
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| 402 | |
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| 403 | [Reading files] |
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| 404 | reader - access rpfits/sdfits files |
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| 405 | read - read in integrations |
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| 406 | summary - list info about all integrations |
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| 407 | |
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| 408 | [General] |
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| 409 | commands - this command |
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| 410 | print - print details about a variable |
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| 411 | list_scans - list all scantables created bt the user |
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| 412 | del - delete the given variable from memory |
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| 413 | range - create a list of values, e.g. |
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| 414 | range(3) = [0,1,2], range(2,5) = [2,3,4] |
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| 415 | help - print help for one of the listed functions |
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| 416 | execfile - execute an asap script, e.g. execfile('myscript') |
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| 417 | list_rcparameters - print out a list of possible values to be |
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| 418 | put into $HOME/.asaprc |
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| 419 | mask_and,mask_or, |
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| 420 | mask_not - boolean operations on masks created with |
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| 421 | scantable.create_mask |
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| 422 | |
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| 423 | Note: |
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| 424 | How to use this with help: |
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| 425 | # function 'summary' |
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| 426 | [xxx] is just a category |
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| 427 | Every 'sub-level' in this list should be replaces by a '.' Period when |
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| 428 | using help |
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| 429 | Example: |
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| 430 | ASAP> help scantable # to get info on ths scantable |
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| 431 | ASAP> help scantable.summary # to get help on the scantable's |
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| 432 | ASAP> help average_time |
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| 433 | |
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| 434 | """ |
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| 435 | print x |
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| 436 | return |
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| 437 | |
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| 438 | def welcome(): |
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| 439 | return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package |
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| 440 | |
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| 441 | Please report any bugs to: |
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| 442 | asap@atnf.csiro.au |
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| 443 | |
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| 444 | [IMPORTANT: ASAP is 0-based] |
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| 445 | Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__) |
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