| [100] | 1 | """
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| 2 | This is the ATNF Single Dish Analysis package.
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| 3 |
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| 4 | """
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| [1080] | 5 | import os,sys,shutil, platform
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| [226] | 6 |
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| [1080] | 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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| [1171] | 20 | # Allow user defined data location
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| 21 | if os.environ.has_key("ASAPDATA"):
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| 22 | if os.path.exists(os.environ["ASAPDATA"]):
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| 23 | asapdata = os.environ["ASAPDATA"]
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| [1371] | 24 | # use AIPSPATH if defined and "data" dir present
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| 25 | if not os.environ.has_key("AIPSPATH") or \
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| 26 | not os.path.exists(os.environ["AIPSPATH"].split()[0]+"/data"):
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| [1316] | 27 | os.environ["AIPSPATH"] = "%s %s somwhere" % ( asapdata, plf)
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| [1171] | 28 | # set up user space
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| [1080] | 29 | userdir = os.environ["HOME"]+"/.asap"
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| 30 | if not os.path.exists(userdir):
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| 31 | print 'First time ASAP use. Setting up ~/.asap'
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| 32 | os.mkdir(userdir)
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| 33 | shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap")
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| [1434] | 34 | shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
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| 35 | userdir+"/ipy_user_conf.py")
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| [1080] | 36 | f = file(userdir+"/asapuserfuncs.py", "w")
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| 37 | f.close()
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| 38 | f = file(userdir+"/ipythonrc", "w")
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| 39 | f.close()
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| [1472] | 40 | else:
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| 41 | # upgrade to support later ipython versions
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| 42 | if not os.path.exists(userdir+"/ipy_user_conf.py"):
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| 43 | shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
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| 44 | userdir+"/ipy_user_conf.py")
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| 45 |
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| [1171] | 46 | # remove from namespace
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| [1080] | 47 | del asapdata, userdir, shutil, platform
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| 48 |
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| [513] | 49 | def _validate_bool(b):
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| [226] | 50 | 'Convert b to a boolean or raise'
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| 51 | bl = b.lower()
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| 52 | if bl in ('f', 'no', 'false', '0', 0): return False
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| 53 | elif bl in ('t', 'yes', 'true', '1', 1): return True
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| 54 | else:
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| 55 | raise ValueError('Could not convert "%s" to boolean' % b)
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| 56 |
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| [513] | 57 | def _validate_int(s):
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| [226] | 58 | 'convert s to int or raise'
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| 59 | try: return int(s)
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| 60 | except ValueError:
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| 61 | raise ValueError('Could not convert "%s" to int' % s)
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| 62 |
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| [513] | 63 | def _asap_fname():
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| [226] | 64 | """
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| 65 | Return the path to the rc file
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| 66 |
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| 67 | Search order:
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| 68 |
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| 69 | * current working dir
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| 70 | * environ var ASAPRC
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| [274] | 71 | * HOME/.asaprc
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| [706] | 72 |
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| [226] | 73 | """
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| 74 |
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| 75 | fname = os.path.join( os.getcwd(), '.asaprc')
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| 76 | if os.path.exists(fname): return fname
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| 77 |
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| 78 | if os.environ.has_key('ASAPRC'):
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| 79 | path = os.environ['ASAPRC']
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| 80 | if os.path.exists(path):
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| 81 | fname = os.path.join(path, '.asaprc')
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| 82 | if os.path.exists(fname):
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| 83 | return fname
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| 84 |
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| 85 | if os.environ.has_key('HOME'):
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| 86 | home = os.environ['HOME']
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| 87 | fname = os.path.join(home, '.asaprc')
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| 88 | if os.path.exists(fname):
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| 89 | return fname
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| 90 | return None
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| 91 |
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| [706] | 92 |
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| [226] | 93 | defaultParams = {
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| 94 | # general
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| [513] | 95 | 'verbose' : [True, _validate_bool],
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| 96 | 'useplotter' : [True, _validate_bool],
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| [542] | 97 | 'insitu' : [True, _validate_bool],
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| [706] | 98 |
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| [226] | 99 | # plotting
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| [706] | 100 | 'plotter.gui' : [True, _validate_bool],
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| [226] | 101 | 'plotter.stacking' : ['p', str],
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| 102 | 'plotter.panelling' : ['s', str],
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| [700] | 103 | 'plotter.colours' : ['', str],
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| 104 | 'plotter.linestyles' : ['', str],
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| [710] | 105 | 'plotter.decimate' : [False, _validate_bool],
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| 106 | 'plotter.ganged' : [True, _validate_bool],
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| [1022] | 107 | 'plotter.histogram' : [False, _validate_bool],
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| [1097] | 108 | 'plotter.papertype' : ['A4', str],
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| [1513] | 109 | 'plotter.xaxisformatting' : ['asap', str],
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| [710] | 110 |
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| [226] | 111 | # scantable
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| 112 | 'scantable.save' : ['ASAP', str],
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| [513] | 113 | 'scantable.autoaverage' : [True, _validate_bool],
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| [226] | 114 | 'scantable.freqframe' : ['LSRK', str], #default frequency frame
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| [1076] | 115 | 'scantable.verbosesummary' : [False, _validate_bool],
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| [1422] | 116 | 'scantable.storage' : ['memory', str],
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| [1504] | 117 | 'scantable.history' : [True, _validate_bool],
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| 118 | 'scantable.reference' : ['.*(e|w|_R)$', str]
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| [226] | 119 | # fitter
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| 120 | }
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| 121 |
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| [255] | 122 | def list_rcparameters():
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| [706] | 123 |
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| [255] | 124 | print """
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| [737] | 125 | # general
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| 126 | # print verbose output
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| 127 | verbose : True
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| [255] | 128 |
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| [737] | 129 | # preload a default plotter
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| 130 | useplotter : True
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| [255] | 131 |
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| [737] | 132 | # apply operations on the input scantable or return new one
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| 133 | insitu : True
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| [706] | 134 |
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| [737] | 135 | # plotting
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| [710] | 136 |
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| [737] | 137 | # do we want a GUI or plot to a file
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| 138 | plotter.gui : True
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| [710] | 139 |
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| [737] | 140 | # default mode for colour stacking
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| 141 | plotter.stacking : Pol
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| [255] | 142 |
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| [737] | 143 | # default mode for panelling
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| 144 | plotter.panelling : scan
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| [255] | 145 |
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| [737] | 146 | # push panels together, to share axislabels
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| 147 | plotter.ganged : True
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| [710] | 148 |
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| [1513] | 149 | # decimate the number of points plotted by a factor of
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| [737] | 150 | # nchan/1024
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| 151 | plotter.decimate : False
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| [733] | 152 |
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| [737] | 153 | # default colours/linestyles
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| 154 | plotter.colours :
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| 155 | plotter.linestyles :
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| [700] | 156 |
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| [1022] | 157 | # enable/disable histogram plotting
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| 158 | plotter.histogram : False
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| 159 |
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| [1097] | 160 | # ps paper type
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| 161 | plotter.papertype : A4
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| 162 |
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| [1513] | 163 | # The formatting style of the xaxis
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| 164 | plotter.xaxisformatting : 'asap' or 'mpl'
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| 165 |
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| [737] | 166 | # scantable
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| [1076] | 167 |
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| [1259] | 168 | # default storage of scantable ('memory'/'disk')
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| [1076] | 169 | scantable.storage : memory
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| [1422] | 170 |
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| 171 | # write history of each call to scantable
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| 172 | scantable.history : True
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| 173 |
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| [737] | 174 | # default ouput format when saving
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| 175 | scantable.save : ASAP
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| [1422] | 176 |
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| [737] | 177 | # auto averaging on read
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| 178 | scantable.autoaverage : True
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| [255] | 179 |
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| [737] | 180 | # default frequency frame to set when function
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| [1097] | 181 | # scantable.set_freqframe is called
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| [737] | 182 | scantable.freqframe : LSRK
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| [255] | 183 |
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| [737] | 184 | # Control the level of information printed by summary
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| 185 | scantable.verbosesummary : False
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| [706] | 186 |
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| [1504] | 187 | # Control the identification of reference (off) scans
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| 188 | # This is has to be a regular expression
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| 189 | scantable.reference : .*(e|w|_R)$
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| [737] | 190 | # Fitter
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| 191 | """
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| [706] | 192 |
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| [226] | 193 | def rc_params():
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| 194 | 'Return the default params updated from the values in the rc file'
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| [706] | 195 |
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| [513] | 196 | fname = _asap_fname()
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| [706] | 197 |
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| [226] | 198 | if fname is None or not os.path.exists(fname):
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| 199 | message = 'could not find rc file; returning defaults'
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| 200 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
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| 201 | #print message
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| 202 | return ret
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| [706] | 203 |
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| [226] | 204 | cnt = 0
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| 205 | for line in file(fname):
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| 206 | cnt +=1
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| 207 | line = line.strip()
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| 208 | if not len(line): continue
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| 209 | if line.startswith('#'): continue
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| 210 | tup = line.split(':',1)
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| 211 | if len(tup) !=2:
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| 212 | print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
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| 213 | continue
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| [706] | 214 |
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| [226] | 215 | key, val = tup
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| 216 | key = key.strip()
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| 217 | if not defaultParams.has_key(key):
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| 218 | print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
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| 219 | continue
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| [706] | 220 |
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| [226] | 221 | default, converter = defaultParams[key]
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| 222 |
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| 223 | ind = val.find('#')
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| 224 | if ind>=0: val = val[:ind] # ignore trailing comments
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| 225 | val = val.strip()
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| 226 | try: cval = converter(val) # try to convert to proper type or raise
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| [1080] | 227 | except ValueError, msg:
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| [226] | 228 | 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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| 229 | continue
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| 230 | else:
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| 231 | # Alles Klar, update dict
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| 232 | defaultParams[key][0] = cval
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| 233 |
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| 234 | # strip the conveter funcs and return
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| 235 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
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| [466] | 236 | print ('loaded rc file %s'%fname)
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| [226] | 237 |
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| 238 | return ret
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| 239 |
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| 240 |
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| 241 | # this is the instance used by the asap classes
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| [706] | 242 | rcParams = rc_params()
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| [226] | 243 |
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| 244 | rcParamsDefault = dict(rcParams.items()) # a copy
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| 245 |
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| 246 | def rc(group, **kwargs):
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| 247 | """
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| 248 | Set the current rc params. Group is the grouping for the rc, eg
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| [379] | 249 | for scantable.save the group is 'scantable', for plotter.stacking, the
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| 250 | group is 'plotter', and so on. kwargs is a list of attribute
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| [226] | 251 | name/value pairs, eg
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| 252 |
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| [379] | 253 | rc('scantable', save='SDFITS')
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| [226] | 254 |
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| 255 | sets the current rc params and is equivalent to
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| [706] | 256 |
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| [379] | 257 | rcParams['scantable.save'] = 'SDFITS'
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| [226] | 258 |
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| 259 | Use rcdefaults to restore the default rc params after changes.
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| 260 | """
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| 261 |
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| [379] | 262 | aliases = {}
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| [706] | 263 |
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| [226] | 264 | for k,v in kwargs.items():
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| 265 | name = aliases.get(k) or k
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| [1422] | 266 | if len(group):
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| 267 | key = '%s.%s' % (group, name)
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| 268 | else:
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| 269 | key = name
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| [226] | 270 | if not rcParams.has_key(key):
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| 271 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
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| [706] | 272 |
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| [226] | 273 | rcParams[key] = v
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| 274 |
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| 275 |
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| 276 | def rcdefaults():
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| 277 | """
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| 278 | Restore the default rc params - the ones that were created at
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| 279 | asap load time
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| 280 | """
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| 281 | rcParams.update(rcParamsDefault)
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| 282 |
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| [1295] | 283 | def _n_bools(n, val):
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| 284 | return [ val for i in xrange(n) ]
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| [513] | 285 |
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| 286 | def _is_sequence_or_number(param, ptype=int):
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| 287 | if isinstance(param,tuple) or isinstance(param,list):
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| [928] | 288 | if len(param) == 0: return True # empty list
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| [513] | 289 | out = True
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| 290 | for p in param:
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| 291 | out &= isinstance(p,ptype)
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| 292 | return out
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| 293 | elif isinstance(param, ptype):
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| 294 | return True
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| 295 | return False
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| 296 |
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| [928] | 297 | def _to_list(param, ptype=int):
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| 298 | if isinstance(param, ptype):
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| 299 | if ptype is str: return param.split()
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| 300 | else: return [param]
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| 301 | if _is_sequence_or_number(param, ptype):
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| 302 | return param
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| 303 | return None
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| [715] | 304 |
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| [944] | 305 | def unique(x):
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| [992] | 306 | """
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| 307 | Return the unique values in a list
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| 308 | Parameters:
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| 309 | x: the list to reduce
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| 310 | Examples:
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| 311 | x = [1,2,3,3,4]
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| 312 | print unique(x)
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| 313 | [1,2,3,4]
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| 314 | """
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| [944] | 315 | return dict([ (val, 1) for val in x]).keys()
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| 316 |
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| [992] | 317 | def list_files(path=".",suffix="rpf"):
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| 318 | """
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| 319 | Return a list files readable by asap, such as rpf, sdfits, mbf, asap
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| 320 | Parameters:
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| 321 | path: The directory to list (default '.')
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| 322 | suffix: The file extension (default rpf)
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| 323 | Example:
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| 324 | files = list_files("data/","sdfits")
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| 325 | print files
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| 326 | ['data/2001-09-01_0332_P363.sdfits',
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| 327 | 'data/2003-04-04_131152_t0002.sdfits',
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| 328 | 'data/Sgr_86p262_best_SPC.sdfits']
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| 329 | """
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| 330 | if not os.path.isdir(path):
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| 331 | return None
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| [1295] | 332 | valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split()
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| [992] | 333 | if not suffix in valid:
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| 334 | return None
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| 335 | files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
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| 336 | return filter(lambda x: x.endswith(suffix),files)
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| 337 |
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| [715] | 338 | # workaround for ipython, which redirects this if banner=0 in ipythonrc
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| 339 | sys.stdout = sys.__stdout__
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| 340 | sys.stderr = sys.__stderr__
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| 341 |
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| 342 | # Logging
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| 343 | from asap._asap import Log as _asaplog
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| 344 | global asaplog
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| [710] | 345 | asaplog=_asaplog()
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| [715] | 346 | if rcParams['verbose']:
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| 347 | asaplog.enable()
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| 348 | else:
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| 349 | asaplog.disable()
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| 350 |
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| 351 | def print_log():
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| 352 | log = asaplog.pop()
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| 353 | if len(log) and rcParams['verbose']: print log
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| 354 | return
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| 355 |
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| [1295] | 356 | def mask_and(a, b):
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| 357 | assert(len(a)==len(b))
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| 358 | return [ a[i] & b[i] for i in xrange(len(a)) ]
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| [1134] | 359 |
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| [1295] | 360 | def mask_or(a, b):
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| 361 | assert(len(a)==len(b))
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| 362 | return [ a[i] | b[i] for i in xrange(len(a)) ]
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| 363 |
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| 364 | def mask_not(a):
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| 365 | return [ not i for i in a ]
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| 366 |
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| [1117] | 367 | from asapfitter import fitter
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| [895] | 368 | from asapreader import reader
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| [944] | 369 | from selector import selector
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| [710] | 370 |
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| [100] | 371 | from asapmath import *
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| [1080] | 372 | from scantable import scantable
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| [1097] | 373 | from asaplinefind import linefinder
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| [1134] | 374 | from linecatalog import linecatalog
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| [285] | 375 |
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| [928] | 376 | if rcParams['useplotter']:
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| [1295] | 377 | try:
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| [1423] | 378 | from asapplotter import asapplotter
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| 379 | gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
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| 380 | if gui:
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| [1422] | 381 | import matplotlib
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| 382 | matplotlib.use("TkAgg")
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| [1423] | 383 | import pylab
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| [1422] | 384 | xyplotter = pylab
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| [1423] | 385 | plotter = asapplotter(gui)
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| 386 | del gui
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| [1295] | 387 | except ImportError:
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| [1423] | 388 | print "Matplotlib not installed. No plotting available"
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| [285] | 389 |
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| [574] | 390 | __date__ = '$Date: 2009-03-13 00:52:52 +0000 (Fri, 13 Mar 2009) $'.split()[1]
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| [1523] | 391 | __version__ = '2.3.0'
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| [100] | 392 |
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| [1193] | 393 | def is_ipython():
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| [1259] | 394 | return '__IP' in dir(sys.modules["__main__"])
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| [1193] | 395 | if is_ipython():
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| [1014] | 396 | def version(): print "ASAP %s(%s)"% (__version__, __date__)
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| [1422] | 397 |
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| [706] | 398 | def list_scans(t = scantable):
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| [1295] | 399 | import types
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| [706] | 400 | globs = sys.modules['__main__'].__dict__.iteritems()
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| 401 | print "The user created scantables are:"
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| 402 | sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
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| 403 | print filter(lambda x: not x.startswith('_'), sts)
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| 404 | return
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| [100] | 405 |
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| [715] | 406 | def commands():
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| 407 | x = """
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| [113] | 408 | [The scan container]
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| 409 | scantable - a container for integrations/scans
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| [182] | 410 | (can open asap/rpfits/sdfits and ms files)
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| [113] | 411 | copy - returns a copy of a scan
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| 412 | get_scan - gets a specific scan out of a scantable
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| [984] | 413 | (by name or number)
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| [1093] | 414 | drop_scan - drops a specific scan out of a scantable
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| 415 | (by number)
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| [984] | 416 | set_selection - set a new subselection of the data
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| 417 | get_selection - get the current selection object
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| [113] | 418 | summary - print info about the scantable contents
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| [182] | 419 | stats - get specified statistic of the spectra in
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| 420 | the scantable
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| 421 | stddev - get the standard deviation of the spectra
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| 422 | in the scantable
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| [113] | 423 | get_tsys - get the TSys
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| 424 | get_time - get the timestamps of the integrations
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| [1351] | 425 | get_inttime - get the integration time
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| [733] | 426 | get_sourcename - get the source names of the scans
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| [794] | 427 | get_azimuth - get the azimuth of the scans
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| 428 | get_elevation - get the elevation of the scans
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| 429 | get_parangle - get the parallactic angle of the scans
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| [876] | 430 | get_unit - get the current unit
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| [513] | 431 | set_unit - set the abcissa unit to be used from this
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| 432 | point on
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| [255] | 433 | get_abcissa - get the abcissa values and name for a given
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| 434 | row (time)
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| [1259] | 435 | get_column_names - get the names of the columns in the scantable
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| 436 | for use with selector.set_query
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| [113] | 437 | set_freqframe - set the frame info for the Spectral Axis
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| 438 | (e.g. 'LSRK')
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| [276] | 439 | set_doppler - set the doppler to be used from this point on
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| [984] | 440 | set_dirframe - set the frame for the direction on the sky
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| [240] | 441 | set_instrument - set the instrument name
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| [1190] | 442 | set_feedtype - set the feed type
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| [255] | 443 | get_fluxunit - get the brightness flux unit
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| [240] | 444 | set_fluxunit - set the brightness flux unit
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| [1508] | 445 | set_sourcetype - set the type of the source - source or reference
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| [188] | 446 | create_mask - return an mask in the current unit
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| 447 | for the given region. The specified regions
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| 448 | are NOT masked
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| [255] | 449 | get_restfreqs - get the current list of rest frequencies
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| 450 | set_restfreqs - set a list of rest frequencies
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| [1471] | 451 | shift_refpix - shift the reference pixel of the IFs
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| 452 | set_spectrum - overwrite the spectrum for a given row
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| 453 | get_spectrum - retrieve the spectrum for a given
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| 454 | get_mask - retrieve the mask for a given
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| [1012] | 455 | flag - flag selected channels in the data
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| [1192] | 456 | lag_flag - flag specified frequency in the data
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| [1151] | 457 | save - save the scantable to disk as either 'ASAP',
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| 458 | 'SDFITS' or 'ASCII'
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| [486] | 459 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
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| [733] | 460 | nscan - the number of scans in the scantable
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| [1422] | 461 | nrow - the number of spectra in the scantable
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| [486] | 462 | history - print the history of the scantable
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| [530] | 463 | get_fit - get a fit which has been stored witnh the data
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| [706] | 464 | average_time - return the (weighted) time average of a scan
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| [513] | 465 | or a list of scans
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| 466 | average_pol - average the polarisations together.
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| [1144] | 467 | average_beam - average the beams together.
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| [992] | 468 | convert_pol - convert to a different polarisation type
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| [690] | 469 | auto_quotient - return the on/off quotient with
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| [1069] | 470 | automatic detection of the on/off scans (closest
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| 471 | in time off is selected)
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| [1144] | 472 | mx_quotient - Form a quotient using MX data (off beams)
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| [1014] | 473 | scale, *, / - return a scan scaled by a given factor
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| 474 | add, +, - - return a scan with given value added
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| [513] | 475 | bin - return a scan with binned channels
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| 476 | resample - return a scan with resampled channels
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| 477 | smooth - return the spectrally smoothed scan
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| 478 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
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| [706] | 479 | auto_poly_baseline - automatically fit a polynomial baseline
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| [780] | 480 | recalc_azel - recalculate azimuth and elevation based on
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| 481 | the pointing
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| [513] | 482 | gain_el - apply gain-elevation correction
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| 483 | opacity - apply opacity correction
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| 484 | convert_flux - convert to and from Jy and Kelvin brightness
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| [255] | 485 | units
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| [513] | 486 | freq_align - align spectra in frequency frame
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| [1014] | 487 | invert_phase - Invert the phase of the cross-correlation
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| [1351] | 488 | swap_linears - Swap XX and YY (or RR LL)
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| [513] | 489 | rotate_xyphase - rotate XY phase of cross correlation
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| 490 | rotate_linpolphase - rotate the phase of the complex
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| 491 | polarization O=Q+iU correlation
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| [733] | 492 | freq_switch - perform frequency switching on the data
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| 493 | stats - Determine the specified statistic, e.g. 'min'
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| 494 | 'max', 'rms' etc.
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| 495 | stddev - Determine the standard deviation of the current
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| 496 | beam/if/pol
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| [1014] | 497 | [Selection]
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| 498 | selector - a selection object to set a subset of a scantable
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| 499 | set_scans - set (a list of) scans by index
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| 500 | set_cycles - set (a list of) cycles by index
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| 501 | set_beams - set (a list of) beamss by index
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| 502 | set_ifs - set (a list of) ifs by index
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| 503 | set_polarisations - set (a list of) polarisations by name
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| 504 | or by index
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| 505 | set_names - set a selection by name (wildcards allowed)
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| 506 | set_tsys - set a selection by tsys thresholds
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| [1259] | 507 | set_query - set a selection by SQL-like query, e.g. BEAMNO==1
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| [1351] | 508 | ( also get_ functions for all these )
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| [1014] | 509 | reset - unset all selections
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| [1351] | 510 | + - merge two selections
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| [733] | 511 |
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| [513] | 512 | [Math] Mainly functions which operate on more than one scantable
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| [100] | 513 |
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| [706] | 514 | average_time - return the (weighted) time average
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| [513] | 515 | of a list of scans
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| 516 | quotient - return the on/off quotient
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| 517 | simple_math - simple mathematical operations on two scantables,
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| 518 | 'add', 'sub', 'mul', 'div'
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| [1069] | 519 | quotient - build quotient of the given on and off scans
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| [1351] | 520 | (matched pairs and 1 off - n on are valid)
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| [1117] | 521 | merge - merge a list of scantables
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| [1069] | 522 |
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| [1151] | 523 | [Line Catalog]
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|---|
| 524 | linecatalog - a linecatalog wrapper, taking an ASCII or
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| 525 | internal format table
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| 526 | summary - print a summary of the current selection
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| 527 | set_name - select a subset by name pattern, e.g. '*OH*'
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| 528 | set_strength_limits - select a subset by line strength limits
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| 529 | set_frequency_limits - select a subset by frequency limits
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| 530 | reset - unset all selections
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| 531 | save - save the current subset to a table (internal
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| 532 | format)
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| 533 | get_row - get the name and frequency from a specific
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| 534 | row in the table
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| [513] | 535 | [Fitting]
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| [113] | 536 | fitter
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| 537 | auto_fit - return a scan where the function is
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| 538 | applied to all Beams/IFs/Pols.
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| 539 | commit - return a new scan where the fits have been
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| 540 | commited.
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| 541 | fit - execute the actual fitting process
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| [984] | 542 | store_fit - store the fit parameters in the data (scantable)
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| [113] | 543 | get_chi2 - get the Chi^2
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| 544 | set_scan - set the scantable to be fit
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| 545 | set_function - set the fitting function
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| 546 | set_parameters - set the parameters for the function(s), and
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| 547 | set if they should be held fixed during fitting
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| [513] | 548 | set_gauss_parameters - same as above but specialised for individual
|
|---|
| 549 | gaussian components
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|---|
| [113] | 550 | get_parameters - get the fitted parameters
|
|---|
| [513] | 551 | plot - plot the resulting fit and/or components and
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|---|
| 552 | residual
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|---|
| [210] | 553 | [Plotter]
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|---|
| 554 | asapplotter - a plotter for asap, default plotter is
|
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| 555 | called 'plotter'
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| [984] | 556 | plot - plot a scantable
|
|---|
| [1151] | 557 | plot_lines - plot a linecatalog overlay
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|---|
| [378] | 558 | save - save the plot to a file ('png' ,'ps' or 'eps')
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| [210] | 559 | set_mode - set the state of the plotter, i.e.
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|---|
| 560 | what is to be plotted 'colour stacked'
|
|---|
| 561 | and what 'panelled'
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| [984] | 562 | set_selection - only plot a selected part of the data
|
|---|
| [733] | 563 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
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|---|
| [255] | 564 | set_legend - specify user labels for the legend indeces
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|---|
| 565 | set_title - specify user labels for the panel indeces
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|---|
| [733] | 566 | set_abcissa - specify a user label for the abcissa
|
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| [255] | 567 | set_ordinate - specify a user label for the ordinate
|
|---|
| [378] | 568 | set_layout - specify the multi-panel layout (rows,cols)
|
|---|
| [733] | 569 | set_colors - specify a set of colours to use
|
|---|
| 570 | set_linestyles - specify a set of linestyles to use if only
|
|---|
| 571 | using one color
|
|---|
| [1151] | 572 | set_font - set general font properties, e.g. 'family'
|
|---|
| [1054] | 573 | set_histogram - plot in historam style
|
|---|
| [733] | 574 | set_mask - set a plotting mask for a specific polarization
|
|---|
| [1171] | 575 | text - draw text annotations either in data or relative
|
|---|
| 576 | coordinates
|
|---|
| 577 | arrow - draw arrow annotations either in data or relative
|
|---|
| 578 | coordinates
|
|---|
| 579 | axhline,axvline - draw horizontal/vertical lines
|
|---|
| 580 | axhspan,axvspan - draw horizontal/vertical regions
|
|---|
| [1175] | 581 |
|
|---|
| 582 | xyplotter - matplotlib/pylab plotting functions
|
|---|
| 583 |
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|---|
| [182] | 584 | [Reading files]
|
|---|
| 585 | reader - access rpfits/sdfits files
|
|---|
| [984] | 586 | open - attach reader to a file
|
|---|
| 587 | close - detach reader from file
|
|---|
| [182] | 588 | read - read in integrations
|
|---|
| 589 | summary - list info about all integrations
|
|---|
| 590 |
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|---|
| [113] | 591 | [General]
|
|---|
| 592 | commands - this command
|
|---|
| 593 | print - print details about a variable
|
|---|
| 594 | list_scans - list all scantables created bt the user
|
|---|
| [992] | 595 | list_files - list all files readable by asap (default rpf)
|
|---|
| [113] | 596 | del - delete the given variable from memory
|
|---|
| 597 | range - create a list of values, e.g.
|
|---|
| 598 | range(3) = [0,1,2], range(2,5) = [2,3,4]
|
|---|
| 599 | help - print help for one of the listed functions
|
|---|
| 600 | execfile - execute an asap script, e.g. execfile('myscript')
|
|---|
| [255] | 601 | list_rcparameters - print out a list of possible values to be
|
|---|
| [274] | 602 | put into $HOME/.asaprc
|
|---|
| [1171] | 603 | rc - set rc parameters from within asap
|
|---|
| [466] | 604 | mask_and,mask_or,
|
|---|
| 605 | mask_not - boolean operations on masks created with
|
|---|
| 606 | scantable.create_mask
|
|---|
| [706] | 607 |
|
|---|
| [210] | 608 | Note:
|
|---|
| 609 | How to use this with help:
|
|---|
| 610 | # function 'summary'
|
|---|
| 611 | [xxx] is just a category
|
|---|
| 612 | Every 'sub-level' in this list should be replaces by a '.' Period when
|
|---|
| [706] | 613 | using help
|
|---|
| [210] | 614 | Example:
|
|---|
| 615 | ASAP> help scantable # to get info on ths scantable
|
|---|
| 616 | ASAP> help scantable.summary # to get help on the scantable's
|
|---|
| 617 | ASAP> help average_time
|
|---|
| 618 |
|
|---|
| [715] | 619 | """
|
|---|
| [1151] | 620 | if rcParams['verbose']:
|
|---|
| 621 | try:
|
|---|
| 622 | from IPython.genutils import page as pager
|
|---|
| 623 | except ImportError:
|
|---|
| 624 | from pydoc import pager
|
|---|
| 625 | pager(x)
|
|---|
| 626 | else:
|
|---|
| 627 | print x
|
|---|
| [715] | 628 | return
|
|---|
| [113] | 629 |
|
|---|
| [706] | 630 | def welcome():
|
|---|
| 631 | return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
|
|---|
| [100] | 632 |
|
|---|
| [1035] | 633 | Please report any bugs via:
|
|---|
| [1378] | 634 | http://svn.atnf.csiro.au/trac/asap/simpleticket
|
|---|
| [100] | 635 |
|
|---|
| [378] | 636 | [IMPORTANT: ASAP is 0-based]
|
|---|
| [706] | 637 | Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
|
|---|
