| [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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| [1589] | 6 | import functools
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| [226] | 7 |
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| [1080] | 8 | # Set up AIPSPATH and first time use of asap i.e. ~/.asap/*
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| 9 | plf = None
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| 10 | if sys.platform == "linux2":
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| 11 | if platform.architecture()[0] == '64bit':
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| 12 | plf = 'linux_64b'
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| 13 | else:
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| 14 | plf = 'linux_gnu'
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| 15 | elif sys.platform == 'darwin':
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| 16 | plf = 'darwin'
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| 17 | else:
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| 18 | # Shouldn't happen - default to linux
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| 19 | plf = 'linux'
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| 20 | asapdata = __path__[-1]
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| [1171] | 21 | # Allow user defined data location
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| 22 | if os.environ.has_key("ASAPDATA"):
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| 23 | if os.path.exists(os.environ["ASAPDATA"]):
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| 24 | asapdata = os.environ["ASAPDATA"]
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| [1371] | 25 | # use AIPSPATH if defined and "data" dir present
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| 26 | if not os.environ.has_key("AIPSPATH") or \
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| 27 | not os.path.exists(os.environ["AIPSPATH"].split()[0]+"/data"):
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| [1316] | 28 | os.environ["AIPSPATH"] = "%s %s somwhere" % ( asapdata, plf)
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| [1171] | 29 | # set up user space
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| [1080] | 30 | userdir = os.environ["HOME"]+"/.asap"
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| 31 | if not os.path.exists(userdir):
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| 32 | print 'First time ASAP use. Setting up ~/.asap'
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| 33 | os.mkdir(userdir)
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| 34 | shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap")
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| [1588] | 35 | shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
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| [1434] | 36 | userdir+"/ipy_user_conf.py")
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| [1080] | 37 | f = file(userdir+"/asapuserfuncs.py", "w")
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| 38 | f.close()
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| 39 | f = file(userdir+"/ipythonrc", "w")
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| 40 | f.close()
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| [1472] | 41 | else:
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| 42 | # upgrade to support later ipython versions
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| 43 | if not os.path.exists(userdir+"/ipy_user_conf.py"):
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| [1588] | 44 | shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
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| [1472] | 45 | userdir+"/ipy_user_conf.py")
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| 46 |
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| [1171] | 47 | # remove from namespace
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| [1080] | 48 | del asapdata, userdir, shutil, platform
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| 49 |
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| [513] | 50 | def _validate_bool(b):
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| [226] | 51 | 'Convert b to a boolean or raise'
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| 52 | bl = b.lower()
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| 53 | if bl in ('f', 'no', 'false', '0', 0): return False
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| 54 | elif bl in ('t', 'yes', 'true', '1', 1): return True
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| 55 | else:
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| 56 | raise ValueError('Could not convert "%s" to boolean' % b)
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| 57 |
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| [513] | 58 | def _validate_int(s):
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| [226] | 59 | 'convert s to int or raise'
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| 60 | try: return int(s)
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| 61 | except ValueError:
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| 62 | raise ValueError('Could not convert "%s" to int' % s)
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| 63 |
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| [513] | 64 | def _asap_fname():
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| [226] | 65 | """
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| 66 | Return the path to the rc file
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| 67 |
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| 68 | Search order:
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| 69 |
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| 70 | * current working dir
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| 71 | * environ var ASAPRC
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| [274] | 72 | * HOME/.asaprc
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| [706] | 73 |
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| [226] | 74 | """
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| 75 |
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| 76 | fname = os.path.join( os.getcwd(), '.asaprc')
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| 77 | if os.path.exists(fname): return fname
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| 78 |
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| 79 | if os.environ.has_key('ASAPRC'):
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| 80 | path = os.environ['ASAPRC']
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| 81 | if os.path.exists(path):
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| 82 | fname = os.path.join(path, '.asaprc')
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| 83 | if os.path.exists(fname):
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| 84 | return fname
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| 85 |
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| 86 | if os.environ.has_key('HOME'):
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| 87 | home = os.environ['HOME']
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| 88 | fname = os.path.join(home, '.asaprc')
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| 89 | if os.path.exists(fname):
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| 90 | return fname
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| 91 | return None
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| 92 |
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| [706] | 93 |
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| [226] | 94 | defaultParams = {
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| 95 | # general
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| [513] | 96 | 'verbose' : [True, _validate_bool],
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| 97 | 'useplotter' : [True, _validate_bool],
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| [542] | 98 | 'insitu' : [True, _validate_bool],
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| [706] | 99 |
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| [226] | 100 | # plotting
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| [706] | 101 | 'plotter.gui' : [True, _validate_bool],
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| [226] | 102 | 'plotter.stacking' : ['p', str],
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| 103 | 'plotter.panelling' : ['s', str],
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| [700] | 104 | 'plotter.colours' : ['', str],
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| 105 | 'plotter.linestyles' : ['', str],
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| [710] | 106 | 'plotter.decimate' : [False, _validate_bool],
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| 107 | 'plotter.ganged' : [True, _validate_bool],
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| [1022] | 108 | 'plotter.histogram' : [False, _validate_bool],
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| [1097] | 109 | 'plotter.papertype' : ['A4', str],
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| [1560] | 110 | 'plotter.axesformatting' : ['mpl', str],
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| [710] | 111 |
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| [226] | 112 | # scantable
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| 113 | 'scantable.save' : ['ASAP', str],
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| [513] | 114 | 'scantable.autoaverage' : [True, _validate_bool],
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| [226] | 115 | 'scantable.freqframe' : ['LSRK', str], #default frequency frame
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| [1076] | 116 | 'scantable.verbosesummary' : [False, _validate_bool],
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| [1422] | 117 | 'scantable.storage' : ['memory', str],
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| [1504] | 118 | 'scantable.history' : [True, _validate_bool],
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| [1586] | 119 | 'scantable.reference' : ['.*(e|w|_R)$', str],
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| 120 | 'scantable.parallactify' : [False, _validate_bool]
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| [226] | 121 | # fitter
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| 122 | }
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| 123 |
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| [255] | 124 | def list_rcparameters():
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| [706] | 125 |
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| [255] | 126 | print """
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| [737] | 127 | # general
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| 128 | # print verbose output
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| 129 | verbose : True
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| [255] | 130 |
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| [737] | 131 | # preload a default plotter
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| 132 | useplotter : True
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| [255] | 133 |
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| [737] | 134 | # apply operations on the input scantable or return new one
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| 135 | insitu : True
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| [706] | 136 |
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| [737] | 137 | # plotting
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| [710] | 138 |
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| [737] | 139 | # do we want a GUI or plot to a file
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| 140 | plotter.gui : True
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| [710] | 141 |
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| [737] | 142 | # default mode for colour stacking
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| 143 | plotter.stacking : Pol
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| [255] | 144 |
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| [737] | 145 | # default mode for panelling
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| 146 | plotter.panelling : scan
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| [255] | 147 |
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| [1560] | 148 | # push panels together, to share axis labels
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| [737] | 149 | plotter.ganged : True
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| [710] | 150 |
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| [1513] | 151 | # decimate the number of points plotted by a factor of
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| [737] | 152 | # nchan/1024
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| 153 | plotter.decimate : False
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| [733] | 154 |
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| [737] | 155 | # default colours/linestyles
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| 156 | plotter.colours :
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| 157 | plotter.linestyles :
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| [700] | 158 |
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| [1022] | 159 | # enable/disable histogram plotting
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| 160 | plotter.histogram : False
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| 161 |
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| [1097] | 162 | # ps paper type
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| 163 | plotter.papertype : A4
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| 164 |
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| [1513] | 165 | # The formatting style of the xaxis
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| [1560] | 166 | plotter.axesformatting : 'mpl' (default) or 'asap' (for old versions of matplotlib)
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| [1513] | 167 |
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| [737] | 168 | # scantable
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| [1076] | 169 |
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| [1259] | 170 | # default storage of scantable ('memory'/'disk')
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| [1076] | 171 | scantable.storage : memory
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| [1422] | 172 |
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| 173 | # write history of each call to scantable
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| 174 | scantable.history : True
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| 175 |
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| [737] | 176 | # default ouput format when saving
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| 177 | scantable.save : ASAP
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| [1422] | 178 |
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| [737] | 179 | # auto averaging on read
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| 180 | scantable.autoaverage : True
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| [255] | 181 |
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| [737] | 182 | # default frequency frame to set when function
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| [1097] | 183 | # scantable.set_freqframe is called
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| [737] | 184 | scantable.freqframe : LSRK
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| [255] | 185 |
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| [737] | 186 | # Control the level of information printed by summary
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| 187 | scantable.verbosesummary : False
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| [706] | 188 |
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| [1504] | 189 | # Control the identification of reference (off) scans
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| 190 | # This is has to be a regular expression
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| 191 | scantable.reference : .*(e|w|_R)$
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| [1560] | 192 |
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| [737] | 193 | # Fitter
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| 194 | """
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| [706] | 195 |
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| [226] | 196 | def rc_params():
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| 197 | 'Return the default params updated from the values in the rc file'
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| [706] | 198 |
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| [513] | 199 | fname = _asap_fname()
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| [706] | 200 |
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| [226] | 201 | if fname is None or not os.path.exists(fname):
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| 202 | message = 'could not find rc file; returning defaults'
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| 203 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
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| 204 | #print message
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| 205 | return ret
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| [706] | 206 |
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| [226] | 207 | cnt = 0
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| 208 | for line in file(fname):
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| 209 | cnt +=1
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| 210 | line = line.strip()
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| 211 | if not len(line): continue
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| 212 | if line.startswith('#'): continue
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| 213 | tup = line.split(':',1)
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| 214 | if len(tup) !=2:
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| 215 | print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
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| 216 | continue
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| [706] | 217 |
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| [226] | 218 | key, val = tup
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| 219 | key = key.strip()
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| 220 | if not defaultParams.has_key(key):
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| 221 | print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
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| 222 | continue
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| [706] | 223 |
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| [226] | 224 | default, converter = defaultParams[key]
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| 225 |
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| 226 | ind = val.find('#')
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| 227 | if ind>=0: val = val[:ind] # ignore trailing comments
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| 228 | val = val.strip()
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| 229 | try: cval = converter(val) # try to convert to proper type or raise
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| [1080] | 230 | except ValueError, msg:
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| [226] | 231 | 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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| 232 | continue
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| 233 | else:
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| 234 | # Alles Klar, update dict
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| 235 | defaultParams[key][0] = cval
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| 236 |
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| 237 | # strip the conveter funcs and return
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| 238 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
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| [466] | 239 | print ('loaded rc file %s'%fname)
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| [226] | 240 |
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| 241 | return ret
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| 242 |
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| 243 |
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| 244 | # this is the instance used by the asap classes
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| [706] | 245 | rcParams = rc_params()
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| [226] | 246 |
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| 247 | rcParamsDefault = dict(rcParams.items()) # a copy
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| 248 |
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| 249 | def rc(group, **kwargs):
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| 250 | """
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| 251 | Set the current rc params. Group is the grouping for the rc, eg
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| [379] | 252 | for scantable.save the group is 'scantable', for plotter.stacking, the
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| 253 | group is 'plotter', and so on. kwargs is a list of attribute
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| [226] | 254 | name/value pairs, eg
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| 255 |
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| [379] | 256 | rc('scantable', save='SDFITS')
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| [226] | 257 |
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| 258 | sets the current rc params and is equivalent to
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| [706] | 259 |
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| [379] | 260 | rcParams['scantable.save'] = 'SDFITS'
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| [226] | 261 |
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| 262 | Use rcdefaults to restore the default rc params after changes.
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| 263 | """
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| 264 |
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| [379] | 265 | aliases = {}
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| [706] | 266 |
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| [226] | 267 | for k,v in kwargs.items():
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| 268 | name = aliases.get(k) or k
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| [1422] | 269 | if len(group):
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| 270 | key = '%s.%s' % (group, name)
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| 271 | else:
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| 272 | key = name
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| [226] | 273 | if not rcParams.has_key(key):
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| 274 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
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| [706] | 275 |
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| [226] | 276 | rcParams[key] = v
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| 277 |
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| 278 |
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| 279 | def rcdefaults():
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| 280 | """
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| 281 | Restore the default rc params - the ones that were created at
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| 282 | asap load time
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| 283 | """
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| 284 | rcParams.update(rcParamsDefault)
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| 285 |
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| [1295] | 286 | def _n_bools(n, val):
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| [1588] | 287 | return [ val for i in xrange(n) ]
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| [513] | 288 |
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| 289 | def _is_sequence_or_number(param, ptype=int):
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| 290 | if isinstance(param,tuple) or isinstance(param,list):
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| [928] | 291 | if len(param) == 0: return True # empty list
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| [513] | 292 | out = True
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| 293 | for p in param:
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| 294 | out &= isinstance(p,ptype)
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| 295 | return out
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| 296 | elif isinstance(param, ptype):
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| 297 | return True
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| 298 | return False
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| 299 |
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| [928] | 300 | def _to_list(param, ptype=int):
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| 301 | if isinstance(param, ptype):
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| 302 | if ptype is str: return param.split()
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| 303 | else: return [param]
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| 304 | if _is_sequence_or_number(param, ptype):
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| 305 | return param
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| 306 | return None
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| [715] | 307 |
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| [944] | 308 | def unique(x):
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| [992] | 309 | """
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| 310 | Return the unique values in a list
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| 311 | Parameters:
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| 312 | x: the list to reduce
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| 313 | Examples:
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| 314 | x = [1,2,3,3,4]
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| 315 | print unique(x)
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| 316 | [1,2,3,4]
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| 317 | """
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| [944] | 318 | return dict([ (val, 1) for val in x]).keys()
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| 319 |
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| [992] | 320 | def list_files(path=".",suffix="rpf"):
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| 321 | """
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| 322 | Return a list files readable by asap, such as rpf, sdfits, mbf, asap
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| 323 | Parameters:
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| 324 | path: The directory to list (default '.')
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| 325 | suffix: The file extension (default rpf)
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| 326 | Example:
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| 327 | files = list_files("data/","sdfits")
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| 328 | print files
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| 329 | ['data/2001-09-01_0332_P363.sdfits',
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| 330 | 'data/2003-04-04_131152_t0002.sdfits',
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| 331 | 'data/Sgr_86p262_best_SPC.sdfits']
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| 332 | """
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| 333 | if not os.path.isdir(path):
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| 334 | return None
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| [1295] | 335 | valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split()
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| [992] | 336 | if not suffix in valid:
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| 337 | return None
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| 338 | files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
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| 339 | return filter(lambda x: x.endswith(suffix),files)
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| 340 |
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| [715] | 341 | # workaround for ipython, which redirects this if banner=0 in ipythonrc
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| 342 | sys.stdout = sys.__stdout__
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| 343 | sys.stderr = sys.__stderr__
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| 344 |
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| 345 | # Logging
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| 346 | from asap._asap import Log as _asaplog
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| 347 | global asaplog
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| [710] | 348 | asaplog=_asaplog()
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| [715] | 349 | if rcParams['verbose']:
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| 350 | asaplog.enable()
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| 351 | else:
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| 352 | asaplog.disable()
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| 353 |
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| [1589] | 354 |
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| 355 | def print_log_dec(f):
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| 356 | @functools.wraps(f)
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| 357 | def wrap_it(*args, **kw):
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| 358 | val = f(*args, **kw)
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| 359 | print_log()
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| 360 | return val
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| 361 | return wrap_it
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| 362 |
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| [715] | 363 | def print_log():
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| [1589] | 364 | log = asaplog.pop().strip()
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| [715] | 365 | if len(log) and rcParams['verbose']: print log
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| 366 | return
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| 367 |
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| [1295] | 368 | def mask_and(a, b):
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| 369 | assert(len(a)==len(b))
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| 370 | return [ a[i] & b[i] for i in xrange(len(a)) ]
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| [1134] | 371 |
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| [1295] | 372 | def mask_or(a, b):
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| 373 | assert(len(a)==len(b))
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| 374 | return [ a[i] | b[i] for i in xrange(len(a)) ]
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| 375 |
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| 376 | def mask_not(a):
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| 377 | return [ not i for i in a ]
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| 378 |
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| [1117] | 379 | from asapfitter import fitter
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| [895] | 380 | from asapreader import reader
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| [944] | 381 | from selector import selector
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| [710] | 382 |
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| [100] | 383 | from asapmath import *
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| [1080] | 384 | from scantable import scantable
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| [1097] | 385 | from asaplinefind import linefinder
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| [1134] | 386 | from linecatalog import linecatalog
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| [285] | 387 |
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| [928] | 388 | if rcParams['useplotter']:
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| [1295] | 389 | try:
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| [1423] | 390 | from asapplotter import asapplotter
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| 391 | gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
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| 392 | if gui:
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| [1422] | 393 | import matplotlib
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| 394 | matplotlib.use("TkAgg")
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| [1423] | 395 | import pylab
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| [1422] | 396 | xyplotter = pylab
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| [1423] | 397 | plotter = asapplotter(gui)
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| 398 | del gui
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| [1295] | 399 | except ImportError:
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| [1423] | 400 | print "Matplotlib not installed. No plotting available"
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| [285] | 401 |
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| [574] | 402 | __date__ = '$Date: 2009-07-02 02:17:20 +0000 (Thu, 02 Jul 2009) $'.split()[1]
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| [1560] | 403 | __version__ = '$Revision: 1589 $'
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| [100] | 404 |
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| [1193] | 405 | def is_ipython():
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| [1259] | 406 | return '__IP' in dir(sys.modules["__main__"])
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| [1589] | 407 |
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| [1193] | 408 | if is_ipython():
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| [1014] | 409 | def version(): print "ASAP %s(%s)"% (__version__, __date__)
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| [1588] | 410 |
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| 411 | def list_scans(t = scantable):
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| [1560] | 412 | import inspect
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| 413 | print "The user created scantables are: ",
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| 414 | globs=inspect.currentframe().f_back.f_locals.copy()
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| 415 | out = [ k for k,v in globs.iteritems() \
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| 416 | if isinstance(v, scantable) and not k.startswith("_") ]
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| 417 | print out
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| 418 | return out
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| [100] | 419 |
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| [715] | 420 | def commands():
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| 421 | x = """
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| [113] | 422 | [The scan container]
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| 423 | scantable - a container for integrations/scans
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| [182] | 424 | (can open asap/rpfits/sdfits and ms files)
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| [113] | 425 | copy - returns a copy of a scan
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| 426 | get_scan - gets a specific scan out of a scantable
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| [984] | 427 | (by name or number)
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| [1093] | 428 | drop_scan - drops a specific scan out of a scantable
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| 429 | (by number)
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| [984] | 430 | set_selection - set a new subselection of the data
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| 431 | get_selection - get the current selection object
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| [113] | 432 | summary - print info about the scantable contents
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| [182] | 433 | stats - get specified statistic of the spectra in
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| 434 | the scantable
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| 435 | stddev - get the standard deviation of the spectra
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| 436 | in the scantable
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| [113] | 437 | get_tsys - get the TSys
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| 438 | get_time - get the timestamps of the integrations
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| [1351] | 439 | get_inttime - get the integration time
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| [733] | 440 | get_sourcename - get the source names of the scans
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| [794] | 441 | get_azimuth - get the azimuth of the scans
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| 442 | get_elevation - get the elevation of the scans
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| 443 | get_parangle - get the parallactic angle of the scans
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| [876] | 444 | get_unit - get the current unit
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| [513] | 445 | set_unit - set the abcissa unit to be used from this
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| 446 | point on
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| [255] | 447 | get_abcissa - get the abcissa values and name for a given
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| 448 | row (time)
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| [1259] | 449 | get_column_names - get the names of the columns in the scantable
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| 450 | for use with selector.set_query
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| [113] | 451 | set_freqframe - set the frame info for the Spectral Axis
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| 452 | (e.g. 'LSRK')
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| [276] | 453 | set_doppler - set the doppler to be used from this point on
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| [984] | 454 | set_dirframe - set the frame for the direction on the sky
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| [240] | 455 | set_instrument - set the instrument name
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| [1190] | 456 | set_feedtype - set the feed type
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| [255] | 457 | get_fluxunit - get the brightness flux unit
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| [240] | 458 | set_fluxunit - set the brightness flux unit
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| [1508] | 459 | set_sourcetype - set the type of the source - source or reference
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| [188] | 460 | create_mask - return an mask in the current unit
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| 461 | for the given region. The specified regions
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| 462 | are NOT masked
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| [255] | 463 | get_restfreqs - get the current list of rest frequencies
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| 464 | set_restfreqs - set a list of rest frequencies
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| [1471] | 465 | shift_refpix - shift the reference pixel of the IFs
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| 466 | set_spectrum - overwrite the spectrum for a given row
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| 467 | get_spectrum - retrieve the spectrum for a given
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| 468 | get_mask - retrieve the mask for a given
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| [1012] | 469 | flag - flag selected channels in the data
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| [1192] | 470 | lag_flag - flag specified frequency in the data
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| [1151] | 471 | save - save the scantable to disk as either 'ASAP',
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| 472 | 'SDFITS' or 'ASCII'
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| [486] | 473 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
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| [733] | 474 | nscan - the number of scans in the scantable
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| [1422] | 475 | nrow - the number of spectra in the scantable
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| [486] | 476 | history - print the history of the scantable
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| [530] | 477 | get_fit - get a fit which has been stored witnh the data
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| [706] | 478 | average_time - return the (weighted) time average of a scan
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| [513] | 479 | or a list of scans
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| 480 | average_pol - average the polarisations together.
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| [1144] | 481 | average_beam - average the beams together.
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| [992] | 482 | convert_pol - convert to a different polarisation type
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| [690] | 483 | auto_quotient - return the on/off quotient with
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| [1069] | 484 | automatic detection of the on/off scans (closest
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| 485 | in time off is selected)
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| [1144] | 486 | mx_quotient - Form a quotient using MX data (off beams)
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| [1014] | 487 | scale, *, / - return a scan scaled by a given factor
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| [1560] | 488 | add, + - return a scan with given value added
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| 489 | sub, - - return a scan with given value subtracted
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| [513] | 490 | bin - return a scan with binned channels
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| 491 | resample - return a scan with resampled channels
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| 492 | smooth - return the spectrally smoothed scan
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| 493 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
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| [706] | 494 | auto_poly_baseline - automatically fit a polynomial baseline
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| [780] | 495 | recalc_azel - recalculate azimuth and elevation based on
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| 496 | the pointing
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| [513] | 497 | gain_el - apply gain-elevation correction
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| 498 | opacity - apply opacity correction
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| 499 | convert_flux - convert to and from Jy and Kelvin brightness
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| [255] | 500 | units
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| [513] | 501 | freq_align - align spectra in frequency frame
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| [1014] | 502 | invert_phase - Invert the phase of the cross-correlation
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| [1351] | 503 | swap_linears - Swap XX and YY (or RR LL)
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| [513] | 504 | rotate_xyphase - rotate XY phase of cross correlation
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| 505 | rotate_linpolphase - rotate the phase of the complex
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| 506 | polarization O=Q+iU correlation
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| [733] | 507 | freq_switch - perform frequency switching on the data
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| 508 | stats - Determine the specified statistic, e.g. 'min'
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| 509 | 'max', 'rms' etc.
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| 510 | stddev - Determine the standard deviation of the current
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| 511 | beam/if/pol
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| [1588] | 512 | get_row_selector - get the selection object for a specified row
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| 513 | number
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| [1014] | 514 | [Selection]
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| 515 | selector - a selection object to set a subset of a scantable
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| 516 | set_scans - set (a list of) scans by index
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| 517 | set_cycles - set (a list of) cycles by index
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| 518 | set_beams - set (a list of) beamss by index
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| 519 | set_ifs - set (a list of) ifs by index
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| 520 | set_polarisations - set (a list of) polarisations by name
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| 521 | or by index
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| 522 | set_names - set a selection by name (wildcards allowed)
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| 523 | set_tsys - set a selection by tsys thresholds
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| [1259] | 524 | set_query - set a selection by SQL-like query, e.g. BEAMNO==1
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| [1351] | 525 | ( also get_ functions for all these )
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| [1014] | 526 | reset - unset all selections
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| [1351] | 527 | + - merge two selections
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| [733] | 528 |
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| [513] | 529 | [Math] Mainly functions which operate on more than one scantable
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| [100] | 530 |
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| [706] | 531 | average_time - return the (weighted) time average
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| [513] | 532 | of a list of scans
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| 533 | quotient - return the on/off quotient
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| 534 | simple_math - simple mathematical operations on two scantables,
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| 535 | 'add', 'sub', 'mul', 'div'
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| [1069] | 536 | quotient - build quotient of the given on and off scans
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| [1351] | 537 | (matched pairs and 1 off - n on are valid)
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| [1117] | 538 | merge - merge a list of scantables
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|---|
| [1069] | 539 |
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|---|
| [1151] | 540 | [Line Catalog]
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|---|
| 541 | linecatalog - a linecatalog wrapper, taking an ASCII or
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| 542 | internal format table
|
|---|
| 543 | summary - print a summary of the current selection
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| 544 | set_name - select a subset by name pattern, e.g. '*OH*'
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|---|
| 545 | set_strength_limits - select a subset by line strength limits
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|---|
| 546 | set_frequency_limits - select a subset by frequency limits
|
|---|
| 547 | reset - unset all selections
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|---|
| 548 | save - save the current subset to a table (internal
|
|---|
| 549 | format)
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|---|
| 550 | get_row - get the name and frequency from a specific
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|---|
| 551 | row in the table
|
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| [513] | 552 | [Fitting]
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| [113] | 553 | fitter
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|---|
| 554 | auto_fit - return a scan where the function is
|
|---|
| 555 | applied to all Beams/IFs/Pols.
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| 556 | commit - return a new scan where the fits have been
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| 557 | commited.
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| 558 | fit - execute the actual fitting process
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| [984] | 559 | store_fit - store the fit parameters in the data (scantable)
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| [113] | 560 | get_chi2 - get the Chi^2
|
|---|
| 561 | set_scan - set the scantable to be fit
|
|---|
| 562 | set_function - set the fitting function
|
|---|
| 563 | set_parameters - set the parameters for the function(s), and
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|---|
| 564 | set if they should be held fixed during fitting
|
|---|
| [513] | 565 | set_gauss_parameters - same as above but specialised for individual
|
|---|
| 566 | gaussian components
|
|---|
| [113] | 567 | get_parameters - get the fitted parameters
|
|---|
| [513] | 568 | plot - plot the resulting fit and/or components and
|
|---|
| 569 | residual
|
|---|
| [210] | 570 | [Plotter]
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|---|
| 571 | asapplotter - a plotter for asap, default plotter is
|
|---|
| 572 | called 'plotter'
|
|---|
| [984] | 573 | plot - plot a scantable
|
|---|
| [1151] | 574 | plot_lines - plot a linecatalog overlay
|
|---|
| [378] | 575 | save - save the plot to a file ('png' ,'ps' or 'eps')
|
|---|
| [210] | 576 | set_mode - set the state of the plotter, i.e.
|
|---|
| 577 | what is to be plotted 'colour stacked'
|
|---|
| 578 | and what 'panelled'
|
|---|
| [984] | 579 | set_selection - only plot a selected part of the data
|
|---|
| [733] | 580 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
|
|---|
| [255] | 581 | set_legend - specify user labels for the legend indeces
|
|---|
| 582 | set_title - specify user labels for the panel indeces
|
|---|
| [733] | 583 | set_abcissa - specify a user label for the abcissa
|
|---|
| [255] | 584 | set_ordinate - specify a user label for the ordinate
|
|---|
| [378] | 585 | set_layout - specify the multi-panel layout (rows,cols)
|
|---|
| [733] | 586 | set_colors - specify a set of colours to use
|
|---|
| 587 | set_linestyles - specify a set of linestyles to use if only
|
|---|
| 588 | using one color
|
|---|
| [1151] | 589 | set_font - set general font properties, e.g. 'family'
|
|---|
| [1054] | 590 | set_histogram - plot in historam style
|
|---|
| [733] | 591 | set_mask - set a plotting mask for a specific polarization
|
|---|
| [1171] | 592 | text - draw text annotations either in data or relative
|
|---|
| 593 | coordinates
|
|---|
| 594 | arrow - draw arrow annotations either in data or relative
|
|---|
| 595 | coordinates
|
|---|
| 596 | axhline,axvline - draw horizontal/vertical lines
|
|---|
| 597 | axhspan,axvspan - draw horizontal/vertical regions
|
|---|
| [1560] | 598 | annotate - draw an arrow with label
|
|---|
| 599 | create_mask - create a scnatble mask interactively
|
|---|
| [1175] | 600 |
|
|---|
| 601 | xyplotter - matplotlib/pylab plotting functions
|
|---|
| 602 |
|
|---|
| [182] | 603 | [Reading files]
|
|---|
| 604 | reader - access rpfits/sdfits files
|
|---|
| [984] | 605 | open - attach reader to a file
|
|---|
| 606 | close - detach reader from file
|
|---|
| [182] | 607 | read - read in integrations
|
|---|
| 608 | summary - list info about all integrations
|
|---|
| 609 |
|
|---|
| [113] | 610 | [General]
|
|---|
| 611 | commands - this command
|
|---|
| 612 | print - print details about a variable
|
|---|
| [1560] | 613 | list_scans - list all scantables created by the user
|
|---|
| [992] | 614 | list_files - list all files readable by asap (default rpf)
|
|---|
| [113] | 615 | del - delete the given variable from memory
|
|---|
| 616 | range - create a list of values, e.g.
|
|---|
| 617 | range(3) = [0,1,2], range(2,5) = [2,3,4]
|
|---|
| 618 | help - print help for one of the listed functions
|
|---|
| 619 | execfile - execute an asap script, e.g. execfile('myscript')
|
|---|
| [255] | 620 | list_rcparameters - print out a list of possible values to be
|
|---|
| [274] | 621 | put into $HOME/.asaprc
|
|---|
| [1171] | 622 | rc - set rc parameters from within asap
|
|---|
| [466] | 623 | mask_and,mask_or,
|
|---|
| 624 | mask_not - boolean operations on masks created with
|
|---|
| 625 | scantable.create_mask
|
|---|
| [706] | 626 |
|
|---|
| [210] | 627 | Note:
|
|---|
| 628 | How to use this with help:
|
|---|
| 629 | # function 'summary'
|
|---|
| 630 | [xxx] is just a category
|
|---|
| 631 | Every 'sub-level' in this list should be replaces by a '.' Period when
|
|---|
| [706] | 632 | using help
|
|---|
| [210] | 633 | Example:
|
|---|
| 634 | ASAP> help scantable # to get info on ths scantable
|
|---|
| 635 | ASAP> help scantable.summary # to get help on the scantable's
|
|---|
| 636 | ASAP> help average_time
|
|---|
| 637 |
|
|---|
| [715] | 638 | """
|
|---|
| [1151] | 639 | if rcParams['verbose']:
|
|---|
| 640 | try:
|
|---|
| 641 | from IPython.genutils import page as pager
|
|---|
| 642 | except ImportError:
|
|---|
| 643 | from pydoc import pager
|
|---|
| 644 | pager(x)
|
|---|
| 645 | else:
|
|---|
| 646 | print x
|
|---|
| [715] | 647 | return
|
|---|
| [113] | 648 |
|
|---|
| [706] | 649 | def welcome():
|
|---|
| 650 | return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
|
|---|
| [100] | 651 |
|
|---|
| [1035] | 652 | Please report any bugs via:
|
|---|
| [1378] | 653 | http://svn.atnf.csiro.au/trac/asap/simpleticket
|
|---|
| [100] | 654 |
|
|---|
| [378] | 655 | [IMPORTANT: ASAP is 0-based]
|
|---|
| [706] | 656 | Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
|
|---|
