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