| [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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| 34 | f = file(userdir+"/asapuserfuncs.py", "w")
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| 35 | f.close()
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| 36 | f = file(userdir+"/ipythonrc", "w")
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| 37 | f.close()
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| [1171] | 38 | # remove from namespace
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| [1080] | 39 | del asapdata, userdir, shutil, platform
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| 40 |
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| [513] | 41 | def _validate_bool(b):
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| [226] | 42 | 'Convert b to a boolean or raise'
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| 43 | bl = b.lower()
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| 44 | if bl in ('f', 'no', 'false', '0', 0): return False
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| 45 | elif bl in ('t', 'yes', 'true', '1', 1): return True
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| 46 | else:
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| 47 | raise ValueError('Could not convert "%s" to boolean' % b)
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| 48 |
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| [513] | 49 | def _validate_int(s):
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| [226] | 50 | 'convert s to int or raise'
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| 51 | try: return int(s)
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| 52 | except ValueError:
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| 53 | raise ValueError('Could not convert "%s" to int' % s)
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| 54 |
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| [513] | 55 | def _asap_fname():
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| [226] | 56 | """
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| 57 | Return the path to the rc file
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| 58 |
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| 59 | Search order:
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| 60 |
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| 61 | * current working dir
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| 62 | * environ var ASAPRC
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| [274] | 63 | * HOME/.asaprc
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| [706] | 64 |
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| [226] | 65 | """
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| 66 |
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| 67 | fname = os.path.join( os.getcwd(), '.asaprc')
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| 68 | if os.path.exists(fname): return fname
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| 69 |
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| 70 | if os.environ.has_key('ASAPRC'):
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| 71 | path = os.environ['ASAPRC']
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| 72 | if os.path.exists(path):
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| 73 | fname = os.path.join(path, '.asaprc')
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| 74 | if os.path.exists(fname):
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| 75 | return fname
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| 76 |
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| 77 | if os.environ.has_key('HOME'):
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| 78 | home = os.environ['HOME']
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| 79 | fname = os.path.join(home, '.asaprc')
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| 80 | if os.path.exists(fname):
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| 81 | return fname
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| 82 | return None
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| 83 |
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| [706] | 84 |
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| [226] | 85 | defaultParams = {
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| 86 | # general
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| [513] | 87 | 'verbose' : [True, _validate_bool],
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| 88 | 'useplotter' : [True, _validate_bool],
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| [542] | 89 | 'insitu' : [True, _validate_bool],
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| [706] | 90 |
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| [226] | 91 | # plotting
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| [706] | 92 | 'plotter.gui' : [True, _validate_bool],
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| [226] | 93 | 'plotter.stacking' : ['p', str],
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| 94 | 'plotter.panelling' : ['s', str],
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| [700] | 95 | 'plotter.colours' : ['', str],
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| 96 | 'plotter.linestyles' : ['', str],
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| [710] | 97 | 'plotter.decimate' : [False, _validate_bool],
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| 98 | 'plotter.ganged' : [True, _validate_bool],
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| [1022] | 99 | 'plotter.histogram' : [False, _validate_bool],
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| [1097] | 100 | 'plotter.papertype' : ['A4', str],
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| [710] | 101 |
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| [226] | 102 | # scantable
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| 103 | 'scantable.save' : ['ASAP', str],
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| [513] | 104 | 'scantable.autoaverage' : [True, _validate_bool],
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| [226] | 105 | 'scantable.freqframe' : ['LSRK', str], #default frequency frame
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| [1076] | 106 | 'scantable.verbosesummary' : [False, _validate_bool],
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| 107 | 'scantable.storage' : ['memory', str]
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| [226] | 108 | # fitter
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| 109 | }
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| 110 |
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| [255] | 111 | def list_rcparameters():
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| [706] | 112 |
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| [255] | 113 | print """
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| [737] | 114 | # general
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| 115 | # print verbose output
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| 116 | verbose : True
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| [255] | 117 |
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| [737] | 118 | # preload a default plotter
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| 119 | useplotter : True
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| [255] | 120 |
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| [737] | 121 | # apply operations on the input scantable or return new one
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| 122 | insitu : True
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| [706] | 123 |
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| [737] | 124 | # plotting
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| [710] | 125 |
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| [737] | 126 | # do we want a GUI or plot to a file
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| 127 | plotter.gui : True
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| [710] | 128 |
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| [737] | 129 | # default mode for colour stacking
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| 130 | plotter.stacking : Pol
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| [255] | 131 |
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| [737] | 132 | # default mode for panelling
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| 133 | plotter.panelling : scan
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| [255] | 134 |
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| [737] | 135 | # push panels together, to share axislabels
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| 136 | plotter.ganged : True
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| [710] | 137 |
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| [737] | 138 | # decimate the number of points plotted bya afactor of
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| 139 | # nchan/1024
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| 140 | plotter.decimate : False
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| [733] | 141 |
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| [737] | 142 | # default colours/linestyles
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| 143 | plotter.colours :
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| 144 | plotter.linestyles :
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| [700] | 145 |
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| [1022] | 146 | # enable/disable histogram plotting
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| 147 | plotter.histogram : False
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| 148 |
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| [1097] | 149 | # ps paper type
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| 150 | plotter.papertype : A4
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| 151 |
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| [737] | 152 | # scantable
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| [1076] | 153 |
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| [1259] | 154 | # default storage of scantable ('memory'/'disk')
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| [1076] | 155 | scantable.storage : memory
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| [737] | 156 | # default ouput format when saving
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| 157 | scantable.save : ASAP
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| 158 | # auto averaging on read
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| 159 | scantable.autoaverage : True
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| [255] | 160 |
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| [737] | 161 | # default frequency frame to set when function
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| [1097] | 162 | # scantable.set_freqframe is called
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| [737] | 163 | scantable.freqframe : LSRK
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| [255] | 164 |
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| [737] | 165 | # Control the level of information printed by summary
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| 166 | scantable.verbosesummary : False
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| [706] | 167 |
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| [737] | 168 | # Fitter
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| 169 | """
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| [706] | 170 |
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| [226] | 171 | def rc_params():
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| 172 | 'Return the default params updated from the values in the rc file'
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| [706] | 173 |
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| [513] | 174 | fname = _asap_fname()
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| [706] | 175 |
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| [226] | 176 | if fname is None or not os.path.exists(fname):
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| 177 | message = 'could not find rc file; returning defaults'
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| 178 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
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| 179 | #print message
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| 180 | return ret
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| [706] | 181 |
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| [226] | 182 | cnt = 0
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| 183 | for line in file(fname):
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| 184 | cnt +=1
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| 185 | line = line.strip()
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| 186 | if not len(line): continue
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| 187 | if line.startswith('#'): continue
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| 188 | tup = line.split(':',1)
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| 189 | if len(tup) !=2:
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| 190 | print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
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| 191 | continue
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| [706] | 192 |
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| [226] | 193 | key, val = tup
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| 194 | key = key.strip()
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| 195 | if not defaultParams.has_key(key):
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| 196 | print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
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| 197 | continue
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| [706] | 198 |
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| [226] | 199 | default, converter = defaultParams[key]
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| 200 |
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| 201 | ind = val.find('#')
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| 202 | if ind>=0: val = val[:ind] # ignore trailing comments
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| 203 | val = val.strip()
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| 204 | try: cval = converter(val) # try to convert to proper type or raise
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| [1080] | 205 | except ValueError, msg:
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| [226] | 206 | 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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| 207 | continue
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| 208 | else:
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| 209 | # Alles Klar, update dict
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| 210 | defaultParams[key][0] = cval
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| 211 |
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| 212 | # strip the conveter funcs and return
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| 213 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
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| [466] | 214 | print ('loaded rc file %s'%fname)
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| [226] | 215 |
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| 216 | return ret
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| 217 |
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| 218 |
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| 219 | # this is the instance used by the asap classes
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| [706] | 220 | rcParams = rc_params()
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| [226] | 221 |
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| 222 | rcParamsDefault = dict(rcParams.items()) # a copy
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| 223 |
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| 224 | def rc(group, **kwargs):
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| 225 | """
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| 226 | Set the current rc params. Group is the grouping for the rc, eg
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| [379] | 227 | for scantable.save the group is 'scantable', for plotter.stacking, the
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| 228 | group is 'plotter', and so on. kwargs is a list of attribute
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| [226] | 229 | name/value pairs, eg
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| 230 |
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| [379] | 231 | rc('scantable', save='SDFITS')
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| [226] | 232 |
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| 233 | sets the current rc params and is equivalent to
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| [706] | 234 |
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| [379] | 235 | rcParams['scantable.save'] = 'SDFITS'
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| [226] | 236 |
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| 237 | Use rcdefaults to restore the default rc params after changes.
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| 238 | """
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| 239 |
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| [379] | 240 | aliases = {}
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| [706] | 241 |
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| [226] | 242 | for k,v in kwargs.items():
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| 243 | name = aliases.get(k) or k
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| 244 | key = '%s.%s' % (group, name)
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| 245 | if not rcParams.has_key(key):
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| 246 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
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| [706] | 247 |
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| [226] | 248 | rcParams[key] = v
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| 249 |
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| 250 |
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| 251 | def rcdefaults():
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| 252 | """
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| 253 | Restore the default rc params - the ones that were created at
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| 254 | asap load time
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| 255 | """
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| 256 | rcParams.update(rcParamsDefault)
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| 257 |
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| [1295] | 258 | def _n_bools(n, val):
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| 259 | return [ val for i in xrange(n) ]
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| [513] | 260 |
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| 261 | def _is_sequence_or_number(param, ptype=int):
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| 262 | if isinstance(param,tuple) or isinstance(param,list):
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| [928] | 263 | if len(param) == 0: return True # empty list
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| [513] | 264 | out = True
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| 265 | for p in param:
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| 266 | out &= isinstance(p,ptype)
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| 267 | return out
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| 268 | elif isinstance(param, ptype):
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| 269 | return True
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| 270 | return False
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| 271 |
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| [928] | 272 | def _to_list(param, ptype=int):
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| 273 | if isinstance(param, ptype):
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| 274 | if ptype is str: return param.split()
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| 275 | else: return [param]
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| 276 | if _is_sequence_or_number(param, ptype):
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| 277 | return param
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| 278 | return None
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| [715] | 279 |
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| [944] | 280 | def unique(x):
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| [992] | 281 | """
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| 282 | Return the unique values in a list
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| 283 | Parameters:
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| 284 | x: the list to reduce
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| 285 | Examples:
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| 286 | x = [1,2,3,3,4]
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| 287 | print unique(x)
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| 288 | [1,2,3,4]
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| 289 | """
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| [944] | 290 | return dict([ (val, 1) for val in x]).keys()
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| 291 |
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| [992] | 292 | def list_files(path=".",suffix="rpf"):
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| 293 | """
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| 294 | Return a list files readable by asap, such as rpf, sdfits, mbf, asap
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| 295 | Parameters:
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| 296 | path: The directory to list (default '.')
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| 297 | suffix: The file extension (default rpf)
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| 298 | Example:
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| 299 | files = list_files("data/","sdfits")
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| 300 | print files
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| 301 | ['data/2001-09-01_0332_P363.sdfits',
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| 302 | 'data/2003-04-04_131152_t0002.sdfits',
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| 303 | 'data/Sgr_86p262_best_SPC.sdfits']
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| 304 | """
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| 305 | if not os.path.isdir(path):
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| 306 | return None
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| [1295] | 307 | valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split()
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| [992] | 308 | if not suffix in valid:
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| 309 | return None
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| 310 | files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
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| 311 | return filter(lambda x: x.endswith(suffix),files)
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| 312 |
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| [715] | 313 | # workaround for ipython, which redirects this if banner=0 in ipythonrc
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| 314 | sys.stdout = sys.__stdout__
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| 315 | sys.stderr = sys.__stderr__
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| 316 |
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| 317 | # Logging
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| 318 | from asap._asap import Log as _asaplog
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| 319 | global asaplog
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| [710] | 320 | asaplog=_asaplog()
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| [715] | 321 | if rcParams['verbose']:
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| 322 | asaplog.enable()
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| 323 | else:
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| 324 | asaplog.disable()
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| 325 |
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| 326 | def print_log():
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| 327 | log = asaplog.pop()
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| 328 | if len(log) and rcParams['verbose']: print log
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| 329 | return
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| 330 |
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| [1295] | 331 | def mask_and(a, b):
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| 332 | assert(len(a)==len(b))
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| 333 | return [ a[i] & b[i] for i in xrange(len(a)) ]
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| [1134] | 334 |
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| [1295] | 335 | def mask_or(a, b):
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| 336 | assert(len(a)==len(b))
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| 337 | return [ a[i] | b[i] for i in xrange(len(a)) ]
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| 338 |
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| 339 | def mask_not(a):
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| 340 | return [ not i for i in a ]
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| 341 |
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| [1117] | 342 | from asapfitter import fitter
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| [895] | 343 | from asapreader import reader
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| [944] | 344 | from selector import selector
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| [710] | 345 |
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| [100] | 346 | from asapmath import *
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| [1080] | 347 | from scantable import scantable
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| [1097] | 348 | from asaplinefind import linefinder
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| [1134] | 349 | from linecatalog import linecatalog
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| [285] | 350 |
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| [928] | 351 | if rcParams['useplotter']:
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| [1295] | 352 | try:
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| 353 | from asapplotter import asapplotter
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| 354 | gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
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| 355 | if gui:
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| 356 | import pylab as xyplotter
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| 357 | plotter = asapplotter(gui)
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| 358 | del gui
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| 359 | except ImportError:
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| 360 | print "Matplotlib not installed. No plotting available"
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| [285] | 361 |
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| [574] | 362 | __date__ = '$Date: 2007-07-12 03:49:25 +0000 (Thu, 12 Jul 2007) $'.split()[1]
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| [1371] | 363 | __version__ = 'trunk'
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| [100] | 364 |
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| [1193] | 365 | def is_ipython():
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| [1259] | 366 | return '__IP' in dir(sys.modules["__main__"])
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| [1193] | 367 | if is_ipython():
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| [1014] | 368 | def version(): print "ASAP %s(%s)"% (__version__, __date__)
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| [706] | 369 | def list_scans(t = scantable):
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| [1295] | 370 | import types
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| [706] | 371 | globs = sys.modules['__main__'].__dict__.iteritems()
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| 372 | print "The user created scantables are:"
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| 373 | sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
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| 374 | print filter(lambda x: not x.startswith('_'), sts)
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| 375 | return
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| [100] | 376 |
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| [715] | 377 | def commands():
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| 378 | x = """
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| [113] | 379 | [The scan container]
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| 380 | scantable - a container for integrations/scans
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| [182] | 381 | (can open asap/rpfits/sdfits and ms files)
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| [113] | 382 | copy - returns a copy of a scan
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| 383 | get_scan - gets a specific scan out of a scantable
|
|---|
| [984] | 384 | (by name or number)
|
|---|
| [1093] | 385 | drop_scan - drops a specific scan out of a scantable
|
|---|
| 386 | (by number)
|
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| [984] | 387 | set_selection - set a new subselection of the data
|
|---|
| 388 | get_selection - get the current selection object
|
|---|
| [113] | 389 | summary - print info about the scantable contents
|
|---|
| [182] | 390 | stats - get specified statistic of the spectra in
|
|---|
| 391 | the scantable
|
|---|
| 392 | stddev - get the standard deviation of the spectra
|
|---|
| 393 | in the scantable
|
|---|
| [113] | 394 | get_tsys - get the TSys
|
|---|
| 395 | get_time - get the timestamps of the integrations
|
|---|
| [1351] | 396 | get_inttime - get the integration time
|
|---|
| [733] | 397 | get_sourcename - get the source names of the scans
|
|---|
| [794] | 398 | get_azimuth - get the azimuth of the scans
|
|---|
| 399 | get_elevation - get the elevation of the scans
|
|---|
| 400 | get_parangle - get the parallactic angle of the scans
|
|---|
| [876] | 401 | get_unit - get the current unit
|
|---|
| [513] | 402 | set_unit - set the abcissa unit to be used from this
|
|---|
| 403 | point on
|
|---|
| [255] | 404 | get_abcissa - get the abcissa values and name for a given
|
|---|
| 405 | row (time)
|
|---|
| [1259] | 406 | get_column_names - get the names of the columns in the scantable
|
|---|
| 407 | for use with selector.set_query
|
|---|
| [113] | 408 | set_freqframe - set the frame info for the Spectral Axis
|
|---|
| 409 | (e.g. 'LSRK')
|
|---|
| [276] | 410 | set_doppler - set the doppler to be used from this point on
|
|---|
| [984] | 411 | set_dirframe - set the frame for the direction on the sky
|
|---|
| [240] | 412 | set_instrument - set the instrument name
|
|---|
| [1190] | 413 | set_feedtype - set the feed type
|
|---|
| [255] | 414 | get_fluxunit - get the brightness flux unit
|
|---|
| [240] | 415 | set_fluxunit - set the brightness flux unit
|
|---|
| [188] | 416 | create_mask - return an mask in the current unit
|
|---|
| 417 | for the given region. The specified regions
|
|---|
| 418 | are NOT masked
|
|---|
| [255] | 419 | get_restfreqs - get the current list of rest frequencies
|
|---|
| 420 | set_restfreqs - set a list of rest frequencies
|
|---|
| [1360] | 421 | shift_refpix - shift the reference pixel of the IFs
|
|---|
| [1012] | 422 | flag - flag selected channels in the data
|
|---|
| [1192] | 423 | lag_flag - flag specified frequency in the data
|
|---|
| [1151] | 424 | save - save the scantable to disk as either 'ASAP',
|
|---|
| 425 | 'SDFITS' or 'ASCII'
|
|---|
| [486] | 426 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
|
|---|
| [733] | 427 | nscan - the number of scans in the scantable
|
|---|
| [984] | 428 | nrow - te number of spectra in the scantable
|
|---|
| [486] | 429 | history - print the history of the scantable
|
|---|
| [530] | 430 | get_fit - get a fit which has been stored witnh the data
|
|---|
| [706] | 431 | average_time - return the (weighted) time average of a scan
|
|---|
| [513] | 432 | or a list of scans
|
|---|
| 433 | average_pol - average the polarisations together.
|
|---|
| [1144] | 434 | average_beam - average the beams together.
|
|---|
| [992] | 435 | convert_pol - convert to a different polarisation type
|
|---|
| [690] | 436 | auto_quotient - return the on/off quotient with
|
|---|
| [1069] | 437 | automatic detection of the on/off scans (closest
|
|---|
| 438 | in time off is selected)
|
|---|
| [1144] | 439 | mx_quotient - Form a quotient using MX data (off beams)
|
|---|
| [1014] | 440 | scale, *, / - return a scan scaled by a given factor
|
|---|
| 441 | add, +, - - return a scan with given value added
|
|---|
| [513] | 442 | bin - return a scan with binned channels
|
|---|
| 443 | resample - return a scan with resampled channels
|
|---|
| 444 | smooth - return the spectrally smoothed scan
|
|---|
| 445 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
|
|---|
| [706] | 446 | auto_poly_baseline - automatically fit a polynomial baseline
|
|---|
| [780] | 447 | recalc_azel - recalculate azimuth and elevation based on
|
|---|
| 448 | the pointing
|
|---|
| [513] | 449 | gain_el - apply gain-elevation correction
|
|---|
| 450 | opacity - apply opacity correction
|
|---|
| 451 | convert_flux - convert to and from Jy and Kelvin brightness
|
|---|
| [255] | 452 | units
|
|---|
| [513] | 453 | freq_align - align spectra in frequency frame
|
|---|
| [1014] | 454 | invert_phase - Invert the phase of the cross-correlation
|
|---|
| [1351] | 455 | swap_linears - Swap XX and YY (or RR LL)
|
|---|
| [513] | 456 | rotate_xyphase - rotate XY phase of cross correlation
|
|---|
| 457 | rotate_linpolphase - rotate the phase of the complex
|
|---|
| 458 | polarization O=Q+iU correlation
|
|---|
| [733] | 459 | freq_switch - perform frequency switching on the data
|
|---|
| 460 | stats - Determine the specified statistic, e.g. 'min'
|
|---|
| 461 | 'max', 'rms' etc.
|
|---|
| 462 | stddev - Determine the standard deviation of the current
|
|---|
| 463 | beam/if/pol
|
|---|
| [1014] | 464 | [Selection]
|
|---|
| 465 | selector - a selection object to set a subset of a scantable
|
|---|
| 466 | set_scans - set (a list of) scans by index
|
|---|
| 467 | set_cycles - set (a list of) cycles by index
|
|---|
| 468 | set_beams - set (a list of) beamss by index
|
|---|
| 469 | set_ifs - set (a list of) ifs by index
|
|---|
| 470 | set_polarisations - set (a list of) polarisations by name
|
|---|
| 471 | or by index
|
|---|
| 472 | set_names - set a selection by name (wildcards allowed)
|
|---|
| 473 | set_tsys - set a selection by tsys thresholds
|
|---|
| [1259] | 474 | set_query - set a selection by SQL-like query, e.g. BEAMNO==1
|
|---|
| [1351] | 475 | ( also get_ functions for all these )
|
|---|
| [1014] | 476 | reset - unset all selections
|
|---|
| [1351] | 477 | + - merge two selections
|
|---|
| [733] | 478 |
|
|---|
| [513] | 479 | [Math] Mainly functions which operate on more than one scantable
|
|---|
| [100] | 480 |
|
|---|
| [706] | 481 | average_time - return the (weighted) time average
|
|---|
| [513] | 482 | of a list of scans
|
|---|
| 483 | quotient - return the on/off quotient
|
|---|
| 484 | simple_math - simple mathematical operations on two scantables,
|
|---|
| 485 | 'add', 'sub', 'mul', 'div'
|
|---|
| [1069] | 486 | quotient - build quotient of the given on and off scans
|
|---|
| [1351] | 487 | (matched pairs and 1 off - n on are valid)
|
|---|
| [1117] | 488 | merge - merge a list of scantables
|
|---|
| [1069] | 489 |
|
|---|
| [1151] | 490 | [Line Catalog]
|
|---|
| 491 | linecatalog - a linecatalog wrapper, taking an ASCII or
|
|---|
| 492 | internal format table
|
|---|
| 493 | summary - print a summary of the current selection
|
|---|
| 494 | set_name - select a subset by name pattern, e.g. '*OH*'
|
|---|
| 495 | set_strength_limits - select a subset by line strength limits
|
|---|
| 496 | set_frequency_limits - select a subset by frequency limits
|
|---|
| 497 | reset - unset all selections
|
|---|
| 498 | save - save the current subset to a table (internal
|
|---|
| 499 | format)
|
|---|
| 500 | get_row - get the name and frequency from a specific
|
|---|
| 501 | row in the table
|
|---|
| [513] | 502 | [Fitting]
|
|---|
| [113] | 503 | fitter
|
|---|
| 504 | auto_fit - return a scan where the function is
|
|---|
| 505 | applied to all Beams/IFs/Pols.
|
|---|
| 506 | commit - return a new scan where the fits have been
|
|---|
| 507 | commited.
|
|---|
| 508 | fit - execute the actual fitting process
|
|---|
| [984] | 509 | store_fit - store the fit parameters in the data (scantable)
|
|---|
| [113] | 510 | get_chi2 - get the Chi^2
|
|---|
| 511 | set_scan - set the scantable to be fit
|
|---|
| 512 | set_function - set the fitting function
|
|---|
| 513 | set_parameters - set the parameters for the function(s), and
|
|---|
| 514 | set if they should be held fixed during fitting
|
|---|
| [513] | 515 | set_gauss_parameters - same as above but specialised for individual
|
|---|
| 516 | gaussian components
|
|---|
| [113] | 517 | get_parameters - get the fitted parameters
|
|---|
| [513] | 518 | plot - plot the resulting fit and/or components and
|
|---|
| 519 | residual
|
|---|
| [210] | 520 | [Plotter]
|
|---|
| 521 | asapplotter - a plotter for asap, default plotter is
|
|---|
| 522 | called 'plotter'
|
|---|
| [984] | 523 | plot - plot a scantable
|
|---|
| [1151] | 524 | plot_lines - plot a linecatalog overlay
|
|---|
| [378] | 525 | save - save the plot to a file ('png' ,'ps' or 'eps')
|
|---|
| [210] | 526 | set_mode - set the state of the plotter, i.e.
|
|---|
| 527 | what is to be plotted 'colour stacked'
|
|---|
| 528 | and what 'panelled'
|
|---|
| [984] | 529 | set_selection - only plot a selected part of the data
|
|---|
| [733] | 530 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
|
|---|
| [255] | 531 | set_legend - specify user labels for the legend indeces
|
|---|
| 532 | set_title - specify user labels for the panel indeces
|
|---|
| [733] | 533 | set_abcissa - specify a user label for the abcissa
|
|---|
| [255] | 534 | set_ordinate - specify a user label for the ordinate
|
|---|
| [378] | 535 | set_layout - specify the multi-panel layout (rows,cols)
|
|---|
| [733] | 536 | set_colors - specify a set of colours to use
|
|---|
| 537 | set_linestyles - specify a set of linestyles to use if only
|
|---|
| 538 | using one color
|
|---|
| [1151] | 539 | set_font - set general font properties, e.g. 'family'
|
|---|
| [1054] | 540 | set_histogram - plot in historam style
|
|---|
| [733] | 541 | set_mask - set a plotting mask for a specific polarization
|
|---|
| [1171] | 542 | text - draw text annotations either in data or relative
|
|---|
| 543 | coordinates
|
|---|
| 544 | arrow - draw arrow annotations either in data or relative
|
|---|
| 545 | coordinates
|
|---|
| 546 | axhline,axvline - draw horizontal/vertical lines
|
|---|
| 547 | axhspan,axvspan - draw horizontal/vertical regions
|
|---|
| [1175] | 548 |
|
|---|
| 549 | xyplotter - matplotlib/pylab plotting functions
|
|---|
| 550 |
|
|---|
| [182] | 551 | [Reading files]
|
|---|
| 552 | reader - access rpfits/sdfits files
|
|---|
| [984] | 553 | open - attach reader to a file
|
|---|
| 554 | close - detach reader from file
|
|---|
| [182] | 555 | read - read in integrations
|
|---|
| 556 | summary - list info about all integrations
|
|---|
| 557 |
|
|---|
| [113] | 558 | [General]
|
|---|
| 559 | commands - this command
|
|---|
| 560 | print - print details about a variable
|
|---|
| 561 | list_scans - list all scantables created bt the user
|
|---|
| [992] | 562 | list_files - list all files readable by asap (default rpf)
|
|---|
| [113] | 563 | del - delete the given variable from memory
|
|---|
| 564 | range - create a list of values, e.g.
|
|---|
| 565 | range(3) = [0,1,2], range(2,5) = [2,3,4]
|
|---|
| 566 | help - print help for one of the listed functions
|
|---|
| 567 | execfile - execute an asap script, e.g. execfile('myscript')
|
|---|
| [255] | 568 | list_rcparameters - print out a list of possible values to be
|
|---|
| [274] | 569 | put into $HOME/.asaprc
|
|---|
| [1171] | 570 | rc - set rc parameters from within asap
|
|---|
| [466] | 571 | mask_and,mask_or,
|
|---|
| 572 | mask_not - boolean operations on masks created with
|
|---|
| 573 | scantable.create_mask
|
|---|
| [706] | 574 |
|
|---|
| [210] | 575 | Note:
|
|---|
| 576 | How to use this with help:
|
|---|
| 577 | # function 'summary'
|
|---|
| 578 | [xxx] is just a category
|
|---|
| 579 | Every 'sub-level' in this list should be replaces by a '.' Period when
|
|---|
| [706] | 580 | using help
|
|---|
| [210] | 581 | Example:
|
|---|
| 582 | ASAP> help scantable # to get info on ths scantable
|
|---|
| 583 | ASAP> help scantable.summary # to get help on the scantable's
|
|---|
| 584 | ASAP> help average_time
|
|---|
| 585 |
|
|---|
| [715] | 586 | """
|
|---|
| [1151] | 587 | if rcParams['verbose']:
|
|---|
| 588 | try:
|
|---|
| 589 | from IPython.genutils import page as pager
|
|---|
| 590 | except ImportError:
|
|---|
| 591 | from pydoc import pager
|
|---|
| 592 | pager(x)
|
|---|
| 593 | else:
|
|---|
| 594 | print x
|
|---|
| [715] | 595 | return
|
|---|
| [113] | 596 |
|
|---|
| [706] | 597 | def welcome():
|
|---|
| 598 | return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
|
|---|
| [100] | 599 |
|
|---|
| [1035] | 600 | Please report any bugs via:
|
|---|
| [1378] | 601 | http://svn.atnf.csiro.au/trac/asap/simpleticket
|
|---|
| [100] | 602 |
|
|---|
| [378] | 603 | [IMPORTANT: ASAP is 0-based]
|
|---|
| [706] | 604 | Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
|
|---|
