| [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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| [1691] | 6 | try:
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| 7 | from functools import wraps as wraps_dec
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| 8 | except ImportError:
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| 9 | from asap.compatibility import wraps as wraps_dec
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| [226] | 10 |
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| [1789] | 11 | # Set up CASAPATH and first time use of asap i.e. ~/.asap/*
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| [1080] | 12 | plf = None
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| 13 | if sys.platform == "linux2":
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| 14 | if platform.architecture()[0] == '64bit':
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| 15 | plf = 'linux_64b'
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| 16 | else:
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| 17 | plf = 'linux_gnu'
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| 18 | elif sys.platform == 'darwin':
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| 19 | plf = 'darwin'
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| 20 | else:
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| 21 | # Shouldn't happen - default to linux
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| 22 | plf = 'linux'
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| 23 | asapdata = __path__[-1]
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| [1171] | 24 | # Allow user defined data location
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| 25 | if os.environ.has_key("ASAPDATA"):
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| 26 | if os.path.exists(os.environ["ASAPDATA"]):
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| 27 | asapdata = os.environ["ASAPDATA"]
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| [1789] | 28 | # use CASAPATH if defined and "data" dir present
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| 29 | if not os.environ.has_key("CASAPATH") or \
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| 30 | not os.path.exists(os.environ["CASAPATH"].split()[0]+"/data"):
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| 31 | os.environ["CASAPATH"] = "%s %s somwhere" % ( asapdata, plf)
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| [1171] | 32 | # set up user space
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| [1080] | 33 | userdir = os.environ["HOME"]+"/.asap"
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| 34 | if not os.path.exists(userdir):
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| 35 | print 'First time ASAP use. Setting up ~/.asap'
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| 36 | os.mkdir(userdir)
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| [1789] | 37 | #shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap")
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| 38 | # commented out by TT on 2009.06.23 for casapy use
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| 39 | ##shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
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| 40 | ## userdir+"/ipy_user_conf.py")
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| [1080] | 41 | f = file(userdir+"/asapuserfuncs.py", "w")
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| 42 | f.close()
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| 43 | f = file(userdir+"/ipythonrc", "w")
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| 44 | f.close()
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| [1789] | 45 | # commented out by TT on 2009.06.23 for casapy use
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| 46 | ##else:
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| [1472] | 47 | # upgrade to support later ipython versions
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| [1789] | 48 | ##if not os.path.exists(userdir+"/ipy_user_conf.py"):
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| 49 | ## shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
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| 50 | ## userdir+"/ipy_user_conf.py")
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| [1472] | 51 |
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| [1171] | 52 | # remove from namespace
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| [1080] | 53 | del asapdata, userdir, shutil, platform
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| 54 |
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| [513] | 55 | def _validate_bool(b):
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| [226] | 56 | 'Convert b to a boolean or raise'
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| 57 | bl = b.lower()
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| 58 | if bl in ('f', 'no', 'false', '0', 0): return False
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| 59 | elif bl in ('t', 'yes', 'true', '1', 1): return True
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| 60 | else:
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| 61 | raise ValueError('Could not convert "%s" to boolean' % b)
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| 62 |
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| [513] | 63 | def _validate_int(s):
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| [226] | 64 | 'convert s to int or raise'
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| 65 | try: return int(s)
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| 66 | except ValueError:
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| 67 | raise ValueError('Could not convert "%s" to int' % s)
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| 68 |
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| [513] | 69 | def _asap_fname():
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| [226] | 70 | """
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| 71 | Return the path to the rc file
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| 72 |
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| 73 | Search order:
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| 74 |
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| 75 | * current working dir
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| 76 | * environ var ASAPRC
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| [274] | 77 | * HOME/.asaprc
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| [706] | 78 |
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| [226] | 79 | """
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| 80 | fname = os.path.join( os.getcwd(), '.asaprc')
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| 81 | if os.path.exists(fname): return fname
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| 82 |
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| 83 | if os.environ.has_key('ASAPRC'):
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| 84 | path = os.environ['ASAPRC']
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| 85 | if os.path.exists(path):
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| 86 | fname = os.path.join(path, '.asaprc')
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| 87 | if os.path.exists(fname):
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| 88 | return fname
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| 89 |
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| 90 | if os.environ.has_key('HOME'):
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| 91 | home = os.environ['HOME']
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| 92 | fname = os.path.join(home, '.asaprc')
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| 93 | if os.path.exists(fname):
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| 94 | return fname
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| 95 | return None
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| 96 |
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| [706] | 97 |
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| [226] | 98 | defaultParams = {
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| 99 | # general
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| [513] | 100 | 'verbose' : [True, _validate_bool],
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| 101 | 'useplotter' : [True, _validate_bool],
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| [542] | 102 | 'insitu' : [True, _validate_bool],
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| [706] | 103 |
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| [226] | 104 | # plotting
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| [706] | 105 | 'plotter.gui' : [True, _validate_bool],
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| [226] | 106 | 'plotter.stacking' : ['p', str],
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| 107 | 'plotter.panelling' : ['s', str],
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| [700] | 108 | 'plotter.colours' : ['', str],
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| 109 | 'plotter.linestyles' : ['', str],
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| [710] | 110 | 'plotter.decimate' : [False, _validate_bool],
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| 111 | 'plotter.ganged' : [True, _validate_bool],
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| [1022] | 112 | 'plotter.histogram' : [False, _validate_bool],
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| [1097] | 113 | 'plotter.papertype' : ['A4', str],
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| [1789] | 114 | ## for older Matplotlib version
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| 115 | #'plotter.axesformatting' : ['mpl', str],
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| 116 | 'plotter.axesformatting' : ['asap', str],
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| [710] | 117 |
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| [226] | 118 | # scantable
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| 119 | 'scantable.save' : ['ASAP', str],
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| [513] | 120 | 'scantable.autoaverage' : [True, _validate_bool],
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| [226] | 121 | 'scantable.freqframe' : ['LSRK', str], #default frequency frame
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| [1076] | 122 | 'scantable.verbosesummary' : [False, _validate_bool],
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| [1422] | 123 | 'scantable.storage' : ['memory', str],
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| [1504] | 124 | 'scantable.history' : [True, _validate_bool],
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| [1586] | 125 | 'scantable.reference' : ['.*(e|w|_R)$', str],
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| 126 | 'scantable.parallactify' : [False, _validate_bool]
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| [226] | 127 | # fitter
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| 128 | }
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| 129 |
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| [255] | 130 | def list_rcparameters():
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| [706] | 131 |
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| [255] | 132 | print """
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| [737] | 133 | # general
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| 134 | # print verbose output
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| 135 | verbose : True
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| [255] | 136 |
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| [737] | 137 | # preload a default plotter
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| 138 | useplotter : True
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| [255] | 139 |
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| [737] | 140 | # apply operations on the input scantable or return new one
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| 141 | insitu : True
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| [706] | 142 |
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| [737] | 143 | # plotting
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| [710] | 144 |
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| [737] | 145 | # do we want a GUI or plot to a file
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| 146 | plotter.gui : True
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| [710] | 147 |
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| [737] | 148 | # default mode for colour stacking
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| 149 | plotter.stacking : Pol
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| [255] | 150 |
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| [737] | 151 | # default mode for panelling
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| 152 | plotter.panelling : scan
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| [255] | 153 |
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| [1560] | 154 | # push panels together, to share axis labels
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| [737] | 155 | plotter.ganged : True
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| [710] | 156 |
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| [1513] | 157 | # decimate the number of points plotted by a factor of
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| [737] | 158 | # nchan/1024
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| 159 | plotter.decimate : False
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| [733] | 160 |
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| [737] | 161 | # default colours/linestyles
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| 162 | plotter.colours :
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| 163 | plotter.linestyles :
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| [700] | 164 |
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| [1022] | 165 | # enable/disable histogram plotting
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| 166 | plotter.histogram : False
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| 167 |
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| [1097] | 168 | # ps paper type
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| 169 | plotter.papertype : A4
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| 170 |
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| [1513] | 171 | # The formatting style of the xaxis
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| [1560] | 172 | plotter.axesformatting : 'mpl' (default) or 'asap' (for old versions of matplotlib)
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| [1513] | 173 |
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| [737] | 174 | # scantable
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| [1076] | 175 |
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| [1259] | 176 | # default storage of scantable ('memory'/'disk')
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| [1076] | 177 | scantable.storage : memory
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| [1422] | 178 |
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| 179 | # write history of each call to scantable
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| 180 | scantable.history : True
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| 181 |
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| [737] | 182 | # default ouput format when saving
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| 183 | scantable.save : ASAP
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| [1422] | 184 |
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| [737] | 185 | # auto averaging on read
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| 186 | scantable.autoaverage : True
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| [255] | 187 |
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| [737] | 188 | # default frequency frame to set when function
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| [1097] | 189 | # scantable.set_freqframe is called
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| [737] | 190 | scantable.freqframe : LSRK
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| [255] | 191 |
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| [737] | 192 | # Control the level of information printed by summary
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| 193 | scantable.verbosesummary : False
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| [706] | 194 |
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| [1504] | 195 | # Control the identification of reference (off) scans
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| 196 | # This is has to be a regular expression
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| [1595] | 197 | scantable.reference : .*(e|w|_R)$
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| [1560] | 198 |
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| [1595] | 199 | # Indicate whether the data was parallactified (total phase offest == 0.0)
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| 200 | scantable.parallactify : False
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| 201 |
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| [737] | 202 | # Fitter
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| 203 | """
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| [706] | 204 |
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| [226] | 205 | def rc_params():
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| 206 | 'Return the default params updated from the values in the rc file'
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| [706] | 207 |
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| [513] | 208 | fname = _asap_fname()
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| [706] | 209 |
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| [226] | 210 | if fname is None or not os.path.exists(fname):
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| 211 | message = 'could not find rc file; returning defaults'
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| 212 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
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| 213 | #print message
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| 214 | return ret
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| [706] | 215 |
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| [226] | 216 | cnt = 0
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| 217 | for line in file(fname):
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| 218 | cnt +=1
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| 219 | line = line.strip()
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| 220 | if not len(line): continue
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| 221 | if line.startswith('#'): continue
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| 222 | tup = line.split(':',1)
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| 223 | if len(tup) !=2:
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| [1789] | 224 | #print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
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| 225 | asaplog.push('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
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| 226 | print_log('WARN')
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| [226] | 227 | continue
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| [706] | 228 |
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| [226] | 229 | key, val = tup
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| 230 | key = key.strip()
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| 231 | if not defaultParams.has_key(key):
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| [1789] | 232 | #print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
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| 233 | asaplog.push('Bad key "%s" on line %d in %s' % (key, cnt, fname))
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| 234 | print_log('WARN')
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| [226] | 235 | continue
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| [706] | 236 |
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| [226] | 237 | default, converter = defaultParams[key]
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| 238 |
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| 239 | ind = val.find('#')
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| 240 | if ind>=0: val = val[:ind] # ignore trailing comments
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| 241 | val = val.strip()
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| 242 | try: cval = converter(val) # try to convert to proper type or raise
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| [1080] | 243 | except ValueError, msg:
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| [1789] | 244 | #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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| 245 | asaplog.push('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, str(msg)))
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| 246 | print_log('WARN')
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| [226] | 247 | continue
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| 248 | else:
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| 249 | # Alles Klar, update dict
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| 250 | defaultParams[key][0] = cval
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| 251 |
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| 252 | # strip the conveter funcs and return
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| 253 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
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| [466] | 254 | print ('loaded rc file %s'%fname)
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| [226] | 255 |
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| 256 | return ret
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| 257 |
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| 258 |
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| 259 | # this is the instance used by the asap classes
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| [706] | 260 | rcParams = rc_params()
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| [226] | 261 |
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| 262 | rcParamsDefault = dict(rcParams.items()) # a copy
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| 263 |
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| 264 | def rc(group, **kwargs):
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| 265 | """
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| 266 | Set the current rc params. Group is the grouping for the rc, eg
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| [379] | 267 | for scantable.save the group is 'scantable', for plotter.stacking, the
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| 268 | group is 'plotter', and so on. kwargs is a list of attribute
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| [226] | 269 | name/value pairs, eg
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| 270 |
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| [379] | 271 | rc('scantable', save='SDFITS')
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| [226] | 272 |
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| 273 | sets the current rc params and is equivalent to
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| [706] | 274 |
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| [379] | 275 | rcParams['scantable.save'] = 'SDFITS'
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| [226] | 276 |
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| 277 | Use rcdefaults to restore the default rc params after changes.
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| 278 | """
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| 279 |
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| [379] | 280 | aliases = {}
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| [706] | 281 |
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| [226] | 282 | for k,v in kwargs.items():
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| 283 | name = aliases.get(k) or k
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| [1422] | 284 | if len(group):
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| 285 | key = '%s.%s' % (group, name)
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| 286 | else:
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| 287 | key = name
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| [226] | 288 | if not rcParams.has_key(key):
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| 289 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
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| [706] | 290 |
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| [226] | 291 | rcParams[key] = v
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| 292 |
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| 293 |
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| 294 | def rcdefaults():
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| 295 | """
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| 296 | Restore the default rc params - the ones that were created at
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| 297 | asap load time
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| 298 | """
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| 299 | rcParams.update(rcParamsDefault)
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| 300 |
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| [1295] | 301 | def _n_bools(n, val):
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| [1588] | 302 | return [ val for i in xrange(n) ]
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| [513] | 303 |
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| 304 | def _is_sequence_or_number(param, ptype=int):
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| 305 | if isinstance(param,tuple) or isinstance(param,list):
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| [928] | 306 | if len(param) == 0: return True # empty list
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| [513] | 307 | out = True
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| 308 | for p in param:
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| 309 | out &= isinstance(p,ptype)
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| 310 | return out
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| 311 | elif isinstance(param, ptype):
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| 312 | return True
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| 313 | return False
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| 314 |
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| [928] | 315 | def _to_list(param, ptype=int):
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| 316 | if isinstance(param, ptype):
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| 317 | if ptype is str: return param.split()
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| 318 | else: return [param]
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| 319 | if _is_sequence_or_number(param, ptype):
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| 320 | return param
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| 321 | return None
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| [715] | 322 |
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| [944] | 323 | def unique(x):
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| [992] | 324 | """
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| 325 | Return the unique values in a list
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| 326 | Parameters:
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| 327 | x: the list to reduce
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| 328 | Examples:
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| 329 | x = [1,2,3,3,4]
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| 330 | print unique(x)
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| 331 | [1,2,3,4]
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| 332 | """
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| [944] | 333 | return dict([ (val, 1) for val in x]).keys()
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| 334 |
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| [992] | 335 | def list_files(path=".",suffix="rpf"):
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| 336 | """
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| 337 | Return a list files readable by asap, such as rpf, sdfits, mbf, asap
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| 338 | Parameters:
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| 339 | path: The directory to list (default '.')
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| 340 | suffix: The file extension (default rpf)
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| 341 | Example:
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| 342 | files = list_files("data/","sdfits")
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| 343 | print files
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| 344 | ['data/2001-09-01_0332_P363.sdfits',
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| 345 | 'data/2003-04-04_131152_t0002.sdfits',
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| 346 | 'data/Sgr_86p262_best_SPC.sdfits']
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| 347 | """
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| 348 | if not os.path.isdir(path):
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| 349 | return None
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| [1295] | 350 | valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split()
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| [992] | 351 | if not suffix in valid:
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| 352 | return None
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| 353 | files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
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| 354 | return filter(lambda x: x.endswith(suffix),files)
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| 355 |
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| [715] | 356 | # workaround for ipython, which redirects this if banner=0 in ipythonrc
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| 357 | sys.stdout = sys.__stdout__
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| 358 | sys.stderr = sys.__stderr__
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| 359 |
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| 360 | # Logging
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| 361 | from asap._asap import Log as _asaplog
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| 362 | global asaplog
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| [710] | 363 | asaplog=_asaplog()
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| [715] | 364 | if rcParams['verbose']:
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| 365 | asaplog.enable()
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| 366 | else:
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| 367 | asaplog.disable()
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| 368 |
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| [1589] | 369 |
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| 370 | def print_log_dec(f):
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| [1691] | 371 | @wraps_dec(f)
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| [1589] | 372 | def wrap_it(*args, **kw):
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| 373 | val = f(*args, **kw)
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| 374 | print_log()
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| 375 | return val
|
|---|
| 376 | return wrap_it
|
|---|
| 377 |
|
|---|
| [1789] | 378 | def print_log(level='INFO'):
|
|---|
| 379 | from taskinit import casalog
|
|---|
| 380 | log = asaplog.pop()
|
|---|
| 381 | #if len(log) and rcParams['verbose']: print log
|
|---|
| 382 | if len(log) and rcParams['verbose']: casalog.post( log, priority=level )
|
|---|
| [715] | 383 | return
|
|---|
| 384 |
|
|---|
| [1295] | 385 | def mask_and(a, b):
|
|---|
| 386 | assert(len(a)==len(b))
|
|---|
| 387 | return [ a[i] & b[i] for i in xrange(len(a)) ]
|
|---|
| [1134] | 388 |
|
|---|
| [1295] | 389 | def mask_or(a, b):
|
|---|
| 390 | assert(len(a)==len(b))
|
|---|
| 391 | return [ a[i] | b[i] for i in xrange(len(a)) ]
|
|---|
| 392 |
|
|---|
| 393 | def mask_not(a):
|
|---|
| 394 | return [ not i for i in a ]
|
|---|
| 395 |
|
|---|
| [1117] | 396 | from asapfitter import fitter
|
|---|
| [895] | 397 | from asapreader import reader
|
|---|
| [944] | 398 | from selector import selector
|
|---|
| [710] | 399 |
|
|---|
| [100] | 400 | from asapmath import *
|
|---|
| [1080] | 401 | from scantable import scantable
|
|---|
| [1097] | 402 | from asaplinefind import linefinder
|
|---|
| [1645] | 403 | from simplelinefinder import simplelinefinder
|
|---|
| [1134] | 404 | from linecatalog import linecatalog
|
|---|
| [1789] | 405 | from interactivemask import interactivemask
|
|---|
| [1689] | 406 | from opacity import skydip
|
|---|
| [1725] | 407 | from opacity import model as opacity_model
|
|---|
| [285] | 408 |
|
|---|
| [928] | 409 | if rcParams['useplotter']:
|
|---|
| [1295] | 410 | try:
|
|---|
| [1423] | 411 | from asapplotter import asapplotter
|
|---|
| 412 | gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
|
|---|
| 413 | if gui:
|
|---|
| [1422] | 414 | import matplotlib
|
|---|
| [1789] | 415 | if not matplotlib.sys.modules['matplotlib.backends']: matplotlib.use("TkAgg")
|
|---|
| [1691] | 416 | from matplotlib import pylab
|
|---|
| [1422] | 417 | xyplotter = pylab
|
|---|
| [1423] | 418 | plotter = asapplotter(gui)
|
|---|
| 419 | del gui
|
|---|
| [1295] | 420 | except ImportError:
|
|---|
| [1789] | 421 | #print "Matplotlib not installed. No plotting available"
|
|---|
| 422 | asaplog.post( "Matplotlib not installed. No plotting available")
|
|---|
| 423 | print_log('WARN')
|
|---|
| [285] | 424 |
|
|---|
| [574] | 425 | __date__ = '$Date: 2010-07-30 06:59:56 +0000 (Fri, 30 Jul 2010) $'.split()[1]
|
|---|
| [1789] | 426 | __version__ = '3.0.0 alma'
|
|---|
| 427 | # nrao casapy specific, get revision number
|
|---|
| 428 | #__revision__ = ' unknown '
|
|---|
| 429 | casapath=os.environ["CASAPATH"].split()
|
|---|
| 430 | #svninfo.txt path
|
|---|
| 431 | if os.path.isdir(casapath[0]+'/'+casapath[1]+'/python/2.5/asap'):
|
|---|
| 432 | # for casa developer environment (linux or darwin)
|
|---|
| 433 | revinfo=casapath[0]+'/'+casapath[1]+'/python/2.5/asap/svninfo.txt'
|
|---|
| 434 | else:
|
|---|
| 435 | # for end-user environments
|
|---|
| 436 | if casapath[1]=='darwin':
|
|---|
| 437 | revinfo=casapath[0]+'/Resources/python/asap/svninfo.txt'
|
|---|
| 438 | else:
|
|---|
| 439 | revinfo=casapath[0]+'/lib/python2.5/asap/svninfo.txt'
|
|---|
| 440 | if os.path.isfile(revinfo):
|
|---|
| 441 | f = file(revinfo)
|
|---|
| 442 | f.readline()
|
|---|
| 443 | revsionno=f.readline()
|
|---|
| 444 | f.close()
|
|---|
| 445 | del f
|
|---|
| 446 | __revision__ = revsionno.rstrip()
|
|---|
| 447 | else:
|
|---|
| 448 | __revision__ = ' unknown '
|
|---|
| [100] | 449 |
|
|---|
| [1193] | 450 | def is_ipython():
|
|---|
| [1725] | 451 | return 'IPython' in sys.modules.keys()
|
|---|
| [1193] | 452 | if is_ipython():
|
|---|
| [1014] | 453 | def version(): print "ASAP %s(%s)"% (__version__, __date__)
|
|---|
| [1588] | 454 |
|
|---|
| 455 | def list_scans(t = scantable):
|
|---|
| [1560] | 456 | import inspect
|
|---|
| 457 | print "The user created scantables are: ",
|
|---|
| 458 | globs=inspect.currentframe().f_back.f_locals.copy()
|
|---|
| 459 | out = [ k for k,v in globs.iteritems() \
|
|---|
| 460 | if isinstance(v, scantable) and not k.startswith("_") ]
|
|---|
| 461 | print out
|
|---|
| 462 | return out
|
|---|
| [100] | 463 |
|
|---|
| [715] | 464 | def commands():
|
|---|
| 465 | x = """
|
|---|
| [113] | 466 | [The scan container]
|
|---|
| 467 | scantable - a container for integrations/scans
|
|---|
| [182] | 468 | (can open asap/rpfits/sdfits and ms files)
|
|---|
| [113] | 469 | copy - returns a copy of a scan
|
|---|
| 470 | get_scan - gets a specific scan out of a scantable
|
|---|
| [984] | 471 | (by name or number)
|
|---|
| [1093] | 472 | drop_scan - drops a specific scan out of a scantable
|
|---|
| 473 | (by number)
|
|---|
| [984] | 474 | set_selection - set a new subselection of the data
|
|---|
| 475 | get_selection - get the current selection object
|
|---|
| [113] | 476 | summary - print info about the scantable contents
|
|---|
| [182] | 477 | stats - get specified statistic of the spectra in
|
|---|
| 478 | the scantable
|
|---|
| 479 | stddev - get the standard deviation of the spectra
|
|---|
| 480 | in the scantable
|
|---|
| [113] | 481 | get_tsys - get the TSys
|
|---|
| 482 | get_time - get the timestamps of the integrations
|
|---|
| [1351] | 483 | get_inttime - get the integration time
|
|---|
| [733] | 484 | get_sourcename - get the source names of the scans
|
|---|
| [794] | 485 | get_azimuth - get the azimuth of the scans
|
|---|
| 486 | get_elevation - get the elevation of the scans
|
|---|
| 487 | get_parangle - get the parallactic angle of the scans
|
|---|
| [1697] | 488 | get_coordinate - get the spectral coordinate for the given row,
|
|---|
| 489 | which can be used for coordinate conversions
|
|---|
| [1739] | 490 | get_weather - get the weather condition parameters
|
|---|
| [876] | 491 | get_unit - get the current unit
|
|---|
| [513] | 492 | set_unit - set the abcissa unit to be used from this
|
|---|
| 493 | point on
|
|---|
| [255] | 494 | get_abcissa - get the abcissa values and name for a given
|
|---|
| 495 | row (time)
|
|---|
| [1259] | 496 | get_column_names - get the names of the columns in the scantable
|
|---|
| 497 | for use with selector.set_query
|
|---|
| [113] | 498 | set_freqframe - set the frame info for the Spectral Axis
|
|---|
| 499 | (e.g. 'LSRK')
|
|---|
| [276] | 500 | set_doppler - set the doppler to be used from this point on
|
|---|
| [984] | 501 | set_dirframe - set the frame for the direction on the sky
|
|---|
| [240] | 502 | set_instrument - set the instrument name
|
|---|
| [1190] | 503 | set_feedtype - set the feed type
|
|---|
| [255] | 504 | get_fluxunit - get the brightness flux unit
|
|---|
| [240] | 505 | set_fluxunit - set the brightness flux unit
|
|---|
| [1508] | 506 | set_sourcetype - set the type of the source - source or reference
|
|---|
| [188] | 507 | create_mask - return an mask in the current unit
|
|---|
| 508 | for the given region. The specified regions
|
|---|
| 509 | are NOT masked
|
|---|
| [255] | 510 | get_restfreqs - get the current list of rest frequencies
|
|---|
| 511 | set_restfreqs - set a list of rest frequencies
|
|---|
| [1471] | 512 | shift_refpix - shift the reference pixel of the IFs
|
|---|
| 513 | set_spectrum - overwrite the spectrum for a given row
|
|---|
| 514 | get_spectrum - retrieve the spectrum for a given
|
|---|
| 515 | get_mask - retrieve the mask for a given
|
|---|
| [1012] | 516 | flag - flag selected channels in the data
|
|---|
| [1192] | 517 | lag_flag - flag specified frequency in the data
|
|---|
| [1151] | 518 | save - save the scantable to disk as either 'ASAP',
|
|---|
| 519 | 'SDFITS' or 'ASCII'
|
|---|
| [486] | 520 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
|
|---|
| [733] | 521 | nscan - the number of scans in the scantable
|
|---|
| [1422] | 522 | nrow - the number of spectra in the scantable
|
|---|
| [486] | 523 | history - print the history of the scantable
|
|---|
| [530] | 524 | get_fit - get a fit which has been stored witnh the data
|
|---|
| [706] | 525 | average_time - return the (weighted) time average of a scan
|
|---|
| [513] | 526 | or a list of scans
|
|---|
| 527 | average_pol - average the polarisations together.
|
|---|
| [1144] | 528 | average_beam - average the beams together.
|
|---|
| [992] | 529 | convert_pol - convert to a different polarisation type
|
|---|
| [690] | 530 | auto_quotient - return the on/off quotient with
|
|---|
| [1069] | 531 | automatic detection of the on/off scans (closest
|
|---|
| 532 | in time off is selected)
|
|---|
| [1144] | 533 | mx_quotient - Form a quotient using MX data (off beams)
|
|---|
| [1014] | 534 | scale, *, / - return a scan scaled by a given factor
|
|---|
| [1560] | 535 | add, + - return a scan with given value added
|
|---|
| 536 | sub, - - return a scan with given value subtracted
|
|---|
| [513] | 537 | bin - return a scan with binned channels
|
|---|
| 538 | resample - return a scan with resampled channels
|
|---|
| 539 | smooth - return the spectrally smoothed scan
|
|---|
| 540 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
|
|---|
| [706] | 541 | auto_poly_baseline - automatically fit a polynomial baseline
|
|---|
| [780] | 542 | recalc_azel - recalculate azimuth and elevation based on
|
|---|
| 543 | the pointing
|
|---|
| [513] | 544 | gain_el - apply gain-elevation correction
|
|---|
| 545 | opacity - apply opacity correction
|
|---|
| 546 | convert_flux - convert to and from Jy and Kelvin brightness
|
|---|
| [255] | 547 | units
|
|---|
| [513] | 548 | freq_align - align spectra in frequency frame
|
|---|
| [1014] | 549 | invert_phase - Invert the phase of the cross-correlation
|
|---|
| [1351] | 550 | swap_linears - Swap XX and YY (or RR LL)
|
|---|
| [513] | 551 | rotate_xyphase - rotate XY phase of cross correlation
|
|---|
| 552 | rotate_linpolphase - rotate the phase of the complex
|
|---|
| 553 | polarization O=Q+iU correlation
|
|---|
| [733] | 554 | freq_switch - perform frequency switching on the data
|
|---|
| 555 | stats - Determine the specified statistic, e.g. 'min'
|
|---|
| 556 | 'max', 'rms' etc.
|
|---|
| 557 | stddev - Determine the standard deviation of the current
|
|---|
| 558 | beam/if/pol
|
|---|
| [1588] | 559 | get_row_selector - get the selection object for a specified row
|
|---|
| 560 | number
|
|---|
| [1014] | 561 | [Selection]
|
|---|
| 562 | selector - a selection object to set a subset of a scantable
|
|---|
| 563 | set_scans - set (a list of) scans by index
|
|---|
| 564 | set_cycles - set (a list of) cycles by index
|
|---|
| 565 | set_beams - set (a list of) beamss by index
|
|---|
| 566 | set_ifs - set (a list of) ifs by index
|
|---|
| 567 | set_polarisations - set (a list of) polarisations by name
|
|---|
| 568 | or by index
|
|---|
| 569 | set_names - set a selection by name (wildcards allowed)
|
|---|
| 570 | set_tsys - set a selection by tsys thresholds
|
|---|
| [1259] | 571 | set_query - set a selection by SQL-like query, e.g. BEAMNO==1
|
|---|
| [1351] | 572 | ( also get_ functions for all these )
|
|---|
| [1014] | 573 | reset - unset all selections
|
|---|
| [1351] | 574 | + - merge two selections
|
|---|
| [733] | 575 |
|
|---|
| [513] | 576 | [Math] Mainly functions which operate on more than one scantable
|
|---|
| [100] | 577 |
|
|---|
| [706] | 578 | average_time - return the (weighted) time average
|
|---|
| [513] | 579 | of a list of scans
|
|---|
| 580 | quotient - return the on/off quotient
|
|---|
| 581 | simple_math - simple mathematical operations on two scantables,
|
|---|
| 582 | 'add', 'sub', 'mul', 'div'
|
|---|
| [1069] | 583 | quotient - build quotient of the given on and off scans
|
|---|
| [1351] | 584 | (matched pairs and 1 off - n on are valid)
|
|---|
| [1117] | 585 | merge - merge a list of scantables
|
|---|
| [1069] | 586 |
|
|---|
| [1151] | 587 | [Line Catalog]
|
|---|
| 588 | linecatalog - a linecatalog wrapper, taking an ASCII or
|
|---|
| 589 | internal format table
|
|---|
| 590 | summary - print a summary of the current selection
|
|---|
| 591 | set_name - select a subset by name pattern, e.g. '*OH*'
|
|---|
| 592 | set_strength_limits - select a subset by line strength limits
|
|---|
| 593 | set_frequency_limits - select a subset by frequency limits
|
|---|
| 594 | reset - unset all selections
|
|---|
| 595 | save - save the current subset to a table (internal
|
|---|
| 596 | format)
|
|---|
| 597 | get_row - get the name and frequency from a specific
|
|---|
| 598 | row in the table
|
|---|
| [513] | 599 | [Fitting]
|
|---|
| [113] | 600 | fitter
|
|---|
| 601 | auto_fit - return a scan where the function is
|
|---|
| 602 | applied to all Beams/IFs/Pols.
|
|---|
| 603 | commit - return a new scan where the fits have been
|
|---|
| 604 | commited.
|
|---|
| 605 | fit - execute the actual fitting process
|
|---|
| [984] | 606 | store_fit - store the fit parameters in the data (scantable)
|
|---|
| [113] | 607 | get_chi2 - get the Chi^2
|
|---|
| 608 | set_scan - set the scantable to be fit
|
|---|
| 609 | set_function - set the fitting function
|
|---|
| 610 | set_parameters - set the parameters for the function(s), and
|
|---|
| 611 | set if they should be held fixed during fitting
|
|---|
| [513] | 612 | set_gauss_parameters - same as above but specialised for individual
|
|---|
| 613 | gaussian components
|
|---|
| [113] | 614 | get_parameters - get the fitted parameters
|
|---|
| [513] | 615 | plot - plot the resulting fit and/or components and
|
|---|
| 616 | residual
|
|---|
| [210] | 617 | [Plotter]
|
|---|
| 618 | asapplotter - a plotter for asap, default plotter is
|
|---|
| 619 | called 'plotter'
|
|---|
| [984] | 620 | plot - plot a scantable
|
|---|
| [1151] | 621 | plot_lines - plot a linecatalog overlay
|
|---|
| [1697] | 622 | plotazel - plot azimuth and elevation versus time
|
|---|
| 623 | plotpointing - plot telescope pointings
|
|---|
| [378] | 624 | save - save the plot to a file ('png' ,'ps' or 'eps')
|
|---|
| [210] | 625 | set_mode - set the state of the plotter, i.e.
|
|---|
| 626 | what is to be plotted 'colour stacked'
|
|---|
| 627 | and what 'panelled'
|
|---|
| [984] | 628 | set_selection - only plot a selected part of the data
|
|---|
| [733] | 629 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
|
|---|
| [255] | 630 | set_legend - specify user labels for the legend indeces
|
|---|
| 631 | set_title - specify user labels for the panel indeces
|
|---|
| [733] | 632 | set_abcissa - specify a user label for the abcissa
|
|---|
| [255] | 633 | set_ordinate - specify a user label for the ordinate
|
|---|
| [378] | 634 | set_layout - specify the multi-panel layout (rows,cols)
|
|---|
| [733] | 635 | set_colors - specify a set of colours to use
|
|---|
| 636 | set_linestyles - specify a set of linestyles to use if only
|
|---|
| 637 | using one color
|
|---|
| [1151] | 638 | set_font - set general font properties, e.g. 'family'
|
|---|
| [1054] | 639 | set_histogram - plot in historam style
|
|---|
| [733] | 640 | set_mask - set a plotting mask for a specific polarization
|
|---|
| [1171] | 641 | text - draw text annotations either in data or relative
|
|---|
| 642 | coordinates
|
|---|
| 643 | arrow - draw arrow annotations either in data or relative
|
|---|
| 644 | coordinates
|
|---|
| 645 | axhline,axvline - draw horizontal/vertical lines
|
|---|
| 646 | axhspan,axvspan - draw horizontal/vertical regions
|
|---|
| [1560] | 647 | annotate - draw an arrow with label
|
|---|
| 648 | create_mask - create a scnatble mask interactively
|
|---|
| [1175] | 649 |
|
|---|
| 650 | xyplotter - matplotlib/pylab plotting functions
|
|---|
| 651 |
|
|---|
| [113] | 652 | [General]
|
|---|
| 653 | commands - this command
|
|---|
| 654 | print - print details about a variable
|
|---|
| [1560] | 655 | list_scans - list all scantables created by the user
|
|---|
| [992] | 656 | list_files - list all files readable by asap (default rpf)
|
|---|
| [113] | 657 | del - delete the given variable from memory
|
|---|
| 658 | range - create a list of values, e.g.
|
|---|
| 659 | range(3) = [0,1,2], range(2,5) = [2,3,4]
|
|---|
| 660 | help - print help for one of the listed functions
|
|---|
| 661 | execfile - execute an asap script, e.g. execfile('myscript')
|
|---|
| [255] | 662 | list_rcparameters - print out a list of possible values to be
|
|---|
| [274] | 663 | put into $HOME/.asaprc
|
|---|
| [1171] | 664 | rc - set rc parameters from within asap
|
|---|
| [466] | 665 | mask_and,mask_or,
|
|---|
| 666 | mask_not - boolean operations on masks created with
|
|---|
| 667 | scantable.create_mask
|
|---|
| [1697] | 668 | skydip - gain opacity values from a sky dip observation
|
|---|
| [1725] | 669 | opacity_model - compute opacities fro given frequencies based on
|
|---|
| 670 | atmospheric model
|
|---|
| [706] | 671 |
|
|---|
| [210] | 672 | Note:
|
|---|
| 673 | How to use this with help:
|
|---|
| 674 | # function 'summary'
|
|---|
| 675 | [xxx] is just a category
|
|---|
| 676 | Every 'sub-level' in this list should be replaces by a '.' Period when
|
|---|
| [706] | 677 | using help
|
|---|
| [210] | 678 | Example:
|
|---|
| 679 | ASAP> help scantable # to get info on ths scantable
|
|---|
| 680 | ASAP> help scantable.summary # to get help on the scantable's
|
|---|
| 681 | ASAP> help average_time
|
|---|
| 682 |
|
|---|
| [715] | 683 | """
|
|---|
| [1151] | 684 | if rcParams['verbose']:
|
|---|
| 685 | try:
|
|---|
| 686 | from IPython.genutils import page as pager
|
|---|
| 687 | except ImportError:
|
|---|
| 688 | from pydoc import pager
|
|---|
| 689 | pager(x)
|
|---|
| 690 | else:
|
|---|
| 691 | print x
|
|---|
| [715] | 692 | return
|
|---|
| [113] | 693 |
|
|---|
| [706] | 694 | def welcome():
|
|---|
| 695 | return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
|
|---|
| [100] | 696 |
|
|---|
| [1035] | 697 | Please report any bugs via:
|
|---|
| [1378] | 698 | http://svn.atnf.csiro.au/trac/asap/simpleticket
|
|---|
| [100] | 699 |
|
|---|
| [378] | 700 | [IMPORTANT: ASAP is 0-based]
|
|---|
| [706] | 701 | Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
|
|---|
