| [100] | 1 | """
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| 2 | This is the ATNF Single Dish Analysis package.
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| 3 |
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| 4 | """
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| [1080] | 5 | import os,sys,shutil, platform
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| [226] | 6 |
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| [1080] | 7 | # Set up AIPSPATH and first time use of asap i.e. ~/.asap/*
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| 8 | plf = None
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| 9 | if sys.platform == "linux2":
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| 10 | if platform.architecture()[0] == '64bit':
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| 11 | plf = 'linux_64b'
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| 12 | else:
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| 13 | plf = 'linux_gnu'
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| 14 | elif sys.platform == 'darwin':
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| 15 | plf = 'darwin'
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| 16 | else:
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| 17 | # Shouldn't happen - default to linux
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| 18 | plf = 'linux'
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| 19 | asapdata = __path__[-1]
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| [1171] | 20 | # Allow user defined data location
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| 21 | if os.environ.has_key("ASAPDATA"):
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| 22 | if os.path.exists(os.environ["ASAPDATA"]):
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| 23 | asapdata = os.environ["ASAPDATA"]
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| [1371] | 24 | # use AIPSPATH if defined and "data" dir present
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| 25 | if not os.environ.has_key("AIPSPATH") or \
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| 26 | not os.path.exists(os.environ["AIPSPATH"].split()[0]+"/data"):
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| [1316] | 27 | os.environ["AIPSPATH"] = "%s %s somwhere" % ( asapdata, plf)
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| [1171] | 28 | # set up user space
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| [1080] | 29 | userdir = os.environ["HOME"]+"/.asap"
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| 30 | if not os.path.exists(userdir):
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| 31 | print 'First time ASAP use. Setting up ~/.asap'
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| 32 | os.mkdir(userdir)
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| 33 | shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap")
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| [1434] | 34 | shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
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| 35 | userdir+"/ipy_user_conf.py")
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| [1080] | 36 | f = file(userdir+"/asapuserfuncs.py", "w")
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| 37 | f.close()
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| 38 | f = file(userdir+"/ipythonrc", "w")
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| 39 | f.close()
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| [1171] | 40 | # remove from namespace
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| [1080] | 41 | del asapdata, userdir, shutil, platform
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| 42 |
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| [513] | 43 | def _validate_bool(b):
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| [226] | 44 | 'Convert b to a boolean or raise'
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| 45 | bl = b.lower()
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| 46 | if bl in ('f', 'no', 'false', '0', 0): return False
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| 47 | elif bl in ('t', 'yes', 'true', '1', 1): return True
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| 48 | else:
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| 49 | raise ValueError('Could not convert "%s" to boolean' % b)
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| 50 |
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| [513] | 51 | def _validate_int(s):
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| [226] | 52 | 'convert s to int or raise'
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| 53 | try: return int(s)
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| 54 | except ValueError:
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| 55 | raise ValueError('Could not convert "%s" to int' % s)
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| 56 |
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| [513] | 57 | def _asap_fname():
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| [226] | 58 | """
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| 59 | Return the path to the rc file
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| 60 |
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| 61 | Search order:
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| 62 |
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| 63 | * current working dir
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| 64 | * environ var ASAPRC
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| [274] | 65 | * HOME/.asaprc
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| [706] | 66 |
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| [226] | 67 | """
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| 68 |
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| 69 | fname = os.path.join( os.getcwd(), '.asaprc')
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| 70 | if os.path.exists(fname): return fname
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| 71 |
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| 72 | if os.environ.has_key('ASAPRC'):
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| 73 | path = os.environ['ASAPRC']
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| 74 | if os.path.exists(path):
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| 75 | fname = os.path.join(path, '.asaprc')
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| 76 | if os.path.exists(fname):
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| 77 | return fname
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| 78 |
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| 79 | if os.environ.has_key('HOME'):
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| 80 | home = os.environ['HOME']
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| 81 | fname = os.path.join(home, '.asaprc')
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| 82 | if os.path.exists(fname):
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| 83 | return fname
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| 84 | return None
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| 85 |
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| [706] | 86 |
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| [226] | 87 | defaultParams = {
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| 88 | # general
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| [513] | 89 | 'verbose' : [True, _validate_bool],
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| 90 | 'useplotter' : [True, _validate_bool],
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| [542] | 91 | 'insitu' : [True, _validate_bool],
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| [706] | 92 |
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| [226] | 93 | # plotting
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| [706] | 94 | 'plotter.gui' : [True, _validate_bool],
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| [226] | 95 | 'plotter.stacking' : ['p', str],
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| 96 | 'plotter.panelling' : ['s', str],
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| [700] | 97 | 'plotter.colours' : ['', str],
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| 98 | 'plotter.linestyles' : ['', str],
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| [710] | 99 | 'plotter.decimate' : [False, _validate_bool],
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| 100 | 'plotter.ganged' : [True, _validate_bool],
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| [1022] | 101 | 'plotter.histogram' : [False, _validate_bool],
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| [1097] | 102 | 'plotter.papertype' : ['A4', str],
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| [710] | 103 |
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| [226] | 104 | # scantable
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| 105 | 'scantable.save' : ['ASAP', str],
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| [513] | 106 | 'scantable.autoaverage' : [True, _validate_bool],
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| [226] | 107 | 'scantable.freqframe' : ['LSRK', str], #default frequency frame
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| [1076] | 108 | 'scantable.verbosesummary' : [False, _validate_bool],
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| [1422] | 109 | 'scantable.storage' : ['memory', str],
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| 110 | 'scantable.history' : [True, _validate_bool]
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| [226] | 111 | # fitter
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| 112 | }
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| 113 |
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| [255] | 114 | def list_rcparameters():
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| [706] | 115 |
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| [255] | 116 | print """
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| [737] | 117 | # general
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| 118 | # print verbose output
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| 119 | verbose : True
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| [255] | 120 |
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| [737] | 121 | # preload a default plotter
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| 122 | useplotter : True
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| [255] | 123 |
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| [737] | 124 | # apply operations on the input scantable or return new one
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| 125 | insitu : True
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| [706] | 126 |
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| [737] | 127 | # plotting
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| [710] | 128 |
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| [737] | 129 | # do we want a GUI or plot to a file
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| 130 | plotter.gui : True
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| [710] | 131 |
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| [737] | 132 | # default mode for colour stacking
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| 133 | plotter.stacking : Pol
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| [255] | 134 |
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| [737] | 135 | # default mode for panelling
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| 136 | plotter.panelling : scan
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| [255] | 137 |
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| [737] | 138 | # push panels together, to share axislabels
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| 139 | plotter.ganged : True
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| [710] | 140 |
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| [737] | 141 | # decimate the number of points plotted bya afactor of
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| 142 | # nchan/1024
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| 143 | plotter.decimate : False
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| [733] | 144 |
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| [737] | 145 | # default colours/linestyles
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| 146 | plotter.colours :
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| 147 | plotter.linestyles :
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| [700] | 148 |
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| [1022] | 149 | # enable/disable histogram plotting
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| 150 | plotter.histogram : False
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| 151 |
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| [1097] | 152 | # ps paper type
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| 153 | plotter.papertype : A4
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| 154 |
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| [737] | 155 | # scantable
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| [1076] | 156 |
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| [1259] | 157 | # default storage of scantable ('memory'/'disk')
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| [1076] | 158 | scantable.storage : memory
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| [1422] | 159 |
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| 160 | # write history of each call to scantable
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| 161 | scantable.history : True
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| 162 |
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| [737] | 163 | # default ouput format when saving
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| 164 | scantable.save : ASAP
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| [1422] | 165 |
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| [737] | 166 | # auto averaging on read
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| 167 | scantable.autoaverage : True
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| [255] | 168 |
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| [737] | 169 | # default frequency frame to set when function
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| [1097] | 170 | # scantable.set_freqframe is called
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| [737] | 171 | scantable.freqframe : LSRK
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| [255] | 172 |
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| [737] | 173 | # Control the level of information printed by summary
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| 174 | scantable.verbosesummary : False
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| [706] | 175 |
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| [737] | 176 | # Fitter
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| 177 | """
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| [706] | 178 |
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| [226] | 179 | def rc_params():
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| 180 | 'Return the default params updated from the values in the rc file'
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| [706] | 181 |
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| [513] | 182 | fname = _asap_fname()
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| [706] | 183 |
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| [226] | 184 | if fname is None or not os.path.exists(fname):
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| 185 | message = 'could not find rc file; returning defaults'
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| 186 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
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| 187 | #print message
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| 188 | return ret
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| [706] | 189 |
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| [226] | 190 | cnt = 0
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| 191 | for line in file(fname):
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| 192 | cnt +=1
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| 193 | line = line.strip()
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| 194 | if not len(line): continue
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| 195 | if line.startswith('#'): continue
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| 196 | tup = line.split(':',1)
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| 197 | if len(tup) !=2:
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| 198 | print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
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| 199 | continue
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| [706] | 200 |
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| [226] | 201 | key, val = tup
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| 202 | key = key.strip()
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| 203 | if not defaultParams.has_key(key):
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| 204 | print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
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| 205 | continue
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| [706] | 206 |
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| [226] | 207 | default, converter = defaultParams[key]
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| 208 |
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| 209 | ind = val.find('#')
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| 210 | if ind>=0: val = val[:ind] # ignore trailing comments
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| 211 | val = val.strip()
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| 212 | try: cval = converter(val) # try to convert to proper type or raise
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| [1080] | 213 | except ValueError, msg:
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| [226] | 214 | 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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| 215 | continue
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| 216 | else:
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| 217 | # Alles Klar, update dict
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| 218 | defaultParams[key][0] = cval
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| 219 |
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| 220 | # strip the conveter funcs and return
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| 221 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
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| [466] | 222 | print ('loaded rc file %s'%fname)
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| [226] | 223 |
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| 224 | return ret
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| 225 |
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| 226 |
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| 227 | # this is the instance used by the asap classes
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| [706] | 228 | rcParams = rc_params()
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| [226] | 229 |
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| 230 | rcParamsDefault = dict(rcParams.items()) # a copy
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| 231 |
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| 232 | def rc(group, **kwargs):
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| 233 | """
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| 234 | Set the current rc params. Group is the grouping for the rc, eg
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| [379] | 235 | for scantable.save the group is 'scantable', for plotter.stacking, the
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| 236 | group is 'plotter', and so on. kwargs is a list of attribute
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| [226] | 237 | name/value pairs, eg
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| 238 |
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| [379] | 239 | rc('scantable', save='SDFITS')
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| [226] | 240 |
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| 241 | sets the current rc params and is equivalent to
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| [706] | 242 |
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| [379] | 243 | rcParams['scantable.save'] = 'SDFITS'
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| [226] | 244 |
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| 245 | Use rcdefaults to restore the default rc params after changes.
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| 246 | """
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| 247 |
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| [379] | 248 | aliases = {}
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| [706] | 249 |
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| [226] | 250 | for k,v in kwargs.items():
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| 251 | name = aliases.get(k) or k
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| [1422] | 252 | if len(group):
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| 253 | key = '%s.%s' % (group, name)
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| 254 | else:
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| 255 | key = name
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| [226] | 256 | if not rcParams.has_key(key):
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| 257 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
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| [706] | 258 |
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| [226] | 259 | rcParams[key] = v
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| 260 |
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| 261 |
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| 262 | def rcdefaults():
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| 263 | """
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| 264 | Restore the default rc params - the ones that were created at
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| 265 | asap load time
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| 266 | """
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| 267 | rcParams.update(rcParamsDefault)
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| 268 |
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| [1295] | 269 | def _n_bools(n, val):
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| 270 | return [ val for i in xrange(n) ]
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| [513] | 271 |
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| 272 | def _is_sequence_or_number(param, ptype=int):
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| 273 | if isinstance(param,tuple) or isinstance(param,list):
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| [928] | 274 | if len(param) == 0: return True # empty list
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| [513] | 275 | out = True
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| 276 | for p in param:
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| 277 | out &= isinstance(p,ptype)
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| 278 | return out
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| 279 | elif isinstance(param, ptype):
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| 280 | return True
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| 281 | return False
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| 282 |
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| [928] | 283 | def _to_list(param, ptype=int):
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| 284 | if isinstance(param, ptype):
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| 285 | if ptype is str: return param.split()
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| 286 | else: return [param]
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| 287 | if _is_sequence_or_number(param, ptype):
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| 288 | return param
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| 289 | return None
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| [715] | 290 |
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| [944] | 291 | def unique(x):
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| [992] | 292 | """
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| 293 | Return the unique values in a list
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| 294 | Parameters:
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| 295 | x: the list to reduce
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| 296 | Examples:
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| 297 | x = [1,2,3,3,4]
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| 298 | print unique(x)
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| 299 | [1,2,3,4]
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| 300 | """
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| [944] | 301 | return dict([ (val, 1) for val in x]).keys()
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| 302 |
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| [992] | 303 | def list_files(path=".",suffix="rpf"):
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| 304 | """
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| 305 | Return a list files readable by asap, such as rpf, sdfits, mbf, asap
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| 306 | Parameters:
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| 307 | path: The directory to list (default '.')
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| 308 | suffix: The file extension (default rpf)
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| 309 | Example:
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| 310 | files = list_files("data/","sdfits")
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| 311 | print files
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| 312 | ['data/2001-09-01_0332_P363.sdfits',
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| 313 | 'data/2003-04-04_131152_t0002.sdfits',
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| 314 | 'data/Sgr_86p262_best_SPC.sdfits']
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| 315 | """
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| 316 | if not os.path.isdir(path):
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| 317 | return None
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| [1295] | 318 | valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split()
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| [992] | 319 | if not suffix in valid:
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| 320 | return None
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| 321 | files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
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| 322 | return filter(lambda x: x.endswith(suffix),files)
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| 323 |
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| [715] | 324 | # workaround for ipython, which redirects this if banner=0 in ipythonrc
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| 325 | sys.stdout = sys.__stdout__
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| 326 | sys.stderr = sys.__stderr__
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| 327 |
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| 328 | # Logging
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| 329 | from asap._asap import Log as _asaplog
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| 330 | global asaplog
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| [710] | 331 | asaplog=_asaplog()
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| [715] | 332 | if rcParams['verbose']:
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| 333 | asaplog.enable()
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| 334 | else:
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| 335 | asaplog.disable()
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| 336 |
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| 337 | def print_log():
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| 338 | log = asaplog.pop()
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| 339 | if len(log) and rcParams['verbose']: print log
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| 340 | return
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| 341 |
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| [1295] | 342 | def mask_and(a, b):
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| 343 | assert(len(a)==len(b))
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| 344 | return [ a[i] & b[i] for i in xrange(len(a)) ]
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| [1134] | 345 |
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| [1295] | 346 | def mask_or(a, b):
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| 347 | assert(len(a)==len(b))
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| 348 | return [ a[i] | b[i] for i in xrange(len(a)) ]
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| 349 |
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| 350 | def mask_not(a):
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| 351 | return [ not i for i in a ]
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| 352 |
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| [1117] | 353 | from asapfitter import fitter
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| [895] | 354 | from asapreader import reader
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| [944] | 355 | from selector import selector
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| [710] | 356 |
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| [100] | 357 | from asapmath import *
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| [1080] | 358 | from scantable import scantable
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| [1097] | 359 | from asaplinefind import linefinder
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| [1134] | 360 | from linecatalog import linecatalog
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| [285] | 361 |
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| [928] | 362 | if rcParams['useplotter']:
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| [1295] | 363 | try:
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| [1423] | 364 | from asapplotter import asapplotter
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| 365 | gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
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| 366 | if gui:
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| [1422] | 367 | import matplotlib
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| 368 | matplotlib.use("TkAgg")
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| [1423] | 369 | import pylab
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| [1422] | 370 | xyplotter = pylab
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| [1423] | 371 | plotter = asapplotter(gui)
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| 372 | del gui
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| [1295] | 373 | except ImportError:
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| [1423] | 374 | print "Matplotlib not installed. No plotting available"
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| [285] | 375 |
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| [574] | 376 | __date__ = '$Date: 2008-08-28 03:55:49 +0000 (Thu, 28 Aug 2008) $'.split()[1]
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| [1371] | 377 | __version__ = 'trunk'
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| [100] | 378 |
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| [1193] | 379 | def is_ipython():
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| [1259] | 380 | return '__IP' in dir(sys.modules["__main__"])
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| [1193] | 381 | if is_ipython():
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| [1014] | 382 | def version(): print "ASAP %s(%s)"% (__version__, __date__)
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| [1422] | 383 |
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| [706] | 384 | def list_scans(t = scantable):
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| [1295] | 385 | import types
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| [706] | 386 | globs = sys.modules['__main__'].__dict__.iteritems()
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| 387 | print "The user created scantables are:"
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| 388 | sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
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| 389 | print filter(lambda x: not x.startswith('_'), sts)
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| 390 | return
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| [100] | 391 |
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| [715] | 392 | def commands():
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| 393 | x = """
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| [113] | 394 | [The scan container]
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| 395 | scantable - a container for integrations/scans
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| [182] | 396 | (can open asap/rpfits/sdfits and ms files)
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| [113] | 397 | copy - returns a copy of a scan
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| 398 | get_scan - gets a specific scan out of a scantable
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| [984] | 399 | (by name or number)
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| [1093] | 400 | drop_scan - drops a specific scan out of a scantable
|
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| 401 | (by number)
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| [984] | 402 | set_selection - set a new subselection of the data
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| 403 | get_selection - get the current selection object
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| [113] | 404 | summary - print info about the scantable contents
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| [182] | 405 | stats - get specified statistic of the spectra in
|
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| 406 | the scantable
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| 407 | stddev - get the standard deviation of the spectra
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| 408 | in the scantable
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| [113] | 409 | get_tsys - get the TSys
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| 410 | get_time - get the timestamps of the integrations
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| [1351] | 411 | get_inttime - get the integration time
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| [733] | 412 | get_sourcename - get the source names of the scans
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| [794] | 413 | get_azimuth - get the azimuth of the scans
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| 414 | get_elevation - get the elevation of the scans
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| 415 | get_parangle - get the parallactic angle of the scans
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| [876] | 416 | get_unit - get the current unit
|
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| [513] | 417 | set_unit - set the abcissa unit to be used from this
|
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| 418 | point on
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| [255] | 419 | get_abcissa - get the abcissa values and name for a given
|
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| 420 | row (time)
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| [1259] | 421 | get_column_names - get the names of the columns in the scantable
|
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| 422 | for use with selector.set_query
|
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| [113] | 423 | set_freqframe - set the frame info for the Spectral Axis
|
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| 424 | (e.g. 'LSRK')
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| [276] | 425 | set_doppler - set the doppler to be used from this point on
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| [984] | 426 | set_dirframe - set the frame for the direction on the sky
|
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| [240] | 427 | set_instrument - set the instrument name
|
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| [1190] | 428 | set_feedtype - set the feed type
|
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| [255] | 429 | get_fluxunit - get the brightness flux unit
|
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| [240] | 430 | set_fluxunit - set the brightness flux unit
|
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| [188] | 431 | create_mask - return an mask in the current unit
|
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| 432 | for the given region. The specified regions
|
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| 433 | are NOT masked
|
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| [255] | 434 | get_restfreqs - get the current list of rest frequencies
|
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| 435 | set_restfreqs - set a list of rest frequencies
|
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| [1422] | 436 | shift_refpix - shift the reference pixel of the IFs
|
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| [1012] | 437 | flag - flag selected channels in the data
|
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| [1192] | 438 | lag_flag - flag specified frequency in the data
|
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| [1151] | 439 | save - save the scantable to disk as either 'ASAP',
|
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| 440 | 'SDFITS' or 'ASCII'
|
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| [486] | 441 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
|
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| [733] | 442 | nscan - the number of scans in the scantable
|
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| [1422] | 443 | nrow - the number of spectra in the scantable
|
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| [486] | 444 | history - print the history of the scantable
|
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| [530] | 445 | get_fit - get a fit which has been stored witnh the data
|
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| [706] | 446 | average_time - return the (weighted) time average of a scan
|
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| [513] | 447 | or a list of scans
|
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| 448 | average_pol - average the polarisations together.
|
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| [1144] | 449 | average_beam - average the beams together.
|
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| [992] | 450 | convert_pol - convert to a different polarisation type
|
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| [690] | 451 | auto_quotient - return the on/off quotient with
|
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| [1069] | 452 | automatic detection of the on/off scans (closest
|
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| 453 | in time off is selected)
|
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| [1144] | 454 | mx_quotient - Form a quotient using MX data (off beams)
|
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| [1014] | 455 | scale, *, / - return a scan scaled by a given factor
|
|---|
| 456 | add, +, - - return a scan with given value added
|
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| [513] | 457 | bin - return a scan with binned channels
|
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| 458 | resample - return a scan with resampled channels
|
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| 459 | smooth - return the spectrally smoothed scan
|
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| 460 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
|
|---|
| [706] | 461 | auto_poly_baseline - automatically fit a polynomial baseline
|
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| [780] | 462 | recalc_azel - recalculate azimuth and elevation based on
|
|---|
| 463 | the pointing
|
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| [513] | 464 | gain_el - apply gain-elevation correction
|
|---|
| 465 | opacity - apply opacity correction
|
|---|
| 466 | convert_flux - convert to and from Jy and Kelvin brightness
|
|---|
| [255] | 467 | units
|
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| [513] | 468 | freq_align - align spectra in frequency frame
|
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| [1014] | 469 | invert_phase - Invert the phase of the cross-correlation
|
|---|
| [1351] | 470 | swap_linears - Swap XX and YY (or RR LL)
|
|---|
| [513] | 471 | rotate_xyphase - rotate XY phase of cross correlation
|
|---|
| 472 | rotate_linpolphase - rotate the phase of the complex
|
|---|
| 473 | polarization O=Q+iU correlation
|
|---|
| [733] | 474 | freq_switch - perform frequency switching on the data
|
|---|
| 475 | stats - Determine the specified statistic, e.g. 'min'
|
|---|
| 476 | 'max', 'rms' etc.
|
|---|
| 477 | stddev - Determine the standard deviation of the current
|
|---|
| 478 | beam/if/pol
|
|---|
| [1014] | 479 | [Selection]
|
|---|
| 480 | selector - a selection object to set a subset of a scantable
|
|---|
| 481 | set_scans - set (a list of) scans by index
|
|---|
| 482 | set_cycles - set (a list of) cycles by index
|
|---|
| 483 | set_beams - set (a list of) beamss by index
|
|---|
| 484 | set_ifs - set (a list of) ifs by index
|
|---|
| 485 | set_polarisations - set (a list of) polarisations by name
|
|---|
| 486 | or by index
|
|---|
| 487 | set_names - set a selection by name (wildcards allowed)
|
|---|
| 488 | set_tsys - set a selection by tsys thresholds
|
|---|
| [1259] | 489 | set_query - set a selection by SQL-like query, e.g. BEAMNO==1
|
|---|
| [1351] | 490 | ( also get_ functions for all these )
|
|---|
| [1014] | 491 | reset - unset all selections
|
|---|
| [1351] | 492 | + - merge two selections
|
|---|
| [733] | 493 |
|
|---|
| [513] | 494 | [Math] Mainly functions which operate on more than one scantable
|
|---|
| [100] | 495 |
|
|---|
| [706] | 496 | average_time - return the (weighted) time average
|
|---|
| [513] | 497 | of a list of scans
|
|---|
| 498 | quotient - return the on/off quotient
|
|---|
| 499 | simple_math - simple mathematical operations on two scantables,
|
|---|
| 500 | 'add', 'sub', 'mul', 'div'
|
|---|
| [1069] | 501 | quotient - build quotient of the given on and off scans
|
|---|
| [1351] | 502 | (matched pairs and 1 off - n on are valid)
|
|---|
| [1117] | 503 | merge - merge a list of scantables
|
|---|
| [1069] | 504 |
|
|---|
| [1151] | 505 | [Line Catalog]
|
|---|
| 506 | linecatalog - a linecatalog wrapper, taking an ASCII or
|
|---|
| 507 | internal format table
|
|---|
| 508 | summary - print a summary of the current selection
|
|---|
| 509 | set_name - select a subset by name pattern, e.g. '*OH*'
|
|---|
| 510 | set_strength_limits - select a subset by line strength limits
|
|---|
| 511 | set_frequency_limits - select a subset by frequency limits
|
|---|
| 512 | reset - unset all selections
|
|---|
| 513 | save - save the current subset to a table (internal
|
|---|
| 514 | format)
|
|---|
| 515 | get_row - get the name and frequency from a specific
|
|---|
| 516 | row in the table
|
|---|
| [513] | 517 | [Fitting]
|
|---|
| [113] | 518 | fitter
|
|---|
| 519 | auto_fit - return a scan where the function is
|
|---|
| 520 | applied to all Beams/IFs/Pols.
|
|---|
| 521 | commit - return a new scan where the fits have been
|
|---|
| 522 | commited.
|
|---|
| 523 | fit - execute the actual fitting process
|
|---|
| [984] | 524 | store_fit - store the fit parameters in the data (scantable)
|
|---|
| [113] | 525 | get_chi2 - get the Chi^2
|
|---|
| 526 | set_scan - set the scantable to be fit
|
|---|
| 527 | set_function - set the fitting function
|
|---|
| 528 | set_parameters - set the parameters for the function(s), and
|
|---|
| 529 | set if they should be held fixed during fitting
|
|---|
| [513] | 530 | set_gauss_parameters - same as above but specialised for individual
|
|---|
| 531 | gaussian components
|
|---|
| [113] | 532 | get_parameters - get the fitted parameters
|
|---|
| [513] | 533 | plot - plot the resulting fit and/or components and
|
|---|
| 534 | residual
|
|---|
| [210] | 535 | [Plotter]
|
|---|
| 536 | asapplotter - a plotter for asap, default plotter is
|
|---|
| 537 | called 'plotter'
|
|---|
| [984] | 538 | plot - plot a scantable
|
|---|
| [1151] | 539 | plot_lines - plot a linecatalog overlay
|
|---|
| [378] | 540 | save - save the plot to a file ('png' ,'ps' or 'eps')
|
|---|
| [210] | 541 | set_mode - set the state of the plotter, i.e.
|
|---|
| 542 | what is to be plotted 'colour stacked'
|
|---|
| 543 | and what 'panelled'
|
|---|
| [984] | 544 | set_selection - only plot a selected part of the data
|
|---|
| [733] | 545 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
|
|---|
| [255] | 546 | set_legend - specify user labels for the legend indeces
|
|---|
| 547 | set_title - specify user labels for the panel indeces
|
|---|
| [733] | 548 | set_abcissa - specify a user label for the abcissa
|
|---|
| [255] | 549 | set_ordinate - specify a user label for the ordinate
|
|---|
| [378] | 550 | set_layout - specify the multi-panel layout (rows,cols)
|
|---|
| [733] | 551 | set_colors - specify a set of colours to use
|
|---|
| 552 | set_linestyles - specify a set of linestyles to use if only
|
|---|
| 553 | using one color
|
|---|
| [1151] | 554 | set_font - set general font properties, e.g. 'family'
|
|---|
| [1054] | 555 | set_histogram - plot in historam style
|
|---|
| [733] | 556 | set_mask - set a plotting mask for a specific polarization
|
|---|
| [1171] | 557 | text - draw text annotations either in data or relative
|
|---|
| 558 | coordinates
|
|---|
| 559 | arrow - draw arrow annotations either in data or relative
|
|---|
| 560 | coordinates
|
|---|
| 561 | axhline,axvline - draw horizontal/vertical lines
|
|---|
| 562 | axhspan,axvspan - draw horizontal/vertical regions
|
|---|
| [1175] | 563 |
|
|---|
| 564 | xyplotter - matplotlib/pylab plotting functions
|
|---|
| 565 |
|
|---|
| [182] | 566 | [Reading files]
|
|---|
| 567 | reader - access rpfits/sdfits files
|
|---|
| [984] | 568 | open - attach reader to a file
|
|---|
| 569 | close - detach reader from file
|
|---|
| [182] | 570 | read - read in integrations
|
|---|
| 571 | summary - list info about all integrations
|
|---|
| 572 |
|
|---|
| [113] | 573 | [General]
|
|---|
| 574 | commands - this command
|
|---|
| 575 | print - print details about a variable
|
|---|
| 576 | list_scans - list all scantables created bt the user
|
|---|
| [992] | 577 | list_files - list all files readable by asap (default rpf)
|
|---|
| [113] | 578 | del - delete the given variable from memory
|
|---|
| 579 | range - create a list of values, e.g.
|
|---|
| 580 | range(3) = [0,1,2], range(2,5) = [2,3,4]
|
|---|
| 581 | help - print help for one of the listed functions
|
|---|
| 582 | execfile - execute an asap script, e.g. execfile('myscript')
|
|---|
| [255] | 583 | list_rcparameters - print out a list of possible values to be
|
|---|
| [274] | 584 | put into $HOME/.asaprc
|
|---|
| [1171] | 585 | rc - set rc parameters from within asap
|
|---|
| [466] | 586 | mask_and,mask_or,
|
|---|
| 587 | mask_not - boolean operations on masks created with
|
|---|
| 588 | scantable.create_mask
|
|---|
| [706] | 589 |
|
|---|
| [210] | 590 | Note:
|
|---|
| 591 | How to use this with help:
|
|---|
| 592 | # function 'summary'
|
|---|
| 593 | [xxx] is just a category
|
|---|
| 594 | Every 'sub-level' in this list should be replaces by a '.' Period when
|
|---|
| [706] | 595 | using help
|
|---|
| [210] | 596 | Example:
|
|---|
| 597 | ASAP> help scantable # to get info on ths scantable
|
|---|
| 598 | ASAP> help scantable.summary # to get help on the scantable's
|
|---|
| 599 | ASAP> help average_time
|
|---|
| 600 |
|
|---|
| [715] | 601 | """
|
|---|
| [1151] | 602 | if rcParams['verbose']:
|
|---|
| 603 | try:
|
|---|
| 604 | from IPython.genutils import page as pager
|
|---|
| 605 | except ImportError:
|
|---|
| 606 | from pydoc import pager
|
|---|
| 607 | pager(x)
|
|---|
| 608 | else:
|
|---|
| 609 | print x
|
|---|
| [715] | 610 | return
|
|---|
| [113] | 611 |
|
|---|
| [706] | 612 | def welcome():
|
|---|
| 613 | return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
|
|---|
| [100] | 614 |
|
|---|
| [1035] | 615 | Please report any bugs via:
|
|---|
| [1378] | 616 | http://svn.atnf.csiro.au/trac/asap/simpleticket
|
|---|
| [100] | 617 |
|
|---|
| [378] | 618 | [IMPORTANT: ASAP is 0-based]
|
|---|
| [706] | 619 | Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
|
|---|
