[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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[1757] | 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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[1456] | 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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[1456] | 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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[1445] | 37 | #shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap") |
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[1603] | 38 | # commented out by TT on 2009.06.23 for casapy use |
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[1757] | 39 | ##shutil.copyfile(asapdata+"/data/ipy_user_conf.py", |
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[1603] | 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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[1603] | 45 | # commented out by TT on 2009.06.23 for casapy use |
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| 46 | ##else: |
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| 47 | # upgrade to support later ipython versions |
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| 48 | ##if not os.path.exists(userdir+"/ipy_user_conf.py"): |
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[1757] | 49 | ## shutil.copyfile(asapdata+"/data/ipy_user_conf.py", |
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[1603] | 50 | ## userdir+"/ipy_user_conf.py") |
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| 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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[1757] | 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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[1603] | 123 | 'scantable.storage' : ['memory', str], |
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| 124 | 'scantable.history' : [True, _validate_bool], |
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[1757] | 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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[1757] | 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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[1603] | 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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[1603] | 171 | # The formatting style of the xaxis |
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[1757] | 172 | plotter.axesformatting : 'mpl' (default) or 'asap' (for old versions of matplotlib) |
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[1603] | 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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[1603] | 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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[1603] | 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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[1603] | 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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[1757] | 197 | scantable.reference : .*(e|w|_R)$ |
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| 198 | |
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| 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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[1612] | 224 | #print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname)) |
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[1614] | 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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[1612] | 232 | #print ('Bad key "%s" on line %d in %s' % (key, cnt, fname)) |
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[1614] | 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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[1612] | 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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[1676] | 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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[1614] | 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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[1603] | 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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[1757] | 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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[1757] | 369 | |
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| 370 | def print_log_dec(f): |
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| 371 | @wraps_dec(f) |
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| 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 |
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| 376 | return wrap_it |
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| 377 | |
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[1614] | 378 | def print_log(level='INFO'): |
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[1660] | 379 | from taskinit import casalog |
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[715] | 380 | log = asaplog.pop() |
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[1612] | 381 | #if len(log) and rcParams['verbose']: print log |
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[1614] | 382 | if len(log) and rcParams['verbose']: casalog.post( log, priority=level ) |
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[715] | 383 | return |
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| 384 | |
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[1295] | 385 | def mask_and(a, b): |
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| 386 | assert(len(a)==len(b)) |
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| 387 | return [ a[i] & b[i] for i in xrange(len(a)) ] |
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[1134] | 388 | |
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[1295] | 389 | def mask_or(a, b): |
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| 390 | assert(len(a)==len(b)) |
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| 391 | return [ a[i] | b[i] for i in xrange(len(a)) ] |
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| 392 | |
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| 393 | def mask_not(a): |
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| 394 | return [ not i for i in a ] |
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| 395 | |
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[1117] | 396 | from asapfitter import fitter |
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[895] | 397 | from asapreader import reader |
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[944] | 398 | from selector import selector |
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[710] | 399 | |
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[100] | 400 | from asapmath import * |
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[1080] | 401 | from scantable import scantable |
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[1097] | 402 | from asaplinefind import linefinder |
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[1757] | 403 | from simplelinefinder import simplelinefinder |
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[1134] | 404 | from linecatalog import linecatalog |
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[1460] | 405 | from interactivemask import interactivemask |
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[1757] | 406 | from opacity import skydip |
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| 407 | from opacity import model as opacity_model |
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[285] | 408 | |
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[928] | 409 | if rcParams['useplotter']: |
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[1295] | 410 | try: |
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[1603] | 411 | from asapplotter import asapplotter |
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| 412 | gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui'] |
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| 413 | if gui: |
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| 414 | import matplotlib |
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[1729] | 415 | if not matplotlib.sys.modules['matplotlib.backends']: matplotlib.use("TkAgg") |
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[1757] | 416 | from matplotlib import pylab |
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[1603] | 417 | xyplotter = pylab |
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| 418 | plotter = asapplotter(gui) |
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| 419 | del gui |
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[1295] | 420 | except ImportError: |
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[1612] | 421 | #print "Matplotlib not installed. No plotting available" |
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[1614] | 422 | asaplog.post( "Matplotlib not installed. No plotting available") |
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| 423 | print_log('WARN') |
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[285] | 424 | |
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[574] | 425 | __date__ = '$Date: 2010-06-09 09:03:06 +0000 (Wed, 09 Jun 2010) $'.split()[1] |
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[1757] | 426 | __version__ = '3.0.0 alma' |
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[1445] | 427 | # nrao casapy specific, get revision number |
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[1494] | 428 | #__revision__ = ' unknown ' |
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[1456] | 429 | casapath=os.environ["CASAPATH"].split() |
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[1624] | 430 | #svninfo.txt path |
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| 431 | if os.path.isdir(casapath[0]+'/'+casapath[1]+'/python/2.5/asap'): |
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| 432 | # for casa developer environment (linux or darwin) |
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| 433 | revinfo=casapath[0]+'/'+casapath[1]+'/python/2.5/asap/svninfo.txt' |
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| 434 | else: |
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| 435 | # for end-user environments |
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| 436 | if casapath[1]=='darwin': |
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| 437 | revinfo=casapath[0]+'/Resources/python/asap/svninfo.txt' |
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| 438 | else: |
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| 439 | revinfo=casapath[0]+'/lib/python2.5/asap/svninfo.txt' |
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[1445] | 440 | if os.path.isfile(revinfo): |
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| 441 | f = file(revinfo) |
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[1605] | 442 | f.readline() |
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[1445] | 443 | revsionno=f.readline() |
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| 444 | f.close() |
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[1662] | 445 | del f |
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[1445] | 446 | __revision__ = revsionno.rstrip() |
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[1494] | 447 | else: |
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| 448 | __revision__ = ' unknown ' |
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[100] | 449 | |
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[1193] | 450 | def is_ipython(): |
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[1757] | 451 | return 'IPython' in sys.modules.keys() |
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[1193] | 452 | if is_ipython(): |
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[1014] | 453 | def version(): print "ASAP %s(%s)"% (__version__, __date__) |
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[1757] | 454 | |
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[706] | 455 | def list_scans(t = scantable): |
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[1757] | 456 | import inspect |
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| 457 | print "The user created scantables are: ", |
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| 458 | globs=inspect.currentframe().f_back.f_locals.copy() |
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| 459 | out = [ k for k,v in globs.iteritems() \ |
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| 460 | if isinstance(v, scantable) and not k.startswith("_") ] |
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| 461 | print out |
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| 462 | return out |
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[100] | 463 | |
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[715] | 464 | def commands(): |
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| 465 | x = """ |
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[113] | 466 | [The scan container] |
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| 467 | scantable - a container for integrations/scans |
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[182] | 468 | (can open asap/rpfits/sdfits and ms files) |
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[113] | 469 | copy - returns a copy of a scan |
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| 470 | get_scan - gets a specific scan out of a scantable |
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[984] | 471 | (by name or number) |
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[1093] | 472 | drop_scan - drops a specific scan out of a scantable |
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| 473 | (by number) |
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[984] | 474 | set_selection - set a new subselection of the data |
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| 475 | get_selection - get the current selection object |
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[113] | 476 | summary - print info about the scantable contents |
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[182] | 477 | stats - get specified statistic of the spectra in |
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| 478 | the scantable |
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| 479 | stddev - get the standard deviation of the spectra |
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| 480 | in the scantable |
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[113] | 481 | get_tsys - get the TSys |
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| 482 | get_time - get the timestamps of the integrations |
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[1351] | 483 | get_inttime - get the integration time |
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[733] | 484 | get_sourcename - get the source names of the scans |
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[794] | 485 | get_azimuth - get the azimuth of the scans |
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| 486 | get_elevation - get the elevation of the scans |
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| 487 | get_parangle - get the parallactic angle of the scans |
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[1757] | 488 | get_coordinate - get the spectral coordinate for the given row, |
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| 489 | which can be used for coordinate conversions |
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| 490 | get_weather - get the weather condition parameters |
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[876] | 491 | get_unit - get the current unit |
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[513] | 492 | set_unit - set the abcissa unit to be used from this |
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| 493 | point on |
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[255] | 494 | get_abcissa - get the abcissa values and name for a given |
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| 495 | row (time) |
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[1259] | 496 | get_column_names - get the names of the columns in the scantable |
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| 497 | for use with selector.set_query |
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[113] | 498 | set_freqframe - set the frame info for the Spectral Axis |
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| 499 | (e.g. 'LSRK') |
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[276] | 500 | set_doppler - set the doppler to be used from this point on |
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[984] | 501 | set_dirframe - set the frame for the direction on the sky |
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[240] | 502 | set_instrument - set the instrument name |
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[1190] | 503 | set_feedtype - set the feed type |
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[255] | 504 | get_fluxunit - get the brightness flux unit |
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[240] | 505 | set_fluxunit - set the brightness flux unit |
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[1603] | 506 | set_sourcetype - set the type of the source - source or reference |
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[188] | 507 | create_mask - return an mask in the current unit |
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| 508 | for the given region. The specified regions |
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| 509 | are NOT masked |
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[255] | 510 | get_restfreqs - get the current list of rest frequencies |
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| 511 | set_restfreqs - set a list of rest frequencies |
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[1603] | 512 | shift_refpix - shift the reference pixel of the IFs |
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| 513 | set_spectrum - overwrite the spectrum for a given row |
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| 514 | get_spectrum - retrieve the spectrum for a given |
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| 515 | get_mask - retrieve the mask for a given |
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[1012] | 516 | flag - flag selected channels in the data |
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[1192] | 517 | lag_flag - flag specified frequency in the data |
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[1151] | 518 | save - save the scantable to disk as either 'ASAP', |
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| 519 | 'SDFITS' or 'ASCII' |
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[486] | 520 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans |
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[733] | 521 | nscan - the number of scans in the scantable |
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[1603] | 522 | nrow - the number of spectra in the scantable |
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[486] | 523 | history - print the history of the scantable |
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[530] | 524 | get_fit - get a fit which has been stored witnh the data |
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[706] | 525 | average_time - return the (weighted) time average of a scan |
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[513] | 526 | or a list of scans |
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| 527 | average_pol - average the polarisations together. |
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[1144] | 528 | average_beam - average the beams together. |
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[992] | 529 | convert_pol - convert to a different polarisation type |
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[690] | 530 | auto_quotient - return the on/off quotient with |
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[1069] | 531 | automatic detection of the on/off scans (closest |
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| 532 | in time off is selected) |
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[1144] | 533 | mx_quotient - Form a quotient using MX data (off beams) |
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[1014] | 534 | scale, *, / - return a scan scaled by a given factor |
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[1757] | 535 | add, + - return a scan with given value added |
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| 536 | sub, - - return a scan with given value subtracted |
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[513] | 537 | bin - return a scan with binned channels |
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| 538 | resample - return a scan with resampled channels |
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| 539 | smooth - return the spectrally smoothed scan |
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| 540 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols |
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[706] | 541 | auto_poly_baseline - automatically fit a polynomial baseline |
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[780] | 542 | recalc_azel - recalculate azimuth and elevation based on |
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| 543 | the pointing |
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[513] | 544 | gain_el - apply gain-elevation correction |
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| 545 | opacity - apply opacity correction |
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| 546 | convert_flux - convert to and from Jy and Kelvin brightness |
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[255] | 547 | units |
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[513] | 548 | freq_align - align spectra in frequency frame |
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[1014] | 549 | invert_phase - Invert the phase of the cross-correlation |
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[1351] | 550 | swap_linears - Swap XX and YY (or RR LL) |
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[513] | 551 | rotate_xyphase - rotate XY phase of cross correlation |
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| 552 | rotate_linpolphase - rotate the phase of the complex |
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| 553 | polarization O=Q+iU correlation |
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[733] | 554 | freq_switch - perform frequency switching on the data |
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| 555 | stats - Determine the specified statistic, e.g. 'min' |
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| 556 | 'max', 'rms' etc. |
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| 557 | stddev - Determine the standard deviation of the current |
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| 558 | beam/if/pol |
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[1757] | 559 | get_row_selector - get the selection object for a specified row |
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| 560 | number |
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[1014] | 561 | [Selection] |
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| 562 | selector - a selection object to set a subset of a scantable |
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| 563 | set_scans - set (a list of) scans by index |
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| 564 | set_cycles - set (a list of) cycles by index |
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| 565 | set_beams - set (a list of) beamss by index |
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| 566 | set_ifs - set (a list of) ifs by index |
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| 567 | set_polarisations - set (a list of) polarisations by name |
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| 568 | or by index |
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| 569 | set_names - set a selection by name (wildcards allowed) |
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| 570 | set_tsys - set a selection by tsys thresholds |
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[1259] | 571 | set_query - set a selection by SQL-like query, e.g. BEAMNO==1 |
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[1351] | 572 | ( also get_ functions for all these ) |
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[1014] | 573 | reset - unset all selections |
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[1351] | 574 | + - merge two selections |
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[733] | 575 | |
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[513] | 576 | [Math] Mainly functions which operate on more than one scantable |
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[100] | 577 | |
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[706] | 578 | average_time - return the (weighted) time average |
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[513] | 579 | of a list of scans |
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| 580 | quotient - return the on/off quotient |
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| 581 | simple_math - simple mathematical operations on two scantables, |
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| 582 | 'add', 'sub', 'mul', 'div' |
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[1069] | 583 | quotient - build quotient of the given on and off scans |
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[1351] | 584 | (matched pairs and 1 off - n on are valid) |
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[1117] | 585 | merge - merge a list of scantables |
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[1069] | 586 | |
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[1151] | 587 | [Line Catalog] |
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| 588 | linecatalog - a linecatalog wrapper, taking an ASCII or |
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| 589 | internal format table |
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| 590 | summary - print a summary of the current selection |
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| 591 | set_name - select a subset by name pattern, e.g. '*OH*' |
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| 592 | set_strength_limits - select a subset by line strength limits |
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| 593 | set_frequency_limits - select a subset by frequency limits |
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| 594 | reset - unset all selections |
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| 595 | save - save the current subset to a table (internal |
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| 596 | format) |
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| 597 | get_row - get the name and frequency from a specific |
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| 598 | row in the table |
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[513] | 599 | [Fitting] |
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[113] | 600 | fitter |
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| 601 | auto_fit - return a scan where the function is |
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| 602 | applied to all Beams/IFs/Pols. |
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| 603 | commit - return a new scan where the fits have been |
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| 604 | commited. |
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| 605 | fit - execute the actual fitting process |
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[984] | 606 | store_fit - store the fit parameters in the data (scantable) |
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[113] | 607 | get_chi2 - get the Chi^2 |
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| 608 | set_scan - set the scantable to be fit |
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| 609 | set_function - set the fitting function |
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| 610 | set_parameters - set the parameters for the function(s), and |
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| 611 | set if they should be held fixed during fitting |
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[513] | 612 | set_gauss_parameters - same as above but specialised for individual |
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| 613 | gaussian components |
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[113] | 614 | get_parameters - get the fitted parameters |
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[513] | 615 | plot - plot the resulting fit and/or components and |
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| 616 | residual |
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[210] | 617 | [Plotter] |
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| 618 | asapplotter - a plotter for asap, default plotter is |
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| 619 | called 'plotter' |
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[984] | 620 | plot - plot a scantable |
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[1151] | 621 | plot_lines - plot a linecatalog overlay |
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[1757] | 622 | plotazel - plot azimuth and elevation versus time |
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| 623 | plotpointing - plot telescope pointings |
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[378] | 624 | save - save the plot to a file ('png' ,'ps' or 'eps') |
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[210] | 625 | set_mode - set the state of the plotter, i.e. |
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| 626 | what is to be plotted 'colour stacked' |
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| 627 | and what 'panelled' |
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[984] | 628 | set_selection - only plot a selected part of the data |
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[733] | 629 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax] |
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[255] | 630 | set_legend - specify user labels for the legend indeces |
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| 631 | set_title - specify user labels for the panel indeces |
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[733] | 632 | set_abcissa - specify a user label for the abcissa |
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[255] | 633 | set_ordinate - specify a user label for the ordinate |
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[378] | 634 | set_layout - specify the multi-panel layout (rows,cols) |
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[733] | 635 | set_colors - specify a set of colours to use |
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| 636 | set_linestyles - specify a set of linestyles to use if only |
---|
| 637 | using one color |
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[1151] | 638 | set_font - set general font properties, e.g. 'family' |
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[1054] | 639 | set_histogram - plot in historam style |
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[733] | 640 | set_mask - set a plotting mask for a specific polarization |
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[1171] | 641 | text - draw text annotations either in data or relative |
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| 642 | coordinates |
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| 643 | arrow - draw arrow annotations either in data or relative |
---|
| 644 | coordinates |
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| 645 | axhline,axvline - draw horizontal/vertical lines |
---|
| 646 | axhspan,axvspan - draw horizontal/vertical regions |
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[1757] | 647 | annotate - draw an arrow with label |
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| 648 | create_mask - create a scnatble mask interactively |
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[1175] | 649 | |
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| 650 | xyplotter - matplotlib/pylab plotting functions |
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| 651 | |
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[113] | 652 | [General] |
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| 653 | commands - this command |
---|
| 654 | print - print details about a variable |
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[1757] | 655 | list_scans - list all scantables created by the user |
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[992] | 656 | list_files - list all files readable by asap (default rpf) |
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[113] | 657 | del - delete the given variable from memory |
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| 658 | range - create a list of values, e.g. |
---|
| 659 | range(3) = [0,1,2], range(2,5) = [2,3,4] |
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| 660 | help - print help for one of the listed functions |
---|
| 661 | execfile - execute an asap script, e.g. execfile('myscript') |
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[255] | 662 | list_rcparameters - print out a list of possible values to be |
---|
[274] | 663 | put into $HOME/.asaprc |
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[1171] | 664 | rc - set rc parameters from within asap |
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[466] | 665 | mask_and,mask_or, |
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| 666 | mask_not - boolean operations on masks created with |
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| 667 | scantable.create_mask |
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[1757] | 668 | skydip - gain opacity values from a sky dip observation |
---|
| 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__) |
---|