[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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[1456] | 7 | # Set up CASAPATH and first time use of asap i.e. ~/.asap/* |
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[1080] | 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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[1456] | 24 | # use CASAPATH if defined and "data" dir present |
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| 25 | if not os.environ.has_key("CASAPATH") or \ |
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| 26 | not os.path.exists(os.environ["CASAPATH"].split()[0]+"/data"): |
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| 27 | os.environ["CASAPATH"] = "%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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[1445] | 33 | #shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap") |
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[1603] | 34 | # commented out by TT on 2009.06.23 for casapy use |
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| 35 | ##shutil.copyfile(asapdata+"/data/ipy_user_conf.py", |
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| 36 | ## userdir+"/ipy_user_conf.py") |
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[1080] | 37 | f = file(userdir+"/asapuserfuncs.py", "w") |
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| 38 | f.close() |
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| 39 | f = file(userdir+"/ipythonrc", "w") |
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| 40 | f.close() |
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[1603] | 41 | # commented out by TT on 2009.06.23 for casapy use |
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| 42 | ##else: |
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| 43 | # upgrade to support later ipython versions |
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| 44 | ##if not os.path.exists(userdir+"/ipy_user_conf.py"): |
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| 45 | ## shutil.copyfile(asapdata+"/data/ipy_user_conf.py", |
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| 46 | ## userdir+"/ipy_user_conf.py") |
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| 47 | |
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[1171] | 48 | # remove from namespace |
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[1080] | 49 | del asapdata, userdir, shutil, platform |
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| 50 | |
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[513] | 51 | def _validate_bool(b): |
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[226] | 52 | 'Convert b to a boolean or raise' |
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| 53 | bl = b.lower() |
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| 54 | if bl in ('f', 'no', 'false', '0', 0): return False |
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| 55 | elif bl in ('t', 'yes', 'true', '1', 1): return True |
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| 56 | else: |
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| 57 | raise ValueError('Could not convert "%s" to boolean' % b) |
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| 58 | |
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[513] | 59 | def _validate_int(s): |
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[226] | 60 | 'convert s to int or raise' |
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| 61 | try: return int(s) |
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| 62 | except ValueError: |
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| 63 | raise ValueError('Could not convert "%s" to int' % s) |
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| 64 | |
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[513] | 65 | def _asap_fname(): |
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[226] | 66 | """ |
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| 67 | Return the path to the rc file |
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| 68 | |
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| 69 | Search order: |
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| 70 | |
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| 71 | * current working dir |
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| 72 | * environ var ASAPRC |
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[274] | 73 | * HOME/.asaprc |
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[706] | 74 | |
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[226] | 75 | """ |
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| 76 | |
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| 77 | fname = os.path.join( os.getcwd(), '.asaprc') |
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| 78 | if os.path.exists(fname): return fname |
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| 79 | |
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| 80 | if os.environ.has_key('ASAPRC'): |
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| 81 | path = os.environ['ASAPRC'] |
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| 82 | if os.path.exists(path): |
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| 83 | fname = os.path.join(path, '.asaprc') |
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| 84 | if os.path.exists(fname): |
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| 85 | return fname |
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| 86 | |
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| 87 | if os.environ.has_key('HOME'): |
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| 88 | home = os.environ['HOME'] |
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| 89 | fname = os.path.join(home, '.asaprc') |
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| 90 | if os.path.exists(fname): |
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| 91 | return fname |
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| 92 | return None |
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| 93 | |
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[706] | 94 | |
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[226] | 95 | defaultParams = { |
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| 96 | # general |
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[513] | 97 | 'verbose' : [True, _validate_bool], |
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| 98 | 'useplotter' : [True, _validate_bool], |
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[542] | 99 | 'insitu' : [True, _validate_bool], |
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[706] | 100 | |
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[226] | 101 | # plotting |
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[706] | 102 | 'plotter.gui' : [True, _validate_bool], |
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[226] | 103 | 'plotter.stacking' : ['p', str], |
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| 104 | 'plotter.panelling' : ['s', str], |
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[700] | 105 | 'plotter.colours' : ['', str], |
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| 106 | 'plotter.linestyles' : ['', str], |
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[710] | 107 | 'plotter.decimate' : [False, _validate_bool], |
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| 108 | 'plotter.ganged' : [True, _validate_bool], |
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[1022] | 109 | 'plotter.histogram' : [False, _validate_bool], |
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[1097] | 110 | 'plotter.papertype' : ['A4', str], |
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[1603] | 111 | 'plotter.xaxisformatting' : ['asap', str], |
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[710] | 112 | |
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[226] | 113 | # scantable |
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| 114 | 'scantable.save' : ['ASAP', str], |
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[513] | 115 | 'scantable.autoaverage' : [True, _validate_bool], |
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[226] | 116 | 'scantable.freqframe' : ['LSRK', str], #default frequency frame |
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[1076] | 117 | 'scantable.verbosesummary' : [False, _validate_bool], |
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[1603] | 118 | 'scantable.storage' : ['memory', str], |
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| 119 | 'scantable.history' : [True, _validate_bool], |
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| 120 | 'scantable.reference' : ['.*(e|w|_R)$', str] |
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[226] | 121 | # fitter |
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| 122 | } |
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| 123 | |
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[255] | 124 | def list_rcparameters(): |
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[706] | 125 | |
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[255] | 126 | print """ |
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[737] | 127 | # general |
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| 128 | # print verbose output |
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| 129 | verbose : True |
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[255] | 130 | |
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[737] | 131 | # preload a default plotter |
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| 132 | useplotter : True |
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[255] | 133 | |
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[737] | 134 | # apply operations on the input scantable or return new one |
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| 135 | insitu : True |
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[706] | 136 | |
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[737] | 137 | # plotting |
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[710] | 138 | |
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[737] | 139 | # do we want a GUI or plot to a file |
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| 140 | plotter.gui : True |
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[710] | 141 | |
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[737] | 142 | # default mode for colour stacking |
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| 143 | plotter.stacking : Pol |
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[255] | 144 | |
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[737] | 145 | # default mode for panelling |
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| 146 | plotter.panelling : scan |
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[255] | 147 | |
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[737] | 148 | # push panels together, to share axislabels |
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| 149 | plotter.ganged : True |
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[710] | 150 | |
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[1603] | 151 | # decimate the number of points plotted by a factor of |
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[737] | 152 | # nchan/1024 |
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| 153 | plotter.decimate : False |
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[733] | 154 | |
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[737] | 155 | # default colours/linestyles |
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| 156 | plotter.colours : |
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| 157 | plotter.linestyles : |
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[700] | 158 | |
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[1022] | 159 | # enable/disable histogram plotting |
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| 160 | plotter.histogram : False |
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| 161 | |
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[1097] | 162 | # ps paper type |
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| 163 | plotter.papertype : A4 |
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| 164 | |
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[1603] | 165 | # The formatting style of the xaxis |
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| 166 | plotter.xaxisformatting : 'asap' or 'mpl' |
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| 167 | |
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[737] | 168 | # scantable |
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[1076] | 169 | |
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[1259] | 170 | # default storage of scantable ('memory'/'disk') |
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[1076] | 171 | scantable.storage : memory |
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[1603] | 172 | |
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| 173 | # write history of each call to scantable |
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| 174 | scantable.history : True |
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| 175 | |
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[737] | 176 | # default ouput format when saving |
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| 177 | scantable.save : ASAP |
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[1603] | 178 | |
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[737] | 179 | # auto averaging on read |
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| 180 | scantable.autoaverage : True |
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[255] | 181 | |
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[737] | 182 | # default frequency frame to set when function |
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[1097] | 183 | # scantable.set_freqframe is called |
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[737] | 184 | scantable.freqframe : LSRK |
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[255] | 185 | |
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[737] | 186 | # Control the level of information printed by summary |
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| 187 | scantable.verbosesummary : False |
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[706] | 188 | |
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[1603] | 189 | # Control the identification of reference (off) scans |
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| 190 | # This is has to be a regular expression |
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| 191 | scantable.reference : .*(e|w|_R)$ |
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[737] | 192 | # Fitter |
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| 193 | """ |
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[706] | 194 | |
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[226] | 195 | def rc_params(): |
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| 196 | 'Return the default params updated from the values in the rc file' |
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[706] | 197 | |
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[513] | 198 | fname = _asap_fname() |
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[706] | 199 | |
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[226] | 200 | if fname is None or not os.path.exists(fname): |
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| 201 | message = 'could not find rc file; returning defaults' |
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| 202 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
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| 203 | #print message |
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| 204 | return ret |
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[706] | 205 | |
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[226] | 206 | cnt = 0 |
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| 207 | for line in file(fname): |
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| 208 | cnt +=1 |
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| 209 | line = line.strip() |
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| 210 | if not len(line): continue |
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| 211 | if line.startswith('#'): continue |
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| 212 | tup = line.split(':',1) |
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| 213 | if len(tup) !=2: |
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[1612] | 214 | #print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname)) |
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[1614] | 215 | asaplog.push('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname)) |
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| 216 | print_log('WARN') |
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[226] | 217 | continue |
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[706] | 218 | |
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[226] | 219 | key, val = tup |
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| 220 | key = key.strip() |
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| 221 | if not defaultParams.has_key(key): |
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[1612] | 222 | #print ('Bad key "%s" on line %d in %s' % (key, cnt, fname)) |
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[1614] | 223 | asaplog.push('Bad key "%s" on line %d in %s' % (key, cnt, fname)) |
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| 224 | print_log('WARN') |
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[226] | 225 | continue |
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[706] | 226 | |
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[226] | 227 | default, converter = defaultParams[key] |
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| 228 | |
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| 229 | ind = val.find('#') |
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| 230 | if ind>=0: val = val[:ind] # ignore trailing comments |
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| 231 | val = val.strip() |
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| 232 | try: cval = converter(val) # try to convert to proper type or raise |
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[1080] | 233 | except ValueError, msg: |
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[1612] | 234 | #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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[1627] | 235 | asaplog.push('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg.message)) |
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[1614] | 236 | print_log('WARN') |
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[226] | 237 | continue |
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| 238 | else: |
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| 239 | # Alles Klar, update dict |
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| 240 | defaultParams[key][0] = cval |
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| 241 | |
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| 242 | # strip the conveter funcs and return |
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| 243 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
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[466] | 244 | print ('loaded rc file %s'%fname) |
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[226] | 245 | |
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| 246 | return ret |
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| 247 | |
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| 248 | |
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| 249 | # this is the instance used by the asap classes |
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[706] | 250 | rcParams = rc_params() |
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[226] | 251 | |
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| 252 | rcParamsDefault = dict(rcParams.items()) # a copy |
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| 253 | |
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| 254 | def rc(group, **kwargs): |
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| 255 | """ |
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| 256 | Set the current rc params. Group is the grouping for the rc, eg |
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[379] | 257 | for scantable.save the group is 'scantable', for plotter.stacking, the |
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| 258 | group is 'plotter', and so on. kwargs is a list of attribute |
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[226] | 259 | name/value pairs, eg |
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| 260 | |
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[379] | 261 | rc('scantable', save='SDFITS') |
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[226] | 262 | |
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| 263 | sets the current rc params and is equivalent to |
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[706] | 264 | |
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[379] | 265 | rcParams['scantable.save'] = 'SDFITS' |
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[226] | 266 | |
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| 267 | Use rcdefaults to restore the default rc params after changes. |
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| 268 | """ |
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| 269 | |
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[379] | 270 | aliases = {} |
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[706] | 271 | |
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[226] | 272 | for k,v in kwargs.items(): |
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| 273 | name = aliases.get(k) or k |
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[1603] | 274 | if len(group): |
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| 275 | key = '%s.%s' % (group, name) |
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| 276 | else: |
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| 277 | key = name |
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[226] | 278 | if not rcParams.has_key(key): |
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| 279 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name)) |
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[706] | 280 | |
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[226] | 281 | rcParams[key] = v |
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| 282 | |
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| 283 | |
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| 284 | def rcdefaults(): |
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| 285 | """ |
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| 286 | Restore the default rc params - the ones that were created at |
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| 287 | asap load time |
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| 288 | """ |
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| 289 | rcParams.update(rcParamsDefault) |
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| 290 | |
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[1295] | 291 | def _n_bools(n, val): |
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| 292 | return [ val for i in xrange(n) ] |
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[513] | 293 | |
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| 294 | def _is_sequence_or_number(param, ptype=int): |
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| 295 | if isinstance(param,tuple) or isinstance(param,list): |
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[928] | 296 | if len(param) == 0: return True # empty list |
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[513] | 297 | out = True |
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| 298 | for p in param: |
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| 299 | out &= isinstance(p,ptype) |
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| 300 | return out |
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| 301 | elif isinstance(param, ptype): |
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| 302 | return True |
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| 303 | return False |
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| 304 | |
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[928] | 305 | def _to_list(param, ptype=int): |
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| 306 | if isinstance(param, ptype): |
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| 307 | if ptype is str: return param.split() |
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| 308 | else: return [param] |
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| 309 | if _is_sequence_or_number(param, ptype): |
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| 310 | return param |
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| 311 | return None |
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[715] | 312 | |
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[944] | 313 | def unique(x): |
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[992] | 314 | """ |
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| 315 | Return the unique values in a list |
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| 316 | Parameters: |
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| 317 | x: the list to reduce |
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| 318 | Examples: |
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| 319 | x = [1,2,3,3,4] |
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| 320 | print unique(x) |
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| 321 | [1,2,3,4] |
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| 322 | """ |
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[944] | 323 | return dict([ (val, 1) for val in x]).keys() |
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| 324 | |
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[992] | 325 | def list_files(path=".",suffix="rpf"): |
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| 326 | """ |
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| 327 | Return a list files readable by asap, such as rpf, sdfits, mbf, asap |
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| 328 | Parameters: |
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| 329 | path: The directory to list (default '.') |
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| 330 | suffix: The file extension (default rpf) |
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| 331 | Example: |
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| 332 | files = list_files("data/","sdfits") |
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| 333 | print files |
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| 334 | ['data/2001-09-01_0332_P363.sdfits', |
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| 335 | 'data/2003-04-04_131152_t0002.sdfits', |
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| 336 | 'data/Sgr_86p262_best_SPC.sdfits'] |
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| 337 | """ |
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| 338 | if not os.path.isdir(path): |
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| 339 | return None |
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[1295] | 340 | valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split() |
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[992] | 341 | if not suffix in valid: |
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| 342 | return None |
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| 343 | files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)] |
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| 344 | return filter(lambda x: x.endswith(suffix),files) |
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| 345 | |
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[715] | 346 | # workaround for ipython, which redirects this if banner=0 in ipythonrc |
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| 347 | sys.stdout = sys.__stdout__ |
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| 348 | sys.stderr = sys.__stderr__ |
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| 349 | |
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| 350 | # Logging |
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[1612] | 351 | from taskinit import * |
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[715] | 352 | from asap._asap import Log as _asaplog |
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| 353 | global asaplog |
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[710] | 354 | asaplog=_asaplog() |
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[715] | 355 | if rcParams['verbose']: |
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| 356 | asaplog.enable() |
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| 357 | else: |
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| 358 | asaplog.disable() |
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| 359 | |
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[1614] | 360 | def print_log(level='INFO'): |
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[715] | 361 | log = asaplog.pop() |
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[1612] | 362 | #if len(log) and rcParams['verbose']: print log |
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[1614] | 363 | if len(log) and rcParams['verbose']: casalog.post( log, priority=level ) |
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[715] | 364 | return |
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| 365 | |
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[1295] | 366 | def mask_and(a, b): |
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| 367 | assert(len(a)==len(b)) |
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| 368 | return [ a[i] & b[i] for i in xrange(len(a)) ] |
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[1134] | 369 | |
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[1295] | 370 | def mask_or(a, b): |
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| 371 | assert(len(a)==len(b)) |
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| 372 | return [ a[i] | b[i] for i in xrange(len(a)) ] |
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| 373 | |
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| 374 | def mask_not(a): |
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| 375 | return [ not i for i in a ] |
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| 376 | |
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[1117] | 377 | from asapfitter import fitter |
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[895] | 378 | from asapreader import reader |
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[944] | 379 | from selector import selector |
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[710] | 380 | |
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[100] | 381 | from asapmath import * |
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[1080] | 382 | from scantable import scantable |
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[1097] | 383 | from asaplinefind import linefinder |
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[1134] | 384 | from linecatalog import linecatalog |
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[1460] | 385 | from interactivemask import interactivemask |
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[285] | 386 | |
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[928] | 387 | if rcParams['useplotter']: |
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[1295] | 388 | try: |
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[1603] | 389 | from asapplotter import asapplotter |
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| 390 | gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui'] |
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| 391 | if gui: |
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| 392 | import matplotlib |
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| 393 | matplotlib.use("TkAgg") |
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| 394 | import pylab |
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| 395 | xyplotter = pylab |
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| 396 | plotter = asapplotter(gui) |
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| 397 | del gui |
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[1295] | 398 | except ImportError: |
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[1612] | 399 | #print "Matplotlib not installed. No plotting available" |
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[1614] | 400 | asaplog.post( "Matplotlib not installed. No plotting available") |
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| 401 | print_log('WARN') |
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[285] | 402 | |
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[574] | 403 | __date__ = '$Date: 2009-09-03 05:15:48 +0000 (Thu, 03 Sep 2009) $'.split()[1] |
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[1603] | 404 | __version__ = '2.3.1 alma' |
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[1445] | 405 | # nrao casapy specific, get revision number |
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[1494] | 406 | #__revision__ = ' unknown ' |
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[1456] | 407 | casapath=os.environ["CASAPATH"].split() |
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[1624] | 408 | #svninfo.txt path |
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| 409 | if os.path.isdir(casapath[0]+'/'+casapath[1]+'/python/2.5/asap'): |
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| 410 | # for casa developer environment (linux or darwin) |
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| 411 | revinfo=casapath[0]+'/'+casapath[1]+'/python/2.5/asap/svninfo.txt' |
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| 412 | else: |
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| 413 | # for end-user environments |
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| 414 | if casapath[1]=='darwin': |
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| 415 | revinfo=casapath[0]+'/Resources/python/asap/svninfo.txt' |
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| 416 | else: |
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| 417 | revinfo=casapath[0]+'/lib/python2.5/asap/svninfo.txt' |
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[1445] | 418 | if os.path.isfile(revinfo): |
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| 419 | f = file(revinfo) |
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[1605] | 420 | f.readline() |
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[1445] | 421 | revsionno=f.readline() |
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| 422 | f.close() |
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| 423 | __revision__ = revsionno.rstrip() |
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[1494] | 424 | else: |
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| 425 | __revision__ = ' unknown ' |
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[100] | 426 | |
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[1193] | 427 | def is_ipython(): |
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[1259] | 428 | return '__IP' in dir(sys.modules["__main__"]) |
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[1193] | 429 | if is_ipython(): |
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[1014] | 430 | def version(): print "ASAP %s(%s)"% (__version__, __date__) |
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[706] | 431 | def list_scans(t = scantable): |
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[1295] | 432 | import types |
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[706] | 433 | globs = sys.modules['__main__'].__dict__.iteritems() |
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| 434 | print "The user created scantables are:" |
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| 435 | sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs)) |
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| 436 | print filter(lambda x: not x.startswith('_'), sts) |
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| 437 | return |
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[100] | 438 | |
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[715] | 439 | def commands(): |
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| 440 | x = """ |
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[113] | 441 | [The scan container] |
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| 442 | scantable - a container for integrations/scans |
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[182] | 443 | (can open asap/rpfits/sdfits and ms files) |
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[113] | 444 | copy - returns a copy of a scan |
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| 445 | get_scan - gets a specific scan out of a scantable |
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[984] | 446 | (by name or number) |
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[1093] | 447 | drop_scan - drops a specific scan out of a scantable |
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| 448 | (by number) |
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[984] | 449 | set_selection - set a new subselection of the data |
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| 450 | get_selection - get the current selection object |
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[113] | 451 | summary - print info about the scantable contents |
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[182] | 452 | stats - get specified statistic of the spectra in |
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| 453 | the scantable |
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| 454 | stddev - get the standard deviation of the spectra |
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| 455 | in the scantable |
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[113] | 456 | get_tsys - get the TSys |
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| 457 | get_time - get the timestamps of the integrations |
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[1351] | 458 | get_inttime - get the integration time |
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[733] | 459 | get_sourcename - get the source names of the scans |
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[794] | 460 | get_azimuth - get the azimuth of the scans |
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| 461 | get_elevation - get the elevation of the scans |
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| 462 | get_parangle - get the parallactic angle of the scans |
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[876] | 463 | get_unit - get the current unit |
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[513] | 464 | set_unit - set the abcissa unit to be used from this |
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| 465 | point on |
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[255] | 466 | get_abcissa - get the abcissa values and name for a given |
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| 467 | row (time) |
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[1259] | 468 | get_column_names - get the names of the columns in the scantable |
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| 469 | for use with selector.set_query |
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[113] | 470 | set_freqframe - set the frame info for the Spectral Axis |
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| 471 | (e.g. 'LSRK') |
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[276] | 472 | set_doppler - set the doppler to be used from this point on |
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[984] | 473 | set_dirframe - set the frame for the direction on the sky |
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[240] | 474 | set_instrument - set the instrument name |
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[1190] | 475 | set_feedtype - set the feed type |
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[255] | 476 | get_fluxunit - get the brightness flux unit |
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[240] | 477 | set_fluxunit - set the brightness flux unit |
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[1603] | 478 | set_sourcetype - set the type of the source - source or reference |
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[188] | 479 | create_mask - return an mask in the current unit |
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| 480 | for the given region. The specified regions |
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| 481 | are NOT masked |
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[255] | 482 | get_restfreqs - get the current list of rest frequencies |
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| 483 | set_restfreqs - set a list of rest frequencies |
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[1603] | 484 | shift_refpix - shift the reference pixel of the IFs |
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| 485 | set_spectrum - overwrite the spectrum for a given row |
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| 486 | get_spectrum - retrieve the spectrum for a given |
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| 487 | get_mask - retrieve the mask for a given |
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[1012] | 488 | flag - flag selected channels in the data |
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[1192] | 489 | lag_flag - flag specified frequency in the data |
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[1151] | 490 | save - save the scantable to disk as either 'ASAP', |
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| 491 | 'SDFITS' or 'ASCII' |
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[486] | 492 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans |
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[733] | 493 | nscan - the number of scans in the scantable |
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[1603] | 494 | nrow - the number of spectra in the scantable |
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[486] | 495 | history - print the history of the scantable |
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[530] | 496 | get_fit - get a fit which has been stored witnh the data |
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[706] | 497 | average_time - return the (weighted) time average of a scan |
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[513] | 498 | or a list of scans |
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| 499 | average_pol - average the polarisations together. |
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[1144] | 500 | average_beam - average the beams together. |
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[992] | 501 | convert_pol - convert to a different polarisation type |
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[690] | 502 | auto_quotient - return the on/off quotient with |
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[1069] | 503 | automatic detection of the on/off scans (closest |
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| 504 | in time off is selected) |
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[1144] | 505 | mx_quotient - Form a quotient using MX data (off beams) |
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[1014] | 506 | scale, *, / - return a scan scaled by a given factor |
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| 507 | add, +, - - return a scan with given value added |
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[513] | 508 | bin - return a scan with binned channels |
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| 509 | resample - return a scan with resampled channels |
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| 510 | smooth - return the spectrally smoothed scan |
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| 511 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols |
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[706] | 512 | auto_poly_baseline - automatically fit a polynomial baseline |
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[780] | 513 | recalc_azel - recalculate azimuth and elevation based on |
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| 514 | the pointing |
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[513] | 515 | gain_el - apply gain-elevation correction |
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| 516 | opacity - apply opacity correction |
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| 517 | convert_flux - convert to and from Jy and Kelvin brightness |
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[255] | 518 | units |
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[513] | 519 | freq_align - align spectra in frequency frame |
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[1014] | 520 | invert_phase - Invert the phase of the cross-correlation |
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[1351] | 521 | swap_linears - Swap XX and YY (or RR LL) |
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[513] | 522 | rotate_xyphase - rotate XY phase of cross correlation |
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| 523 | rotate_linpolphase - rotate the phase of the complex |
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| 524 | polarization O=Q+iU correlation |
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[733] | 525 | freq_switch - perform frequency switching on the data |
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| 526 | stats - Determine the specified statistic, e.g. 'min' |
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| 527 | 'max', 'rms' etc. |
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| 528 | stddev - Determine the standard deviation of the current |
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| 529 | beam/if/pol |
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[1014] | 530 | [Selection] |
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| 531 | selector - a selection object to set a subset of a scantable |
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| 532 | set_scans - set (a list of) scans by index |
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| 533 | set_cycles - set (a list of) cycles by index |
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| 534 | set_beams - set (a list of) beamss by index |
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| 535 | set_ifs - set (a list of) ifs by index |
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| 536 | set_polarisations - set (a list of) polarisations by name |
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| 537 | or by index |
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| 538 | set_names - set a selection by name (wildcards allowed) |
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| 539 | set_tsys - set a selection by tsys thresholds |
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[1259] | 540 | set_query - set a selection by SQL-like query, e.g. BEAMNO==1 |
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[1351] | 541 | ( also get_ functions for all these ) |
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[1014] | 542 | reset - unset all selections |
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[1351] | 543 | + - merge two selections |
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[733] | 544 | |
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[513] | 545 | [Math] Mainly functions which operate on more than one scantable |
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[100] | 546 | |
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[706] | 547 | average_time - return the (weighted) time average |
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[513] | 548 | of a list of scans |
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| 549 | quotient - return the on/off quotient |
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| 550 | simple_math - simple mathematical operations on two scantables, |
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| 551 | 'add', 'sub', 'mul', 'div' |
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[1069] | 552 | quotient - build quotient of the given on and off scans |
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[1351] | 553 | (matched pairs and 1 off - n on are valid) |
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[1117] | 554 | merge - merge a list of scantables |
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[1069] | 555 | |
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[1151] | 556 | [Line Catalog] |
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| 557 | linecatalog - a linecatalog wrapper, taking an ASCII or |
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| 558 | internal format table |
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| 559 | summary - print a summary of the current selection |
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| 560 | set_name - select a subset by name pattern, e.g. '*OH*' |
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| 561 | set_strength_limits - select a subset by line strength limits |
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| 562 | set_frequency_limits - select a subset by frequency limits |
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| 563 | reset - unset all selections |
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| 564 | save - save the current subset to a table (internal |
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| 565 | format) |
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| 566 | get_row - get the name and frequency from a specific |
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| 567 | row in the table |
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[513] | 568 | [Fitting] |
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[113] | 569 | fitter |
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| 570 | auto_fit - return a scan where the function is |
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| 571 | applied to all Beams/IFs/Pols. |
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| 572 | commit - return a new scan where the fits have been |
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| 573 | commited. |
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| 574 | fit - execute the actual fitting process |
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[984] | 575 | store_fit - store the fit parameters in the data (scantable) |
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[113] | 576 | get_chi2 - get the Chi^2 |
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| 577 | set_scan - set the scantable to be fit |
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| 578 | set_function - set the fitting function |
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| 579 | set_parameters - set the parameters for the function(s), and |
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| 580 | set if they should be held fixed during fitting |
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[513] | 581 | set_gauss_parameters - same as above but specialised for individual |
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| 582 | gaussian components |
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[113] | 583 | get_parameters - get the fitted parameters |
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[513] | 584 | plot - plot the resulting fit and/or components and |
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| 585 | residual |
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[210] | 586 | [Plotter] |
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| 587 | asapplotter - a plotter for asap, default plotter is |
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| 588 | called 'plotter' |
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[984] | 589 | plot - plot a scantable |
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[1151] | 590 | plot_lines - plot a linecatalog overlay |
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[378] | 591 | save - save the plot to a file ('png' ,'ps' or 'eps') |
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[210] | 592 | set_mode - set the state of the plotter, i.e. |
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| 593 | what is to be plotted 'colour stacked' |
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| 594 | and what 'panelled' |
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[984] | 595 | set_selection - only plot a selected part of the data |
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[733] | 596 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax] |
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[255] | 597 | set_legend - specify user labels for the legend indeces |
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| 598 | set_title - specify user labels for the panel indeces |
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[733] | 599 | set_abcissa - specify a user label for the abcissa |
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[255] | 600 | set_ordinate - specify a user label for the ordinate |
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[378] | 601 | set_layout - specify the multi-panel layout (rows,cols) |
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[733] | 602 | set_colors - specify a set of colours to use |
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| 603 | set_linestyles - specify a set of linestyles to use if only |
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| 604 | using one color |
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[1151] | 605 | set_font - set general font properties, e.g. 'family' |
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[1054] | 606 | set_histogram - plot in historam style |
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[733] | 607 | set_mask - set a plotting mask for a specific polarization |
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[1171] | 608 | text - draw text annotations either in data or relative |
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| 609 | coordinates |
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| 610 | arrow - draw arrow annotations either in data or relative |
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| 611 | coordinates |
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| 612 | axhline,axvline - draw horizontal/vertical lines |
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| 613 | axhspan,axvspan - draw horizontal/vertical regions |
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[1175] | 614 | |
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| 615 | xyplotter - matplotlib/pylab plotting functions |
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| 616 | |
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[182] | 617 | [Reading files] |
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| 618 | reader - access rpfits/sdfits files |
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[984] | 619 | open - attach reader to a file |
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| 620 | close - detach reader from file |
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[182] | 621 | read - read in integrations |
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| 622 | summary - list info about all integrations |
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| 623 | |
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[113] | 624 | [General] |
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| 625 | commands - this command |
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| 626 | print - print details about a variable |
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| 627 | list_scans - list all scantables created bt the user |
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[992] | 628 | list_files - list all files readable by asap (default rpf) |
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[113] | 629 | del - delete the given variable from memory |
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| 630 | range - create a list of values, e.g. |
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| 631 | range(3) = [0,1,2], range(2,5) = [2,3,4] |
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| 632 | help - print help for one of the listed functions |
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| 633 | execfile - execute an asap script, e.g. execfile('myscript') |
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[255] | 634 | list_rcparameters - print out a list of possible values to be |
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[274] | 635 | put into $HOME/.asaprc |
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[1171] | 636 | rc - set rc parameters from within asap |
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[466] | 637 | mask_and,mask_or, |
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| 638 | mask_not - boolean operations on masks created with |
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| 639 | scantable.create_mask |
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[706] | 640 | |
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[210] | 641 | Note: |
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| 642 | How to use this with help: |
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| 643 | # function 'summary' |
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| 644 | [xxx] is just a category |
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| 645 | Every 'sub-level' in this list should be replaces by a '.' Period when |
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[706] | 646 | using help |
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[210] | 647 | Example: |
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| 648 | ASAP> help scantable # to get info on ths scantable |
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| 649 | ASAP> help scantable.summary # to get help on the scantable's |
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| 650 | ASAP> help average_time |
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| 651 | |
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[715] | 652 | """ |
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[1151] | 653 | if rcParams['verbose']: |
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| 654 | try: |
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| 655 | from IPython.genutils import page as pager |
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| 656 | except ImportError: |
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| 657 | from pydoc import pager |
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| 658 | pager(x) |
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| 659 | else: |
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| 660 | print x |
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[715] | 661 | return |
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[113] | 662 | |
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[706] | 663 | def welcome(): |
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| 664 | return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package |
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[100] | 665 | |
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[1035] | 666 | Please report any bugs via: |
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[1378] | 667 | http://svn.atnf.csiro.au/trac/asap/simpleticket |
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[100] | 668 | |
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[378] | 669 | [IMPORTANT: ASAP is 0-based] |
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[706] | 670 | Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__) |
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