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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5 | import os,sys,shutil, platform
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6 |
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7 | # Set up AIPSPATH and first time use of asap i.e. ~/.asap/*
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8 | plf = None
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9 | if sys.platform == "linux2":
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10 | if platform.architecture()[0] == '64bit':
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11 | plf = 'linux_64b'
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12 | else:
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13 | plf = 'linux_gnu'
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14 | elif sys.platform == 'darwin':
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15 | plf = 'darwin'
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16 | else:
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17 | # Shouldn't happen - default to linux
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18 | plf = 'linux'
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19 | asapdata = __path__[-1]
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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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24 | os.environ["AIPSPATH"] = "%s %s somwhere" % ( asapdata, plf)
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25 | # set up user space
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26 | userdir = os.environ["HOME"]+"/.asap"
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27 | if not os.path.exists(userdir):
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28 | print 'First time ASAP use. Setting up ~/.asap'
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29 | os.mkdir(userdir)
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30 | shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap")
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31 | f = file(userdir+"/asapuserfuncs.py", "w")
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32 | f.close()
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33 | f = file(userdir+"/ipythonrc", "w")
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34 | f.close()
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35 | # remove from namespace
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36 | del asapdata, userdir, shutil, platform
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37 |
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38 | def _validate_bool(b):
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39 | 'Convert b to a boolean or raise'
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40 | bl = b.lower()
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41 | if bl in ('f', 'no', 'false', '0', 0): return False
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42 | elif bl in ('t', 'yes', 'true', '1', 1): return True
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43 | else:
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44 | raise ValueError('Could not convert "%s" to boolean' % b)
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45 |
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46 | def _validate_int(s):
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47 | 'convert s to int or raise'
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48 | try: return int(s)
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49 | except ValueError:
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50 | raise ValueError('Could not convert "%s" to int' % s)
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51 |
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52 | def _asap_fname():
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53 | """
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54 | Return the path to the rc file
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55 |
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56 | Search order:
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57 |
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58 | * current working dir
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59 | * environ var ASAPRC
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60 | * HOME/.asaprc
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61 |
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62 | """
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63 |
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64 | fname = os.path.join( os.getcwd(), '.asaprc')
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65 | if os.path.exists(fname): return fname
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66 |
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67 | if os.environ.has_key('ASAPRC'):
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68 | path = os.environ['ASAPRC']
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69 | if os.path.exists(path):
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70 | fname = os.path.join(path, '.asaprc')
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71 | if os.path.exists(fname):
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72 | return fname
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73 |
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74 | if os.environ.has_key('HOME'):
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75 | home = os.environ['HOME']
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76 | fname = os.path.join(home, '.asaprc')
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77 | if os.path.exists(fname):
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78 | return fname
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79 | return None
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80 |
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81 |
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82 | defaultParams = {
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83 | # general
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84 | 'verbose' : [True, _validate_bool],
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85 | 'useplotter' : [True, _validate_bool],
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86 | 'insitu' : [True, _validate_bool],
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87 |
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88 | # plotting
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89 | 'plotter.gui' : [True, _validate_bool],
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90 | 'plotter.stacking' : ['p', str],
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91 | 'plotter.panelling' : ['s', str],
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92 | 'plotter.colours' : ['', str],
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93 | 'plotter.linestyles' : ['', str],
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94 | 'plotter.decimate' : [False, _validate_bool],
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95 | 'plotter.ganged' : [True, _validate_bool],
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96 | 'plotter.histogram' : [False, _validate_bool],
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97 | 'plotter.papertype' : ['A4', str],
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98 |
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99 | # scantable
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100 | 'scantable.save' : ['ASAP', str],
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101 | 'scantable.autoaverage' : [True, _validate_bool],
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102 | 'scantable.freqframe' : ['LSRK', str], #default frequency frame
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103 | 'scantable.verbosesummary' : [False, _validate_bool],
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104 | 'scantable.storage' : ['memory', str]
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105 | # fitter
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106 | }
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107 |
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108 | def list_rcparameters():
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109 |
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110 | print """
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111 | # general
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112 | # print verbose output
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113 | verbose : True
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114 |
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115 | # preload a default plotter
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116 | useplotter : True
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117 |
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118 | # apply operations on the input scantable or return new one
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119 | insitu : True
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120 |
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121 | # plotting
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122 |
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123 | # do we want a GUI or plot to a file
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124 | plotter.gui : True
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125 |
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126 | # default mode for colour stacking
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127 | plotter.stacking : Pol
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128 |
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129 | # default mode for panelling
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130 | plotter.panelling : scan
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131 |
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132 | # push panels together, to share axislabels
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133 | plotter.ganged : True
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134 |
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135 | # decimate the number of points plotted bya afactor of
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136 | # nchan/1024
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137 | plotter.decimate : False
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138 |
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139 | # default colours/linestyles
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140 | plotter.colours :
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141 | plotter.linestyles :
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142 |
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143 | # enable/disable histogram plotting
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144 | plotter.histogram : False
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145 |
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146 | # ps paper type
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147 | plotter.papertype : A4
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148 |
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149 | # scantable
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150 |
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151 | # default storage of scantable ('memory'/'disk')
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152 | scantable.storage : memory
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153 | # default ouput format when saving
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154 | scantable.save : ASAP
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155 | # auto averaging on read
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156 | scantable.autoaverage : True
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157 |
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158 | # default frequency frame to set when function
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159 | # scantable.set_freqframe is called
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160 | scantable.freqframe : LSRK
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161 |
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162 | # Control the level of information printed by summary
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163 | scantable.verbosesummary : False
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164 |
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165 | # Fitter
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166 | """
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167 |
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168 | def rc_params():
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169 | 'Return the default params updated from the values in the rc file'
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170 |
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171 | fname = _asap_fname()
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172 |
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173 | if fname is None or not os.path.exists(fname):
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174 | message = 'could not find rc file; returning defaults'
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175 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
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176 | #print message
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177 | return ret
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178 |
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179 | cnt = 0
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180 | for line in file(fname):
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181 | cnt +=1
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182 | line = line.strip()
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183 | if not len(line): continue
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184 | if line.startswith('#'): continue
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185 | tup = line.split(':',1)
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186 | if len(tup) !=2:
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187 | print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
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188 | continue
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189 |
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190 | key, val = tup
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191 | key = key.strip()
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192 | if not defaultParams.has_key(key):
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193 | print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
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194 | continue
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195 |
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196 | default, converter = defaultParams[key]
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197 |
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198 | ind = val.find('#')
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199 | if ind>=0: val = val[:ind] # ignore trailing comments
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200 | val = val.strip()
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201 | try: cval = converter(val) # try to convert to proper type or raise
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202 | except ValueError, msg:
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203 | 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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204 | continue
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205 | else:
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206 | # Alles Klar, update dict
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207 | defaultParams[key][0] = cval
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208 |
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209 | # strip the conveter funcs and return
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210 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
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211 | print ('loaded rc file %s'%fname)
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212 |
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213 | return ret
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214 |
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215 |
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216 | # this is the instance used by the asap classes
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217 | rcParams = rc_params()
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218 |
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219 | rcParamsDefault = dict(rcParams.items()) # a copy
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220 |
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221 | def rc(group, **kwargs):
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222 | """
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223 | Set the current rc params. Group is the grouping for the rc, eg
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224 | for scantable.save the group is 'scantable', for plotter.stacking, the
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225 | group is 'plotter', and so on. kwargs is a list of attribute
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226 | name/value pairs, eg
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227 |
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228 | rc('scantable', save='SDFITS')
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229 |
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230 | sets the current rc params and is equivalent to
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231 |
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232 | rcParams['scantable.save'] = 'SDFITS'
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233 |
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234 | Use rcdefaults to restore the default rc params after changes.
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235 | """
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236 |
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237 | aliases = {}
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238 |
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239 | for k,v in kwargs.items():
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240 | name = aliases.get(k) or k
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241 | key = '%s.%s' % (group, name)
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242 | if not rcParams.has_key(key):
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243 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
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244 |
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245 | rcParams[key] = v
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246 |
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247 |
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248 | def rcdefaults():
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249 | """
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250 | Restore the default rc params - the ones that were created at
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251 | asap load time
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252 | """
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253 | rcParams.update(rcParamsDefault)
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254 |
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255 |
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256 | def _is_sequence_or_number(param, ptype=int):
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257 | if isinstance(param,tuple) or isinstance(param,list):
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258 | if len(param) == 0: return True # empty list
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259 | out = True
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260 | for p in param:
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261 | out &= isinstance(p,ptype)
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262 | return out
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263 | elif isinstance(param, ptype):
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264 | return True
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265 | return False
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266 |
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267 | def _to_list(param, ptype=int):
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268 | if isinstance(param, ptype):
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269 | if ptype is str: return param.split()
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270 | else: return [param]
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271 | if _is_sequence_or_number(param, ptype):
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272 | return param
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273 | return None
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274 |
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275 | def unique(x):
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276 | """
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277 | Return the unique values in a list
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278 | Parameters:
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279 | x: the list to reduce
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280 | Examples:
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281 | x = [1,2,3,3,4]
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282 | print unique(x)
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283 | [1,2,3,4]
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284 | """
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285 | return dict([ (val, 1) for val in x]).keys()
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286 |
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287 | def list_files(path=".",suffix="rpf"):
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288 | """
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289 | Return a list files readable by asap, such as rpf, sdfits, mbf, asap
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290 | Parameters:
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291 | path: The directory to list (default '.')
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292 | suffix: The file extension (default rpf)
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293 | Example:
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294 | files = list_files("data/","sdfits")
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295 | print files
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296 | ['data/2001-09-01_0332_P363.sdfits',
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297 | 'data/2003-04-04_131152_t0002.sdfits',
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298 | 'data/Sgr_86p262_best_SPC.sdfits']
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299 | """
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300 | import os
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301 | if not os.path.isdir(path):
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302 | return None
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303 | valid = "rpf sdf sdfits mbf asap".split()
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304 | if not suffix in valid:
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305 | return None
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306 | files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
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307 | return filter(lambda x: x.endswith(suffix),files)
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308 |
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309 | # workaround for ipython, which redirects this if banner=0 in ipythonrc
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310 | sys.stdout = sys.__stdout__
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311 | sys.stderr = sys.__stderr__
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312 |
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313 | # Logging
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314 | from asap._asap import Log as _asaplog
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315 | global asaplog
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316 | asaplog=_asaplog()
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317 | if rcParams['verbose']:
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318 | asaplog.enable()
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319 | else:
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320 | asaplog.disable()
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321 |
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322 | def print_log():
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323 | log = asaplog.pop()
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324 | if len(log) and rcParams['verbose']: print log
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325 | return
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326 |
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327 | try:
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328 | import numpy.core as NUM
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329 | except ImportError:
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330 | try:
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331 | import numarray as NUM
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332 | except ImportError:
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333 | raise ImportError("You need to have numpy or numarray installed")
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334 |
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335 | from asapfitter import fitter
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336 | from asapreader import reader
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337 | from selector import selector
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338 |
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339 | from asapmath import *
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340 | from scantable import scantable
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341 | from asaplinefind import linefinder
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342 | from linecatalog import linecatalog
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343 |
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344 | mask_and = NUM.logical_and
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345 | mask_or = NUM.logical_or
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346 | mask_not = NUM.logical_not
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347 |
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348 | if rcParams['useplotter']:
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349 | from asapplotter import asapplotter
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350 | gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
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351 | if gui:
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352 | import pylab as xyplotter
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353 | plotter = asapplotter(gui)
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354 | del gui
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355 |
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356 | __date__ = '$Date: 2006-09-11 05:03:57 +0000 (Mon, 11 Sep 2006) $'.split()[1]
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357 | __version__ = '2.1'
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358 |
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359 | def is_ipython():
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360 | return '__IP' in dir(sys.modules["__main__"])
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361 | if is_ipython():
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362 | def version(): print "ASAP %s(%s)"% (__version__, __date__)
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363 | def list_scans(t = scantable):
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364 | import sys, types
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365 | globs = sys.modules['__main__'].__dict__.iteritems()
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366 | print "The user created scantables are:"
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367 | sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
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368 | print filter(lambda x: not x.startswith('_'), sts)
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369 | return
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370 |
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371 | def commands():
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372 | x = """
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373 | [The scan container]
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374 | scantable - a container for integrations/scans
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375 | (can open asap/rpfits/sdfits and ms files)
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376 | copy - returns a copy of a scan
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377 | get_scan - gets a specific scan out of a scantable
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378 | (by name or number)
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379 | drop_scan - drops a specific scan out of a scantable
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380 | (by number)
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381 | set_selection - set a new subselection of the data
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382 | get_selection - get the current selection object
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383 | summary - print info about the scantable contents
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384 | stats - get specified statistic of the spectra in
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385 | the scantable
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386 | stddev - get the standard deviation of the spectra
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387 | in the scantable
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388 | get_tsys - get the TSys
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389 | get_time - get the timestamps of the integrations
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390 | get_sourcename - get the source names of the scans
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391 | get_azimuth - get the azimuth of the scans
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392 | get_elevation - get the elevation of the scans
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393 | get_parangle - get the parallactic angle of the scans
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394 | get_unit - get the current unit
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395 | set_unit - set the abcissa unit to be used from this
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396 | point on
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397 | get_abcissa - get the abcissa values and name for a given
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398 | row (time)
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399 | get_column_names - get the names of the columns in the scantable
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400 | for use with selector.set_query
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401 | set_freqframe - set the frame info for the Spectral Axis
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402 | (e.g. 'LSRK')
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403 | set_doppler - set the doppler to be used from this point on
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404 | set_dirframe - set the frame for the direction on the sky
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405 | set_instrument - set the instrument name
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406 | set_feedtype - set the feed type
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407 | get_fluxunit - get the brightness flux unit
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408 | set_fluxunit - set the brightness flux unit
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409 | create_mask - return an mask in the current unit
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410 | for the given region. The specified regions
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411 | are NOT masked
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412 | get_restfreqs - get the current list of rest frequencies
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413 | set_restfreqs - set a list of rest frequencies
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414 | flag - flag selected channels in the data
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415 | lag_flag - flag specified frequency in the data
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416 | save - save the scantable to disk as either 'ASAP',
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417 | 'SDFITS' or 'ASCII'
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418 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
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419 | nscan - the number of scans in the scantable
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420 | nrow - te number of spectra in the scantable
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421 | history - print the history of the scantable
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422 | get_fit - get a fit which has been stored witnh the data
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423 | average_time - return the (weighted) time average of a scan
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424 | or a list of scans
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425 | average_pol - average the polarisations together.
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426 | average_beam - average the beams together.
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427 | convert_pol - convert to a different polarisation type
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428 | auto_quotient - return the on/off quotient with
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429 | automatic detection of the on/off scans (closest
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430 | in time off is selected)
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431 | mx_quotient - Form a quotient using MX data (off beams)
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432 | scale, *, / - return a scan scaled by a given factor
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433 | add, +, - - return a scan with given value added
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434 | bin - return a scan with binned channels
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435 | resample - return a scan with resampled channels
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436 | smooth - return the spectrally smoothed scan
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437 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
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438 | auto_poly_baseline - automatically fit a polynomial baseline
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439 | recalc_azel - recalculate azimuth and elevation based on
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440 | the pointing
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441 | gain_el - apply gain-elevation correction
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442 | opacity - apply opacity correction
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443 | convert_flux - convert to and from Jy and Kelvin brightness
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444 | units
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445 | freq_align - align spectra in frequency frame
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446 | invert_phase - Invert the phase of the cross-correlation
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447 | swap_linears - Swap XX and YY
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448 | rotate_xyphase - rotate XY phase of cross correlation
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449 | rotate_linpolphase - rotate the phase of the complex
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450 | polarization O=Q+iU correlation
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451 | freq_switch - perform frequency switching on the data
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452 | stats - Determine the specified statistic, e.g. 'min'
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453 | 'max', 'rms' etc.
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454 | stddev - Determine the standard deviation of the current
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455 | beam/if/pol
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456 | [Selection]
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457 | selector - a selection object to set a subset of a scantable
|
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458 | set_scans - set (a list of) scans by index
|
---|
459 | set_cycles - set (a list of) cycles by index
|
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460 | set_beams - set (a list of) beamss by index
|
---|
461 | set_ifs - set (a list of) ifs by index
|
---|
462 | set_polarisations - set (a list of) polarisations by name
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---|
463 | or by index
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---|
464 | set_names - set a selection by name (wildcards allowed)
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---|
465 | set_tsys - set a selection by tsys thresholds
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466 | set_query - set a selection by SQL-like query, e.g. BEAMNO==1
|
---|
467 | reset - unset all selections
|
---|
468 | + - merge to selections
|
---|
469 |
|
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470 | [Math] Mainly functions which operate on more than one scantable
|
---|
471 |
|
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472 | average_time - return the (weighted) time average
|
---|
473 | of a list of scans
|
---|
474 | quotient - return the on/off quotient
|
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475 | simple_math - simple mathematical operations on two scantables,
|
---|
476 | 'add', 'sub', 'mul', 'div'
|
---|
477 | quotient - build quotient of the given on and off scans
|
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478 | (matched pairs and 1 off/n on are valid)
|
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479 | merge - merge a list of scantables
|
---|
480 |
|
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481 | [Line Catalog]
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482 | linecatalog - a linecatalog wrapper, taking an ASCII or
|
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483 | internal format table
|
---|
484 | summary - print a summary of the current selection
|
---|
485 | set_name - select a subset by name pattern, e.g. '*OH*'
|
---|
486 | set_strength_limits - select a subset by line strength limits
|
---|
487 | set_frequency_limits - select a subset by frequency limits
|
---|
488 | reset - unset all selections
|
---|
489 | save - save the current subset to a table (internal
|
---|
490 | format)
|
---|
491 | get_row - get the name and frequency from a specific
|
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492 | row in the table
|
---|
493 | [Fitting]
|
---|
494 | fitter
|
---|
495 | auto_fit - return a scan where the function is
|
---|
496 | applied to all Beams/IFs/Pols.
|
---|
497 | commit - return a new scan where the fits have been
|
---|
498 | commited.
|
---|
499 | fit - execute the actual fitting process
|
---|
500 | store_fit - store the fit parameters in the data (scantable)
|
---|
501 | get_chi2 - get the Chi^2
|
---|
502 | set_scan - set the scantable to be fit
|
---|
503 | set_function - set the fitting function
|
---|
504 | set_parameters - set the parameters for the function(s), and
|
---|
505 | set if they should be held fixed during fitting
|
---|
506 | set_gauss_parameters - same as above but specialised for individual
|
---|
507 | gaussian components
|
---|
508 | get_parameters - get the fitted parameters
|
---|
509 | plot - plot the resulting fit and/or components and
|
---|
510 | residual
|
---|
511 | [Plotter]
|
---|
512 | asapplotter - a plotter for asap, default plotter is
|
---|
513 | called 'plotter'
|
---|
514 | plot - plot a scantable
|
---|
515 | plot_lines - plot a linecatalog overlay
|
---|
516 | save - save the plot to a file ('png' ,'ps' or 'eps')
|
---|
517 | set_mode - set the state of the plotter, i.e.
|
---|
518 | what is to be plotted 'colour stacked'
|
---|
519 | and what 'panelled'
|
---|
520 | set_selection - only plot a selected part of the data
|
---|
521 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
|
---|
522 | set_legend - specify user labels for the legend indeces
|
---|
523 | set_title - specify user labels for the panel indeces
|
---|
524 | set_abcissa - specify a user label for the abcissa
|
---|
525 | set_ordinate - specify a user label for the ordinate
|
---|
526 | set_layout - specify the multi-panel layout (rows,cols)
|
---|
527 | set_colors - specify a set of colours to use
|
---|
528 | set_linestyles - specify a set of linestyles to use if only
|
---|
529 | using one color
|
---|
530 | set_font - set general font properties, e.g. 'family'
|
---|
531 | set_histogram - plot in historam style
|
---|
532 | set_mask - set a plotting mask for a specific polarization
|
---|
533 | text - draw text annotations either in data or relative
|
---|
534 | coordinates
|
---|
535 | arrow - draw arrow annotations either in data or relative
|
---|
536 | coordinates
|
---|
537 | axhline,axvline - draw horizontal/vertical lines
|
---|
538 | axhspan,axvspan - draw horizontal/vertical regions
|
---|
539 |
|
---|
540 | xyplotter - matplotlib/pylab plotting functions
|
---|
541 |
|
---|
542 | [Reading files]
|
---|
543 | reader - access rpfits/sdfits files
|
---|
544 | open - attach reader to a file
|
---|
545 | close - detach reader from file
|
---|
546 | read - read in integrations
|
---|
547 | summary - list info about all integrations
|
---|
548 |
|
---|
549 | [General]
|
---|
550 | commands - this command
|
---|
551 | print - print details about a variable
|
---|
552 | list_scans - list all scantables created bt the user
|
---|
553 | list_files - list all files readable by asap (default rpf)
|
---|
554 | del - delete the given variable from memory
|
---|
555 | range - create a list of values, e.g.
|
---|
556 | range(3) = [0,1,2], range(2,5) = [2,3,4]
|
---|
557 | help - print help for one of the listed functions
|
---|
558 | execfile - execute an asap script, e.g. execfile('myscript')
|
---|
559 | list_rcparameters - print out a list of possible values to be
|
---|
560 | put into $HOME/.asaprc
|
---|
561 | rc - set rc parameters from within asap
|
---|
562 | mask_and,mask_or,
|
---|
563 | mask_not - boolean operations on masks created with
|
---|
564 | scantable.create_mask
|
---|
565 |
|
---|
566 | Note:
|
---|
567 | How to use this with help:
|
---|
568 | # function 'summary'
|
---|
569 | [xxx] is just a category
|
---|
570 | Every 'sub-level' in this list should be replaces by a '.' Period when
|
---|
571 | using help
|
---|
572 | Example:
|
---|
573 | ASAP> help scantable # to get info on ths scantable
|
---|
574 | ASAP> help scantable.summary # to get help on the scantable's
|
---|
575 | ASAP> help average_time
|
---|
576 |
|
---|
577 | """
|
---|
578 | if rcParams['verbose']:
|
---|
579 | try:
|
---|
580 | from IPython.genutils import page as pager
|
---|
581 | except ImportError:
|
---|
582 | from pydoc import pager
|
---|
583 | pager(x)
|
---|
584 | else:
|
---|
585 | print x
|
---|
586 | return
|
---|
587 |
|
---|
588 | def welcome():
|
---|
589 | return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
|
---|
590 |
|
---|
591 | Please report any bugs via:
|
---|
592 | http://sourcecode.atnf.csiro.au/cgi-bin/trac_asap.cgi/newticket
|
---|
593 |
|
---|
594 | [IMPORTANT: ASAP is 0-based]
|
---|
595 | Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
|
---|