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 |
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6 | |
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7 | def _validate_bool(b): |
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8 | 'Convert b to a boolean or raise' |
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9 | bl = b.lower() |
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10 | if bl in ('f', 'no', 'false', '0', 0): return False |
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11 | elif bl in ('t', 'yes', 'true', '1', 1): return True |
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12 | else: |
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13 | raise ValueError('Could not convert "%s" to boolean' % b) |
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14 | |
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15 | def _validate_int(s): |
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16 | 'convert s to int or raise' |
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17 | try: return int(s) |
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18 | except ValueError: |
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19 | raise ValueError('Could not convert "%s" to int' % s) |
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20 | |
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21 | def _asap_fname(): |
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22 | """ |
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23 | Return the path to the rc file |
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24 | |
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25 | Search order: |
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26 | |
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27 | * current working dir |
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28 | * environ var ASAPRC |
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29 | * HOME/.asaprc |
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30 | |
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31 | """ |
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32 | |
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33 | fname = os.path.join( os.getcwd(), '.asaprc') |
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34 | if os.path.exists(fname): return fname |
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35 | |
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36 | if os.environ.has_key('ASAPRC'): |
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37 | path = os.environ['ASAPRC'] |
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38 | if os.path.exists(path): |
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39 | fname = os.path.join(path, '.asaprc') |
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40 | if os.path.exists(fname): |
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41 | return fname |
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42 | |
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43 | if os.environ.has_key('HOME'): |
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44 | home = os.environ['HOME'] |
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45 | fname = os.path.join(home, '.asaprc') |
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46 | if os.path.exists(fname): |
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47 | return fname |
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48 | return None |
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49 | |
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50 | |
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51 | defaultParams = { |
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52 | # general |
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53 | 'verbose' : [True, _validate_bool], |
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54 | 'useplotter' : [True, _validate_bool], |
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55 | 'insitu' : [True, _validate_bool], |
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56 | |
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57 | # plotting |
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58 | 'plotter.gui' : [True, _validate_bool], |
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59 | 'plotter.stacking' : ['p', str], |
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60 | 'plotter.panelling' : ['s', str], |
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61 | 'plotter.colours' : ['', str], |
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62 | 'plotter.linestyles' : ['', str], |
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63 | 'plotter.decimate' : [False, _validate_bool], |
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64 | 'plotter.ganged' : [True, _validate_bool], |
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65 | |
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66 | # scantable |
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67 | 'scantable.save' : ['ASAP', str], |
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68 | 'scantable.autoaverage' : [True, _validate_bool], |
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69 | 'scantable.freqframe' : ['LSRK', str], #default frequency frame |
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70 | 'scantable.allaxes' : [True, _validate_bool], # apply action to all axes |
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71 | 'scantable.plotter' : [True, _validate_bool], # use internal plotter |
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72 | 'scantable.verbosesummary' : [False, _validate_bool] |
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73 | |
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74 | # fitter |
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75 | } |
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76 | |
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77 | def list_rcparameters(): |
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78 | |
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79 | print """ |
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80 | # general |
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81 | # print verbose output |
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82 | verbose : True |
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83 | |
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84 | # preload a default plotter |
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85 | useplotter : True |
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86 | |
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87 | # apply operations on the input scantable or return new one |
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88 | insitu : True |
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89 | |
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90 | # plotting |
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91 | |
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92 | # do we want a GUI or plot to a file |
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93 | plotter.gui : True |
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94 | |
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95 | # default mode for colour stacking |
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96 | plotter.stacking : Pol |
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97 | |
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98 | # default mode for panelling |
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99 | plotter.panelling : scan |
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100 | |
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101 | # push panels together, to share axislabels |
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102 | plotter.ganged : True |
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103 | |
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104 | # decimate the number of points plotted bya afactor of |
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105 | # nchan/1024 |
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106 | plotter.decimate : False |
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107 | |
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108 | # default colours/linestyles |
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109 | plotter.colours : |
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110 | plotter.linestyles : |
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111 | |
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112 | # scantable |
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113 | # default ouput format when saving |
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114 | scantable.save : ASAP |
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115 | # auto averaging on read |
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116 | scantable.autoaverage : True |
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117 | |
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118 | # default frequency frame to set when function |
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119 | # scantable.set_freqfrmae is called |
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120 | scantable.freqframe : LSRK |
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121 | |
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122 | # apply action to all axes not just the cursor location |
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123 | scantable.allaxes : True |
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124 | |
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125 | # use internal plotter |
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126 | scantable.plotter : True |
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127 | |
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128 | # Control the level of information printed by summary |
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129 | scantable.verbosesummary : False |
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130 | |
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131 | # Fitter |
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132 | """ |
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133 | |
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134 | def rc_params(): |
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135 | 'Return the default params updated from the values in the rc file' |
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136 | |
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137 | fname = _asap_fname() |
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138 | |
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139 | if fname is None or not os.path.exists(fname): |
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140 | message = 'could not find rc file; returning defaults' |
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141 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
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142 | #print message |
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143 | return ret |
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144 | |
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145 | cnt = 0 |
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146 | for line in file(fname): |
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147 | cnt +=1 |
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148 | line = line.strip() |
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149 | if not len(line): continue |
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150 | if line.startswith('#'): continue |
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151 | tup = line.split(':',1) |
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152 | if len(tup) !=2: |
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153 | print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname)) |
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154 | continue |
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155 | |
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156 | key, val = tup |
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157 | key = key.strip() |
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158 | if not defaultParams.has_key(key): |
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159 | print ('Bad key "%s" on line %d in %s' % (key, cnt, fname)) |
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160 | continue |
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161 | |
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162 | default, converter = defaultParams[key] |
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163 | |
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164 | ind = val.find('#') |
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165 | if ind>=0: val = val[:ind] # ignore trailing comments |
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166 | val = val.strip() |
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167 | try: cval = converter(val) # try to convert to proper type or raise |
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168 | except Exception, msg: |
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169 | 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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170 | continue |
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171 | else: |
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172 | # Alles Klar, update dict |
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173 | defaultParams[key][0] = cval |
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174 | |
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175 | # strip the conveter funcs and return |
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176 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
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177 | print ('loaded rc file %s'%fname) |
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178 | |
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179 | return ret |
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180 | |
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181 | |
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182 | # this is the instance used by the asap classes |
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183 | rcParams = rc_params() |
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184 | |
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185 | rcParamsDefault = dict(rcParams.items()) # a copy |
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186 | |
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187 | def rc(group, **kwargs): |
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188 | """ |
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189 | Set the current rc params. Group is the grouping for the rc, eg |
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190 | for scantable.save the group is 'scantable', for plotter.stacking, the |
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191 | group is 'plotter', and so on. kwargs is a list of attribute |
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192 | name/value pairs, eg |
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193 | |
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194 | rc('scantable', save='SDFITS') |
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195 | |
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196 | sets the current rc params and is equivalent to |
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197 | |
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198 | rcParams['scantable.save'] = 'SDFITS' |
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199 | |
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200 | Use rcdefaults to restore the default rc params after changes. |
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201 | """ |
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202 | |
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203 | aliases = {} |
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204 | |
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205 | for k,v in kwargs.items(): |
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206 | name = aliases.get(k) or k |
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207 | key = '%s.%s' % (group, name) |
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208 | if not rcParams.has_key(key): |
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209 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name)) |
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210 | |
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211 | rcParams[key] = v |
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212 | |
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213 | |
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214 | def rcdefaults(): |
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215 | """ |
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216 | Restore the default rc params - the ones that were created at |
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217 | asap load time |
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218 | """ |
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219 | rcParams.update(rcParamsDefault) |
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220 | |
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221 | |
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222 | def _is_sequence_or_number(param, ptype=int): |
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223 | if isinstance(param,tuple) or isinstance(param,list): |
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224 | out = True |
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225 | for p in param: |
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226 | out &= isinstance(p,ptype) |
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227 | return out |
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228 | elif isinstance(param, ptype): |
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229 | return True |
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230 | return False |
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231 | |
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232 | |
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233 | # workaround for ipython, which redirects this if banner=0 in ipythonrc |
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234 | sys.stdout = sys.__stdout__ |
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235 | sys.stderr = sys.__stderr__ |
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236 | |
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237 | # Logging |
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238 | from asap._asap import Log as _asaplog |
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239 | global asaplog |
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240 | asaplog=_asaplog() |
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241 | if rcParams['verbose']: |
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242 | asaplog.enable() |
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243 | else: |
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244 | asaplog.disable() |
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245 | |
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246 | def print_log(): |
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247 | log = asaplog.pop() |
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248 | if len(log) and rcParams['verbose']: print log |
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249 | return |
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250 | |
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251 | from asapfitter import * |
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252 | from asapreader import reader |
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253 | |
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254 | from asapmath import * |
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255 | from scantable import * |
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256 | from asaplinefind import * |
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257 | from asapfit import * |
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258 | |
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259 | from numarray import logical_and as mask_and |
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260 | from numarray import logical_or as mask_or |
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261 | from numarray import logical_not as mask_not |
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262 | |
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263 | if rcParams['useplotter']: |
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264 | from asapplotter import * |
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265 | gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui'] |
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266 | plotter = asapplotter(gui) |
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267 | del gui |
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268 | |
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269 | __date__ = '$Date: 2005-12-14 00:19:21 +0000 (Wed, 14 Dec 2005) $'.split()[1] |
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270 | __version__ = '2.0a' |
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271 | |
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272 | if rcParams['verbose']: |
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273 | def list_scans(t = scantable): |
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274 | import sys, types |
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275 | globs = sys.modules['__main__'].__dict__.iteritems() |
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276 | print "The user created scantables are:" |
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277 | sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs)) |
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278 | print filter(lambda x: not x.startswith('_'), sts) |
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279 | return |
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280 | |
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281 | def commands(): |
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282 | x = """ |
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283 | [The scan container] |
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284 | scantable - a container for integrations/scans |
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285 | (can open asap/rpfits/sdfits and ms files) |
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286 | copy - returns a copy of a scan |
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287 | get_scan - gets a specific scan out of a scantable |
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288 | (by name or number) |
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289 | summary - print info about the scantable contents |
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290 | set_cursor - set a specific Beam/IF/Pol 'cursor' for |
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291 | further use |
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292 | get_cursor - print out the current cursor position |
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293 | stats - get specified statistic of the spectra in |
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294 | the scantable |
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295 | stddev - get the standard deviation of the spectra |
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296 | in the scantable |
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297 | get_tsys - get the TSys |
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298 | get_time - get the timestamps of the integrations |
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299 | get_sourcename - get the source names of the scans |
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300 | get_azimuth - get the azimuth of the scans |
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301 | get_elevation - get the elevation of the scans |
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302 | get_parangle - get the parallactic angle of the scans |
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303 | get_unit - get the currnt unit |
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304 | set_unit - set the abcissa unit to be used from this |
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305 | point on |
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306 | get_abcissa - get the abcissa values and name for a given |
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307 | row (time) |
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308 | set_freqframe - set the frame info for the Spectral Axis |
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309 | (e.g. 'LSRK') |
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310 | set_doppler - set the doppler to be used from this point on |
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311 | set_instrument - set the instrument name |
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312 | get_fluxunit - get the brightness flux unit |
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313 | set_fluxunit - set the brightness flux unit |
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314 | create_mask - return an mask in the current unit |
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315 | for the given region. The specified regions |
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316 | are NOT masked |
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317 | get_restfreqs - get the current list of rest frequencies |
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318 | set_restfreqs - set a list of rest frequencies |
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319 | lines - print list of known spectral lines |
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320 | flag_spectrum - flag a whole Beam/IF/Pol |
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321 | save - save the scantable to disk as either 'ASAP' |
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322 | or 'SDFITS' |
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323 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans |
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324 | nscan - the number of scans in the scantable |
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325 | nrow - te number of integrations in the scantable |
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326 | history - print the history of the scantable |
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327 | get_fit - get a fit which has been stored witnh the data |
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328 | average_time - return the (weighted) time average of a scan |
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329 | or a list of scans |
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330 | average_pol - average the polarisations together. |
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331 | The dimension won't be reduced and |
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332 | all polarisations will contain the |
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333 | averaged spectrum. |
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334 | auto_quotient - return the on/off quotient with |
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335 | automatic detection of the on/off scans |
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336 | (matched pairs and 1 off - n on) |
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337 | quotient - return the on/off quotient |
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338 | scale - return a scan scaled by a given factor |
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339 | add - return a scan with given value added |
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340 | bin - return a scan with binned channels |
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341 | resample - return a scan with resampled channels |
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342 | smooth - return the spectrally smoothed scan |
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343 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols |
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344 | auto_poly_baseline - automatically fit a polynomial baseline |
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345 | recalc_azel - recalculate azimuth and elevation based on |
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346 | the pointing |
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347 | gain_el - apply gain-elevation correction |
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348 | opacity - apply opacity correction |
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349 | convert_flux - convert to and from Jy and Kelvin brightness |
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350 | units |
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351 | freq_align - align spectra in frequency frame |
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352 | rotate_xyphase - rotate XY phase of cross correlation |
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353 | rotate_linpolphase - rotate the phase of the complex |
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354 | polarization O=Q+iU correlation |
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355 | freq_switch - perform frequency switching on the data |
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356 | stats - Determine the specified statistic, e.g. 'min' |
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357 | 'max', 'rms' etc. |
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358 | stddev - Determine the standard deviation of the current |
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359 | beam/if/pol |
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360 | |
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361 | [Math] Mainly functions which operate on more than one scantable |
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362 | |
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363 | average_time - return the (weighted) time average |
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364 | of a list of scans |
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365 | quotient - return the on/off quotient |
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366 | simple_math - simple mathematical operations on two scantables, |
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367 | 'add', 'sub', 'mul', 'div' |
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368 | [Fitting] |
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369 | fitter |
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370 | auto_fit - return a scan where the function is |
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371 | applied to all Beams/IFs/Pols. |
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372 | commit - return a new scan where the fits have been |
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373 | commited. |
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374 | fit - execute the actual fitting process |
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375 | store_fit - store the fit paramaters in the data (scantable) |
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376 | get_chi2 - get the Chi^2 |
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377 | set_scan - set the scantable to be fit |
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378 | set_function - set the fitting function |
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379 | set_parameters - set the parameters for the function(s), and |
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380 | set if they should be held fixed during fitting |
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381 | set_gauss_parameters - same as above but specialised for individual |
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382 | gaussian components |
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383 | get_parameters - get the fitted parameters |
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384 | plot - plot the resulting fit and/or components and |
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385 | residual |
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386 | [Plotter] |
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387 | asapplotter - a plotter for asap, default plotter is |
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388 | called 'plotter' |
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389 | plot - plot a (list of) scantable |
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390 | save - save the plot to a file ('png' ,'ps' or 'eps') |
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391 | set_mode - set the state of the plotter, i.e. |
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392 | what is to be plotted 'colour stacked' |
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393 | and what 'panelled' |
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394 | set_cursor - only plot a selected part of the data |
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395 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax] |
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396 | set_legend - specify user labels for the legend indeces |
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397 | set_title - specify user labels for the panel indeces |
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398 | set_abcissa - specify a user label for the abcissa |
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399 | set_ordinate - specify a user label for the ordinate |
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400 | set_layout - specify the multi-panel layout (rows,cols) |
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401 | set_colors - specify a set of colours to use |
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402 | set_linestyles - specify a set of linestyles to use if only |
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403 | using one color |
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404 | set_mask - set a plotting mask for a specific polarization |
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405 | |
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406 | [Reading files] |
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407 | reader - access rpfits/sdfits files |
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408 | read - read in integrations |
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409 | summary - list info about all integrations |
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410 | |
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411 | [General] |
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412 | commands - this command |
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413 | print - print details about a variable |
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414 | list_scans - list all scantables created bt the user |
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415 | del - delete the given variable from memory |
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416 | range - create a list of values, e.g. |
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417 | range(3) = [0,1,2], range(2,5) = [2,3,4] |
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418 | help - print help for one of the listed functions |
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419 | execfile - execute an asap script, e.g. execfile('myscript') |
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420 | list_rcparameters - print out a list of possible values to be |
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421 | put into $HOME/.asaprc |
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422 | mask_and,mask_or, |
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423 | mask_not - boolean operations on masks created with |
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424 | scantable.create_mask |
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425 | |
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426 | Note: |
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427 | How to use this with help: |
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428 | # function 'summary' |
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429 | [xxx] is just a category |
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430 | Every 'sub-level' in this list should be replaces by a '.' Period when |
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431 | using help |
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432 | Example: |
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433 | ASAP> help scantable # to get info on ths scantable |
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434 | ASAP> help scantable.summary # to get help on the scantable's |
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435 | ASAP> help average_time |
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436 | |
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437 | """ |
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438 | print x |
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439 | return |
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440 | |
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441 | def welcome(): |
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442 | return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package |
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443 | |
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444 | Please report any bugs to: |
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445 | asap@atnf.csiro.au |
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446 | |
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447 | [IMPORTANT: ASAP is 0-based] |
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448 | Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__) |
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