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' : [False, validate_bool],
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56 |
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57 | # plotting
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58 | 'plotter.stacking' : ['p', str],
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59 | 'plotter.panelling' : ['s', str],
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60 |
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61 | # scantable
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62 | 'scantable.save' : ['ASAP', str],
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63 | 'scantable.autoaverage' : [True, validate_bool],
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64 | 'scantable.freqframe' : ['LSRK', str], #default frequency frame
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65 | 'scantable.allaxes' : [True, validate_bool], # apply action to all axes
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66 | 'scantable.plotter' : [True, validate_bool], # use internal plotter
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67 | 'scantable.verbosesummary' : [False, validate_bool]
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68 |
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69 | # fitter
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70 | }
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71 |
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72 | def list_rcparameters():
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73 |
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74 | print """
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75 | # general
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76 | # print verbose output
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77 | 'verbose' : True
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78 |
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79 | # preload a default plotter
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80 | 'useplotter' : True
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81 |
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82 | # apply operations on the input scantable or return new one
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83 | 'insitu' : False
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84 |
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85 | # plotting
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86 | # default mode for colour stacking
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87 | 'plotter.stacking' : 'Pol'
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88 |
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89 | # default mode for panelling
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90 | 'plotter.panelling' : 'scan'
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91 |
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92 | # scantable
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93 | # default ouput format when saving
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94 | 'scantable.save' : 'ASAP'
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95 | # auto averaging on read
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96 | 'scantable.autoaverage' : True
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97 |
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98 | # default frequency frame to set when function
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99 | # scantable.set_freqfrmae is called
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100 | 'scantable.freqframe' : 'LSRK'
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101 |
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102 | # apply action to all axes not just the cursor location
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103 | 'scantable.allaxes' : True
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104 |
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105 | # use internal plotter
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106 | 'scantable.plotter' : True
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107 |
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108 | # Control the level of information printed by summary
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109 | 'scantable.verbosesummary' : False
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110 |
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111 | # Fitter
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112 | """
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113 |
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114 | def rc_params():
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115 | 'Return the default params updated from the values in the rc file'
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116 |
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117 | fname = asap_fname()
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118 |
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119 | if fname is None or not os.path.exists(fname):
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120 | message = 'could not find rc file; returning defaults'
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121 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
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122 | #print message
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123 | return ret
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124 |
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125 | cnt = 0
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126 | for line in file(fname):
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127 | cnt +=1
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128 | line = line.strip()
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129 | if not len(line): continue
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130 | if line.startswith('#'): continue
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131 | tup = line.split(':',1)
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132 | if len(tup) !=2:
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133 | print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
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134 | continue
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135 |
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136 | key, val = tup
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137 | key = key.strip()
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138 | if not defaultParams.has_key(key):
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139 | print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
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140 | continue
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141 |
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142 | default, converter = defaultParams[key]
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143 |
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144 | ind = val.find('#')
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145 | if ind>=0: val = val[:ind] # ignore trailing comments
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146 | val = val.strip()
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147 | try: cval = converter(val) # try to convert to proper type or raise
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148 | except Exception, msg:
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149 | 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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150 | continue
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151 | else:
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152 | # Alles Klar, update dict
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153 | defaultParams[key][0] = cval
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154 |
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155 | # strip the conveter funcs and return
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156 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
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157 | verbose.report('loaded rc file %s'%fname)
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158 |
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159 | return ret
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160 |
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161 |
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162 | # this is the instance used by the asap classes
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163 | rcParams = rc_params()
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164 |
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165 | rcParamsDefault = dict(rcParams.items()) # a copy
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166 |
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167 | def rc(group, **kwargs):
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168 | """
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169 | Set the current rc params. Group is the grouping for the rc, eg
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170 | for scantable.save the group is 'scantable', for plotter.stacking, the
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171 | group is 'plotter', and so on. kwargs is a list of attribute
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172 | name/value pairs, eg
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173 |
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174 | rc('scantable', save='SDFITS')
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175 |
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176 | sets the current rc params and is equivalent to
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177 |
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178 | rcParams['scantable.save'] = 'SDFITS'
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179 |
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180 | Use rcdefaults to restore the default rc params after changes.
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181 | """
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182 |
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183 | aliases = {}
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184 |
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185 | for k,v in kwargs.items():
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186 | name = aliases.get(k) or k
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187 | key = '%s.%s' % (group, name)
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188 | if not rcParams.has_key(key):
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189 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
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190 |
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191 | rcParams[key] = v
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192 |
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193 |
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194 | def rcdefaults():
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195 | """
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196 | Restore the default rc params - the ones that were created at
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197 | asap load time
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198 | """
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199 | rcParams.update(rcParamsDefault)
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200 |
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201 | from asapfitter import *
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202 | from asapreader import reader
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203 | from asapmath import *
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204 | from scantable import *
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205 | from asaplinefind import *
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206 |
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207 | if rcParams['useplotter']:
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208 | if os.environ.has_key('DISPLAY'):
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209 | print "Initialising asapplotter with the name 'plotter' ..."
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210 | import asapplotter
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211 | plotter = asapplotter.asapplotter()
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212 | else:
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213 | print "No $DISPLAY set. Disabling plotter.\n"
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214 |
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215 | #from numarray ones,zeros
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216 |
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217 |
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218 | __date__ = '$Date: 2005-02-09 11:30:35 +0000 (Wed, 09 Feb 2005) $'
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219 | __version__ = '0.2'
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220 |
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221 | def list_scans(t = scantable):
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222 | import sys, types
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223 | #meta_t = type(t)
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224 | #if meta_t == types.InstanceType:
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225 | # t = t.__class__
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226 | #elif meta_t not in [types.ClassType, types.TypeType]:
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227 | # t = meta_t
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228 | globs = sys.modules['__main__'].__dict__.iteritems()
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229 | print "The user created scantables are:"
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230 | x = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
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231 | print x
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232 |
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233 | def commands():
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234 | x = """
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235 | [The scan container]
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236 | scantable - a container for integrations/scans
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237 | (can open asap/rpfits/sdfits and ms files)
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238 | copy - returns a copy of a scan
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239 | get_scan - gets a specific scan out of a scantable
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240 | summary - print info about the scantable contents
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241 | set_cursor - set a specific Beam/IF/Pol 'cursor' for
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242 | further use
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243 | get_cursor - print out the current cursor position
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244 | stats - get specified statistic of the spectra in
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245 | the scantable
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246 | stddev - get the standard deviation of the spectra
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247 | in the scantable
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248 | get_tsys - get the TSys
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249 | get_time - get the timestamps of the integrations
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250 | get_unit - get the currnt unit
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251 | set_unit - set the abcissa unit to be used from this point on
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252 | get_abcissa - get the abcissa values and name for a given
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253 | row (time)
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254 | set_freqframe - set the frame info for the Spectral Axis
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255 | (e.g. 'LSRK')
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256 | set_doppler - set the doppler to be used from this point on
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257 | set_instrument - set the instrument name
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258 | get_fluxunit - get the brightness flux unit
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259 | set_fluxunit - set the brightness flux unit
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260 | create_mask - return an mask in the current unit
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261 | for the given region. The specified regions
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262 | are NOT masked
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263 | get_restfreqs - get the current list of rest frequencies
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264 | set_restfreqs - set a list of rest frequencies
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265 | lines - print list of known spectral lines
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266 | flag_spectrum - flag a whole Beam/IF/Pol
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267 | save - save the scantable to disk as either 'ASAP'
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268 | or 'SDFITS'
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269 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
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270 | [Math]
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271 | average_time - return the (weighted) time average of a scan
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272 | or a list of scans
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273 | average_pol - average the polarisations together.
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274 | The dimension won't be reduced and
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275 | all polarisations will contain the
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276 | averaged spectrum.
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277 | quotient - return the on/off quotient
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278 | simple_math - simple mathematical operations on two scantables,
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279 | 'add', 'sub', 'mul', 'div'
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280 | scale - return a scan scaled by a given factor
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281 | add - return a scan with given value added
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282 | bin - return a scan with binned channels
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283 | resample - return a scan with resampled channels
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284 | smooth - return the spectrally smoothed scan
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285 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
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286 | gain_el - apply gain-elevation correction
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287 | opacity - apply opacity correction
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288 | convert_flux - convert to and from Jy and Kelvin brightness
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289 | units
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290 |
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291 | fitter
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292 | auto_fit - return a scan where the function is
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293 | applied to all Beams/IFs/Pols.
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294 | commit - return a new scan where the fits have been
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295 | commited.
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296 | fit - execute the actual fitting process
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297 | get_chi2 - get the Chi^2
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298 | set_scan - set the scantable to be fit
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299 | set_function - set the fitting function
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300 | set_parameters - set the parameters for the function(s), and
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301 | set if they should be held fixed during fitting
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302 | get_parameters - get the fitted parameters
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303 | [Plotter]
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304 | asapplotter - a plotter for asap, default plotter is
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305 | called 'plotter'
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306 | plot - plot a (list of) scantable
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307 | save - save the plot to a file ('png' ,'ps' or 'eps')
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308 | set_mode - set the state of the plotter, i.e.
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309 | what is to be plotted 'colour stacked'
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310 | and what 'panelled'
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311 | set_range - set the abcissa 'zoom' range
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312 | set_legend - specify user labels for the legend indeces
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313 | set_title - specify user labels for the panel indeces
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314 | set_ordinate - specify a user label for the ordinate
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315 | set_abcissa - specify a user label for the abcissa
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316 | set_layout - specify the multi-panel layout (rows,cols)
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317 |
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318 | [Reading files]
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319 | reader - access rpfits/sdfits files
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320 | read - read in integrations
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321 | summary - list info about all integrations
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322 |
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323 | [General]
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324 | commands - this command
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325 | print - print details about a variable
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326 | list_scans - list all scantables created bt the user
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327 | del - delete the given variable from memory
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328 | range - create a list of values, e.g.
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329 | range(3) = [0,1,2], range(2,5) = [2,3,4]
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330 | help - print help for one of the listed functions
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331 | execfile - execute an asap script, e.g. execfile('myscript')
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332 | list_rcparameters - print out a list of possible values to be
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333 | put into $HOME/.asaprc
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334 | Note:
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335 | How to use this with help:
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336 | # function 'summary'
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337 | [xxx] is just a category
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338 | Every 'sub-level' in this list should be replaces by a '.' Period when
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339 | using help
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340 | Example:
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341 | ASAP> help scantable # to get info on ths scantable
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342 | ASAP> help scantable.summary # to get help on the scantable's
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343 | ASAP> help average_time
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344 |
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345 | """
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346 | print x
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347 | return
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348 |
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349 | print """Welcome to ASAP - the ATNF Single Dish Analysis Package
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350 | This is a testing pre-release %s
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351 |
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352 | Please report any bugs to:
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353 | Malte.Marquarding@csiro.au
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354 |
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355 | [IMPORTANT: ASAP is 0-based]
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356 | Type commands() to get a list of all available ASAP commands.
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357 | """ % (__version__)
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