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 | |
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68 | # fitter |
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69 | } |
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70 | |
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71 | def list_rcparameters(): |
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72 | |
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73 | print """ |
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74 | # general |
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75 | # print verbose output |
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76 | 'verbose' : True |
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77 | |
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78 | # preload a default plotter |
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79 | 'useplotter' : True |
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80 | |
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81 | # apply operations on the input scantable or return new one |
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82 | 'insitu' : False |
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83 | |
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84 | # plotting |
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85 | # default mode for colour stacking |
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86 | 'plotter.stacking' : 'Pol' |
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87 | |
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88 | # default mode for panelling |
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89 | 'plotter.panelling' : 'scan' |
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90 | |
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91 | # scantable |
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92 | # default ouput format when saving |
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93 | 'scantable.save' : 'ASAP' |
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94 | # auto averaging on read |
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95 | 'scantable.autoaverage' : True |
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96 | |
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97 | # default frequency frame to set when function |
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98 | # scantable.set_freqfrmae is called |
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99 | 'scantable.freqframe' : 'LSRK' |
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100 | |
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101 | # apply action to all axes not just the cursor location |
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102 | 'scantable.allaxes' : True |
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103 | |
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104 | # use internal plotter |
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105 | 'scantable.plotter' : True |
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106 | |
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107 | # Fitter |
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108 | """ |
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109 | |
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110 | def rc_params(): |
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111 | 'Return the default params updated from the values in the rc file' |
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112 | |
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113 | fname = asap_fname() |
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114 | |
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115 | if fname is None or not os.path.exists(fname): |
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116 | message = 'could not find rc file; returning defaults' |
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117 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
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118 | #print message |
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119 | return ret |
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120 | |
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121 | cnt = 0 |
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122 | for line in file(fname): |
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123 | cnt +=1 |
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124 | line = line.strip() |
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125 | if not len(line): continue |
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126 | if line.startswith('#'): continue |
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127 | tup = line.split(':',1) |
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128 | if len(tup) !=2: |
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129 | print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname)) |
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130 | continue |
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131 | |
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132 | key, val = tup |
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133 | key = key.strip() |
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134 | if not defaultParams.has_key(key): |
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135 | print ('Bad key "%s" on line %d in %s' % (key, cnt, fname)) |
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136 | continue |
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137 | |
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138 | default, converter = defaultParams[key] |
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139 | |
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140 | ind = val.find('#') |
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141 | if ind>=0: val = val[:ind] # ignore trailing comments |
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142 | val = val.strip() |
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143 | try: cval = converter(val) # try to convert to proper type or raise |
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144 | except Exception, msg: |
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145 | 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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146 | continue |
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147 | else: |
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148 | # Alles Klar, update dict |
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149 | defaultParams[key][0] = cval |
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150 | |
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151 | # strip the conveter funcs and return |
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152 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
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153 | verbose.report('loaded rc file %s'%fname) |
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154 | |
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155 | return ret |
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156 | |
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157 | |
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158 | # this is the instance used by the asap classes |
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159 | rcParams = rc_params() |
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160 | |
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161 | rcParamsDefault = dict(rcParams.items()) # a copy |
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162 | |
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163 | def rc(group, **kwargs): |
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164 | """ |
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165 | Set the current rc params. Group is the grouping for the rc, eg |
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166 | for lines.linewidth the group is 'lines', for axes.facecolor, the |
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167 | group is 'axes', and so on. kwargs is a list of attribute |
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168 | name/value pairs, eg |
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169 | |
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170 | rc('lines', linewidth=2, color='r') |
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171 | |
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172 | sets the current rc params and is equivalent to |
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173 | |
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174 | rcParams['lines.linewidth'] = 2 |
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175 | rcParams['lines.color'] = 'r' |
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176 | |
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177 | |
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178 | Note you can use python's kwargs dictionary facility to store |
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179 | dictionaries of default parameters. Eg, you can customize the |
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180 | font rc as follows |
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181 | |
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182 | font = {'family' : 'monospace', |
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183 | 'weight' : 'bold', |
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184 | 'size' : 'larger', |
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185 | } |
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186 | |
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187 | rc('font', **font) # pass in the font dict as kwargs |
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188 | |
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189 | This enables you to easily switch between several configurations. |
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190 | Use rcdefaults to restore the default rc params after changes. |
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191 | """ |
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192 | |
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193 | aliases = { |
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194 | } |
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195 | |
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196 | for k,v in kwargs.items(): |
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197 | name = aliases.get(k) or k |
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198 | key = '%s.%s' % (group, name) |
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199 | if not rcParams.has_key(key): |
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200 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name)) |
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201 | |
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202 | rcParams[key] = v |
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203 | |
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204 | |
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205 | def rcdefaults(): |
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206 | """ |
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207 | Restore the default rc params - the ones that were created at |
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208 | asap load time |
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209 | """ |
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210 | rcParams.update(rcParamsDefault) |
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211 | |
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212 | from asapfitter import * |
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213 | from asapreader import reader |
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214 | from asapmath import * |
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215 | from scantable import * |
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216 | from asaplinefind import * |
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217 | |
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218 | if rcParams['useplotter']: |
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219 | if os.environ.has_key('DISPLAY'): |
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220 | print "Initialising plotter..." |
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221 | import asapplotter |
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222 | plotter = asapplotter.asapplotter() |
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223 | else: |
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224 | print "No $DISPLAY set. Disabling plotter\n" |
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225 | |
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226 | #from numarray ones,zeros |
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227 | |
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228 | __date__ = '$Date: 2005-01-25 15:00:39 +0000 (Tue, 25 Jan 2005) $' |
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229 | __version__ = '0.2' |
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230 | |
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231 | def list_scans(t = scantable): |
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232 | import sys, types |
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233 | #meta_t = type(t) |
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234 | #if meta_t == types.InstanceType: |
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235 | # t = t.__class__ |
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236 | #elif meta_t not in [types.ClassType, types.TypeType]: |
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237 | # t = meta_t |
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238 | globs = sys.modules['__main__'].__dict__.iteritems() |
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239 | print "The user created scantables are:" |
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240 | x = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs)) |
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241 | print x |
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242 | |
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243 | def commands(): |
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244 | x = """ |
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245 | [The scan container] |
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246 | scantable - a container for integrations/scans |
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247 | (can open asap/rpfits/sdfits and ms files) |
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248 | copy - returns a copy of a scan |
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249 | get_scan - gets a specific scan out of a scantable |
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250 | summary - print info about the scantable contents |
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251 | set_cursor - set a specific Beam/IF/Pol 'cursor' for |
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252 | further use |
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253 | get_cursor - print out the current cursor position |
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254 | stats - get specified statistic of the spectra in |
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255 | the scantable |
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256 | stddev - get the standard deviation of the spectra |
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257 | in the scantable |
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258 | get_tsys - get the TSys |
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259 | get_time - get the timestamps of the integrations |
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260 | get_unit - get the currnt unit |
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261 | set_unit - set the abcissa unit to be used from this point on |
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262 | get_abcissa - get the abcissa values and name for a given |
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263 | row (time) |
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264 | set_freqframe - set the frame info for the Spectral Axis |
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265 | (e.g. 'LSRK') |
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266 | set_doppler - set the doppler to be used from this point on |
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267 | set_instrument - set the instrument name |
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268 | get_fluxunit - get the brightness flux unit |
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269 | set_fluxunit - set the brightness flux unit |
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270 | create_mask - return an mask in the current unit |
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271 | for the given region. The specified regions |
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272 | are NOT masked |
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273 | get_restfreqs - get the current list of rest frequencies |
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274 | set_restfreqs - set a list of rest frequencies |
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275 | flag_spectrum - flag a whole Beam/IF/Pol |
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276 | save - save the scantable to disk as either 'ASAP' |
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277 | or 'SDFITS' |
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278 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans |
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279 | [Math] |
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280 | average_time - return the (weighted) time average of a scan |
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281 | or a list of scans |
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282 | average_pol - average the polarisations together. |
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283 | The dimension won't be reduced and |
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284 | all polarisations will contain the |
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285 | averaged spectrum. |
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286 | quotient - return the on/off quotient |
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287 | simple_math - simple mathematical operations on two scantables, |
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288 | 'add', 'sub', 'mul', 'div' |
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289 | scale - return a scan scaled by a given factor |
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290 | add - return a scan with given value added |
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291 | bin - return a scan with binned channels |
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292 | resample - return a scan with resampled channels |
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293 | smooth - return the spectrally smoothed scan |
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294 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols |
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295 | gain_el - apply gain-elevation correction |
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296 | opacity - apply opacity correction |
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297 | convert_flux - convert to and from Jy and Kelvin brightness |
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298 | units |
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299 | |
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300 | fitter |
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301 | auto_fit - return a scan where the function is |
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302 | applied to all Beams/IFs/Pols. |
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303 | commit - return a new scan where the fits have been |
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304 | commited. |
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305 | fit - execute the actual fitting process |
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306 | get_chi2 - get the Chi^2 |
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307 | set_scan - set the scantable to be fit |
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308 | set_function - set the fitting function |
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309 | set_parameters - set the parameters for the function(s), and |
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310 | set if they should be held fixed during fitting |
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311 | get_parameters - get the fitted parameters |
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312 | [Plotter] |
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313 | asapplotter - a plotter for asap, default plotter is |
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314 | called 'plotter' |
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315 | plot - plot a (list of) scantable |
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316 | set_mode - set the state of the plotter, i.e. |
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317 | what is to be plotted 'colour stacked' |
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318 | and what 'panelled' |
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319 | set_range - set the abcissa 'zoom' range |
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320 | set_legend - specify user labels for the legend indeces |
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321 | set_title - specify user labels for the panel indeces |
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322 | set_ordinate - specify a user label for the ordinate |
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323 | set_abcissa - specify a user label for the abcissa |
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324 | |
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325 | [Reading files] |
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326 | reader - access rpfits/sdfits files |
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327 | read - read in integrations |
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328 | summary - list info about all integrations |
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329 | |
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330 | [General] |
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331 | commands - this command |
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332 | print - print details about a variable |
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333 | list_scans - list all scantables created bt the user |
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334 | del - delete the given variable from memory |
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335 | range - create a list of values, e.g. |
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336 | range(3) = [0,1,2], range(2,5) = [2,3,4] |
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337 | help - print help for one of the listed functions |
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338 | execfile - execute an asap script, e.g. execfile('myscript') |
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339 | list_rcparameters - print out a list of possible values to be |
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340 | put into $HOME/.asaprc |
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341 | Note: |
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342 | How to use this with help: |
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343 | # function 'summary' |
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344 | [xxx] is just a category |
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345 | Every 'sub-level' in this list should be replaces by a '.' Period when |
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346 | using help |
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347 | Example: |
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348 | ASAP> help scantable # to get info on ths scantable |
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349 | ASAP> help scantable.summary # to get help on the scantable's |
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350 | ASAP> help average_time |
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351 | |
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352 | """ |
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353 | print x |
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354 | return |
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355 | |
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356 | print """Welcome to ASAP - the ATNF Single Dish Analysis Package |
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357 | This is a testing pre-release v0.2 |
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358 | |
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359 | Please report any bugs to: |
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360 | Malte.Marquarding@csiro.au |
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361 | |
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362 | [NOTE: ASAP is 0-based] |
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363 | Type commands() to get a list of all available ASAP commands. |
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364 | """ |
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