1 | """ |
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2 | This is the ATNF Single Dish Analysis package. |
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3 | |
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4 | """ |
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5 | import os,sys,shutil, platform |
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6 | |
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7 | # Set up AIPSPATH and first time use of asap i.e. ~/.asap/* |
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8 | plf = None |
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9 | if sys.platform == "linux2": |
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10 | if platform.architecture()[0] == '64bit': |
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11 | plf = 'linux_64b' |
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12 | else: |
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13 | plf = 'linux_gnu' |
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14 | elif sys.platform == 'darwin': |
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15 | plf = 'darwin' |
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16 | else: |
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17 | # Shouldn't happen - default to linux |
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18 | plf = 'linux' |
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19 | asapdata = __path__[-1] |
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20 | # Allow user defined data location |
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21 | if os.environ.has_key("ASAPDATA"): |
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22 | if os.path.exists(os.environ["ASAPDATA"]): |
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23 | asapdata = os.environ["ASAPDATA"] |
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24 | if not os.environ.has_key("AIPSPATH"): |
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25 | os.environ["AIPSPATH"] = "%s %s somwhere" % ( asapdata, plf) |
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26 | # set up user space |
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27 | userdir = os.environ["HOME"]+"/.asap" |
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28 | if not os.path.exists(userdir): |
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29 | print 'First time ASAP use. Setting up ~/.asap' |
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30 | os.mkdir(userdir) |
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31 | shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap") |
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32 | f = file(userdir+"/asapuserfuncs.py", "w") |
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33 | f.close() |
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34 | f = file(userdir+"/ipythonrc", "w") |
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35 | f.close() |
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36 | # remove from namespace |
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37 | del asapdata, userdir, shutil, platform |
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38 | |
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39 | def _validate_bool(b): |
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40 | 'Convert b to a boolean or raise' |
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41 | bl = b.lower() |
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42 | if bl in ('f', 'no', 'false', '0', 0): return False |
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43 | elif bl in ('t', 'yes', 'true', '1', 1): return True |
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44 | else: |
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45 | raise ValueError('Could not convert "%s" to boolean' % b) |
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46 | |
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47 | def _validate_int(s): |
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48 | 'convert s to int or raise' |
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49 | try: return int(s) |
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50 | except ValueError: |
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51 | raise ValueError('Could not convert "%s" to int' % s) |
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52 | |
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53 | def _asap_fname(): |
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54 | """ |
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55 | Return the path to the rc file |
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56 | |
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57 | Search order: |
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58 | |
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59 | * current working dir |
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60 | * environ var ASAPRC |
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61 | * HOME/.asaprc |
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62 | |
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63 | """ |
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64 | |
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65 | fname = os.path.join( os.getcwd(), '.asaprc') |
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66 | if os.path.exists(fname): return fname |
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67 | |
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68 | if os.environ.has_key('ASAPRC'): |
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69 | path = os.environ['ASAPRC'] |
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70 | if os.path.exists(path): |
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71 | fname = os.path.join(path, '.asaprc') |
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72 | if os.path.exists(fname): |
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73 | return fname |
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74 | |
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75 | if os.environ.has_key('HOME'): |
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76 | home = os.environ['HOME'] |
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77 | fname = os.path.join(home, '.asaprc') |
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78 | if os.path.exists(fname): |
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79 | return fname |
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80 | return None |
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81 | |
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82 | |
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83 | defaultParams = { |
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84 | # general |
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85 | 'verbose' : [True, _validate_bool], |
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86 | 'useplotter' : [True, _validate_bool], |
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87 | 'insitu' : [True, _validate_bool], |
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88 | |
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89 | # plotting |
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90 | 'plotter.gui' : [True, _validate_bool], |
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91 | 'plotter.stacking' : ['p', str], |
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92 | 'plotter.panelling' : ['s', str], |
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93 | 'plotter.colours' : ['', str], |
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94 | 'plotter.linestyles' : ['', str], |
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95 | 'plotter.decimate' : [False, _validate_bool], |
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96 | 'plotter.ganged' : [True, _validate_bool], |
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97 | 'plotter.histogram' : [False, _validate_bool], |
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98 | 'plotter.papertype' : ['A4', str], |
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99 | |
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100 | # scantable |
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101 | 'scantable.save' : ['ASAP', str], |
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102 | 'scantable.autoaverage' : [True, _validate_bool], |
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103 | 'scantable.freqframe' : ['LSRK', str], #default frequency frame |
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104 | 'scantable.verbosesummary' : [False, _validate_bool], |
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105 | 'scantable.storage' : ['memory', str] |
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106 | # fitter |
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107 | } |
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108 | |
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109 | def list_rcparameters(): |
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110 | |
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111 | print """ |
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112 | # general |
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113 | # print verbose output |
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114 | verbose : True |
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115 | |
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116 | # preload a default plotter |
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117 | useplotter : True |
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118 | |
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119 | # apply operations on the input scantable or return new one |
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120 | insitu : True |
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121 | |
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122 | # plotting |
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123 | |
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124 | # do we want a GUI or plot to a file |
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125 | plotter.gui : True |
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126 | |
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127 | # default mode for colour stacking |
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128 | plotter.stacking : Pol |
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129 | |
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130 | # default mode for panelling |
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131 | plotter.panelling : scan |
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132 | |
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133 | # push panels together, to share axislabels |
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134 | plotter.ganged : True |
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135 | |
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136 | # decimate the number of points plotted bya afactor of |
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137 | # nchan/1024 |
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138 | plotter.decimate : False |
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139 | |
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140 | # default colours/linestyles |
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141 | plotter.colours : |
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142 | plotter.linestyles : |
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143 | |
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144 | # enable/disable histogram plotting |
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145 | plotter.histogram : False |
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146 | |
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147 | # ps paper type |
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148 | plotter.papertype : A4 |
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149 | |
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150 | # scantable |
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151 | |
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152 | # default storage of scantable ('memory'/'disk') |
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153 | scantable.storage : memory |
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154 | # default ouput format when saving |
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155 | scantable.save : ASAP |
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156 | # auto averaging on read |
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157 | scantable.autoaverage : True |
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158 | |
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159 | # default frequency frame to set when function |
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160 | # scantable.set_freqframe is called |
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161 | scantable.freqframe : LSRK |
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162 | |
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163 | # Control the level of information printed by summary |
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164 | scantable.verbosesummary : False |
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165 | |
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166 | # Fitter |
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167 | """ |
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168 | |
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169 | def rc_params(): |
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170 | 'Return the default params updated from the values in the rc file' |
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171 | |
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172 | fname = _asap_fname() |
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173 | |
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174 | if fname is None or not os.path.exists(fname): |
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175 | message = 'could not find rc file; returning defaults' |
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176 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
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177 | #print message |
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178 | return ret |
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179 | |
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180 | cnt = 0 |
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181 | for line in file(fname): |
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182 | cnt +=1 |
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183 | line = line.strip() |
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184 | if not len(line): continue |
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185 | if line.startswith('#'): continue |
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186 | tup = line.split(':',1) |
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187 | if len(tup) !=2: |
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188 | print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname)) |
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189 | continue |
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190 | |
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191 | key, val = tup |
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192 | key = key.strip() |
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193 | if not defaultParams.has_key(key): |
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194 | print ('Bad key "%s" on line %d in %s' % (key, cnt, fname)) |
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195 | continue |
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196 | |
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197 | default, converter = defaultParams[key] |
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198 | |
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199 | ind = val.find('#') |
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200 | if ind>=0: val = val[:ind] # ignore trailing comments |
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201 | val = val.strip() |
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202 | try: cval = converter(val) # try to convert to proper type or raise |
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203 | except ValueError, msg: |
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204 | 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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205 | continue |
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206 | else: |
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207 | # Alles Klar, update dict |
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208 | defaultParams[key][0] = cval |
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209 | |
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210 | # strip the conveter funcs and return |
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211 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
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212 | print ('loaded rc file %s'%fname) |
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213 | |
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214 | return ret |
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215 | |
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216 | |
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217 | # this is the instance used by the asap classes |
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218 | rcParams = rc_params() |
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219 | |
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220 | rcParamsDefault = dict(rcParams.items()) # a copy |
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221 | |
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222 | def rc(group, **kwargs): |
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223 | """ |
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224 | Set the current rc params. Group is the grouping for the rc, eg |
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225 | for scantable.save the group is 'scantable', for plotter.stacking, the |
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226 | group is 'plotter', and so on. kwargs is a list of attribute |
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227 | name/value pairs, eg |
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228 | |
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229 | rc('scantable', save='SDFITS') |
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230 | |
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231 | sets the current rc params and is equivalent to |
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232 | |
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233 | rcParams['scantable.save'] = 'SDFITS' |
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234 | |
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235 | Use rcdefaults to restore the default rc params after changes. |
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236 | """ |
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237 | |
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238 | aliases = {} |
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239 | |
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240 | for k,v in kwargs.items(): |
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241 | name = aliases.get(k) or k |
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242 | key = '%s.%s' % (group, name) |
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243 | if not rcParams.has_key(key): |
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244 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name)) |
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245 | |
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246 | rcParams[key] = v |
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247 | |
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248 | |
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249 | def rcdefaults(): |
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250 | """ |
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251 | Restore the default rc params - the ones that were created at |
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252 | asap load time |
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253 | """ |
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254 | rcParams.update(rcParamsDefault) |
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255 | |
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256 | def _n_bools(n, val): |
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257 | return [ val for i in xrange(n) ] |
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258 | |
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259 | def _is_sequence_or_number(param, ptype=int): |
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260 | if isinstance(param,tuple) or isinstance(param,list): |
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261 | if len(param) == 0: return True # empty list |
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262 | out = True |
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263 | for p in param: |
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264 | out &= isinstance(p,ptype) |
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265 | return out |
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266 | elif isinstance(param, ptype): |
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267 | return True |
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268 | return False |
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269 | |
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270 | def _to_list(param, ptype=int): |
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271 | if isinstance(param, ptype): |
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272 | if ptype is str: return param.split() |
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273 | else: return [param] |
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274 | if _is_sequence_or_number(param, ptype): |
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275 | return param |
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276 | return None |
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277 | |
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278 | def unique(x): |
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279 | """ |
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280 | Return the unique values in a list |
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281 | Parameters: |
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282 | x: the list to reduce |
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283 | Examples: |
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284 | x = [1,2,3,3,4] |
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285 | print unique(x) |
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286 | [1,2,3,4] |
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287 | """ |
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288 | return dict([ (val, 1) for val in x]).keys() |
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289 | |
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290 | def list_files(path=".",suffix="rpf"): |
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291 | """ |
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292 | Return a list files readable by asap, such as rpf, sdfits, mbf, asap |
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293 | Parameters: |
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294 | path: The directory to list (default '.') |
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295 | suffix: The file extension (default rpf) |
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296 | Example: |
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297 | files = list_files("data/","sdfits") |
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298 | print files |
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299 | ['data/2001-09-01_0332_P363.sdfits', |
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300 | 'data/2003-04-04_131152_t0002.sdfits', |
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301 | 'data/Sgr_86p262_best_SPC.sdfits'] |
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302 | """ |
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303 | if not os.path.isdir(path): |
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304 | return None |
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305 | valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split() |
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306 | if not suffix in valid: |
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307 | return None |
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308 | files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)] |
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309 | return filter(lambda x: x.endswith(suffix),files) |
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310 | |
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311 | # workaround for ipython, which redirects this if banner=0 in ipythonrc |
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312 | sys.stdout = sys.__stdout__ |
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313 | sys.stderr = sys.__stderr__ |
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314 | |
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315 | # Logging |
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316 | from asap._asap import Log as _asaplog |
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317 | global asaplog |
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318 | asaplog=_asaplog() |
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319 | if rcParams['verbose']: |
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320 | asaplog.enable() |
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321 | else: |
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322 | asaplog.disable() |
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323 | |
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324 | def print_log(): |
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325 | log = asaplog.pop() |
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326 | if len(log) and rcParams['verbose']: print log |
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327 | return |
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328 | |
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329 | def mask_and(a, b): |
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330 | assert(len(a)==len(b)) |
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331 | return [ a[i] & b[i] for i in xrange(len(a)) ] |
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332 | |
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333 | def mask_or(a, b): |
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334 | assert(len(a)==len(b)) |
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335 | return [ a[i] | b[i] for i in xrange(len(a)) ] |
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336 | |
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337 | def mask_not(a): |
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338 | return [ not i for i in a ] |
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339 | |
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340 | from asapfitter import fitter |
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341 | from asapreader import reader |
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342 | from selector import selector |
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343 | |
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344 | from asapmath import * |
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345 | from scantable import scantable |
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346 | from asaplinefind import linefinder |
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347 | from linecatalog import linecatalog |
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348 | |
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349 | if rcParams['useplotter']: |
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350 | try: |
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351 | from asapplotter import asapplotter |
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352 | gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui'] |
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353 | if gui: |
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354 | import pylab as xyplotter |
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355 | plotter = asapplotter(gui) |
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356 | del gui |
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357 | except ImportError: |
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358 | print "Matplotlib not installed. No plotting available" |
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359 | |
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360 | __date__ = '$Date: 2007-03-02 00:02:27 +0000 (Fri, 02 Mar 2007) $'.split()[1] |
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361 | __version__ = '2.1.2' |
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362 | |
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363 | def is_ipython(): |
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364 | return '__IP' in dir(sys.modules["__main__"]) |
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365 | if is_ipython(): |
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366 | def version(): print "ASAP %s(%s)"% (__version__, __date__) |
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367 | def list_scans(t = scantable): |
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368 | import types |
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369 | globs = sys.modules['__main__'].__dict__.iteritems() |
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370 | print "The user created scantables are:" |
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371 | sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs)) |
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372 | print filter(lambda x: not x.startswith('_'), sts) |
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373 | return |
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374 | |
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375 | def commands(): |
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376 | x = """ |
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377 | [The scan container] |
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378 | scantable - a container for integrations/scans |
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379 | (can open asap/rpfits/sdfits and ms files) |
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380 | copy - returns a copy of a scan |
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381 | get_scan - gets a specific scan out of a scantable |
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382 | (by name or number) |
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383 | drop_scan - drops a specific scan out of a scantable |
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384 | (by number) |
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385 | set_selection - set a new subselection of the data |
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386 | get_selection - get the current selection object |
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387 | summary - print info about the scantable contents |
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388 | stats - get specified statistic of the spectra in |
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389 | the scantable |
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390 | stddev - get the standard deviation of the spectra |
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391 | in the scantable |
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392 | get_tsys - get the TSys |
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393 | get_time - get the timestamps of the integrations |
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394 | get_sourcename - get the source names of the scans |
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395 | get_azimuth - get the azimuth of the scans |
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396 | get_elevation - get the elevation of the scans |
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397 | get_parangle - get the parallactic angle of the scans |
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398 | get_unit - get the current unit |
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399 | set_unit - set the abcissa unit to be used from this |
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400 | point on |
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401 | get_abcissa - get the abcissa values and name for a given |
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402 | row (time) |
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403 | get_column_names - get the names of the columns in the scantable |
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404 | for use with selector.set_query |
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405 | set_freqframe - set the frame info for the Spectral Axis |
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406 | (e.g. 'LSRK') |
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407 | set_doppler - set the doppler to be used from this point on |
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408 | set_dirframe - set the frame for the direction on the sky |
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409 | set_instrument - set the instrument name |
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410 | set_feedtype - set the feed type |
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411 | get_fluxunit - get the brightness flux unit |
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412 | set_fluxunit - set the brightness flux unit |
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413 | create_mask - return an mask in the current unit |
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414 | for the given region. The specified regions |
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415 | are NOT masked |
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416 | get_restfreqs - get the current list of rest frequencies |
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417 | set_restfreqs - set a list of rest frequencies |
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418 | flag - flag selected channels in the data |
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419 | lag_flag - flag specified frequency in the data |
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420 | save - save the scantable to disk as either 'ASAP', |
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421 | 'SDFITS' or 'ASCII' |
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422 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans |
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423 | nscan - the number of scans in the scantable |
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424 | nrow - te number of spectra in the scantable |
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425 | history - print the history of the scantable |
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426 | get_fit - get a fit which has been stored witnh the data |
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427 | average_time - return the (weighted) time average of a scan |
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428 | or a list of scans |
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429 | average_pol - average the polarisations together. |
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430 | average_beam - average the beams together. |
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431 | convert_pol - convert to a different polarisation type |
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432 | auto_quotient - return the on/off quotient with |
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433 | automatic detection of the on/off scans (closest |
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434 | in time off is selected) |
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435 | mx_quotient - Form a quotient using MX data (off beams) |
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436 | scale, *, / - return a scan scaled by a given factor |
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437 | add, +, - - return a scan with given value added |
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438 | bin - return a scan with binned channels |
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439 | resample - return a scan with resampled channels |
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440 | smooth - return the spectrally smoothed scan |
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441 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols |
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442 | auto_poly_baseline - automatically fit a polynomial baseline |
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443 | recalc_azel - recalculate azimuth and elevation based on |
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444 | the pointing |
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445 | gain_el - apply gain-elevation correction |
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446 | opacity - apply opacity correction |
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447 | convert_flux - convert to and from Jy and Kelvin brightness |
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448 | units |
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449 | freq_align - align spectra in frequency frame |
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450 | invert_phase - Invert the phase of the cross-correlation |
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451 | swap_linears - Swap XX and YY |
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452 | rotate_xyphase - rotate XY phase of cross correlation |
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453 | rotate_linpolphase - rotate the phase of the complex |
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454 | polarization O=Q+iU correlation |
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455 | freq_switch - perform frequency switching on the data |
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456 | stats - Determine the specified statistic, e.g. 'min' |
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457 | 'max', 'rms' etc. |
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458 | stddev - Determine the standard deviation of the current |
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459 | beam/if/pol |
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460 | [Selection] |
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461 | selector - a selection object to set a subset of a scantable |
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462 | set_scans - set (a list of) scans by index |
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463 | set_cycles - set (a list of) cycles by index |
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464 | set_beams - set (a list of) beamss by index |
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465 | set_ifs - set (a list of) ifs by index |
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466 | set_polarisations - set (a list of) polarisations by name |
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467 | or by index |
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468 | set_names - set a selection by name (wildcards allowed) |
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469 | set_tsys - set a selection by tsys thresholds |
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470 | set_query - set a selection by SQL-like query, e.g. BEAMNO==1 |
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471 | reset - unset all selections |
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472 | + - merge to selections |
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473 | |
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474 | [Math] Mainly functions which operate on more than one scantable |
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475 | |
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476 | average_time - return the (weighted) time average |
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477 | of a list of scans |
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478 | quotient - return the on/off quotient |
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479 | simple_math - simple mathematical operations on two scantables, |
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480 | 'add', 'sub', 'mul', 'div' |
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481 | quotient - build quotient of the given on and off scans |
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482 | (matched pairs and 1 off/n on are valid) |
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483 | merge - merge a list of scantables |
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484 | |
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485 | [Line Catalog] |
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486 | linecatalog - a linecatalog wrapper, taking an ASCII or |
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487 | internal format table |
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488 | summary - print a summary of the current selection |
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489 | set_name - select a subset by name pattern, e.g. '*OH*' |
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490 | set_strength_limits - select a subset by line strength limits |
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491 | set_frequency_limits - select a subset by frequency limits |
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492 | reset - unset all selections |
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493 | save - save the current subset to a table (internal |
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494 | format) |
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495 | get_row - get the name and frequency from a specific |
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496 | row in the table |
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497 | [Fitting] |
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498 | fitter |
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499 | auto_fit - return a scan where the function is |
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500 | applied to all Beams/IFs/Pols. |
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501 | commit - return a new scan where the fits have been |
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502 | commited. |
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503 | fit - execute the actual fitting process |
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504 | store_fit - store the fit parameters in the data (scantable) |
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505 | get_chi2 - get the Chi^2 |
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506 | set_scan - set the scantable to be fit |
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507 | set_function - set the fitting function |
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508 | set_parameters - set the parameters for the function(s), and |
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509 | set if they should be held fixed during fitting |
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510 | set_gauss_parameters - same as above but specialised for individual |
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511 | gaussian components |
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512 | get_parameters - get the fitted parameters |
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513 | plot - plot the resulting fit and/or components and |
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514 | residual |
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515 | [Plotter] |
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516 | asapplotter - a plotter for asap, default plotter is |
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517 | called 'plotter' |
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518 | plot - plot a scantable |
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519 | plot_lines - plot a linecatalog overlay |
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520 | save - save the plot to a file ('png' ,'ps' or 'eps') |
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521 | set_mode - set the state of the plotter, i.e. |
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522 | what is to be plotted 'colour stacked' |
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523 | and what 'panelled' |
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524 | set_selection - only plot a selected part of the data |
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525 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax] |
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526 | set_legend - specify user labels for the legend indeces |
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527 | set_title - specify user labels for the panel indeces |
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528 | set_abcissa - specify a user label for the abcissa |
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529 | set_ordinate - specify a user label for the ordinate |
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530 | set_layout - specify the multi-panel layout (rows,cols) |
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531 | set_colors - specify a set of colours to use |
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532 | set_linestyles - specify a set of linestyles to use if only |
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533 | using one color |
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534 | set_font - set general font properties, e.g. 'family' |
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535 | set_histogram - plot in historam style |
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536 | set_mask - set a plotting mask for a specific polarization |
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537 | text - draw text annotations either in data or relative |
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538 | coordinates |
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539 | arrow - draw arrow annotations either in data or relative |
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540 | coordinates |
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541 | axhline,axvline - draw horizontal/vertical lines |
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542 | axhspan,axvspan - draw horizontal/vertical regions |
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543 | |
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544 | xyplotter - matplotlib/pylab plotting functions |
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545 | |
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546 | [Reading files] |
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547 | reader - access rpfits/sdfits files |
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548 | open - attach reader to a file |
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549 | close - detach reader from file |
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550 | read - read in integrations |
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551 | summary - list info about all integrations |
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552 | |
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553 | [General] |
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554 | commands - this command |
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555 | print - print details about a variable |
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556 | list_scans - list all scantables created bt the user |
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557 | list_files - list all files readable by asap (default rpf) |
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558 | del - delete the given variable from memory |
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559 | range - create a list of values, e.g. |
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560 | range(3) = [0,1,2], range(2,5) = [2,3,4] |
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561 | help - print help for one of the listed functions |
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562 | execfile - execute an asap script, e.g. execfile('myscript') |
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563 | list_rcparameters - print out a list of possible values to be |
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564 | put into $HOME/.asaprc |
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565 | rc - set rc parameters from within asap |
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566 | mask_and,mask_or, |
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567 | mask_not - boolean operations on masks created with |
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568 | scantable.create_mask |
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569 | |
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570 | Note: |
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571 | How to use this with help: |
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572 | # function 'summary' |
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573 | [xxx] is just a category |
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574 | Every 'sub-level' in this list should be replaces by a '.' Period when |
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575 | using help |
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576 | Example: |
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577 | ASAP> help scantable # to get info on ths scantable |
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578 | ASAP> help scantable.summary # to get help on the scantable's |
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579 | ASAP> help average_time |
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580 | |
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581 | """ |
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582 | if rcParams['verbose']: |
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583 | try: |
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584 | from IPython.genutils import page as pager |
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585 | except ImportError: |
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586 | from pydoc import pager |
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587 | pager(x) |
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588 | else: |
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589 | print x |
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590 | return |
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591 | |
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592 | def welcome(): |
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593 | return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package |
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594 | |
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595 | Please report any bugs via: |
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596 | http://sourcecode.atnf.csiro.au/cgi-bin/trac_asap.cgi/newticket |
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597 | |
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598 | [IMPORTANT: ASAP is 0-based] |
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599 | Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__) |
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