1 | from asap._asap import sdtable |
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2 | from asap import rcParams |
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3 | from numarray import ones,zeros |
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4 | import sys |
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5 | |
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6 | class scantable(sdtable): |
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7 | """ |
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8 | The ASAP container for scans |
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9 | """ |
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10 | |
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11 | def __init__(self, filename, unit=None): |
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12 | """ |
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13 | Create a scantable from a saved one or make a reference |
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14 | Parameters: |
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15 | filename: the name of an asap table on disk |
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16 | or |
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17 | the name of a rpfits/sdfits/ms file |
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18 | (integrations within scans are auto averaged |
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19 | and the whole file is read) |
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20 | or |
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21 | [advanced] a reference to an existing |
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22 | scantable |
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23 | unit: brightness unit; must be consistent with K or Jy. |
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24 | Over-rides the default selected by the reader |
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25 | (input rpfits/sdfits/ms) or replaces the value |
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26 | in existing scantables |
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27 | """ |
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28 | self._vb = rcParams['verbose'] |
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29 | self._p = None |
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30 | from os import stat as st |
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31 | import stat |
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32 | if isinstance(filename,sdtable): |
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33 | sdtable.__init__(self, filename) |
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34 | if unit is not None: |
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35 | self.set_fluxunit(unit) |
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36 | else: |
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37 | try: |
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38 | mode = st(filename)[stat.ST_MODE] |
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39 | except OSError: |
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40 | print "File not found" |
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41 | return |
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42 | if stat.S_ISDIR(mode): |
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43 | # crude check if asap table |
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44 | if stat.S_ISREG(st(filename+'/table.info')[stat.ST_MODE]): |
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45 | sdtable.__init__(self, filename) |
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46 | if unit is not None: |
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47 | self.set_fluxunit(unit) |
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48 | else: |
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49 | print 'The given file is not a valid asap table' |
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50 | return |
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51 | else: |
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52 | autoav = rcParams['scantable.autoaverage'] |
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53 | |
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54 | from asap._asap import sdreader |
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55 | ifSel = -1 |
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56 | beamSel = -1 |
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57 | r = sdreader(filename,ifSel,beamSel) |
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58 | print 'Importing data...' |
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59 | r.read([-1]) |
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60 | tbl = r.getdata() |
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61 | if unit is not None: |
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62 | tbl.set_fluxunit(unit) |
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63 | if autoav: |
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64 | from asap._asap import average |
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65 | tmp = tuple([tbl]) |
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66 | print 'Auto averaging integrations...' |
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67 | tbl2 = average(tmp,(),True,'none') |
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68 | sdtable.__init__(self,tbl2) |
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69 | del r,tbl |
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70 | else: |
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71 | sdtable.__init__(self,tbl) |
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72 | |
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73 | def save(self, name=None, format=None, overwrite=False): |
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74 | """ |
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75 | Store the scantable on disk. This can be an asap (aips++) Table, SDFITS, |
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76 | Image FITS or MS2 format. |
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77 | Parameters: |
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78 | name: the name of the outputfile. For format="FITS" this |
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79 | is the directory file name into which all the files will |
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80 | be written (default is 'asap_FITS') |
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81 | format: an optional file format. Default is ASAP. |
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82 | Allowed are - 'ASAP' (save as ASAP [aips++] Table), |
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83 | 'SDFITS' (save as SDFITS file) |
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84 | 'FITS' (saves each row as a FITS Image) |
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85 | 'ASCII' (saves as ascii text file) |
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86 | 'MS2' (saves as an aips++ |
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87 | MeasurementSet V2) |
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88 | overwrite: if the file should be overwritten if it exists. |
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89 | The default False is to return with warning |
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90 | without writing the output |
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91 | Example: |
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92 | scan.save('myscan.asap') |
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93 | scan.save('myscan.sdfits','SDFITS') |
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94 | """ |
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95 | if format is None: format = rcParams['scantable.save'] |
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96 | suffix = '.'+format.lower() |
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97 | if name is None or name =="": |
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98 | name = 'scantable'+suffix |
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99 | print "No filename given. Using default name %s..." % name |
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100 | from os import path |
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101 | if path.isfile(name) or path.isdir(name): |
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102 | if not overwrite: |
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103 | print "File %s already exists." % name |
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104 | return |
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105 | if format == 'ASAP': |
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106 | self._save(name) |
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107 | else: |
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108 | from asap._asap import sdwriter as _sw |
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109 | w = _sw(format) |
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110 | w.write(self, name) |
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111 | return |
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112 | |
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113 | def copy(self): |
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114 | """ |
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115 | Return a copy of this scantable. |
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116 | Parameters: |
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117 | none |
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118 | Example: |
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119 | copiedscan = scan.copy() |
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120 | """ |
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121 | sd = scantable(sdtable._copy(self)) |
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122 | return sd |
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123 | |
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124 | def get_scan(self, scanid=None): |
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125 | """ |
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126 | Return a specific scan (by scanno) or collection of scans (by |
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127 | source name) in a new scantable. |
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128 | Parameters: |
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129 | scanid: a scanno or a source name |
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130 | Example: |
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131 | scan.get_scan('323p459') |
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132 | # gets all scans containing the source '323p459' |
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133 | """ |
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134 | if scanid is None: |
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135 | print "Please specify a scan no or name to retrieve from the scantable" |
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136 | try: |
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137 | if type(scanid) is str: |
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138 | s = sdtable._getsource(self,scanid) |
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139 | return scantable(s) |
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140 | elif type(scanid) is int: |
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141 | s = sdtable._getscan(self,scanid) |
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142 | return scantable(s) |
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143 | except RuntimeError: |
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144 | print "Couldn't find any match." |
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145 | |
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146 | def __str__(self): |
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147 | return sdtable._summary(self) |
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148 | |
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149 | def summary(self,filename=None): |
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150 | """ |
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151 | Print a summary of the contents of this scantable. |
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152 | Parameters: |
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153 | filename: the name of a file to write the putput to |
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154 | Default - no file output |
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155 | """ |
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156 | info = sdtable._summary(self) |
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157 | if filename is not None: |
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158 | if filename is "": |
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159 | filename = 'scantable_summary.txt' |
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160 | data = open(filename, 'w') |
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161 | data.write(info) |
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162 | data.close() |
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163 | print info |
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164 | |
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165 | def set_cursor(self, thebeam=0,theif=0,thepol=0): |
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166 | """ |
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167 | Set the spectrum for individual operations. |
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168 | Parameters: |
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169 | thebeam,theif,thepol: a number |
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170 | Example: |
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171 | scan.set_cursor(0,0,1) |
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172 | pol1sig = scan.stats(all=False) # returns std dev for beam=0 |
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173 | # if=0, pol=1 |
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174 | """ |
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175 | self.setbeam(thebeam) |
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176 | self.setpol(thepol) |
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177 | self.setif(theif) |
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178 | return |
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179 | |
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180 | def get_cursor(self): |
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181 | """ |
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182 | Return/print a the current 'cursor' into the Beam/IF/Pol cube. |
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183 | Parameters: |
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184 | none |
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185 | Returns: |
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186 | a list of values (currentBeam,currentIF,currentPol) |
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187 | Example: |
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188 | none |
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189 | """ |
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190 | i = self.getbeam() |
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191 | j = self.getif() |
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192 | k = self.getpol() |
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193 | if self._vb: |
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194 | print "--------------------------------------------------" |
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195 | print " Cursor position" |
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196 | print "--------------------------------------------------" |
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197 | out = 'Beam=%d IF=%d Pol=%d ' % (i,j,k) |
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198 | print out |
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199 | return i,j,k |
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200 | |
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201 | def stats(self, stat='stddev', mask=None, all=None): |
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202 | """ |
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203 | Determine the specified statistic of the current beam/if/pol |
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204 | Takes a 'mask' as an optional parameter to specify which |
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205 | channels should be excluded. |
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206 | Parameters: |
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207 | stat: 'min', 'max', 'sumsq', 'sum', 'mean' |
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208 | 'var', 'stddev', 'avdev', 'rms', 'median' |
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209 | mask: an optional mask specifying where the statistic |
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210 | should be determined. |
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211 | all: if true show all (default or .asaprc) rather |
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212 | that the cursor selected spectrum of Beam/IF/Pol |
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213 | |
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214 | Example: |
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215 | scan.set_unit('channel') |
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216 | msk = scan.create_mask([100,200],[500,600]) |
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217 | scan.stats(stat='mean', mask=m) |
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218 | """ |
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219 | if all is None: all = rcParams['scantable.allaxes'] |
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220 | from asap._asap import stats as _stats |
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221 | from numarray import array,zeros,Float |
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222 | if mask == None: |
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223 | mask = ones(self.nchan()) |
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224 | axes = ['Beam','IF','Pol','Time'] |
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225 | |
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226 | if all: |
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227 | n = self.nbeam()*self.nif()*self.npol()*self.nrow() |
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228 | shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()] |
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229 | arr = array(zeros(n),shape=shp,type=Float) |
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230 | |
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231 | for i in range(self.nbeam()): |
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232 | self.setbeam(i) |
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233 | for j in range(self.nif()): |
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234 | self.setif(j) |
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235 | for k in range(self.npol()): |
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236 | self.setpol(k) |
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237 | arr[i,j,k,:] = _stats(self,mask,stat,-1) |
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238 | retval = {'axes': axes, 'data': arr, 'cursor':None} |
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239 | tm = [self._gettime(val) for val in range(self.nrow())] |
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240 | if self._vb: |
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241 | self._print_values(retval,stat,tm) |
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242 | return retval |
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243 | |
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244 | else: |
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245 | i,j,k = (self.getbeam(),self.getif(),self.getpol()) |
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246 | statval = _stats(self,mask,stat,-1) |
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247 | out = '' |
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248 | for l in range(self.nrow()): |
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249 | tm = self._gettime(l) |
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250 | out += 'Time[%s]:\n' % (tm) |
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251 | if self.nbeam() > 1: out += ' Beam[%d] ' % (i) |
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252 | if self.nif() > 1: out += ' IF[%d] ' % (j) |
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253 | if self.npol() > 1: out += ' Pol[%d] ' % (k) |
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254 | out += '= %3.3f\n' % (statval[l]) |
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255 | out += "--------------------------------------------------\n" |
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256 | |
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257 | if self._vb: |
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258 | print "--------------------------------------------------" |
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259 | print " ",stat |
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260 | print "--------------------------------------------------" |
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261 | print out |
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262 | retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)} |
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263 | return retval |
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264 | |
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265 | def stddev(self,mask=None, all=None): |
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266 | """ |
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267 | Determine the standard deviation of the current beam/if/pol |
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268 | Takes a 'mask' as an optional parameter to specify which |
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269 | channels should be excluded. |
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270 | Parameters: |
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271 | mask: an optional mask specifying where the standard |
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272 | deviation should be determined. |
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273 | all: optional flag to show all or a cursor selected |
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274 | spectrum of Beam/IF/Pol. Default is all or taken |
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275 | from .asaprc |
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276 | |
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277 | Example: |
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278 | scan.set_unit('channel') |
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279 | msk = scan.create_mask([100,200],[500,600]) |
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280 | scan.stddev(mask=m) |
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281 | """ |
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282 | if all is None: all = rcParams['scantable.allaxes'] |
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283 | return self.stats(stat='stddev',mask=mask, all=all); |
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284 | |
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285 | def get_tsys(self, all=None): |
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286 | """ |
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287 | Return the System temperatures. |
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288 | Parameters: |
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289 | all: optional parameter to get the Tsys values for all |
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290 | Beams/IFs/Pols (default) or just the one selected |
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291 | with scantable.set_cursor() |
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292 | [True or False] |
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293 | Returns: |
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294 | a list of Tsys values. |
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295 | """ |
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296 | if all is None: all = rcParams['scantable.allaxes'] |
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297 | from numarray import array,zeros,Float |
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298 | axes = ['Beam','IF','Pol','Time'] |
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299 | |
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300 | if all: |
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301 | n = self.nbeam()*self.nif()*self.npol()*self.nrow() |
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302 | shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()] |
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303 | arr = array(zeros(n),shape=shp,type=Float) |
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304 | |
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305 | for i in range(self.nbeam()): |
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306 | self.setbeam(i) |
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307 | for j in range(self.nif()): |
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308 | self.setif(j) |
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309 | for k in range(self.npol()): |
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310 | self.setpol(k) |
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311 | arr[i,j,k,:] = self._gettsys() |
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312 | retval = {'axes': axes, 'data': arr, 'cursor':None} |
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313 | tm = [self._gettime(val) for val in range(self.nrow())] |
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314 | if self._vb: |
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315 | self._print_values(retval,'Tsys',tm) |
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316 | return retval |
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317 | |
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318 | else: |
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319 | i,j,k = (self.getbeam(),self.getif(),self.getpol()) |
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320 | statval = self._gettsys() |
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321 | out = '' |
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322 | for l in range(self.nrow()): |
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323 | tm = self._gettime(l) |
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324 | out += 'Time[%s]:\n' % (tm) |
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325 | if self.nbeam() > 1: out += ' Beam[%d] ' % (i) |
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326 | if self.nif() > 1: out += ' IF[%d] ' % (j) |
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327 | if self.npol() > 1: out += ' Pol[%d] ' % (k) |
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328 | out += '= %3.3f\n' % (statval[l]) |
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329 | out += "--------------------------------------------------\n" |
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330 | |
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331 | if self._vb: |
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332 | print "--------------------------------------------------" |
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333 | print " TSys" |
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334 | print "--------------------------------------------------" |
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335 | print out |
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336 | retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)} |
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337 | return retval |
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338 | |
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339 | def get_time(self): |
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340 | """ |
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341 | Get a list of time stamps for the observations. |
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342 | Return a string for each integration in the scantable. |
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343 | Parameters: |
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344 | none |
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345 | Example: |
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346 | none |
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347 | """ |
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348 | out = [] |
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349 | for i in range(self.nrow()): |
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350 | out.append(self._gettime(i)) |
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351 | return out |
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352 | |
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353 | def set_unit(self, unit='channel'): |
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354 | """ |
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355 | Set the unit for all following operations on this scantable |
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356 | Parameters: |
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357 | unit: optional unit, default is 'channel' |
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358 | one of '*Hz','km/s','channel', '' |
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359 | """ |
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360 | |
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361 | if unit in ['','pixel', 'channel']: |
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362 | unit = '' |
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363 | inf = list(self._getcoordinfo()) |
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364 | inf[0] = unit |
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365 | self._setcoordinfo(inf) |
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366 | if self._p: self.plot() |
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367 | |
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368 | def set_doppler(self, doppler='RADIO'): |
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369 | """ |
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370 | Set the doppler for all following operations on this scantable. |
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371 | Parameters: |
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372 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
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373 | """ |
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374 | |
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375 | inf = list(self._getcoordinfo()) |
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376 | inf[2] = doppler |
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377 | self._setcoordinfo(inf) |
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378 | if self._p: self.plot() |
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379 | |
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380 | def set_freqframe(self, frame=None): |
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381 | """ |
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382 | Set the frame type of the Spectral Axis. |
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383 | Parameters: |
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384 | frame: an optional frame type, default 'LSRK'. |
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385 | Examples: |
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386 | scan.set_freqframe('BARY') |
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387 | """ |
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388 | if not frame: frame = rcParams['scantable.freqframe'] |
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389 | valid = ['REST','TOPO','LSRD','LSRK','BARY', \ |
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390 | 'GEO','GALACTO','LGROUP','CMB'] |
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391 | if frame in valid: |
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392 | inf = list(self._getcoordinfo()) |
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393 | inf[1] = frame |
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394 | self._setcoordinfo(inf) |
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395 | else: |
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396 | print "Please specify a valid freq type. Valid types are:\n",valid |
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397 | |
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398 | def get_unit(self): |
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399 | """ |
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400 | Get the default unit set in this scantable |
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401 | Parameters: |
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402 | Returns: |
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403 | A unit string |
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404 | """ |
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405 | inf = self._getcoordinfo() |
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406 | unit = inf[0] |
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407 | if unit == '': unit = 'channel' |
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408 | return unit |
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409 | |
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410 | def get_abcissa(self, rowno=0): |
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411 | """ |
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412 | Get the abcissa in the current coordinate setup for the currently |
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413 | selected Beam/IF/Pol |
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414 | Parameters: |
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415 | rowno: an optional row number in the scantable. Default is the |
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416 | first row, i.e. rowno=0 |
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417 | Returns: |
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418 | The abcissa values and it's format string. |
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419 | """ |
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420 | abc = self._getabcissa(rowno) |
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421 | lbl = self._getabcissalabel(rowno) |
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422 | return abc, lbl |
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423 | |
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424 | def create_mask(self, *args, **kwargs): |
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425 | """ |
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426 | Compute and return a mask based on [min,max] windows. |
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427 | The specified windows are to be INCLUDED, when the mask is |
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428 | applied. |
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429 | Parameters: |
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430 | [min,max],[min2,max2],... |
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431 | Pairs of start/end points specifying the regions |
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432 | to be masked |
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433 | invert: optional argument. If specified as True, |
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434 | return an inverted mask, i.e. the regions |
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435 | specified are EXCLUDED |
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436 | Example: |
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437 | scan.set_unit('channel') |
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438 | |
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439 | a) |
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440 | msk = scan.set_mask([400,500],[800,900]) |
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441 | # masks everything outside 400 and 500 |
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442 | # and 800 and 900 in the unit 'channel' |
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443 | |
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444 | b) |
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445 | msk = scan.set_mask([400,500],[800,900], invert=True) |
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446 | # masks the regions between 400 and 500 |
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447 | # and 800 and 900 in the unit 'channel' |
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448 | |
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449 | """ |
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450 | u = self._getcoordinfo()[0] |
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451 | if self._vb: |
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452 | if u == "": u = "channel" |
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453 | print "The current mask window unit is", u |
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454 | n = self.nchan() |
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455 | data = self._getabcissa() |
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456 | msk = zeros(n) |
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457 | for window in args: |
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458 | if (len(window) != 2 or window[0] > window[1] ): |
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459 | print "A window needs to be defined as [min,max]" |
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460 | return |
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461 | for i in range(n): |
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462 | if data[i] >= window[0] and data[i] < window[1]: |
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463 | msk[i] = 1 |
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464 | if kwargs.has_key('invert'): |
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465 | if kwargs.get('invert'): |
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466 | from numarray import logical_not |
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467 | msk = logical_not(msk) |
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468 | return msk |
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469 | |
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470 | def set_restfreqs(self, freqs, unit='Hz'): |
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471 | """ |
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472 | Set the restfrequency(s) for this scantable. |
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473 | Parameters: |
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474 | freqs: one or more frequencies |
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475 | unit: optional 'unit', default 'Hz' |
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476 | Example: |
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477 | scan.set_restfreqs([1000000000.0]) |
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478 | """ |
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479 | if type(freqs) is float or int: |
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480 | freqs = (freqs) |
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481 | sdtable._setrestfreqs(self,freqs, unit) |
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482 | return |
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483 | def get_restfreqs(self): |
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484 | """ |
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485 | Get the restfrequency(s) stored in this scantable. |
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486 | The return value(s) are always of unit 'Hz' |
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487 | Parameters: |
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488 | none |
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489 | Returns: |
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490 | a list of doubles |
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491 | """ |
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492 | return list(self._getrestfreqs()) |
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493 | |
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494 | def flag_spectrum(self, thebeam, theif, thepol): |
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495 | """ |
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496 | This flags a selected spectrum in the scan 'for good'. |
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497 | USE WITH CARE - not reversible. |
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498 | Use masks for non-permanent exclusion of channels. |
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499 | Parameters: |
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500 | thebeam,theif,thepol: all have to be explicitly |
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501 | specified |
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502 | Example: |
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503 | scan.flag_spectrum(0,0,1) |
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504 | flags the spectrum for Beam=0, IF=0, Pol=1 |
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505 | """ |
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506 | if (thebeam < self.nbeam() and theif < self.nif() and thepol < self.npol()): |
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507 | stable.setbeam(thebeam) |
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508 | stable.setif(theif) |
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509 | stable.setpol(thepol) |
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510 | stable._flag(self) |
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511 | else: |
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512 | print "Please specify a valid (Beam/IF/Pol)" |
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513 | return |
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514 | |
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515 | def plot(self, what='spectrum',col='Pol', panel=None): |
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516 | """ |
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517 | Plot the spectra contained in the scan. Alternatively you can also |
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518 | Plot Tsys vs Time |
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519 | Parameters: |
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520 | what: a choice of 'spectrum' (default) or 'tsys' |
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521 | col: which out of Beams/IFs/Pols should be colour stacked |
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522 | panel: set up multiple panels, currently not working. |
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523 | """ |
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524 | print "Warning! Not fully functional. Use plotter.plot() instead" |
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525 | |
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526 | validcol = {'Beam':self.nbeam(),'IF':self.nif(),'Pol':self.npol()} |
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527 | |
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528 | validyax = ['spectrum','tsys'] |
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529 | from asap.asaplot import ASAPlot |
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530 | if not self._p: |
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531 | self._p = ASAPlot() |
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532 | #print "Plotting not enabled" |
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533 | #return |
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534 | if self._p.is_dead: |
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535 | del self._p |
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536 | self._p = ASAPlot() |
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537 | npan = 1 |
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538 | x = None |
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539 | if what == 'tsys': |
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540 | n = self.nrow() |
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541 | if n < 2: |
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542 | print "Only one integration. Can't plot." |
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543 | return |
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544 | self._p.hold() |
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545 | self._p.clear() |
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546 | if panel == 'Time': |
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547 | npan = self.nrow() |
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548 | self._p.set_panels(rows=npan) |
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549 | xlab,ylab,tlab = None,None,None |
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550 | self._vb = False |
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551 | sel = self.get_cursor() |
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552 | for i in range(npan): |
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553 | if npan > 1: |
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554 | self._p.subplot(i) |
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555 | for j in range(validcol[col]): |
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556 | x = None |
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557 | y = None |
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558 | m = None |
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559 | tlab = self._getsourcename(i) |
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560 | import re |
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561 | tlab = re.sub('_S','',tlab) |
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562 | if col == 'Beam': |
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563 | self.setbeam(j) |
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564 | elif col == 'IF': |
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565 | self.setif(j) |
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566 | elif col == 'Pol': |
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567 | self.setpol(j) |
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568 | if what == 'tsys': |
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569 | x = range(self.nrow()) |
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570 | xlab = 'Time [pixel]' |
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571 | m = list(ones(len(x))) |
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572 | y = [] |
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573 | ylab = r'$T_{sys}$' |
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574 | for k in range(len(x)): |
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575 | y.append(self._gettsys(k)) |
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576 | else: |
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577 | x,xlab = self.get_abcissa(i) |
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578 | y = self._getspectrum(i) |
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579 | ylab = r'Flux' |
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580 | m = self._getmask(i) |
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581 | llab = col+' '+str(j) |
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582 | self._p.set_line(label=llab) |
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583 | self._p.plot(x,y,m) |
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584 | self._p.set_axes('xlabel',xlab) |
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585 | self._p.set_axes('ylabel',ylab) |
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586 | self._p.set_axes('title',tlab) |
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587 | self._p.release() |
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588 | self.set_cursor(sel[0],sel[1],sel[2]) |
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589 | self._vb = rcParams['verbose'] |
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590 | return |
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591 | |
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592 | print out |
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593 | |
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594 | def _print_values(self, dat, label='', timestamps=[]): |
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595 | d = dat['data'] |
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596 | a = dat['axes'] |
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597 | shp = d.getshape() |
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598 | out = '' |
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599 | for i in range(shp[3]): |
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600 | out += '%s [%s]:\n' % (a[3],timestamps[i]) |
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601 | t = d[:,:,:,i] |
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602 | for j in range(shp[0]): |
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603 | if shp[0] > 1: out += ' %s[%d] ' % (a[0],j) |
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604 | for k in range(shp[1]): |
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605 | if shp[1] > 1: out += ' %s[%d] ' % (a[1],k) |
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606 | for l in range(shp[2]): |
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607 | if shp[2] > 1: out += ' %s[%d] ' % (a[2],l) |
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608 | out += '= %3.3f\n' % (t[j,k,l]) |
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609 | out += "--------------------------------------------------\n" |
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610 | print "--------------------------------------------------" |
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611 | print " ", label |
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612 | print "--------------------------------------------------" |
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613 | print out |
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