1 | from asap._asap import sdtable |
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2 | from asap import rcParams |
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3 | from asap import print_log |
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4 | from numarray import ones,zeros |
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5 | import sys |
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6 | |
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7 | class scantable(sdtable): |
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8 | """ |
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9 | The ASAP container for scans |
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10 | """ |
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11 | |
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12 | def __init__(self, filename, average=None, unit=None): |
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13 | """ |
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14 | Create a scantable from a saved one or make a reference |
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15 | Parameters: |
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16 | filename: the name of an asap table on disk |
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17 | or |
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18 | the name of a rpfits/sdfits/ms file |
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19 | (integrations within scans are auto averaged |
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20 | and the whole file is read) |
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21 | or |
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22 | [advanced] a reference to an existing |
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23 | scantable |
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24 | average: average all integrations withinb a scan on read. |
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25 | The default (True) is taken from .asaprc. |
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26 | unit: brightness unit; must be consistent with K or Jy. |
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27 | Over-rides the default selected by the reader |
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28 | (input rpfits/sdfits/ms) or replaces the value |
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29 | in existing scantables |
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30 | """ |
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31 | if average is None or type(average) is not bool: |
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32 | average = rcParams['scantable.autoaverage'] |
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33 | |
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34 | varlist = vars() |
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35 | self._p = None |
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36 | from asap import asaplog |
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37 | if isinstance(filename,sdtable): |
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38 | sdtable.__init__(self, filename) |
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39 | if unit is not None: |
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40 | self.set_fluxunit(unit) |
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41 | else: |
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42 | import os.path |
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43 | if not os.path.exists(filename): |
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44 | s = "File '%s' not found." % (filename) |
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45 | if rcParams['verbose']: |
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46 | asaplog.push(s) |
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47 | print asaplog.pop().strip() |
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48 | return |
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49 | raise IOError(s) |
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50 | filename = os.path.expandvars(filename) |
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51 | if os.path.isdir(filename): |
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52 | # crude check if asap table |
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53 | if os.path.exists(filename+'/table.info'): |
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54 | sdtable.__init__(self, filename) |
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55 | if unit is not None: |
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56 | self.set_fluxunit(unit) |
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57 | else: |
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58 | msg = "The given file '%s'is not a valid asap table." % (filename) |
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59 | if rcParams['verbose']: |
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60 | print msg |
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61 | return |
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62 | else: |
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63 | raise IOError(msg) |
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64 | else: |
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65 | from asap._asap import sdreader |
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66 | ifSel = -1 |
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67 | beamSel = -1 |
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68 | r = sdreader() |
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69 | r._open(filename,ifSel,beamSel) |
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70 | asaplog.push('Importing data...') |
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71 | print_log() |
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72 | r._read([-1]) |
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73 | tbl = r._getdata() |
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74 | if unit is not None: |
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75 | tbl.set_fluxunit(unit) |
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76 | if average: |
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77 | from asap._asap import average as _av |
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78 | asaplog.push('Auto averaging integrations...') |
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79 | print_log() |
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80 | tbl2 = _av((tbl,),(),True,'none') |
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81 | sdtable.__init__(self,tbl2) |
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82 | del tbl2 |
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83 | else: |
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84 | sdtable.__init__(self,tbl) |
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85 | del r,tbl |
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86 | self._add_history("scantable", varlist) |
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87 | print_log() |
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88 | |
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89 | def save(self, name=None, format=None, stokes=False, overwrite=False): |
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90 | """ |
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91 | Store the scantable on disk. This can be an asap (aips++) Table, SDFITS, |
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92 | Image FITS or MS2 format. |
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93 | Parameters: |
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94 | name: the name of the outputfile. For format="FITS" this |
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95 | is the directory file name into which all the files |
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96 | will be written (default is 'asap_FITS'). For format |
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97 | "ASCII" this is the root file name (data in 'name'.txt |
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98 | and header in 'name'_header.txt) |
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99 | format: an optional file format. Default is ASAP. |
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100 | Allowed are - 'ASAP' (save as ASAP [aips++] Table), |
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101 | 'SDFITS' (save as SDFITS file) |
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102 | 'FITS' (saves each row as a FITS Image) |
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103 | 'ASCII' (saves as ascii text file) |
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104 | 'MS2' (saves as an aips++ |
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105 | MeasurementSet V2) |
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106 | stokes: Convert to Stokes parameters (only available |
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107 | currently with FITS and ASCII formats. |
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108 | Default is False. |
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109 | overwrite: If the file should be overwritten if it exists. |
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110 | The default False is to return with warning |
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111 | without writing the output. USE WITH CARE. |
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112 | Example: |
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113 | scan.save('myscan.asap') |
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114 | scan.save('myscan.sdfits','SDFITS') |
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115 | """ |
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116 | from os import path |
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117 | if format is None: format = rcParams['scantable.save'] |
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118 | suffix = '.'+format.lower() |
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119 | if name is None or name =="": |
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120 | name = 'scantable'+suffix |
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121 | from asap import asaplog |
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122 | msg = "No filename given. Using default name %s..." % name |
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123 | asaplog.push(msg) |
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124 | name = path.expandvars(name) |
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125 | if path.isfile(name) or path.isdir(name): |
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126 | if not overwrite: |
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127 | msg = "File %s exists." % name |
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128 | if rcParams['verbose']: |
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129 | print msg |
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130 | return |
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131 | else: |
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132 | raise IOError(msg) |
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133 | format2 = format.upper() |
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134 | if format2 == 'ASAP': |
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135 | self._save(name) |
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136 | else: |
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137 | from asap._asap import sdwriter as _sw |
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138 | w = _sw(format2) |
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139 | w.write(self, name, stokes) |
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140 | |
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141 | print_log() |
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142 | return |
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143 | |
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144 | def copy(self): |
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145 | """ |
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146 | Return a copy of this scantable. |
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147 | Parameters: |
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148 | none |
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149 | Example: |
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150 | copiedscan = scan.copy() |
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151 | """ |
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152 | sd = scantable(sdtable._copy(self)) |
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153 | return sd |
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154 | |
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155 | def get_scan(self, scanid=None): |
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156 | """ |
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157 | Return a specific scan (by scanno) or collection of scans (by |
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158 | source name) in a new scantable. |
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159 | Parameters: |
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160 | scanid: a (list of) scanno or a source name, unix-style |
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161 | patterns are accepted for source name matching, e.g. |
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162 | '*_R' gets all 'ref scans |
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163 | Example: |
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164 | # get all scans containing the source '323p459' |
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165 | newscan = scan.get_scan('323p459') |
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166 | # get all 'off' scans |
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167 | refscans = scan.get_scan('*_R') |
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168 | # get a susbset of scans by scanno (as listed in scan.summary()) |
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169 | newscan = scan.get_scan([0,2,7,10]) |
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170 | """ |
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171 | if scanid is None: |
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172 | if rcParams['verbose']: |
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173 | print "Please specify a scan no or name to retrieve from the scantable" |
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174 | return |
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175 | else: |
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176 | raise RuntimeError("No scan given") |
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177 | |
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178 | try: |
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179 | if type(scanid) is str: |
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180 | s = sdtable._getsource(self,scanid) |
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181 | return scantable(s) |
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182 | elif type(scanid) is int: |
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183 | s = sdtable._getscan(self,[scanid]) |
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184 | return scantable(s) |
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185 | elif type(scanid) is list: |
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186 | s = sdtable._getscan(self,scanid) |
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187 | return scantable(s) |
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188 | else: |
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189 | msg = "Illegal scanid type, use 'int' or 'list' if ints." |
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190 | if rcParams['verbose']: |
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191 | print msg |
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192 | else: |
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193 | raise TypeError(msg) |
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194 | except RuntimeError: |
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195 | if rcParams['verbose']: print "Couldn't find any match." |
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196 | else: raise |
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197 | |
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198 | def __str__(self): |
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199 | return sdtable._summary(self,True) |
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200 | |
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201 | def summary(self,filename=None, verbose=None): |
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202 | """ |
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203 | Print a summary of the contents of this scantable. |
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204 | Parameters: |
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205 | filename: the name of a file to write the putput to |
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206 | Default - no file output |
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207 | verbose: print extra info such as the frequency table |
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208 | The default (False) is taken from .asaprc |
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209 | """ |
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210 | info = sdtable._summary(self, verbose) |
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211 | if verbose is None: verbose = rcParams['scantable.verbosesummary'] |
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212 | if filename is not None: |
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213 | if filename is "": |
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214 | filename = 'scantable_summary.txt' |
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215 | from os.path import expandvars, isdir |
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216 | filename = expandvars(filename) |
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217 | if not isdir(filename): |
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218 | data = open(filename, 'w') |
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219 | data.write(info) |
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220 | data.close() |
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221 | else: |
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222 | msg = "Illegal file name '%s'." % (filename) |
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223 | if rcParams['verbose']: |
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224 | print msg |
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225 | else: |
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226 | raise IOError(msg) |
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227 | if rcParams['verbose']: |
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228 | try: |
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229 | from IPython.genutils import page as pager |
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230 | except ImportError: |
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231 | from pydoc import pager |
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232 | pager(info) |
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233 | else: |
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234 | return info |
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235 | |
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236 | def set_cursor(self, beam=0, IF=0, pol=0): |
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237 | """ |
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238 | Set the spectrum for individual operations. |
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239 | Parameters: |
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240 | beam, IF, pol: a number |
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241 | Example: |
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242 | scan.set_cursor(0,0,1) |
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243 | pol1sig = scan.stats(all=False) # returns std dev for beam=0 |
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244 | # if=0, pol=1 |
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245 | """ |
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246 | varlist = vars() |
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247 | self.setbeam(beam) |
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248 | self.setpol(pol) |
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249 | self.setif(IF) |
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250 | self._add_history("set_cursor",varlist) |
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251 | return |
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252 | |
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253 | def get_cursor(self): |
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254 | """ |
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255 | Return/print a the current 'cursor' into the Beam/IF/Pol cube. |
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256 | Parameters: |
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257 | none |
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258 | Returns: |
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259 | a list of values (currentBeam,currentIF,currentPol) |
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260 | Example: |
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261 | none |
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262 | """ |
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263 | i = self.getbeam() |
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264 | j = self.getif() |
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265 | k = self.getpol() |
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266 | from asap import asaplog |
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267 | out = "--------------------------------------------------\n" |
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268 | out += " Cursor position\n" |
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269 | out += "--------------------------------------------------\n" |
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270 | out += 'Beam=%d IF=%d Pol=%d ' % (i,j,k) |
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271 | asaplog.push(out) |
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272 | print_log() |
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273 | return i,j,k |
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274 | |
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275 | def stats(self, stat='stddev', mask=None, allaxes=None): |
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276 | """ |
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277 | Determine the specified statistic of the current beam/if/pol |
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278 | Takes a 'mask' as an optional parameter to specify which |
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279 | channels should be excluded. |
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280 | Parameters: |
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281 | stat: 'min', 'max', 'sumsq', 'sum', 'mean' |
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282 | 'var', 'stddev', 'avdev', 'rms', 'median' |
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283 | mask: an optional mask specifying where the statistic |
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284 | should be determined. |
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285 | allaxes: if True apply to all spectra. Otherwise |
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286 | apply only to the selected (beam/pol/if)spectra only. |
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287 | The default is taken from .asaprc (True if none) |
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288 | Example: |
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289 | scan.set_unit('channel') |
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290 | msk = scan.create_mask([100,200],[500,600]) |
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291 | scan.stats(stat='mean', mask=m) |
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292 | """ |
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293 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
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294 | from asap._asap import stats as _stats |
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295 | from numarray import array,zeros,Float |
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296 | if mask == None: |
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297 | mask = ones(self.nchan()) |
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298 | axes = ['Beam','IF','Pol','Time'] |
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299 | |
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300 | beamSel,IFSel,polSel = (self.getbeam(),self.getif(),self.getpol()) |
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301 | if allaxes: |
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302 | n = self.nbeam()*self.nif()*self.npol()*self.nrow() |
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303 | shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()] |
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304 | arr = array(zeros(n),shape=shp,type=Float) |
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305 | |
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306 | for i in range(self.nbeam()): |
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307 | self.setbeam(i) |
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308 | for j in range(self.nif()): |
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309 | self.setif(j) |
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310 | for k in range(self.npol()): |
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311 | self.setpol(k) |
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312 | arr[i,j,k,:] = _stats(self,mask,stat,-1) |
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313 | retval = {'axes': axes, 'data': arr, 'cursor':None} |
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314 | tm = [self._gettime(val) for val in range(self.nrow())] |
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315 | if rcParams['verbose']: |
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316 | self._print_values(retval,stat,tm) |
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317 | self.setbeam(beamSel) |
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318 | self.setif(IFSel) |
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319 | self.setpol(polSel) |
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320 | return retval |
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321 | |
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322 | else: |
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323 | statval = _stats(self,mask,stat,-1) |
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324 | out = '' |
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325 | for l in range(self.nrow()): |
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326 | tm = self._gettime(l) |
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327 | out += 'Time[%s]:\n' % (tm) |
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328 | if self.nbeam() > 1: out += ' Beam[%d] ' % (beamSel) |
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329 | if self.nif() > 1: out += ' IF[%d] ' % (IFSel) |
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330 | if self.npol() > 1: out += ' Pol[%d] ' % (polSel) |
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331 | out += '= %3.3f\n' % (statval[l]) |
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332 | out += "--------------------------------------------------\n" |
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333 | |
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334 | if rcParams['verbose']: |
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335 | print "--------------------------------------------------" |
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336 | print " ",stat |
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337 | print "--------------------------------------------------" |
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338 | print out |
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339 | retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)} |
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340 | return retval |
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341 | |
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342 | def stddev(self,mask=None, allaxes=None): |
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343 | """ |
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344 | Determine the standard deviation of the current beam/if/pol |
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345 | Takes a 'mask' as an optional parameter to specify which |
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346 | channels should be excluded. |
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347 | Parameters: |
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348 | mask: an optional mask specifying where the standard |
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349 | deviation should be determined. |
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350 | allaxes: optional flag to show all or a cursor selected |
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351 | spectrum of Beam/IF/Pol. Default is all or taken |
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352 | from .asaprc |
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353 | |
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354 | Example: |
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355 | scan.set_unit('channel') |
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356 | msk = scan.create_mask([100,200],[500,600]) |
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357 | scan.stddev(mask=m) |
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358 | """ |
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359 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
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360 | return self.stats(stat='stddev',mask=mask, allaxes=allaxes); |
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361 | |
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362 | def get_tsys(self, allaxes=None): |
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363 | """ |
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364 | Return the System temperatures. |
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365 | Parameters: |
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366 | allaxes: if True apply to all spectra. Otherwise |
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367 | apply only to the selected (beam/pol/if)spectra only. |
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368 | The default is taken from .asaprc (True if none) |
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369 | Returns: |
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370 | a list of Tsys values. |
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371 | """ |
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372 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
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373 | from numarray import array,zeros,Float |
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374 | axes = ['Beam','IF','Pol','Time'] |
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375 | |
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376 | if allaxes: |
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377 | n = self.nbeam()*self.nif()*self.npol()*self.nrow() |
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378 | shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()] |
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379 | arr = array(zeros(n),shape=shp,type=Float) |
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380 | |
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381 | for i in range(self.nbeam()): |
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382 | self.setbeam(i) |
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383 | for j in range(self.nif()): |
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384 | self.setif(j) |
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385 | for k in range(self.npol()): |
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386 | self.setpol(k) |
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387 | arr[i,j,k,:] = self._gettsys() |
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388 | retval = {'axes': axes, 'data': arr, 'cursor':None} |
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389 | tm = [self._gettime(val) for val in range(self.nrow())] |
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390 | if rcParams['verbose']: |
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391 | self._print_values(retval,'Tsys',tm) |
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392 | return retval |
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393 | |
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394 | else: |
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395 | i,j,k = (self.getbeam(),self.getif(),self.getpol()) |
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396 | statval = self._gettsys() |
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397 | out = '' |
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398 | for l in range(self.nrow()): |
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399 | tm = self._gettime(l) |
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400 | out += 'Time[%s]:\n' % (tm) |
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401 | if self.nbeam() > 1: out += ' Beam[%d] ' % (i) |
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402 | if self.nif() > 1: out += ' IF[%d] ' % (j) |
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403 | if self.npol() > 1: out += ' Pol[%d] ' % (k) |
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404 | out += '= %3.3f\n' % (statval[l]) |
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405 | out += "--------------------------------------------------\n" |
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406 | |
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407 | if rcParams['verbose']: |
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408 | print "--------------------------------------------------" |
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409 | print " TSys" |
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410 | print "--------------------------------------------------" |
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411 | print out |
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412 | retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)} |
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413 | return retval |
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414 | |
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415 | def get_time(self, row=-1): |
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416 | """ |
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417 | Get a list of time stamps for the observations. |
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418 | Return a string for each integration in the scantable. |
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419 | Parameters: |
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420 | row: row no of integration. Default -1 return all rows |
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421 | Example: |
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422 | none |
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423 | """ |
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424 | out = [] |
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425 | if row == -1: |
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426 | for i in range(self.nrow()): |
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427 | out.append(self._gettime(i)) |
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428 | return out |
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429 | else: |
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430 | if row < self.nrow(): |
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431 | return self._gettime(row) |
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432 | |
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433 | def get_sourcename(self, row=-1): |
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434 | """ |
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435 | Get a list source names for the observations. |
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436 | Return a string for each integration in the scantable. |
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437 | Parameters: |
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438 | row: row no of integration. Default -1 return all rows |
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439 | Example: |
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440 | none |
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441 | """ |
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442 | out = [] |
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443 | if row == -1: |
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444 | return [self._getsourcename(i) for i in range(self.nrow())] |
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445 | else: |
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446 | if 0 <= row < self.nrow(): |
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447 | return self._getsourcename(row) |
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448 | |
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449 | def get_elevation(self, row=-1): |
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450 | """ |
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451 | Get a list of elevations for the observations. |
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452 | Return a float for each integration in the scantable. |
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453 | Parameters: |
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454 | row: row no of integration. Default -1 return all rows |
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455 | Example: |
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456 | none |
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457 | """ |
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458 | out = [] |
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459 | if row == -1: |
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460 | return [self._getelevation(i) for i in range(self.nrow())] |
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461 | else: |
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462 | if 0 <= row < self.nrow(): |
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463 | return self._getelevation(row) |
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464 | |
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465 | def get_azimuth(self, row=-1): |
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466 | """ |
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467 | Get a list of azimuths for the observations. |
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468 | Return a float for each integration in the scantable. |
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469 | Parameters: |
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470 | row: row no of integration. Default -1 return all rows |
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471 | Example: |
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472 | none |
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473 | """ |
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474 | out = [] |
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475 | if row == -1: |
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476 | return [self._getazimuth(i) for i in range(self.nrow())] |
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477 | else: |
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478 | if 0 <= row < self.nrow(): |
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479 | return self._getazimuth(row) |
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480 | |
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481 | def get_parangle(self, row=-1): |
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482 | """ |
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483 | Get a list of parallactic angles for the observations. |
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484 | Return a float for each integration in the scantable. |
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485 | Parameters: |
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486 | row: row no of integration. Default -1 return all rows |
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487 | Example: |
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488 | none |
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489 | """ |
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490 | out = [] |
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491 | if row == -1: |
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492 | return [self._getparangle(i) for i in range(self.nrow())] |
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493 | else: |
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494 | if 0 <= row < self.nrow(): |
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495 | return self._getparangle(row) |
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496 | |
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497 | def set_unit(self, unit='channel'): |
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498 | """ |
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499 | Set the unit for all following operations on this scantable |
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500 | Parameters: |
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501 | unit: optional unit, default is 'channel' |
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502 | one of '*Hz','km/s','channel', '' |
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503 | """ |
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504 | varlist = vars() |
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505 | if unit in ['','pixel', 'channel']: |
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506 | unit = '' |
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507 | inf = list(self._getcoordinfo()) |
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508 | inf[0] = unit |
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509 | self._setcoordinfo(inf) |
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510 | if self._p: self.plot() |
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511 | self._add_history("set_unit",varlist) |
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512 | |
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513 | def set_instrument(self, instr): |
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514 | """ |
---|
515 | Set the instrument for subsequent processing |
---|
516 | Parameters: |
---|
517 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
---|
518 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
---|
519 | """ |
---|
520 | self._setInstrument(instr) |
---|
521 | self._add_history("set_instument",vars()) |
---|
522 | print_log() |
---|
523 | |
---|
524 | def set_doppler(self, doppler='RADIO'): |
---|
525 | """ |
---|
526 | Set the doppler for all following operations on this scantable. |
---|
527 | Parameters: |
---|
528 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
---|
529 | """ |
---|
530 | varlist = vars() |
---|
531 | inf = list(self._getcoordinfo()) |
---|
532 | inf[2] = doppler |
---|
533 | self._setcoordinfo(inf) |
---|
534 | if self._p: self.plot() |
---|
535 | self._add_history("set_doppler",vars()) |
---|
536 | print_log() |
---|
537 | |
---|
538 | def set_freqframe(self, frame=None): |
---|
539 | """ |
---|
540 | Set the frame type of the Spectral Axis. |
---|
541 | Parameters: |
---|
542 | frame: an optional frame type, default 'LSRK'. Valid frames are: |
---|
543 | 'REST','TOPO','LSRD','LSRK','BARY', |
---|
544 | 'GEO','GALACTO','LGROUP','CMB' |
---|
545 | Examples: |
---|
546 | scan.set_freqframe('BARY') |
---|
547 | """ |
---|
548 | if frame is None: frame = rcParams['scantable.freqframe'] |
---|
549 | varlist = vars() |
---|
550 | valid = ['REST','TOPO','LSRD','LSRK','BARY', \ |
---|
551 | 'GEO','GALACTO','LGROUP','CMB'] |
---|
552 | |
---|
553 | if frame in valid: |
---|
554 | inf = list(self._getcoordinfo()) |
---|
555 | inf[1] = frame |
---|
556 | self._setcoordinfo(inf) |
---|
557 | self._add_history("set_freqframe",varlist) |
---|
558 | else: |
---|
559 | msg = "Please specify a valid freq type. Valid types are:\n",valid |
---|
560 | if rcParams['verbose']: |
---|
561 | print msg |
---|
562 | else: |
---|
563 | raise TypeError(msg) |
---|
564 | print_log() |
---|
565 | |
---|
566 | def get_unit(self): |
---|
567 | """ |
---|
568 | Get the default unit set in this scantable |
---|
569 | Parameters: |
---|
570 | Returns: |
---|
571 | A unit string |
---|
572 | """ |
---|
573 | inf = self._getcoordinfo() |
---|
574 | unit = inf[0] |
---|
575 | if unit == '': unit = 'channel' |
---|
576 | return unit |
---|
577 | |
---|
578 | def get_abcissa(self, rowno=0): |
---|
579 | """ |
---|
580 | Get the abcissa in the current coordinate setup for the currently |
---|
581 | selected Beam/IF/Pol |
---|
582 | Parameters: |
---|
583 | rowno: an optional row number in the scantable. Default is the |
---|
584 | first row, i.e. rowno=0 |
---|
585 | Returns: |
---|
586 | The abcissa values and it's format string (as a dictionary) |
---|
587 | """ |
---|
588 | abc = self._getabcissa(rowno) |
---|
589 | lbl = self._getabcissalabel(rowno) |
---|
590 | print_log() |
---|
591 | return abc, lbl |
---|
592 | |
---|
593 | def create_mask(self, *args, **kwargs): |
---|
594 | """ |
---|
595 | Compute and return a mask based on [min,max] windows. |
---|
596 | The specified windows are to be INCLUDED, when the mask is |
---|
597 | applied. |
---|
598 | Parameters: |
---|
599 | [min,max],[min2,max2],... |
---|
600 | Pairs of start/end points specifying the regions |
---|
601 | to be masked |
---|
602 | invert: optional argument. If specified as True, |
---|
603 | return an inverted mask, i.e. the regions |
---|
604 | specified are EXCLUDED |
---|
605 | row: create the mask using the specified row for |
---|
606 | unit conversions, default is row=0 |
---|
607 | only necessary if frequency varies over rows. |
---|
608 | Example: |
---|
609 | scan.set_unit('channel') |
---|
610 | |
---|
611 | a) |
---|
612 | msk = scan.set_mask([400,500],[800,900]) |
---|
613 | # masks everything outside 400 and 500 |
---|
614 | # and 800 and 900 in the unit 'channel' |
---|
615 | |
---|
616 | b) |
---|
617 | msk = scan.set_mask([400,500],[800,900], invert=True) |
---|
618 | # masks the regions between 400 and 500 |
---|
619 | # and 800 and 900 in the unit 'channel' |
---|
620 | |
---|
621 | """ |
---|
622 | row = 0 |
---|
623 | if kwargs.has_key("row"): |
---|
624 | row = kwargs.get("row") |
---|
625 | data = self._getabcissa(row) |
---|
626 | u = self._getcoordinfo()[0] |
---|
627 | if rcParams['verbose']: |
---|
628 | if u == "": u = "channel" |
---|
629 | from asap import asaplog |
---|
630 | msg = "The current mask window unit is %s" % u |
---|
631 | asaplog.push(msg) |
---|
632 | n = self.nchan() |
---|
633 | msk = zeros(n) |
---|
634 | # test if args is a 'list' or a 'normal *args - UGLY!!! |
---|
635 | |
---|
636 | ws = (isinstance(args[-1][-1],int) or isinstance(args[-1][-1],float)) and args or args[0] |
---|
637 | for window in ws: |
---|
638 | if (len(window) != 2 or window[0] > window[1] ): |
---|
639 | raise TypeError("A window needs to be defined as [min,max]") |
---|
640 | for i in range(n): |
---|
641 | if data[i] >= window[0] and data[i] < window[1]: |
---|
642 | msk[i] = 1 |
---|
643 | if kwargs.has_key('invert'): |
---|
644 | if kwargs.get('invert'): |
---|
645 | from numarray import logical_not |
---|
646 | msk = logical_not(msk) |
---|
647 | print_log() |
---|
648 | return msk |
---|
649 | |
---|
650 | def get_restfreqs(self): |
---|
651 | """ |
---|
652 | Get the restfrequency(s) stored in this scantable. |
---|
653 | The return value(s) are always of unit 'Hz' |
---|
654 | Parameters: |
---|
655 | none |
---|
656 | Returns: |
---|
657 | a list of doubles |
---|
658 | """ |
---|
659 | return list(self._getrestfreqs()) |
---|
660 | |
---|
661 | def lines(self): |
---|
662 | """ |
---|
663 | Print the list of known spectral lines |
---|
664 | """ |
---|
665 | l = sdtable._lines(self) |
---|
666 | if rcParams['verbose']: |
---|
667 | print l |
---|
668 | else: |
---|
669 | return l |
---|
670 | |
---|
671 | def set_restfreqs(self, freqs=None, unit='Hz', lines=None, source=None, |
---|
672 | theif=None): |
---|
673 | """ |
---|
674 | Select the restfrequency for the specified source and IF OR |
---|
675 | replace for all IFs. If the 'freqs' argument holds a scalar, |
---|
676 | then that rest frequency will be applied to the selected |
---|
677 | data (and added to the list of available rest frequencies). |
---|
678 | In this way, you can set a rest frequency for each |
---|
679 | source and IF combination. If the 'freqs' argument holds |
---|
680 | a vector, then it MUST be of length the number of IFs |
---|
681 | (and the available restfrequencies will be replaced by |
---|
682 | this vector). In this case, *all* data ('source' and |
---|
683 | 'theif' are ignored) have the restfrequency set per IF according |
---|
684 | to the corresponding value you give in the 'freqs' vector. |
---|
685 | E.g. 'freqs=[1e9,2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
686 | IF 1 gets restfreq 2e9. |
---|
687 | |
---|
688 | You can also specify the frequencies via known line names |
---|
689 | in the argument 'lines'. Use 'freqs' or 'lines'. 'freqs' |
---|
690 | takes precedence. See the list of known names via function |
---|
691 | scantable.lines() |
---|
692 | Parameters: |
---|
693 | freqs: list of rest frequencies |
---|
694 | unit: unit for rest frequency (default 'Hz') |
---|
695 | lines: list of known spectral lines names (alternative to freqs). |
---|
696 | See possible list via scantable.lines() |
---|
697 | source: Source name (blank means all) |
---|
698 | theif: IF (-1 means all) |
---|
699 | Example: |
---|
700 | scan.set_restfreqs(freqs=1.4e9, source='NGC253', theif=2) |
---|
701 | scan.set_restfreqs(freqs=[1.4e9,1.67e9]) |
---|
702 | """ |
---|
703 | varlist = vars() |
---|
704 | if source is None: |
---|
705 | source = "" |
---|
706 | if theif is None: |
---|
707 | theif = -1 |
---|
708 | t = type(freqs) |
---|
709 | if t is int or t is float: |
---|
710 | freqs = [freqs] |
---|
711 | if freqs is None: |
---|
712 | freqs = [] |
---|
713 | t = type(lines) |
---|
714 | if t is str: |
---|
715 | lines = [lines] |
---|
716 | if lines is None: |
---|
717 | lines = [] |
---|
718 | sdtable._setrestfreqs(self, freqs, unit, lines, source, theif) |
---|
719 | self._add_history("set_restfreqs", varlist) |
---|
720 | |
---|
721 | |
---|
722 | |
---|
723 | def flag_spectrum(self, thebeam, theif, thepol): |
---|
724 | """ |
---|
725 | This flags a selected spectrum in the scan 'for good'. |
---|
726 | USE WITH CARE - not reversible. |
---|
727 | Use masks for non-permanent exclusion of channels. |
---|
728 | Parameters: |
---|
729 | thebeam,theif,thepol: all have to be explicitly |
---|
730 | specified |
---|
731 | Example: |
---|
732 | scan.flag_spectrum(0,0,1) |
---|
733 | flags the spectrum for Beam=0, IF=0, Pol=1 |
---|
734 | """ |
---|
735 | if (thebeam < self.nbeam() and |
---|
736 | theif < self.nif() and |
---|
737 | thepol < self.npol()): |
---|
738 | sdtable.setbeam(self, thebeam) |
---|
739 | sdtable.setif(self, theif) |
---|
740 | sdtable.setpol(self, thepol) |
---|
741 | sdtable._flag(self) |
---|
742 | self._add_history("flag_spectrum", vars()) |
---|
743 | else: |
---|
744 | print "Please specify a valid (Beam/IF/Pol)" |
---|
745 | return |
---|
746 | |
---|
747 | def _print_values(self, dat, label='', timestamps=[]): |
---|
748 | d = dat['data'] |
---|
749 | a = dat['axes'] |
---|
750 | shp = d.getshape() |
---|
751 | out = '' |
---|
752 | for i in range(shp[3]): |
---|
753 | out += '%s [%s]:\n' % (a[3],timestamps[i]) |
---|
754 | t = d[:,:,:,i] |
---|
755 | for j in range(shp[0]): |
---|
756 | if shp[0] > 1: out += ' %s[%d] ' % (a[0],j) |
---|
757 | for k in range(shp[1]): |
---|
758 | if shp[1] > 1: out += ' %s[%d] ' % (a[1],k) |
---|
759 | for l in range(shp[2]): |
---|
760 | if shp[2] > 1: out += ' %s[%d] ' % (a[2],l) |
---|
761 | out += '= %3.3f\n' % (t[j,k,l]) |
---|
762 | out += "-"*80 |
---|
763 | out += "\n" |
---|
764 | print "-"*80 |
---|
765 | print " ", label |
---|
766 | print "-"*80 |
---|
767 | print out |
---|
768 | |
---|
769 | def history(self): |
---|
770 | hist = list(self._gethistory()) |
---|
771 | out = "-"*80 |
---|
772 | for h in hist: |
---|
773 | if h.startswith("---"): |
---|
774 | out += "\n"+h |
---|
775 | else: |
---|
776 | items = h.split("##") |
---|
777 | date = items[0] |
---|
778 | func = items[1] |
---|
779 | items = items[2:] |
---|
780 | out += "\n"+date+"\n" |
---|
781 | out += "Function: %s\n Parameters:" % (func) |
---|
782 | for i in items: |
---|
783 | s = i.split("=") |
---|
784 | out += "\n %s = %s" % (s[0],s[1]) |
---|
785 | out += "\n"+"-"*80 |
---|
786 | try: |
---|
787 | from IPython.genutils import page as pager |
---|
788 | except ImportError: |
---|
789 | from pydoc import pager |
---|
790 | pager(out) |
---|
791 | return |
---|
792 | |
---|
793 | # |
---|
794 | # Maths business |
---|
795 | # |
---|
796 | |
---|
797 | def average_time(self, mask=None, scanav=False, weight='tint'): |
---|
798 | """ |
---|
799 | Return the (time) average of a scan, or apply it 'insitu'. |
---|
800 | Note: |
---|
801 | in channels only |
---|
802 | The cursor of the output scan is set to 0. |
---|
803 | Parameters: |
---|
804 | one scan or comma separated scans |
---|
805 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
806 | weighting) |
---|
807 | scanav: True averages each scan separately |
---|
808 | False (default) averages all scans together, |
---|
809 | weight: Weighting scheme. 'none', 'var' (1/var(spec) |
---|
810 | weighted), 'tsys' (1/Tsys**2 weighted), 'tint' |
---|
811 | (integration time weighted) or 'tintsys' (Tint/Tsys**2). |
---|
812 | The default is 'tint' |
---|
813 | Example: |
---|
814 | # time average the scantable without using a mask |
---|
815 | newscan = scan.average_time() |
---|
816 | """ |
---|
817 | varlist = vars() |
---|
818 | if weight is None: weight = 'tint' |
---|
819 | if mask is None: mask = () |
---|
820 | from asap._asap import average as _av |
---|
821 | s = scantable(_av((self,), mask, scanav, weight)) |
---|
822 | s._add_history("average_time",varlist) |
---|
823 | print_log() |
---|
824 | return s |
---|
825 | |
---|
826 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None, |
---|
827 | allaxes=None): |
---|
828 | """ |
---|
829 | Return a scan where all spectra are converted to either |
---|
830 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
831 | By default the function tries to look the values up internally. |
---|
832 | If it can't find them (or if you want to over-ride), you must |
---|
833 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
834 | also if you don't set it). jyperk takes precedence if you set both. |
---|
835 | Parameters: |
---|
836 | jyperk: the Jy / K conversion factor |
---|
837 | eta: the aperture efficiency |
---|
838 | d: the geomtric diameter (metres) |
---|
839 | insitu: if False a new scantable is returned. |
---|
840 | Otherwise, the scaling is done in-situ |
---|
841 | The default is taken from .asaprc (False) |
---|
842 | allaxes: if True apply to all spectra. Otherwise |
---|
843 | apply only to the selected (beam/pol/if)spectra only |
---|
844 | The default is taken from .asaprc (True if none) |
---|
845 | """ |
---|
846 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
847 | if insitu is None: insitu = rcParams['insitu'] |
---|
848 | varlist = vars() |
---|
849 | if jyperk is None: jyperk = -1.0 |
---|
850 | if d is None: d = -1.0 |
---|
851 | if eta is None: eta = -1.0 |
---|
852 | if not insitu: |
---|
853 | from asap._asap import convertflux as _convert |
---|
854 | s = scantable(_convert(self, d, eta, jyperk, allaxes)) |
---|
855 | s._add_history("convert_flux", varlist) |
---|
856 | print_log() |
---|
857 | return s |
---|
858 | else: |
---|
859 | from asap._asap import convertflux_insitu as _convert |
---|
860 | _convert(self, d, eta, jyperk, allaxes) |
---|
861 | self._add_history("convert_flux", varlist) |
---|
862 | print_log() |
---|
863 | return |
---|
864 | |
---|
865 | def gain_el(self, poly=None, filename="", method="linear", |
---|
866 | insitu=None, allaxes=None): |
---|
867 | """ |
---|
868 | Return a scan after applying a gain-elevation correction. |
---|
869 | The correction can be made via either a polynomial or a |
---|
870 | table-based interpolation (and extrapolation if necessary). |
---|
871 | You specify polynomial coefficients, an ascii table or neither. |
---|
872 | If you specify neither, then a polynomial correction will be made |
---|
873 | with built in coefficients known for certain telescopes (an error |
---|
874 | will occur if the instrument is not known). |
---|
875 | The data and Tsys are *divided* by the scaling factors. |
---|
876 | Parameters: |
---|
877 | poly: Polynomial coefficients (default None) to compute a |
---|
878 | gain-elevation correction as a function of |
---|
879 | elevation (in degrees). |
---|
880 | filename: The name of an ascii file holding correction factors. |
---|
881 | The first row of the ascii file must give the column |
---|
882 | names and these MUST include columns |
---|
883 | "ELEVATION" (degrees) and "FACTOR" (multiply data |
---|
884 | by this) somewhere. |
---|
885 | The second row must give the data type of the |
---|
886 | column. Use 'R' for Real and 'I' for Integer. |
---|
887 | An example file would be |
---|
888 | (actual factors are arbitrary) : |
---|
889 | |
---|
890 | TIME ELEVATION FACTOR |
---|
891 | R R R |
---|
892 | 0.1 0 0.8 |
---|
893 | 0.2 20 0.85 |
---|
894 | 0.3 40 0.9 |
---|
895 | 0.4 60 0.85 |
---|
896 | 0.5 80 0.8 |
---|
897 | 0.6 90 0.75 |
---|
898 | method: Interpolation method when correcting from a table. |
---|
899 | Values are "nearest", "linear" (default), "cubic" |
---|
900 | and "spline" |
---|
901 | insitu: if False a new scantable is returned. |
---|
902 | Otherwise, the scaling is done in-situ |
---|
903 | The default is taken from .asaprc (False) |
---|
904 | allaxes: If True apply to all spectra. Otherwise |
---|
905 | apply only to the selected (beam/pol/if) spectra only |
---|
906 | The default is taken from .asaprc (True if none) |
---|
907 | """ |
---|
908 | |
---|
909 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
910 | if insitu is None: insitu = rcParams['insitu'] |
---|
911 | varlist = vars() |
---|
912 | if poly is None: |
---|
913 | poly = () |
---|
914 | from os.path import expandvars |
---|
915 | filename = expandvars(filename) |
---|
916 | if not insitu: |
---|
917 | from asap._asap import gainel as _gainEl |
---|
918 | s = scantable(_gainEl(self, poly, filename, method, allaxes)) |
---|
919 | s._add_history("gain_el", varlist) |
---|
920 | print_log() |
---|
921 | return s |
---|
922 | else: |
---|
923 | from asap._asap import gainel_insitu as _gainEl |
---|
924 | _gainEl(self, poly, filename, method, allaxes) |
---|
925 | self._add_history("gain_el", varlist) |
---|
926 | print_log() |
---|
927 | return |
---|
928 | |
---|
929 | def freq_align(self, reftime=None, method='cubic', perif=False, |
---|
930 | insitu=None): |
---|
931 | """ |
---|
932 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
933 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
934 | set_freqframe. |
---|
935 | Parameters: |
---|
936 | reftime: reference time to align at. By default, the time of |
---|
937 | the first row of data is used. |
---|
938 | method: Interpolation method for regridding the spectra. |
---|
939 | Choose from "nearest", "linear", "cubic" (default) |
---|
940 | and "spline" |
---|
941 | perif: Generate aligners per freqID (no doppler tracking) or |
---|
942 | per IF (scan-based doppler tracking) |
---|
943 | insitu: if False a new scantable is returned. |
---|
944 | Otherwise, the scaling is done in-situ |
---|
945 | The default is taken from .asaprc (False) |
---|
946 | """ |
---|
947 | if insitu is None: insitu = rcParams['insitu'] |
---|
948 | varlist = vars() |
---|
949 | if reftime is None: reftime = '' |
---|
950 | perfreqid = not perif |
---|
951 | if not insitu: |
---|
952 | from asap._asap import freq_align as _align |
---|
953 | s = scantable(_align(self, reftime, method, perfreqid)) |
---|
954 | s._add_history("freq_align", varlist) |
---|
955 | print_log() |
---|
956 | return s |
---|
957 | else: |
---|
958 | from asap._asap import freq_align_insitu as _align |
---|
959 | _align(self, reftime, method, perfreqid) |
---|
960 | self._add_history("freq_align", varlist) |
---|
961 | print_log() |
---|
962 | return |
---|
963 | |
---|
964 | def opacity(self, tau, insitu=None, allaxes=None): |
---|
965 | """ |
---|
966 | Apply an opacity correction. The data |
---|
967 | and Tsys are multiplied by the correction factor. |
---|
968 | Parameters: |
---|
969 | tau: Opacity from which the correction factor is |
---|
970 | exp(tau*ZD) |
---|
971 | where ZD is the zenith-distance |
---|
972 | insitu: if False a new scantable is returned. |
---|
973 | Otherwise, the scaling is done in-situ |
---|
974 | The default is taken from .asaprc (False) |
---|
975 | allaxes: if True apply to all spectra. Otherwise |
---|
976 | apply only to the selected (beam/pol/if)spectra only |
---|
977 | The default is taken from .asaprc (True if none) |
---|
978 | """ |
---|
979 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
980 | if insitu is None: insitu = rcParams['insitu'] |
---|
981 | varlist = vars() |
---|
982 | if not insitu: |
---|
983 | from asap._asap import opacity as _opacity |
---|
984 | s = scantable(_opacity(self, tau, allaxes)) |
---|
985 | s._add_history("opacity", varlist) |
---|
986 | print_log() |
---|
987 | return s |
---|
988 | else: |
---|
989 | from asap._asap import opacity_insitu as _opacity |
---|
990 | _opacity(self, tau, allaxes) |
---|
991 | self._add_history("opacity", varlist) |
---|
992 | print_log() |
---|
993 | return |
---|
994 | |
---|
995 | def bin(self, width=5, insitu=None): |
---|
996 | """ |
---|
997 | Return a scan where all spectra have been binned up. |
---|
998 | width: The bin width (default=5) in pixels |
---|
999 | insitu: if False a new scantable is returned. |
---|
1000 | Otherwise, the scaling is done in-situ |
---|
1001 | The default is taken from .asaprc (False) |
---|
1002 | """ |
---|
1003 | if insitu is None: insitu = rcParams['insitu'] |
---|
1004 | varlist = vars() |
---|
1005 | if not insitu: |
---|
1006 | from asap._asap import bin as _bin |
---|
1007 | s = scantable(_bin(self, width)) |
---|
1008 | s._add_history("bin",varlist) |
---|
1009 | print_log() |
---|
1010 | return s |
---|
1011 | else: |
---|
1012 | from asap._asap import bin_insitu as _bin |
---|
1013 | _bin(self, width) |
---|
1014 | self._add_history("bin",varlist) |
---|
1015 | print_log() |
---|
1016 | return |
---|
1017 | |
---|
1018 | |
---|
1019 | def resample(self, width=5, method='cubic', insitu=None): |
---|
1020 | """ |
---|
1021 | Return a scan where all spectra have been binned up |
---|
1022 | width: The bin width (default=5) in pixels |
---|
1023 | method: Interpolation method when correcting from a table. |
---|
1024 | Values are "nearest", "linear", "cubic" (default) |
---|
1025 | and "spline" |
---|
1026 | insitu: if False a new scantable is returned. |
---|
1027 | Otherwise, the scaling is done in-situ |
---|
1028 | The default is taken from .asaprc (False) |
---|
1029 | """ |
---|
1030 | if insitu is None: insitu = rcParams['insitu'] |
---|
1031 | varlist = vars() |
---|
1032 | if not insitu: |
---|
1033 | from asap._asap import resample as _resample |
---|
1034 | s = scantable(_resample(self, method, width)) |
---|
1035 | s._add_history("resample",varlist) |
---|
1036 | print_log() |
---|
1037 | return s |
---|
1038 | else: |
---|
1039 | from asap._asap import resample_insitu as _resample |
---|
1040 | _resample(self, method, width) |
---|
1041 | self._add_history("resample",varlist) |
---|
1042 | print_log() |
---|
1043 | return |
---|
1044 | |
---|
1045 | def average_pol(self, mask=None, weight='none', insitu=None): |
---|
1046 | """ |
---|
1047 | Average the Polarisations together. |
---|
1048 | The polarisation cursor of the output scan is set to 0 |
---|
1049 | Parameters: |
---|
1050 | mask: An optional mask defining the region, where the |
---|
1051 | averaging will be applied. The output will have all |
---|
1052 | specified points masked. |
---|
1053 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
1054 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
1055 | insitu: if False a new scantable is returned. |
---|
1056 | Otherwise, the scaling is done in-situ |
---|
1057 | The default is taken from .asaprc (False) |
---|
1058 | """ |
---|
1059 | if insitu is None: insitu = rcParams['insitu'] |
---|
1060 | varlist = vars() |
---|
1061 | |
---|
1062 | if mask is None: |
---|
1063 | mask = () |
---|
1064 | if not insitu: |
---|
1065 | from asap._asap import averagepol as _avpol |
---|
1066 | s = scantable(_avpol(self, mask, weight)) |
---|
1067 | s._add_history("average_pol",varlist) |
---|
1068 | print_log() |
---|
1069 | return s |
---|
1070 | else: |
---|
1071 | from asap._asap import averagepol_insitu as _avpol |
---|
1072 | _avpol(self, mask, weight) |
---|
1073 | self._add_history("average_pol",varlist) |
---|
1074 | print_log() |
---|
1075 | return |
---|
1076 | |
---|
1077 | def smooth(self, kernel="hanning", width=5.0, insitu=None, allaxes=None): |
---|
1078 | """ |
---|
1079 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
1080 | Parameters: |
---|
1081 | scan: The input scan |
---|
1082 | kernel: The type of smoothing kernel. Select from |
---|
1083 | 'hanning' (default), 'gaussian' and 'boxcar'. |
---|
1084 | The first three characters are sufficient. |
---|
1085 | width: The width of the kernel in pixels. For hanning this is |
---|
1086 | ignored otherwise it defauls to 5 pixels. |
---|
1087 | For 'gaussian' it is the Full Width Half |
---|
1088 | Maximum. For 'boxcar' it is the full width. |
---|
1089 | insitu: if False a new scantable is returned. |
---|
1090 | Otherwise, the scaling is done in-situ |
---|
1091 | The default is taken from .asaprc (False) |
---|
1092 | allaxes: If True (default) apply to all spectra. Otherwise |
---|
1093 | apply only to the selected (beam/pol/if)spectra only |
---|
1094 | The default is taken from .asaprc (True if none) |
---|
1095 | Example: |
---|
1096 | none |
---|
1097 | """ |
---|
1098 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
1099 | if insitu is None: insitu = rcParams['insitu'] |
---|
1100 | varlist = vars() |
---|
1101 | if not insitu: |
---|
1102 | from asap._asap import smooth as _smooth |
---|
1103 | s = scantable(_smooth(self,kernel,width,allaxes)) |
---|
1104 | s._add_history("smooth", varlist) |
---|
1105 | print_log() |
---|
1106 | return s |
---|
1107 | else: |
---|
1108 | from asap._asap import smooth_insitu as _smooth |
---|
1109 | _smooth(self,kernel,width,allaxes) |
---|
1110 | self._add_history("smooth", varlist) |
---|
1111 | print_log() |
---|
1112 | return |
---|
1113 | |
---|
1114 | def poly_baseline(self, mask=None, order=0, insitu=None, allaxes=None): |
---|
1115 | """ |
---|
1116 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
1117 | Parameters: |
---|
1118 | scan: a scantable |
---|
1119 | mask: an optional mask |
---|
1120 | order: the order of the polynomial (default is 0) |
---|
1121 | insitu: if False a new scantable is returned. |
---|
1122 | Otherwise, the scaling is done in-situ |
---|
1123 | The default is taken from .asaprc (False) |
---|
1124 | allaxes: If True (default) apply to all spectra. Otherwise |
---|
1125 | apply only to the selected (beam/pol/if)spectra only |
---|
1126 | The default is taken from .asaprc (True if none) |
---|
1127 | Example: |
---|
1128 | # return a scan baselined by a third order polynomial, |
---|
1129 | # not using a mask |
---|
1130 | bscan = scan.poly_baseline(order=3) |
---|
1131 | """ |
---|
1132 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
1133 | if insitu is None: insitu = rcParams['insitu'] |
---|
1134 | varlist = vars() |
---|
1135 | if mask is None: |
---|
1136 | from numarray import ones |
---|
1137 | mask = list(ones(self.nchan())) |
---|
1138 | from asap.asapfitter import fitter |
---|
1139 | f = fitter() |
---|
1140 | f.set_scan(self, mask) |
---|
1141 | f.set_function(poly=order) |
---|
1142 | sf = f.auto_fit(insitu,allaxes) |
---|
1143 | if insitu: |
---|
1144 | self._add_history("poly_baseline", varlist) |
---|
1145 | print_log() |
---|
1146 | return |
---|
1147 | else: |
---|
1148 | sf._add_history("poly_baseline", varlist) |
---|
1149 | print_log() |
---|
1150 | return sf |
---|
1151 | |
---|
1152 | def auto_poly_baseline(self, mask=None, edge=(0,0), order=0, |
---|
1153 | threshold=3,insitu=None): |
---|
1154 | """ |
---|
1155 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
1156 | Spectral lines are detected first using linefinder and masked out |
---|
1157 | to avoid them affecting the baseline solution. |
---|
1158 | |
---|
1159 | Parameters: |
---|
1160 | mask: an optional mask retreived from scantable |
---|
1161 | edge: an optional number of channel to drop at |
---|
1162 | the edge of spectrum. If only one value is |
---|
1163 | specified, the same number will be dropped from |
---|
1164 | both sides of the spectrum. Default is to keep |
---|
1165 | all channels |
---|
1166 | order: the order of the polynomial (default is 0) |
---|
1167 | threshold: the threshold used by line finder. It is better to |
---|
1168 | keep it large as only strong lines affect the |
---|
1169 | baseline solution. |
---|
1170 | insitu: if False a new scantable is returned. |
---|
1171 | Otherwise, the scaling is done in-situ |
---|
1172 | The default is taken from .asaprc (False) |
---|
1173 | |
---|
1174 | Example: |
---|
1175 | scan2=scan.auto_poly_baseline(order=7) |
---|
1176 | """ |
---|
1177 | if insitu is None: insitu = rcParams['insitu'] |
---|
1178 | varlist = vars() |
---|
1179 | from asap.asapfitter import fitter |
---|
1180 | from asap.asaplinefind import linefinder |
---|
1181 | from asap import _is_sequence_or_number as _is_valid |
---|
1182 | |
---|
1183 | if not _is_valid(edge, int): |
---|
1184 | |
---|
1185 | raise RuntimeError, "Parameter 'edge' has to be an integer or a \ |
---|
1186 | pair of integers specified as a tuple" |
---|
1187 | |
---|
1188 | # setup fitter |
---|
1189 | f = fitter() |
---|
1190 | f.set_function(poly=order) |
---|
1191 | |
---|
1192 | # setup line finder |
---|
1193 | fl=linefinder() |
---|
1194 | fl.set_options(threshold=threshold) |
---|
1195 | |
---|
1196 | if not insitu: |
---|
1197 | workscan=self.copy() |
---|
1198 | else: |
---|
1199 | workscan=self |
---|
1200 | |
---|
1201 | sel=workscan.get_cursor() |
---|
1202 | rows=range(workscan.nrow()) |
---|
1203 | from asap import asaplog |
---|
1204 | for i in range(workscan.nbeam()): |
---|
1205 | workscan.setbeam(i) |
---|
1206 | for j in range(workscan.nif()): |
---|
1207 | workscan.setif(j) |
---|
1208 | for k in range(workscan.npol()): |
---|
1209 | workscan.setpol(k) |
---|
1210 | asaplog.push("Processing:") |
---|
1211 | msg = 'Beam[%d], IF[%d], Pol[%d]' % (i,j,k) |
---|
1212 | asaplog.push(msg) |
---|
1213 | for iRow in rows: |
---|
1214 | fl.set_scan(workscan,mask,edge) |
---|
1215 | fl.find_lines(iRow) |
---|
1216 | f.set_scan(workscan, fl.get_mask()) |
---|
1217 | f.x=workscan._getabcissa(iRow) |
---|
1218 | f.y=workscan._getspectrum(iRow) |
---|
1219 | f.data=None |
---|
1220 | f.fit() |
---|
1221 | x=f.get_parameters() |
---|
1222 | workscan._setspectrum(f.fitter.getresidual(),iRow) |
---|
1223 | workscan.set_cursor(sel[0],sel[1],sel[2]) |
---|
1224 | if not insitu: |
---|
1225 | return workscan |
---|
1226 | |
---|
1227 | def rotate_linpolphase(self, angle, allaxes=None): |
---|
1228 | """ |
---|
1229 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
1230 | This is always done in situ in the raw data. So if you call this |
---|
1231 | function more than once then each call rotates the phase further. |
---|
1232 | Parameters: |
---|
1233 | angle: The angle (degrees) to rotate (add) by. |
---|
1234 | allaxes: If True apply to all spectra. Otherwise |
---|
1235 | apply only to the selected (beam/pol/if)spectra only. |
---|
1236 | The default is taken from .asaprc (True if none) |
---|
1237 | Examples: |
---|
1238 | scan.rotate_linpolphase(2.3) |
---|
1239 | """ |
---|
1240 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
1241 | varlist = vars() |
---|
1242 | from asap._asap import _rotate_linpolphase as _rotate |
---|
1243 | _rotate(self, angle, allaxes) |
---|
1244 | self._add_history("rotate_linpolphase", varlist) |
---|
1245 | print_log() |
---|
1246 | return |
---|
1247 | |
---|
1248 | |
---|
1249 | def rotate_xyphase(self, angle, allaxes=None): |
---|
1250 | """ |
---|
1251 | Rotate the phase of the XY correlation. This is always done in situ |
---|
1252 | in the data. So if you call this function more than once |
---|
1253 | then each call rotates the phase further. |
---|
1254 | Parameters: |
---|
1255 | angle: The angle (degrees) to rotate (add) by. |
---|
1256 | allaxes: If True apply to all spectra. Otherwise |
---|
1257 | apply only to the selected (beam/pol/if)spectra only. |
---|
1258 | The default is taken from .asaprc (True if none) |
---|
1259 | Examples: |
---|
1260 | scan.rotate_xyphase(2.3) |
---|
1261 | """ |
---|
1262 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
1263 | varlist = vars() |
---|
1264 | from asap._asap import _rotate_xyphase |
---|
1265 | _rotate_xyphase(self, angle, allaxes) |
---|
1266 | self._add_history("rotate_xyphase", varlist) |
---|
1267 | print_log() |
---|
1268 | return |
---|
1269 | |
---|
1270 | |
---|
1271 | def add(self, offset, insitu=None, allaxes=None): |
---|
1272 | """ |
---|
1273 | Return a scan where all spectra have the offset added |
---|
1274 | Parameters: |
---|
1275 | offset: the offset |
---|
1276 | insitu: if False a new scantable is returned. |
---|
1277 | Otherwise, the scaling is done in-situ |
---|
1278 | The default is taken from .asaprc (False) |
---|
1279 | allaxes: if True apply to all spectra. Otherwise |
---|
1280 | apply only to the selected (beam/pol/if)spectra only |
---|
1281 | The default is taken from .asaprc (True if none) |
---|
1282 | """ |
---|
1283 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
1284 | if insitu is None: insitu = rcParams['insitu'] |
---|
1285 | varlist = vars() |
---|
1286 | if not insitu: |
---|
1287 | from asap._asap import add as _add |
---|
1288 | s = scantable(_add(self, offset, allaxes)) |
---|
1289 | s._add_history("add",varlist) |
---|
1290 | print_log() |
---|
1291 | return s |
---|
1292 | else: |
---|
1293 | from asap._asap import add_insitu as _add |
---|
1294 | _add(self, offset, allaxes) |
---|
1295 | self._add_history("add",varlist) |
---|
1296 | print_log() |
---|
1297 | return |
---|
1298 | |
---|
1299 | def scale(self, factor, insitu=None, allaxes=None, tsys=True): |
---|
1300 | """ |
---|
1301 | Return a scan where all spectra are scaled by the give 'factor' |
---|
1302 | Parameters: |
---|
1303 | factor: the scaling factor |
---|
1304 | insitu: if False a new scantable is returned. |
---|
1305 | Otherwise, the scaling is done in-situ |
---|
1306 | The default is taken from .asaprc (False) |
---|
1307 | allaxes: if True apply to all spectra. Otherwise |
---|
1308 | apply only to the selected (beam/pol/if)spectra only. |
---|
1309 | The default is taken from .asaprc (True if none) |
---|
1310 | tsys: if True (default) then apply the operation to Tsys |
---|
1311 | as well as the data |
---|
1312 | """ |
---|
1313 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
1314 | if insitu is None: insitu = rcParams['insitu'] |
---|
1315 | varlist = vars() |
---|
1316 | if not insitu: |
---|
1317 | from asap._asap import scale as _scale |
---|
1318 | s = scantable(_scale(self, factor, allaxes, tsys)) |
---|
1319 | s._add_history("scale",varlist) |
---|
1320 | print_log() |
---|
1321 | return s |
---|
1322 | else: |
---|
1323 | from asap._asap import scale_insitu as _scale |
---|
1324 | _scale(self, factor, allaxes, tsys) |
---|
1325 | self._add_history("scale",varlist) |
---|
1326 | print_log() |
---|
1327 | return |
---|
1328 | |
---|
1329 | def auto_quotient(self, mode='suffix', preserve=True): |
---|
1330 | """ |
---|
1331 | This function allows to build quotients automatically. |
---|
1332 | It assumes the observation to have the same numer of |
---|
1333 | "ons" and "offs" |
---|
1334 | It will support "closest off in time" in the future |
---|
1335 | Parameters: |
---|
1336 | mode: the on/off detection mode; 'suffix' (default) |
---|
1337 | 'suffix' identifies 'off' scans by the |
---|
1338 | trailing '_R' (Mopra/Parkes) or |
---|
1339 | '_e'/'_w' (Tid) |
---|
1340 | preserve: you can preserve (default) the continuum or |
---|
1341 | remove it. The equations used are |
---|
1342 | preserve: Output = Toff * (on/off) - Toff |
---|
1343 | remove: Output = Tref * (on/off) - Ton |
---|
1344 | """ |
---|
1345 | modes = ["suffix","time"] |
---|
1346 | if not mode in modes: |
---|
1347 | print "please provide valid mode. Valid modes are %s" % (modes) |
---|
1348 | return None |
---|
1349 | from asap._asap import quotient as _quot |
---|
1350 | if mode == "suffix": |
---|
1351 | srcs = self.get_scan("*[^_ewR]") |
---|
1352 | refs = self.get_scan("*[_ewR]") |
---|
1353 | if isinstance(srcs,scantable) and isinstance(refs,scantable): |
---|
1354 | from asap import asaplog |
---|
1355 | ns,nr = srcs.nrow(),refs.nrow() |
---|
1356 | msg = "Found %i Off and %i On scans" % (ns,nr) |
---|
1357 | asaplog.push(msg) |
---|
1358 | if nr > ns: |
---|
1359 | asaplog("Found more Off integrations than On scans - dropping excess Offs.") |
---|
1360 | refs = refs.get_scan(range(ns)) |
---|
1361 | print_log() |
---|
1362 | return scantable(_quot(srcs,refs, preserve)) |
---|
1363 | else: |
---|
1364 | msg = "Couldn't find any on/off pairs" |
---|
1365 | if rcParams['verbose']: |
---|
1366 | print msg |
---|
1367 | return |
---|
1368 | else: |
---|
1369 | raise RuntimeError() |
---|
1370 | else: |
---|
1371 | if rcParams['verbose']: print "not yet implemented" |
---|
1372 | return None |
---|
1373 | |
---|
1374 | def quotient(self, other, isreference=True, preserve=True): |
---|
1375 | """ |
---|
1376 | Return the quotient of a 'source' (on) scan and a 'reference' (off) |
---|
1377 | scan. |
---|
1378 | The reference can have just one row, even if the signal has many. |
---|
1379 | Otherwise they must have the same number of rows. |
---|
1380 | The cursor of the output scan is set to 0 |
---|
1381 | Parameters: |
---|
1382 | other: the 'other' scan |
---|
1383 | isreference: if the 'other' scan is the reference (default) |
---|
1384 | or source |
---|
1385 | preserve: you can preserve (default) the continuum or |
---|
1386 | remove it. The equations used are |
---|
1387 | preserve: Output = Toff * (on/off) - Toff |
---|
1388 | remove: Output = Tref * (on/off) - Ton |
---|
1389 | Example: |
---|
1390 | # src is a scantable for an 'on' scan, ref for an 'off' scantable |
---|
1391 | q1 = src.quotient(ref) |
---|
1392 | q2 = ref.quotient(src, isreference=False) |
---|
1393 | # gives the same result |
---|
1394 | """ |
---|
1395 | from asap._asap import quotient as _quot |
---|
1396 | try: |
---|
1397 | s = None |
---|
1398 | if isreference: |
---|
1399 | s = scantable(_quot(self, other, preserve)) |
---|
1400 | else: |
---|
1401 | s = scantable(_quot(other, self, preserve)) |
---|
1402 | print_log() |
---|
1403 | return s |
---|
1404 | except RuntimeError,e: |
---|
1405 | if rcParams['verbose']: |
---|
1406 | print e |
---|
1407 | return |
---|
1408 | else: raise |
---|
1409 | |
---|
1410 | def freq_switch(self, insitu=None): |
---|
1411 | """ |
---|
1412 | Apply frequency switching to the data. |
---|
1413 | Parameters: |
---|
1414 | insitu: if False a new scantable is returned. |
---|
1415 | Otherwise, the swictching is done in-situ |
---|
1416 | The default is taken from .asaprc (False) |
---|
1417 | Example: |
---|
1418 | none |
---|
1419 | """ |
---|
1420 | if insitu is None: insitu = rcParams['insitu'] |
---|
1421 | varlist = vars() |
---|
1422 | try: |
---|
1423 | if insitu: |
---|
1424 | from asap._asap import _frequency_switch_insitu |
---|
1425 | _frequency_switch_insitu(self) |
---|
1426 | self._add_history("freq_switch", varlist) |
---|
1427 | print_log() |
---|
1428 | return |
---|
1429 | else: |
---|
1430 | from asap._asap import _frequency_switch |
---|
1431 | sf = scantable(_frequency_switch(self)) |
---|
1432 | sf._add_history("freq_switch", varlist) |
---|
1433 | print_log() |
---|
1434 | return sf |
---|
1435 | except RuntimeError,e: |
---|
1436 | if rcParams['verbose']: print e |
---|
1437 | else: raise |
---|
1438 | |
---|
1439 | def recalc_azel(self): |
---|
1440 | """ |
---|
1441 | Recalculate the azimuth and elevation for each position. |
---|
1442 | Parameters: |
---|
1443 | none |
---|
1444 | Example: |
---|
1445 | """ |
---|
1446 | varlist = vars() |
---|
1447 | self._recalc_azel() |
---|
1448 | self._add_history("recalc_azel", varlist) |
---|
1449 | print_log() |
---|
1450 | return |
---|
1451 | |
---|
1452 | def __add__(self, other): |
---|
1453 | varlist = vars() |
---|
1454 | s = None |
---|
1455 | if isinstance(other, scantable): |
---|
1456 | from asap._asap import b_operate as _bop |
---|
1457 | s = scantable(_bop(self, other, 'add', True)) |
---|
1458 | elif isinstance(other, float): |
---|
1459 | from asap._asap import add as _add |
---|
1460 | s = scantable(_add(self, other, True)) |
---|
1461 | else: |
---|
1462 | raise TypeError("Other input is not a scantable or float value") |
---|
1463 | s._add_history("operator +", varlist) |
---|
1464 | print_log() |
---|
1465 | return s |
---|
1466 | |
---|
1467 | def __sub__(self, other): |
---|
1468 | """ |
---|
1469 | implicit on all axes and on Tsys |
---|
1470 | """ |
---|
1471 | varlist = vars() |
---|
1472 | s = None |
---|
1473 | if isinstance(other, scantable): |
---|
1474 | from asap._asap import b_operate as _bop |
---|
1475 | s = scantable(_bop(self, other, 'sub', True)) |
---|
1476 | elif isinstance(other, float): |
---|
1477 | from asap._asap import add as _add |
---|
1478 | s = scantable(_add(self, -other, True)) |
---|
1479 | else: |
---|
1480 | raise TypeError("Other input is not a scantable or float value") |
---|
1481 | s._add_history("operator -", varlist) |
---|
1482 | print_log() |
---|
1483 | return s |
---|
1484 | |
---|
1485 | def __mul__(self, other): |
---|
1486 | """ |
---|
1487 | implicit on all axes and on Tsys |
---|
1488 | """ |
---|
1489 | varlist = vars() |
---|
1490 | s = None |
---|
1491 | if isinstance(other, scantable): |
---|
1492 | from asap._asap import b_operate as _bop |
---|
1493 | s = scantable(_bop(self, other, 'mul', True)) |
---|
1494 | elif isinstance(other, float): |
---|
1495 | if other == 0.0: |
---|
1496 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
1497 | from asap._asap import scale as _sca |
---|
1498 | s = scantable(_sca(self, other, True)) |
---|
1499 | else: |
---|
1500 | raise TypeError("Other input is not a scantable or float value") |
---|
1501 | s._add_history("operator *", varlist) |
---|
1502 | print_log() |
---|
1503 | return s |
---|
1504 | |
---|
1505 | |
---|
1506 | def __div__(self, other): |
---|
1507 | """ |
---|
1508 | implicit on all axes and on Tsys |
---|
1509 | """ |
---|
1510 | varlist = vars() |
---|
1511 | s = None |
---|
1512 | if isinstance(other, scantable): |
---|
1513 | from asap._asap import b_operate as _bop |
---|
1514 | s = scantable(_bop(self, other, 'div', True)) |
---|
1515 | elif isinstance(other, float): |
---|
1516 | if other == 0.0: |
---|
1517 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
1518 | from asap._asap import scale as _sca |
---|
1519 | s = scantable(_sca(self, 1.0/other, True)) |
---|
1520 | else: |
---|
1521 | raise TypeError("Other input is not a scantable or float value") |
---|
1522 | s._add_history("operator /", varlist) |
---|
1523 | print_log() |
---|
1524 | return s |
---|
1525 | |
---|
1526 | def get_fit(self, row=0): |
---|
1527 | """ |
---|
1528 | Print or return the stored fits for a row in the scantable |
---|
1529 | Parameters: |
---|
1530 | row: the row which the fit has been applied to. |
---|
1531 | """ |
---|
1532 | if row > self.nrow(): |
---|
1533 | return |
---|
1534 | from asap import asapfit |
---|
1535 | fit = asapfit(self._getfit(row)) |
---|
1536 | if rcParams['verbose']: |
---|
1537 | print fit |
---|
1538 | return |
---|
1539 | else: |
---|
1540 | return fit.as_dict() |
---|
1541 | |
---|
1542 | def _add_history(self, funcname, parameters): |
---|
1543 | # create date |
---|
1544 | sep = "##" |
---|
1545 | from datetime import datetime |
---|
1546 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
1547 | hist = dstr+sep |
---|
1548 | hist += funcname+sep#cdate+sep |
---|
1549 | if parameters.has_key('self'): del parameters['self'] |
---|
1550 | for k,v in parameters.iteritems(): |
---|
1551 | if type(v) is dict: |
---|
1552 | for k2,v2 in v.iteritems(): |
---|
1553 | hist += k2 |
---|
1554 | hist += "=" |
---|
1555 | if isinstance(v2,scantable): |
---|
1556 | hist += 'scantable' |
---|
1557 | elif k2 == 'mask': |
---|
1558 | if isinstance(v2,list) or isinstance(v2,tuple): |
---|
1559 | hist += str(self._zip_mask(v2)) |
---|
1560 | else: |
---|
1561 | hist += str(v2) |
---|
1562 | else: |
---|
1563 | hist += str(v2) |
---|
1564 | else: |
---|
1565 | hist += k |
---|
1566 | hist += "=" |
---|
1567 | if isinstance(v,scantable): |
---|
1568 | hist += 'scantable' |
---|
1569 | elif k == 'mask': |
---|
1570 | if isinstance(v,list) or isinstance(v,tuple): |
---|
1571 | hist += str(self._zip_mask(v)) |
---|
1572 | else: |
---|
1573 | hist += str(v) |
---|
1574 | else: |
---|
1575 | hist += str(v) |
---|
1576 | hist += sep |
---|
1577 | hist = hist[:-2] # remove trailing '##' |
---|
1578 | self._addhistory(hist) |
---|
1579 | |
---|
1580 | |
---|
1581 | def _zip_mask(self, mask): |
---|
1582 | mask = list(mask) |
---|
1583 | i = 0 |
---|
1584 | segments = [] |
---|
1585 | while mask[i:].count(1): |
---|
1586 | i += mask[i:].index(1) |
---|
1587 | if mask[i:].count(0): |
---|
1588 | j = i + mask[i:].index(0) |
---|
1589 | else: |
---|
1590 | j = len(mask) |
---|
1591 | segments.append([i,j]) |
---|
1592 | i = j |
---|
1593 | return segments |
---|
1594 | |
---|
1595 | def _get_ordinate_label(self): |
---|
1596 | fu = "("+self.get_fluxunit()+")" |
---|
1597 | import re |
---|
1598 | lbl = "Intensity" |
---|
1599 | if re.match(".K.",fu): |
---|
1600 | lbl = "Brightness Temperature "+ fu |
---|
1601 | elif re.match(".Jy.",fu): |
---|
1602 | lbl = "Flux density "+ fu |
---|
1603 | return lbl |
---|
1604 | |
---|