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