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, asaplog |
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4 | from asap import selector |
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5 | from numarray import ones,zeros |
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6 | import sys |
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7 | |
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8 | class scantable(Scantable): |
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9 | """ |
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10 | The ASAP container for scans |
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11 | """ |
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12 | |
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13 | def __init__(self, filename, average=None, unit=None): |
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14 | """ |
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15 | Create a scantable from a saved one or make a reference |
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16 | Parameters: |
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17 | filename: the name of an asap table on disk |
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18 | or |
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19 | the name of a rpfits/sdfits/ms file |
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20 | (integrations within scans are auto averaged |
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21 | and the whole file is read) |
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22 | or |
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23 | [advanced] a reference to an existing |
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24 | scantable |
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25 | average: average all integrations withinb a scan on read. |
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26 | The default (True) is taken from .asaprc. |
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27 | unit: brightness unit; must be consistent with K or Jy. |
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28 | Over-rides the default selected by the reader |
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29 | (input rpfits/sdfits/ms) or replaces the value |
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30 | in existing scantables |
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31 | """ |
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32 | if average is None: |
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33 | average = rcParams['scantable.autoaverage'] |
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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 | if isinstance(filename, Scantable): |
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38 | Scantable.__init__(self, filename) |
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39 | else: |
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40 | if isinstance(filename,str): |
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41 | import os.path |
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42 | filename = os.path.expandvars(filename) |
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43 | filename = os.path.expanduser(filename) |
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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 | 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 | Scantable.__init__(self, filename, "memory") |
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55 | if unit is not None: |
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56 | self.set_fluxunit(unit) |
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57 | self.set_freqframe(rcParams['scantable.freqframe']) |
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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 | self._fill([filename],unit, average) |
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67 | elif (isinstance(filename,list) or isinstance(filename,tuple)) \ |
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68 | and isinstance(filename[-1], str): |
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69 | self._fill(filename, unit, average) |
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70 | print_log() |
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71 | |
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72 | def save(self, name=None, format=None, overwrite=False): |
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73 | """ |
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74 | Store the scantable on disk. This can be an asap (aips++) Table, SDFITS, |
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75 | Image FITS or MS2 format. |
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76 | Parameters: |
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77 | name: the name of the outputfile. For format="FITS" this |
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78 | is the directory file name into which all the files |
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79 | will be written (default is 'asap_FITS'). For format |
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80 | "ASCII" this is the root file name (data in 'name'.txt |
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81 | and header in 'name'_header.txt) |
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82 | format: an optional file format. Default is ASAP. |
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83 | Allowed are - 'ASAP' (save as ASAP [aips++] Table), |
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84 | 'SDFITS' (save as SDFITS file) |
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85 | 'FITS' (saves each row as a FITS Image) |
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86 | 'ASCII' (saves as ascii text file) |
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87 | 'MS2' (saves as an aips++ |
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88 | MeasurementSet V2) |
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89 | overwrite: If the file should be overwritten if it exists. |
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90 | The default False is to return with warning |
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91 | without writing the output. USE WITH CARE. |
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92 | Example: |
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93 | scan.save('myscan.asap') |
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94 | scan.save('myscan.sdfits','SDFITS') |
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95 | """ |
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96 | from os import path |
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97 | if format is None: format = rcParams['scantable.save'] |
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98 | suffix = '.'+format.lower() |
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99 | if name is None or name =="": |
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100 | name = 'scantable'+suffix |
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101 | from asap import asaplog |
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102 | msg = "No filename given. Using default name %s..." % name |
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103 | asaplog.push(msg) |
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104 | name = path.expandvars(name) |
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105 | if path.isfile(name) or path.isdir(name): |
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106 | if not overwrite: |
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107 | msg = "File %s exists." % name |
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108 | if rcParams['verbose']: |
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109 | print msg |
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110 | return |
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111 | else: |
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112 | raise IOError(msg) |
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113 | format2 = format.upper() |
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114 | if format2 == 'ASAP': |
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115 | self._save(name) |
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116 | else: |
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117 | from asap._asap import stwriter as stw |
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118 | w = stw(format2) |
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119 | w.write(self, name) |
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120 | print_log() |
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121 | return |
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122 | |
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123 | def copy(self): |
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124 | """ |
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125 | Return a copy of this scantable. |
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126 | Parameters: |
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127 | none |
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128 | Example: |
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129 | copiedscan = scan.copy() |
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130 | """ |
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131 | sd = scantable(Scantable._copy(self)) |
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132 | return sd |
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133 | |
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134 | def get_scan(self, scanid=None): |
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135 | """ |
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136 | Return a specific scan (by scanno) or collection of scans (by |
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137 | source name) in a new scantable. |
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138 | Parameters: |
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139 | scanid: a (list of) scanno or a source name, unix-style |
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140 | patterns are accepted for source name matching, e.g. |
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141 | '*_R' gets all 'ref scans |
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142 | Example: |
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143 | # get all scans containing the source '323p459' |
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144 | newscan = scan.get_scan('323p459') |
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145 | # get all 'off' scans |
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146 | refscans = scan.get_scan('*_R') |
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147 | # get a susbset of scans by scanno (as listed in scan.summary()) |
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148 | newscan = scan.get_scan([0,2,7,10]) |
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149 | """ |
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150 | if scanid is None: |
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151 | if rcParams['verbose']: |
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152 | print "Please specify a scan no or name to retrieve from the scantable" |
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153 | return |
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154 | else: |
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155 | raise RuntimeError("No scan given") |
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156 | |
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157 | try: |
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158 | bsel = self.get_selection() |
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159 | sel = selector() |
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160 | if type(scanid) is str: |
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161 | sel.set_name(scanid) |
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162 | self.set_selection(bsel+sel) |
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163 | scopy = self._copy() |
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164 | self.set_selection(bsel) |
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165 | return scantable(scopy) |
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166 | elif type(scanid) is int: |
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167 | sel.set_scans([scanid]) |
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168 | self.set_selection(bsel+sel) |
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169 | scopy = self._copy() |
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170 | self.set_selection(bsel) |
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171 | return scantable(scopy) |
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172 | elif type(scanid) is list: |
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173 | sel.set_scans(scanid) |
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174 | self.set_selection(sel) |
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175 | scopy = self._copy() |
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176 | self.set_selection(bsel) |
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177 | return scantable(scopy) |
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178 | else: |
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179 | msg = "Illegal scanid type, use 'int' or 'list' if ints." |
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180 | if rcParams['verbose']: |
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181 | print msg |
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182 | else: |
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183 | raise TypeError(msg) |
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184 | except RuntimeError: |
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185 | if rcParams['verbose']: print "Couldn't find any match." |
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186 | else: raise |
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187 | |
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188 | def __str__(self): |
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189 | return Scantable._summary(self,True) |
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190 | |
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191 | def summary(self, filename=None): |
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192 | """ |
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193 | Print a summary of the contents of this scantable. |
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194 | Parameters: |
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195 | filename: the name of a file to write the putput to |
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196 | Default - no file output |
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197 | verbose: print extra info such as the frequency table |
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198 | The default (False) is taken from .asaprc |
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199 | """ |
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200 | info = Scantable._summary(self, True) |
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201 | #if verbose is None: verbose = rcParams['scantable.verbosesummary'] |
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202 | if filename is not None: |
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203 | if filename is "": |
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204 | filename = 'scantable_summary.txt' |
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205 | from os.path import expandvars, isdir |
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206 | filename = expandvars(filename) |
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207 | if not isdir(filename): |
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208 | data = open(filename, 'w') |
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209 | data.write(info) |
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210 | data.close() |
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211 | else: |
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212 | msg = "Illegal file name '%s'." % (filename) |
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213 | if rcParams['verbose']: |
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214 | print msg |
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215 | else: |
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216 | raise IOError(msg) |
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217 | if rcParams['verbose']: |
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218 | try: |
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219 | from IPython.genutils import page as pager |
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220 | except ImportError: |
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221 | from pydoc import pager |
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222 | pager(info) |
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223 | else: |
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224 | return info |
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225 | |
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226 | |
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227 | def get_selection(self): |
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228 | """ |
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229 | Get the selection object currently set on this scantable. |
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230 | Parameters: |
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231 | none |
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232 | Example: |
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233 | sel = scan.get_selection() |
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234 | sel.set_ifs(0) # select IF 0 |
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235 | scan.set_selection(sel) # apply modified selection |
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236 | """ |
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237 | return selector(self._getselection()) |
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238 | |
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239 | def set_selection(self, selection=selector()): |
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240 | """ |
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241 | Select a subset of the data. All following operations on this scantable |
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242 | are only applied to thi selection. |
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243 | Parameters: |
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244 | selection: a selector object (default unset the selection) |
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245 | Examples: |
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246 | sel = selector() # create a selection object |
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247 | self.set_scans([0,3]) # select SCANNO 0 and 3 |
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248 | scan.set_selection(sel) # set the selection |
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249 | scan.summary() # will only print summary of scanno 0 an 3 |
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250 | scan.set_selection() # unset the selection |
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251 | """ |
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252 | self._setselection(selection) |
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253 | |
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254 | def set_cursor(self, beam=0, IF=0, pol=0): |
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255 | print "DEPRECATED - use set_selection" |
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256 | |
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257 | def get_cursor(self): |
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258 | print "DEPRECATED - use get_selection" |
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259 | |
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260 | def stats(self, stat='stddev', mask=None): |
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261 | """ |
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262 | Determine the specified statistic of the current beam/if/pol |
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263 | Takes a 'mask' as an optional parameter to specify which |
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264 | channels should be excluded. |
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265 | Parameters: |
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266 | stat: 'min', 'max', 'sumsq', 'sum', 'mean' |
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267 | 'var', 'stddev', 'avdev', 'rms', 'median' |
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268 | mask: an optional mask specifying where the statistic |
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269 | should be determined. |
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270 | Example: |
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271 | scan.set_unit('channel') |
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272 | msk = scan.create_mask([100,200],[500,600]) |
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273 | scan.stats(stat='mean', mask=m) |
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274 | """ |
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275 | from numarray import array,zeros,Float |
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276 | if mask == None: |
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277 | mask = [] |
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278 | axes = ['Beam','IF','Pol','Time'] |
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279 | if not self._check_ifs(): |
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280 | raise ValueError("Cannot apply mask as the IFs have different number of channels" |
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281 | "Please use setselection() to select individual IFs") |
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282 | |
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283 | statvals = self._math._stats(self, mask, stat) |
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284 | out = '' |
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285 | axes = [] |
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286 | for i in range(self.nrow()): |
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287 | axis = [] |
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288 | axis.append(self.getscan(i)) |
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289 | axis.append(self.getbeam(i)) |
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290 | axis.append(self.getif(i)) |
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291 | axis.append(self.getpol(i)) |
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292 | axis.append(self.getcycle(i)) |
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293 | axes.append(axis) |
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294 | tm = self._gettime(i) |
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295 | src = self._getsourcename(i) |
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296 | out += 'Scan[%d] (%s) ' % (axis[0], src) |
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297 | out += 'Time[%s]:\n' % (tm) |
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298 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1]) |
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299 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2]) |
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300 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3]) |
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301 | out += '= %3.3f\n' % (statvals[i]) |
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302 | out += "--------------------------------------------------\n" |
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303 | |
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304 | if rcParams['verbose']: |
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305 | print "--------------------------------------------------" |
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306 | print " ",stat |
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307 | print "--------------------------------------------------" |
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308 | print out |
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309 | retval = { 'axesnames': ['scanno','beamno','ifno','polno','cycleno'], |
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310 | 'axes' : axes, |
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311 | 'data': statvals} |
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312 | return retval |
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313 | |
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314 | def stddev(self,mask=None): |
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315 | """ |
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316 | Determine the standard deviation of the current beam/if/pol |
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317 | Takes a 'mask' as an optional parameter to specify which |
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318 | channels should be excluded. |
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319 | Parameters: |
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320 | mask: an optional mask specifying where the standard |
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321 | deviation should be determined. |
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322 | |
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323 | Example: |
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324 | scan.set_unit('channel') |
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325 | msk = scan.create_mask([100,200],[500,600]) |
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326 | scan.stddev(mask=m) |
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327 | """ |
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328 | return self.stats(stat='stddev',mask=mask); |
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329 | |
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330 | |
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331 | def column_names(self): |
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332 | """ |
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333 | Return a list of column names, which can be used for selection. |
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334 | """ |
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335 | return list(Scantable.column_names(self)) |
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336 | |
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337 | def get_tsys(self): |
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338 | """ |
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339 | Return the System temperatures. |
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340 | Parameters: |
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341 | |
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342 | Returns: |
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343 | a list of Tsys values for the current selection |
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344 | """ |
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345 | |
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346 | return self._row_callback(self._gettsys, "Tsys") |
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347 | |
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348 | def _row_callback(self, callback, label): |
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349 | axes = [] |
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350 | axesnames = ['scanno','beamno','ifno','polno','cycleno'] |
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351 | out = "" |
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352 | outvec =[] |
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353 | for i in range(self.nrow()): |
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354 | axis = [] |
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355 | axis.append(self.getscan(i)) |
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356 | axis.append(self.getbeam(i)) |
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357 | axis.append(self.getif(i)) |
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358 | axis.append(self.getpol(i)) |
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359 | axis.append(self.getcycle(i)) |
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360 | axes.append(axis) |
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361 | tm = self._gettime(i) |
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362 | src = self._getsourcename(i) |
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363 | out += 'Scan[%d] (%s) ' % (axis[0], src) |
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364 | out += 'Time[%s]:\n' % (tm) |
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365 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1]) |
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366 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2]) |
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367 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3]) |
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368 | outvec.append(callback(i)) |
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369 | out += '= %3.3f\n' % (outvec[i]) |
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370 | out += "--------------------------------------------------\n" |
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371 | if rcParams['verbose']: |
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372 | print "--------------------------------------------------" |
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373 | print " %s" % (label) |
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374 | print "--------------------------------------------------" |
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375 | print out |
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376 | retval = {'axesnames': axesnames, 'axes': axes, 'data': outvec} |
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377 | return retval |
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378 | |
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379 | |
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380 | def get_time(self, row=-1): |
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381 | """ |
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382 | Get a list of time stamps for the observations. |
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383 | Return a string for each integration in the scantable. |
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384 | Parameters: |
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385 | row: row no of integration. Default -1 return all rows |
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386 | Example: |
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387 | none |
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388 | """ |
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389 | out = [] |
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390 | if row == -1: |
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391 | for i in range(self.nrow()): |
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392 | out.append(self._gettime(i)) |
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393 | return out |
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394 | else: |
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395 | if row < self.nrow(): |
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396 | return self._gettime(row) |
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397 | |
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398 | def get_sourcename(self, row=-1): |
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399 | """ |
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400 | Get a list source names for the observations. |
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401 | Return a string for each integration in the scantable. |
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402 | Parameters: |
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403 | row: row no of integration. Default -1 return all rows |
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404 | Example: |
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405 | none |
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406 | """ |
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407 | out = [] |
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408 | if row == -1: |
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409 | return [self._getsourcename(i) for i in range(self.nrow())] |
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410 | else: |
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411 | if 0 <= row < self.nrow(): |
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412 | return self._getsourcename(row) |
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413 | |
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414 | def get_elevation(self, row=-1): |
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415 | """ |
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416 | Get a list of elevations for the observations. |
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417 | Return a float for each integration in the scantable. |
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418 | Parameters: |
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419 | row: row no of integration. Default -1 return all rows |
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420 | Example: |
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421 | none |
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422 | """ |
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423 | out = [] |
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424 | if row == -1: |
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425 | return [self._getelevation(i) for i in range(self.nrow())] |
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426 | else: |
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427 | if 0 <= row < self.nrow(): |
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428 | return self._getelevation(row) |
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429 | |
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430 | def get_azimuth(self, row=-1): |
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431 | """ |
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432 | Get a list of azimuths for the observations. |
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433 | Return a float for each integration in the scantable. |
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434 | Parameters: |
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435 | row: row no of integration. Default -1 return all rows |
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436 | Example: |
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437 | none |
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438 | """ |
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439 | out = [] |
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440 | if row == -1: |
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441 | return [self._getazimuth(i) for i in range(self.nrow())] |
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442 | else: |
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443 | if 0 <= row < self.nrow(): |
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444 | return self._getazimuth(row) |
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445 | |
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446 | def get_parangle(self, row=-1): |
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447 | """ |
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448 | Get a list of parallactic angles for the observations. |
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449 | Return a float for each integration in the scantable. |
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450 | Parameters: |
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451 | row: row no of integration. Default -1 return all rows |
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452 | Example: |
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453 | none |
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454 | """ |
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455 | out = [] |
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456 | if row == -1: |
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457 | return [self._getparangle(i) for i in range(self.nrow())] |
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458 | else: |
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459 | if 0 <= row < self.nrow(): |
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460 | return self._getparangle(row) |
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461 | |
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462 | def set_unit(self, unit='channel'): |
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463 | """ |
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464 | Set the unit for all following operations on this scantable |
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465 | Parameters: |
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466 | unit: optional unit, default is 'channel' |
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467 | one of '*Hz','km/s','channel', '' |
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468 | """ |
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469 | varlist = vars() |
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470 | if unit in ['','pixel', 'channel']: |
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471 | unit = '' |
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472 | inf = list(self._getcoordinfo()) |
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473 | inf[0] = unit |
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474 | self._setcoordinfo(inf) |
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475 | self._add_history("set_unit",varlist) |
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476 | |
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477 | def set_instrument(self, instr): |
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478 | """ |
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479 | Set the instrument for subsequent processing |
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480 | Parameters: |
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481 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
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482 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
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483 | """ |
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484 | self._setInstrument(instr) |
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485 | self._add_history("set_instument",vars()) |
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486 | print_log() |
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487 | |
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488 | def set_doppler(self, doppler='RADIO'): |
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489 | """ |
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490 | Set the doppler for all following operations on this scantable. |
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491 | Parameters: |
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492 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
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493 | """ |
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494 | varlist = vars() |
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495 | inf = list(self._getcoordinfo()) |
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496 | inf[2] = doppler |
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497 | self._setcoordinfo(inf) |
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498 | self._add_history("set_doppler",vars()) |
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499 | print_log() |
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500 | |
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501 | def set_freqframe(self, frame=None): |
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502 | """ |
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503 | Set the frame type of the Spectral Axis. |
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504 | Parameters: |
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505 | frame: an optional frame type, default 'LSRK'. Valid frames are: |
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506 | 'REST','TOPO','LSRD','LSRK','BARY', |
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507 | 'GEO','GALACTO','LGROUP','CMB' |
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508 | Examples: |
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509 | scan.set_freqframe('BARY') |
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510 | """ |
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511 | if frame is None: frame = rcParams['scantable.freqframe'] |
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512 | varlist = vars() |
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513 | valid = ['REST','TOPO','LSRD','LSRK','BARY', \ |
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514 | 'GEO','GALACTO','LGROUP','CMB'] |
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515 | |
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516 | if frame in valid: |
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517 | inf = list(self._getcoordinfo()) |
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518 | inf[1] = frame |
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519 | self._setcoordinfo(inf) |
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520 | self._add_history("set_freqframe",varlist) |
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521 | else: |
---|
522 | msg = "Please specify a valid freq type. Valid types are:\n",valid |
---|
523 | if rcParams['verbose']: |
---|
524 | print msg |
---|
525 | else: |
---|
526 | raise TypeError(msg) |
---|
527 | print_log() |
---|
528 | |
---|
529 | def set_dirframe(self, frame=""): |
---|
530 | """ |
---|
531 | Set the frame type of the Direction on the sky. |
---|
532 | Parameters: |
---|
533 | frame: an optional frame type, default ''. Valid frames are: |
---|
534 | 'J2000', 'B1950', 'GALACTIC' |
---|
535 | Examples: |
---|
536 | scan.set_dirframe('GALACTIC') |
---|
537 | """ |
---|
538 | varlist = vars() |
---|
539 | try: |
---|
540 | Scantable.set_dirframe(self, frame) |
---|
541 | except RuntimeError,msg: |
---|
542 | if rcParams['verbose']: |
---|
543 | print msg |
---|
544 | else: |
---|
545 | raise |
---|
546 | self._add_history("set_dirframe",varlist) |
---|
547 | |
---|
548 | def get_unit(self): |
---|
549 | """ |
---|
550 | Get the default unit set in this scantable |
---|
551 | Parameters: |
---|
552 | Returns: |
---|
553 | A unit string |
---|
554 | """ |
---|
555 | inf = self._getcoordinfo() |
---|
556 | unit = inf[0] |
---|
557 | if unit == '': unit = 'channel' |
---|
558 | return unit |
---|
559 | |
---|
560 | def get_abcissa(self, rowno=0): |
---|
561 | """ |
---|
562 | Get the abcissa in the current coordinate setup for the currently |
---|
563 | selected Beam/IF/Pol |
---|
564 | Parameters: |
---|
565 | rowno: an optional row number in the scantable. Default is the |
---|
566 | first row, i.e. rowno=0 |
---|
567 | Returns: |
---|
568 | The abcissa values and it's format string (as a dictionary) |
---|
569 | """ |
---|
570 | abc = self._getabcissa(rowno) |
---|
571 | lbl = self._getabcissalabel(rowno) |
---|
572 | print_log() |
---|
573 | return abc, lbl |
---|
574 | |
---|
575 | def flag(self, mask=[]): |
---|
576 | """ |
---|
577 | Flag the selected data using an optional channel mask. |
---|
578 | Parameters: |
---|
579 | mask: an optional channel mask, created with create_mask. Default |
---|
580 | (no mask) is all channels. |
---|
581 | """ |
---|
582 | varlist = vars() |
---|
583 | try: |
---|
584 | self._flag(mask) |
---|
585 | except RuntimeError,msg: |
---|
586 | if rcParams['verbose']: |
---|
587 | print msg |
---|
588 | return |
---|
589 | else: raise |
---|
590 | self._add_history("flag", varlist) |
---|
591 | |
---|
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 | if not self._check_ifs(): |
---|
632 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
633 | asaplog.push(msg) |
---|
634 | n = self.nchan() |
---|
635 | msk = zeros(n) |
---|
636 | # test if args is a 'list' or a 'normal *args - UGLY!!! |
---|
637 | |
---|
638 | ws = (isinstance(args[-1][-1],int) or isinstance(args[-1][-1],float)) and args or args[0] |
---|
639 | for window in ws: |
---|
640 | if (len(window) != 2 or window[0] > window[1] ): |
---|
641 | raise TypeError("A window needs to be defined as [min,max]") |
---|
642 | for i in range(n): |
---|
643 | if data[i] >= window[0] and data[i] < window[1]: |
---|
644 | msk[i] = 1 |
---|
645 | if kwargs.has_key('invert'): |
---|
646 | if kwargs.get('invert'): |
---|
647 | from numarray import logical_not |
---|
648 | msk = logical_not(msk) |
---|
649 | print_log() |
---|
650 | return msk |
---|
651 | |
---|
652 | def get_restfreqs(self): |
---|
653 | """ |
---|
654 | Get the restfrequency(s) stored in this scantable. |
---|
655 | The return value(s) are always of unit 'Hz' |
---|
656 | Parameters: |
---|
657 | none |
---|
658 | Returns: |
---|
659 | a list of doubles |
---|
660 | """ |
---|
661 | return list(self._getrestfreqs()) |
---|
662 | |
---|
663 | |
---|
664 | def set_restfreqs(self, freqs=None, unit='Hz'): |
---|
665 | """ |
---|
666 | Set or replace the restfrequency specified and |
---|
667 | If the 'freqs' argument holds a scalar, |
---|
668 | then that rest frequency will be applied to all the selected |
---|
669 | data. If the 'freqs' argument holds |
---|
670 | a vector, then it MUST be of equal or smaller length than |
---|
671 | the number of IFs (and the available restfrequencies will be |
---|
672 | replaced by this vector). In this case, *all* data have |
---|
673 | the restfrequency set per IF according |
---|
674 | to the corresponding value you give in the 'freqs' vector. |
---|
675 | E.g. 'freqs=[1e9,2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
676 | IF 1 gets restfreq 2e9. |
---|
677 | You can also specify the frequencies via known line names |
---|
678 | from the built-in Lovas table. |
---|
679 | Parameters: |
---|
680 | freqs: list of rest frequency values or string idenitfiers |
---|
681 | unit: unit for rest frequency (default 'Hz') |
---|
682 | |
---|
683 | Example: |
---|
684 | # set the given restfrequency for the whole table |
---|
685 | scan.set_restfreqs(freqs=1.4e9) |
---|
686 | # If thee number of IFs in the data is >= 2 the IF0 gets the first |
---|
687 | # value IF1 the second... |
---|
688 | scan.set_restfreqs(freqs=[1.4e9,1.67e9]) |
---|
689 | #set the given restfrequency for the whole table (by name) |
---|
690 | scan.set_restfreqs(freqs="OH1667") |
---|
691 | |
---|
692 | Note: |
---|
693 | To do more sophisticate Restfrequency setting, e.g. on a |
---|
694 | source and IF basis, use scantable.set_selection() before using |
---|
695 | this function. |
---|
696 | # provide your scantable is call scan |
---|
697 | selection = selector() |
---|
698 | selection.set_name("ORION*") |
---|
699 | selection.set_ifs([1]) |
---|
700 | scan.set_selection(selection) |
---|
701 | scan.set_restfreqs(freqs=86.6e9) |
---|
702 | |
---|
703 | """ |
---|
704 | varlist = vars() |
---|
705 | |
---|
706 | t = type(freqs) |
---|
707 | if isinstance(freqs, int) or isinstance(freqs,float): |
---|
708 | self._setrestfreqs(freqs, unit) |
---|
709 | elif isinstance(freqs, list) or isinstance(freqs,tuple): |
---|
710 | if isinstance(freqs[-1], int) or isinstance(freqs[-1],float): |
---|
711 | sel = selector() |
---|
712 | savesel = self._getselection() |
---|
713 | for i in xrange(len(freqs)): |
---|
714 | sel.set_ifs([i]) |
---|
715 | self._setselection(sel) |
---|
716 | self._setrestfreqs(freqs[i], unit) |
---|
717 | self._setselection(savesel) |
---|
718 | elif isinstance(freqs[-1], str): |
---|
719 | # not yet implemented |
---|
720 | pass |
---|
721 | else: |
---|
722 | return |
---|
723 | self._add_history("set_restfreqs", varlist) |
---|
724 | |
---|
725 | |
---|
726 | |
---|
727 | def history(self): |
---|
728 | hist = list(self._gethistory()) |
---|
729 | out = "-"*80 |
---|
730 | for h in hist: |
---|
731 | if h.startswith("---"): |
---|
732 | out += "\n"+h |
---|
733 | else: |
---|
734 | items = h.split("##") |
---|
735 | date = items[0] |
---|
736 | func = items[1] |
---|
737 | items = items[2:] |
---|
738 | out += "\n"+date+"\n" |
---|
739 | out += "Function: %s\n Parameters:" % (func) |
---|
740 | for i in items: |
---|
741 | s = i.split("=") |
---|
742 | out += "\n %s = %s" % (s[0],s[1]) |
---|
743 | out += "\n"+"-"*80 |
---|
744 | try: |
---|
745 | from IPython.genutils import page as pager |
---|
746 | except ImportError: |
---|
747 | from pydoc import pager |
---|
748 | pager(out) |
---|
749 | return |
---|
750 | |
---|
751 | # |
---|
752 | # Maths business |
---|
753 | # |
---|
754 | |
---|
755 | def average_time(self, mask=None, scanav=False, weight='tint', align=False): |
---|
756 | """ |
---|
757 | Return the (time) average of a scan, or apply it 'insitu'. |
---|
758 | Note: |
---|
759 | in channels only |
---|
760 | The cursor of the output scan is set to 0. |
---|
761 | Parameters: |
---|
762 | one scan or comma separated scans |
---|
763 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
764 | weighting) |
---|
765 | scanav: True averages each scan separately |
---|
766 | False (default) averages all scans together, |
---|
767 | weight: Weighting scheme. 'none', 'var' (1/var(spec) |
---|
768 | weighted), 'tsys' (1/Tsys**2 weighted), 'tint' |
---|
769 | (integration time weighted) or 'tintsys' (Tint/Tsys**2). |
---|
770 | The default is 'tint' |
---|
771 | align: align the spectra in velocity before averaging. It takes |
---|
772 | the time of the first spectrum as reference time. |
---|
773 | Example: |
---|
774 | # time average the scantable without using a mask |
---|
775 | newscan = scan.average_time() |
---|
776 | """ |
---|
777 | varlist = vars() |
---|
778 | if weight is None: weight = 'TINT' |
---|
779 | if mask is None: mask = () |
---|
780 | if scanav: |
---|
781 | scanav = "SCAN" |
---|
782 | else: |
---|
783 | scanav = "NONE" |
---|
784 | scan = (self,) |
---|
785 | try: |
---|
786 | if align: |
---|
787 | scan = (self.freq_align(insitu=False),) |
---|
788 | s = scantable(self._math._average(scan, mask, weight.upper(), |
---|
789 | scanav)) |
---|
790 | except RuntimeError,msg: |
---|
791 | if rcParams['verbose']: |
---|
792 | print msg |
---|
793 | return |
---|
794 | else: raise |
---|
795 | s._add_history("average_time",varlist) |
---|
796 | print_log() |
---|
797 | return s |
---|
798 | |
---|
799 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None): |
---|
800 | """ |
---|
801 | Return a scan where all spectra are converted to either |
---|
802 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
803 | By default the function tries to look the values up internally. |
---|
804 | If it can't find them (or if you want to over-ride), you must |
---|
805 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
806 | also if you don't set it). jyperk takes precedence if you set both. |
---|
807 | Parameters: |
---|
808 | jyperk: the Jy / K conversion factor |
---|
809 | eta: the aperture efficiency |
---|
810 | d: the geomtric diameter (metres) |
---|
811 | insitu: if False a new scantable is returned. |
---|
812 | Otherwise, the scaling is done in-situ |
---|
813 | The default is taken from .asaprc (False) |
---|
814 | allaxes: if True apply to all spectra. Otherwise |
---|
815 | apply only to the selected (beam/pol/if)spectra only |
---|
816 | The default is taken from .asaprc (True if none) |
---|
817 | """ |
---|
818 | if insitu is None: insitu = rcParams['insitu'] |
---|
819 | self._math._setinsitu(insitu) |
---|
820 | varlist = vars() |
---|
821 | if jyperk is None: jyperk = -1.0 |
---|
822 | if d is None: d = -1.0 |
---|
823 | if eta is None: eta = -1.0 |
---|
824 | s = scantable(self._math._convertflux(self, d, eta, jyperk)) |
---|
825 | s._add_history("convert_flux", varlist) |
---|
826 | print_log() |
---|
827 | if insitu: self._assign(s) |
---|
828 | else: return s |
---|
829 | |
---|
830 | def gain_el(self, poly=None, filename="", method="linear", insitu=None): |
---|
831 | """ |
---|
832 | Return a scan after applying a gain-elevation correction. |
---|
833 | The correction can be made via either a polynomial or a |
---|
834 | table-based interpolation (and extrapolation if necessary). |
---|
835 | You specify polynomial coefficients, an ascii table or neither. |
---|
836 | If you specify neither, then a polynomial correction will be made |
---|
837 | with built in coefficients known for certain telescopes (an error |
---|
838 | will occur if the instrument is not known). |
---|
839 | The data and Tsys are *divided* by the scaling factors. |
---|
840 | Parameters: |
---|
841 | poly: Polynomial coefficients (default None) to compute a |
---|
842 | gain-elevation correction as a function of |
---|
843 | elevation (in degrees). |
---|
844 | filename: The name of an ascii file holding correction factors. |
---|
845 | The first row of the ascii file must give the column |
---|
846 | names and these MUST include columns |
---|
847 | "ELEVATION" (degrees) and "FACTOR" (multiply data |
---|
848 | by this) somewhere. |
---|
849 | The second row must give the data type of the |
---|
850 | column. Use 'R' for Real and 'I' for Integer. |
---|
851 | An example file would be |
---|
852 | (actual factors are arbitrary) : |
---|
853 | |
---|
854 | TIME ELEVATION FACTOR |
---|
855 | R R R |
---|
856 | 0.1 0 0.8 |
---|
857 | 0.2 20 0.85 |
---|
858 | 0.3 40 0.9 |
---|
859 | 0.4 60 0.85 |
---|
860 | 0.5 80 0.8 |
---|
861 | 0.6 90 0.75 |
---|
862 | method: Interpolation method when correcting from a table. |
---|
863 | Values are "nearest", "linear" (default), "cubic" |
---|
864 | and "spline" |
---|
865 | insitu: if False a new scantable is returned. |
---|
866 | Otherwise, the scaling is done in-situ |
---|
867 | The default is taken from .asaprc (False) |
---|
868 | """ |
---|
869 | |
---|
870 | if insitu is None: insitu = rcParams['insitu'] |
---|
871 | self._math._setinsitu(insitu) |
---|
872 | varlist = vars() |
---|
873 | if poly is None: |
---|
874 | poly = () |
---|
875 | from os.path import expandvars |
---|
876 | filename = expandvars(filename) |
---|
877 | s = scantable(self._math._gainel(self, poly, filename, method)) |
---|
878 | s._add_history("gain_el", varlist) |
---|
879 | print_log() |
---|
880 | if insitu: self._assign(s) |
---|
881 | else: return s |
---|
882 | |
---|
883 | def freq_align(self, reftime=None, method='cubic', insitu=None): |
---|
884 | """ |
---|
885 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
886 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
887 | set_freqframe. |
---|
888 | Parameters: |
---|
889 | reftime: reference time to align at. By default, the time of |
---|
890 | the first row of data is used. |
---|
891 | method: Interpolation method for regridding the spectra. |
---|
892 | Choose from "nearest", "linear", "cubic" (default) |
---|
893 | and "spline" |
---|
894 | insitu: if False a new scantable is returned. |
---|
895 | Otherwise, the scaling is done in-situ |
---|
896 | The default is taken from .asaprc (False) |
---|
897 | """ |
---|
898 | if insitu is None: insitu = rcParams["insitu"] |
---|
899 | self._math._setinsitu(insitu) |
---|
900 | varlist = vars() |
---|
901 | if reftime is None: reftime = "" |
---|
902 | s = scantable(self._math._freq_align(self, reftime, method)) |
---|
903 | s._add_history("freq_align", varlist) |
---|
904 | print_log() |
---|
905 | if insitu: self._assign(s) |
---|
906 | else: return s |
---|
907 | |
---|
908 | def opacity(self, tau, insitu=None): |
---|
909 | """ |
---|
910 | Apply an opacity correction. The data |
---|
911 | and Tsys are multiplied by the correction factor. |
---|
912 | Parameters: |
---|
913 | tau: Opacity from which the correction factor is |
---|
914 | exp(tau*ZD) |
---|
915 | where ZD is the zenith-distance |
---|
916 | insitu: if False a new scantable is returned. |
---|
917 | Otherwise, the scaling is done in-situ |
---|
918 | The default is taken from .asaprc (False) |
---|
919 | """ |
---|
920 | if insitu is None: insitu = rcParams['insitu'] |
---|
921 | self._math._setinsitu(insitu) |
---|
922 | varlist = vars() |
---|
923 | s = scantable(self._math._opacity(self, tau)) |
---|
924 | s._add_history("opacity", varlist) |
---|
925 | print_log() |
---|
926 | if insitu: self._assign(s) |
---|
927 | else: return s |
---|
928 | |
---|
929 | def bin(self, width=5, insitu=None): |
---|
930 | """ |
---|
931 | Return a scan where all spectra have been binned up. |
---|
932 | width: The bin width (default=5) in pixels |
---|
933 | insitu: if False a new scantable is returned. |
---|
934 | Otherwise, the scaling is done in-situ |
---|
935 | The default is taken from .asaprc (False) |
---|
936 | """ |
---|
937 | if insitu is None: insitu = rcParams['insitu'] |
---|
938 | self._math._setinsitu(insitu) |
---|
939 | varlist = vars() |
---|
940 | s = scantable(self._math._bin(self, width)) |
---|
941 | s._add_history("bin",varlist) |
---|
942 | print_log() |
---|
943 | if insitu: self._assign(s) |
---|
944 | else: return s |
---|
945 | |
---|
946 | |
---|
947 | def resample(self, width=5, method='cubic', insitu=None): |
---|
948 | """ |
---|
949 | Return a scan where all spectra have been binned up |
---|
950 | width: The bin width (default=5) in pixels |
---|
951 | method: Interpolation method when correcting from a table. |
---|
952 | Values are "nearest", "linear", "cubic" (default) |
---|
953 | and "spline" |
---|
954 | insitu: if False a new scantable is returned. |
---|
955 | Otherwise, the scaling is done in-situ |
---|
956 | The default is taken from .asaprc (False) |
---|
957 | """ |
---|
958 | if insitu is None: insitu = rcParams['insitu'] |
---|
959 | self._math._setinsitu(insitu) |
---|
960 | varlist = vars() |
---|
961 | s = scantable(self._math._resample(self, method, width)) |
---|
962 | s._add_history("resample",varlist) |
---|
963 | print_log() |
---|
964 | if insitu: self._assign(s) |
---|
965 | else: return s |
---|
966 | |
---|
967 | |
---|
968 | def average_pol(self, mask=None, weight='none'): |
---|
969 | """ |
---|
970 | Average the Polarisations together. |
---|
971 | Parameters: |
---|
972 | mask: An optional mask defining the region, where the |
---|
973 | averaging will be applied. The output will have all |
---|
974 | specified points masked. |
---|
975 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
976 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
977 | """ |
---|
978 | varlist = vars() |
---|
979 | if mask is None: |
---|
980 | mask = () |
---|
981 | s = scantable(self._math._averagepol(self, mask, weight.upper())) |
---|
982 | s._add_history("average_pol",varlist) |
---|
983 | print_log() |
---|
984 | return s |
---|
985 | |
---|
986 | def convert_pol(self, poltype=None): |
---|
987 | """ |
---|
988 | Convert the data to a different polarisation type. |
---|
989 | Parameters: |
---|
990 | poltype: The new polarisation type. Valid types are: |
---|
991 | "linear", "stokes" and "circular" |
---|
992 | """ |
---|
993 | varlist = vars() |
---|
994 | try: |
---|
995 | s = scantable(self._math._convertpol(self, poltype)) |
---|
996 | except RuntimeError,msg: |
---|
997 | if rcParams['verbose']: |
---|
998 | print msg |
---|
999 | return |
---|
1000 | else: |
---|
1001 | raise |
---|
1002 | s._add_history("convert_pol",varlist) |
---|
1003 | print_log() |
---|
1004 | return s |
---|
1005 | |
---|
1006 | def smooth(self, kernel="hanning", width=5.0, insitu=None): |
---|
1007 | """ |
---|
1008 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
1009 | Parameters: |
---|
1010 | scan: The input scan |
---|
1011 | kernel: The type of smoothing kernel. Select from |
---|
1012 | 'hanning' (default), 'gaussian' and 'boxcar'. |
---|
1013 | The first three characters are sufficient. |
---|
1014 | width: The width of the kernel in pixels. For hanning this is |
---|
1015 | ignored otherwise it defauls to 5 pixels. |
---|
1016 | For 'gaussian' it is the Full Width Half |
---|
1017 | Maximum. For 'boxcar' it is the full width. |
---|
1018 | insitu: if False a new scantable is returned. |
---|
1019 | Otherwise, the scaling is done in-situ |
---|
1020 | The default is taken from .asaprc (False) |
---|
1021 | Example: |
---|
1022 | none |
---|
1023 | """ |
---|
1024 | if insitu is None: insitu = rcParams['insitu'] |
---|
1025 | self._math._setinsitu(insitu) |
---|
1026 | varlist = vars() |
---|
1027 | s = scantable(self._math._smooth(self,kernel,width)) |
---|
1028 | s._add_history("smooth", varlist) |
---|
1029 | print_log() |
---|
1030 | if insitu: self._assign(s) |
---|
1031 | else: return s |
---|
1032 | |
---|
1033 | |
---|
1034 | def poly_baseline(self, mask=None, order=0, insitu=None): |
---|
1035 | """ |
---|
1036 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
1037 | Parameters: |
---|
1038 | scan: a scantable |
---|
1039 | mask: an optional mask |
---|
1040 | order: the order of the polynomial (default is 0) |
---|
1041 | insitu: if False a new scantable is returned. |
---|
1042 | Otherwise, the scaling is done in-situ |
---|
1043 | The default is taken from .asaprc (False) |
---|
1044 | allaxes: If True (default) apply to all spectra. Otherwise |
---|
1045 | apply only to the selected (beam/pol/if)spectra only |
---|
1046 | The default is taken from .asaprc (True if none) |
---|
1047 | Example: |
---|
1048 | # return a scan baselined by a third order polynomial, |
---|
1049 | # not using a mask |
---|
1050 | bscan = scan.poly_baseline(order=3) |
---|
1051 | """ |
---|
1052 | if insitu is None: insitu = rcParams['insitu'] |
---|
1053 | varlist = vars() |
---|
1054 | if mask is None: |
---|
1055 | from numarray import ones |
---|
1056 | mask = list(ones(self.nchan(-1))) |
---|
1057 | from asap.asapfitter import fitter |
---|
1058 | f = fitter() |
---|
1059 | f.set_scan(self, mask) |
---|
1060 | f.set_function(poly=order) |
---|
1061 | s = f.auto_fit(insitu) |
---|
1062 | s._add_history("poly_baseline", varlist) |
---|
1063 | print_log() |
---|
1064 | if insitu: self._assign(s) |
---|
1065 | else: return s |
---|
1066 | |
---|
1067 | def auto_poly_baseline(self, mask=[], edge=(0,0), order=0, |
---|
1068 | threshold=3, insitu=None): |
---|
1069 | """ |
---|
1070 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
1071 | Spectral lines are detected first using linefinder and masked out |
---|
1072 | to avoid them affecting the baseline solution. |
---|
1073 | |
---|
1074 | Parameters: |
---|
1075 | mask: an optional mask retreived from scantable |
---|
1076 | edge: an optional number of channel to drop at |
---|
1077 | the edge of spectrum. If only one value is |
---|
1078 | specified, the same number will be dropped from |
---|
1079 | both sides of the spectrum. Default is to keep |
---|
1080 | all channels. Nested tuples represent individual |
---|
1081 | edge selection for different IFs (a number of spectral |
---|
1082 | channels can be different) |
---|
1083 | order: the order of the polynomial (default is 0) |
---|
1084 | threshold: the threshold used by line finder. It is better to |
---|
1085 | keep it large as only strong lines affect the |
---|
1086 | baseline solution. |
---|
1087 | insitu: if False a new scantable is returned. |
---|
1088 | Otherwise, the scaling is done in-situ |
---|
1089 | The default is taken from .asaprc (False) |
---|
1090 | |
---|
1091 | Example: |
---|
1092 | scan2=scan.auto_poly_baseline(order=7) |
---|
1093 | """ |
---|
1094 | if insitu is None: insitu = rcParams['insitu'] |
---|
1095 | varlist = vars() |
---|
1096 | from asap.asapfitter import fitter |
---|
1097 | from asap.asaplinefind import linefinder |
---|
1098 | from asap import _is_sequence_or_number as _is_valid |
---|
1099 | |
---|
1100 | # check whether edge is set up for each IF individually |
---|
1101 | individualEdge = False; |
---|
1102 | if len(edge)>1: |
---|
1103 | if isinstance(edge[0],list) or isinstance(edge[0],tuple): |
---|
1104 | individualEdge = True; |
---|
1105 | |
---|
1106 | if not _is_valid(edge, int) and not individualEdge: |
---|
1107 | raise ValueError, "Parameter 'edge' has to be an integer or a \ |
---|
1108 | pair of integers specified as a tuple. Nested tuples are allowed \ |
---|
1109 | to make individual selection for different IFs." |
---|
1110 | |
---|
1111 | curedge = (0,0) |
---|
1112 | if individualEdge: |
---|
1113 | for edge_par in edge: |
---|
1114 | if not _is_valid(edge,int): |
---|
1115 | raise ValueError, "Each element of the 'edge' tuple has \ |
---|
1116 | to be a pair of integers or an integer." |
---|
1117 | else: |
---|
1118 | curedge = edge; |
---|
1119 | |
---|
1120 | # setup fitter |
---|
1121 | f = fitter() |
---|
1122 | f.set_function(poly=order) |
---|
1123 | |
---|
1124 | # setup line finder |
---|
1125 | fl=linefinder() |
---|
1126 | fl.set_options(threshold=threshold) |
---|
1127 | |
---|
1128 | if not insitu: |
---|
1129 | workscan=self.copy() |
---|
1130 | else: |
---|
1131 | workscan=self |
---|
1132 | |
---|
1133 | fl.set_scan(workscan) |
---|
1134 | |
---|
1135 | rows=range(workscan.nrow()) |
---|
1136 | from asap import asaplog |
---|
1137 | asaplog.push("Processing:") |
---|
1138 | for r in rows: |
---|
1139 | 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)) |
---|
1140 | asaplog.push(msg, False) |
---|
1141 | |
---|
1142 | # figure out edge parameter |
---|
1143 | if individualEdge: |
---|
1144 | if len(edge)>=workscan.getif(r): |
---|
1145 | raise RuntimeError, "Number of edge elements appear to be less than the number of IFs" |
---|
1146 | curedge = edge[workscan.getif(r)] |
---|
1147 | |
---|
1148 | # setup line finder |
---|
1149 | fl.find_lines(r,mask,curedge) |
---|
1150 | f.set_scan(workscan, fl.get_mask()) |
---|
1151 | f.x = workscan._getabcissa(r) |
---|
1152 | f.y = workscan._getspectrum(r) |
---|
1153 | f.data = None |
---|
1154 | f.fit() |
---|
1155 | x = f.get_parameters() |
---|
1156 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
1157 | workscan._add_history("poly_baseline", varlist) |
---|
1158 | if insitu: |
---|
1159 | self._assign(workscan) |
---|
1160 | else: |
---|
1161 | return workscan |
---|
1162 | |
---|
1163 | def rotate_linpolphase(self, angle): |
---|
1164 | """ |
---|
1165 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
1166 | This is always done in situ in the raw data. So if you call this |
---|
1167 | function more than once then each call rotates the phase further. |
---|
1168 | Parameters: |
---|
1169 | angle: The angle (degrees) to rotate (add) by. |
---|
1170 | Examples: |
---|
1171 | scan.rotate_linpolphase(2.3) |
---|
1172 | """ |
---|
1173 | varlist = vars() |
---|
1174 | self._math._rotate_linpolphase(self, angle) |
---|
1175 | self._add_history("rotate_linpolphase", varlist) |
---|
1176 | print_log() |
---|
1177 | return |
---|
1178 | |
---|
1179 | |
---|
1180 | def rotate_xyphase(self, angle): |
---|
1181 | """ |
---|
1182 | Rotate the phase of the XY correlation. This is always done in situ |
---|
1183 | in the data. So if you call this function more than once |
---|
1184 | then each call rotates the phase further. |
---|
1185 | Parameters: |
---|
1186 | angle: The angle (degrees) to rotate (add) by. |
---|
1187 | Examples: |
---|
1188 | scan.rotate_xyphase(2.3) |
---|
1189 | """ |
---|
1190 | varlist = vars() |
---|
1191 | self._math._rotate_xyphase(self, angle) |
---|
1192 | self._add_history("rotate_xyphase", varlist) |
---|
1193 | print_log() |
---|
1194 | return |
---|
1195 | |
---|
1196 | def swap_linears(self): |
---|
1197 | """ |
---|
1198 | Swap the linear polarisations XX and YY |
---|
1199 | """ |
---|
1200 | varlist = vars() |
---|
1201 | self._math._swap_linears(self) |
---|
1202 | self._add_history("swap_linears", varlist) |
---|
1203 | print_log() |
---|
1204 | return |
---|
1205 | |
---|
1206 | def invert_phase(self): |
---|
1207 | """ |
---|
1208 | Invert the phase of the complex polarisation |
---|
1209 | """ |
---|
1210 | varlist = vars() |
---|
1211 | self._math._invert_phase(self) |
---|
1212 | self._add_history("invert_phase", varlist) |
---|
1213 | print_log() |
---|
1214 | return |
---|
1215 | |
---|
1216 | def add(self, offset, insitu=None): |
---|
1217 | """ |
---|
1218 | Return a scan where all spectra have the offset added |
---|
1219 | Parameters: |
---|
1220 | offset: the offset |
---|
1221 | insitu: if False a new scantable is returned. |
---|
1222 | Otherwise, the scaling is done in-situ |
---|
1223 | The default is taken from .asaprc (False) |
---|
1224 | """ |
---|
1225 | if insitu is None: insitu = rcParams['insitu'] |
---|
1226 | self._math._setinsitu(insitu) |
---|
1227 | varlist = vars() |
---|
1228 | s = scantable(self._math._unaryop(self, offset, "ADD", False)) |
---|
1229 | s._add_history("add",varlist) |
---|
1230 | print_log() |
---|
1231 | if insitu: |
---|
1232 | self._assign(s) |
---|
1233 | else: |
---|
1234 | return s |
---|
1235 | |
---|
1236 | def scale(self, factor, tsys=True, insitu=None,): |
---|
1237 | """ |
---|
1238 | Return a scan where all spectra are scaled by the give 'factor' |
---|
1239 | Parameters: |
---|
1240 | factor: the scaling factor |
---|
1241 | insitu: if False a new scantable is returned. |
---|
1242 | Otherwise, the scaling is done in-situ |
---|
1243 | The default is taken from .asaprc (False) |
---|
1244 | tsys: if True (default) then apply the operation to Tsys |
---|
1245 | as well as the data |
---|
1246 | """ |
---|
1247 | if insitu is None: insitu = rcParams['insitu'] |
---|
1248 | self._math._setinsitu(insitu) |
---|
1249 | varlist = vars() |
---|
1250 | s = scantable(self._math._unaryop(self, factor, "MUL", tsys)) |
---|
1251 | s._add_history("scale",varlist) |
---|
1252 | print_log() |
---|
1253 | if insitu: |
---|
1254 | self._assign(s) |
---|
1255 | else: |
---|
1256 | return s |
---|
1257 | |
---|
1258 | def auto_quotient(self, mode='time', preserve=True): |
---|
1259 | """ |
---|
1260 | This function allows to build quotients automatically. |
---|
1261 | It assumes the observation to have the same numer of |
---|
1262 | "ons" and "offs" |
---|
1263 | It will support "closest off in time" in the future |
---|
1264 | Parameters: |
---|
1265 | mode: the on/off detection mode; 'suffix' (default) |
---|
1266 | 'suffix' identifies 'off' scans by the |
---|
1267 | trailing '_R' (Mopra/Parkes) or |
---|
1268 | '_e'/'_w' (Tid) |
---|
1269 | preserve: you can preserve (default) the continuum or |
---|
1270 | remove it. The equations used are |
---|
1271 | preserve: Output = Toff * (on/off) - Toff |
---|
1272 | remove: Output = Tref * (on/off) - Ton |
---|
1273 | """ |
---|
1274 | modes = ["time"] |
---|
1275 | if not mode in modes: |
---|
1276 | msg = "please provide valid mode. Valid modes are %s" % (modes) |
---|
1277 | raise ValueError(msg) |
---|
1278 | varlist = vars() |
---|
1279 | s = scantable(self._math._quotient(self, mode, preserve)) |
---|
1280 | s._add_history("auto_quotient",varlist) |
---|
1281 | print_log() |
---|
1282 | return s |
---|
1283 | |
---|
1284 | |
---|
1285 | |
---|
1286 | |
---|
1287 | def freq_switch(self, insitu=None): |
---|
1288 | """ |
---|
1289 | Apply frequency switching to the data. |
---|
1290 | Parameters: |
---|
1291 | insitu: if False a new scantable is returned. |
---|
1292 | Otherwise, the swictching is done in-situ |
---|
1293 | The default is taken from .asaprc (False) |
---|
1294 | Example: |
---|
1295 | none |
---|
1296 | """ |
---|
1297 | if insitu is None: insitu = rcParams['insitu'] |
---|
1298 | self._math._setinsitu(insitu) |
---|
1299 | varlist = vars() |
---|
1300 | s = scantable(self._math._freqswitch(self)) |
---|
1301 | s._add_history("freq_switch",varlist) |
---|
1302 | print_log() |
---|
1303 | if insitu: self._assign(s) |
---|
1304 | else: return s |
---|
1305 | |
---|
1306 | def recalc_azel(self): |
---|
1307 | """ |
---|
1308 | Recalculate the azimuth and elevation for each position. |
---|
1309 | Parameters: |
---|
1310 | none |
---|
1311 | Example: |
---|
1312 | """ |
---|
1313 | varlist = vars() |
---|
1314 | self._recalcazel() |
---|
1315 | self._add_history("recalc_azel", varlist) |
---|
1316 | print_log() |
---|
1317 | return |
---|
1318 | |
---|
1319 | def __add__(self, other): |
---|
1320 | varlist = vars() |
---|
1321 | s = None |
---|
1322 | if isinstance(other, scantable): |
---|
1323 | print "scantable + scantable NYI" |
---|
1324 | return |
---|
1325 | elif isinstance(other, float): |
---|
1326 | s = scantable(self._math._unaryop(self, other, "ADD", False)) |
---|
1327 | else: |
---|
1328 | raise TypeError("Other input is not a scantable or float value") |
---|
1329 | s._add_history("operator +", varlist) |
---|
1330 | print_log() |
---|
1331 | return s |
---|
1332 | |
---|
1333 | def __sub__(self, other): |
---|
1334 | """ |
---|
1335 | implicit on all axes and on Tsys |
---|
1336 | """ |
---|
1337 | varlist = vars() |
---|
1338 | s = None |
---|
1339 | if isinstance(other, scantable): |
---|
1340 | print "scantable - scantable NYI" |
---|
1341 | return |
---|
1342 | elif isinstance(other, float): |
---|
1343 | s = scantable(self._math._unaryop(self, other, "SUB", False)) |
---|
1344 | else: |
---|
1345 | raise TypeError("Other input is not a scantable or float value") |
---|
1346 | s._add_history("operator -", varlist) |
---|
1347 | print_log() |
---|
1348 | return s |
---|
1349 | |
---|
1350 | def __mul__(self, other): |
---|
1351 | """ |
---|
1352 | implicit on all axes and on Tsys |
---|
1353 | """ |
---|
1354 | varlist = vars() |
---|
1355 | s = None |
---|
1356 | if isinstance(other, scantable): |
---|
1357 | print "scantable * scantable NYI" |
---|
1358 | return |
---|
1359 | elif isinstance(other, float): |
---|
1360 | s = scantable(self._math._unaryop(self, other, "MUL", False)) |
---|
1361 | else: |
---|
1362 | raise TypeError("Other input is not a scantable or float value") |
---|
1363 | s._add_history("operator *", varlist) |
---|
1364 | print_log() |
---|
1365 | return s |
---|
1366 | |
---|
1367 | |
---|
1368 | def __div__(self, other): |
---|
1369 | """ |
---|
1370 | implicit on all axes and on Tsys |
---|
1371 | """ |
---|
1372 | varlist = vars() |
---|
1373 | s = None |
---|
1374 | if isinstance(other, scantable): |
---|
1375 | print "scantable / scantable NYI" |
---|
1376 | return |
---|
1377 | elif isinstance(other, float): |
---|
1378 | if other == 0.0: |
---|
1379 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
1380 | s = scantable(self._math._unaryop(self, other, "DIV", False)) |
---|
1381 | else: |
---|
1382 | raise TypeError("Other input is not a scantable or float value") |
---|
1383 | s._add_history("operator /", varlist) |
---|
1384 | print_log() |
---|
1385 | return s |
---|
1386 | |
---|
1387 | def get_fit(self, row=0): |
---|
1388 | """ |
---|
1389 | Print or return the stored fits for a row in the scantable |
---|
1390 | Parameters: |
---|
1391 | row: the row which the fit has been applied to. |
---|
1392 | """ |
---|
1393 | if row > self.nrow(): |
---|
1394 | return |
---|
1395 | from asap.asapfit import asapfit |
---|
1396 | fit = asapfit(self._getfit(row)) |
---|
1397 | if rcParams['verbose']: |
---|
1398 | print fit |
---|
1399 | return |
---|
1400 | else: |
---|
1401 | return fit.as_dict() |
---|
1402 | |
---|
1403 | def _add_history(self, funcname, parameters): |
---|
1404 | # create date |
---|
1405 | sep = "##" |
---|
1406 | from datetime import datetime |
---|
1407 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
1408 | hist = dstr+sep |
---|
1409 | hist += funcname+sep#cdate+sep |
---|
1410 | if parameters.has_key('self'): del parameters['self'] |
---|
1411 | for k,v in parameters.iteritems(): |
---|
1412 | if type(v) is dict: |
---|
1413 | for k2,v2 in v.iteritems(): |
---|
1414 | hist += k2 |
---|
1415 | hist += "=" |
---|
1416 | if isinstance(v2,scantable): |
---|
1417 | hist += 'scantable' |
---|
1418 | elif k2 == 'mask': |
---|
1419 | if isinstance(v2,list) or isinstance(v2,tuple): |
---|
1420 | hist += str(self._zip_mask(v2)) |
---|
1421 | else: |
---|
1422 | hist += str(v2) |
---|
1423 | else: |
---|
1424 | hist += str(v2) |
---|
1425 | else: |
---|
1426 | hist += k |
---|
1427 | hist += "=" |
---|
1428 | if isinstance(v,scantable): |
---|
1429 | hist += 'scantable' |
---|
1430 | elif k == 'mask': |
---|
1431 | if isinstance(v,list) or isinstance(v,tuple): |
---|
1432 | hist += str(self._zip_mask(v)) |
---|
1433 | else: |
---|
1434 | hist += str(v) |
---|
1435 | else: |
---|
1436 | hist += str(v) |
---|
1437 | hist += sep |
---|
1438 | hist = hist[:-2] # remove trailing '##' |
---|
1439 | self._addhistory(hist) |
---|
1440 | |
---|
1441 | |
---|
1442 | def _zip_mask(self, mask): |
---|
1443 | mask = list(mask) |
---|
1444 | i = 0 |
---|
1445 | segments = [] |
---|
1446 | while mask[i:].count(1): |
---|
1447 | i += mask[i:].index(1) |
---|
1448 | if mask[i:].count(0): |
---|
1449 | j = i + mask[i:].index(0) |
---|
1450 | else: |
---|
1451 | j = len(mask) |
---|
1452 | segments.append([i,j]) |
---|
1453 | i = j |
---|
1454 | return segments |
---|
1455 | |
---|
1456 | def _get_ordinate_label(self): |
---|
1457 | fu = "("+self.get_fluxunit()+")" |
---|
1458 | import re |
---|
1459 | lbl = "Intensity" |
---|
1460 | if re.match(".K.",fu): |
---|
1461 | lbl = "Brightness Temperature "+ fu |
---|
1462 | elif re.match(".Jy.",fu): |
---|
1463 | lbl = "Flux density "+ fu |
---|
1464 | return lbl |
---|
1465 | |
---|
1466 | def _check_ifs(self): |
---|
1467 | nchans = [self.nchan(i) for i in range(self.nif(-1))] |
---|
1468 | nchans = filter(lambda t: t > 0, nchans) |
---|
1469 | return (sum(nchans)/len(nchans) == nchans[0]) |
---|
1470 | |
---|
1471 | def _fill(self, names, unit, average): |
---|
1472 | import os |
---|
1473 | varlist = vars() |
---|
1474 | from asap._asap import stfiller |
---|
1475 | first = True |
---|
1476 | fullnames = [] |
---|
1477 | for name in names: |
---|
1478 | name = os.path.expandvars(name) |
---|
1479 | name = os.path.expanduser(name) |
---|
1480 | if not os.path.exists(name): |
---|
1481 | msg = "File '%s' does not exists" % (name) |
---|
1482 | if rcParams['verbose']: |
---|
1483 | asaplog.push(msg) |
---|
1484 | print asaplog.pop().strip() |
---|
1485 | return |
---|
1486 | raise IOError(msg) |
---|
1487 | fullnames.append(name) |
---|
1488 | if average: |
---|
1489 | asaplog.push('Auto averaging integrations') |
---|
1490 | for name in fullnames: |
---|
1491 | r = stfiller() |
---|
1492 | msg = "Importing %s..." % (name) |
---|
1493 | asaplog.push(msg,False) |
---|
1494 | print_log() |
---|
1495 | r._open(name,-1,-1) |
---|
1496 | r._read() |
---|
1497 | tbl = r._getdata() |
---|
1498 | if average: |
---|
1499 | tbl = self._math._average((tbl,),(),'NONE','SCAN') |
---|
1500 | #tbl = tbl2 |
---|
1501 | if not first: |
---|
1502 | tbl = self._math._merge([self, tbl]) |
---|
1503 | #tbl = tbl2 |
---|
1504 | Scantable.__init__(self, tbl) |
---|
1505 | r._close() |
---|
1506 | del r,tbl |
---|
1507 | first = False |
---|
1508 | if unit is not None: |
---|
1509 | self.set_fluxunit(unit) |
---|
1510 | self.set_freqframe(rcParams['scantable.freqframe']) |
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1511 | #self._add_history("scantable", varlist) |
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1512 | |
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