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 asap import asaplog |
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5 | from asap import selector |
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6 | from asap import NUM |
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7 | from asap import linecatalog |
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8 | |
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9 | class scantable(Scantable): |
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10 | """ |
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11 | The ASAP container for scans |
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12 | """ |
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13 | |
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14 | def __init__(self, filename, average=None, unit=None): |
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15 | """ |
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16 | Create a scantable from a saved one or make a reference |
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17 | Parameters: |
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18 | filename: the name of an asap table on disk |
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19 | or |
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20 | the name of a rpfits/sdfits/ms file |
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21 | (integrations within scans are auto averaged |
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22 | and the whole file is read) |
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23 | or |
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24 | [advanced] a reference to an existing |
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25 | scantable |
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26 | average: average all integrations withinb a scan on read. |
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27 | The default (True) is taken from .asaprc. |
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28 | unit: brightness unit; must be consistent with K or Jy. |
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29 | Over-rides the default selected by the reader |
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30 | (input rpfits/sdfits/ms) or replaces the value |
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31 | in existing scantables |
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32 | """ |
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33 | if average is None: |
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34 | average = rcParams['scantable.autoaverage'] |
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35 | varlist = vars() |
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36 | from asap._asap import stmath |
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37 | self._math = stmath() |
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38 | if isinstance(filename, Scantable): |
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39 | Scantable.__init__(self, filename) |
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40 | else: |
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41 | if isinstance(filename, str): |
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42 | import os.path |
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43 | filename = os.path.expandvars(filename) |
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44 | filename = os.path.expanduser(filename) |
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45 | if not os.path.exists(filename): |
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46 | s = "File '%s' not found." % (filename) |
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47 | if rcParams['verbose']: |
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48 | asaplog.push(s) |
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49 | print asaplog.pop().strip() |
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50 | return |
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51 | raise IOError(s) |
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52 | if os.path.isdir(filename) \ |
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53 | and not os.path.exists(filename+'/table.f1'): |
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54 | # crude check if asap table |
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55 | if os.path.exists(filename+'/table.info'): |
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56 | ondisk = rcParams['scantable.storage'] == 'disk' |
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57 | Scantable.__init__(self, filename, ondisk) |
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58 | if unit is not None: |
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59 | self.set_fluxunit(unit) |
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60 | self.set_freqframe(rcParams['scantable.freqframe']) |
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61 | else: |
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62 | msg = "The given file '%s'is not a valid " \ |
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63 | "asap table." % (filename) |
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64 | if rcParams['verbose']: |
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65 | print msg |
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66 | return |
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67 | else: |
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68 | raise IOError(msg) |
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69 | else: |
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70 | self._fill([filename], unit, average) |
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71 | elif (isinstance(filename, list) or isinstance(filename, tuple)) \ |
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72 | and isinstance(filename[-1], str): |
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73 | self._fill(filename, unit, average) |
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74 | self._add_history("scantable", varlist) |
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75 | print_log() |
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76 | |
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77 | def save(self, name=None, format=None, overwrite=False): |
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78 | """ |
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79 | Store the scantable on disk. This can be an asap (aips++) Table, SDFITS, |
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80 | Image FITS or MS2 format. |
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81 | Parameters: |
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82 | name: the name of the outputfile. For format "ASCII" |
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83 | this is the root file name (data in 'name'.txt |
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84 | and header in 'name'_header.txt) |
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85 | format: an optional file format. Default is ASAP. |
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86 | Allowed are - 'ASAP' (save as ASAP [aips++] Table), |
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87 | 'SDFITS' (save as SDFITS file) |
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88 | 'ASCII' (saves as ascii text file) |
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89 | 'MS2' (saves as an aips++ |
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90 | MeasurementSet V2) |
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91 | overwrite: If the file should be overwritten if it exists. |
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92 | The default False is to return with warning |
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93 | without writing the output. USE WITH CARE. |
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94 | Example: |
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95 | scan.save('myscan.asap') |
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96 | scan.save('myscan.sdfits', 'SDFITS') |
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97 | """ |
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98 | from os import path |
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99 | if format is None: format = rcParams['scantable.save'] |
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100 | suffix = '.'+format.lower() |
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101 | if name is None or name == "": |
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102 | name = 'scantable'+suffix |
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103 | msg = "No filename given. Using default name %s..." % name |
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104 | asaplog.push(msg) |
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105 | name = path.expandvars(name) |
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106 | if path.isfile(name) or path.isdir(name): |
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107 | if not overwrite: |
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108 | msg = "File %s exists." % name |
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109 | if rcParams['verbose']: |
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110 | print msg |
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111 | return |
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112 | else: |
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113 | raise IOError(msg) |
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114 | format2 = format.upper() |
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115 | if format2 == 'ASAP': |
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116 | self._save(name) |
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117 | else: |
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118 | from asap._asap import stwriter as stw |
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119 | writer = stw(format2) |
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120 | writer.write(self, name) |
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121 | print_log() |
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122 | return |
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123 | |
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124 | def copy(self): |
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125 | """ |
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126 | Return a copy of this scantable. |
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127 | Parameters: |
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128 | none |
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129 | Example: |
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130 | copiedscan = scan.copy() |
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131 | """ |
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132 | sd = scantable(Scantable._copy(self)) |
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133 | return sd |
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134 | |
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135 | def drop_scan(self, scanid=None): |
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136 | """ |
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137 | Return a new scantable where the specified scan number(s) has(have) |
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138 | been dropped. |
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139 | Parameters: |
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140 | scanid: a (list of) scan number(s) |
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141 | """ |
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142 | from asap import _is_sequence_or_number as _is_valid |
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143 | from asap import _to_list |
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144 | from asap import unique |
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145 | if not _is_valid(scanid): |
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146 | if rcParams['verbose']: |
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147 | print "Please specify a scanno to drop from the scantable" |
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148 | return |
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149 | else: |
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150 | raise RuntimeError("No scan given") |
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151 | try: |
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152 | scanid = _to_list(scanid) |
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153 | allscans = unique([ self.getscan(i) for i in range(self.nrow())]) |
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154 | for sid in scanid: allscans.remove(sid) |
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155 | if len(allscans) == 0: |
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156 | raise ValueError("Can't remove all scans") |
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157 | except ValueError: |
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158 | if rcParams['verbose']: |
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159 | print "Couldn't find any match." |
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160 | return |
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161 | else: raise |
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162 | try: |
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163 | bsel = self.get_selection() |
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164 | sel = selector() |
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165 | sel.set_scans(allscans) |
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166 | self.set_selection(bsel+sel) |
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167 | scopy = self._copy() |
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168 | self.set_selection(bsel) |
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169 | return scantable(scopy) |
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170 | except RuntimeError: |
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171 | if rcParams['verbose']: |
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172 | print "Couldn't find any match." |
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173 | else: |
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174 | raise |
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175 | |
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176 | |
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177 | def get_scan(self, scanid=None): |
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178 | """ |
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179 | Return a specific scan (by scanno) or collection of scans (by |
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180 | source name) in a new scantable. |
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181 | Parameters: |
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182 | scanid: a (list of) scanno or a source name, unix-style |
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183 | patterns are accepted for source name matching, e.g. |
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184 | '*_R' gets all 'ref scans |
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185 | Example: |
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186 | # get all scans containing the source '323p459' |
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187 | newscan = scan.get_scan('323p459') |
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188 | # get all 'off' scans |
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189 | refscans = scan.get_scan('*_R') |
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190 | # get a susbset of scans by scanno (as listed in scan.summary()) |
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191 | newscan = scan.get_scan([0, 2, 7, 10]) |
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192 | """ |
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193 | if scanid is None: |
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194 | if rcParams['verbose']: |
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195 | print "Please specify a scan no or name to " \ |
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196 | "retrieve from the scantable" |
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197 | return |
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198 | else: |
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199 | raise RuntimeError("No scan given") |
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200 | |
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201 | try: |
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202 | bsel = self.get_selection() |
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203 | sel = selector() |
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204 | if type(scanid) is str: |
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205 | sel.set_name(scanid) |
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206 | self.set_selection(bsel+sel) |
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207 | scopy = self._copy() |
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208 | self.set_selection(bsel) |
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209 | return scantable(scopy) |
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210 | elif type(scanid) is int: |
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211 | sel.set_scans([scanid]) |
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212 | self.set_selection(bsel+sel) |
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213 | scopy = self._copy() |
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214 | self.set_selection(bsel) |
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215 | return scantable(scopy) |
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216 | elif type(scanid) is list: |
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217 | sel.set_scans(scanid) |
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218 | self.set_selection(sel) |
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219 | scopy = self._copy() |
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220 | self.set_selection(bsel) |
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221 | return scantable(scopy) |
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222 | else: |
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223 | msg = "Illegal scanid type, use 'int' or 'list' if ints." |
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224 | if rcParams['verbose']: |
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225 | print msg |
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226 | else: |
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227 | raise TypeError(msg) |
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228 | except RuntimeError: |
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229 | if rcParams['verbose']: print "Couldn't find any match." |
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230 | else: raise |
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231 | |
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232 | def __str__(self): |
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233 | return Scantable._summary(self, True) |
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234 | |
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235 | def summary(self, filename=None): |
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236 | """ |
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237 | Print a summary of the contents of this scantable. |
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238 | Parameters: |
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239 | filename: the name of a file to write the putput to |
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240 | Default - no file output |
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241 | verbose: print extra info such as the frequency table |
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242 | The default (False) is taken from .asaprc |
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243 | """ |
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244 | info = Scantable._summary(self, True) |
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245 | #if verbose is None: verbose = rcParams['scantable.verbosesummary'] |
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246 | if filename is not None: |
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247 | if filename is "": |
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248 | filename = 'scantable_summary.txt' |
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249 | from os.path import expandvars, isdir |
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250 | filename = expandvars(filename) |
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251 | if not isdir(filename): |
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252 | data = open(filename, 'w') |
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253 | data.write(info) |
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254 | data.close() |
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255 | else: |
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256 | msg = "Illegal file name '%s'." % (filename) |
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257 | if rcParams['verbose']: |
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258 | print msg |
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259 | else: |
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260 | raise IOError(msg) |
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261 | if rcParams['verbose']: |
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262 | try: |
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263 | from IPython.genutils import page as pager |
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264 | except ImportError: |
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265 | from pydoc import pager |
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266 | pager(info) |
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267 | else: |
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268 | return info |
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269 | |
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270 | |
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271 | def get_selection(self): |
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272 | """ |
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273 | Get the selection object currently set on this scantable. |
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274 | Parameters: |
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275 | none |
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276 | Example: |
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277 | sel = scan.get_selection() |
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278 | sel.set_ifs(0) # select IF 0 |
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279 | scan.set_selection(sel) # apply modified selection |
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280 | """ |
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281 | return selector(self._getselection()) |
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282 | |
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283 | def set_selection(self, selection=selector()): |
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284 | """ |
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285 | Select a subset of the data. All following operations on this scantable |
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286 | are only applied to thi selection. |
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287 | Parameters: |
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288 | selection: a selector object (default unset the selection) |
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289 | Examples: |
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290 | sel = selector() # create a selection object |
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291 | self.set_scans([0, 3]) # select SCANNO 0 and 3 |
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292 | scan.set_selection(sel) # set the selection |
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293 | scan.summary() # will only print summary of scanno 0 an 3 |
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294 | scan.set_selection() # unset the selection |
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295 | """ |
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296 | self._setselection(selection) |
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297 | |
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298 | def stats(self, stat='stddev', mask=None): |
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299 | """ |
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300 | Determine the specified statistic of the current beam/if/pol |
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301 | Takes a 'mask' as an optional parameter to specify which |
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302 | channels should be excluded. |
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303 | Parameters: |
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304 | stat: 'min', 'max', 'sumsq', 'sum', 'mean' |
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305 | 'var', 'stddev', 'avdev', 'rms', 'median' |
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306 | mask: an optional mask specifying where the statistic |
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307 | should be determined. |
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308 | Example: |
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309 | scan.set_unit('channel') |
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310 | msk = scan.create_mask([100, 200], [500, 600]) |
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311 | scan.stats(stat='mean', mask=m) |
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312 | """ |
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313 | if mask == None: |
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314 | mask = [] |
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315 | axes = ['Beam', 'IF', 'Pol', 'Time'] |
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316 | if not self._check_ifs(): |
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317 | raise ValueError("Cannot apply mask as the IFs have different " |
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318 | "number of channels. Please use setselection() " |
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319 | "to select individual IFs") |
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320 | |
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321 | statvals = self._math._stats(self, mask, stat) |
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322 | out = '' |
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323 | axes = [] |
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324 | for i in range(self.nrow()): |
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325 | axis = [] |
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326 | axis.append(self.getscan(i)) |
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327 | axis.append(self.getbeam(i)) |
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328 | axis.append(self.getif(i)) |
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329 | axis.append(self.getpol(i)) |
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330 | axis.append(self.getcycle(i)) |
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331 | axes.append(axis) |
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332 | tm = self._gettime(i) |
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333 | src = self._getsourcename(i) |
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334 | out += 'Scan[%d] (%s) ' % (axis[0], src) |
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335 | out += 'Time[%s]:\n' % (tm) |
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336 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1]) |
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337 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2]) |
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338 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3]) |
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339 | out += '= %3.3f\n' % (statvals[i]) |
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340 | out += "--------------------------------------------------\n" |
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341 | |
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342 | if rcParams['verbose']: |
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343 | print "--------------------------------------------------" |
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344 | print " ", stat |
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345 | print "--------------------------------------------------" |
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346 | print out |
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347 | return |
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348 | else: |
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349 | retval = { 'axesnames': ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'], |
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350 | 'axes' : axes, |
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351 | 'data': statvals} |
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352 | return retval |
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353 | |
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354 | def stddev(self, mask=None): |
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355 | """ |
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356 | Determine the standard deviation of the current beam/if/pol |
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357 | Takes a 'mask' as an optional parameter to specify which |
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358 | channels should be excluded. |
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359 | Parameters: |
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360 | mask: an optional mask specifying where the standard |
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361 | deviation should be determined. |
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362 | |
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363 | Example: |
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364 | scan.set_unit('channel') |
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365 | msk = scan.create_mask([100, 200], [500, 600]) |
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366 | scan.stddev(mask=m) |
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367 | """ |
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368 | return self.stats(stat='stddev', mask=mask); |
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369 | |
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370 | |
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371 | def get_column_names(self): |
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372 | """ |
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373 | Return a list of column names, which can be used for selection. |
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374 | """ |
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375 | return list(Scantable.get_column_names(self)) |
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376 | |
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377 | def get_tsys(self): |
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378 | """ |
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379 | Return the System temperatures. |
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380 | Parameters: |
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381 | |
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382 | Returns: |
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383 | a list of Tsys values for the current selection |
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384 | """ |
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385 | |
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386 | return self._row_callback(self._gettsys, "Tsys") |
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387 | |
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388 | def _row_callback(self, callback, label): |
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389 | axes = [] |
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390 | axesnames = ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'] |
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391 | out = "" |
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392 | outvec = [] |
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393 | for i in range(self.nrow()): |
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394 | axis = [] |
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395 | axis.append(self.getscan(i)) |
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396 | axis.append(self.getbeam(i)) |
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397 | axis.append(self.getif(i)) |
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398 | axis.append(self.getpol(i)) |
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399 | axis.append(self.getcycle(i)) |
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400 | axes.append(axis) |
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401 | tm = self._gettime(i) |
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402 | src = self._getsourcename(i) |
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403 | out += 'Scan[%d] (%s) ' % (axis[0], src) |
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404 | out += 'Time[%s]:\n' % (tm) |
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405 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1]) |
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406 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2]) |
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407 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3]) |
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408 | outvec.append(callback(i)) |
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409 | out += '= %3.3f\n' % (outvec[i]) |
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410 | out += "--------------------------------------------------\n" |
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411 | if rcParams['verbose']: |
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412 | print "--------------------------------------------------" |
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413 | print " %s" % (label) |
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414 | print "--------------------------------------------------" |
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415 | print out |
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416 | # disabled because the vector seems more useful |
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417 | #retval = {'axesnames': axesnames, 'axes': axes, 'data': outvec} |
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418 | return outvec |
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419 | |
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420 | def _get_column(self, callback, row=-1): |
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421 | """ |
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422 | """ |
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423 | if row == -1: |
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424 | return [callback(i) for i in range(self.nrow())] |
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425 | else: |
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426 | if 0 <= row < self.nrow(): |
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427 | return callback(row) |
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428 | |
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429 | |
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430 | def get_time(self, row=-1): |
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431 | """ |
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432 | Get a list of time stamps for the observations. |
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433 | Return a string 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 | from time import strptime |
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440 | from datetime import datetime |
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441 | times = self._get_column(self._gettime, row) |
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442 | format = "%Y/%m/%d/%H:%M:%S" |
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443 | if isinstance(times, list): |
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444 | return [datetime(*strptime(i, format)[:6]) for i in times] |
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445 | else: |
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446 | return datetime(*strptime(times, format)[:6]) |
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447 | |
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448 | def get_sourcename(self, row=-1): |
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449 | """ |
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450 | Get a list source names for the observations. |
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451 | Return a string for each integration in the scantable. |
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452 | Parameters: |
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453 | row: row no of integration. Default -1 return all rows |
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454 | Example: |
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455 | none |
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456 | """ |
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457 | return self._get_column(self._getsourcename, row) |
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458 | |
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459 | def get_elevation(self, row=-1): |
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460 | """ |
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461 | Get a list of elevations for the observations. |
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462 | Return a float for each integration in the scantable. |
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463 | Parameters: |
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464 | row: row no of integration. Default -1 return all rows |
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465 | Example: |
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466 | none |
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467 | """ |
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468 | return self._get_column(self._getelevation, row) |
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469 | |
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470 | def get_azimuth(self, row=-1): |
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471 | """ |
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472 | Get a list of azimuths for the observations. |
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473 | Return a float for each integration in the scantable. |
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474 | Parameters: |
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475 | row: row no of integration. Default -1 return all rows |
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476 | Example: |
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477 | none |
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478 | """ |
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479 | return self._get_column(self._getazimuth, row) |
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480 | |
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481 | def get_parangle(self, row=-1): |
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482 | """ |
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483 | Get a list of parallactic angles for the observations. |
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484 | Return a float for each integration in the scantable. |
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485 | Parameters: |
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486 | row: row no of integration. Default -1 return all rows |
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487 | Example: |
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488 | none |
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489 | """ |
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490 | return self._get_column(self._getparangle, row) |
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491 | |
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492 | def get_direction(self, row=-1): |
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493 | """ |
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494 | Get a list of Positions on the sky (direction) for the observations. |
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495 | Return a float for each integration in the scantable. |
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496 | Parameters: |
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497 | row: row no of integration. Default -1 return all rows |
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498 | Example: |
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499 | none |
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500 | """ |
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501 | return self._get_column(self._getdirection, row) |
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502 | |
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503 | def set_unit(self, unit='channel'): |
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504 | """ |
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505 | Set the unit for all following operations on this scantable |
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506 | Parameters: |
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507 | unit: optional unit, default is 'channel' |
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508 | one of '*Hz', 'km/s', 'channel', '' |
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509 | """ |
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510 | varlist = vars() |
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511 | if unit in ['', 'pixel', 'channel']: |
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512 | unit = '' |
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513 | inf = list(self._getcoordinfo()) |
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514 | inf[0] = unit |
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515 | self._setcoordinfo(inf) |
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516 | self._add_history("set_unit", varlist) |
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517 | |
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518 | def set_instrument(self, instr): |
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519 | """ |
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520 | Set the instrument for subsequent processing |
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521 | Parameters: |
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522 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
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523 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
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524 | """ |
---|
525 | self._setInstrument(instr) |
---|
526 | self._add_history("set_instument", vars()) |
---|
527 | print_log() |
---|
528 | |
---|
529 | def set_feedtype(self, feedtype): |
---|
530 | """ |
---|
531 | Overwrite the feed type, which might not be set correctly. |
---|
532 | Parameters: |
---|
533 | feedtype: 'linear' or 'circular' |
---|
534 | """ |
---|
535 | self._setfeedtype(feedtype) |
---|
536 | self._add_history("set_feedtype", vars()) |
---|
537 | print_log() |
---|
538 | |
---|
539 | def set_doppler(self, doppler='RADIO'): |
---|
540 | """ |
---|
541 | Set the doppler for all following operations on this scantable. |
---|
542 | Parameters: |
---|
543 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
---|
544 | """ |
---|
545 | varlist = vars() |
---|
546 | inf = list(self._getcoordinfo()) |
---|
547 | inf[2] = doppler |
---|
548 | self._setcoordinfo(inf) |
---|
549 | self._add_history("set_doppler", vars()) |
---|
550 | print_log() |
---|
551 | |
---|
552 | def set_freqframe(self, frame=None): |
---|
553 | """ |
---|
554 | Set the frame type of the Spectral Axis. |
---|
555 | Parameters: |
---|
556 | frame: an optional frame type, default 'LSRK'. Valid frames are: |
---|
557 | 'REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', |
---|
558 | 'GEO', 'GALACTO', 'LGROUP', 'CMB' |
---|
559 | Examples: |
---|
560 | scan.set_freqframe('BARY') |
---|
561 | """ |
---|
562 | if frame is None: frame = rcParams['scantable.freqframe'] |
---|
563 | varlist = vars() |
---|
564 | valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
565 | 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
566 | |
---|
567 | if frame in valid: |
---|
568 | inf = list(self._getcoordinfo()) |
---|
569 | inf[1] = frame |
---|
570 | self._setcoordinfo(inf) |
---|
571 | self._add_history("set_freqframe", varlist) |
---|
572 | else: |
---|
573 | msg = "Please specify a valid freq type. Valid types are:\n", valid |
---|
574 | if rcParams['verbose']: |
---|
575 | print msg |
---|
576 | else: |
---|
577 | raise TypeError(msg) |
---|
578 | print_log() |
---|
579 | |
---|
580 | def set_dirframe(self, frame=""): |
---|
581 | """ |
---|
582 | Set the frame type of the Direction on the sky. |
---|
583 | Parameters: |
---|
584 | frame: an optional frame type, default ''. Valid frames are: |
---|
585 | 'J2000', 'B1950', 'GALACTIC' |
---|
586 | Examples: |
---|
587 | scan.set_dirframe('GALACTIC') |
---|
588 | """ |
---|
589 | varlist = vars() |
---|
590 | try: |
---|
591 | Scantable.set_dirframe(self, frame) |
---|
592 | except RuntimeError, msg: |
---|
593 | if rcParams['verbose']: |
---|
594 | print msg |
---|
595 | else: |
---|
596 | raise |
---|
597 | self._add_history("set_dirframe", varlist) |
---|
598 | |
---|
599 | def get_unit(self): |
---|
600 | """ |
---|
601 | Get the default unit set in this scantable |
---|
602 | Parameters: |
---|
603 | Returns: |
---|
604 | A unit string |
---|
605 | """ |
---|
606 | inf = self._getcoordinfo() |
---|
607 | unit = inf[0] |
---|
608 | if unit == '': unit = 'channel' |
---|
609 | return unit |
---|
610 | |
---|
611 | def get_abcissa(self, rowno=0): |
---|
612 | """ |
---|
613 | Get the abcissa in the current coordinate setup for the currently |
---|
614 | selected Beam/IF/Pol |
---|
615 | Parameters: |
---|
616 | rowno: an optional row number in the scantable. Default is the |
---|
617 | first row, i.e. rowno=0 |
---|
618 | Returns: |
---|
619 | The abcissa values and it's format string (as a dictionary) |
---|
620 | """ |
---|
621 | abc = self._getabcissa(rowno) |
---|
622 | lbl = self._getabcissalabel(rowno) |
---|
623 | print_log() |
---|
624 | return abc, lbl |
---|
625 | |
---|
626 | def flag(self, mask=None): |
---|
627 | """ |
---|
628 | Flag the selected data using an optional channel mask. |
---|
629 | Parameters: |
---|
630 | mask: an optional channel mask, created with create_mask. Default |
---|
631 | (no mask) is all channels. |
---|
632 | """ |
---|
633 | varlist = vars() |
---|
634 | if mask is None: |
---|
635 | mask = [] |
---|
636 | try: |
---|
637 | self._flag(mask) |
---|
638 | except RuntimeError, msg: |
---|
639 | if rcParams['verbose']: |
---|
640 | print msg |
---|
641 | return |
---|
642 | else: raise |
---|
643 | self._add_history("flag", varlist) |
---|
644 | |
---|
645 | def lag_flag(self, frequency, width=0.0, unit="GHz", insitu=None): |
---|
646 | """ |
---|
647 | Flag the data in 'lag' space by providing a frequency to remove. |
---|
648 | Flagged data in the scantable gets set to 0.0 before the fft. |
---|
649 | No taper is applied. |
---|
650 | Parameters: |
---|
651 | frequency: the frequency (really a period within the bandwidth) to remove |
---|
652 | width: the width of the frequency to remove, to remove a range |
---|
653 | of frequencies aroung the centre. |
---|
654 | unit: the frequency unit (default "GHz") |
---|
655 | Notes: |
---|
656 | It is recommended to flag edges of the band or strong signals beforehand. |
---|
657 | """ |
---|
658 | if insitu is None: insitu = rcParams['insitu'] |
---|
659 | self._math._setinsitu(insitu) |
---|
660 | varlist = vars() |
---|
661 | base = { "GHz": 100000000., "MHz": 1000000., "kHz": 1000., "Hz": 1. } |
---|
662 | if not base.has_key(unit): |
---|
663 | raise ValueError("%s is not a valid unit." % unit) |
---|
664 | try: |
---|
665 | s = scantable(self._math._lag_flag(self, frequency*base[unit], |
---|
666 | width*base[unit])) |
---|
667 | except RuntimeError, msg: |
---|
668 | if rcParams['verbose']: |
---|
669 | print msg |
---|
670 | return |
---|
671 | else: raise |
---|
672 | s._add_history("lag_flag", varlist) |
---|
673 | print_log() |
---|
674 | if insitu: |
---|
675 | self._assign(s) |
---|
676 | else: |
---|
677 | return s |
---|
678 | |
---|
679 | |
---|
680 | def create_mask(self, *args, **kwargs): |
---|
681 | """ |
---|
682 | Compute and return a mask based on [min, max] windows. |
---|
683 | The specified windows are to be INCLUDED, when the mask is |
---|
684 | applied. |
---|
685 | Parameters: |
---|
686 | [min, max], [min2, max2], ... |
---|
687 | Pairs of start/end points (inclusive)specifying the regions |
---|
688 | to be masked |
---|
689 | invert: optional argument. If specified as True, |
---|
690 | return an inverted mask, i.e. the regions |
---|
691 | specified are EXCLUDED |
---|
692 | row: create the mask using the specified row for |
---|
693 | unit conversions, default is row=0 |
---|
694 | only necessary if frequency varies over rows. |
---|
695 | Example: |
---|
696 | scan.set_unit('channel') |
---|
697 | a) |
---|
698 | msk = scan.create_mask([400, 500], [800, 900]) |
---|
699 | # masks everything outside 400 and 500 |
---|
700 | # and 800 and 900 in the unit 'channel' |
---|
701 | |
---|
702 | b) |
---|
703 | msk = scan.create_mask([400, 500], [800, 900], invert=True) |
---|
704 | # masks the regions between 400 and 500 |
---|
705 | # and 800 and 900 in the unit 'channel' |
---|
706 | c) |
---|
707 | mask only channel 400 |
---|
708 | msk = scan.create_mask([400, 400]) |
---|
709 | """ |
---|
710 | row = 0 |
---|
711 | if kwargs.has_key("row"): |
---|
712 | row = kwargs.get("row") |
---|
713 | data = self._getabcissa(row) |
---|
714 | u = self._getcoordinfo()[0] |
---|
715 | if rcParams['verbose']: |
---|
716 | if u == "": u = "channel" |
---|
717 | msg = "The current mask window unit is %s" % u |
---|
718 | i = self._check_ifs() |
---|
719 | if not i: |
---|
720 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
721 | asaplog.push(msg) |
---|
722 | n = self.nchan() |
---|
723 | msk = NUM.zeros(n) |
---|
724 | # test if args is a 'list' or a 'normal *args - UGLY!!! |
---|
725 | |
---|
726 | ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \ |
---|
727 | and args or args[0] |
---|
728 | for window in ws: |
---|
729 | if (len(window) != 2 or window[0] > window[1] ): |
---|
730 | raise TypeError("A window needs to be defined as [min, max]") |
---|
731 | for i in range(n): |
---|
732 | if data[i] >= window[0] and data[i] <= window[1]: |
---|
733 | msk[i] = 1 |
---|
734 | if kwargs.has_key('invert'): |
---|
735 | if kwargs.get('invert'): |
---|
736 | msk = NUM.logical_not(msk) |
---|
737 | print_log() |
---|
738 | return msk |
---|
739 | |
---|
740 | def get_restfreqs(self): |
---|
741 | """ |
---|
742 | Get the restfrequency(s) stored in this scantable. |
---|
743 | The return value(s) are always of unit 'Hz' |
---|
744 | Parameters: |
---|
745 | none |
---|
746 | Returns: |
---|
747 | a list of doubles |
---|
748 | """ |
---|
749 | return list(self._getrestfreqs()) |
---|
750 | |
---|
751 | |
---|
752 | def set_restfreqs(self, freqs=None, unit='Hz'): |
---|
753 | """ |
---|
754 | Set or replace the restfrequency specified and |
---|
755 | If the 'freqs' argument holds a scalar, |
---|
756 | then that rest frequency will be applied to all the selected |
---|
757 | data. If the 'freqs' argument holds |
---|
758 | a vector, then it MUST be of equal or smaller length than |
---|
759 | the number of IFs (and the available restfrequencies will be |
---|
760 | replaced by this vector). In this case, *all* data have |
---|
761 | the restfrequency set per IF according |
---|
762 | to the corresponding value you give in the 'freqs' vector. |
---|
763 | E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
764 | IF 1 gets restfreq 2e9. |
---|
765 | You can also specify the frequencies via a linecatalog/ |
---|
766 | |
---|
767 | Parameters: |
---|
768 | freqs: list of rest frequency values or string idenitfiers |
---|
769 | unit: unit for rest frequency (default 'Hz') |
---|
770 | |
---|
771 | Example: |
---|
772 | # set the given restfrequency for the whole table |
---|
773 | scan.set_restfreqs(freqs=1.4e9) |
---|
774 | # If thee number of IFs in the data is >= 2 the IF0 gets the first |
---|
775 | # value IF1 the second... |
---|
776 | scan.set_restfreqs(freqs=[1.4e9, 1.67e9]) |
---|
777 | #set the given restfrequency for the whole table (by name) |
---|
778 | scan.set_restfreqs(freqs="OH1667") |
---|
779 | |
---|
780 | Note: |
---|
781 | To do more sophisticate Restfrequency setting, e.g. on a |
---|
782 | source and IF basis, use scantable.set_selection() before using |
---|
783 | this function. |
---|
784 | # provide your scantable is call scan |
---|
785 | selection = selector() |
---|
786 | selection.set_name("ORION*") |
---|
787 | selection.set_ifs([1]) |
---|
788 | scan.set_selection(selection) |
---|
789 | scan.set_restfreqs(freqs=86.6e9) |
---|
790 | |
---|
791 | """ |
---|
792 | varlist = vars() |
---|
793 | from asap import linecatalog |
---|
794 | # simple value |
---|
795 | if isinstance(freqs, int) or isinstance(freqs, float): |
---|
796 | self._setrestfreqs(freqs, "",unit) |
---|
797 | # list of values |
---|
798 | elif isinstance(freqs, list) or isinstance(freqs, tuple): |
---|
799 | # list values are scalars |
---|
800 | if isinstance(freqs[-1], int) or isinstance(freqs[-1], float): |
---|
801 | sel = selector() |
---|
802 | savesel = self._getselection() |
---|
803 | for i in xrange(len(freqs)): |
---|
804 | sel.set_ifs([i]) |
---|
805 | self._setselection(sel) |
---|
806 | self._setrestfreqs(freqs[i], "",unit) |
---|
807 | self._setselection(savesel) |
---|
808 | # list values are tuples, (value, name) |
---|
809 | elif isinstance(freqs[-1], dict): |
---|
810 | sel = selector() |
---|
811 | savesel = self._getselection() |
---|
812 | for i in xrange(len(freqs)): |
---|
813 | sel.set_ifs([i]) |
---|
814 | self._setselection(sel) |
---|
815 | self._setrestfreqs(freqs[i]["value"], |
---|
816 | freqs[i]["name"], "MHz") |
---|
817 | self._setselection(savesel) |
---|
818 | # freqs are to be taken from a linecatalog |
---|
819 | elif isinstance(freqs, linecatalog): |
---|
820 | sel = selector() |
---|
821 | savesel = self._getselection() |
---|
822 | for i in xrange(freqs.nrow()): |
---|
823 | sel.set_ifs([i]) |
---|
824 | self._setselection(sel) |
---|
825 | self._setrestfreqs(freqs.get_frequency(i), |
---|
826 | freqs.get_name(i), "MHz") |
---|
827 | # ensure that we are not iterating past nIF |
---|
828 | if i == self.nif()-1: break |
---|
829 | self._setselection(savesel) |
---|
830 | else: |
---|
831 | return |
---|
832 | self._add_history("set_restfreqs", varlist) |
---|
833 | |
---|
834 | |
---|
835 | |
---|
836 | def history(self, filename=None): |
---|
837 | """ |
---|
838 | Print the history. Optionally to a file. |
---|
839 | """ |
---|
840 | hist = list(self._gethistory()) |
---|
841 | out = "-"*80 |
---|
842 | for h in hist: |
---|
843 | if h.startswith("---"): |
---|
844 | out += "\n"+h |
---|
845 | else: |
---|
846 | items = h.split("##") |
---|
847 | date = items[0] |
---|
848 | func = items[1] |
---|
849 | items = items[2:] |
---|
850 | out += "\n"+date+"\n" |
---|
851 | out += "Function: %s\n Parameters:" % (func) |
---|
852 | for i in items: |
---|
853 | s = i.split("=") |
---|
854 | out += "\n %s = %s" % (s[0], s[1]) |
---|
855 | out += "\n"+"-"*80 |
---|
856 | if filename is not None: |
---|
857 | if filename is "": |
---|
858 | filename = 'scantable_history.txt' |
---|
859 | import os |
---|
860 | filename = os.path.expandvars(os.path.expanduser(filename)) |
---|
861 | if not os.path.isdir(filename): |
---|
862 | data = open(filename, 'w') |
---|
863 | data.write(out) |
---|
864 | data.close() |
---|
865 | else: |
---|
866 | msg = "Illegal file name '%s'." % (filename) |
---|
867 | if rcParams['verbose']: |
---|
868 | print msg |
---|
869 | else: |
---|
870 | raise IOError(msg) |
---|
871 | if rcParams['verbose']: |
---|
872 | try: |
---|
873 | from IPython.genutils import page as pager |
---|
874 | except ImportError: |
---|
875 | from pydoc import pager |
---|
876 | pager(out) |
---|
877 | else: |
---|
878 | return out |
---|
879 | return |
---|
880 | # |
---|
881 | # Maths business |
---|
882 | # |
---|
883 | |
---|
884 | def average_time(self, mask=None, scanav=False, weight='tint', align=False): |
---|
885 | """ |
---|
886 | Return the (time) weighted average of a scan. |
---|
887 | Note: |
---|
888 | in channels only - align if necessary |
---|
889 | Parameters: |
---|
890 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
891 | weighting) |
---|
892 | scanav: True averages each scan separately |
---|
893 | False (default) averages all scans together, |
---|
894 | weight: Weighting scheme. |
---|
895 | 'none' (mean no weight) |
---|
896 | 'var' (1/var(spec) weighted) |
---|
897 | 'tsys' (1/Tsys**2 weighted) |
---|
898 | 'tint' (integration time weighted) |
---|
899 | 'tintsys' (Tint/Tsys**2) |
---|
900 | 'median' ( median averaging) |
---|
901 | The default is 'tint' |
---|
902 | align: align the spectra in velocity before averaging. It takes |
---|
903 | the time of the first spectrum as reference time. |
---|
904 | Example: |
---|
905 | # time average the scantable without using a mask |
---|
906 | newscan = scan.average_time() |
---|
907 | """ |
---|
908 | varlist = vars() |
---|
909 | if weight is None: weight = 'TINT' |
---|
910 | if mask is None: mask = () |
---|
911 | if scanav: scanav = "SCAN" |
---|
912 | else: scanav = "NONE" |
---|
913 | scan = (self, ) |
---|
914 | try: |
---|
915 | if align: |
---|
916 | scan = (self.freq_align(insitu=False), ) |
---|
917 | s = None |
---|
918 | if weight.upper() == 'MEDIAN': |
---|
919 | s = scantable(self._math._averagechannel(scan[0], 'MEDIAN', |
---|
920 | scanav)) |
---|
921 | else: |
---|
922 | s = scantable(self._math._average(scan, mask, weight.upper(), |
---|
923 | scanav)) |
---|
924 | except RuntimeError, msg: |
---|
925 | if rcParams['verbose']: |
---|
926 | print msg |
---|
927 | return |
---|
928 | else: raise |
---|
929 | s._add_history("average_time", varlist) |
---|
930 | print_log() |
---|
931 | return s |
---|
932 | |
---|
933 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None): |
---|
934 | """ |
---|
935 | Return a scan where all spectra are converted to either |
---|
936 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
937 | By default the function tries to look the values up internally. |
---|
938 | If it can't find them (or if you want to over-ride), you must |
---|
939 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
940 | also if you don't set it). jyperk takes precedence if you set both. |
---|
941 | Parameters: |
---|
942 | jyperk: the Jy / K conversion factor |
---|
943 | eta: the aperture efficiency |
---|
944 | d: the geomtric diameter (metres) |
---|
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 | if jyperk is None: jyperk = -1.0 |
---|
953 | if d is None: d = -1.0 |
---|
954 | if eta is None: eta = -1.0 |
---|
955 | s = scantable(self._math._convertflux(self, d, eta, jyperk)) |
---|
956 | s._add_history("convert_flux", varlist) |
---|
957 | print_log() |
---|
958 | if insitu: self._assign(s) |
---|
959 | else: return s |
---|
960 | |
---|
961 | def gain_el(self, poly=None, filename="", method="linear", insitu=None): |
---|
962 | """ |
---|
963 | Return a scan after applying a gain-elevation correction. |
---|
964 | The correction can be made via either a polynomial or a |
---|
965 | table-based interpolation (and extrapolation if necessary). |
---|
966 | You specify polynomial coefficients, an ascii table or neither. |
---|
967 | If you specify neither, then a polynomial correction will be made |
---|
968 | with built in coefficients known for certain telescopes (an error |
---|
969 | will occur if the instrument is not known). |
---|
970 | The data and Tsys are *divided* by the scaling factors. |
---|
971 | Parameters: |
---|
972 | poly: Polynomial coefficients (default None) to compute a |
---|
973 | gain-elevation correction as a function of |
---|
974 | elevation (in degrees). |
---|
975 | filename: The name of an ascii file holding correction factors. |
---|
976 | The first row of the ascii file must give the column |
---|
977 | names and these MUST include columns |
---|
978 | "ELEVATION" (degrees) and "FACTOR" (multiply data |
---|
979 | by this) somewhere. |
---|
980 | The second row must give the data type of the |
---|
981 | column. Use 'R' for Real and 'I' for Integer. |
---|
982 | An example file would be |
---|
983 | (actual factors are arbitrary) : |
---|
984 | |
---|
985 | TIME ELEVATION FACTOR |
---|
986 | R R R |
---|
987 | 0.1 0 0.8 |
---|
988 | 0.2 20 0.85 |
---|
989 | 0.3 40 0.9 |
---|
990 | 0.4 60 0.85 |
---|
991 | 0.5 80 0.8 |
---|
992 | 0.6 90 0.75 |
---|
993 | method: Interpolation method when correcting from a table. |
---|
994 | Values are "nearest", "linear" (default), "cubic" |
---|
995 | and "spline" |
---|
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 | """ |
---|
1000 | |
---|
1001 | if insitu is None: insitu = rcParams['insitu'] |
---|
1002 | self._math._setinsitu(insitu) |
---|
1003 | varlist = vars() |
---|
1004 | if poly is None: |
---|
1005 | poly = () |
---|
1006 | from os.path import expandvars |
---|
1007 | filename = expandvars(filename) |
---|
1008 | s = scantable(self._math._gainel(self, poly, filename, method)) |
---|
1009 | s._add_history("gain_el", varlist) |
---|
1010 | print_log() |
---|
1011 | if insitu: self._assign(s) |
---|
1012 | else: return s |
---|
1013 | |
---|
1014 | def freq_align(self, reftime=None, method='cubic', insitu=None): |
---|
1015 | """ |
---|
1016 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
1017 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
1018 | set_freqframe. |
---|
1019 | Parameters: |
---|
1020 | reftime: reference time to align at. By default, the time of |
---|
1021 | the first row of data is used. |
---|
1022 | method: Interpolation method for regridding the spectra. |
---|
1023 | Choose from "nearest", "linear", "cubic" (default) |
---|
1024 | and "spline" |
---|
1025 | insitu: if False a new scantable is returned. |
---|
1026 | Otherwise, the scaling is done in-situ |
---|
1027 | The default is taken from .asaprc (False) |
---|
1028 | """ |
---|
1029 | if insitu is None: insitu = rcParams["insitu"] |
---|
1030 | self._math._setinsitu(insitu) |
---|
1031 | varlist = vars() |
---|
1032 | if reftime is None: reftime = "" |
---|
1033 | s = scantable(self._math._freq_align(self, reftime, method)) |
---|
1034 | s._add_history("freq_align", varlist) |
---|
1035 | print_log() |
---|
1036 | if insitu: self._assign(s) |
---|
1037 | else: return s |
---|
1038 | |
---|
1039 | def opacity(self, tau, insitu=None): |
---|
1040 | """ |
---|
1041 | Apply an opacity correction. The data |
---|
1042 | and Tsys are multiplied by the correction factor. |
---|
1043 | Parameters: |
---|
1044 | tau: Opacity from which the correction factor is |
---|
1045 | exp(tau*ZD) |
---|
1046 | where ZD is the zenith-distance |
---|
1047 | insitu: if False a new scantable is returned. |
---|
1048 | Otherwise, the scaling is done in-situ |
---|
1049 | The default is taken from .asaprc (False) |
---|
1050 | """ |
---|
1051 | if insitu is None: insitu = rcParams['insitu'] |
---|
1052 | self._math._setinsitu(insitu) |
---|
1053 | varlist = vars() |
---|
1054 | s = scantable(self._math._opacity(self, tau)) |
---|
1055 | s._add_history("opacity", varlist) |
---|
1056 | print_log() |
---|
1057 | if insitu: self._assign(s) |
---|
1058 | else: return s |
---|
1059 | |
---|
1060 | def bin(self, width=5, insitu=None): |
---|
1061 | """ |
---|
1062 | Return a scan where all spectra have been binned up. |
---|
1063 | width: The bin width (default=5) in pixels |
---|
1064 | insitu: if False a new scantable is returned. |
---|
1065 | Otherwise, the scaling is done in-situ |
---|
1066 | The default is taken from .asaprc (False) |
---|
1067 | """ |
---|
1068 | if insitu is None: insitu = rcParams['insitu'] |
---|
1069 | self._math._setinsitu(insitu) |
---|
1070 | varlist = vars() |
---|
1071 | s = scantable(self._math._bin(self, width)) |
---|
1072 | s._add_history("bin", varlist) |
---|
1073 | print_log() |
---|
1074 | if insitu: self._assign(s) |
---|
1075 | else: return s |
---|
1076 | |
---|
1077 | |
---|
1078 | def resample(self, width=5, method='cubic', insitu=None): |
---|
1079 | """ |
---|
1080 | Return a scan where all spectra have been binned up |
---|
1081 | width: The bin width (default=5) in pixels |
---|
1082 | method: Interpolation method when correcting from a table. |
---|
1083 | Values are "nearest", "linear", "cubic" (default) |
---|
1084 | and "spline" |
---|
1085 | insitu: if False a new scantable is returned. |
---|
1086 | Otherwise, the scaling is done in-situ |
---|
1087 | The default is taken from .asaprc (False) |
---|
1088 | """ |
---|
1089 | if insitu is None: insitu = rcParams['insitu'] |
---|
1090 | self._math._setinsitu(insitu) |
---|
1091 | varlist = vars() |
---|
1092 | s = scantable(self._math._resample(self, method, width)) |
---|
1093 | s._add_history("resample", varlist) |
---|
1094 | print_log() |
---|
1095 | if insitu: self._assign(s) |
---|
1096 | else: return s |
---|
1097 | |
---|
1098 | |
---|
1099 | def average_pol(self, mask=None, weight='none'): |
---|
1100 | """ |
---|
1101 | Average the Polarisations together. |
---|
1102 | Parameters: |
---|
1103 | mask: An optional mask defining the region, where the |
---|
1104 | averaging will be applied. The output will have all |
---|
1105 | specified points masked. |
---|
1106 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
1107 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
1108 | """ |
---|
1109 | varlist = vars() |
---|
1110 | if mask is None: |
---|
1111 | mask = () |
---|
1112 | s = scantable(self._math._averagepol(self, mask, weight.upper())) |
---|
1113 | s._add_history("average_pol", varlist) |
---|
1114 | print_log() |
---|
1115 | return s |
---|
1116 | |
---|
1117 | def average_beam(self, mask=None, weight='none'): |
---|
1118 | """ |
---|
1119 | Average the Beams together. |
---|
1120 | Parameters: |
---|
1121 | mask: An optional mask defining the region, where the |
---|
1122 | averaging will be applied. The output will have all |
---|
1123 | specified points masked. |
---|
1124 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
1125 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
1126 | """ |
---|
1127 | varlist = vars() |
---|
1128 | if mask is None: |
---|
1129 | mask = () |
---|
1130 | s = scantable(self._math._averagebeams(self, mask, weight.upper())) |
---|
1131 | s._add_history("average_beam", varlist) |
---|
1132 | print_log() |
---|
1133 | return s |
---|
1134 | |
---|
1135 | def convert_pol(self, poltype=None): |
---|
1136 | """ |
---|
1137 | Convert the data to a different polarisation type. |
---|
1138 | Parameters: |
---|
1139 | poltype: The new polarisation type. Valid types are: |
---|
1140 | "linear", "stokes" and "circular" |
---|
1141 | """ |
---|
1142 | varlist = vars() |
---|
1143 | try: |
---|
1144 | s = scantable(self._math._convertpol(self, poltype)) |
---|
1145 | except RuntimeError, msg: |
---|
1146 | if rcParams['verbose']: |
---|
1147 | print msg |
---|
1148 | return |
---|
1149 | else: |
---|
1150 | raise |
---|
1151 | s._add_history("convert_pol", varlist) |
---|
1152 | print_log() |
---|
1153 | return s |
---|
1154 | |
---|
1155 | def smooth(self, kernel="hanning", width=5.0, insitu=None): |
---|
1156 | """ |
---|
1157 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
1158 | Parameters: |
---|
1159 | scan: The input scan |
---|
1160 | kernel: The type of smoothing kernel. Select from |
---|
1161 | 'hanning' (default), 'gaussian' and 'boxcar'. |
---|
1162 | The first three characters are sufficient. |
---|
1163 | width: The width of the kernel in pixels. For hanning this is |
---|
1164 | ignored otherwise it defauls to 5 pixels. |
---|
1165 | For 'gaussian' it is the Full Width Half |
---|
1166 | Maximum. For 'boxcar' it is the full width. |
---|
1167 | insitu: if False a new scantable is returned. |
---|
1168 | Otherwise, the scaling is done in-situ |
---|
1169 | The default is taken from .asaprc (False) |
---|
1170 | Example: |
---|
1171 | none |
---|
1172 | """ |
---|
1173 | if insitu is None: insitu = rcParams['insitu'] |
---|
1174 | self._math._setinsitu(insitu) |
---|
1175 | varlist = vars() |
---|
1176 | s = scantable(self._math._smooth(self, kernel.lower(), width)) |
---|
1177 | s._add_history("smooth", varlist) |
---|
1178 | print_log() |
---|
1179 | if insitu: self._assign(s) |
---|
1180 | else: return s |
---|
1181 | |
---|
1182 | |
---|
1183 | def poly_baseline(self, mask=None, order=0, plot=False, insitu=None): |
---|
1184 | """ |
---|
1185 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
1186 | Parameters: |
---|
1187 | scan: a scantable |
---|
1188 | mask: an optional mask |
---|
1189 | order: the order of the polynomial (default is 0) |
---|
1190 | plot: plot the fit and the residual. In this each |
---|
1191 | indivual fit has to be approved, by typing 'y' |
---|
1192 | or 'n' |
---|
1193 | insitu: if False a new scantable is returned. |
---|
1194 | Otherwise, the scaling is done in-situ |
---|
1195 | The default is taken from .asaprc (False) |
---|
1196 | Example: |
---|
1197 | # return a scan baselined by a third order polynomial, |
---|
1198 | # not using a mask |
---|
1199 | bscan = scan.poly_baseline(order=3) |
---|
1200 | """ |
---|
1201 | if insitu is None: insitu = rcParams['insitu'] |
---|
1202 | varlist = vars() |
---|
1203 | if mask is None: |
---|
1204 | mask = list(NUM.ones(self.nchan(-1))) |
---|
1205 | from asap.asapfitter import fitter |
---|
1206 | f = fitter() |
---|
1207 | f.set_scan(self, mask) |
---|
1208 | f.set_function(poly=order) |
---|
1209 | s = f.auto_fit(insitu, plot=plot) |
---|
1210 | s._add_history("poly_baseline", varlist) |
---|
1211 | print_log() |
---|
1212 | if insitu: self._assign(s) |
---|
1213 | else: return s |
---|
1214 | |
---|
1215 | def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0, |
---|
1216 | threshold=3, plot=False, insitu=None): |
---|
1217 | """ |
---|
1218 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
1219 | Spectral lines are detected first using linefinder and masked out |
---|
1220 | to avoid them affecting the baseline solution. |
---|
1221 | |
---|
1222 | Parameters: |
---|
1223 | mask: an optional mask retreived from scantable |
---|
1224 | edge: an optional number of channel to drop at |
---|
1225 | the edge of spectrum. If only one value is |
---|
1226 | specified, the same number will be dropped from |
---|
1227 | both sides of the spectrum. Default is to keep |
---|
1228 | all channels. Nested tuples represent individual |
---|
1229 | edge selection for different IFs (a number of spectral |
---|
1230 | channels can be different) |
---|
1231 | order: the order of the polynomial (default is 0) |
---|
1232 | threshold: the threshold used by line finder. It is better to |
---|
1233 | keep it large as only strong lines affect the |
---|
1234 | baseline solution. |
---|
1235 | plot: plot the fit and the residual. In this each |
---|
1236 | indivual fit has to be approved, by typing 'y' |
---|
1237 | or 'n' |
---|
1238 | insitu: if False a new scantable is returned. |
---|
1239 | Otherwise, the scaling is done in-situ |
---|
1240 | The default is taken from .asaprc (False) |
---|
1241 | |
---|
1242 | Example: |
---|
1243 | scan2=scan.auto_poly_baseline(order=7) |
---|
1244 | """ |
---|
1245 | if insitu is None: insitu = rcParams['insitu'] |
---|
1246 | varlist = vars() |
---|
1247 | from asap.asapfitter import fitter |
---|
1248 | from asap.asaplinefind import linefinder |
---|
1249 | from asap import _is_sequence_or_number as _is_valid |
---|
1250 | |
---|
1251 | # check whether edge is set up for each IF individually |
---|
1252 | individualedge = False; |
---|
1253 | if len(edge) > 1: |
---|
1254 | if isinstance(edge[0], list) or isinstance(edge[0], tuple): |
---|
1255 | individualedge = True; |
---|
1256 | |
---|
1257 | if not _is_valid(edge, int) and not individualedge: |
---|
1258 | raise ValueError, "Parameter 'edge' has to be an integer or a \ |
---|
1259 | pair of integers specified as a tuple. Nested tuples are allowed \ |
---|
1260 | to make individual selection for different IFs." |
---|
1261 | |
---|
1262 | curedge = (0, 0) |
---|
1263 | if individualedge: |
---|
1264 | for edgepar in edge: |
---|
1265 | if not _is_valid(edgepar, int): |
---|
1266 | raise ValueError, "Each element of the 'edge' tuple has \ |
---|
1267 | to be a pair of integers or an integer." |
---|
1268 | else: |
---|
1269 | curedge = edge; |
---|
1270 | |
---|
1271 | # setup fitter |
---|
1272 | f = fitter() |
---|
1273 | f.set_function(poly=order) |
---|
1274 | |
---|
1275 | # setup line finder |
---|
1276 | fl = linefinder() |
---|
1277 | fl.set_options(threshold=threshold) |
---|
1278 | |
---|
1279 | if not insitu: |
---|
1280 | workscan = self.copy() |
---|
1281 | else: |
---|
1282 | workscan = self |
---|
1283 | |
---|
1284 | fl.set_scan(workscan) |
---|
1285 | |
---|
1286 | rows = range(workscan.nrow()) |
---|
1287 | asaplog.push("Processing:") |
---|
1288 | for r in rows: |
---|
1289 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \ |
---|
1290 | (workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \ |
---|
1291 | workscan.getpol(r), workscan.getcycle(r)) |
---|
1292 | asaplog.push(msg, False) |
---|
1293 | |
---|
1294 | # figure out edge parameter |
---|
1295 | if individualedge: |
---|
1296 | if len(edge) >= workscan.getif(r): |
---|
1297 | raise RuntimeError, "Number of edge elements appear to " \ |
---|
1298 | "be less than the number of IFs" |
---|
1299 | curedge = edge[workscan.getif(r)] |
---|
1300 | |
---|
1301 | # setup line finder |
---|
1302 | fl.find_lines(r, mask, curedge) |
---|
1303 | f.set_scan(workscan, fl.get_mask()) |
---|
1304 | f.x = workscan._getabcissa(r) |
---|
1305 | f.y = workscan._getspectrum(r) |
---|
1306 | f.data = None |
---|
1307 | f.fit() |
---|
1308 | x = f.get_parameters() |
---|
1309 | if plot: |
---|
1310 | f.plot(residual=True) |
---|
1311 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
1312 | if x.upper() == 'N': |
---|
1313 | continue |
---|
1314 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
1315 | if plot: |
---|
1316 | f._p.unmap() |
---|
1317 | f._p = None |
---|
1318 | workscan._add_history("auto_poly_baseline", varlist) |
---|
1319 | if insitu: |
---|
1320 | self._assign(workscan) |
---|
1321 | else: |
---|
1322 | return workscan |
---|
1323 | |
---|
1324 | def rotate_linpolphase(self, angle): |
---|
1325 | """ |
---|
1326 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
1327 | This is always done in situ in the raw data. So if you call this |
---|
1328 | function more than once then each call rotates the phase further. |
---|
1329 | Parameters: |
---|
1330 | angle: The angle (degrees) to rotate (add) by. |
---|
1331 | Examples: |
---|
1332 | scan.rotate_linpolphase(2.3) |
---|
1333 | """ |
---|
1334 | varlist = vars() |
---|
1335 | self._math._rotate_linpolphase(self, angle) |
---|
1336 | self._add_history("rotate_linpolphase", varlist) |
---|
1337 | print_log() |
---|
1338 | return |
---|
1339 | |
---|
1340 | |
---|
1341 | def rotate_xyphase(self, angle): |
---|
1342 | """ |
---|
1343 | Rotate the phase of the XY correlation. This is always done in situ |
---|
1344 | in the data. So if you call this function more than once |
---|
1345 | then each call rotates the phase further. |
---|
1346 | Parameters: |
---|
1347 | angle: The angle (degrees) to rotate (add) by. |
---|
1348 | Examples: |
---|
1349 | scan.rotate_xyphase(2.3) |
---|
1350 | """ |
---|
1351 | varlist = vars() |
---|
1352 | self._math._rotate_xyphase(self, angle) |
---|
1353 | self._add_history("rotate_xyphase", varlist) |
---|
1354 | print_log() |
---|
1355 | return |
---|
1356 | |
---|
1357 | def swap_linears(self): |
---|
1358 | """ |
---|
1359 | Swap the linear polarisations XX and YY |
---|
1360 | """ |
---|
1361 | varlist = vars() |
---|
1362 | self._math._swap_linears(self) |
---|
1363 | self._add_history("swap_linears", varlist) |
---|
1364 | print_log() |
---|
1365 | return |
---|
1366 | |
---|
1367 | def invert_phase(self): |
---|
1368 | """ |
---|
1369 | Invert the phase of the complex polarisation |
---|
1370 | """ |
---|
1371 | varlist = vars() |
---|
1372 | self._math._invert_phase(self) |
---|
1373 | self._add_history("invert_phase", varlist) |
---|
1374 | print_log() |
---|
1375 | return |
---|
1376 | |
---|
1377 | def add(self, offset, insitu=None): |
---|
1378 | """ |
---|
1379 | Return a scan where all spectra have the offset added |
---|
1380 | Parameters: |
---|
1381 | offset: the offset |
---|
1382 | insitu: if False a new scantable is returned. |
---|
1383 | Otherwise, the scaling is done in-situ |
---|
1384 | The default is taken from .asaprc (False) |
---|
1385 | """ |
---|
1386 | if insitu is None: insitu = rcParams['insitu'] |
---|
1387 | self._math._setinsitu(insitu) |
---|
1388 | varlist = vars() |
---|
1389 | s = scantable(self._math._unaryop(self, offset, "ADD", False)) |
---|
1390 | s._add_history("add", varlist) |
---|
1391 | print_log() |
---|
1392 | if insitu: |
---|
1393 | self._assign(s) |
---|
1394 | else: |
---|
1395 | return s |
---|
1396 | |
---|
1397 | def scale(self, factor, tsys=True, insitu=None, ): |
---|
1398 | """ |
---|
1399 | Return a scan where all spectra are scaled by the give 'factor' |
---|
1400 | Parameters: |
---|
1401 | factor: the scaling factor |
---|
1402 | insitu: if False a new scantable is returned. |
---|
1403 | Otherwise, the scaling is done in-situ |
---|
1404 | The default is taken from .asaprc (False) |
---|
1405 | tsys: if True (default) then apply the operation to Tsys |
---|
1406 | as well as the data |
---|
1407 | """ |
---|
1408 | if insitu is None: insitu = rcParams['insitu'] |
---|
1409 | self._math._setinsitu(insitu) |
---|
1410 | varlist = vars() |
---|
1411 | s = scantable(self._math._unaryop(self, factor, "MUL", tsys)) |
---|
1412 | s._add_history("scale", varlist) |
---|
1413 | print_log() |
---|
1414 | if insitu: |
---|
1415 | self._assign(s) |
---|
1416 | else: |
---|
1417 | return s |
---|
1418 | |
---|
1419 | def auto_quotient(self, mode='time', preserve=True): |
---|
1420 | """ |
---|
1421 | This function allows to build quotients automatically. |
---|
1422 | It assumes the observation to have the same numer of |
---|
1423 | "ons" and "offs" |
---|
1424 | It will support "closest off in time" in the future |
---|
1425 | Parameters: |
---|
1426 | mode: the on/off detection mode; 'suffix' (default) |
---|
1427 | 'suffix' identifies 'off' scans by the |
---|
1428 | trailing '_R' (Mopra/Parkes) or |
---|
1429 | '_e'/'_w' (Tid) |
---|
1430 | preserve: you can preserve (default) the continuum or |
---|
1431 | remove it. The equations used are |
---|
1432 | preserve: Output = Toff * (on/off) - Toff |
---|
1433 | remove: Output = Toff * (on/off) - Ton |
---|
1434 | """ |
---|
1435 | modes = ["time"] |
---|
1436 | if not mode in modes: |
---|
1437 | msg = "please provide valid mode. Valid modes are %s" % (modes) |
---|
1438 | raise ValueError(msg) |
---|
1439 | varlist = vars() |
---|
1440 | s = scantable(self._math._auto_quotient(self, mode, preserve)) |
---|
1441 | s._add_history("auto_quotient", varlist) |
---|
1442 | print_log() |
---|
1443 | return s |
---|
1444 | |
---|
1445 | def mx_quotient(self, mask = None, weight='median', preserve=True): |
---|
1446 | """ |
---|
1447 | Form a quotient using "off" beams when observing in "MX" mode. |
---|
1448 | Parameters: |
---|
1449 | mask: an optional mask to be used when weight == 'stddev' |
---|
1450 | weight: How to average the off beams. Default is 'median'. |
---|
1451 | preserve: you can preserve (default) the continuum or |
---|
1452 | remove it. The equations used are |
---|
1453 | preserve: Output = Toff * (on/off) - Toff |
---|
1454 | remove: Output = Toff * (on/off) - Ton |
---|
1455 | """ |
---|
1456 | if mask is None: mask = () |
---|
1457 | varlist = vars() |
---|
1458 | on = scantable(self._math._mx_extract(self, 'on')) |
---|
1459 | preoff = scantable(self._math._mx_extract(self, 'off')) |
---|
1460 | off = preoff.average_time(mask=mask, weight=weight, scanav=False) |
---|
1461 | from asapmath import quotient |
---|
1462 | q = quotient(on, off, preserve) |
---|
1463 | q._add_history("mx_quotient", varlist) |
---|
1464 | print_log() |
---|
1465 | return q |
---|
1466 | |
---|
1467 | def freq_switch(self, insitu=None): |
---|
1468 | """ |
---|
1469 | Apply frequency switching to the data. |
---|
1470 | Parameters: |
---|
1471 | insitu: if False a new scantable is returned. |
---|
1472 | Otherwise, the swictching is done in-situ |
---|
1473 | The default is taken from .asaprc (False) |
---|
1474 | Example: |
---|
1475 | none |
---|
1476 | """ |
---|
1477 | if insitu is None: insitu = rcParams['insitu'] |
---|
1478 | self._math._setinsitu(insitu) |
---|
1479 | varlist = vars() |
---|
1480 | s = scantable(self._math._freqswitch(self)) |
---|
1481 | s._add_history("freq_switch", varlist) |
---|
1482 | print_log() |
---|
1483 | if insitu: self._assign(s) |
---|
1484 | else: return s |
---|
1485 | |
---|
1486 | def recalc_azel(self): |
---|
1487 | """ |
---|
1488 | Recalculate the azimuth and elevation for each position. |
---|
1489 | Parameters: |
---|
1490 | none |
---|
1491 | Example: |
---|
1492 | """ |
---|
1493 | varlist = vars() |
---|
1494 | self._recalcazel() |
---|
1495 | self._add_history("recalc_azel", varlist) |
---|
1496 | print_log() |
---|
1497 | return |
---|
1498 | |
---|
1499 | def __add__(self, other): |
---|
1500 | varlist = vars() |
---|
1501 | s = None |
---|
1502 | if isinstance(other, scantable): |
---|
1503 | print "scantable + scantable NYI" |
---|
1504 | return |
---|
1505 | elif isinstance(other, float): |
---|
1506 | s = scantable(self._math._unaryop(self, other, "ADD", False)) |
---|
1507 | else: |
---|
1508 | raise TypeError("Other input is not a scantable or float value") |
---|
1509 | s._add_history("operator +", varlist) |
---|
1510 | print_log() |
---|
1511 | return s |
---|
1512 | |
---|
1513 | def __sub__(self, other): |
---|
1514 | """ |
---|
1515 | implicit on all axes and on Tsys |
---|
1516 | """ |
---|
1517 | varlist = vars() |
---|
1518 | s = None |
---|
1519 | if isinstance(other, scantable): |
---|
1520 | print "scantable - scantable NYI" |
---|
1521 | return |
---|
1522 | elif isinstance(other, float): |
---|
1523 | s = scantable(self._math._unaryop(self, other, "SUB", False)) |
---|
1524 | else: |
---|
1525 | raise TypeError("Other input is not a scantable or float value") |
---|
1526 | s._add_history("operator -", varlist) |
---|
1527 | print_log() |
---|
1528 | return s |
---|
1529 | |
---|
1530 | def __mul__(self, other): |
---|
1531 | """ |
---|
1532 | implicit on all axes and on Tsys |
---|
1533 | """ |
---|
1534 | varlist = vars() |
---|
1535 | s = None |
---|
1536 | if isinstance(other, scantable): |
---|
1537 | print "scantable * scantable NYI" |
---|
1538 | return |
---|
1539 | elif isinstance(other, float): |
---|
1540 | s = scantable(self._math._unaryop(self, other, "MUL", False)) |
---|
1541 | else: |
---|
1542 | raise TypeError("Other input is not a scantable or float value") |
---|
1543 | s._add_history("operator *", varlist) |
---|
1544 | print_log() |
---|
1545 | return s |
---|
1546 | |
---|
1547 | |
---|
1548 | def __div__(self, other): |
---|
1549 | """ |
---|
1550 | implicit on all axes and on Tsys |
---|
1551 | """ |
---|
1552 | varlist = vars() |
---|
1553 | s = None |
---|
1554 | if isinstance(other, scantable): |
---|
1555 | print "scantable / scantable NYI" |
---|
1556 | return |
---|
1557 | elif isinstance(other, float): |
---|
1558 | if other == 0.0: |
---|
1559 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
1560 | s = scantable(self._math._unaryop(self, other, "DIV", False)) |
---|
1561 | else: |
---|
1562 | raise TypeError("Other input is not a scantable or float value") |
---|
1563 | s._add_history("operator /", varlist) |
---|
1564 | print_log() |
---|
1565 | return s |
---|
1566 | |
---|
1567 | def get_fit(self, row=0): |
---|
1568 | """ |
---|
1569 | Print or return the stored fits for a row in the scantable |
---|
1570 | Parameters: |
---|
1571 | row: the row which the fit has been applied to. |
---|
1572 | """ |
---|
1573 | if row > self.nrow(): |
---|
1574 | return |
---|
1575 | from asap.asapfit import asapfit |
---|
1576 | fit = asapfit(self._getfit(row)) |
---|
1577 | if rcParams['verbose']: |
---|
1578 | print fit |
---|
1579 | return |
---|
1580 | else: |
---|
1581 | return fit.as_dict() |
---|
1582 | |
---|
1583 | def _add_history(self, funcname, parameters): |
---|
1584 | # create date |
---|
1585 | sep = "##" |
---|
1586 | from datetime import datetime |
---|
1587 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
1588 | hist = dstr+sep |
---|
1589 | hist += funcname+sep#cdate+sep |
---|
1590 | if parameters.has_key('self'): del parameters['self'] |
---|
1591 | for k, v in parameters.iteritems(): |
---|
1592 | if type(v) is dict: |
---|
1593 | for k2, v2 in v.iteritems(): |
---|
1594 | hist += k2 |
---|
1595 | hist += "=" |
---|
1596 | if isinstance(v2, scantable): |
---|
1597 | hist += 'scantable' |
---|
1598 | elif k2 == 'mask': |
---|
1599 | if isinstance(v2, list) or isinstance(v2, tuple): |
---|
1600 | hist += str(self._zip_mask(v2)) |
---|
1601 | else: |
---|
1602 | hist += str(v2) |
---|
1603 | else: |
---|
1604 | hist += str(v2) |
---|
1605 | else: |
---|
1606 | hist += k |
---|
1607 | hist += "=" |
---|
1608 | if isinstance(v, scantable): |
---|
1609 | hist += 'scantable' |
---|
1610 | elif k == 'mask': |
---|
1611 | if isinstance(v, list) or isinstance(v, tuple): |
---|
1612 | hist += str(self._zip_mask(v)) |
---|
1613 | else: |
---|
1614 | hist += str(v) |
---|
1615 | else: |
---|
1616 | hist += str(v) |
---|
1617 | hist += sep |
---|
1618 | hist = hist[:-2] # remove trailing '##' |
---|
1619 | self._addhistory(hist) |
---|
1620 | |
---|
1621 | |
---|
1622 | def _zip_mask(self, mask): |
---|
1623 | mask = list(mask) |
---|
1624 | i = 0 |
---|
1625 | segments = [] |
---|
1626 | while mask[i:].count(1): |
---|
1627 | i += mask[i:].index(1) |
---|
1628 | if mask[i:].count(0): |
---|
1629 | j = i + mask[i:].index(0) |
---|
1630 | else: |
---|
1631 | j = len(mask) |
---|
1632 | segments.append([i, j]) |
---|
1633 | i = j |
---|
1634 | return segments |
---|
1635 | |
---|
1636 | def _get_ordinate_label(self): |
---|
1637 | fu = "("+self.get_fluxunit()+")" |
---|
1638 | import re |
---|
1639 | lbl = "Intensity" |
---|
1640 | if re.match(".K.", fu): |
---|
1641 | lbl = "Brightness Temperature "+ fu |
---|
1642 | elif re.match(".Jy.", fu): |
---|
1643 | lbl = "Flux density "+ fu |
---|
1644 | return lbl |
---|
1645 | |
---|
1646 | def _check_ifs(self): |
---|
1647 | nchans = [self.nchan(i) for i in range(self.nif(-1))] |
---|
1648 | nchans = filter(lambda t: t > 0, nchans) |
---|
1649 | return (sum(nchans)/len(nchans) == nchans[0]) |
---|
1650 | |
---|
1651 | def _fill(self, names, unit, average): |
---|
1652 | import os |
---|
1653 | from asap._asap import stfiller |
---|
1654 | first = True |
---|
1655 | fullnames = [] |
---|
1656 | for name in names: |
---|
1657 | name = os.path.expandvars(name) |
---|
1658 | name = os.path.expanduser(name) |
---|
1659 | if not os.path.exists(name): |
---|
1660 | msg = "File '%s' does not exists" % (name) |
---|
1661 | if rcParams['verbose']: |
---|
1662 | asaplog.push(msg) |
---|
1663 | print asaplog.pop().strip() |
---|
1664 | return |
---|
1665 | raise IOError(msg) |
---|
1666 | fullnames.append(name) |
---|
1667 | if average: |
---|
1668 | asaplog.push('Auto averaging integrations') |
---|
1669 | stype = int(rcParams['scantable.storage'].lower() == 'disk') |
---|
1670 | for name in fullnames: |
---|
1671 | tbl = Scantable(stype) |
---|
1672 | r = stfiller(tbl) |
---|
1673 | msg = "Importing %s..." % (name) |
---|
1674 | asaplog.push(msg, False) |
---|
1675 | print_log() |
---|
1676 | r._open(name, -1, -1) |
---|
1677 | r._read() |
---|
1678 | #tbl = r._getdata() |
---|
1679 | if average: |
---|
1680 | tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN') |
---|
1681 | #tbl = tbl2 |
---|
1682 | if not first: |
---|
1683 | tbl = self._math._merge([self, tbl]) |
---|
1684 | #tbl = tbl2 |
---|
1685 | Scantable.__init__(self, tbl) |
---|
1686 | r._close() |
---|
1687 | del r, tbl |
---|
1688 | first = False |
---|
1689 | if unit is not None: |
---|
1690 | self.set_fluxunit(unit) |
---|
1691 | self.set_freqframe(rcParams['scantable.freqframe']) |
---|
1692 | |
---|