1 | import os |
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2 | try: |
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3 | from functools import wraps as wraps_dec |
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4 | except ImportError: |
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5 | from asap.compatibility import wraps as wraps_dec |
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6 | |
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7 | from asap._asap import Scantable |
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8 | from asap import rcParams |
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9 | from asap import print_log, print_log_dec |
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10 | from asap import asaplog |
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11 | from asap import selector |
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12 | from asap import linecatalog |
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13 | from asap.coordinate import coordinate |
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14 | from asap import _n_bools, mask_not, mask_and, mask_or |
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15 | |
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16 | |
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17 | def preserve_selection(func): |
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18 | @wraps_dec(func) |
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19 | def wrap(obj, *args, **kw): |
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20 | basesel = obj.get_selection() |
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21 | val = func(obj, *args, **kw) |
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22 | obj.set_selection(basesel) |
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23 | return val |
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24 | return wrap |
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25 | |
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26 | |
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27 | def is_scantable(filename): |
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28 | return (os.path.isdir(filename) |
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29 | and not os.path.exists(filename+'/table.f1') |
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30 | and os.path.exists(filename+'/table.info')) |
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31 | |
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32 | |
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33 | class scantable(Scantable): |
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34 | """ |
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35 | The ASAP container for scans |
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36 | """ |
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37 | @print_log_dec |
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38 | def __init__(self, filename, average=None, unit=None, parallactify=None): |
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39 | """ |
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40 | Create a scantable from a saved one or make a reference |
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41 | Parameters: |
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42 | filename: the name of an asap table on disk |
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43 | or |
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44 | the name of a rpfits/sdfits/ms file |
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45 | (integrations within scans are auto averaged |
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46 | and the whole file is read) |
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47 | or |
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48 | [advanced] a reference to an existing |
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49 | scantable |
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50 | average: average all integrations withinb a scan on read. |
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51 | The default (True) is taken from .asaprc. |
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52 | unit: brightness unit; must be consistent with K or Jy. |
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53 | Over-rides the default selected by the reader |
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54 | (input rpfits/sdfits/ms) or replaces the value |
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55 | in existing scantables |
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56 | parallactify: Indcicate that the data had been parallatified. |
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57 | Default is taken form rc file. |
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58 | """ |
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59 | if average is None: |
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60 | average = rcParams['scantable.autoaverage'] |
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61 | parallactify = parallactify or rcParams['scantable.parallactify'] |
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62 | varlist = vars() |
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63 | from asap._asap import stmath |
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64 | self._math = stmath() |
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65 | if isinstance(filename, Scantable): |
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66 | Scantable.__init__(self, filename) |
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67 | else: |
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68 | if isinstance(filename, str): |
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69 | filename = os.path.expandvars(filename) |
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70 | filename = os.path.expanduser(filename) |
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71 | if not os.path.exists(filename): |
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72 | s = "File '%s' not found." % (filename) |
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73 | if rcParams['verbose']: |
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74 | asaplog.push(s) |
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75 | return |
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76 | raise IOError(s) |
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77 | if is_scantable(filename): |
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78 | ondisk = rcParams['scantable.storage'] == 'disk' |
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79 | Scantable.__init__(self, filename, ondisk) |
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80 | if unit is not None: |
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81 | self.set_fluxunit(unit) |
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82 | self.set_freqframe(rcParams['scantable.freqframe']) |
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83 | else: |
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84 | self._fill([filename], unit, average) |
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85 | elif (isinstance(filename, list) or isinstance(filename, tuple)) \ |
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86 | and isinstance(filename[-1], str): |
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87 | self._fill(filename, unit, average) |
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88 | self.parallactify(parallactify) |
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89 | self._add_history("scantable", varlist) |
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90 | |
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91 | @print_log_dec |
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92 | def save(self, name=None, format=None, overwrite=False): |
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93 | """ |
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94 | Store the scantable on disk. This can be an asap (aips++) Table, |
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95 | SDFITS or MS2 format. |
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96 | Parameters: |
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97 | name: the name of the outputfile. For format "ASCII" |
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98 | this is the root file name (data in 'name'.txt |
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99 | and header in 'name'_header.txt) |
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100 | format: an optional file format. Default is ASAP. |
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101 | Allowed are - 'ASAP' (save as ASAP [aips++] Table), |
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102 | 'SDFITS' (save as SDFITS file) |
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103 | 'ASCII' (saves as ascii text file) |
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104 | 'MS2' (saves as an aips++ |
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105 | MeasurementSet V2) |
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106 | 'FITS' (save as image FITS - not |
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107 | readable by class) |
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108 | 'CLASS' (save as FITS readable by CLASS) |
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109 | overwrite: If the file should be overwritten if it exists. |
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110 | The default False is to return with warning |
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111 | without writing the output. USE WITH CARE. |
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112 | Example: |
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113 | scan.save('myscan.asap') |
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114 | scan.save('myscan.sdfits', 'SDFITS') |
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115 | """ |
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116 | from os import path |
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117 | format = format or rcParams['scantable.save'] |
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118 | suffix = '.'+format.lower() |
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119 | if name is None or name == "": |
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120 | name = 'scantable'+suffix |
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121 | msg = "No filename given. Using default name %s..." % name |
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122 | asaplog.push(msg) |
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123 | name = path.expandvars(name) |
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124 | if path.isfile(name) or path.isdir(name): |
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125 | if not overwrite: |
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126 | msg = "File %s exists." % name |
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127 | if rcParams['verbose']: |
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128 | print msg |
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129 | return |
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130 | else: |
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131 | raise IOError(msg) |
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132 | format2 = format.upper() |
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133 | if format2 == 'ASAP': |
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134 | self._save(name) |
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135 | else: |
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136 | from asap._asap import stwriter as stw |
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137 | writer = stw(format2) |
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138 | writer.write(self, name) |
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139 | return |
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140 | |
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141 | def copy(self): |
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142 | """ |
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143 | Return a copy of this scantable. |
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144 | Note: |
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145 | This makes a full (deep) copy. scan2 = scan1 makes a reference. |
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146 | Parameters: |
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147 | none |
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148 | Example: |
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149 | copiedscan = scan.copy() |
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150 | """ |
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151 | sd = scantable(Scantable._copy(self)) |
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152 | return sd |
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153 | |
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154 | def drop_scan(self, scanid=None): |
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155 | """ |
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156 | Return a new scantable where the specified scan number(s) has(have) |
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157 | been dropped. |
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158 | Parameters: |
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159 | scanid: a (list of) scan number(s) |
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160 | """ |
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161 | from asap import _is_sequence_or_number as _is_valid |
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162 | from asap import _to_list |
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163 | from asap import unique |
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164 | if not _is_valid(scanid): |
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165 | if rcParams['verbose']: |
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166 | print "Please specify a scanno to drop from the scantable" |
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167 | return |
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168 | else: |
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169 | raise RuntimeError("No scan given") |
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170 | try: |
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171 | scanid = _to_list(scanid) |
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172 | allscans = unique([ self.getscan(i) for i in range(self.nrow())]) |
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173 | for sid in scanid: allscans.remove(sid) |
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174 | if len(allscans) == 0: |
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175 | raise ValueError("Can't remove all scans") |
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176 | except ValueError: |
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177 | if rcParams['verbose']: |
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178 | print "Couldn't find any match." |
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179 | return |
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180 | else: raise |
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181 | try: |
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182 | sel = selector(scans=allscans) |
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183 | return self._select_copy(sel) |
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184 | except RuntimeError: |
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185 | if rcParams['verbose']: |
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186 | print "Couldn't find any match." |
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187 | else: |
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188 | raise |
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189 | |
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190 | def _select_copy(self, selection): |
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191 | orig = self.get_selection() |
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192 | self.set_selection(orig+selection) |
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193 | cp = self.copy() |
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194 | self.set_selection(orig) |
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195 | return cp |
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196 | |
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197 | def get_scan(self, scanid=None): |
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198 | """ |
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199 | Return a specific scan (by scanno) or collection of scans (by |
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200 | source name) in a new scantable. |
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201 | Note: |
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202 | See scantable.drop_scan() for the inverse operation. |
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203 | Parameters: |
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204 | scanid: a (list of) scanno or a source name, unix-style |
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205 | patterns are accepted for source name matching, e.g. |
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206 | '*_R' gets all 'ref scans |
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207 | Example: |
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208 | # get all scans containing the source '323p459' |
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209 | newscan = scan.get_scan('323p459') |
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210 | # get all 'off' scans |
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211 | refscans = scan.get_scan('*_R') |
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212 | # get a susbset of scans by scanno (as listed in scan.summary()) |
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213 | newscan = scan.get_scan([0, 2, 7, 10]) |
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214 | """ |
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215 | if scanid is None: |
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216 | if rcParams['verbose']: |
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217 | print "Please specify a scan no or name to " \ |
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218 | "retrieve from the scantable" |
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219 | return |
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220 | else: |
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221 | raise RuntimeError("No scan given") |
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222 | |
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223 | try: |
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224 | bsel = self.get_selection() |
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225 | sel = selector() |
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226 | if type(scanid) is str: |
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227 | sel.set_name(scanid) |
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228 | return self._select_copy(sel) |
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229 | elif type(scanid) is int: |
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230 | sel.set_scans([scanid]) |
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231 | return self._select_copy(sel) |
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232 | elif type(scanid) is list: |
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233 | sel.set_scans(scanid) |
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234 | return self._select_copy(sel) |
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235 | else: |
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236 | msg = "Illegal scanid type, use 'int' or 'list' if ints." |
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237 | if rcParams['verbose']: |
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238 | print msg |
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239 | else: |
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240 | raise TypeError(msg) |
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241 | except RuntimeError: |
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242 | if rcParams['verbose']: print "Couldn't find any match." |
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243 | else: raise |
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244 | |
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245 | def __str__(self): |
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246 | return Scantable._summary(self, True) |
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247 | |
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248 | def summary(self, filename=None): |
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249 | """ |
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250 | Print a summary of the contents of this scantable. |
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251 | Parameters: |
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252 | filename: the name of a file to write the putput to |
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253 | Default - no file output |
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254 | """ |
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255 | info = Scantable._summary(self, True) |
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256 | if filename is not None: |
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257 | if filename is "": |
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258 | filename = 'scantable_summary.txt' |
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259 | from os.path import expandvars, isdir |
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260 | filename = expandvars(filename) |
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261 | if not isdir(filename): |
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262 | data = open(filename, 'w') |
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263 | data.write(info) |
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264 | data.close() |
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265 | else: |
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266 | msg = "Illegal file name '%s'." % (filename) |
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267 | if rcParams['verbose']: |
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268 | print msg |
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269 | else: |
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270 | raise IOError(msg) |
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271 | if rcParams['verbose']: |
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272 | try: |
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273 | from IPython.genutils import page as pager |
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274 | except ImportError: |
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275 | from pydoc import pager |
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276 | pager(info) |
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277 | else: |
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278 | return info |
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279 | |
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280 | def get_spectrum(self, rowno): |
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281 | """Return the spectrum for the current row in the scantable as a list. |
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282 | Parameters: |
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283 | rowno: the row number to retrieve the spectrum from |
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284 | """ |
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285 | return self._getspectrum(rowno) |
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286 | |
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287 | def get_mask(self, rowno): |
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288 | """Return the mask for the current row in the scantable as a list. |
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289 | Parameters: |
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290 | rowno: the row number to retrieve the mask from |
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291 | """ |
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292 | return self._getmask(rowno) |
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293 | |
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294 | def set_spectrum(self, spec, rowno): |
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295 | """Return the spectrum for the current row in the scantable as a list. |
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296 | Parameters: |
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297 | spec: the spectrum |
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298 | rowno: the row number to set the spectrum for |
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299 | """ |
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300 | assert(len(spec) == self.nchan()) |
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301 | return self._setspectrum(spec, rowno) |
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302 | |
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303 | def get_coordinate(self, rowno): |
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304 | """Return the (spectral) coordinate for a a given 'rowno'. |
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305 | NOTE: |
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306 | * This coordinate is only valid until a scantable method modifies |
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307 | the frequency axis. |
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308 | * This coordinate does contain the original frequency set-up |
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309 | NOT the new frame. The conversions however are done using the user |
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310 | specified frame (e.g. LSRK/TOPO). To get the 'real' coordinate, |
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311 | use scantable.freq_align first. Without it there is no closure, |
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312 | i.e. |
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313 | c = myscan.get_coordinate(0) |
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314 | c.to_frequency(c.get_reference_pixel()) != c.get_reference_value() |
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315 | |
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316 | Parameters: |
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317 | rowno: the row number for the spectral coordinate |
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318 | |
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319 | """ |
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320 | return coordinate(Scantable.get_coordinate(self, rowno)) |
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321 | |
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322 | def get_selection(self): |
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323 | """ |
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324 | Get the selection object currently set on this scantable. |
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325 | Parameters: |
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326 | none |
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327 | Example: |
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328 | sel = scan.get_selection() |
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329 | sel.set_ifs(0) # select IF 0 |
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330 | scan.set_selection(sel) # apply modified selection |
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331 | """ |
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332 | return selector(self._getselection()) |
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333 | |
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334 | def set_selection(self, selection=None, **kw): |
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335 | """ |
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336 | Select a subset of the data. All following operations on this scantable |
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337 | are only applied to thi selection. |
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338 | Parameters: |
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339 | selection: a selector object (default unset the selection), |
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340 | |
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341 | or |
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342 | |
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343 | any combination of |
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344 | "pols", "ifs", "beams", "scans", "cycles", "name", "query" |
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345 | |
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346 | Examples: |
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347 | sel = selector() # create a selection object |
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348 | self.set_scans([0, 3]) # select SCANNO 0 and 3 |
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349 | scan.set_selection(sel) # set the selection |
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350 | scan.summary() # will only print summary of scanno 0 an 3 |
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351 | scan.set_selection() # unset the selection |
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352 | # or the equivalent |
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353 | scan.set_selection(scans=[0,3]) |
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354 | scan.summary() # will only print summary of scanno 0 an 3 |
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355 | scan.set_selection() # unset the selection |
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356 | """ |
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357 | if selection is None: |
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358 | # reset |
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359 | if len(kw) == 0: |
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360 | selection = selector() |
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361 | else: |
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362 | # try keywords |
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363 | for k in kw: |
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364 | if k not in selector.fields: |
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365 | raise KeyError("Invalid selection key '%s', valid keys are %s" % (k, selector.fields)) |
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366 | selection = selector(**kw) |
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367 | self._setselection(selection) |
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368 | |
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369 | def stats(self, stat='stddev', mask=None): |
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370 | """ |
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371 | Determine the specified statistic of the current beam/if/pol |
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372 | Takes a 'mask' as an optional parameter to specify which |
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373 | channels should be excluded. |
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374 | Parameters: |
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375 | stat: 'min', 'max', 'sumsq', 'sum', 'mean' |
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376 | 'var', 'stddev', 'avdev', 'rms', 'median' |
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377 | mask: an optional mask specifying where the statistic |
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378 | should be determined. |
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379 | Example: |
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380 | scan.set_unit('channel') |
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381 | msk = scan.create_mask([100, 200], [500, 600]) |
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382 | scan.stats(stat='mean', mask=m) |
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383 | """ |
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384 | mask = mask or [] |
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385 | if not self._check_ifs(): |
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386 | raise ValueError("Cannot apply mask as the IFs have different " |
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387 | "number of channels. Please use setselection() " |
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388 | "to select individual IFs") |
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389 | |
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390 | statvals = self._math._stats(self, mask, stat) |
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391 | def cb(i): |
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392 | return statvals[i] |
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393 | |
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394 | return self._row_callback(cb, stat) |
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395 | |
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396 | def stddev(self, mask=None): |
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397 | """ |
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398 | Determine the standard deviation of the current beam/if/pol |
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399 | Takes a 'mask' as an optional parameter to specify which |
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400 | channels should be excluded. |
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401 | Parameters: |
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402 | mask: an optional mask specifying where the standard |
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403 | deviation should be determined. |
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404 | |
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405 | Example: |
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406 | scan.set_unit('channel') |
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407 | msk = scan.create_mask([100, 200], [500, 600]) |
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408 | scan.stddev(mask=m) |
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409 | """ |
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410 | return self.stats(stat='stddev', mask=mask); |
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411 | |
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412 | |
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413 | def get_column_names(self): |
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414 | """ |
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415 | Return a list of column names, which can be used for selection. |
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416 | """ |
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417 | return list(Scantable.get_column_names(self)) |
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418 | |
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419 | def get_tsys(self, row=-1): |
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420 | """ |
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421 | Return the System temperatures. |
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422 | Returns: |
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423 | a list of Tsys values for the current selection |
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424 | """ |
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425 | if row > -1: |
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426 | return self._get_column(self._gettsys, row) |
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427 | return self._row_callback(self._gettsys, "Tsys") |
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428 | |
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429 | |
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430 | def get_weather(self, row=-1): |
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431 | values = self._get_column(self._get_weather, row) |
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432 | if row > -1: |
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433 | return {'temperature': values[0], |
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434 | 'pressure': values[1], 'humidity' : values[2], |
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435 | 'windspeed' : values[3], 'windaz' : values[4] |
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436 | } |
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437 | else: |
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438 | out = [] |
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439 | for r in values: |
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440 | |
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441 | out.append({'temperature': r[0], |
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442 | 'pressure': r[1], 'humidity' : r[2], |
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443 | 'windspeed' : r[3], 'windaz' : r[4] |
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444 | }) |
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445 | return out |
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446 | |
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447 | def _row_callback(self, callback, label): |
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448 | out = "" |
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449 | outvec = [] |
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450 | sep = '-'*50 |
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451 | for i in range(self.nrow()): |
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452 | tm = self._gettime(i) |
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453 | src = self._getsourcename(i) |
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454 | out += 'Scan[%d] (%s) ' % (self.getscan(i), src) |
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455 | out += 'Time[%s]:\n' % (tm) |
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456 | if self.nbeam(-1) > 1: |
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457 | out += ' Beam[%d] ' % (self.getbeam(i)) |
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458 | if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i)) |
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459 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i)) |
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460 | outvec.append(callback(i)) |
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461 | out += '= %3.3f\n' % (outvec[i]) |
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462 | out += sep+'\n' |
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463 | if rcParams['verbose']: |
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464 | print sep |
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465 | print " %s" % (label) |
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466 | print sep |
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467 | print out |
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468 | return outvec |
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469 | |
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470 | def _get_column(self, callback, row=-1): |
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471 | """ |
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472 | """ |
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473 | if row == -1: |
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474 | return [callback(i) for i in range(self.nrow())] |
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475 | else: |
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476 | if 0 <= row < self.nrow(): |
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477 | return callback(row) |
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478 | |
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479 | |
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480 | def get_time(self, row=-1, asdatetime=False): |
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481 | """ |
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482 | Get a list of time stamps for the observations. |
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483 | Return a datetime object for each integration time stamp in the scantable. |
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484 | Parameters: |
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485 | row: row no of integration. Default -1 return all rows |
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486 | asdatetime: return values as datetime objects rather than strings |
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487 | Example: |
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488 | none |
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489 | """ |
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490 | from time import strptime |
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491 | from datetime import datetime |
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492 | times = self._get_column(self._gettime, row) |
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493 | if not asdatetime: |
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494 | return times |
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495 | format = "%Y/%m/%d/%H:%M:%S" |
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496 | if isinstance(times, list): |
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497 | return [datetime(*strptime(i, format)[:6]) for i in times] |
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498 | else: |
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499 | return datetime(*strptime(times, format)[:6]) |
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500 | |
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501 | |
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502 | def get_inttime(self, row=-1): |
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503 | """ |
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504 | Get a list of integration times for the observations. |
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505 | Return a time in seconds for each integration in the scantable. |
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506 | Parameters: |
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507 | row: row no of integration. Default -1 return all rows. |
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508 | Example: |
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509 | none |
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510 | """ |
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511 | return self._get_column(self._getinttime, row) |
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512 | |
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513 | |
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514 | def get_sourcename(self, row=-1): |
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515 | """ |
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516 | Get a list source names for the observations. |
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517 | Return a string for each integration in the scantable. |
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518 | Parameters: |
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519 | row: row no of integration. Default -1 return all rows. |
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520 | Example: |
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521 | none |
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522 | """ |
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523 | return self._get_column(self._getsourcename, row) |
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524 | |
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525 | def get_elevation(self, row=-1): |
---|
526 | """ |
---|
527 | Get a list of elevations for the observations. |
---|
528 | Return a float for each integration in the scantable. |
---|
529 | Parameters: |
---|
530 | row: row no of integration. Default -1 return all rows. |
---|
531 | Example: |
---|
532 | none |
---|
533 | """ |
---|
534 | return self._get_column(self._getelevation, row) |
---|
535 | |
---|
536 | def get_azimuth(self, row=-1): |
---|
537 | """ |
---|
538 | Get a list of azimuths for the observations. |
---|
539 | Return a float for each integration in the scantable. |
---|
540 | Parameters: |
---|
541 | row: row no of integration. Default -1 return all rows. |
---|
542 | Example: |
---|
543 | none |
---|
544 | """ |
---|
545 | return self._get_column(self._getazimuth, row) |
---|
546 | |
---|
547 | def get_parangle(self, row=-1): |
---|
548 | """ |
---|
549 | Get a list of parallactic angles for the observations. |
---|
550 | Return a float for each integration in the scantable. |
---|
551 | Parameters: |
---|
552 | row: row no of integration. Default -1 return all rows. |
---|
553 | Example: |
---|
554 | none |
---|
555 | """ |
---|
556 | return self._get_column(self._getparangle, row) |
---|
557 | |
---|
558 | def get_direction(self, row=-1): |
---|
559 | """ |
---|
560 | Get a list of Positions on the sky (direction) for the observations. |
---|
561 | Return a string for each integration in the scantable. |
---|
562 | Parameters: |
---|
563 | row: row no of integration. Default -1 return all rows |
---|
564 | Example: |
---|
565 | none |
---|
566 | """ |
---|
567 | return self._get_column(self._getdirection, row) |
---|
568 | |
---|
569 | def get_directionval(self, row=-1): |
---|
570 | """ |
---|
571 | Get a list of Positions on the sky (direction) for the observations. |
---|
572 | Return a float for each integration in the scantable. |
---|
573 | Parameters: |
---|
574 | row: row no of integration. Default -1 return all rows |
---|
575 | Example: |
---|
576 | none |
---|
577 | """ |
---|
578 | return self._get_column(self._getdirectionvec, row) |
---|
579 | |
---|
580 | @print_log_dec |
---|
581 | def set_unit(self, unit='channel'): |
---|
582 | """ |
---|
583 | Set the unit for all following operations on this scantable |
---|
584 | Parameters: |
---|
585 | unit: optional unit, default is 'channel' |
---|
586 | one of '*Hz', 'km/s', 'channel', '' |
---|
587 | """ |
---|
588 | varlist = vars() |
---|
589 | if unit in ['', 'pixel', 'channel']: |
---|
590 | unit = '' |
---|
591 | inf = list(self._getcoordinfo()) |
---|
592 | inf[0] = unit |
---|
593 | self._setcoordinfo(inf) |
---|
594 | self._add_history("set_unit", varlist) |
---|
595 | |
---|
596 | @print_log_dec |
---|
597 | def set_instrument(self, instr): |
---|
598 | """ |
---|
599 | Set the instrument for subsequent processing. |
---|
600 | Parameters: |
---|
601 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
---|
602 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
---|
603 | """ |
---|
604 | self._setInstrument(instr) |
---|
605 | self._add_history("set_instument", vars()) |
---|
606 | |
---|
607 | @print_log_dec |
---|
608 | def set_feedtype(self, feedtype): |
---|
609 | """ |
---|
610 | Overwrite the feed type, which might not be set correctly. |
---|
611 | Parameters: |
---|
612 | feedtype: 'linear' or 'circular' |
---|
613 | """ |
---|
614 | self._setfeedtype(feedtype) |
---|
615 | self._add_history("set_feedtype", vars()) |
---|
616 | |
---|
617 | @print_log_dec |
---|
618 | def set_doppler(self, doppler='RADIO'): |
---|
619 | """ |
---|
620 | Set the doppler for all following operations on this scantable. |
---|
621 | Parameters: |
---|
622 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
---|
623 | """ |
---|
624 | varlist = vars() |
---|
625 | inf = list(self._getcoordinfo()) |
---|
626 | inf[2] = doppler |
---|
627 | self._setcoordinfo(inf) |
---|
628 | self._add_history("set_doppler", vars()) |
---|
629 | |
---|
630 | @print_log_dec |
---|
631 | def set_freqframe(self, frame=None): |
---|
632 | """ |
---|
633 | Set the frame type of the Spectral Axis. |
---|
634 | Parameters: |
---|
635 | frame: an optional frame type, default 'LSRK'. Valid frames are: |
---|
636 | 'REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', |
---|
637 | 'GEO', 'GALACTO', 'LGROUP', 'CMB' |
---|
638 | Examples: |
---|
639 | scan.set_freqframe('BARY') |
---|
640 | """ |
---|
641 | frame = frame or rcParams['scantable.freqframe'] |
---|
642 | varlist = vars() |
---|
643 | valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
644 | 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
645 | |
---|
646 | if frame in valid: |
---|
647 | inf = list(self._getcoordinfo()) |
---|
648 | inf[1] = frame |
---|
649 | self._setcoordinfo(inf) |
---|
650 | self._add_history("set_freqframe", varlist) |
---|
651 | else: |
---|
652 | msg = "Please specify a valid freq type. Valid types are:\n", valid |
---|
653 | if rcParams['verbose']: |
---|
654 | print msg |
---|
655 | else: |
---|
656 | raise TypeError(msg) |
---|
657 | |
---|
658 | def set_dirframe(self, frame=""): |
---|
659 | """ |
---|
660 | Set the frame type of the Direction on the sky. |
---|
661 | Parameters: |
---|
662 | frame: an optional frame type, default ''. Valid frames are: |
---|
663 | 'J2000', 'B1950', 'GALACTIC' |
---|
664 | Examples: |
---|
665 | scan.set_dirframe('GALACTIC') |
---|
666 | """ |
---|
667 | varlist = vars() |
---|
668 | try: |
---|
669 | Scantable.set_dirframe(self, frame) |
---|
670 | except RuntimeError, msg: |
---|
671 | if rcParams['verbose']: |
---|
672 | print msg |
---|
673 | else: |
---|
674 | raise |
---|
675 | self._add_history("set_dirframe", varlist) |
---|
676 | |
---|
677 | def get_unit(self): |
---|
678 | """ |
---|
679 | Get the default unit set in this scantable |
---|
680 | Returns: |
---|
681 | A unit string |
---|
682 | """ |
---|
683 | inf = self._getcoordinfo() |
---|
684 | unit = inf[0] |
---|
685 | if unit == '': unit = 'channel' |
---|
686 | return unit |
---|
687 | |
---|
688 | def get_abcissa(self, rowno=0): |
---|
689 | """ |
---|
690 | Get the abcissa in the current coordinate setup for the currently |
---|
691 | selected Beam/IF/Pol |
---|
692 | Parameters: |
---|
693 | rowno: an optional row number in the scantable. Default is the |
---|
694 | first row, i.e. rowno=0 |
---|
695 | Returns: |
---|
696 | The abcissa values and the format string (as a dictionary) |
---|
697 | """ |
---|
698 | abc = self._getabcissa(rowno) |
---|
699 | lbl = self._getabcissalabel(rowno) |
---|
700 | return abc, lbl |
---|
701 | |
---|
702 | def flag(self, mask=None): |
---|
703 | """ |
---|
704 | Flag the selected data using an optional channel mask. |
---|
705 | Parameters: |
---|
706 | mask: an optional channel mask, created with create_mask. Default |
---|
707 | (no mask) is all channels. |
---|
708 | """ |
---|
709 | varlist = vars() |
---|
710 | mask = mask or [] |
---|
711 | try: |
---|
712 | self._flag(mask) |
---|
713 | except RuntimeError, msg: |
---|
714 | if rcParams['verbose']: |
---|
715 | print msg |
---|
716 | return |
---|
717 | else: raise |
---|
718 | self._add_history("flag", varlist) |
---|
719 | |
---|
720 | @print_log_dec |
---|
721 | def lag_flag(self, start, end, unit="MHz", insitu=None): |
---|
722 | """ |
---|
723 | Flag the data in 'lag' space by providing a frequency to remove. |
---|
724 | Flagged data in the scantable gets interpolated over the region. |
---|
725 | No taper is applied. |
---|
726 | Parameters: |
---|
727 | start: the start frequency (really a period within the |
---|
728 | bandwidth) or period to remove |
---|
729 | end: the end frequency or period to remove |
---|
730 | unit: the frequency unit (default "MHz") or "" for |
---|
731 | explicit lag channels |
---|
732 | Notes: |
---|
733 | It is recommended to flag edges of the band or strong |
---|
734 | signals beforehand. |
---|
735 | """ |
---|
736 | if insitu is None: insitu = rcParams['insitu'] |
---|
737 | self._math._setinsitu(insitu) |
---|
738 | varlist = vars() |
---|
739 | base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1.} |
---|
740 | if not (unit == "" or base.has_key(unit)): |
---|
741 | raise ValueError("%s is not a valid unit." % unit) |
---|
742 | try: |
---|
743 | if unit == "": |
---|
744 | s = scantable(self._math._lag_flag(self, start, end, "lags")) |
---|
745 | else: |
---|
746 | s = scantable(self._math._lag_flag(self, start*base[unit], |
---|
747 | end*base[unit], "frequency")) |
---|
748 | except RuntimeError, msg: |
---|
749 | if rcParams['verbose']: |
---|
750 | print msg |
---|
751 | return |
---|
752 | else: raise |
---|
753 | s._add_history("lag_flag", varlist) |
---|
754 | if insitu: |
---|
755 | self._assign(s) |
---|
756 | else: |
---|
757 | return s |
---|
758 | |
---|
759 | @print_log_dec |
---|
760 | def create_mask(self, *args, **kwargs): |
---|
761 | """ |
---|
762 | Compute and return a mask based on [min, max] windows. |
---|
763 | The specified windows are to be INCLUDED, when the mask is |
---|
764 | applied. |
---|
765 | Parameters: |
---|
766 | [min, max], [min2, max2], ... |
---|
767 | Pairs of start/end points (inclusive)specifying the regions |
---|
768 | to be masked |
---|
769 | invert: optional argument. If specified as True, |
---|
770 | return an inverted mask, i.e. the regions |
---|
771 | specified are EXCLUDED |
---|
772 | row: create the mask using the specified row for |
---|
773 | unit conversions, default is row=0 |
---|
774 | only necessary if frequency varies over rows. |
---|
775 | Example: |
---|
776 | scan.set_unit('channel') |
---|
777 | a) |
---|
778 | msk = scan.create_mask([400, 500], [800, 900]) |
---|
779 | # masks everything outside 400 and 500 |
---|
780 | # and 800 and 900 in the unit 'channel' |
---|
781 | |
---|
782 | b) |
---|
783 | msk = scan.create_mask([400, 500], [800, 900], invert=True) |
---|
784 | # masks the regions between 400 and 500 |
---|
785 | # and 800 and 900 in the unit 'channel' |
---|
786 | c) |
---|
787 | mask only channel 400 |
---|
788 | msk = scan.create_mask([400]) |
---|
789 | """ |
---|
790 | row = kwargs.get("row", 0) |
---|
791 | data = self._getabcissa(row) |
---|
792 | u = self._getcoordinfo()[0] |
---|
793 | if rcParams['verbose']: |
---|
794 | if u == "": u = "channel" |
---|
795 | msg = "The current mask window unit is %s" % u |
---|
796 | i = self._check_ifs() |
---|
797 | if not i: |
---|
798 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
799 | asaplog.push(msg) |
---|
800 | n = self.nchan() |
---|
801 | msk = _n_bools(n, False) |
---|
802 | # test if args is a 'list' or a 'normal *args - UGLY!!! |
---|
803 | |
---|
804 | ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \ |
---|
805 | and args or args[0] |
---|
806 | for window in ws: |
---|
807 | if len(window) == 1: |
---|
808 | window = [window[0], window[0]] |
---|
809 | if len(window) == 0 or len(window) > 2: |
---|
810 | raise ValueError("A window needs to be defined as [start(, end)]") |
---|
811 | if window[0] > window[1]: |
---|
812 | tmp = window[0] |
---|
813 | window[0] = window[1] |
---|
814 | window[1] = tmp |
---|
815 | for i in range(n): |
---|
816 | if data[i] >= window[0] and data[i] <= window[1]: |
---|
817 | msk[i] = True |
---|
818 | if kwargs.has_key('invert'): |
---|
819 | if kwargs.get('invert'): |
---|
820 | msk = mask_not(msk) |
---|
821 | return msk |
---|
822 | |
---|
823 | def get_restfreqs(self): |
---|
824 | """ |
---|
825 | Get the restfrequency(s) stored in this scantable. |
---|
826 | The return value(s) are always of unit 'Hz' |
---|
827 | Parameters: |
---|
828 | none |
---|
829 | Returns: |
---|
830 | a list of doubles |
---|
831 | """ |
---|
832 | return list(self._getrestfreqs()) |
---|
833 | |
---|
834 | |
---|
835 | def set_restfreqs(self, freqs=None, unit='Hz'): |
---|
836 | """ |
---|
837 | Set or replace the restfrequency specified and |
---|
838 | If the 'freqs' argument holds a scalar, |
---|
839 | then that rest frequency will be applied to all the selected |
---|
840 | data. If the 'freqs' argument holds |
---|
841 | a vector, then it MUST be of equal or smaller length than |
---|
842 | the number of IFs (and the available restfrequencies will be |
---|
843 | replaced by this vector). In this case, *all* data have |
---|
844 | the restfrequency set per IF according |
---|
845 | to the corresponding value you give in the 'freqs' vector. |
---|
846 | E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
847 | IF 1 gets restfreq 2e9. |
---|
848 | You can also specify the frequencies via a linecatalog. |
---|
849 | |
---|
850 | Parameters: |
---|
851 | freqs: list of rest frequency values or string idenitfiers |
---|
852 | unit: unit for rest frequency (default 'Hz') |
---|
853 | |
---|
854 | Example: |
---|
855 | # set the given restfrequency for the whole table |
---|
856 | scan.set_restfreqs(freqs=1.4e9) |
---|
857 | # If thee number of IFs in the data is >= 2 IF0 gets the first |
---|
858 | # value IF1 the second... |
---|
859 | scan.set_restfreqs(freqs=[1.4e9, 1.67e9]) |
---|
860 | #set the given restfrequency for the whole table (by name) |
---|
861 | scan.set_restfreqs(freqs="OH1667") |
---|
862 | |
---|
863 | Note: |
---|
864 | To do more sophisticate Restfrequency setting, e.g. on a |
---|
865 | source and IF basis, use scantable.set_selection() before using |
---|
866 | this function. |
---|
867 | # provide your scantable is called scan |
---|
868 | selection = selector() |
---|
869 | selection.set_name("ORION*") |
---|
870 | selection.set_ifs([1]) |
---|
871 | scan.set_selection(selection) |
---|
872 | scan.set_restfreqs(freqs=86.6e9) |
---|
873 | |
---|
874 | """ |
---|
875 | varlist = vars() |
---|
876 | from asap import linecatalog |
---|
877 | # simple value |
---|
878 | if isinstance(freqs, int) or isinstance(freqs, float): |
---|
879 | self._setrestfreqs(freqs, "",unit) |
---|
880 | # list of values |
---|
881 | elif isinstance(freqs, list) or isinstance(freqs, tuple): |
---|
882 | # list values are scalars |
---|
883 | if isinstance(freqs[-1], int) or isinstance(freqs[-1], float): |
---|
884 | sel = selector() |
---|
885 | savesel = self._getselection() |
---|
886 | iflist = self.getifnos() |
---|
887 | for i in xrange(len(freqs)): |
---|
888 | sel.set_ifs(iflist[i]) |
---|
889 | self._setselection(sel) |
---|
890 | self._setrestfreqs(freqs[i], "",unit) |
---|
891 | self._setselection(savesel) |
---|
892 | # list values are tuples, (value, name) |
---|
893 | elif isinstance(freqs[-1], dict): |
---|
894 | sel = selector() |
---|
895 | savesel = self._getselection() |
---|
896 | iflist = self.getifnos() |
---|
897 | for i in xrange(len(freqs)): |
---|
898 | sel.set_ifs(iflist[i]) |
---|
899 | self._setselection(sel) |
---|
900 | self._setrestfreqs(freqs[i]["value"], |
---|
901 | freqs[i]["name"], "MHz") |
---|
902 | self._setselection(savesel) |
---|
903 | # freqs are to be taken from a linecatalog |
---|
904 | elif isinstance(freqs, linecatalog): |
---|
905 | sel = selector() |
---|
906 | savesel = self._getselection() |
---|
907 | iflist = self.getifnos() |
---|
908 | for i in xrange(freqs.nrow()): |
---|
909 | sel.set_ifs(iflist[i]) |
---|
910 | self._setselection(sel) |
---|
911 | self._setrestfreqs(freqs.get_frequency(i), |
---|
912 | freqs.get_name(i), "MHz") |
---|
913 | # ensure that we are not iterating past nIF |
---|
914 | if i == self.nif()-1: break |
---|
915 | self._setselection(savesel) |
---|
916 | else: |
---|
917 | return |
---|
918 | self._add_history("set_restfreqs", varlist) |
---|
919 | |
---|
920 | def shift_refpix(self, delta): |
---|
921 | """ |
---|
922 | Shift the reference pixel of the Spectra Coordinate by an |
---|
923 | integer amount. |
---|
924 | Parameters: |
---|
925 | delta: the amount to shift by |
---|
926 | Note: |
---|
927 | Be careful using this with broadband data. |
---|
928 | """ |
---|
929 | Scantable.shift_refpix(self, delta) |
---|
930 | |
---|
931 | def history(self, filename=None): |
---|
932 | """ |
---|
933 | Print the history. Optionally to a file. |
---|
934 | Parameters: |
---|
935 | filename: The name of the file to save the history to. |
---|
936 | """ |
---|
937 | hist = list(self._gethistory()) |
---|
938 | out = "-"*80 |
---|
939 | for h in hist: |
---|
940 | if h.startswith("---"): |
---|
941 | out += "\n"+h |
---|
942 | else: |
---|
943 | items = h.split("##") |
---|
944 | date = items[0] |
---|
945 | func = items[1] |
---|
946 | items = items[2:] |
---|
947 | out += "\n"+date+"\n" |
---|
948 | out += "Function: %s\n Parameters:" % (func) |
---|
949 | for i in items: |
---|
950 | s = i.split("=") |
---|
951 | out += "\n %s = %s" % (s[0], s[1]) |
---|
952 | out += "\n"+"-"*80 |
---|
953 | if filename is not None: |
---|
954 | if filename is "": |
---|
955 | filename = 'scantable_history.txt' |
---|
956 | import os |
---|
957 | filename = os.path.expandvars(os.path.expanduser(filename)) |
---|
958 | if not os.path.isdir(filename): |
---|
959 | data = open(filename, 'w') |
---|
960 | data.write(out) |
---|
961 | data.close() |
---|
962 | else: |
---|
963 | msg = "Illegal file name '%s'." % (filename) |
---|
964 | if rcParams['verbose']: |
---|
965 | print msg |
---|
966 | else: |
---|
967 | raise IOError(msg) |
---|
968 | if rcParams['verbose']: |
---|
969 | try: |
---|
970 | from IPython.genutils import page as pager |
---|
971 | except ImportError: |
---|
972 | from pydoc import pager |
---|
973 | pager(out) |
---|
974 | else: |
---|
975 | return out |
---|
976 | return |
---|
977 | # |
---|
978 | # Maths business |
---|
979 | # |
---|
980 | @print_log_dec |
---|
981 | def average_time(self, mask=None, scanav=False, weight='tint', align=False): |
---|
982 | """ |
---|
983 | Return the (time) weighted average of a scan. |
---|
984 | Note: |
---|
985 | in channels only - align if necessary |
---|
986 | Parameters: |
---|
987 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
988 | weighting) |
---|
989 | scanav: True averages each scan separately |
---|
990 | False (default) averages all scans together, |
---|
991 | weight: Weighting scheme. |
---|
992 | 'none' (mean no weight) |
---|
993 | 'var' (1/var(spec) weighted) |
---|
994 | 'tsys' (1/Tsys**2 weighted) |
---|
995 | 'tint' (integration time weighted) |
---|
996 | 'tintsys' (Tint/Tsys**2) |
---|
997 | 'median' ( median averaging) |
---|
998 | The default is 'tint' |
---|
999 | align: align the spectra in velocity before averaging. It takes |
---|
1000 | the time of the first spectrum as reference time. |
---|
1001 | Example: |
---|
1002 | # time average the scantable without using a mask |
---|
1003 | newscan = scan.average_time() |
---|
1004 | """ |
---|
1005 | varlist = vars() |
---|
1006 | weight = weight or 'TINT' |
---|
1007 | mask = mask or () |
---|
1008 | scanav = (scanav and 'SCAN') or 'NONE' |
---|
1009 | scan = (self, ) |
---|
1010 | try: |
---|
1011 | if align: |
---|
1012 | scan = (self.freq_align(insitu=False), ) |
---|
1013 | s = None |
---|
1014 | if weight.upper() == 'MEDIAN': |
---|
1015 | s = scantable(self._math._averagechannel(scan[0], 'MEDIAN', |
---|
1016 | scanav)) |
---|
1017 | else: |
---|
1018 | s = scantable(self._math._average(scan, mask, weight.upper(), |
---|
1019 | scanav)) |
---|
1020 | except RuntimeError, msg: |
---|
1021 | if rcParams['verbose']: |
---|
1022 | print msg |
---|
1023 | return |
---|
1024 | else: raise |
---|
1025 | s._add_history("average_time", varlist) |
---|
1026 | return s |
---|
1027 | |
---|
1028 | @print_log_dec |
---|
1029 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None): |
---|
1030 | """ |
---|
1031 | Return a scan where all spectra are converted to either |
---|
1032 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
1033 | By default the function tries to look the values up internally. |
---|
1034 | If it can't find them (or if you want to over-ride), you must |
---|
1035 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
1036 | also if you don't set it). jyperk takes precedence if you set both. |
---|
1037 | Parameters: |
---|
1038 | jyperk: the Jy / K conversion factor |
---|
1039 | eta: the aperture efficiency |
---|
1040 | d: the geomtric diameter (metres) |
---|
1041 | insitu: if False a new scantable is returned. |
---|
1042 | Otherwise, the scaling is done in-situ |
---|
1043 | The default is taken from .asaprc (False) |
---|
1044 | """ |
---|
1045 | if insitu is None: insitu = rcParams['insitu'] |
---|
1046 | self._math._setinsitu(insitu) |
---|
1047 | varlist = vars() |
---|
1048 | jyperk = jyperk or -1.0 |
---|
1049 | d = d or -1.0 |
---|
1050 | eta = eta or -1.0 |
---|
1051 | s = scantable(self._math._convertflux(self, d, eta, jyperk)) |
---|
1052 | s._add_history("convert_flux", varlist) |
---|
1053 | if insitu: self._assign(s) |
---|
1054 | else: return s |
---|
1055 | |
---|
1056 | @print_log_dec |
---|
1057 | def gain_el(self, poly=None, filename="", method="linear", insitu=None): |
---|
1058 | """ |
---|
1059 | Return a scan after applying a gain-elevation correction. |
---|
1060 | The correction can be made via either a polynomial or a |
---|
1061 | table-based interpolation (and extrapolation if necessary). |
---|
1062 | You specify polynomial coefficients, an ascii table or neither. |
---|
1063 | If you specify neither, then a polynomial correction will be made |
---|
1064 | with built in coefficients known for certain telescopes (an error |
---|
1065 | will occur if the instrument is not known). |
---|
1066 | The data and Tsys are *divided* by the scaling factors. |
---|
1067 | Parameters: |
---|
1068 | poly: Polynomial coefficients (default None) to compute a |
---|
1069 | gain-elevation correction as a function of |
---|
1070 | elevation (in degrees). |
---|
1071 | filename: The name of an ascii file holding correction factors. |
---|
1072 | The first row of the ascii file must give the column |
---|
1073 | names and these MUST include columns |
---|
1074 | "ELEVATION" (degrees) and "FACTOR" (multiply data |
---|
1075 | by this) somewhere. |
---|
1076 | The second row must give the data type of the |
---|
1077 | column. Use 'R' for Real and 'I' for Integer. |
---|
1078 | An example file would be |
---|
1079 | (actual factors are arbitrary) : |
---|
1080 | |
---|
1081 | TIME ELEVATION FACTOR |
---|
1082 | R R R |
---|
1083 | 0.1 0 0.8 |
---|
1084 | 0.2 20 0.85 |
---|
1085 | 0.3 40 0.9 |
---|
1086 | 0.4 60 0.85 |
---|
1087 | 0.5 80 0.8 |
---|
1088 | 0.6 90 0.75 |
---|
1089 | method: Interpolation method when correcting from a table. |
---|
1090 | Values are "nearest", "linear" (default), "cubic" |
---|
1091 | and "spline" |
---|
1092 | insitu: if False a new scantable is returned. |
---|
1093 | Otherwise, the scaling is done in-situ |
---|
1094 | The default is taken from .asaprc (False) |
---|
1095 | """ |
---|
1096 | |
---|
1097 | if insitu is None: insitu = rcParams['insitu'] |
---|
1098 | self._math._setinsitu(insitu) |
---|
1099 | varlist = vars() |
---|
1100 | poly = poly or () |
---|
1101 | from os.path import expandvars |
---|
1102 | filename = expandvars(filename) |
---|
1103 | s = scantable(self._math._gainel(self, poly, filename, method)) |
---|
1104 | s._add_history("gain_el", varlist) |
---|
1105 | if insitu: |
---|
1106 | self._assign(s) |
---|
1107 | else: |
---|
1108 | return s |
---|
1109 | |
---|
1110 | @print_log_dec |
---|
1111 | def freq_align(self, reftime=None, method='cubic', insitu=None): |
---|
1112 | """ |
---|
1113 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
1114 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
1115 | set_freqframe. |
---|
1116 | Parameters: |
---|
1117 | reftime: reference time to align at. By default, the time of |
---|
1118 | the first row of data is used. |
---|
1119 | method: Interpolation method for regridding the spectra. |
---|
1120 | Choose from "nearest", "linear", "cubic" (default) |
---|
1121 | and "spline" |
---|
1122 | insitu: if False a new scantable is returned. |
---|
1123 | Otherwise, the scaling is done in-situ |
---|
1124 | The default is taken from .asaprc (False) |
---|
1125 | """ |
---|
1126 | if insitu is None: insitu = rcParams["insitu"] |
---|
1127 | self._math._setinsitu(insitu) |
---|
1128 | varlist = vars() |
---|
1129 | reftime = reftime or "" |
---|
1130 | s = scantable(self._math._freq_align(self, reftime, method)) |
---|
1131 | s._add_history("freq_align", varlist) |
---|
1132 | if insitu: self._assign(s) |
---|
1133 | else: return s |
---|
1134 | |
---|
1135 | @print_log_dec |
---|
1136 | def opacity(self, tau=None, insitu=None): |
---|
1137 | """ |
---|
1138 | Apply an opacity correction. The data |
---|
1139 | and Tsys are multiplied by the correction factor. |
---|
1140 | Parameters: |
---|
1141 | tau: (list of) opacity from which the correction factor is |
---|
1142 | exp(tau*ZD) |
---|
1143 | where ZD is the zenith-distance. |
---|
1144 | If a list is provided, it has to be of length nIF, |
---|
1145 | nIF*nPol or 1 and in order of IF/POL, e.g. |
---|
1146 | [opif0pol0, opif0pol1, opif1pol0 ...] |
---|
1147 | if tau is `None` the opacities are determined from a |
---|
1148 | model. |
---|
1149 | insitu: if False a new scantable is returned. |
---|
1150 | Otherwise, the scaling is done in-situ |
---|
1151 | The default is taken from .asaprc (False) |
---|
1152 | """ |
---|
1153 | if insitu is None: insitu = rcParams['insitu'] |
---|
1154 | self._math._setinsitu(insitu) |
---|
1155 | varlist = vars() |
---|
1156 | if not hasattr(tau, "__len__"): |
---|
1157 | tau = [tau] |
---|
1158 | s = scantable(self._math._opacity(self, tau)) |
---|
1159 | s._add_history("opacity", varlist) |
---|
1160 | if insitu: self._assign(s) |
---|
1161 | else: return s |
---|
1162 | |
---|
1163 | @print_log_dec |
---|
1164 | def bin(self, width=5, insitu=None): |
---|
1165 | """ |
---|
1166 | Return a scan where all spectra have been binned up. |
---|
1167 | Parameters: |
---|
1168 | width: The bin width (default=5) in pixels |
---|
1169 | insitu: if False a new scantable is returned. |
---|
1170 | Otherwise, the scaling is done in-situ |
---|
1171 | The default is taken from .asaprc (False) |
---|
1172 | """ |
---|
1173 | if insitu is None: insitu = rcParams['insitu'] |
---|
1174 | self._math._setinsitu(insitu) |
---|
1175 | varlist = vars() |
---|
1176 | s = scantable(self._math._bin(self, width)) |
---|
1177 | s._add_history("bin", varlist) |
---|
1178 | if insitu: |
---|
1179 | self._assign(s) |
---|
1180 | else: |
---|
1181 | return s |
---|
1182 | |
---|
1183 | @print_log_dec |
---|
1184 | def resample(self, width=5, method='cubic', insitu=None): |
---|
1185 | """ |
---|
1186 | Return a scan where all spectra have been binned up. |
---|
1187 | |
---|
1188 | Parameters: |
---|
1189 | width: The bin width (default=5) in pixels |
---|
1190 | method: Interpolation method when correcting from a table. |
---|
1191 | Values are "nearest", "linear", "cubic" (default) |
---|
1192 | and "spline" |
---|
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 | """ |
---|
1197 | if insitu is None: insitu = rcParams['insitu'] |
---|
1198 | self._math._setinsitu(insitu) |
---|
1199 | varlist = vars() |
---|
1200 | s = scantable(self._math._resample(self, method, width)) |
---|
1201 | s._add_history("resample", varlist) |
---|
1202 | if insitu: self._assign(s) |
---|
1203 | else: return s |
---|
1204 | |
---|
1205 | @print_log_dec |
---|
1206 | def average_pol(self, mask=None, weight='none'): |
---|
1207 | """ |
---|
1208 | Average the Polarisations together. |
---|
1209 | Parameters: |
---|
1210 | mask: An optional mask defining the region, where the |
---|
1211 | averaging will be applied. The output will have all |
---|
1212 | specified points masked. |
---|
1213 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
1214 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
1215 | """ |
---|
1216 | varlist = vars() |
---|
1217 | mask = mask or () |
---|
1218 | s = scantable(self._math._averagepol(self, mask, weight.upper())) |
---|
1219 | s._add_history("average_pol", varlist) |
---|
1220 | return s |
---|
1221 | |
---|
1222 | @print_log_dec |
---|
1223 | def average_beam(self, mask=None, weight='none'): |
---|
1224 | """ |
---|
1225 | Average the Beams together. |
---|
1226 | Parameters: |
---|
1227 | mask: An optional mask defining the region, where the |
---|
1228 | averaging will be applied. The output will have all |
---|
1229 | specified points masked. |
---|
1230 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
1231 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
1232 | """ |
---|
1233 | varlist = vars() |
---|
1234 | mask = mask or () |
---|
1235 | s = scantable(self._math._averagebeams(self, mask, weight.upper())) |
---|
1236 | s._add_history("average_beam", varlist) |
---|
1237 | return s |
---|
1238 | |
---|
1239 | def parallactify(self, pflag): |
---|
1240 | """ |
---|
1241 | Set a flag to inidcate whether this data should be treated as having |
---|
1242 | been 'parallactified' (total phase == 0.0) |
---|
1243 | Parameters: |
---|
1244 | pflag: Bool inidcating whether to turn this on (True) or |
---|
1245 | off (False) |
---|
1246 | """ |
---|
1247 | varlist = vars() |
---|
1248 | self._parallactify(pflag) |
---|
1249 | self._add_history("parallactify", varlist) |
---|
1250 | |
---|
1251 | @print_log_dec |
---|
1252 | def convert_pol(self, poltype=None): |
---|
1253 | """ |
---|
1254 | Convert the data to a different polarisation type. |
---|
1255 | Note that you will need cross-polarisation terms for most conversions. |
---|
1256 | Parameters: |
---|
1257 | poltype: The new polarisation type. Valid types are: |
---|
1258 | "linear", "circular", "stokes" and "linpol" |
---|
1259 | """ |
---|
1260 | varlist = vars() |
---|
1261 | try: |
---|
1262 | s = scantable(self._math._convertpol(self, poltype)) |
---|
1263 | except RuntimeError, msg: |
---|
1264 | if rcParams['verbose']: |
---|
1265 | print msg |
---|
1266 | return |
---|
1267 | else: |
---|
1268 | raise |
---|
1269 | s._add_history("convert_pol", varlist) |
---|
1270 | return s |
---|
1271 | |
---|
1272 | @print_log_dec |
---|
1273 | def smooth(self, kernel="hanning", width=5.0, order=2, insitu=None): |
---|
1274 | """ |
---|
1275 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
1276 | Parameters: |
---|
1277 | kernel: The type of smoothing kernel. Select from |
---|
1278 | 'hanning' (default), 'gaussian', 'boxcar', 'rmedian' |
---|
1279 | or 'poly' |
---|
1280 | width: The width of the kernel in pixels. For hanning this is |
---|
1281 | ignored otherwise it defauls to 5 pixels. |
---|
1282 | For 'gaussian' it is the Full Width Half |
---|
1283 | Maximum. For 'boxcar' it is the full width. |
---|
1284 | For 'rmedian' and 'poly' it is the half width. |
---|
1285 | order: Optional parameter for 'poly' kernel (default is 2), to |
---|
1286 | specify the order of the polnomial. Ignored by all other |
---|
1287 | kernels. |
---|
1288 | insitu: if False a new scantable is returned. |
---|
1289 | Otherwise, the scaling is done in-situ |
---|
1290 | The default is taken from .asaprc (False) |
---|
1291 | Example: |
---|
1292 | none |
---|
1293 | """ |
---|
1294 | if insitu is None: insitu = rcParams['insitu'] |
---|
1295 | self._math._setinsitu(insitu) |
---|
1296 | varlist = vars() |
---|
1297 | s = scantable(self._math._smooth(self, kernel.lower(), width, order)) |
---|
1298 | s._add_history("smooth", varlist) |
---|
1299 | if insitu: self._assign(s) |
---|
1300 | else: return s |
---|
1301 | |
---|
1302 | @print_log_dec |
---|
1303 | def poly_baseline(self, mask=None, order=0, plot=False, uselin=False, |
---|
1304 | insitu=None): |
---|
1305 | """ |
---|
1306 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
1307 | Parameters: |
---|
1308 | mask: an optional mask |
---|
1309 | order: the order of the polynomial (default is 0) |
---|
1310 | plot: plot the fit and the residual. In this each |
---|
1311 | indivual fit has to be approved, by typing 'y' |
---|
1312 | or 'n' |
---|
1313 | uselin: use linear polynomial fit |
---|
1314 | insitu: if False a new scantable is returned. |
---|
1315 | Otherwise, the scaling is done in-situ |
---|
1316 | The default is taken from .asaprc (False) |
---|
1317 | Example: |
---|
1318 | # return a scan baselined by a third order polynomial, |
---|
1319 | # not using a mask |
---|
1320 | bscan = scan.poly_baseline(order=3) |
---|
1321 | """ |
---|
1322 | if insitu is None: insitu = rcParams['insitu'] |
---|
1323 | varlist = vars() |
---|
1324 | if mask is None: |
---|
1325 | mask = [True for i in xrange(self.nchan(-1))] |
---|
1326 | from asap.asapfitter import fitter |
---|
1327 | try: |
---|
1328 | f = fitter() |
---|
1329 | f.set_scan(self, mask) |
---|
1330 | #f.set_function(poly=order) |
---|
1331 | if uselin: |
---|
1332 | f.set_function(lpoly=order) |
---|
1333 | else: |
---|
1334 | f.set_function(poly=order) |
---|
1335 | s = f.auto_fit(insitu, plot=plot) |
---|
1336 | s._add_history("poly_baseline", varlist) |
---|
1337 | if insitu: self._assign(s) |
---|
1338 | else: return s |
---|
1339 | except RuntimeError: |
---|
1340 | msg = "The fit failed, possibly because it didn't converge." |
---|
1341 | if rcParams['verbose']: |
---|
1342 | print msg |
---|
1343 | return |
---|
1344 | else: |
---|
1345 | raise RuntimeError(msg) |
---|
1346 | |
---|
1347 | def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0, |
---|
1348 | threshold=3, chan_avg_limit=1, plot=False, |
---|
1349 | insitu=None): |
---|
1350 | """ |
---|
1351 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
1352 | Spectral lines are detected first using linefinder and masked out |
---|
1353 | to avoid them affecting the baseline solution. |
---|
1354 | |
---|
1355 | Parameters: |
---|
1356 | mask: an optional mask retreived from scantable |
---|
1357 | edge: an optional number of channel to drop at |
---|
1358 | the edge of spectrum. If only one value is |
---|
1359 | specified, the same number will be dropped from |
---|
1360 | both sides of the spectrum. Default is to keep |
---|
1361 | all channels. Nested tuples represent individual |
---|
1362 | edge selection for different IFs (a number of spectral |
---|
1363 | channels can be different) |
---|
1364 | order: the order of the polynomial (default is 0) |
---|
1365 | threshold: the threshold used by line finder. It is better to |
---|
1366 | keep it large as only strong lines affect the |
---|
1367 | baseline solution. |
---|
1368 | chan_avg_limit: |
---|
1369 | a maximum number of consequtive spectral channels to |
---|
1370 | average during the search of weak and broad lines. |
---|
1371 | The default is no averaging (and no search for weak |
---|
1372 | lines). If such lines can affect the fitted baseline |
---|
1373 | (e.g. a high order polynomial is fitted), increase this |
---|
1374 | parameter (usually values up to 8 are reasonable). Most |
---|
1375 | users of this method should find the default value |
---|
1376 | sufficient. |
---|
1377 | plot: plot the fit and the residual. In this each |
---|
1378 | indivual fit has to be approved, by typing 'y' |
---|
1379 | or 'n' |
---|
1380 | insitu: if False a new scantable is returned. |
---|
1381 | Otherwise, the scaling is done in-situ |
---|
1382 | The default is taken from .asaprc (False) |
---|
1383 | |
---|
1384 | Example: |
---|
1385 | scan2=scan.auto_poly_baseline(order=7) |
---|
1386 | """ |
---|
1387 | if insitu is None: insitu = rcParams['insitu'] |
---|
1388 | varlist = vars() |
---|
1389 | from asap.asapfitter import fitter |
---|
1390 | from asap.asaplinefind import linefinder |
---|
1391 | from asap import _is_sequence_or_number as _is_valid |
---|
1392 | |
---|
1393 | # check whether edge is set up for each IF individually |
---|
1394 | individualedge = False; |
---|
1395 | if len(edge) > 1: |
---|
1396 | if isinstance(edge[0], list) or isinstance(edge[0], tuple): |
---|
1397 | individualedge = True; |
---|
1398 | |
---|
1399 | if not _is_valid(edge, int) and not individualedge: |
---|
1400 | raise ValueError, "Parameter 'edge' has to be an integer or a \ |
---|
1401 | pair of integers specified as a tuple. Nested tuples are allowed \ |
---|
1402 | to make individual selection for different IFs." |
---|
1403 | |
---|
1404 | curedge = (0, 0) |
---|
1405 | if individualedge: |
---|
1406 | for edgepar in edge: |
---|
1407 | if not _is_valid(edgepar, int): |
---|
1408 | raise ValueError, "Each element of the 'edge' tuple has \ |
---|
1409 | to be a pair of integers or an integer." |
---|
1410 | else: |
---|
1411 | curedge = edge; |
---|
1412 | |
---|
1413 | # setup fitter |
---|
1414 | f = fitter() |
---|
1415 | f.set_function(poly=order) |
---|
1416 | |
---|
1417 | # setup line finder |
---|
1418 | fl = linefinder() |
---|
1419 | fl.set_options(threshold=threshold,avg_limit=chan_avg_limit) |
---|
1420 | |
---|
1421 | if not insitu: |
---|
1422 | workscan = self.copy() |
---|
1423 | else: |
---|
1424 | workscan = self |
---|
1425 | |
---|
1426 | fl.set_scan(workscan) |
---|
1427 | |
---|
1428 | rows = range(workscan.nrow()) |
---|
1429 | asaplog.push("Processing:") |
---|
1430 | for r in rows: |
---|
1431 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \ |
---|
1432 | (workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \ |
---|
1433 | workscan.getpol(r), workscan.getcycle(r)) |
---|
1434 | asaplog.push(msg, False) |
---|
1435 | |
---|
1436 | # figure out edge parameter |
---|
1437 | if individualedge: |
---|
1438 | if len(edge) >= workscan.getif(r): |
---|
1439 | raise RuntimeError, "Number of edge elements appear to " \ |
---|
1440 | "be less than the number of IFs" |
---|
1441 | curedge = edge[workscan.getif(r)] |
---|
1442 | |
---|
1443 | # setup line finder |
---|
1444 | fl.find_lines(r, mask, curedge) |
---|
1445 | f.set_data(workscan._getabcissa(r), workscan._getspectrum(r), |
---|
1446 | mask_and(workscan._getmask(r), fl.get_mask())) |
---|
1447 | f.fit() |
---|
1448 | x = f.get_parameters() |
---|
1449 | if plot: |
---|
1450 | f.plot(residual=True) |
---|
1451 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
1452 | if x.upper() == 'N': |
---|
1453 | continue |
---|
1454 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
1455 | if plot: |
---|
1456 | f._p.unmap() |
---|
1457 | f._p = None |
---|
1458 | workscan._add_history("auto_poly_baseline", varlist) |
---|
1459 | if insitu: |
---|
1460 | self._assign(workscan) |
---|
1461 | else: |
---|
1462 | return workscan |
---|
1463 | |
---|
1464 | @print_log_dec |
---|
1465 | def rotate_linpolphase(self, angle): |
---|
1466 | """ |
---|
1467 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
1468 | This is always done in situ in the raw data. So if you call this |
---|
1469 | function more than once then each call rotates the phase further. |
---|
1470 | Parameters: |
---|
1471 | angle: The angle (degrees) to rotate (add) by. |
---|
1472 | Examples: |
---|
1473 | scan.rotate_linpolphase(2.3) |
---|
1474 | """ |
---|
1475 | varlist = vars() |
---|
1476 | self._math._rotate_linpolphase(self, angle) |
---|
1477 | self._add_history("rotate_linpolphase", varlist) |
---|
1478 | return |
---|
1479 | |
---|
1480 | @print_log_dec |
---|
1481 | def rotate_xyphase(self, angle): |
---|
1482 | """ |
---|
1483 | Rotate the phase of the XY correlation. This is always done in situ |
---|
1484 | in the data. So if you call this function more than once |
---|
1485 | then each call rotates the phase further. |
---|
1486 | Parameters: |
---|
1487 | angle: The angle (degrees) to rotate (add) by. |
---|
1488 | Examples: |
---|
1489 | scan.rotate_xyphase(2.3) |
---|
1490 | """ |
---|
1491 | varlist = vars() |
---|
1492 | self._math._rotate_xyphase(self, angle) |
---|
1493 | self._add_history("rotate_xyphase", varlist) |
---|
1494 | return |
---|
1495 | |
---|
1496 | @print_log_dec |
---|
1497 | def swap_linears(self): |
---|
1498 | """ |
---|
1499 | Swap the linear polarisations XX and YY, or better the first two |
---|
1500 | polarisations as this also works for ciculars. |
---|
1501 | """ |
---|
1502 | varlist = vars() |
---|
1503 | self._math._swap_linears(self) |
---|
1504 | self._add_history("swap_linears", varlist) |
---|
1505 | return |
---|
1506 | |
---|
1507 | @print_log_dec |
---|
1508 | def invert_phase(self): |
---|
1509 | """ |
---|
1510 | Invert the phase of the complex polarisation |
---|
1511 | """ |
---|
1512 | varlist = vars() |
---|
1513 | self._math._invert_phase(self) |
---|
1514 | self._add_history("invert_phase", varlist) |
---|
1515 | return |
---|
1516 | |
---|
1517 | @print_log_dec |
---|
1518 | def add(self, offset, insitu=None): |
---|
1519 | """ |
---|
1520 | Return a scan where all spectra have the offset added |
---|
1521 | Parameters: |
---|
1522 | offset: the offset |
---|
1523 | insitu: if False a new scantable is returned. |
---|
1524 | Otherwise, the scaling is done in-situ |
---|
1525 | The default is taken from .asaprc (False) |
---|
1526 | """ |
---|
1527 | if insitu is None: insitu = rcParams['insitu'] |
---|
1528 | self._math._setinsitu(insitu) |
---|
1529 | varlist = vars() |
---|
1530 | s = scantable(self._math._unaryop(self, offset, "ADD", False)) |
---|
1531 | s._add_history("add", varlist) |
---|
1532 | if insitu: |
---|
1533 | self._assign(s) |
---|
1534 | else: |
---|
1535 | return s |
---|
1536 | |
---|
1537 | @print_log_dec |
---|
1538 | def scale(self, factor, tsys=True, insitu=None): |
---|
1539 | """ |
---|
1540 | Return a scan where all spectra are scaled by the give 'factor' |
---|
1541 | Parameters: |
---|
1542 | factor: the scaling factor |
---|
1543 | insitu: if False a new scantable is returned. |
---|
1544 | Otherwise, the scaling is done in-situ |
---|
1545 | The default is taken from .asaprc (False) |
---|
1546 | tsys: if True (default) then apply the operation to Tsys |
---|
1547 | as well as the data |
---|
1548 | """ |
---|
1549 | if insitu is None: insitu = rcParams['insitu'] |
---|
1550 | self._math._setinsitu(insitu) |
---|
1551 | varlist = vars() |
---|
1552 | s = scantable(self._math._unaryop(self, factor, "MUL", tsys)) |
---|
1553 | s._add_history("scale", varlist) |
---|
1554 | if insitu: |
---|
1555 | self._assign(s) |
---|
1556 | else: |
---|
1557 | return s |
---|
1558 | |
---|
1559 | def set_sourcetype(self, match, matchtype="pattern", |
---|
1560 | sourcetype="reference"): |
---|
1561 | """ |
---|
1562 | Set the type of the source to be an source or reference scan |
---|
1563 | using the provided pattern: |
---|
1564 | Parameters: |
---|
1565 | match: a Unix style pattern, regular expression or selector |
---|
1566 | matchtype: 'pattern' (default) UNIX style pattern or |
---|
1567 | 'regex' regular expression |
---|
1568 | sourcetype: the type of the source to use (source/reference) |
---|
1569 | """ |
---|
1570 | varlist = vars() |
---|
1571 | basesel = self.get_selection() |
---|
1572 | stype = -1 |
---|
1573 | if sourcetype.lower().startswith("r"): |
---|
1574 | stype = 1 |
---|
1575 | elif sourcetype.lower().startswith("s"): |
---|
1576 | stype = 0 |
---|
1577 | else: |
---|
1578 | raise ValueError("Illegal sourcetype use s(ource) or r(eference)") |
---|
1579 | if matchtype.lower().startswith("p"): |
---|
1580 | matchtype = "pattern" |
---|
1581 | elif matchtype.lower().startswith("r"): |
---|
1582 | matchtype = "regex" |
---|
1583 | else: |
---|
1584 | raise ValueError("Illegal matchtype, use p(attern) or r(egex)") |
---|
1585 | sel = selector() |
---|
1586 | if isinstance(match, selector): |
---|
1587 | sel = match |
---|
1588 | else: |
---|
1589 | sel.set_query("SRCNAME == %s('%s')" % (matchtype, match)) |
---|
1590 | self.set_selection(basesel+sel) |
---|
1591 | self._setsourcetype(stype) |
---|
1592 | self.set_selection(basesel) |
---|
1593 | self._add_history("set_sourcetype", varlist) |
---|
1594 | |
---|
1595 | @print_log_dec |
---|
1596 | def auto_quotient(self, preserve=True, mode='paired'): |
---|
1597 | """ |
---|
1598 | This function allows to build quotients automatically. |
---|
1599 | It assumes the observation to have the same numer of |
---|
1600 | "ons" and "offs" |
---|
1601 | Parameters: |
---|
1602 | preserve: you can preserve (default) the continuum or |
---|
1603 | remove it. The equations used are |
---|
1604 | preserve: Output = Toff * (on/off) - Toff |
---|
1605 | remove: Output = Toff * (on/off) - Ton |
---|
1606 | mode: the on/off detection mode |
---|
1607 | 'paired' (default) |
---|
1608 | identifies 'off' scans by the |
---|
1609 | trailing '_R' (Mopra/Parkes) or |
---|
1610 | '_e'/'_w' (Tid) and matches |
---|
1611 | on/off pairs from the observing pattern |
---|
1612 | 'time' |
---|
1613 | finds the closest off in time |
---|
1614 | |
---|
1615 | """ |
---|
1616 | modes = ["time", "paired"] |
---|
1617 | if not mode in modes: |
---|
1618 | msg = "please provide valid mode. Valid modes are %s" % (modes) |
---|
1619 | raise ValueError(msg) |
---|
1620 | varlist = vars() |
---|
1621 | s = None |
---|
1622 | if mode.lower() == "paired": |
---|
1623 | basesel = self.get_selection() |
---|
1624 | sel = selector()+basesel |
---|
1625 | sel.set_query("SRCTYPE==1") |
---|
1626 | self.set_selection(sel) |
---|
1627 | offs = self.copy() |
---|
1628 | sel.set_query("SRCTYPE==0") |
---|
1629 | self.set_selection(sel) |
---|
1630 | ons = self.copy() |
---|
1631 | s = scantable(self._math._quotient(ons, offs, preserve)) |
---|
1632 | self.set_selection(basesel) |
---|
1633 | elif mode.lower() == "time": |
---|
1634 | s = scantable(self._math._auto_quotient(self, mode, preserve)) |
---|
1635 | s._add_history("auto_quotient", varlist) |
---|
1636 | return s |
---|
1637 | |
---|
1638 | @print_log_dec |
---|
1639 | def mx_quotient(self, mask = None, weight='median', preserve=True): |
---|
1640 | """ |
---|
1641 | Form a quotient using "off" beams when observing in "MX" mode. |
---|
1642 | Parameters: |
---|
1643 | mask: an optional mask to be used when weight == 'stddev' |
---|
1644 | weight: How to average the off beams. Default is 'median'. |
---|
1645 | preserve: you can preserve (default) the continuum or |
---|
1646 | remove it. The equations used are |
---|
1647 | preserve: Output = Toff * (on/off) - Toff |
---|
1648 | remove: Output = Toff * (on/off) - Ton |
---|
1649 | """ |
---|
1650 | mask = mask or () |
---|
1651 | varlist = vars() |
---|
1652 | on = scantable(self._math._mx_extract(self, 'on')) |
---|
1653 | preoff = scantable(self._math._mx_extract(self, 'off')) |
---|
1654 | off = preoff.average_time(mask=mask, weight=weight, scanav=False) |
---|
1655 | from asapmath import quotient |
---|
1656 | q = quotient(on, off, preserve) |
---|
1657 | q._add_history("mx_quotient", varlist) |
---|
1658 | return q |
---|
1659 | |
---|
1660 | @print_log_dec |
---|
1661 | def freq_switch(self, insitu=None): |
---|
1662 | """ |
---|
1663 | Apply frequency switching to the data. |
---|
1664 | Parameters: |
---|
1665 | insitu: if False a new scantable is returned. |
---|
1666 | Otherwise, the swictching is done in-situ |
---|
1667 | The default is taken from .asaprc (False) |
---|
1668 | Example: |
---|
1669 | none |
---|
1670 | """ |
---|
1671 | if insitu is None: insitu = rcParams['insitu'] |
---|
1672 | self._math._setinsitu(insitu) |
---|
1673 | varlist = vars() |
---|
1674 | s = scantable(self._math._freqswitch(self)) |
---|
1675 | s._add_history("freq_switch", varlist) |
---|
1676 | if insitu: self._assign(s) |
---|
1677 | else: return s |
---|
1678 | |
---|
1679 | @print_log_dec |
---|
1680 | def recalc_azel(self): |
---|
1681 | """ |
---|
1682 | Recalculate the azimuth and elevation for each position. |
---|
1683 | Parameters: |
---|
1684 | none |
---|
1685 | Example: |
---|
1686 | """ |
---|
1687 | varlist = vars() |
---|
1688 | self._recalcazel() |
---|
1689 | self._add_history("recalc_azel", varlist) |
---|
1690 | return |
---|
1691 | |
---|
1692 | @print_log_dec |
---|
1693 | def __add__(self, other): |
---|
1694 | varlist = vars() |
---|
1695 | s = None |
---|
1696 | if isinstance(other, scantable): |
---|
1697 | s = scantable(self._math._binaryop(self, other, "ADD")) |
---|
1698 | elif isinstance(other, float): |
---|
1699 | s = scantable(self._math._unaryop(self, other, "ADD", False)) |
---|
1700 | else: |
---|
1701 | raise TypeError("Other input is not a scantable or float value") |
---|
1702 | s._add_history("operator +", varlist) |
---|
1703 | return s |
---|
1704 | |
---|
1705 | @print_log_dec |
---|
1706 | def __sub__(self, other): |
---|
1707 | """ |
---|
1708 | implicit on all axes and on Tsys |
---|
1709 | """ |
---|
1710 | varlist = vars() |
---|
1711 | s = None |
---|
1712 | if isinstance(other, scantable): |
---|
1713 | s = scantable(self._math._binaryop(self, other, "SUB")) |
---|
1714 | elif isinstance(other, float): |
---|
1715 | s = scantable(self._math._unaryop(self, other, "SUB", False)) |
---|
1716 | else: |
---|
1717 | raise TypeError("Other input is not a scantable or float value") |
---|
1718 | s._add_history("operator -", varlist) |
---|
1719 | return s |
---|
1720 | |
---|
1721 | @print_log_dec |
---|
1722 | def __mul__(self, other): |
---|
1723 | """ |
---|
1724 | implicit on all axes and on Tsys |
---|
1725 | """ |
---|
1726 | varlist = vars() |
---|
1727 | s = None |
---|
1728 | if isinstance(other, scantable): |
---|
1729 | s = scantable(self._math._binaryop(self, other, "MUL")) |
---|
1730 | elif isinstance(other, float): |
---|
1731 | s = scantable(self._math._unaryop(self, other, "MUL", False)) |
---|
1732 | else: |
---|
1733 | raise TypeError("Other input is not a scantable or float value") |
---|
1734 | s._add_history("operator *", varlist) |
---|
1735 | return s |
---|
1736 | |
---|
1737 | |
---|
1738 | @print_log_dec |
---|
1739 | def __div__(self, other): |
---|
1740 | """ |
---|
1741 | implicit on all axes and on Tsys |
---|
1742 | """ |
---|
1743 | varlist = vars() |
---|
1744 | s = None |
---|
1745 | if isinstance(other, scantable): |
---|
1746 | s = scantable(self._math._binaryop(self, other, "DIV")) |
---|
1747 | elif isinstance(other, float): |
---|
1748 | if other == 0.0: |
---|
1749 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
1750 | s = scantable(self._math._unaryop(self, other, "DIV", False)) |
---|
1751 | else: |
---|
1752 | raise TypeError("Other input is not a scantable or float value") |
---|
1753 | s._add_history("operator /", varlist) |
---|
1754 | return s |
---|
1755 | |
---|
1756 | def get_fit(self, row=0): |
---|
1757 | """ |
---|
1758 | Print or return the stored fits for a row in the scantable |
---|
1759 | Parameters: |
---|
1760 | row: the row which the fit has been applied to. |
---|
1761 | """ |
---|
1762 | if row > self.nrow(): |
---|
1763 | return |
---|
1764 | from asap.asapfit import asapfit |
---|
1765 | fit = asapfit(self._getfit(row)) |
---|
1766 | if rcParams['verbose']: |
---|
1767 | print fit |
---|
1768 | return |
---|
1769 | else: |
---|
1770 | return fit.as_dict() |
---|
1771 | |
---|
1772 | def flag_nans(self): |
---|
1773 | """ |
---|
1774 | Utility function to flag NaN values in the scantable. |
---|
1775 | """ |
---|
1776 | import numpy |
---|
1777 | basesel = self.get_selection() |
---|
1778 | for i in range(self.nrow()): |
---|
1779 | sel = self.get_row_selector(i) |
---|
1780 | self.set_selection(basesel+sel) |
---|
1781 | nans = numpy.isnan(self._getspectrum(0)) |
---|
1782 | if numpy.any(nans): |
---|
1783 | bnans = [ bool(v) for v in nans] |
---|
1784 | self.flag(bnans) |
---|
1785 | self.set_selection(basesel) |
---|
1786 | |
---|
1787 | def get_row_selector(self, rowno): |
---|
1788 | return selector(beams=self.getbeam(rowno), |
---|
1789 | ifs=self.getif(rowno), |
---|
1790 | pols=self.getpol(rowno), |
---|
1791 | scans=self.getscan(rowno), |
---|
1792 | cycles=self.getcycle(rowno)) |
---|
1793 | |
---|
1794 | def _add_history(self, funcname, parameters): |
---|
1795 | if not rcParams['scantable.history']: |
---|
1796 | return |
---|
1797 | # create date |
---|
1798 | sep = "##" |
---|
1799 | from datetime import datetime |
---|
1800 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
1801 | hist = dstr+sep |
---|
1802 | hist += funcname+sep#cdate+sep |
---|
1803 | if parameters.has_key('self'): del parameters['self'] |
---|
1804 | for k, v in parameters.iteritems(): |
---|
1805 | if type(v) is dict: |
---|
1806 | for k2, v2 in v.iteritems(): |
---|
1807 | hist += k2 |
---|
1808 | hist += "=" |
---|
1809 | if isinstance(v2, scantable): |
---|
1810 | hist += 'scantable' |
---|
1811 | elif k2 == 'mask': |
---|
1812 | if isinstance(v2, list) or isinstance(v2, tuple): |
---|
1813 | hist += str(self._zip_mask(v2)) |
---|
1814 | else: |
---|
1815 | hist += str(v2) |
---|
1816 | else: |
---|
1817 | hist += str(v2) |
---|
1818 | else: |
---|
1819 | hist += k |
---|
1820 | hist += "=" |
---|
1821 | if isinstance(v, scantable): |
---|
1822 | hist += 'scantable' |
---|
1823 | elif k == 'mask': |
---|
1824 | if isinstance(v, list) or isinstance(v, tuple): |
---|
1825 | hist += str(self._zip_mask(v)) |
---|
1826 | else: |
---|
1827 | hist += str(v) |
---|
1828 | else: |
---|
1829 | hist += str(v) |
---|
1830 | hist += sep |
---|
1831 | hist = hist[:-2] # remove trailing '##' |
---|
1832 | self._addhistory(hist) |
---|
1833 | |
---|
1834 | |
---|
1835 | def _zip_mask(self, mask): |
---|
1836 | mask = list(mask) |
---|
1837 | i = 0 |
---|
1838 | segments = [] |
---|
1839 | while mask[i:].count(1): |
---|
1840 | i += mask[i:].index(1) |
---|
1841 | if mask[i:].count(0): |
---|
1842 | j = i + mask[i:].index(0) |
---|
1843 | else: |
---|
1844 | j = len(mask) |
---|
1845 | segments.append([i, j]) |
---|
1846 | i = j |
---|
1847 | return segments |
---|
1848 | |
---|
1849 | def _get_ordinate_label(self): |
---|
1850 | fu = "("+self.get_fluxunit()+")" |
---|
1851 | import re |
---|
1852 | lbl = "Intensity" |
---|
1853 | if re.match(".K.", fu): |
---|
1854 | lbl = "Brightness Temperature "+ fu |
---|
1855 | elif re.match(".Jy.", fu): |
---|
1856 | lbl = "Flux density "+ fu |
---|
1857 | return lbl |
---|
1858 | |
---|
1859 | def _check_ifs(self): |
---|
1860 | nchans = [self.nchan(i) for i in range(self.nif(-1))] |
---|
1861 | nchans = filter(lambda t: t > 0, nchans) |
---|
1862 | return (sum(nchans)/len(nchans) == nchans[0]) |
---|
1863 | |
---|
1864 | def _fill(self, names, unit, average): |
---|
1865 | import os |
---|
1866 | from asap._asap import stfiller |
---|
1867 | first = True |
---|
1868 | fullnames = [] |
---|
1869 | for name in names: |
---|
1870 | name = os.path.expandvars(name) |
---|
1871 | name = os.path.expanduser(name) |
---|
1872 | if not os.path.exists(name): |
---|
1873 | msg = "File '%s' does not exists" % (name) |
---|
1874 | if rcParams['verbose']: |
---|
1875 | asaplog.push(msg) |
---|
1876 | print asaplog.pop().strip() |
---|
1877 | return |
---|
1878 | raise IOError(msg) |
---|
1879 | fullnames.append(name) |
---|
1880 | if average: |
---|
1881 | asaplog.push('Auto averaging integrations') |
---|
1882 | stype = int(rcParams['scantable.storage'].lower() == 'disk') |
---|
1883 | for name in fullnames: |
---|
1884 | tbl = Scantable(stype) |
---|
1885 | r = stfiller(tbl) |
---|
1886 | rx = rcParams['scantable.reference'] |
---|
1887 | r._setreferenceexpr(rx) |
---|
1888 | msg = "Importing %s..." % (name) |
---|
1889 | asaplog.push(msg, False) |
---|
1890 | print_log() |
---|
1891 | r._open(name, -1, -1) |
---|
1892 | r._read() |
---|
1893 | if average: |
---|
1894 | tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN') |
---|
1895 | if not first: |
---|
1896 | tbl = self._math._merge([self, tbl]) |
---|
1897 | Scantable.__init__(self, tbl) |
---|
1898 | r._close() |
---|
1899 | del r, tbl |
---|
1900 | first = False |
---|
1901 | if unit is not None: |
---|
1902 | self.set_fluxunit(unit) |
---|
1903 | self.set_freqframe(rcParams['scantable.freqframe']) |
---|
1904 | |
---|
1905 | def __getitem__(self, key): |
---|
1906 | if key < 0: |
---|
1907 | key += self.nrow() |
---|
1908 | if key >= self.nrow(): |
---|
1909 | raise IndexError("Row index out of range.") |
---|
1910 | return self._getspectrum(key) |
---|
1911 | |
---|
1912 | def __setitem__(self, key, value): |
---|
1913 | if key < 0: |
---|
1914 | key += self.nrow() |
---|
1915 | if key >= self.nrow(): |
---|
1916 | raise IndexError("Row index out of range.") |
---|
1917 | if not hasattr(value, "__len__") or \ |
---|
1918 | len(value) > self.nchan(self.getif(key)): |
---|
1919 | raise ValueError("Spectrum length doesn't match.") |
---|
1920 | return self._setspectrum(value, key) |
---|
1921 | |
---|
1922 | def __len__(self): |
---|
1923 | return self.nrow() |
---|
1924 | |
---|
1925 | def __iter__(self): |
---|
1926 | for i in range(len(self)): |
---|
1927 | yield self[i] |
---|