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.env import is_casapy
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8 | from asap._asap import Scantable
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9 | from asap._asap import filler
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10 | from asap.parameters import rcParams
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11 | from asap.logging import asaplog, print_log, print_log_dec
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12 | from asap.selector import selector
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13 | from asap.linecatalog import linecatalog
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14 | from asap.coordinate import coordinate
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15 | from asap.utils import _n_bools, mask_not, mask_and, mask_or
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16 |
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17 |
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18 | def preserve_selection(func):
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19 | @wraps_dec(func)
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20 | def wrap(obj, *args, **kw):
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21 | basesel = obj.get_selection()
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22 | val = func(obj, *args, **kw)
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23 | obj.set_selection(basesel)
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24 | return val
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25 | return wrap
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26 |
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27 |
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28 | def is_scantable(filename):
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29 | return (os.path.isdir(filename)
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30 | and not os.path.exists(filename+'/table.f1')
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31 | and os.path.exists(filename+'/table.info'))
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32 |
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33 |
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34 | class scantable(Scantable):
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35 | """
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36 | The ASAP container for scans
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37 | """
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38 |
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39 | @print_log_dec
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40 | def __init__(self, filename, average=None, unit=None, getpt=None,
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41 | antenna=None, parallactify=None):
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42 | """
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43 | Create a scantable from a saved one or make a reference
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44 | Parameters:
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45 | filename: the name of an asap table on disk
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46 | or
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47 | the name of a rpfits/sdfits/ms file
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48 | (integrations within scans are auto averaged
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49 | and the whole file is read)
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50 | or
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51 | [advanced] a reference to an existing
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52 | scantable
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53 | average: average all integrations withinb a scan on read.
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54 | The default (True) is taken from .asaprc.
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55 | unit: brightness unit; must be consistent with K or Jy.
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56 | Over-rides the default selected by the filler
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57 | (input rpfits/sdfits/ms) or replaces the value
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58 | in existing scantables
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59 | getpt: for MeasurementSet input data only:
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60 | If True, all pointing data are filled.
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61 | The deafult is False, which makes time to load
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62 | the MS data faster in some cases.
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63 | antenna: Antenna selection. integer (id) or string (name
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64 | or id).
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65 | parallactify: Indicate that the data had been parallatified.
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66 | Default is taken form rc file.
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67 | """
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68 | if average is None:
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69 | average = rcParams['scantable.autoaverage']
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70 | if getpt is None:
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71 | getpt = True
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72 | if antenna is not None:
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73 | asaplog.push("Antenna selection currently unsupported."
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74 | "Using '0'")
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75 | print_log('WARN')
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76 | if antenna is None:
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77 | antenna = ''
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78 | elif type(antenna) == int:
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79 | antenna = '%s' % antenna
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80 | elif type(antenna) == list:
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81 | tmpstr = ''
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82 | for i in range( len(antenna) ):
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83 | if type(antenna[i]) == int:
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84 | tmpstr = tmpstr + ('%s,'%(antenna[i]))
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85 | elif type(antenna[i]) == str:
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86 | tmpstr=tmpstr+antenna[i]+','
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87 | else:
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88 | asaplog.push('Bad antenna selection.')
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89 | print_log('ERROR')
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90 | return
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91 | antenna = tmpstr.rstrip(',')
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92 | parallactify = parallactify or rcParams['scantable.parallactify']
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93 | varlist = vars()
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94 | from asap._asap import stmath
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95 | self._math = stmath( rcParams['insitu'] )
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96 | if isinstance(filename, Scantable):
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97 | Scantable.__init__(self, filename)
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98 | else:
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99 | if isinstance(filename, str):
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100 | filename = os.path.expandvars(filename)
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101 | filename = os.path.expanduser(filename)
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102 | if not os.path.exists(filename):
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103 | s = "File '%s' not found." % (filename)
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104 | if rcParams['verbose']:
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105 | asaplog.push(s)
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106 | print_log('ERROR')
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107 | return
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108 | raise IOError(s)
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109 | if is_scantable(filename):
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110 | ondisk = rcParams['scantable.storage'] == 'disk'
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111 | Scantable.__init__(self, filename, ondisk)
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112 | if unit is not None:
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113 | self.set_fluxunit(unit)
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114 | # do not reset to the default freqframe
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115 | #self.set_freqframe(rcParams['scantable.freqframe'])
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116 | elif os.path.isdir(filename) \
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117 | and not os.path.exists(filename+'/table.f1'):
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118 | msg = "The given file '%s'is not a valid " \
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119 | "asap table." % (filename)
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120 | if rcParams['verbose']:
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121 | #print msg
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122 | asaplog.push( msg )
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123 | print_log( 'ERROR' )
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124 | return
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125 | else:
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126 | raise IOError(msg)
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127 | else:
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128 | self._fill([filename], unit, average, getpt, antenna)
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129 | elif (isinstance(filename, list) or isinstance(filename, tuple)) \
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130 | and isinstance(filename[-1], str):
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131 | self._fill(filename, unit, average, getpt, antenna)
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132 | self.parallactify(parallactify)
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133 | self._add_history("scantable", varlist)
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134 | print_log()
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135 |
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136 | @print_log_dec
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137 | def save(self, name=None, format=None, overwrite=False):
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138 | """
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139 | Store the scantable on disk. This can be an asap (aips++) Table,
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140 | SDFITS or MS2 format.
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141 | Parameters:
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142 | name: the name of the outputfile. For format "ASCII"
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143 | this is the root file name (data in 'name'.txt
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144 | and header in 'name'_header.txt)
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145 | format: an optional file format. Default is ASAP.
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146 | Allowed are - 'ASAP' (save as ASAP [aips++] Table),
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147 | 'SDFITS' (save as SDFITS file)
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148 | 'ASCII' (saves as ascii text file)
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149 | 'MS2' (saves as an aips++
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150 | MeasurementSet V2)
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151 | 'FITS' (save as image FITS - not
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152 | readable by class)
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153 | 'CLASS' (save as FITS readable by CLASS)
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154 | overwrite: If the file should be overwritten if it exists.
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155 | The default False is to return with warning
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156 | without writing the output. USE WITH CARE.
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157 | Example:
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158 | scan.save('myscan.asap')
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159 | scan.save('myscan.sdfits', 'SDFITS')
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160 | """
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161 | from os import path
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162 | format = format or rcParams['scantable.save']
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163 | suffix = '.'+format.lower()
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164 | if name is None or name == "":
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165 | name = 'scantable'+suffix
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166 | msg = "No filename given. Using default name %s..." % name
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167 | asaplog.push(msg)
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168 | name = path.expandvars(name)
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169 | if path.isfile(name) or path.isdir(name):
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170 | if not overwrite:
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171 | msg = "File %s exists." % name
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172 | if rcParams['verbose']:
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173 | #print msg
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174 | asaplog.push( msg )
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175 | print_log( 'ERROR' )
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176 | return
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177 | else:
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178 | raise IOError(msg)
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179 | format2 = format.upper()
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180 | if format2 == 'ASAP':
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181 | self._save(name)
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182 | else:
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183 | from asap._asap import stwriter as stw
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184 | writer = stw(format2)
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185 | writer.write(self, name)
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186 | print_log()
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187 | return
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188 |
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189 | def copy(self):
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190 | """
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191 | Return a copy of this scantable.
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192 | Note:
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193 | This makes a full (deep) copy. scan2 = scan1 makes a reference.
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194 | Parameters:
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195 | none
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196 | Example:
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197 | copiedscan = scan.copy()
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198 | """
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199 | sd = scantable(Scantable._copy(self))
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200 | return sd
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201 |
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202 | def drop_scan(self, scanid=None):
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203 | """
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204 | Return a new scantable where the specified scan number(s) has(have)
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205 | been dropped.
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206 | Parameters:
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207 | scanid: a (list of) scan number(s)
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208 | """
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209 | from asap import _is_sequence_or_number as _is_valid
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210 | from asap import _to_list
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211 | from asap import unique
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212 | if not _is_valid(scanid):
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213 | if rcParams['verbose']:
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214 | #print "Please specify a scanno to drop from the scantable"
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215 | asaplog.push( 'Please specify a scanno to drop from the scantable' )
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216 | print_log( 'ERROR' )
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217 | return
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218 | else:
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219 | raise RuntimeError("No scan given")
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220 | try:
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221 | scanid = _to_list(scanid)
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222 | allscans = unique([ self.getscan(i) for i in range(self.nrow())])
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223 | for sid in scanid: allscans.remove(sid)
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224 | if len(allscans) == 0:
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225 | raise ValueError("Can't remove all scans")
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226 | except ValueError:
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227 | if rcParams['verbose']:
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228 | #print "Couldn't find any match."
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229 | print_log()
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230 | asaplog.push( "Couldn't find any match." )
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231 | print_log( 'ERROR' )
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232 | return
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233 | else: raise
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234 | try:
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235 | sel = selector(scans=allscans)
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236 | return self._select_copy(sel)
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237 | except RuntimeError:
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238 | if rcParams['verbose']:
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239 | #print "Couldn't find any match."
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240 | print_log()
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241 | asaplog.push( "Couldn't find any match." )
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242 | print_log( 'ERROR' )
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243 | else:
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244 | raise
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245 |
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246 | def _select_copy(self, selection):
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247 | orig = self.get_selection()
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248 | self.set_selection(orig+selection)
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249 | cp = self.copy()
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250 | self.set_selection(orig)
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251 | return cp
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252 |
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253 | def get_scan(self, scanid=None):
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254 | """
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255 | Return a specific scan (by scanno) or collection of scans (by
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256 | source name) in a new scantable.
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257 | Note:
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258 | See scantable.drop_scan() for the inverse operation.
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259 | Parameters:
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260 | scanid: a (list of) scanno or a source name, unix-style
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261 | patterns are accepted for source name matching, e.g.
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262 | '*_R' gets all 'ref scans
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263 | Example:
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264 | # get all scans containing the source '323p459'
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265 | newscan = scan.get_scan('323p459')
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266 | # get all 'off' scans
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267 | refscans = scan.get_scan('*_R')
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268 | # get a susbset of scans by scanno (as listed in scan.summary())
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269 | newscan = scan.get_scan([0, 2, 7, 10])
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270 | """
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271 | if scanid is None:
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272 | if rcParams['verbose']:
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273 | #print "Please specify a scan no or name to " \
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274 | # "retrieve from the scantable"
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275 | asaplog.push( 'Please specify a scan no or name to retrieve from the scantable' )
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276 | print_log( 'ERROR' )
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277 | return
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278 | else:
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279 | raise RuntimeError("No scan given")
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280 |
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281 | try:
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282 | bsel = self.get_selection()
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283 | sel = selector()
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284 | if type(scanid) is str:
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285 | sel.set_name(scanid)
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286 | return self._select_copy(sel)
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287 | elif type(scanid) is int:
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288 | sel.set_scans([scanid])
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289 | return self._select_copy(sel)
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290 | elif type(scanid) is list:
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291 | sel.set_scans(scanid)
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292 | return self._select_copy(sel)
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293 | else:
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294 | msg = "Illegal scanid type, use 'int' or 'list' if ints."
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295 | if rcParams['verbose']:
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296 | #print msg
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297 | asaplog.push( msg )
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298 | print_log( 'ERROR' )
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299 | else:
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300 | raise TypeError(msg)
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301 | except RuntimeError:
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302 | if rcParams['verbose']:
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303 | #print "Couldn't find any match."
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304 | print_log()
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305 | asaplog.push( "Couldn't find any match." )
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306 | print_log( 'ERROR' )
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307 | else: raise
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308 |
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309 | def __str__(self):
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310 | return Scantable._summary(self, True)
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311 |
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312 | def summary(self, filename=None):
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313 | """
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314 | Print a summary of the contents of this scantable.
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315 | Parameters:
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316 | filename: the name of a file to write the putput to
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317 | Default - no file output
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318 | """
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319 | info = Scantable._summary(self, True)
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320 | if filename is not None:
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321 | if filename is "":
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322 | filename = 'scantable_summary.txt'
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323 | from os.path import expandvars, isdir
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324 | filename = expandvars(filename)
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325 | if not isdir(filename):
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326 | data = open(filename, 'w')
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327 | data.write(info)
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328 | data.close()
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329 | else:
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330 | msg = "Illegal file name '%s'." % (filename)
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331 | if rcParams['verbose']:
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332 | #print msg
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333 | asaplog.push( msg )
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334 | print_log( 'ERROR' )
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335 | else:
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336 | raise IOError(msg)
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337 | if rcParams['verbose']:
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338 | try:
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339 | from IPython.genutils import page as pager
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340 | except ImportError:
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341 | from pydoc import pager
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342 | pager(info)
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343 | else:
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344 | return info
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345 |
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346 | def get_spectrum(self, rowno):
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347 | """Return the spectrum for the current row in the scantable as a list.
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348 | Parameters:
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349 | rowno: the row number to retrieve the spectrum from
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350 | """
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351 | return self._getspectrum(rowno)
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352 |
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353 | def get_mask(self, rowno):
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354 | """Return the mask for the current row in the scantable as a list.
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355 | Parameters:
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356 | rowno: the row number to retrieve the mask from
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357 | """
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358 | return self._getmask(rowno)
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359 |
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360 | def set_spectrum(self, spec, rowno):
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361 | """Return the spectrum for the current row in the scantable as a list.
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362 | Parameters:
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363 | spec: the spectrum
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364 | rowno: the row number to set the spectrum for
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365 | """
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366 | assert(len(spec) == self.nchan())
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367 | return self._setspectrum(spec, rowno)
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368 |
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369 | def get_coordinate(self, rowno):
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370 | """Return the (spectral) coordinate for a a given 'rowno'.
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371 | NOTE:
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372 | * This coordinate is only valid until a scantable method modifies
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373 | the frequency axis.
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374 | * This coordinate does contain the original frequency set-up
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375 | NOT the new frame. The conversions however are done using the user
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376 | specified frame (e.g. LSRK/TOPO). To get the 'real' coordinate,
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377 | use scantable.freq_align first. Without it there is no closure,
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378 | i.e.
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379 | c = myscan.get_coordinate(0)
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380 | c.to_frequency(c.get_reference_pixel()) != c.get_reference_value()
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381 |
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382 | Parameters:
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383 | rowno: the row number for the spectral coordinate
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384 |
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385 | """
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386 | return coordinate(Scantable.get_coordinate(self, rowno))
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387 |
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388 | def get_selection(self):
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389 | """
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390 | Get the selection object currently set on this scantable.
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391 | Parameters:
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392 | none
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393 | Example:
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394 | sel = scan.get_selection()
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395 | sel.set_ifs(0) # select IF 0
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396 | scan.set_selection(sel) # apply modified selection
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397 | """
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398 | return selector(self._getselection())
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399 |
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400 | def set_selection(self, selection=None, **kw):
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401 | """
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402 | Select a subset of the data. All following operations on this scantable
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403 | are only applied to thi selection.
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404 | Parameters:
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405 | selection: a selector object (default unset the selection),
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406 |
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407 | or
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408 |
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409 | any combination of
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410 | "pols", "ifs", "beams", "scans", "cycles", "name", "query"
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411 |
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412 | Examples:
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413 | sel = selector() # create a selection object
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414 | self.set_scans([0, 3]) # select SCANNO 0 and 3
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415 | scan.set_selection(sel) # set the selection
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416 | scan.summary() # will only print summary of scanno 0 an 3
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417 | scan.set_selection() # unset the selection
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418 | # or the equivalent
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419 | scan.set_selection(scans=[0,3])
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420 | scan.summary() # will only print summary of scanno 0 an 3
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421 | scan.set_selection() # unset the selection
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422 | """
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423 | if selection is None:
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424 | # reset
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425 | if len(kw) == 0:
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426 | selection = selector()
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427 | else:
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428 | # try keywords
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429 | for k in kw:
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430 | if k not in selector.fields:
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431 | raise KeyError("Invalid selection key '%s', valid keys are %s" % (k, selector.fields))
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432 | selection = selector(**kw)
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433 | self._setselection(selection)
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434 |
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435 | def get_row(self, row=0, insitu=None):
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436 | """
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437 | Select a row in the scantable.
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438 | Return a scantable with single row.
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439 | Parameters:
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440 | row: row no of integration, default is 0.
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441 | insitu: if False a new scantable is returned.
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442 | Otherwise, the scaling is done in-situ
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443 | The default is taken from .asaprc (False)
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444 | """
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445 | if insitu is None: insitu = rcParams['insitu']
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446 | if not insitu:
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447 | workscan = self.copy()
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448 | else:
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449 | workscan = self
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450 | # Select a row
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451 | sel=selector()
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452 | sel.set_scans([workscan.getscan(row)])
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453 | sel.set_cycles([workscan.getcycle(row)])
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454 | sel.set_beams([workscan.getbeam(row)])
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455 | sel.set_ifs([workscan.getif(row)])
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456 | sel.set_polarisations([workscan.getpol(row)])
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457 | sel.set_name(workscan._getsourcename(row))
|
---|
458 | workscan.set_selection(sel)
|
---|
459 | if not workscan.nrow() == 1:
|
---|
460 | msg = "Cloud not identify single row. %d rows selected."%(workscan.nrow())
|
---|
461 | raise RuntimeError(msg)
|
---|
462 | del sel
|
---|
463 | if insitu:
|
---|
464 | self._assign(workscan)
|
---|
465 | else:
|
---|
466 | return workscan
|
---|
467 |
|
---|
468 | #def stats(self, stat='stddev', mask=None):
|
---|
469 | def stats(self, stat='stddev', mask=None, form='3.3f'):
|
---|
470 | """
|
---|
471 | Determine the specified statistic of the current beam/if/pol
|
---|
472 | Takes a 'mask' as an optional parameter to specify which
|
---|
473 | channels should be excluded.
|
---|
474 | Parameters:
|
---|
475 | stat: 'min', 'max', 'min_abc', 'max_abc', 'sumsq', 'sum',
|
---|
476 | 'mean', 'var', 'stddev', 'avdev', 'rms', 'median'
|
---|
477 | mask: an optional mask specifying where the statistic
|
---|
478 | should be determined.
|
---|
479 | form: format string to print statistic values
|
---|
480 | Example:
|
---|
481 | scan.set_unit('channel')
|
---|
482 | msk = scan.create_mask([100, 200], [500, 600])
|
---|
483 | scan.stats(stat='mean', mask=m)
|
---|
484 | """
|
---|
485 | mask = mask or []
|
---|
486 | if not self._check_ifs():
|
---|
487 | raise ValueError("Cannot apply mask as the IFs have different "
|
---|
488 | "number of channels. Please use setselection() "
|
---|
489 | "to select individual IFs")
|
---|
490 | rtnabc = False
|
---|
491 | if stat.lower().endswith('_abc'): rtnabc = True
|
---|
492 | getchan = False
|
---|
493 | if stat.lower().startswith('min') or stat.lower().startswith('max'):
|
---|
494 | chan = self._math._minmaxchan(self, mask, stat)
|
---|
495 | getchan = True
|
---|
496 | statvals = []
|
---|
497 | if not rtnabc: statvals = self._math._stats(self, mask, stat)
|
---|
498 |
|
---|
499 | #def cb(i):
|
---|
500 | # return statvals[i]
|
---|
501 |
|
---|
502 | #return self._row_callback(cb, stat)
|
---|
503 |
|
---|
504 | label=stat
|
---|
505 | #callback=cb
|
---|
506 | out = ""
|
---|
507 | #outvec = []
|
---|
508 | sep = '-'*50
|
---|
509 | for i in range(self.nrow()):
|
---|
510 | refstr = ''
|
---|
511 | statunit= ''
|
---|
512 | if getchan:
|
---|
513 | qx, qy = self.chan2data(rowno=i, chan=chan[i])
|
---|
514 | if rtnabc:
|
---|
515 | statvals.append(qx['value'])
|
---|
516 | refstr = ('(value: %'+form) % (qy['value'])+' ['+qy['unit']+'])'
|
---|
517 | statunit= '['+qx['unit']+']'
|
---|
518 | else:
|
---|
519 | refstr = ('(@ %'+form) % (qx['value'])+' ['+qx['unit']+'])'
|
---|
520 |
|
---|
521 | tm = self._gettime(i)
|
---|
522 | src = self._getsourcename(i)
|
---|
523 | out += 'Scan[%d] (%s) ' % (self.getscan(i), src)
|
---|
524 | out += 'Time[%s]:\n' % (tm)
|
---|
525 | if self.nbeam(-1) > 1:
|
---|
526 | out += ' Beam[%d] ' % (self.getbeam(i))
|
---|
527 | if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i))
|
---|
528 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i))
|
---|
529 | #outvec.append(callback(i))
|
---|
530 | #out += ('= %'+form) % (outvec[i]) +' '+refstr+'\n'
|
---|
531 | out += ('= %'+form) % (statvals[i]) +' '+refstr+'\n'
|
---|
532 | out += sep+"\n"
|
---|
533 |
|
---|
534 | if rcParams['verbose']:
|
---|
535 | import os
|
---|
536 | if os.environ.has_key( 'USER' ):
|
---|
537 | usr=os.environ['USER']
|
---|
538 | else:
|
---|
539 | import commands
|
---|
540 | usr=commands.getoutput( 'whoami' )
|
---|
541 | tmpfile='/tmp/tmp_'+usr+'_casapy_asap_scantable_stats'
|
---|
542 | f=open(tmpfile,'w')
|
---|
543 | print >> f, sep
|
---|
544 | print >> f, ' %s %s' % (label, statunit)
|
---|
545 | print >> f, sep
|
---|
546 | print >> f, out
|
---|
547 | f.close()
|
---|
548 | f=open(tmpfile,'r')
|
---|
549 | x=f.readlines()
|
---|
550 | f.close()
|
---|
551 | blanc=''
|
---|
552 | asaplog.push(blanc.join(x), False)
|
---|
553 | #for xx in x:
|
---|
554 | # asaplog.push( xx, False )
|
---|
555 | print_log()
|
---|
556 | return statvals
|
---|
557 |
|
---|
558 | def chan2data(self, rowno=0, chan=0):
|
---|
559 | """
|
---|
560 | Returns channel/frequency/velocity and spectral value
|
---|
561 | at an arbitrary row and channel in the scantable.
|
---|
562 | Parameters:
|
---|
563 | rowno: a row number in the scantable. Default is the
|
---|
564 | first row, i.e. rowno=0
|
---|
565 | chan: a channel in the scantable. Default is the first
|
---|
566 | channel, i.e. pos=0
|
---|
567 | """
|
---|
568 | if isinstance(rowno, int) and isinstance(chan, int):
|
---|
569 | qx = {'unit': self.get_unit(),
|
---|
570 | 'value': self._getabcissa(rowno)[chan]}
|
---|
571 | qy = {'unit': self.get_fluxunit(),
|
---|
572 | 'value': self._getspectrum(rowno)[chan]}
|
---|
573 | return qx, qy
|
---|
574 |
|
---|
575 | def stddev(self, mask=None):
|
---|
576 | """
|
---|
577 | Determine the standard deviation of the current beam/if/pol
|
---|
578 | Takes a 'mask' as an optional parameter to specify which
|
---|
579 | channels should be excluded.
|
---|
580 | Parameters:
|
---|
581 | mask: an optional mask specifying where the standard
|
---|
582 | deviation should be determined.
|
---|
583 |
|
---|
584 | Example:
|
---|
585 | scan.set_unit('channel')
|
---|
586 | msk = scan.create_mask([100, 200], [500, 600])
|
---|
587 | scan.stddev(mask=m)
|
---|
588 | """
|
---|
589 | return self.stats(stat='stddev', mask=mask);
|
---|
590 |
|
---|
591 |
|
---|
592 | def get_column_names(self):
|
---|
593 | """
|
---|
594 | Return a list of column names, which can be used for selection.
|
---|
595 | """
|
---|
596 | return list(Scantable.get_column_names(self))
|
---|
597 |
|
---|
598 | def get_tsys(self, row=-1):
|
---|
599 | """
|
---|
600 | Return the System temperatures.
|
---|
601 | Returns:
|
---|
602 | a list of Tsys values for the current selection
|
---|
603 | """
|
---|
604 | if row > -1:
|
---|
605 | return self._get_column(self._gettsys, row)
|
---|
606 | return self._row_callback(self._gettsys, "Tsys")
|
---|
607 |
|
---|
608 |
|
---|
609 | def get_weather(self, row=-1):
|
---|
610 | values = self._get_column(self._get_weather, row)
|
---|
611 | if row > -1:
|
---|
612 | return {'temperature': values[0],
|
---|
613 | 'pressure': values[1], 'humidity' : values[2],
|
---|
614 | 'windspeed' : values[3], 'windaz' : values[4]
|
---|
615 | }
|
---|
616 | else:
|
---|
617 | out = []
|
---|
618 | for r in values:
|
---|
619 |
|
---|
620 | out.append({'temperature': r[0],
|
---|
621 | 'pressure': r[1], 'humidity' : r[2],
|
---|
622 | 'windspeed' : r[3], 'windaz' : r[4]
|
---|
623 | })
|
---|
624 | return out
|
---|
625 |
|
---|
626 | def _row_callback(self, callback, label):
|
---|
627 | out = ""
|
---|
628 | outvec = []
|
---|
629 | sep = '-'*50
|
---|
630 | for i in range(self.nrow()):
|
---|
631 | tm = self._gettime(i)
|
---|
632 | src = self._getsourcename(i)
|
---|
633 | out += 'Scan[%d] (%s) ' % (self.getscan(i), src)
|
---|
634 | out += 'Time[%s]:\n' % (tm)
|
---|
635 | if self.nbeam(-1) > 1:
|
---|
636 | out += ' Beam[%d] ' % (self.getbeam(i))
|
---|
637 | if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i))
|
---|
638 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i))
|
---|
639 | outvec.append(callback(i))
|
---|
640 | out += '= %3.3f\n' % (outvec[i])
|
---|
641 | out += sep+'\n'
|
---|
642 | if rcParams['verbose']:
|
---|
643 | asaplog.push(sep)
|
---|
644 | asaplog.push(" %s" % (label))
|
---|
645 | asaplog.push(sep)
|
---|
646 | asaplog.push(out)
|
---|
647 | print_log()
|
---|
648 | return outvec
|
---|
649 |
|
---|
650 | def _get_column(self, callback, row=-1):
|
---|
651 | """
|
---|
652 | """
|
---|
653 | if row == -1:
|
---|
654 | return [callback(i) for i in range(self.nrow())]
|
---|
655 | else:
|
---|
656 | if 0 <= row < self.nrow():
|
---|
657 | return callback(row)
|
---|
658 |
|
---|
659 |
|
---|
660 | def get_time(self, row=-1, asdatetime=False):
|
---|
661 | """
|
---|
662 | Get a list of time stamps for the observations.
|
---|
663 | Return a datetime object for each integration time stamp in the scantable.
|
---|
664 | Parameters:
|
---|
665 | row: row no of integration. Default -1 return all rows
|
---|
666 | asdatetime: return values as datetime objects rather than strings
|
---|
667 | Example:
|
---|
668 | none
|
---|
669 | """
|
---|
670 | from time import strptime
|
---|
671 | from datetime import datetime
|
---|
672 | times = self._get_column(self._gettime, row)
|
---|
673 | if not asdatetime:
|
---|
674 | return times
|
---|
675 | format = "%Y/%m/%d/%H:%M:%S"
|
---|
676 | if isinstance(times, list):
|
---|
677 | return [datetime(*strptime(i, format)[:6]) for i in times]
|
---|
678 | else:
|
---|
679 | return datetime(*strptime(times, format)[:6])
|
---|
680 |
|
---|
681 |
|
---|
682 | def get_inttime(self, row=-1):
|
---|
683 | """
|
---|
684 | Get a list of integration times for the observations.
|
---|
685 | Return a time in seconds for each integration in the scantable.
|
---|
686 | Parameters:
|
---|
687 | row: row no of integration. Default -1 return all rows.
|
---|
688 | Example:
|
---|
689 | none
|
---|
690 | """
|
---|
691 | return self._get_column(self._getinttime, row)
|
---|
692 |
|
---|
693 |
|
---|
694 | def get_sourcename(self, row=-1):
|
---|
695 | """
|
---|
696 | Get a list source names for the observations.
|
---|
697 | Return a string for each integration in the scantable.
|
---|
698 | Parameters:
|
---|
699 | row: row no of integration. Default -1 return all rows.
|
---|
700 | Example:
|
---|
701 | none
|
---|
702 | """
|
---|
703 | return self._get_column(self._getsourcename, row)
|
---|
704 |
|
---|
705 | def get_elevation(self, row=-1):
|
---|
706 | """
|
---|
707 | Get a list of elevations for the observations.
|
---|
708 | Return a float for each integration in the scantable.
|
---|
709 | Parameters:
|
---|
710 | row: row no of integration. Default -1 return all rows.
|
---|
711 | Example:
|
---|
712 | none
|
---|
713 | """
|
---|
714 | return self._get_column(self._getelevation, row)
|
---|
715 |
|
---|
716 | def get_azimuth(self, row=-1):
|
---|
717 | """
|
---|
718 | Get a list of azimuths for the observations.
|
---|
719 | Return a float for each integration in the scantable.
|
---|
720 | Parameters:
|
---|
721 | row: row no of integration. Default -1 return all rows.
|
---|
722 | Example:
|
---|
723 | none
|
---|
724 | """
|
---|
725 | return self._get_column(self._getazimuth, row)
|
---|
726 |
|
---|
727 | def get_parangle(self, row=-1):
|
---|
728 | """
|
---|
729 | Get a list of parallactic angles for the observations.
|
---|
730 | Return a float for each integration in the scantable.
|
---|
731 | Parameters:
|
---|
732 | row: row no of integration. Default -1 return all rows.
|
---|
733 | Example:
|
---|
734 | none
|
---|
735 | """
|
---|
736 | return self._get_column(self._getparangle, row)
|
---|
737 |
|
---|
738 | def get_direction(self, row=-1):
|
---|
739 | """
|
---|
740 | Get a list of Positions on the sky (direction) for the observations.
|
---|
741 | Return a string for each integration in the scantable.
|
---|
742 | Parameters:
|
---|
743 | row: row no of integration. Default -1 return all rows
|
---|
744 | Example:
|
---|
745 | none
|
---|
746 | """
|
---|
747 | return self._get_column(self._getdirection, row)
|
---|
748 |
|
---|
749 | def get_directionval(self, row=-1):
|
---|
750 | """
|
---|
751 | Get a list of Positions on the sky (direction) for the observations.
|
---|
752 | Return a float for each integration in the scantable.
|
---|
753 | Parameters:
|
---|
754 | row: row no of integration. Default -1 return all rows
|
---|
755 | Example:
|
---|
756 | none
|
---|
757 | """
|
---|
758 | return self._get_column(self._getdirectionvec, row)
|
---|
759 |
|
---|
760 | @print_log_dec
|
---|
761 | def set_unit(self, unit='channel'):
|
---|
762 | """
|
---|
763 | Set the unit for all following operations on this scantable
|
---|
764 | Parameters:
|
---|
765 | unit: optional unit, default is 'channel'
|
---|
766 | one of '*Hz', 'km/s', 'channel', ''
|
---|
767 | """
|
---|
768 | varlist = vars()
|
---|
769 | if unit in ['', 'pixel', 'channel']:
|
---|
770 | unit = ''
|
---|
771 | inf = list(self._getcoordinfo())
|
---|
772 | inf[0] = unit
|
---|
773 | self._setcoordinfo(inf)
|
---|
774 | self._add_history("set_unit", varlist)
|
---|
775 |
|
---|
776 | @print_log_dec
|
---|
777 | def set_instrument(self, instr):
|
---|
778 | """
|
---|
779 | Set the instrument for subsequent processing.
|
---|
780 | Parameters:
|
---|
781 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA',
|
---|
782 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART'
|
---|
783 | """
|
---|
784 | self._setInstrument(instr)
|
---|
785 | self._add_history("set_instument", vars())
|
---|
786 | print_log()
|
---|
787 |
|
---|
788 | @print_log_dec
|
---|
789 | def set_feedtype(self, feedtype):
|
---|
790 | """
|
---|
791 | Overwrite the feed type, which might not be set correctly.
|
---|
792 | Parameters:
|
---|
793 | feedtype: 'linear' or 'circular'
|
---|
794 | """
|
---|
795 | self._setfeedtype(feedtype)
|
---|
796 | self._add_history("set_feedtype", vars())
|
---|
797 | print_log()
|
---|
798 |
|
---|
799 | @print_log_dec
|
---|
800 | def set_doppler(self, doppler='RADIO'):
|
---|
801 | """
|
---|
802 | Set the doppler for all following operations on this scantable.
|
---|
803 | Parameters:
|
---|
804 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA'
|
---|
805 | """
|
---|
806 | varlist = vars()
|
---|
807 | inf = list(self._getcoordinfo())
|
---|
808 | inf[2] = doppler
|
---|
809 | self._setcoordinfo(inf)
|
---|
810 | self._add_history("set_doppler", vars())
|
---|
811 | print_log()
|
---|
812 |
|
---|
813 | @print_log_dec
|
---|
814 | def set_freqframe(self, frame=None):
|
---|
815 | """
|
---|
816 | Set the frame type of the Spectral Axis.
|
---|
817 | Parameters:
|
---|
818 | frame: an optional frame type, default 'LSRK'. Valid frames are:
|
---|
819 | 'TOPO', 'LSRD', 'LSRK', 'BARY',
|
---|
820 | 'GEO', 'GALACTO', 'LGROUP', 'CMB'
|
---|
821 | Examples:
|
---|
822 | scan.set_freqframe('BARY')
|
---|
823 | """
|
---|
824 | frame = frame or rcParams['scantable.freqframe']
|
---|
825 | varlist = vars()
|
---|
826 | # "REST" is not implemented in casacore
|
---|
827 | #valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \
|
---|
828 | # 'GEO', 'GALACTO', 'LGROUP', 'CMB']
|
---|
829 | valid = ['TOPO', 'LSRD', 'LSRK', 'BARY', \
|
---|
830 | 'GEO', 'GALACTO', 'LGROUP', 'CMB']
|
---|
831 |
|
---|
832 | if frame in valid:
|
---|
833 | inf = list(self._getcoordinfo())
|
---|
834 | inf[1] = frame
|
---|
835 | self._setcoordinfo(inf)
|
---|
836 | self._add_history("set_freqframe", varlist)
|
---|
837 | else:
|
---|
838 | msg = "Please specify a valid freq type. Valid types are:\n", valid
|
---|
839 | if rcParams['verbose']:
|
---|
840 | #print msg
|
---|
841 | asaplog.push( msg )
|
---|
842 | print_log( 'ERROR' )
|
---|
843 | else:
|
---|
844 | raise TypeError(msg)
|
---|
845 | print_log()
|
---|
846 |
|
---|
847 | def set_dirframe(self, frame=""):
|
---|
848 | """
|
---|
849 | Set the frame type of the Direction on the sky.
|
---|
850 | Parameters:
|
---|
851 | frame: an optional frame type, default ''. Valid frames are:
|
---|
852 | 'J2000', 'B1950', 'GALACTIC'
|
---|
853 | Examples:
|
---|
854 | scan.set_dirframe('GALACTIC')
|
---|
855 | """
|
---|
856 | varlist = vars()
|
---|
857 | try:
|
---|
858 | Scantable.set_dirframe(self, frame)
|
---|
859 | except RuntimeError, msg:
|
---|
860 | if rcParams['verbose']:
|
---|
861 | #print msg
|
---|
862 | print_log()
|
---|
863 | asaplog.push( str(msg) )
|
---|
864 | print_log( 'ERROR' )
|
---|
865 | else:
|
---|
866 | raise
|
---|
867 | self._add_history("set_dirframe", varlist)
|
---|
868 |
|
---|
869 | def get_unit(self):
|
---|
870 | """
|
---|
871 | Get the default unit set in this scantable
|
---|
872 | Returns:
|
---|
873 | A unit string
|
---|
874 | """
|
---|
875 | inf = self._getcoordinfo()
|
---|
876 | unit = inf[0]
|
---|
877 | if unit == '': unit = 'channel'
|
---|
878 | return unit
|
---|
879 |
|
---|
880 | def get_abcissa(self, rowno=0):
|
---|
881 | """
|
---|
882 | Get the abcissa in the current coordinate setup for the currently
|
---|
883 | selected Beam/IF/Pol
|
---|
884 | Parameters:
|
---|
885 | rowno: an optional row number in the scantable. Default is the
|
---|
886 | first row, i.e. rowno=0
|
---|
887 | Returns:
|
---|
888 | The abcissa values and the format string (as a dictionary)
|
---|
889 | """
|
---|
890 | abc = self._getabcissa(rowno)
|
---|
891 | lbl = self._getabcissalabel(rowno)
|
---|
892 | print_log()
|
---|
893 | return abc, lbl
|
---|
894 |
|
---|
895 | def flag(self, mask=None, unflag=False):
|
---|
896 | """
|
---|
897 | Flag the selected data using an optional channel mask.
|
---|
898 | Parameters:
|
---|
899 | mask: an optional channel mask, created with create_mask. Default
|
---|
900 | (no mask) is all channels.
|
---|
901 | unflag: if True, unflag the data
|
---|
902 | """
|
---|
903 | varlist = vars()
|
---|
904 | mask = mask or []
|
---|
905 | try:
|
---|
906 | self._flag(mask, unflag)
|
---|
907 | except RuntimeError, msg:
|
---|
908 | if rcParams['verbose']:
|
---|
909 | #print msg
|
---|
910 | print_log()
|
---|
911 | asaplog.push( str(msg) )
|
---|
912 | print_log( 'ERROR' )
|
---|
913 | return
|
---|
914 | else: raise
|
---|
915 | self._add_history("flag", varlist)
|
---|
916 |
|
---|
917 | def flag_row(self, rows=[], unflag=False):
|
---|
918 | """
|
---|
919 | Flag the selected data in row-based manner.
|
---|
920 | Parameters:
|
---|
921 | rows: list of row numbers to be flagged. Default is no row
|
---|
922 | (must be explicitly specified to execute row-based flagging).
|
---|
923 | unflag: if True, unflag the data.
|
---|
924 | """
|
---|
925 | varlist = vars()
|
---|
926 | try:
|
---|
927 | self._flag_row(rows, unflag)
|
---|
928 | except RuntimeError, msg:
|
---|
929 | if rcParams['verbose']:
|
---|
930 | print_log()
|
---|
931 | asaplog.push( str(msg) )
|
---|
932 | print_log('ERROR')
|
---|
933 | return
|
---|
934 | else: raise
|
---|
935 | self._add_history("flag_row", varlist)
|
---|
936 |
|
---|
937 | def clip(self, uthres=None, dthres=None, clipoutside=True, unflag=False):
|
---|
938 | """
|
---|
939 | Flag the selected data outside a specified range (in channel-base)
|
---|
940 | Parameters:
|
---|
941 | uthres: upper threshold.
|
---|
942 | dthres: lower threshold
|
---|
943 | clipoutside: True for flagging data outside the range [dthres:uthres].
|
---|
944 | False for glagging data inside the range.
|
---|
945 | unflag : if True, unflag the data.
|
---|
946 | """
|
---|
947 | varlist = vars()
|
---|
948 | try:
|
---|
949 | self._clip(uthres, dthres, clipoutside, unflag)
|
---|
950 | except RuntimeError, msg:
|
---|
951 | if rcParams['verbose']:
|
---|
952 | print_log()
|
---|
953 | asaplog.push(str(msg))
|
---|
954 | print_log('ERROR')
|
---|
955 | return
|
---|
956 | else: raise
|
---|
957 | self._add_history("clip", varlist)
|
---|
958 |
|
---|
959 | @print_log_dec
|
---|
960 | def lag_flag(self, start, end, unit="MHz", insitu=None):
|
---|
961 | #def lag_flag(self, frequency, width=0.0, unit="GHz", insitu=None):
|
---|
962 | """
|
---|
963 | Flag the data in 'lag' space by providing a frequency to remove.
|
---|
964 | Flagged data in the scantable gets interpolated over the region.
|
---|
965 | No taper is applied.
|
---|
966 | Parameters:
|
---|
967 | start: the start frequency (really a period within the
|
---|
968 | bandwidth) or period to remove
|
---|
969 | end: the end frequency or period to remove
|
---|
970 | unit: the frequency unit (default "MHz") or "" for
|
---|
971 | explicit lag channels
|
---|
972 | Notes:
|
---|
973 | It is recommended to flag edges of the band or strong
|
---|
974 | signals beforehand.
|
---|
975 | """
|
---|
976 | if insitu is None: insitu = rcParams['insitu']
|
---|
977 | self._math._setinsitu(insitu)
|
---|
978 | varlist = vars()
|
---|
979 | base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1.}
|
---|
980 | if not (unit == "" or base.has_key(unit)):
|
---|
981 | raise ValueError("%s is not a valid unit." % unit)
|
---|
982 | try:
|
---|
983 | if unit == "":
|
---|
984 | s = scantable(self._math._lag_flag(self, start, end, "lags"))
|
---|
985 | else:
|
---|
986 | s = scantable(self._math._lag_flag(self, start*base[unit],
|
---|
987 | end*base[unit], "frequency"))
|
---|
988 | except RuntimeError, msg:
|
---|
989 | if rcParams['verbose']:
|
---|
990 | #print msg
|
---|
991 | print_log()
|
---|
992 | asaplog.push( str(msg) )
|
---|
993 | print_log( 'ERROR' )
|
---|
994 | return
|
---|
995 | else: raise
|
---|
996 | s._add_history("lag_flag", varlist)
|
---|
997 | print_log()
|
---|
998 | if insitu:
|
---|
999 | self._assign(s)
|
---|
1000 | else:
|
---|
1001 | return s
|
---|
1002 |
|
---|
1003 | @print_log_dec
|
---|
1004 | def create_mask(self, *args, **kwargs):
|
---|
1005 | """
|
---|
1006 | Compute and return a mask based on [min, max] windows.
|
---|
1007 | The specified windows are to be INCLUDED, when the mask is
|
---|
1008 | applied.
|
---|
1009 | Parameters:
|
---|
1010 | [min, max], [min2, max2], ...
|
---|
1011 | Pairs of start/end points (inclusive)specifying the regions
|
---|
1012 | to be masked
|
---|
1013 | invert: optional argument. If specified as True,
|
---|
1014 | return an inverted mask, i.e. the regions
|
---|
1015 | specified are EXCLUDED
|
---|
1016 | row: create the mask using the specified row for
|
---|
1017 | unit conversions, default is row=0
|
---|
1018 | only necessary if frequency varies over rows.
|
---|
1019 | Example:
|
---|
1020 | scan.set_unit('channel')
|
---|
1021 | a)
|
---|
1022 | msk = scan.create_mask([400, 500], [800, 900])
|
---|
1023 | # masks everything outside 400 and 500
|
---|
1024 | # and 800 and 900 in the unit 'channel'
|
---|
1025 |
|
---|
1026 | b)
|
---|
1027 | msk = scan.create_mask([400, 500], [800, 900], invert=True)
|
---|
1028 | # masks the regions between 400 and 500
|
---|
1029 | # and 800 and 900 in the unit 'channel'
|
---|
1030 | c)
|
---|
1031 | mask only channel 400
|
---|
1032 | msk = scan.create_mask([400])
|
---|
1033 | """
|
---|
1034 | row = kwargs.get("row", 0)
|
---|
1035 | data = self._getabcissa(row)
|
---|
1036 | u = self._getcoordinfo()[0]
|
---|
1037 | if rcParams['verbose']:
|
---|
1038 | if u == "": u = "channel"
|
---|
1039 | msg = "The current mask window unit is %s" % u
|
---|
1040 | i = self._check_ifs()
|
---|
1041 | if not i:
|
---|
1042 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
|
---|
1043 | asaplog.push(msg)
|
---|
1044 | n = self.nchan()
|
---|
1045 | msk = _n_bools(n, False)
|
---|
1046 | # test if args is a 'list' or a 'normal *args - UGLY!!!
|
---|
1047 |
|
---|
1048 | ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \
|
---|
1049 | and args or args[0]
|
---|
1050 | for window in ws:
|
---|
1051 | if len(window) == 1:
|
---|
1052 | window = [window[0], window[0]]
|
---|
1053 | if len(window) == 0 or len(window) > 2:
|
---|
1054 | raise ValueError("A window needs to be defined as [start(, end)]")
|
---|
1055 | if window[0] > window[1]:
|
---|
1056 | tmp = window[0]
|
---|
1057 | window[0] = window[1]
|
---|
1058 | window[1] = tmp
|
---|
1059 | for i in range(n):
|
---|
1060 | if data[i] >= window[0] and data[i] <= window[1]:
|
---|
1061 | msk[i] = True
|
---|
1062 | if kwargs.has_key('invert'):
|
---|
1063 | if kwargs.get('invert'):
|
---|
1064 | msk = mask_not(msk)
|
---|
1065 | print_log()
|
---|
1066 | return msk
|
---|
1067 |
|
---|
1068 | def get_masklist(self, mask=None, row=0):
|
---|
1069 | """
|
---|
1070 | Compute and return a list of mask windows, [min, max].
|
---|
1071 | Parameters:
|
---|
1072 | mask: channel mask, created with create_mask.
|
---|
1073 | row: calcutate the masklist using the specified row
|
---|
1074 | for unit conversions, default is row=0
|
---|
1075 | only necessary if frequency varies over rows.
|
---|
1076 | Returns:
|
---|
1077 | [min, max], [min2, max2], ...
|
---|
1078 | Pairs of start/end points (inclusive)specifying
|
---|
1079 | the masked regions
|
---|
1080 | """
|
---|
1081 | if not (isinstance(mask,list) or isinstance(mask, tuple)):
|
---|
1082 | raise TypeError("The mask should be list or tuple.")
|
---|
1083 | if len(mask) < 2:
|
---|
1084 | raise TypeError("The mask elements should be > 1")
|
---|
1085 | if self.nchan() != len(mask):
|
---|
1086 | msg = "Number of channels in scantable != number of mask elements"
|
---|
1087 | raise TypeError(msg)
|
---|
1088 | data = self._getabcissa(row)
|
---|
1089 | u = self._getcoordinfo()[0]
|
---|
1090 | if rcParams['verbose']:
|
---|
1091 | if u == "": u = "channel"
|
---|
1092 | msg = "The current mask window unit is %s" % u
|
---|
1093 | i = self._check_ifs()
|
---|
1094 | if not i:
|
---|
1095 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
|
---|
1096 | asaplog.push(msg)
|
---|
1097 | masklist=[]
|
---|
1098 | ist, ien = None, None
|
---|
1099 | ist, ien=self.get_mask_indices(mask)
|
---|
1100 | if ist is not None and ien is not None:
|
---|
1101 | for i in xrange(len(ist)):
|
---|
1102 | range=[data[ist[i]],data[ien[i]]]
|
---|
1103 | range.sort()
|
---|
1104 | masklist.append([range[0],range[1]])
|
---|
1105 | return masklist
|
---|
1106 |
|
---|
1107 | def get_mask_indices(self, mask=None):
|
---|
1108 | """
|
---|
1109 | Compute and Return lists of mask start indices and mask end indices.
|
---|
1110 | Parameters:
|
---|
1111 | mask: channel mask, created with create_mask.
|
---|
1112 | Returns:
|
---|
1113 | List of mask start indices and that of mask end indices,
|
---|
1114 | i.e., [istart1,istart2,....], [iend1,iend2,....].
|
---|
1115 | """
|
---|
1116 | if not (isinstance(mask,list) or isinstance(mask, tuple)):
|
---|
1117 | raise TypeError("The mask should be list or tuple.")
|
---|
1118 | if len(mask) < 2:
|
---|
1119 | raise TypeError("The mask elements should be > 1")
|
---|
1120 | istart=[]
|
---|
1121 | iend=[]
|
---|
1122 | if mask[0]: istart.append(0)
|
---|
1123 | for i in range(len(mask)-1):
|
---|
1124 | if not mask[i] and mask[i+1]:
|
---|
1125 | istart.append(i+1)
|
---|
1126 | elif mask[i] and not mask[i+1]:
|
---|
1127 | iend.append(i)
|
---|
1128 | if mask[len(mask)-1]: iend.append(len(mask)-1)
|
---|
1129 | if len(istart) != len(iend):
|
---|
1130 | raise RuntimeError("Numbers of mask start != mask end.")
|
---|
1131 | for i in range(len(istart)):
|
---|
1132 | if istart[i] > iend[i]:
|
---|
1133 | raise RuntimeError("Mask start index > mask end index")
|
---|
1134 | break
|
---|
1135 | return istart,iend
|
---|
1136 |
|
---|
1137 | # def get_restfreqs(self):
|
---|
1138 | # """
|
---|
1139 | # Get the restfrequency(s) stored in this scantable.
|
---|
1140 | # The return value(s) are always of unit 'Hz'
|
---|
1141 | # Parameters:
|
---|
1142 | # none
|
---|
1143 | # Returns:
|
---|
1144 | # a list of doubles
|
---|
1145 | # """
|
---|
1146 | # return list(self._getrestfreqs())
|
---|
1147 |
|
---|
1148 | def get_restfreqs(self, ids=None):
|
---|
1149 | """
|
---|
1150 | Get the restfrequency(s) stored in this scantable.
|
---|
1151 | The return value(s) are always of unit 'Hz'
|
---|
1152 | Parameters:
|
---|
1153 | ids: (optional) a list of MOLECULE_ID for that restfrequency(s) to
|
---|
1154 | be retrieved
|
---|
1155 | Returns:
|
---|
1156 | dictionary containing ids and a list of doubles for each id
|
---|
1157 | """
|
---|
1158 | if ids is None:
|
---|
1159 | rfreqs={}
|
---|
1160 | idlist = self.getmolnos()
|
---|
1161 | for i in idlist:
|
---|
1162 | rfreqs[i]=list(self._getrestfreqs(i))
|
---|
1163 | return rfreqs
|
---|
1164 | else:
|
---|
1165 | if type(ids)==list or type(ids)==tuple:
|
---|
1166 | rfreqs={}
|
---|
1167 | for i in ids:
|
---|
1168 | rfreqs[i]=list(self._getrestfreqs(i))
|
---|
1169 | return rfreqs
|
---|
1170 | else:
|
---|
1171 | return list(self._getrestfreqs(ids))
|
---|
1172 | #return list(self._getrestfreqs(ids))
|
---|
1173 |
|
---|
1174 | def set_restfreqs(self, freqs=None, unit='Hz'):
|
---|
1175 | """
|
---|
1176 | ********NEED TO BE UPDATED begin************
|
---|
1177 | Set or replace the restfrequency specified and
|
---|
1178 | If the 'freqs' argument holds a scalar,
|
---|
1179 | then that rest frequency will be applied to all the selected
|
---|
1180 | data. If the 'freqs' argument holds
|
---|
1181 | a vector, then it MUST be of equal or smaller length than
|
---|
1182 | the number of IFs (and the available restfrequencies will be
|
---|
1183 | replaced by this vector). In this case, *all* data have
|
---|
1184 | the restfrequency set per IF according
|
---|
1185 | to the corresponding value you give in the 'freqs' vector.
|
---|
1186 | E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and
|
---|
1187 | IF 1 gets restfreq 2e9.
|
---|
1188 | ********NEED TO BE UPDATED end************
|
---|
1189 | You can also specify the frequencies via a linecatalog.
|
---|
1190 |
|
---|
1191 | Parameters:
|
---|
1192 | freqs: list of rest frequency values or string idenitfiers
|
---|
1193 | unit: unit for rest frequency (default 'Hz')
|
---|
1194 |
|
---|
1195 | Example:
|
---|
1196 | # set the given restfrequency for the all currently selected IFs
|
---|
1197 | scan.set_restfreqs(freqs=1.4e9)
|
---|
1198 | # set multiple restfrequencies to all the selected data
|
---|
1199 | scan.set_restfreqs(freqs=[1.4e9, 1.41e9, 1.42e9])
|
---|
1200 | # If the number of IFs in the data is >= 2 the IF0 gets the first
|
---|
1201 | # value IF1 the second... NOTE that freqs needs to be
|
---|
1202 | # specified in list of list (e.g. [[],[],...] ).
|
---|
1203 | scan.set_restfreqs(freqs=[[1.4e9],[1.67e9]])
|
---|
1204 | #set the given restfrequency for the whole table (by name)
|
---|
1205 | scan.set_restfreqs(freqs="OH1667")
|
---|
1206 |
|
---|
1207 | Note:
|
---|
1208 | To do more sophisticate Restfrequency setting, e.g. on a
|
---|
1209 | source and IF basis, use scantable.set_selection() before using
|
---|
1210 | this function.
|
---|
1211 | # provide your scantable is called scan
|
---|
1212 | selection = selector()
|
---|
1213 | selection.set_name("ORION*")
|
---|
1214 | selection.set_ifs([1])
|
---|
1215 | scan.set_selection(selection)
|
---|
1216 | scan.set_restfreqs(freqs=86.6e9)
|
---|
1217 |
|
---|
1218 | """
|
---|
1219 | varlist = vars()
|
---|
1220 | from asap import linecatalog
|
---|
1221 | # simple value
|
---|
1222 | if isinstance(freqs, int) or isinstance(freqs, float):
|
---|
1223 | # TT mod
|
---|
1224 | #self._setrestfreqs(freqs, "",unit)
|
---|
1225 | self._setrestfreqs([freqs], [""],unit)
|
---|
1226 | # list of values
|
---|
1227 | elif isinstance(freqs, list) or isinstance(freqs, tuple):
|
---|
1228 | # list values are scalars
|
---|
1229 | if isinstance(freqs[-1], int) or isinstance(freqs[-1], float):
|
---|
1230 | self._setrestfreqs(freqs, [""], unit)
|
---|
1231 | # list values are tuples, (value, name)
|
---|
1232 | elif isinstance(freqs[-1], dict):
|
---|
1233 | #sel = selector()
|
---|
1234 | #savesel = self._getselection()
|
---|
1235 | #iflist = self.getifnos()
|
---|
1236 | #for i in xrange(len(freqs)):
|
---|
1237 | # sel.set_ifs(iflist[i])
|
---|
1238 | # self._setselection(sel)
|
---|
1239 | # self._setrestfreqs(freqs[i], "",unit)
|
---|
1240 | #self._setselection(savesel)
|
---|
1241 | self._setrestfreqs(freqs["value"],
|
---|
1242 | freqs["name"], unit)
|
---|
1243 | elif isinstance(freqs[-1], list) or isinstance(freqs[-1], tuple):
|
---|
1244 | sel = selector()
|
---|
1245 | savesel = self._getselection()
|
---|
1246 | iflist = self.getifnos()
|
---|
1247 | if len(freqs)>len(iflist):
|
---|
1248 | raise ValueError("number of elements in list of list exeeds the current IF selections")
|
---|
1249 | for i in xrange(len(freqs)):
|
---|
1250 | sel.set_ifs(iflist[i])
|
---|
1251 | self._setselection(sel)
|
---|
1252 | self._setrestfreqs(freqs[i], [""], unit)
|
---|
1253 | self._setselection(savesel)
|
---|
1254 | # freqs are to be taken from a linecatalog
|
---|
1255 | elif isinstance(freqs, linecatalog):
|
---|
1256 | sel = selector()
|
---|
1257 | savesel = self._getselection()
|
---|
1258 | for i in xrange(freqs.nrow()):
|
---|
1259 | sel.set_ifs(iflist[i])
|
---|
1260 | self._setselection(sel)
|
---|
1261 | self._setrestfreqs(freqs.get_frequency(i),
|
---|
1262 | freqs.get_name(i), "MHz")
|
---|
1263 | # ensure that we are not iterating past nIF
|
---|
1264 | if i == self.nif()-1: break
|
---|
1265 | self._setselection(savesel)
|
---|
1266 | else:
|
---|
1267 | return
|
---|
1268 | self._add_history("set_restfreqs", varlist)
|
---|
1269 |
|
---|
1270 | def shift_refpix(self, delta):
|
---|
1271 | """
|
---|
1272 | Shift the reference pixel of the Spectra Coordinate by an
|
---|
1273 | integer amount.
|
---|
1274 | Parameters:
|
---|
1275 | delta: the amount to shift by
|
---|
1276 | Note:
|
---|
1277 | Be careful using this with broadband data.
|
---|
1278 | """
|
---|
1279 | Scantable.shift_refpix(self, delta)
|
---|
1280 |
|
---|
1281 | def history(self, filename=None):
|
---|
1282 | """
|
---|
1283 | Print the history. Optionally to a file.
|
---|
1284 | Parameters:
|
---|
1285 | filename: The name of the file to save the history to.
|
---|
1286 | """
|
---|
1287 | hist = list(self._gethistory())
|
---|
1288 | out = "-"*80
|
---|
1289 | for h in hist:
|
---|
1290 | if h.startswith("---"):
|
---|
1291 | out += "\n"+h
|
---|
1292 | else:
|
---|
1293 | items = h.split("##")
|
---|
1294 | date = items[0]
|
---|
1295 | func = items[1]
|
---|
1296 | items = items[2:]
|
---|
1297 | out += "\n"+date+"\n"
|
---|
1298 | out += "Function: %s\n Parameters:" % (func)
|
---|
1299 | for i in items:
|
---|
1300 | s = i.split("=")
|
---|
1301 | out += "\n %s = %s" % (s[0], s[1])
|
---|
1302 | out += "\n"+"-"*80
|
---|
1303 | if filename is not None:
|
---|
1304 | if filename is "":
|
---|
1305 | filename = 'scantable_history.txt'
|
---|
1306 | import os
|
---|
1307 | filename = os.path.expandvars(os.path.expanduser(filename))
|
---|
1308 | if not os.path.isdir(filename):
|
---|
1309 | data = open(filename, 'w')
|
---|
1310 | data.write(out)
|
---|
1311 | data.close()
|
---|
1312 | else:
|
---|
1313 | msg = "Illegal file name '%s'." % (filename)
|
---|
1314 | if rcParams['verbose']:
|
---|
1315 | #print msg
|
---|
1316 | asaplog.push( msg )
|
---|
1317 | print_log( 'ERROR' )
|
---|
1318 | else:
|
---|
1319 | raise IOError(msg)
|
---|
1320 | if rcParams['verbose']:
|
---|
1321 | try:
|
---|
1322 | from IPython.genutils import page as pager
|
---|
1323 | except ImportError:
|
---|
1324 | from pydoc import pager
|
---|
1325 | pager(out)
|
---|
1326 | else:
|
---|
1327 | return out
|
---|
1328 | return
|
---|
1329 | #
|
---|
1330 | # Maths business
|
---|
1331 | #
|
---|
1332 | @print_log_dec
|
---|
1333 | def average_time(self, mask=None, scanav=False, weight='tint', align=False):
|
---|
1334 | """
|
---|
1335 | Return the (time) weighted average of a scan.
|
---|
1336 | Note:
|
---|
1337 | in channels only - align if necessary
|
---|
1338 | Parameters:
|
---|
1339 | mask: an optional mask (only used for 'var' and 'tsys'
|
---|
1340 | weighting)
|
---|
1341 | scanav: True averages each scan separately
|
---|
1342 | False (default) averages all scans together,
|
---|
1343 | weight: Weighting scheme.
|
---|
1344 | 'none' (mean no weight)
|
---|
1345 | 'var' (1/var(spec) weighted)
|
---|
1346 | 'tsys' (1/Tsys**2 weighted)
|
---|
1347 | 'tint' (integration time weighted)
|
---|
1348 | 'tintsys' (Tint/Tsys**2)
|
---|
1349 | 'median' ( median averaging)
|
---|
1350 | The default is 'tint'
|
---|
1351 | align: align the spectra in velocity before averaging. It takes
|
---|
1352 | the time of the first spectrum as reference time.
|
---|
1353 | Example:
|
---|
1354 | # time average the scantable without using a mask
|
---|
1355 | newscan = scan.average_time()
|
---|
1356 | """
|
---|
1357 | varlist = vars()
|
---|
1358 | weight = weight or 'TINT'
|
---|
1359 | mask = mask or ()
|
---|
1360 | scanav = (scanav and 'SCAN') or 'NONE'
|
---|
1361 | scan = (self, )
|
---|
1362 | try:
|
---|
1363 | if align:
|
---|
1364 | scan = (self.freq_align(insitu=False), )
|
---|
1365 | s = None
|
---|
1366 | if weight.upper() == 'MEDIAN':
|
---|
1367 | s = scantable(self._math._averagechannel(scan[0], 'MEDIAN',
|
---|
1368 | scanav))
|
---|
1369 | else:
|
---|
1370 | s = scantable(self._math._average(scan, mask, weight.upper(),
|
---|
1371 | scanav))
|
---|
1372 | except RuntimeError, msg:
|
---|
1373 | if rcParams['verbose']:
|
---|
1374 | #print msg
|
---|
1375 | print_log()
|
---|
1376 | asaplog.push( str(msg) )
|
---|
1377 | print_log( 'ERROR' )
|
---|
1378 | return
|
---|
1379 | else: raise
|
---|
1380 | s._add_history("average_time", varlist)
|
---|
1381 | print_log()
|
---|
1382 | return s
|
---|
1383 |
|
---|
1384 | @print_log_dec
|
---|
1385 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None):
|
---|
1386 | """
|
---|
1387 | Return a scan where all spectra are converted to either
|
---|
1388 | Jansky or Kelvin depending upon the flux units of the scan table.
|
---|
1389 | By default the function tries to look the values up internally.
|
---|
1390 | If it can't find them (or if you want to over-ride), you must
|
---|
1391 | specify EITHER jyperk OR eta (and D which it will try to look up
|
---|
1392 | also if you don't set it). jyperk takes precedence if you set both.
|
---|
1393 | Parameters:
|
---|
1394 | jyperk: the Jy / K conversion factor
|
---|
1395 | eta: the aperture efficiency
|
---|
1396 | d: the geomtric diameter (metres)
|
---|
1397 | insitu: if False a new scantable is returned.
|
---|
1398 | Otherwise, the scaling is done in-situ
|
---|
1399 | The default is taken from .asaprc (False)
|
---|
1400 | """
|
---|
1401 | if insitu is None: insitu = rcParams['insitu']
|
---|
1402 | self._math._setinsitu(insitu)
|
---|
1403 | varlist = vars()
|
---|
1404 | jyperk = jyperk or -1.0
|
---|
1405 | d = d or -1.0
|
---|
1406 | eta = eta or -1.0
|
---|
1407 | s = scantable(self._math._convertflux(self, d, eta, jyperk))
|
---|
1408 | s._add_history("convert_flux", varlist)
|
---|
1409 | print_log()
|
---|
1410 | if insitu: self._assign(s)
|
---|
1411 | else: return s
|
---|
1412 |
|
---|
1413 | @print_log_dec
|
---|
1414 | def gain_el(self, poly=None, filename="", method="linear", insitu=None):
|
---|
1415 | """
|
---|
1416 | Return a scan after applying a gain-elevation correction.
|
---|
1417 | The correction can be made via either a polynomial or a
|
---|
1418 | table-based interpolation (and extrapolation if necessary).
|
---|
1419 | You specify polynomial coefficients, an ascii table or neither.
|
---|
1420 | If you specify neither, then a polynomial correction will be made
|
---|
1421 | with built in coefficients known for certain telescopes (an error
|
---|
1422 | will occur if the instrument is not known).
|
---|
1423 | The data and Tsys are *divided* by the scaling factors.
|
---|
1424 | Parameters:
|
---|
1425 | poly: Polynomial coefficients (default None) to compute a
|
---|
1426 | gain-elevation correction as a function of
|
---|
1427 | elevation (in degrees).
|
---|
1428 | filename: The name of an ascii file holding correction factors.
|
---|
1429 | The first row of the ascii file must give the column
|
---|
1430 | names and these MUST include columns
|
---|
1431 | "ELEVATION" (degrees) and "FACTOR" (multiply data
|
---|
1432 | by this) somewhere.
|
---|
1433 | The second row must give the data type of the
|
---|
1434 | column. Use 'R' for Real and 'I' for Integer.
|
---|
1435 | An example file would be
|
---|
1436 | (actual factors are arbitrary) :
|
---|
1437 |
|
---|
1438 | TIME ELEVATION FACTOR
|
---|
1439 | R R R
|
---|
1440 | 0.1 0 0.8
|
---|
1441 | 0.2 20 0.85
|
---|
1442 | 0.3 40 0.9
|
---|
1443 | 0.4 60 0.85
|
---|
1444 | 0.5 80 0.8
|
---|
1445 | 0.6 90 0.75
|
---|
1446 | method: Interpolation method when correcting from a table.
|
---|
1447 | Values are "nearest", "linear" (default), "cubic"
|
---|
1448 | and "spline"
|
---|
1449 | insitu: if False a new scantable is returned.
|
---|
1450 | Otherwise, the scaling is done in-situ
|
---|
1451 | The default is taken from .asaprc (False)
|
---|
1452 | """
|
---|
1453 |
|
---|
1454 | if insitu is None: insitu = rcParams['insitu']
|
---|
1455 | self._math._setinsitu(insitu)
|
---|
1456 | varlist = vars()
|
---|
1457 | poly = poly or ()
|
---|
1458 | from os.path import expandvars
|
---|
1459 | filename = expandvars(filename)
|
---|
1460 | s = scantable(self._math._gainel(self, poly, filename, method))
|
---|
1461 | s._add_history("gain_el", varlist)
|
---|
1462 | print_log()
|
---|
1463 | if insitu:
|
---|
1464 | self._assign(s)
|
---|
1465 | else:
|
---|
1466 | return s
|
---|
1467 |
|
---|
1468 | @print_log_dec
|
---|
1469 | def freq_align(self, reftime=None, method='cubic', insitu=None):
|
---|
1470 | """
|
---|
1471 | Return a scan where all rows have been aligned in frequency/velocity.
|
---|
1472 | The alignment frequency frame (e.g. LSRK) is that set by function
|
---|
1473 | set_freqframe.
|
---|
1474 | Parameters:
|
---|
1475 | reftime: reference time to align at. By default, the time of
|
---|
1476 | the first row of data is used.
|
---|
1477 | method: Interpolation method for regridding the spectra.
|
---|
1478 | Choose from "nearest", "linear", "cubic" (default)
|
---|
1479 | and "spline"
|
---|
1480 | insitu: if False a new scantable is returned.
|
---|
1481 | Otherwise, the scaling is done in-situ
|
---|
1482 | The default is taken from .asaprc (False)
|
---|
1483 | """
|
---|
1484 | if insitu is None: insitu = rcParams["insitu"]
|
---|
1485 | self._math._setinsitu(insitu)
|
---|
1486 | varlist = vars()
|
---|
1487 | reftime = reftime or ""
|
---|
1488 | s = scantable(self._math._freq_align(self, reftime, method))
|
---|
1489 | s._add_history("freq_align", varlist)
|
---|
1490 | print_log()
|
---|
1491 | if insitu: self._assign(s)
|
---|
1492 | else: return s
|
---|
1493 |
|
---|
1494 | @print_log_dec
|
---|
1495 | def opacity(self, tau=None, insitu=None):
|
---|
1496 | """
|
---|
1497 | Apply an opacity correction. The data
|
---|
1498 | and Tsys are multiplied by the correction factor.
|
---|
1499 | Parameters:
|
---|
1500 | tau: (list of) opacity from which the correction factor is
|
---|
1501 | exp(tau*ZD)
|
---|
1502 | where ZD is the zenith-distance.
|
---|
1503 | If a list is provided, it has to be of length nIF,
|
---|
1504 | nIF*nPol or 1 and in order of IF/POL, e.g.
|
---|
1505 | [opif0pol0, opif0pol1, opif1pol0 ...]
|
---|
1506 | if tau is `None` the opacities are determined from a
|
---|
1507 | model.
|
---|
1508 | insitu: if False a new scantable is returned.
|
---|
1509 | Otherwise, the scaling is done in-situ
|
---|
1510 | The default is taken from .asaprc (False)
|
---|
1511 | """
|
---|
1512 | if insitu is None: insitu = rcParams['insitu']
|
---|
1513 | self._math._setinsitu(insitu)
|
---|
1514 | varlist = vars()
|
---|
1515 | if not hasattr(tau, "__len__"):
|
---|
1516 | tau = [tau]
|
---|
1517 | s = scantable(self._math._opacity(self, tau))
|
---|
1518 | s._add_history("opacity", varlist)
|
---|
1519 | print_log()
|
---|
1520 | if insitu: self._assign(s)
|
---|
1521 | else: return s
|
---|
1522 |
|
---|
1523 | @print_log_dec
|
---|
1524 | def bin(self, width=5, insitu=None):
|
---|
1525 | """
|
---|
1526 | Return a scan where all spectra have been binned up.
|
---|
1527 | Parameters:
|
---|
1528 | width: The bin width (default=5) in pixels
|
---|
1529 | insitu: if False a new scantable is returned.
|
---|
1530 | Otherwise, the scaling is done in-situ
|
---|
1531 | The default is taken from .asaprc (False)
|
---|
1532 | """
|
---|
1533 | if insitu is None: insitu = rcParams['insitu']
|
---|
1534 | self._math._setinsitu(insitu)
|
---|
1535 | varlist = vars()
|
---|
1536 | s = scantable(self._math._bin(self, width))
|
---|
1537 | s._add_history("bin", varlist)
|
---|
1538 | print_log()
|
---|
1539 | if insitu:
|
---|
1540 | self._assign(s)
|
---|
1541 | else:
|
---|
1542 | return s
|
---|
1543 |
|
---|
1544 | @print_log_dec
|
---|
1545 | def resample(self, width=5, method='cubic', insitu=None):
|
---|
1546 | """
|
---|
1547 | Return a scan where all spectra have been binned up.
|
---|
1548 |
|
---|
1549 | Parameters:
|
---|
1550 | width: The bin width (default=5) in pixels
|
---|
1551 | method: Interpolation method when correcting from a table.
|
---|
1552 | Values are "nearest", "linear", "cubic" (default)
|
---|
1553 | and "spline"
|
---|
1554 | insitu: if False a new scantable is returned.
|
---|
1555 | Otherwise, the scaling is done in-situ
|
---|
1556 | The default is taken from .asaprc (False)
|
---|
1557 | """
|
---|
1558 | if insitu is None: insitu = rcParams['insitu']
|
---|
1559 | self._math._setinsitu(insitu)
|
---|
1560 | varlist = vars()
|
---|
1561 | s = scantable(self._math._resample(self, method, width))
|
---|
1562 | s._add_history("resample", varlist)
|
---|
1563 | print_log()
|
---|
1564 | if insitu: self._assign(s)
|
---|
1565 | else: return s
|
---|
1566 |
|
---|
1567 | @print_log_dec
|
---|
1568 | def average_pol(self, mask=None, weight='none'):
|
---|
1569 | """
|
---|
1570 | Average the Polarisations together.
|
---|
1571 | Parameters:
|
---|
1572 | mask: An optional mask defining the region, where the
|
---|
1573 | averaging will be applied. The output will have all
|
---|
1574 | specified points masked.
|
---|
1575 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
|
---|
1576 | weighted), or 'tsys' (1/Tsys**2 weighted)
|
---|
1577 | """
|
---|
1578 | varlist = vars()
|
---|
1579 | mask = mask or ()
|
---|
1580 | s = scantable(self._math._averagepol(self, mask, weight.upper()))
|
---|
1581 | s._add_history("average_pol", varlist)
|
---|
1582 | print_log()
|
---|
1583 | return s
|
---|
1584 |
|
---|
1585 | @print_log_dec
|
---|
1586 | def average_beam(self, mask=None, weight='none'):
|
---|
1587 | """
|
---|
1588 | Average the Beams together.
|
---|
1589 | Parameters:
|
---|
1590 | mask: An optional mask defining the region, where the
|
---|
1591 | averaging will be applied. The output will have all
|
---|
1592 | specified points masked.
|
---|
1593 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
|
---|
1594 | weighted), or 'tsys' (1/Tsys**2 weighted)
|
---|
1595 | """
|
---|
1596 | varlist = vars()
|
---|
1597 | mask = mask or ()
|
---|
1598 | s = scantable(self._math._averagebeams(self, mask, weight.upper()))
|
---|
1599 | s._add_history("average_beam", varlist)
|
---|
1600 | print_log()
|
---|
1601 | return s
|
---|
1602 |
|
---|
1603 | def parallactify(self, pflag):
|
---|
1604 | """
|
---|
1605 | Set a flag to indicate whether this data should be treated as having
|
---|
1606 | been 'parallactified' (total phase == 0.0)
|
---|
1607 | Parameters:
|
---|
1608 | pflag: Bool indicating whether to turn this on (True) or
|
---|
1609 | off (False)
|
---|
1610 | """
|
---|
1611 | varlist = vars()
|
---|
1612 | self._parallactify(pflag)
|
---|
1613 | self._add_history("parallactify", varlist)
|
---|
1614 |
|
---|
1615 | @print_log_dec
|
---|
1616 | def convert_pol(self, poltype=None):
|
---|
1617 | """
|
---|
1618 | Convert the data to a different polarisation type.
|
---|
1619 | Note that you will need cross-polarisation terms for most conversions.
|
---|
1620 | Parameters:
|
---|
1621 | poltype: The new polarisation type. Valid types are:
|
---|
1622 | "linear", "circular", "stokes" and "linpol"
|
---|
1623 | """
|
---|
1624 | varlist = vars()
|
---|
1625 | try:
|
---|
1626 | s = scantable(self._math._convertpol(self, poltype))
|
---|
1627 | except RuntimeError, msg:
|
---|
1628 | if rcParams['verbose']:
|
---|
1629 | #print msg
|
---|
1630 | print_log()
|
---|
1631 | asaplog.push( str(msg) )
|
---|
1632 | print_log( 'ERROR' )
|
---|
1633 | return
|
---|
1634 | else:
|
---|
1635 | raise
|
---|
1636 | s._add_history("convert_pol", varlist)
|
---|
1637 | print_log()
|
---|
1638 | return s
|
---|
1639 |
|
---|
1640 | @print_log_dec
|
---|
1641 | def smooth(self, kernel="hanning", width=5.0, order=2, plot=False, insitu=None):
|
---|
1642 | """
|
---|
1643 | Smooth the spectrum by the specified kernel (conserving flux).
|
---|
1644 | Parameters:
|
---|
1645 | kernel: The type of smoothing kernel. Select from
|
---|
1646 | 'hanning' (default), 'gaussian', 'boxcar', 'rmedian'
|
---|
1647 | or 'poly'
|
---|
1648 | width: The width of the kernel in pixels. For hanning this is
|
---|
1649 | ignored otherwise it defauls to 5 pixels.
|
---|
1650 | For 'gaussian' it is the Full Width Half
|
---|
1651 | Maximum. For 'boxcar' it is the full width.
|
---|
1652 | For 'rmedian' and 'poly' it is the half width.
|
---|
1653 | order: Optional parameter for 'poly' kernel (default is 2), to
|
---|
1654 | specify the order of the polnomial. Ignored by all other
|
---|
1655 | kernels.
|
---|
1656 | plot: plot the original and the smoothed spectra.
|
---|
1657 | In this each indivual fit has to be approved, by
|
---|
1658 | typing 'y' or 'n'
|
---|
1659 | insitu: if False a new scantable is returned.
|
---|
1660 | Otherwise, the scaling is done in-situ
|
---|
1661 | The default is taken from .asaprc (False)
|
---|
1662 | Example:
|
---|
1663 | none
|
---|
1664 | """
|
---|
1665 | if insitu is None: insitu = rcParams['insitu']
|
---|
1666 | self._math._setinsitu(insitu)
|
---|
1667 | varlist = vars()
|
---|
1668 |
|
---|
1669 | if plot: orgscan = self.copy()
|
---|
1670 |
|
---|
1671 | s = scantable(self._math._smooth(self, kernel.lower(), width, order))
|
---|
1672 | s._add_history("smooth", varlist)
|
---|
1673 |
|
---|
1674 | if plot:
|
---|
1675 | if rcParams['plotter.gui']:
|
---|
1676 | from asap.asaplotgui import asaplotgui as asaplot
|
---|
1677 | else:
|
---|
1678 | from asap.asaplot import asaplot
|
---|
1679 | self._p=asaplot()
|
---|
1680 | self._p.set_panels()
|
---|
1681 | ylab=s._get_ordinate_label()
|
---|
1682 | #self._p.palette(0,["#777777","red"])
|
---|
1683 | for r in xrange(s.nrow()):
|
---|
1684 | xsm=s._getabcissa(r)
|
---|
1685 | ysm=s._getspectrum(r)
|
---|
1686 | xorg=orgscan._getabcissa(r)
|
---|
1687 | yorg=orgscan._getspectrum(r)
|
---|
1688 | self._p.clear()
|
---|
1689 | self._p.hold()
|
---|
1690 | self._p.set_axes('ylabel',ylab)
|
---|
1691 | self._p.set_axes('xlabel',s._getabcissalabel(r))
|
---|
1692 | self._p.set_axes('title',s._getsourcename(r))
|
---|
1693 | self._p.set_line(label='Original',color="#777777")
|
---|
1694 | self._p.plot(xorg,yorg)
|
---|
1695 | self._p.set_line(label='Smoothed',color="red")
|
---|
1696 | self._p.plot(xsm,ysm)
|
---|
1697 | ### Ugly part for legend
|
---|
1698 | for i in [0,1]:
|
---|
1699 | self._p.subplots[0]['lines'].append([self._p.subplots[0]['axes'].lines[i]])
|
---|
1700 | self._p.release()
|
---|
1701 | ### Ugly part for legend
|
---|
1702 | self._p.subplots[0]['lines']=[]
|
---|
1703 | res = raw_input("Accept smoothing ([y]/n): ")
|
---|
1704 | if res.upper() == 'N':
|
---|
1705 | s._setspectrum(yorg, r)
|
---|
1706 | self._p.unmap()
|
---|
1707 | self._p = None
|
---|
1708 | del orgscan
|
---|
1709 |
|
---|
1710 | print_log()
|
---|
1711 | if insitu: self._assign(s)
|
---|
1712 | else: return s
|
---|
1713 |
|
---|
1714 | @print_log_dec
|
---|
1715 | def poly_baseline(self, mask=None, order=0, plot=False, uselin=False,
|
---|
1716 | insitu=None):
|
---|
1717 | """
|
---|
1718 | Return a scan which has been baselined (all rows) by a polynomial.
|
---|
1719 | Parameters:
|
---|
1720 | mask: an optional mask
|
---|
1721 | order: the order of the polynomial (default is 0)
|
---|
1722 | plot: plot the fit and the residual. In this each
|
---|
1723 | indivual fit has to be approved, by typing 'y'
|
---|
1724 | or 'n'
|
---|
1725 | uselin: use linear polynomial fit
|
---|
1726 | insitu: if False a new scantable is returned.
|
---|
1727 | Otherwise, the scaling is done in-situ
|
---|
1728 | The default is taken from .asaprc (False)
|
---|
1729 | Example:
|
---|
1730 | # return a scan baselined by a third order polynomial,
|
---|
1731 | # not using a mask
|
---|
1732 | bscan = scan.poly_baseline(order=3)
|
---|
1733 | """
|
---|
1734 | if insitu is None: insitu = rcParams['insitu']
|
---|
1735 | if not insitu:
|
---|
1736 | workscan = self.copy()
|
---|
1737 | else:
|
---|
1738 | workscan = self
|
---|
1739 | varlist = vars()
|
---|
1740 | if mask is None:
|
---|
1741 | mask = [True for i in xrange(self.nchan(-1))]
|
---|
1742 |
|
---|
1743 | from asap.asapfitter import fitter
|
---|
1744 | try:
|
---|
1745 | f = fitter()
|
---|
1746 | if uselin:
|
---|
1747 | f.set_function(lpoly=order)
|
---|
1748 | else:
|
---|
1749 | f.set_function(poly=order)
|
---|
1750 |
|
---|
1751 | rows = range(workscan.nrow())
|
---|
1752 | if len(rows) > 0:
|
---|
1753 | self.blpars = []
|
---|
1754 |
|
---|
1755 | for r in rows:
|
---|
1756 | # take into account flagtra info (CAS-1434)
|
---|
1757 | flagtra = workscan._getmask(r)
|
---|
1758 | actualmask = mask[:]
|
---|
1759 | if len(actualmask) == 0:
|
---|
1760 | actualmask = list(flagtra[:])
|
---|
1761 | else:
|
---|
1762 | if len(actualmask) != len(flagtra):
|
---|
1763 | raise RuntimeError, "Mask and flagtra have different length"
|
---|
1764 | else:
|
---|
1765 | for i in range(0, len(actualmask)):
|
---|
1766 | actualmask[i] = actualmask[i] and flagtra[i]
|
---|
1767 | f.set_scan(workscan, actualmask)
|
---|
1768 | f.x = workscan._getabcissa(r)
|
---|
1769 | f.y = workscan._getspectrum(r)
|
---|
1770 | f.data = None
|
---|
1771 | f.fit()
|
---|
1772 | if plot:
|
---|
1773 | f.plot(residual=True)
|
---|
1774 | x = raw_input("Accept fit ( [y]/n ): ")
|
---|
1775 | if x.upper() == 'N':
|
---|
1776 | self.blpars.append(None)
|
---|
1777 | continue
|
---|
1778 | workscan._setspectrum(f.fitter.getresidual(), r)
|
---|
1779 | self.blpars.append(f.get_parameters())
|
---|
1780 |
|
---|
1781 | if plot:
|
---|
1782 | f._p.unmap()
|
---|
1783 | f._p = None
|
---|
1784 | workscan._add_history("poly_baseline", varlist)
|
---|
1785 | print_log()
|
---|
1786 | if insitu: self._assign(workscan)
|
---|
1787 | else: return workscan
|
---|
1788 | except RuntimeError:
|
---|
1789 | msg = "The fit failed, possibly because it didn't converge."
|
---|
1790 | if rcParams['verbose']:
|
---|
1791 | #print msg
|
---|
1792 | print_log()
|
---|
1793 | asaplog.push( str(msg) )
|
---|
1794 | print_log( 'ERROR' )
|
---|
1795 | return
|
---|
1796 | else:
|
---|
1797 | raise RuntimeError(msg)
|
---|
1798 |
|
---|
1799 |
|
---|
1800 | def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0,
|
---|
1801 | threshold=3, chan_avg_limit=1, plot=False,
|
---|
1802 | insitu=None):
|
---|
1803 | """
|
---|
1804 | Return a scan which has been baselined (all rows) by a polynomial.
|
---|
1805 | Spectral lines are detected first using linefinder and masked out
|
---|
1806 | to avoid them affecting the baseline solution.
|
---|
1807 |
|
---|
1808 | Parameters:
|
---|
1809 | mask: an optional mask retreived from scantable
|
---|
1810 | edge: an optional number of channel to drop at
|
---|
1811 | the edge of spectrum. If only one value is
|
---|
1812 | specified, the same number will be dropped from
|
---|
1813 | both sides of the spectrum. Default is to keep
|
---|
1814 | all channels. Nested tuples represent individual
|
---|
1815 | edge selection for different IFs (a number of spectral
|
---|
1816 | channels can be different)
|
---|
1817 | order: the order of the polynomial (default is 0)
|
---|
1818 | threshold: the threshold used by line finder. It is better to
|
---|
1819 | keep it large as only strong lines affect the
|
---|
1820 | baseline solution.
|
---|
1821 | chan_avg_limit:
|
---|
1822 | a maximum number of consequtive spectral channels to
|
---|
1823 | average during the search of weak and broad lines.
|
---|
1824 | The default is no averaging (and no search for weak
|
---|
1825 | lines). If such lines can affect the fitted baseline
|
---|
1826 | (e.g. a high order polynomial is fitted), increase this
|
---|
1827 | parameter (usually values up to 8 are reasonable). Most
|
---|
1828 | users of this method should find the default value
|
---|
1829 | sufficient.
|
---|
1830 | plot: plot the fit and the residual. In this each
|
---|
1831 | indivual fit has to be approved, by typing 'y'
|
---|
1832 | or 'n'
|
---|
1833 | insitu: if False a new scantable is returned.
|
---|
1834 | Otherwise, the scaling is done in-situ
|
---|
1835 | The default is taken from .asaprc (False)
|
---|
1836 |
|
---|
1837 | Example:
|
---|
1838 | scan2=scan.auto_poly_baseline(order=7)
|
---|
1839 | """
|
---|
1840 | if insitu is None: insitu = rcParams['insitu']
|
---|
1841 | varlist = vars()
|
---|
1842 | from asap.asapfitter import fitter
|
---|
1843 | from asap.asaplinefind import linefinder
|
---|
1844 | from asap import _is_sequence_or_number as _is_valid
|
---|
1845 |
|
---|
1846 | # check whether edge is set up for each IF individually
|
---|
1847 | individualedge = False;
|
---|
1848 | if len(edge) > 1:
|
---|
1849 | if isinstance(edge[0], list) or isinstance(edge[0], tuple):
|
---|
1850 | individualedge = True;
|
---|
1851 |
|
---|
1852 | if not _is_valid(edge, int) and not individualedge:
|
---|
1853 | raise ValueError, "Parameter 'edge' has to be an integer or a \
|
---|
1854 | pair of integers specified as a tuple. Nested tuples are allowed \
|
---|
1855 | to make individual selection for different IFs."
|
---|
1856 |
|
---|
1857 | curedge = (0, 0)
|
---|
1858 | if individualedge:
|
---|
1859 | for edgepar in edge:
|
---|
1860 | if not _is_valid(edgepar, int):
|
---|
1861 | raise ValueError, "Each element of the 'edge' tuple has \
|
---|
1862 | to be a pair of integers or an integer."
|
---|
1863 | else:
|
---|
1864 | curedge = edge;
|
---|
1865 |
|
---|
1866 | # setup fitter
|
---|
1867 | f = fitter()
|
---|
1868 | f.set_function(poly=order)
|
---|
1869 |
|
---|
1870 | # setup line finder
|
---|
1871 | fl = linefinder()
|
---|
1872 | fl.set_options(threshold=threshold,avg_limit=chan_avg_limit)
|
---|
1873 |
|
---|
1874 | if not insitu:
|
---|
1875 | workscan = self.copy()
|
---|
1876 | else:
|
---|
1877 | workscan = self
|
---|
1878 |
|
---|
1879 | fl.set_scan(workscan)
|
---|
1880 |
|
---|
1881 | rows = range(workscan.nrow())
|
---|
1882 | # Save parameters of baseline fits & masklists as a class attribute.
|
---|
1883 | # NOTICE: It does not reflect changes in scantable!
|
---|
1884 | if len(rows) > 0:
|
---|
1885 | self.blpars=[]
|
---|
1886 | self.masklists=[]
|
---|
1887 | asaplog.push("Processing:")
|
---|
1888 | for r in rows:
|
---|
1889 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \
|
---|
1890 | (workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \
|
---|
1891 | workscan.getpol(r), workscan.getcycle(r))
|
---|
1892 | asaplog.push(msg, False)
|
---|
1893 |
|
---|
1894 | # figure out edge parameter
|
---|
1895 | if individualedge:
|
---|
1896 | if len(edge) >= workscan.getif(r):
|
---|
1897 | raise RuntimeError, "Number of edge elements appear to " \
|
---|
1898 | "be less than the number of IFs"
|
---|
1899 | curedge = edge[workscan.getif(r)]
|
---|
1900 |
|
---|
1901 | # take into account flagtra info (CAS-1434)
|
---|
1902 | flagtra = workscan._getmask(r)
|
---|
1903 | actualmask = mask[:]
|
---|
1904 | if len(actualmask) == 0:
|
---|
1905 | actualmask = list(flagtra[:])
|
---|
1906 | else:
|
---|
1907 | if len(actualmask) != len(flagtra):
|
---|
1908 | raise RuntimeError, "Mask and flagtra have different length"
|
---|
1909 | else:
|
---|
1910 | for i in range(0, len(actualmask)):
|
---|
1911 | actualmask[i] = actualmask[i] and flagtra[i]
|
---|
1912 |
|
---|
1913 | # setup line finder
|
---|
1914 | fl.find_lines(r, actualmask, curedge)
|
---|
1915 | outmask=fl.get_mask()
|
---|
1916 | f.set_scan(workscan, fl.get_mask())
|
---|
1917 | f.x = workscan._getabcissa(r)
|
---|
1918 | f.y = workscan._getspectrum(r)
|
---|
1919 | f.data = None
|
---|
1920 | f.fit()
|
---|
1921 |
|
---|
1922 | # Show mask list
|
---|
1923 | masklist=workscan.get_masklist(fl.get_mask(),row=r)
|
---|
1924 | msg = "mask range: "+str(masklist)
|
---|
1925 | asaplog.push(msg, False)
|
---|
1926 |
|
---|
1927 | if plot:
|
---|
1928 | f.plot(residual=True)
|
---|
1929 | x = raw_input("Accept fit ( [y]/n ): ")
|
---|
1930 | if x.upper() == 'N':
|
---|
1931 | self.blpars.append(None)
|
---|
1932 | self.masklists.append(None)
|
---|
1933 | continue
|
---|
1934 |
|
---|
1935 | workscan._setspectrum(f.fitter.getresidual(), r)
|
---|
1936 | self.blpars.append(f.get_parameters())
|
---|
1937 | self.masklists.append(masklist)
|
---|
1938 | if plot:
|
---|
1939 | f._p.unmap()
|
---|
1940 | f._p = None
|
---|
1941 | workscan._add_history("auto_poly_baseline", varlist)
|
---|
1942 | if insitu:
|
---|
1943 | self._assign(workscan)
|
---|
1944 | else:
|
---|
1945 | return workscan
|
---|
1946 |
|
---|
1947 | @print_log_dec
|
---|
1948 | def rotate_linpolphase(self, angle):
|
---|
1949 | """
|
---|
1950 | Rotate the phase of the complex polarization O=Q+iU correlation.
|
---|
1951 | This is always done in situ in the raw data. So if you call this
|
---|
1952 | function more than once then each call rotates the phase further.
|
---|
1953 | Parameters:
|
---|
1954 | angle: The angle (degrees) to rotate (add) by.
|
---|
1955 | Examples:
|
---|
1956 | scan.rotate_linpolphase(2.3)
|
---|
1957 | """
|
---|
1958 | varlist = vars()
|
---|
1959 | self._math._rotate_linpolphase(self, angle)
|
---|
1960 | self._add_history("rotate_linpolphase", varlist)
|
---|
1961 | print_log()
|
---|
1962 | return
|
---|
1963 |
|
---|
1964 | @print_log_dec
|
---|
1965 | def rotate_xyphase(self, angle):
|
---|
1966 | """
|
---|
1967 | Rotate the phase of the XY correlation. This is always done in situ
|
---|
1968 | in the data. So if you call this function more than once
|
---|
1969 | then each call rotates the phase further.
|
---|
1970 | Parameters:
|
---|
1971 | angle: The angle (degrees) to rotate (add) by.
|
---|
1972 | Examples:
|
---|
1973 | scan.rotate_xyphase(2.3)
|
---|
1974 | """
|
---|
1975 | varlist = vars()
|
---|
1976 | self._math._rotate_xyphase(self, angle)
|
---|
1977 | self._add_history("rotate_xyphase", varlist)
|
---|
1978 | print_log()
|
---|
1979 | return
|
---|
1980 |
|
---|
1981 | @print_log_dec
|
---|
1982 | def swap_linears(self):
|
---|
1983 | """
|
---|
1984 | Swap the linear polarisations XX and YY, or better the first two
|
---|
1985 | polarisations as this also works for ciculars.
|
---|
1986 | """
|
---|
1987 | varlist = vars()
|
---|
1988 | self._math._swap_linears(self)
|
---|
1989 | self._add_history("swap_linears", varlist)
|
---|
1990 | print_log()
|
---|
1991 | return
|
---|
1992 |
|
---|
1993 | @print_log_dec
|
---|
1994 | def invert_phase(self):
|
---|
1995 | """
|
---|
1996 | Invert the phase of the complex polarisation
|
---|
1997 | """
|
---|
1998 | varlist = vars()
|
---|
1999 | self._math._invert_phase(self)
|
---|
2000 | self._add_history("invert_phase", varlist)
|
---|
2001 | print_log()
|
---|
2002 | return
|
---|
2003 |
|
---|
2004 | @print_log_dec
|
---|
2005 | def add(self, offset, insitu=None):
|
---|
2006 | """
|
---|
2007 | Return a scan where all spectra have the offset added
|
---|
2008 | Parameters:
|
---|
2009 | offset: the offset
|
---|
2010 | insitu: if False a new scantable is returned.
|
---|
2011 | Otherwise, the scaling is done in-situ
|
---|
2012 | The default is taken from .asaprc (False)
|
---|
2013 | """
|
---|
2014 | if insitu is None: insitu = rcParams['insitu']
|
---|
2015 | self._math._setinsitu(insitu)
|
---|
2016 | varlist = vars()
|
---|
2017 | s = scantable(self._math._unaryop(self, offset, "ADD", False))
|
---|
2018 | s._add_history("add", varlist)
|
---|
2019 | print_log()
|
---|
2020 | if insitu:
|
---|
2021 | self._assign(s)
|
---|
2022 | else:
|
---|
2023 | return s
|
---|
2024 |
|
---|
2025 | @print_log_dec
|
---|
2026 | def scale(self, factor, tsys=True, insitu=None):
|
---|
2027 | """
|
---|
2028 | Return a scan where all spectra are scaled by the give 'factor'
|
---|
2029 | Parameters:
|
---|
2030 | factor: the scaling factor (float or 1D float list)
|
---|
2031 | insitu: if False a new scantable is returned.
|
---|
2032 | Otherwise, the scaling is done in-situ
|
---|
2033 | The default is taken from .asaprc (False)
|
---|
2034 | tsys: if True (default) then apply the operation to Tsys
|
---|
2035 | as well as the data
|
---|
2036 | """
|
---|
2037 | if insitu is None: insitu = rcParams['insitu']
|
---|
2038 | self._math._setinsitu(insitu)
|
---|
2039 | varlist = vars()
|
---|
2040 | s = None
|
---|
2041 | import numpy
|
---|
2042 | if isinstance(factor, list) or isinstance(factor, numpy.ndarray):
|
---|
2043 | if isinstance(factor[0], list) or isinstance(factor[0], numpy.ndarray):
|
---|
2044 | from asapmath import _array2dOp
|
---|
2045 | s = _array2dOp( self.copy(), factor, "MUL", tsys )
|
---|
2046 | else:
|
---|
2047 | s = scantable( self._math._arrayop( self.copy(), factor, "MUL", tsys ) )
|
---|
2048 | else:
|
---|
2049 | s = scantable(self._math._unaryop(self.copy(), factor, "MUL", tsys))
|
---|
2050 | s._add_history("scale", varlist)
|
---|
2051 | print_log()
|
---|
2052 | if insitu:
|
---|
2053 | self._assign(s)
|
---|
2054 | else:
|
---|
2055 | return s
|
---|
2056 |
|
---|
2057 | def set_sourcetype(self, match, matchtype="pattern",
|
---|
2058 | sourcetype="reference"):
|
---|
2059 | """
|
---|
2060 | Set the type of the source to be an source or reference scan
|
---|
2061 | using the provided pattern:
|
---|
2062 | Parameters:
|
---|
2063 | match: a Unix style pattern, regular expression or selector
|
---|
2064 | matchtype: 'pattern' (default) UNIX style pattern or
|
---|
2065 | 'regex' regular expression
|
---|
2066 | sourcetype: the type of the source to use (source/reference)
|
---|
2067 | """
|
---|
2068 | varlist = vars()
|
---|
2069 | basesel = self.get_selection()
|
---|
2070 | stype = -1
|
---|
2071 | if sourcetype.lower().startswith("r"):
|
---|
2072 | stype = 1
|
---|
2073 | elif sourcetype.lower().startswith("s"):
|
---|
2074 | stype = 0
|
---|
2075 | else:
|
---|
2076 | raise ValueError("Illegal sourcetype use s(ource) or r(eference)")
|
---|
2077 | if matchtype.lower().startswith("p"):
|
---|
2078 | matchtype = "pattern"
|
---|
2079 | elif matchtype.lower().startswith("r"):
|
---|
2080 | matchtype = "regex"
|
---|
2081 | else:
|
---|
2082 | raise ValueError("Illegal matchtype, use p(attern) or r(egex)")
|
---|
2083 | sel = selector()
|
---|
2084 | if isinstance(match, selector):
|
---|
2085 | sel = match
|
---|
2086 | else:
|
---|
2087 | sel.set_query("SRCNAME == %s('%s')" % (matchtype, match))
|
---|
2088 | self.set_selection(basesel+sel)
|
---|
2089 | self._setsourcetype(stype)
|
---|
2090 | self.set_selection(basesel)
|
---|
2091 | self._add_history("set_sourcetype", varlist)
|
---|
2092 |
|
---|
2093 | @print_log_dec
|
---|
2094 | def auto_quotient(self, preserve=True, mode='paired', verify=False):
|
---|
2095 | """
|
---|
2096 | This function allows to build quotients automatically.
|
---|
2097 | It assumes the observation to have the same number of
|
---|
2098 | "ons" and "offs"
|
---|
2099 | Parameters:
|
---|
2100 | preserve: you can preserve (default) the continuum or
|
---|
2101 | remove it. The equations used are
|
---|
2102 | preserve: Output = Toff * (on/off) - Toff
|
---|
2103 | remove: Output = Toff * (on/off) - Ton
|
---|
2104 | mode: the on/off detection mode
|
---|
2105 | 'paired' (default)
|
---|
2106 | identifies 'off' scans by the
|
---|
2107 | trailing '_R' (Mopra/Parkes) or
|
---|
2108 | '_e'/'_w' (Tid) and matches
|
---|
2109 | on/off pairs from the observing pattern
|
---|
2110 | 'time'
|
---|
2111 | finds the closest off in time
|
---|
2112 |
|
---|
2113 | """
|
---|
2114 | modes = ["time", "paired"]
|
---|
2115 | if not mode in modes:
|
---|
2116 | msg = "please provide valid mode. Valid modes are %s" % (modes)
|
---|
2117 | raise ValueError(msg)
|
---|
2118 | varlist = vars()
|
---|
2119 | s = None
|
---|
2120 | if mode.lower() == "paired":
|
---|
2121 | basesel = self.get_selection()
|
---|
2122 | sel = selector()+basesel
|
---|
2123 | sel.set_query("SRCTYPE==1")
|
---|
2124 | self.set_selection(sel)
|
---|
2125 | offs = self.copy()
|
---|
2126 | sel.set_query("SRCTYPE==0")
|
---|
2127 | self.set_selection(sel)
|
---|
2128 | ons = self.copy()
|
---|
2129 | s = scantable(self._math._quotient(ons, offs, preserve))
|
---|
2130 | self.set_selection(basesel)
|
---|
2131 | elif mode.lower() == "time":
|
---|
2132 | s = scantable(self._math._auto_quotient(self, mode, preserve))
|
---|
2133 | s._add_history("auto_quotient", varlist)
|
---|
2134 | print_log()
|
---|
2135 | return s
|
---|
2136 |
|
---|
2137 | @print_log_dec
|
---|
2138 | def mx_quotient(self, mask = None, weight='median', preserve=True):
|
---|
2139 | """
|
---|
2140 | Form a quotient using "off" beams when observing in "MX" mode.
|
---|
2141 | Parameters:
|
---|
2142 | mask: an optional mask to be used when weight == 'stddev'
|
---|
2143 | weight: How to average the off beams. Default is 'median'.
|
---|
2144 | preserve: you can preserve (default) the continuum or
|
---|
2145 | remove it. The equations used are
|
---|
2146 | preserve: Output = Toff * (on/off) - Toff
|
---|
2147 | remove: Output = Toff * (on/off) - Ton
|
---|
2148 | """
|
---|
2149 | mask = mask or ()
|
---|
2150 | varlist = vars()
|
---|
2151 | on = scantable(self._math._mx_extract(self, 'on'))
|
---|
2152 | preoff = scantable(self._math._mx_extract(self, 'off'))
|
---|
2153 | off = preoff.average_time(mask=mask, weight=weight, scanav=False)
|
---|
2154 | from asapmath import quotient
|
---|
2155 | q = quotient(on, off, preserve)
|
---|
2156 | q._add_history("mx_quotient", varlist)
|
---|
2157 | print_log()
|
---|
2158 | return q
|
---|
2159 |
|
---|
2160 | @print_log_dec
|
---|
2161 | def freq_switch(self, insitu=None):
|
---|
2162 | """
|
---|
2163 | Apply frequency switching to the data.
|
---|
2164 | Parameters:
|
---|
2165 | insitu: if False a new scantable is returned.
|
---|
2166 | Otherwise, the swictching is done in-situ
|
---|
2167 | The default is taken from .asaprc (False)
|
---|
2168 | Example:
|
---|
2169 | none
|
---|
2170 | """
|
---|
2171 | if insitu is None: insitu = rcParams['insitu']
|
---|
2172 | self._math._setinsitu(insitu)
|
---|
2173 | varlist = vars()
|
---|
2174 | s = scantable(self._math._freqswitch(self))
|
---|
2175 | s._add_history("freq_switch", varlist)
|
---|
2176 | print_log()
|
---|
2177 | if insitu: self._assign(s)
|
---|
2178 | else: return s
|
---|
2179 |
|
---|
2180 | @print_log_dec
|
---|
2181 | def recalc_azel(self):
|
---|
2182 | """
|
---|
2183 | Recalculate the azimuth and elevation for each position.
|
---|
2184 | Parameters:
|
---|
2185 | none
|
---|
2186 | Example:
|
---|
2187 | """
|
---|
2188 | varlist = vars()
|
---|
2189 | self._recalcazel()
|
---|
2190 | self._add_history("recalc_azel", varlist)
|
---|
2191 | print_log()
|
---|
2192 | return
|
---|
2193 |
|
---|
2194 | @print_log_dec
|
---|
2195 | def __add__(self, other):
|
---|
2196 | varlist = vars()
|
---|
2197 | s = None
|
---|
2198 | if isinstance(other, scantable):
|
---|
2199 | s = scantable(self._math._binaryop(self, other, "ADD"))
|
---|
2200 | elif isinstance(other, float):
|
---|
2201 | s = scantable(self._math._unaryop(self, other, "ADD", False))
|
---|
2202 | else:
|
---|
2203 | raise TypeError("Other input is not a scantable or float value")
|
---|
2204 | s._add_history("operator +", varlist)
|
---|
2205 | return s
|
---|
2206 |
|
---|
2207 | @print_log_dec
|
---|
2208 | def __sub__(self, other):
|
---|
2209 | """
|
---|
2210 | implicit on all axes and on Tsys
|
---|
2211 | """
|
---|
2212 | varlist = vars()
|
---|
2213 | s = None
|
---|
2214 | if isinstance(other, scantable):
|
---|
2215 | s = scantable(self._math._binaryop(self, other, "SUB"))
|
---|
2216 | elif isinstance(other, float):
|
---|
2217 | s = scantable(self._math._unaryop(self, other, "SUB", False))
|
---|
2218 | else:
|
---|
2219 | raise TypeError("Other input is not a scantable or float value")
|
---|
2220 | s._add_history("operator -", varlist)
|
---|
2221 | return s
|
---|
2222 |
|
---|
2223 | @print_log_dec
|
---|
2224 | def __mul__(self, other):
|
---|
2225 | """
|
---|
2226 | implicit on all axes and on Tsys
|
---|
2227 | """
|
---|
2228 | varlist = vars()
|
---|
2229 | s = None
|
---|
2230 | if isinstance(other, scantable):
|
---|
2231 | s = scantable(self._math._binaryop(self, other, "MUL"))
|
---|
2232 | elif isinstance(other, float):
|
---|
2233 | s = scantable(self._math._unaryop(self, other, "MUL", False))
|
---|
2234 | else:
|
---|
2235 | raise TypeError("Other input is not a scantable or float value")
|
---|
2236 | s._add_history("operator *", varlist)
|
---|
2237 | return s
|
---|
2238 |
|
---|
2239 |
|
---|
2240 | @print_log_dec
|
---|
2241 | def __div__(self, other):
|
---|
2242 | """
|
---|
2243 | implicit on all axes and on Tsys
|
---|
2244 | """
|
---|
2245 | varlist = vars()
|
---|
2246 | s = None
|
---|
2247 | if isinstance(other, scantable):
|
---|
2248 | s = scantable(self._math._binaryop(self, other, "DIV"))
|
---|
2249 | elif isinstance(other, float):
|
---|
2250 | if other == 0.0:
|
---|
2251 | raise ZeroDivisionError("Dividing by zero is not recommended")
|
---|
2252 | s = scantable(self._math._unaryop(self, other, "DIV", False))
|
---|
2253 | else:
|
---|
2254 | raise TypeError("Other input is not a scantable or float value")
|
---|
2255 | s._add_history("operator /", varlist)
|
---|
2256 | return s
|
---|
2257 |
|
---|
2258 | def get_fit(self, row=0):
|
---|
2259 | """
|
---|
2260 | Print or return the stored fits for a row in the scantable
|
---|
2261 | Parameters:
|
---|
2262 | row: the row which the fit has been applied to.
|
---|
2263 | """
|
---|
2264 | if row > self.nrow():
|
---|
2265 | return
|
---|
2266 | from asap.asapfit import asapfit
|
---|
2267 | fit = asapfit(self._getfit(row))
|
---|
2268 | if rcParams['verbose']:
|
---|
2269 | #print fit
|
---|
2270 | asaplog.push( '%s' %(fit) )
|
---|
2271 | print_log()
|
---|
2272 | return
|
---|
2273 | else:
|
---|
2274 | return fit.as_dict()
|
---|
2275 |
|
---|
2276 | def flag_nans(self):
|
---|
2277 | """
|
---|
2278 | Utility function to flag NaN values in the scantable.
|
---|
2279 | """
|
---|
2280 | import numpy
|
---|
2281 | basesel = self.get_selection()
|
---|
2282 | for i in range(self.nrow()):
|
---|
2283 | sel = self.get_row_selector(i)
|
---|
2284 | self.set_selection(basesel+sel)
|
---|
2285 | nans = numpy.isnan(self._getspectrum(0))
|
---|
2286 | if numpy.any(nans):
|
---|
2287 | bnans = [ bool(v) for v in nans]
|
---|
2288 | self.flag(bnans)
|
---|
2289 | self.set_selection(basesel)
|
---|
2290 |
|
---|
2291 | def get_row_selector(self, rowno):
|
---|
2292 | return selector(beams=self.getbeam(rowno),
|
---|
2293 | ifs=self.getif(rowno),
|
---|
2294 | pols=self.getpol(rowno),
|
---|
2295 | scans=self.getscan(rowno),
|
---|
2296 | cycles=self.getcycle(rowno))
|
---|
2297 |
|
---|
2298 | def _add_history(self, funcname, parameters):
|
---|
2299 | if not rcParams['scantable.history']:
|
---|
2300 | return
|
---|
2301 | # create date
|
---|
2302 | sep = "##"
|
---|
2303 | from datetime import datetime
|
---|
2304 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S')
|
---|
2305 | hist = dstr+sep
|
---|
2306 | hist += funcname+sep#cdate+sep
|
---|
2307 | if parameters.has_key('self'): del parameters['self']
|
---|
2308 | for k, v in parameters.iteritems():
|
---|
2309 | if type(v) is dict:
|
---|
2310 | for k2, v2 in v.iteritems():
|
---|
2311 | hist += k2
|
---|
2312 | hist += "="
|
---|
2313 | if isinstance(v2, scantable):
|
---|
2314 | hist += 'scantable'
|
---|
2315 | elif k2 == 'mask':
|
---|
2316 | if isinstance(v2, list) or isinstance(v2, tuple):
|
---|
2317 | hist += str(self._zip_mask(v2))
|
---|
2318 | else:
|
---|
2319 | hist += str(v2)
|
---|
2320 | else:
|
---|
2321 | hist += str(v2)
|
---|
2322 | else:
|
---|
2323 | hist += k
|
---|
2324 | hist += "="
|
---|
2325 | if isinstance(v, scantable):
|
---|
2326 | hist += 'scantable'
|
---|
2327 | elif k == 'mask':
|
---|
2328 | if isinstance(v, list) or isinstance(v, tuple):
|
---|
2329 | hist += str(self._zip_mask(v))
|
---|
2330 | else:
|
---|
2331 | hist += str(v)
|
---|
2332 | else:
|
---|
2333 | hist += str(v)
|
---|
2334 | hist += sep
|
---|
2335 | hist = hist[:-2] # remove trailing '##'
|
---|
2336 | self._addhistory(hist)
|
---|
2337 |
|
---|
2338 |
|
---|
2339 | def _zip_mask(self, mask):
|
---|
2340 | mask = list(mask)
|
---|
2341 | i = 0
|
---|
2342 | segments = []
|
---|
2343 | while mask[i:].count(1):
|
---|
2344 | i += mask[i:].index(1)
|
---|
2345 | if mask[i:].count(0):
|
---|
2346 | j = i + mask[i:].index(0)
|
---|
2347 | else:
|
---|
2348 | j = len(mask)
|
---|
2349 | segments.append([i, j])
|
---|
2350 | i = j
|
---|
2351 | return segments
|
---|
2352 |
|
---|
2353 | def _get_ordinate_label(self):
|
---|
2354 | fu = "("+self.get_fluxunit()+")"
|
---|
2355 | import re
|
---|
2356 | lbl = "Intensity"
|
---|
2357 | if re.match(".K.", fu):
|
---|
2358 | lbl = "Brightness Temperature "+ fu
|
---|
2359 | elif re.match(".Jy.", fu):
|
---|
2360 | lbl = "Flux density "+ fu
|
---|
2361 | return lbl
|
---|
2362 |
|
---|
2363 | def _check_ifs(self):
|
---|
2364 | nchans = [self.nchan(i) for i in range(self.nif(-1))]
|
---|
2365 | nchans = filter(lambda t: t > 0, nchans)
|
---|
2366 | return (sum(nchans)/len(nchans) == nchans[0])
|
---|
2367 |
|
---|
2368 | def _fill(self, names, unit, average, getpt, antenna):
|
---|
2369 | first = True
|
---|
2370 | fullnames = []
|
---|
2371 | for name in names:
|
---|
2372 | name = os.path.expandvars(name)
|
---|
2373 | name = os.path.expanduser(name)
|
---|
2374 | if not os.path.exists(name):
|
---|
2375 | msg = "File '%s' does not exists" % (name)
|
---|
2376 | if rcParams['verbose']:
|
---|
2377 | asaplog.push(msg)
|
---|
2378 | print_log( 'ERROR' )
|
---|
2379 | return
|
---|
2380 | raise IOError(msg)
|
---|
2381 | fullnames.append(name)
|
---|
2382 | if average:
|
---|
2383 | asaplog.push('Auto averaging integrations')
|
---|
2384 | stype = int(rcParams['scantable.storage'].lower() == 'disk')
|
---|
2385 | for name in fullnames:
|
---|
2386 | tbl = Scantable(stype)
|
---|
2387 | r = filler(tbl)
|
---|
2388 | rx = rcParams['scantable.reference']
|
---|
2389 | r.setreferenceexpr(rx)
|
---|
2390 | msg = "Importing %s..." % (name)
|
---|
2391 | asaplog.push(msg, False)
|
---|
2392 | print_log()
|
---|
2393 | r.open(name)# antenna, -1, -1, getpt)
|
---|
2394 | r.fill()
|
---|
2395 | if average:
|
---|
2396 | tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN')
|
---|
2397 | if not first:
|
---|
2398 | tbl = self._math._merge([self, tbl])
|
---|
2399 | Scantable.__init__(self, tbl)
|
---|
2400 | r.close()
|
---|
2401 | del r, tbl
|
---|
2402 | first = False
|
---|
2403 | if unit is not None:
|
---|
2404 | self.set_fluxunit(unit)
|
---|
2405 | if not is_casapy():
|
---|
2406 | self.set_freqframe(rcParams['scantable.freqframe'])
|
---|
2407 |
|
---|
2408 | def __getitem__(self, key):
|
---|
2409 | if key < 0:
|
---|
2410 | key += self.nrow()
|
---|
2411 | if key >= self.nrow():
|
---|
2412 | raise IndexError("Row index out of range.")
|
---|
2413 | return self._getspectrum(key)
|
---|
2414 |
|
---|
2415 | def __setitem__(self, key, value):
|
---|
2416 | if key < 0:
|
---|
2417 | key += self.nrow()
|
---|
2418 | if key >= self.nrow():
|
---|
2419 | raise IndexError("Row index out of range.")
|
---|
2420 | if not hasattr(value, "__len__") or \
|
---|
2421 | len(value) > self.nchan(self.getif(key)):
|
---|
2422 | raise ValueError("Spectrum length doesn't match.")
|
---|
2423 | return self._setspectrum(value, key)
|
---|
2424 |
|
---|
2425 | def __len__(self):
|
---|
2426 | return self.nrow()
|
---|
2427 |
|
---|
2428 | def __iter__(self):
|
---|
2429 | for i in range(len(self)):
|
---|
2430 | yield self[i]
|
---|