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