def setNoise(self,vexp=None):
"""
Calculate the noise of the dataset, by taking the standard deviation
of the velocity range lower than v_lsr - 2*vexp.
If this is not available, the velocity range is taken to be where it is
smaller than 1.1*vexp.
If the size of the above selection still is too small, None is
returned.
The gas terminal velocity has to have been set previously or passed to
this method as a keyword.
@keyword vexp: The terminal gas velocity, only required if vexp is not
set yet for this LPDataReader object!
(default: None)
@type vexp: float
@return: The noise of the dataset
@rtype: float
"""
if not vexp is None and not self['contents'].has_key('vexp'):
self['contents']['vexp'] = float(vexp)
if not self['contents'].has_key('vexp'):
print 'Cannot set noise without an estimate for the terminal gas'+\
' velocity. Pass as keyword to this method!'
return None
vel = self['contents']['velocity']
flux = self['contents']['flux']
vlsr = self['contents']['vlsr']
vexp = self['contents']['vexp']
noise = Data.getStd(wave=vel,flux=flux,wmin=vlsr-5*vexp,\
wmax=vlsr-2*vexp,minsize=10)
if noise is None:
noise = Data.getStd(wave=vel,flux=flux,wmin=vlsr-3*vexp,\
wmax=vlsr-1.8*vexp,minsize=10)
if noise is None:
noise = Data.getStd(wave=vel,flux=flux,wmin=vlsr-3*vexp,\
wmax=vlsr-1.1*vexp,minsize=10)
if noise is None:
noise = Data.getStd(wave=vel,flux=flux,wmin=vlsr-3*vexp,\
wmax=vlsr-1.1*vexp,minsize=5)
if noise is None:
print 'WARNING! Noise cannot be determined, not enough data ' + \
'points outside the emission line.'
self['contents']['noise'] = noise
def doDataStats(self,method='clipping'):
'''
Calculate mean, std, rms for the data files.
They are saved in self.data_stats.
@keyword method: Std/Mean/RMS determination method. Can be 'clipping'
or 'preset'. The former 1-sigma clips based on
mean/std/... of full spectrum, then takes mean/std/...
of clipped spectrum. Latter takes preset values from
Data.dat.
(default: 'clipping')
@type method: string
'''
method = method.lower()
if method not in ['preset','clipping']: method = 'clipping'
self.data_stats = dict()
if self.instrument:
if not self.data_info: self.setDataInfo()
for filename,data_wave,data_flux,band in \
zip(self.instrument.data_filenames,\
self.instrument.data_wave_list,\
self.instrument.data_flux_list,\
self.instrument.data_ordernames):
these_stats = dict()
iband = self.data_info['bands'].index(band)
these_stats['sigma'] = self.data_info['sigmas'][iband]
if method == 'preset':
w_std_min = self.data_info['w_std_min'][iband]
w_std_max = self.data_info['w_std_max'][iband]
if w_std_min < data_wave[0] or w_std_max > data_wave[-1]:
method = 'clipping'
test_mean = Data.getMean(wave=data_wave,flux=data_flux,\
wmin=w_std_min,wmax=w_std_max)
if test_mean is None:
method = 'clipping'
if method == 'clipping':
totmean = Data.getMean(wave=data_wave,flux=data_flux)
totstd = Data.getStd(wave=data_wave,flux=data_flux)
limits = (-totstd,totstd)
these_stats['mean'] = Data.getMean(flux=data_flux,\
limits=limits)
these_stats['std'] = Data.getStd(flux=data_flux,\
limits=limits)
these_stats['rms'] = Data.getRMS(flux=data_flux-\
these_stats['mean'],\
limits=limits)
else:
these_stats['mean'] = Data.getMean(wave=data_wave,\
flux=data_flux,\
wmin=w_std_min,\
wmax=w_std_max)
these_stats['std'] = Data.getStd(wave=data_wave,\
flux=data_flux,\
wmin=w_std_min,\
wmax=w_std_max)
these_stats['rms'] = Data.getRMS(wave=data_wave,\
flux=data_flux-\
these_stats['mean'],\
wmin=w_std_min,\
wmax=w_std_max)
print '* Data statistics for %s using "%s" method:'\
%(filename,method)
if method == 'preset':
print '* Taken between %.2f and %.2f micron.'\
%(w_std_min,w_std_max)
print 'mean = ',these_stats['mean'],' Jy'
print 'std = ',these_stats['std'],' Jy'
print 'RMS = ',these_stats['rms'],' Jy'
self.data_stats[filename] = these_stats
print '***********************************'