def read_spec(ispec, exten=None, norm=True):
"""Parse spectrum out of the input
If 2 spectra are given, the 2nd is scaled to the first
Parameters
----------
ispec : Spectrum1D, str, list of files (ordered blue to red),
or tuple of arrays
exten : int, optional
FITS extension
Returns
-------
spec : XSpectrum1D
spec_file : str
"""
from specutils.spectrum1d import Spectrum1D
from linetools.spectra import xspectrum1d as lsx
#
if isinstance(ispec,basestring):
spec_fil = ispec
spec = lsx.XSpectrum1D.from_file(spec_fil, exten=exten)
elif isinstance(ispec,Spectrum1D):
spec = ispec
spec_fil = spec.filename # Grab from Spectrum1D
elif isinstance(ispec,tuple):
spec = lsx.XSpectrum1D.from_tuple(ispec)
spec_fil = 'none'
elif isinstance(ispec,list): # Multiple file names
# Loop on the files
for kk,ispecf in enumerate(ispec):
jspec = lsx.XSpectrum1D.from_file(ispecf, exten=exten)
if kk == 0:
spec = jspec
_, xper1 = ltsp.get_flux_plotrange(spec.flux, perc=0.9)
else:
# Scale flux for convenience of plotting (sig is not scaled)
_, xper2 = ltsp.get_flux_plotrange(jspec.flux, perc=0.9)
scl = xper1[1]/xper2[1]
# Splice
spec = spec.splice(jspec, scale=scl)
# Filename
spec_fil = ispec[0]
spec.filename=spec_fil
else:
raise ValueError('Bad input to read_spec: {:s}'.format(type(ispec)))
# Normalize?
if norm:
if hasattr(spec, 'co') and spec.co is not None:
spec.normalize()
# Return
return spec, spec_fil
def init_spec(self):
""" Initialize parameters for plotting the spectrum
"""
#xy min/max
xmin = np.min(self.spec.dispersion.value)
xmax = np.max(self.spec.dispersion.value)
from linetools.spectra.plotting import get_flux_plotrange
ymin, ymax = get_flux_plotrange(self.spec.flux.value)
#QtCore.pyqtRemoveInputHook()
#xdb.set_trace()
#QtCore.pyqtRestoreInputHook()
self.psdict['x_minmax'] = np.array([xmin, xmax])
self.psdict['y_minmax'] = [ymin, ymax]
self.psdict['sv_xy_minmax'] = [[xmin, xmax], [ymin, ymax]]
self.psdict['tmp_xy'] = None
self.psdict['nav'] = ltgu.navigate(0, 0, init=True)
# Analysis dict
self.adict['flg'] = 0 # Column density flag
def test_get_flux_plotrange():
flux = [1, 2, 0.5, np.nan, 0.7, 1.1]
qflux = u.quantity.Quantity(flux)
ref = -0.273, 2.73
np.testing.assert_allclose(get_flux_plotrange(flux), ref)
np.testing.assert_allclose(get_flux_plotrange(qflux), ref)
def read_spec(ispec, exten=None, norm=True, **kwargs):
"""Parse spectrum out of the input
If 2 spectra are given, the 2nd is scaled to the first
Parameters
----------
ispec : XSpectrum1D, str, list of files (ordered blue to red),
or tuple of arrays
exten : int, optional
FITS extension
Returns
-------
spec : XSpectrum1D
spec_file : str
"""
from linetools.spectra import xspectrum1d as lsx
from linetools.spectra import utils as ltsu
from astropy.utils.misc import isiterable
#
if isinstance(ispec,basestring):
spec_fil = ispec
if 'rsp_kwargs' in kwargs.keys():
spec = lsx.XSpectrum1D.from_file(spec_fil, exten=exten, **kwargs['rsp_kwargs'])
else:
spec = lsx.XSpectrum1D.from_file(spec_fil, exten=exten)
elif isinstance(ispec, lsx.XSpectrum1D):
spec = ispec
spec_fil = spec.filename # Grab from Spectrum1D
elif isinstance(ispec,tuple):
spec = lsx.XSpectrum1D.from_tuple(ispec)
spec_fil = 'none'
elif isinstance(ispec,list): # Multiple file names
# Loop on the files
for kk,ispecf in enumerate(ispec):
if isiterable(exten):
iexten = exten[kk]
else:
iexten = exten
jspec = lsx.XSpectrum1D.from_file(ispecf, exten=iexten)
if kk == 0:
spec = jspec
_, xper1 = ltsp.get_flux_plotrange(spec.flux, perc=0.9)
else:
# Scale flux for convenience of plotting (sig is not scaled)
_, xper2 = ltsp.get_flux_plotrange(jspec.flux, perc=0.9)
scl = xper1/xper2
# Splice
#from PyQt4 import QtCore
#QtCore.pyqtRemoveInputHook()
#pdb.set_trace()
#QtCore.pyqtRestoreInputHook()
spec = ltsu.splice_two(spec, jspec)#, scale=scl)
# Filename
spec_fil = ispec[0]
spec.filename=spec_fil
else:
raise ValueError('Bad input to read_spec: {}'.format(type(ispec)))
# Normalize?
if norm:
if spec.co_is_set:
spec.normed=True
# Demand AA for wavelength unit (unless over-ridden)
if spec.wavelength.unit != u.AA:
wvAA = spec.wavelength.to('AA')
spec.wavelength = wvAA
#from PyQt4 import QtCore
#QtCore.pyqtRemoveInputHook()
#pdb.set_trace()
#QtCore.pyqtRestoreInputHook()
# Return
return spec, spec_fil
def navigate(psdict, event, init=False, wave=None, flux=None):
""" Method to Navigate spectrum
Updates the dict
Parameters
----------
init : (False) Initialize
Just pass back valid key strokes
wave, flux : array of floats, optional
The spectrum wavelength and flux values (both unitless). Only
used for the 'y' option.
"""
# Initalize
if init is True:
return ['l','r','b','t','T','i','I', 'o','O',
'[',']','W','Z', 'y', 'Y', '{', '}', 's']
#
if (not isinstance(event.xdata,float)) or (not isinstance(event.ydata,float)):
print('Navigate: You entered the {:s} key out of bounds'.format(
event.key))
return 0
if event.key == 'l': # Set left
psdict['x_minmax'][0] = event.xdata
elif event.key == 'r': # Set Right
psdict['x_minmax'][1] = event.xdata
elif event.key == 'b': # Set Bottom
psdict['y_minmax'][0] = event.ydata
elif event.key == 't': # Set Top
psdict['y_minmax'][1] = event.ydata
elif event.key == 'T': # Set Top to 1.1
psdict['y_minmax'][1] = 1.1
elif event.key == 's': # Select window (i.e. zoom-in)
if psdict['tmp_xy'] is None:
psdict['tmp_xy'] = [event.xdata,event.ydata]
print('Press another s to set the zoom-in window')
else:
psdict['x_minmax'][0] = np.minimum(event.xdata,psdict['tmp_xy'][0])
psdict['x_minmax'][1] = np.maximum(event.xdata,psdict['tmp_xy'][0])
psdict['y_minmax'][0] = np.minimum(event.ydata,psdict['tmp_xy'][1])
psdict['y_minmax'][1] = np.maximum(event.ydata,psdict['tmp_xy'][1])
psdict['tmp_xy'] = None
elif event.key == 'i': # Zoom in (and center)
deltx = (psdict['x_minmax'][1]-psdict['x_minmax'][0])/4.
psdict['x_minmax'] = [event.xdata-deltx, event.xdata+deltx]
elif event.key == 'I': # Zoom in (and center)
deltx = (psdict['x_minmax'][1]-psdict['x_minmax'][0])/16.
psdict['x_minmax'] = [event.xdata-deltx, event.xdata+deltx]
elif event.key == 'o': # Zoom in (and center)
deltx = psdict['x_minmax'][1]-psdict['x_minmax'][0]
psdict['x_minmax'] = [event.xdata-deltx, event.xdata+deltx]
elif event.key == 'O': # Zoom in (and center)
deltx = psdict['x_minmax'][1]-psdict['x_minmax'][0]
psdict['x_minmax'] = [event.xdata-2*deltx, event.xdata+2*deltx]
elif event.key == 'y' and wave is not None and flux is not None:
# guess y limits
x0,x1 = psdict['x_minmax']
y0,y1 = ltsp.get_flux_plotrange(
flux[between(wave, x0, x1)], perc=90, mult_pos=2)
psdict['y_minmax'] = [y0, y1]
elif event.key == 'Y': # Zoom in (and center)
delty = psdict['y_minmax'][1]-psdict['y_minmax'][0]
psdict['y_minmax'] = [event.ydata-delty, event.ydata+delty]
elif event.key in ['[',']','{','}']: # Pan
center = (psdict['x_minmax'][1]+psdict['x_minmax'][0])/2.
deltx = (psdict['x_minmax'][1]-psdict['x_minmax'][0])/2.
if event.key == '[':
new_center = center - deltx
elif event.key == ']':
new_center = center + deltx
elif event.key == '{':
new_center = center - 4*deltx
elif event.key == '}':
new_center = center + 4*deltx
psdict['x_minmax'] = [new_center-deltx, new_center+deltx]
elif event.key == 'W': # Reset the Window
psdict['x_minmax'] = copy.deepcopy(psdict['sv_xy_minmax'][0])
psdict['y_minmax'] = copy.deepcopy(psdict['sv_xy_minmax'][1])
elif event.key == 'Z': # Zero
psdict['y_minmax'][0] = 0.
else:
if not (event.key in ['shift']):
rstr = 'Key {:s} not supported.'.format(event.key)
print(rstr)
return 0
return 1
def test_get_flux_plotrange():
flux = [1, 2, 0.5, np.nan, 0.7, 1.1]
qflux = u.quantity.Quantity(flux)
ref = -0.273, 2.73
np.testing.assert_allclose(get_flux_plotrange(flux), ref)
np.testing.assert_allclose(get_flux_plotrange(qflux), ref)
def read_spec(ispec, exten=None, norm=True, **kwargs):
"""Parse spectrum out of the input
If 2 spectra are given, the 2nd is scaled to the first
Parameters
----------
ispec : Spectrum1D, str, list of files (ordered blue to red),
or tuple of arrays
exten : int, optional
FITS extension
Returns
-------
spec : XSpectrum1D
spec_file : str
"""
from linetools.spectra import xspectrum1d as lsx
#
if isinstance(ispec,basestring):
spec_fil = ispec
if 'rsp_kwargs' in kwargs.keys():
spec = lsx.XSpectrum1D.from_file(spec_fil, exten=exten, **kwargs['rsp_kwargs'])
else:
spec = lsx.XSpectrum1D.from_file(spec_fil, exten=exten)
#from PyQt4 import QtCore
#QtCore.pyqtRemoveInputHook()
#pdb.set_trace()
#QtCore.pyqtRestoreInputHook()
elif isinstance(ispec, lsx.XSpectrum1D):
spec = ispec
spec_fil = spec.filename # Grab from Spectrum1D
elif isinstance(ispec,tuple):
spec = lsx.XSpectrum1D.from_tuple(ispec)
spec_fil = 'none'
elif isinstance(ispec,list): # Multiple file names
# Loop on the files
for kk,ispecf in enumerate(ispec):
jspec = lsx.XSpectrum1D.from_file(ispecf, exten=exten)
if kk == 0:
spec = jspec
_, xper1 = ltsp.get_flux_plotrange(spec.flux, perc=0.9)
else:
# Scale flux for convenience of plotting (sig is not scaled)
_, xper2 = ltsp.get_flux_plotrange(jspec.flux, perc=0.9)
scl = xper1[1]/xper2[1]
# Splice
spec = spec.splice(jspec, scale=scl)
# Filename
spec_fil = ispec[0]
spec.filename=spec_fil
else:
raise ValueError('Bad input to read_spec: {:s}'.format(type(ispec)))
# Normalize?
if norm:
if spec.co_is_set:
spec.normed=True
# Return
return spec, spec_fil