def my_convolution(chann, head, newsize, outspax, psf, instpsf):
#Convolve cube channel with PSF channel
chann = psf_convolve(chann, psf)
#Convolve cube channel with instrument PSF
chann = psf_convolve(chann, instpsf)
#Frebin datacube up to output spaxel scale
newsize = (int(newsize[0]), int(newsize[1]))
#chann *= (head['CDELT1']*head['CDELT2']*1.E-6)
chann = frebin(chann, (newsize[0],newsize[1]), total=True)
#chann /= (outspax[0]*outspax[1]*1.E-6)
return chann
def wavelength_loop(cube, head, wavels, out_cube, newsize, outspax):
'''Function to take input datacube and process it iteratively through
each wavelength channel as follows:
- Generate PSF array for given channel
- Add effect of ADR to channel
- Convolve cube channel with PSF
- Frebin up to chosen output spaxel scale
Inputs:
cube: Datacube
head: Datacube header
wavels: Wavelength array
out_cube: Empty output cube
newsize: tuple containing (x_newsize, y_newsize) array sizes
outspax: output spaxels (x, y) (mas, mas)
Output:
cube: Processed cube
head: Updated header
'''
nspec = wp.NIRSpec()
nspec.pupilopd = None
print 'OPD = ', nspec.pupilopd
oversamp = 1000. / float(outspax[0])
for l in xrange(len(wavels)):
#Print percentage bar
update_progress(n.round(l / float(len(wavels)), 2))
#Create PSF channel
psf = nspec.calcPSF(outfile=None,
source=None,
filter=None,
nlambda=None,
monochromatic=wavels[l] * 1.E-6,
oversample=oversamp,
fov_arcsec=5,
rebin=False)
psf = psf[0].data
#Convolve cube channel with PSF channel
channel = psf_convolve(cube[l, :, :], psf)
#Frebin datacube up to output spaxel scale
newsize = (int(newsize[0]), int(newsize[1]))
channel *= (head['CDELT1'] * head['CDELT2'] * 1.E-6)
channel = frebin(channel, (newsize[0], newsize[1]), total=True)
channel /= (outspax[0] * outspax[1] * 1.E-6)
#Add channel to output cube
out_cube[l, :, :] = channel
return out_cube, head
def pp_wavelength_channel(chann, head, wave, l, newsize, outspax):
'''Function to take input datacube and process it iteratively through
each wavelength channel as follows:
- Generate PSF array for given channel
- Add effect of ADR to channel
- Convolve cube channel with PSF
- Frebin up to chosen output spaxel scale
Inputs:
chann: cube channel
head: Datacube header
wave: wavelength [um]
l: iteration no.
out_cube: Empty output cube
newsize: tuple containing (x_newsize, y_newsize) array sizes
outspax: tuple containing (x, y) output spaxel scales
Output:
cube: Processed cube
head: Updated header
inspax: Input spaxel scale (mas, mas)
outspax: Output spaxel scale (mas, mas)
'''
nspec = wp.NIRSpec()
nspec.pupilopd = None
#print 'OPD = ', nspec.pupilopd
oversamp = 1000. / float(outspax[0])
#Create PSF channel
#print 'Wavelength = ', wave*1.E-6, 'm'
psf = nspec.calcPSF(outfile=None,
source=None,
filter=None,
nlambda=None,
monochromatic=wave * 1.E-6,
oversample=oversamp,
fov_arcsec=5,
rebin=False)
psf = psf[0].data
#Convolve cube channel with PSF channel
chann = psf_convolve(chann, psf)
#Frebin datacube up to output spaxel scale
newsize = (int(newsize[0]), int(newsize[1]))
chann *= (head['CDELT1'] * head['CDELT2'] * 1.E-6)
chann = frebin(chann, (newsize[0], newsize[1]), total=True)
chann /= (outspax[0] * outspax[1] * 1.E-6)
return chann, l
def wavelength_loop(cube, head, wavels, out_cube, newsize, outspax):
'''Function to take input datacube and process it iteratively through
each wavelength channel as follows:
- Generate PSF array for given channel
- Add effect of ADR to channel
- Convolve cube channel with PSF
- Frebin up to chosen output spaxel scale
Inputs:
cube: Datacube
head: Datacube header
wavels: Wavelength array
out_cube: Empty output cube
newsize: tuple containing (x_newsize, y_newsize) array sizes
outspax: output spaxels (x, y) (mas, mas)
Output:
cube: Processed cube
head: Updated header
'''
nspec = wp.NIRSpec()
nspec.pupilopd = None
print 'OPD = ', nspec.pupilopd
oversamp = 1000./float(outspax[0])
for l in xrange(len(wavels)):
#Print percentage bar
update_progress(n.round(l/float(len(wavels)),2))
#Create PSF channel
psf = nspec.calcPSF(outfile=None, source=None, filter=None, nlambda=None,
monochromatic=wavels[l]*1.E-6, oversample=oversamp,
fov_arcsec=5, rebin=False)
psf = psf[0].data
#Convolve cube channel with PSF channel
channel = psf_convolve(cube[l,:,:], psf)
#Frebin datacube up to output spaxel scale
newsize = (int(newsize[0]), int(newsize[1]))
channel *= (head['CDELT1']*head['CDELT2']*1.E-6)
channel = frebin(channel, (newsize[0],newsize[1]), total=True)
channel /= (outspax[0]*outspax[1]*1.E-6)
#Add channel to output cube
out_cube[l,:,:] = channel
return out_cube, head
def pp_wavelength_channel(chann, head, wave, l, newsize, outspax):
'''Function to take input datacube and process it iteratively through
each wavelength channel as follows:
- Generate PSF array for given channel
- Add effect of ADR to channel
- Convolve cube channel with PSF
- Frebin up to chosen output spaxel scale
Inputs:
chann: cube channel
head: Datacube header
wave: wavelength [um]
l: iteration no.
out_cube: Empty output cube
newsize: tuple containing (x_newsize, y_newsize) array sizes
outspax: tuple containing (x, y) output spaxel scales
Output:
cube: Processed cube
head: Updated header
inspax: Input spaxel scale (mas, mas)
outspax: Output spaxel scale (mas, mas)
'''
nspec = wp.NIRSpec()
nspec.pupilopd = None
#print 'OPD = ', nspec.pupilopd
oversamp = 1000./float(outspax[0])
#Create PSF channel
#print 'Wavelength = ', wave*1.E-6, 'm'
psf = nspec.calcPSF(outfile=None, source=None, filter=None, nlambda=None,
monochromatic=wave*1.E-6, oversample=oversamp,
fov_arcsec=5, rebin=False)
psf = psf[0].data
#Convolve cube channel with PSF channel
chann = psf_convolve(chann, psf)
#Frebin datacube up to output spaxel scale
newsize = (int(newsize[0]), int(newsize[1]))
chann *= (head['CDELT1']*head['CDELT2']*1.E-6)
chann = frebin(chann, (newsize[0],newsize[1]), total=True)
chann /= (outspax[0]*outspax[1]*1.E-6)
return chann, l
def wavelength_loop(cube,
head,
wavels,
out_cube,
AO,
psfvars,
adrvals,
newsize,
outspax,
adr_switch='ON'):
'''Function to take input datacube and process it iteratively through
each wavelength channel as follows:
- Generate PSF array for given channel
- Add effect of ADR to channel
- Convolve cube channel with PSF
- Frebin up to chosen output spaxel scale
Inputs:
cube: Datacube
head: Datacube header
wavels: Wavelength array
out_cube: Empty output cube
AO: AO mode [LTAO, SCAO, Gaussian]
psdvars: list containing [psfparams, psfspax, psfsize, [D,eps],
res_jitter, seeing, user_psf, user_psflams]
adrvals: array of ADR values
newsize: tuple containing (x_newsize, y_newsize) array sizes
outspax: tuple containing (x, y) output spaxel scales
adr_switch: ON or OFF. Turns ADR effect on or off.
Output:
cube: Processed cube
head: Updated header
inspax: Input spaxel scale (mas, mas)
outspax: Output spaxel scale (mas, mas)
'''
for l in xrange(len(wavels)):
#Print percentage bar
update_progress(n.round(l / float(len(wavels)), 2))
#Create PSF channel
#If user PSF and 2D image
upsf = psfvars[-2]
upsflams = psfvars[-1]
if type(upsf) != str and type(upsflams) == str:
psf = upsf
#If User PSF and 3D cube
elif type(upsf) != str and type(upsflams) != str:
#Interpolate PSF cube
interp = interp1d(upsflams, upsf, axis=0)
psf = interp(wavels[l])
elif AO == 'LTAO' or AO == 'SCAO' or AO == 'GLAO':
psf = create_psf_channel(psfvars[0], l, psfvars[1],
(head['CDELT1'], head['CDELT2']),
psfvars[2], psfvars[3], psfvars[4])
elif AO == 'Gaussian':
psf = create_Gausspsf_channel(wavels[l],
psfvars[5],
psfvars[3],
psfvars[4],
psfvars[2],
Nyquist=False,
psfspax=psfvars[1],
output_spax=(head['CDELT1'],
head['CDELT2']))
else:
print 'AO = ', AO
raise ValueError('AO choice error!')
#Create instrument PSF array
instpsf = create_instpsf(psfvars[2], psfvars[1], outspax,
(head['CDELT1'], head['CDELT2']))
#Add ADR effect to channel
if adr_switch == 'ON':
cube[l, :, :] = add_ADR(cube[l, :, :], head, adrvals[l], 'spline3')
#Convolve cube channel with PSF channel
channel = psf_convolve(cube[l, :, :], psf)
#Convolve cube channel with instrument PSF
channel = psf_convolve(channel, instpsf)
#Frebin datacube up to output spaxel scale
newsize = (int(newsize[0]), int(newsize[1]))
channel *= (head['CDELT1'] * head['CDELT2'] * 1.E-6)
channel = frebin(channel, (newsize[0], newsize[1]), total=True)
channel /= (outspax[0] * outspax[1] * 1.E-6)
#Correct ADR effect
if adr_switch == 'ON':
adrhead = head.copy()
adrhead['CDELT1'] = outspax[0]
adrhead['CDELT2'] = outspax[1]
channel = add_ADR(channel, adrhead, -1. * adrvals[l], 'spline3')
#Add channel to output cube
out_cube[l, :, :] = channel
return out_cube, head
def pp_wavelength_channel(chann, head, wave, l, AO, psfvars, adrval, newsize,
outspax, adr_switch):
'''Function to take input datacube and process it iteratively through
each wavelength channel as follows:
- Generate PSF array for given channel
- Add effect of ADR to channel
- Convolve cube channel with PSF
- Frebin up to chosen output spaxel scale
Inputs:
chann: cube channel
head: Datacube header
wave: wavelength [um]
l: iteration no.
out_cube: Empty output cube
AO: AO mode [LTAO, SCAO, Gaussian]
psfvars: list containing [psfparams, psfspax, psfsize,
[D,eps], res_jitter, seeing, user_psf,
user_psflams]
adrval: ADR value
newsize: tuple containing (x_newsize, y_newsize) array sizes
outspax: tuple containing (x, y) output spaxel scales
adr_switch: On or OFF. Turns ADR effect on or off
Output:
cube: Processed cube
head: Updated header
inspax: Input spaxel scale (mas, mas)
outspax: Output spaxel scale (mas, mas)
'''
#Create PSF channel
#If user PSF and 2D image
upsf = psfvars[-2]
upsflams = psfvars[-1]
if type(upsf) != str and type(upsflams) == str:
psf = upsf
#If User PSF and 3D cube
elif type(upsf) != str and type(upsflams) != str:
#Interpolate PSF cube
interp = interp1d(upsflams, upsf, axis=0)
psf = interp(wave)
elif AO == 'LTAO' or AO == 'SCAO' or AO == 'GLAO':
psf = create_psf_channel(psfvars[0], l, psfvars[1],
(head['CDELT1'], head['CDELT2']), psfvars[2],
psfvars[3], psfvars[4])
elif AO == 'Gaussian':
psf = create_Gausspsf_channel(wave, psfvars[5], psfvars[3], psfvars[4],
psfvars[2], False, psfvars[1],
(head['CDELT1'], head['CDELT2']))
else:
print 'AO = ', AO
raise ValueError('AO choice or user_PSF error!')
#Create instrument PSF array
instpsf = create_instpsf(psfvars[2], psfvars[1], outspax,
(head['CDELT1'], head['CDELT2']))
#Add ADR effect to channel
if adr_switch == 'ON':
chann = add_ADR(chann, head, adrval, 'spline3')
#Convolve cube channel with PSF channel
chann = psf_convolve(chann, psf)
#Convolve cube channel with instrument PSF
chann = psf_convolve(chann, instpsf)
#Frebin datacube up to output spaxel scale
newsize = (int(newsize[0]), int(newsize[1]))
chann *= (head['CDELT1'] * head['CDELT2'] * 1.E-6)
chann = frebin(chann, (newsize[0], newsize[1]), total=True)
chann /= (outspax[0] * outspax[1] * 1.E-6)
#"Correct" ADR effect
if adr_switch == 'ON':
adrhead = head.copy()
adrhead['CDELT1'] = outspax[0]
adrhead['CDELT2'] = outspax[1]
chann = add_ADR(chann, adrhead, -1. * adrval, 'spline3')
return chann, l