def signif_cube(fluxcube, varcube,wave1,wave2,outfile=None):
nbhdu, errhdu = kt.narrowband(fluxcube,wave1,wave2,varcube=varcube)
signifdat = nbhdu.data/np.sqrt(errhdu.data)
newhdu = nbhdu.copy()
newhdu.data = signifdat
if outfile is not None:
fits.writeto(data=newhdu.data, header=newhdu.header,
filename=outfile, overwrite=True)
#newhdu.writeto(outfile,overwrite=True)
return newhdu
def median_continuum_subtract(cubefile, contwave1, contwave2,
linewave1, linewave2, outfile=None):
"""Find continuum by median flux value and subtract from line regiom
"""
from astropy.io import fits
medhdu = kt.narrowband(cubefile, contwave1, contwave2, mode='median')
linehdu = kt.slice_cube(cubefile, linewave1, linewave2)
dat = linehdu.data - medhdu.data
sumdat = np.sum(dat,axis=0)
medhdu.data = sumdat
if outfile is not None:
try:
fits.writeto(data=medhdu.data, header=medhdu.header,
filename=outfile, overwrite=True)
#medhdu.writeto(outfile, overwrite=True)
except:
import pdb; pdb.set_trace()
return medhdu
def addWcsRtModel(inp,
ref,
outfile,
spatial_scale=0.2,
zgal=0.6942,
center=('12 36 19.811', '+62 12 51.831'),
PA=27):
### Load in the model file
inpdat = fits.open(inp)
rtcube = DataCube(inp, include_wcs=False)
rtcube.wavelength = inpdat[2].data
rtcube.data = inpdat[1].data
wavearr = rtcube.wavelength
### Load in the reference file if necessary
if not isinstance(ref, DataCube):
refcube = DataCube(ref)
else:
refcube = inp
refdat = refcube.data
refwave = refcube.wavelength
nbhdu = transform.narrowband(refcube, 4000., 5000.)
refnb = nbhdu.data
refwcs = WCS(nbhdu.header)
### Rearrange the cube
newdat = np.transpose(rtcube.data, axes=[2, 1, 0])
### Get the pixel scale in the spectral dimension
diff = wavearr[1:] - wavearr[:-1]
if not np.all(diff == diff[0]):
raise ValueError('Wavelength array not uniformly sampled')
spectral_scale = diff[0]
### Set scale and reference positions
wave1 = wavearr[0] * (1. + zgal)
spectral_scale *= (1. + zgal)
### Get the bright pixel from reference cube
brightpix, brightcoords = utils.bright_pix_coords(refnb, refwcs)
### Create the new WCS
newwcs = WCS(naxis=3)
spatscaledeg = spatial_scale * cosmo.arcsec_per_kpc_proper(zgal) / 3600.
print(spatscaledeg)
if center is not None:
cencoords = SkyCoord(center[0], center[1], unit=(u.hourangle, u.deg))
else:
cencoords = brightcoords
newwcs.wcs.crpix = np.array([150.5, 150.5, 1])
newwcs.wcs.crval = np.array([cencoords.ra.deg, cencoords.dec.deg, wave1])
newwcs.wcs.cdelt = np.array([8.0226e-6, 8.0226e-6, spectral_scale])
newwcs.wcs.cunit = ['deg', 'deg', 'Angstrom']
newwcs.wcs.ctype = ('RA---TAN', 'DEC--TAN', 'VAC')
rotangle = np.radians(PA) # Assuming PA given in degrees
psmat = np.array([[
newwcs.wcs.cdelt[0] * np.cos(rotangle),
-newwcs.wcs.cdelt[1] * np.sin(rotangle), 0.
],
[
newwcs.wcs.cdelt[0] * np.sin(rotangle),
newwcs.wcs.cdelt[1] * np.cos(rotangle), 0.
], [0., 0., 1.]])
newwcs.wcs.cd = psmat
newhdu = newwcs.to_fits()
newhdu[0].header['PC3_3'] = spectral_scale
newhdu[0].data = newdat
newhdu.writeto(outfile, overwrite=True)
def addWcsRtModel(inp,
ref,
outfile,
spatial_scale_xy=[0.679, 0.290],
zgal=0.6942,
center=('12 36 19.811', '+62 12 51.831'),
PA=27):
### Load in the model file
inpdat = fits.open(inp)
rtcube = DataCube(inp, include_wcs=False)
rtcube.wavelength = inpdat[2].data
rtcube.data = inpdat[1].data
wavearr = rtcube.wavelength
### Load in the reference file if necessary
if not isinstance(ref, DataCube):
refcube = DataCube(ref)
else:
refcube = inp
refdat = refcube.data
refwave = refcube.wavelength
nbhdu = transform.narrowband(refcube, 4000., 5000.)
refnb = nbhdu.data
refwcs = WCS(nbhdu.header)
### Rearrange the cube and find brightest pixel
newdat = np.transpose(rtcube.data, axes=[2, 1, 0])
sumdat = np.sum(newdat, axis=0)
maxdat = np.max(sumdat)
brightmodpix = np.where(sumdat == maxdat)
print(brightmodpix)
### Get the pixel scale in the spectral dimension
diff = wavearr[1:] - wavearr[:-1]
if not np.all(np.abs(diff - diff[0]) < 1e-3):
import pdb
pdb.set_trace()
raise ValueError('Wavelength array not uniformly sampled')
spectral_scale = diff[0]
### Set scale and reference position in model
wave1 = wavearr[0] * (1. + zgal)
spectral_scale *= (1. + zgal)
### Get the bright pixel from reference cube
brightpix, brightcoords = utils.bright_pix_coords(refnb, refwcs)
### Create the new WCS
newwcs = WCS(naxis=3)
if center is not None:
cencoords = SkyCoord(center[0], center[1], unit=(u.hourangle, u.deg))
else:
cencoords = brightcoords
# coordinates are (y, x, lam) and '1' indexed in FITS files
newwcs.wcs.crpix = np.array(
[brightmodpix[1][0] + 1, brightmodpix[0][0] + 1, 1])
newwcs.wcs.crval = np.array([cencoords.ra.deg, cencoords.dec.deg, wave1])
newwcs.wcs.cdelt = np.array([
spatial_scale_xy[0] / 3600., spatial_scale_xy[1] / 3600.,
spectral_scale
])
newwcs.wcs.cunit = ['deg', 'deg', 'Angstrom']
newwcs.wcs.ctype = ('RA---TAN', 'DEC--TAN', 'VAC')
rotangle = np.radians(PA) # Assuming PA given in degrees
psmat = np.array([[
newwcs.wcs.cdelt[0] * np.cos(rotangle),
-newwcs.wcs.cdelt[1] * np.sin(rotangle), 0.
],
[
newwcs.wcs.cdelt[0] * np.sin(rotangle),
newwcs.wcs.cdelt[1] * np.cos(rotangle), 0.
], [0., 0., 1.]])
newwcs.wcs.cd = psmat
newhdu = newwcs.to_fits()
newhdu[0].header['PC3_3'] = spectral_scale
newhdu[0].data = newdat
newhdu.writeto(outfile, overwrite=True)