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create_N2H+_maps.py
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create_N2H+_maps.py
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from spectral_cube import SpectralCube as SC
import astropy.units as u
from astropy.io import fits
import numpy as np
import GAS
from config import file_N2Hp_base_erode, file_N2Hp_base_erode_rms, \
file_N2Hp_base_erode_TdV, file_N2Hp_base, file_in_N2Hp,\
file_NH3_11, file_NH3_22, file_NH3_11_match, file_NH3_22_match,\
file_NH3_11_match_TdV, file_NH3_11_match_rms,\
file_NH3_22_match_TdV, file_NH3_22_match_rms
#
# From GAS survey
#
do_baseline_N2Hp = False
if do_baseline_N2Hp:
GAS.baseline.rebaseline(file_in_N2Hp, blorder=1,
baselineRegion=[slice(0, 12, 1), slice(25, 85, 1),
slice(119, 145, 1), slice(177, 199, 1)],
windowFunction=None, blankBaseline=False,
flagSpike=False, v0=None, trimEdge=True)
do_baseline_N2Hp_full = False
if do_baseline_N2Hp_full:
GAS.baseline.rebaseline(file_in_N2Hp.replace('.fits', '_full.fits'), blorder=1,
baselineRegion=[slice(0, 126, 1), slice(154, 276, 1),
slice(345, 399, 1), slice(464, 510, 1)],
windowFunction=None, blankBaseline=False,
flagSpike=False, v0=None, trimEdge=False)
do_trim_N2Hp = False
if do_trim_N2Hp:
from skimage.morphology import disk,erosion
cube = SC.read(file_N2Hp_base)
#
spectral_axis = cube.with_spectral_unit(u.km/u.s, velocity_convention='radio').spectral_axis
good_channels = ((spectral_axis > 1.2*u.km/u.s) & (spectral_axis < 2.5*u.km/u.s)) |\
((spectral_axis > 8.5*u.km/u.s) & (spectral_axis < 11.9*u.km/u.s)) |\
((spectral_axis > 14.5*u.km/u.s) & (spectral_axis < 17.7*u.km/u.s))
bad_channels = ~good_channels
# mask original cube
masked_cube = cube.with_mask(bad_channels[:, np.newaxis, np.newaxis])
# get rms and mask pixels noisier than 0.5 K
# after an erosion of the mask
# save the minimal subcube
rms = masked_cube.std(axis=0)
rms_mask = (rms < 0.5)
rms_mask &= erosion(rms_mask, disk(5))
data = cube.unmasked_data[:, :, :] * rms_mask
data[data[:, :, :] == 0.0] = np.nan
subcube = SC(data=data, wcs=cube.wcs, header=cube.header)[:, 23:226, 11:166] * u.K
#
signal_cube = subcube.with_mask(good_channels[:, np.newaxis, np.newaxis])
rms_cube = subcube.with_mask(bad_channels[:, np.newaxis, np.newaxis])
# calcualate rms and integrated itensity maps
rms = rms_cube.std(axis=0)
TdV = signal_cube.moment(order=0, axis=0).to(u.K * u.km/u.s)
# write out the files to be used
TdV.hdu.writeto(file_N2Hp_base_erode_TdV, overwrite=True)
rms.hdu.writeto(file_N2Hp_base_erode_rms, overwrite=True)
subcube.write(file_N2Hp_base_erode, overwrite=True)
do_trim_N2Hp_full = False
if do_trim_N2Hp_full:
from skimage.morphology import disk,erosion
cube = SC.read(file_N2Hp_base.replace('_rebase1.fits', '_full_rebase1.fits'))
#
spectral_axis = cube.with_spectral_unit(u.km/u.s, velocity_convention='radio').spectral_axis
good_channels = ((spectral_axis > 1.2*u.km/u.s) & (spectral_axis < 2.5*u.km/u.s)) | \
((spectral_axis > 8.5*u.km/u.s) & (spectral_axis < 11.9*u.km/u.s)) | \
((spectral_axis > 14.5*u.km/u.s) & (spectral_axis < 17.7*u.km/u.s))
bad_channels = ~good_channels
# mask original cube
masked_cube = cube.with_mask(bad_channels[:, np.newaxis, np.newaxis])
# get rms and mask pixels noisier than 0.5 K
# after an erosion of the mask
# save the minimal subcube
rms = masked_cube.std(axis=0)
rms_mask = (rms < 0.7)
rms_mask &= erosion(rms_mask, disk(5))
data = cube.unmasked_data[:, :, :] * rms_mask
data[data[:, :, :] == 0.0] = np.nan
subcube = SC(data=data, wcs=cube.wcs, header=cube.header)[:, 23:226, 11:166] * u.K
#
signal_cube = subcube.with_mask(good_channels[:, np.newaxis, np.newaxis])
rms_cube = subcube.with_mask(bad_channels[:, np.newaxis, np.newaxis])
# calcualate rms and integrated itensity maps
rms = rms_cube.std(axis=0)
TdV = signal_cube.moment(order=0, axis=0).to(u.K * u.km/u.s)
# write out the files to be used
new_TdV_file = file_N2Hp_base_erode_TdV.replace('rebase1', 'full_rebase1')
TdV.hdu.writeto(new_TdV_file, overwrite=True)
rms.hdu.writeto(file_N2Hp_base_erode_rms.replace('_rebase1', '_full_rebase1'), overwrite=True)
subcube.write(file_N2Hp_base_erode.replace('_rebase1', '_full_rebase1'), overwrite=True)
do_match_11 = False
if do_match_11:
cube = SC.read(file_NH3_11)
cube.allow_huge_operations=True
# maybe use the same in reproject, to avoid the spectral resampling
hd_N2Hp = fits.getheader(file_N2Hp_base_erode)
hd_NH3_11 = cube.header
key_list = ['NAXIS1', 'NAXIS2', 'BMAJ', 'BMIN', 'BPA', 'CRPIX1', 'CRPIX2',
'CDELT1', 'CDELT2', 'CUNIT1', 'CUNIT2', 'CTYPE1', 'CTYPE2',
'CRVAL1', 'CRVAL2']
for key_i in key_list:
hd_NH3_11[key_i] = hd_N2Hp[key_i]
hd_NH3_11.remove('PV2_1', ignore_missing=True)
hd_NH3_11.remove('PV2_2', ignore_missing=True)
# print(hd_N2Hp)
bin_cube = cube.reproject(hd_NH3_11)
bin_cube.write(file_NH3_11_match, overwrite=True)
do_match_22 = False
if do_match_22:
cube = SC.read(file_NH3_22)
# maybe use the same in reproject, to avoid the spectral resampling
hd_N2Hp = fits.getheader(file_N2Hp_base_erode)
hd_NH3_22 = cube.header
key_list = ['NAXIS1', 'NAXIS2', 'BMAJ', 'BMIN', 'BPA', 'CRPIX1', 'CRPIX2',
'CDELT1', 'CDELT2', 'CUNIT1', 'CUNIT2', 'CTYPE1', 'CTYPE2',
'CRVAL1', 'CRVAL2']
for key_i in key_list:
hd_NH3_22[key_i] = hd_N2Hp[key_i]
hd_NH3_22.remove('PV2_1', ignore_missing=True)
hd_NH3_22.remove('PV2_2', ignore_missing=True)
# print(hd_N2Hp)
bin_cube = cube.reproject(hd_NH3_22)
bin_cube.write(file_NH3_22_match, overwrite=True)
do_TdV_11 = False
if do_TdV_11:
cube_f = SC.read(file_NH3_11_match)
# cube = cube_f.with_spectral_unit(u.km/u.s, velocity_convention='radio')
if cube_f.shape[0] > 1018:
cube = (cube_f[12:-1, :, :]).with_spectral_unit(u.km/u.s,
velocity_convention='radio')
else:
cube = cube_f.with_spectral_unit(u.km/u.s, velocity_convention='radio')
#
spectral_axis = cube.spectral_axis
good_channels = ((spectral_axis > -9.8*u.km/u.s) & (spectral_axis < -8.6*u.km/u.s)) |\
((spectral_axis > 1.7*u.km/u.s) & (spectral_axis < 3.6*u.km/u.s)) |\
((spectral_axis > 9.3*u.km/u.s) & (spectral_axis < 11.3*u.km/u.s)) |\
((spectral_axis > 17.2*u.km/u.s) & (spectral_axis < 18.8*u.km/u.s)) |\
((spectral_axis > 29.0*u.km/u.s) & (spectral_axis < 30.5*u.km/u.s))
bad_channels = ~good_channels
# mask original cube
signal_cube = cube.with_mask(good_channels[:, np.newaxis, np.newaxis])
rms_cube = cube.with_mask(bad_channels[:, np.newaxis, np.newaxis])
# calcualate rms and integrated itensity maps
rms = rms_cube.std(axis=0)
TdV = signal_cube.moment(order=0, axis=0).to(u.K * u.km/u.s)
# write out the files to be used
TdV.hdu.writeto(file_NH3_11_match_TdV, overwrite=True)
rms.hdu.writeto(file_NH3_11_match_rms, overwrite=True)
do_TdV_22 = False
if do_TdV_22:
cube_f = SC.read(file_NH3_22_match)
cube = cube_f.with_spectral_unit(u.km/u.s, velocity_convention='radio')
#
spectral_axis = cube.spectral_axis
good_channels = (spectral_axis < 10.71*u.km/u.s) & (spectral_axis > 9.71*u.km/u.s)
bad_channels = ~good_channels
# mask original cube
signal_cube = cube.with_mask(good_channels[:, np.newaxis, np.newaxis])
rms_cube = cube.with_mask(bad_channels[:, np.newaxis, np.newaxis])
# calcualate rms and integrated itensity maps
rms = rms_cube.std(axis=0)
TdV = signal_cube.moment(order=0, axis=0).to(u.K * u.km/u.s)
# write out the files to be used
TdV.hdu.writeto(file_NH3_22_match_TdV, overwrite=True)
rms.hdu.writeto(file_NH3_22_match_rms, overwrite=True)