chanter 0.0.1__py3-none-any.whl

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Files changed (16) hide show
  1. chanter/__init__.py +4 -0
  2. chanter/galaxy_fitter.py +118 -0
  3. chanter/model_galaxy.py +257 -0
  4. chanter/utils/__init__.py +1 -0
  5. chanter/utils/filter_set.py +175 -0
  6. chanter/utils/make_igm_grid.py +234 -0
  7. chanter/utils/make_ssp_grid/ascii_files/bintoascii.py +9 -0
  8. chanter/utils/make_ssp_grid/csv_to_fits.py +24 -0
  9. chanter/utils/make_ssp_grid/get_ssp.py +32 -0
  10. chanter/utils/make_ssp_grid/load_fits_test.py +8 -0
  11. chanter/utils/make_ssp_grid/raw_files/bc03/src/rebuildfitsheader.py +625 -0
  12. chanter/utils/make_ssp_grid/raw_files/bc03/src/rebuildtimeheader.py +48 -0
  13. chanter-0.0.1.dist-info/METADATA +14 -0
  14. chanter-0.0.1.dist-info/RECORD +16 -0
  15. chanter-0.0.1.dist-info/WHEEL +5 -0
  16. chanter-0.0.1.dist-info/top_level.txt +1 -0
chanter/utils/make_igm_grid.py ADDED
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+ import numpy as np
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+ from astropy.io import fits
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+ import os
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+
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+ max_redshift = 10.
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+ igm_redshifts = np.arange(0.0, max_redshift + 0.01, 0.01)
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+ igm_wavelengths = np.arange(1.0, 1225.01, 1.0)
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+ print(igm_redshifts.shape)
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+
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+ coefs = np.loadtxt("/Users/struanstevenson/Desktop/research/CHANTER/lyman_series_coefs_inoue_2014_table2.txt")
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+
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+
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+ def get_Inoue14_trans(rest_wavs, z_obs):
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+ """ Calculate IGM transmission using Inoue et al. (2014) model. """
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+
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+ if isinstance(rest_wavs, float):
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+ rest_wavs = np.array([rest_wavs])
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+
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+ tau_LAF_LS = np.zeros((39, rest_wavs.shape[0]))
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+ tau_DLA_LS = np.zeros((39, rest_wavs.shape[0]))
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+ tau_LAF_LC = np.zeros(rest_wavs.shape[0])
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+ tau_DLA_LC = np.zeros(rest_wavs.shape[0])
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+
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+ # Populate tau_LAF_LS
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+ for j in range(39):
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+
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+ if z_obs < 1.2:
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+ wav_slice = ((rest_wavs*(1.+z_obs) > coefs[j, 1])
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+ & (rest_wavs*(1.+z_obs)
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+ < (1+z_obs)*coefs[j, 1]))
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+
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+ tau_LAF_LS[j, wav_slice] = (coefs[j, 2]
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+ * (rest_wavs[wav_slice]
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+ * (1.+z_obs)/coefs[j, 1])**1.2)
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+
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+ elif z_obs < 4.7:
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+ wav_slice_1 = ((rest_wavs*(1.+z_obs) > coefs[j, 1])
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+ & (rest_wavs*(1.+z_obs) < 2.2*coefs[j, 1]))
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+ wav_slice_2 = ((rest_wavs*(1.+z_obs) > 2.2*coefs[j, 1])
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+ & (rest_wavs*(1.+z_obs)
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+ < (1+z_obs)*coefs[j, 1]))
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+
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+ tau_LAF_LS[j, wav_slice_1] = (coefs[j, 2]
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+ * (rest_wavs[wav_slice_1]
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+ * (1.+z_obs)/coefs[j, 1])**1.2)
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+
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+ tau_LAF_LS[j, wav_slice_2] = (coefs[j, 3]
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+ * (rest_wavs[wav_slice_2]
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+ * (1.+z_obs)/coefs[j, 1])**3.7)
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+
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+ else:
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+ wav_slice_1 = ((rest_wavs*(1.+z_obs) > coefs[j, 1])
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+ & (rest_wavs*(1.+z_obs) < 2.2*coefs[j, 1]))
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+
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+ wav_slice_2 = ((rest_wavs*(1.+z_obs) > 2.2*coefs[j, 1])
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+ & (rest_wavs*(1.+z_obs) < 5.7*coefs[j, 1]))
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+
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+ wav_slice_3 = ((rest_wavs*(1.+z_obs) > 5.7*coefs[j, 1])
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+ & (rest_wavs*(1.+z_obs)
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+ < (1+z_obs)*coefs[j, 1]))
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+
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+ tau_LAF_LS[j, wav_slice_1] = (coefs[j, 2]
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+ * (rest_wavs[wav_slice_1]
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+ * (1.+z_obs)/coefs[j, 1])**1.2)
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+
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+ tau_LAF_LS[j, wav_slice_2] = (coefs[j, 3]
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+ * (rest_wavs[wav_slice_2]
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+ * (1.+z_obs)/coefs[j, 1])**3.7)
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+
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+ tau_LAF_LS[j, wav_slice_3] = (coefs[j, 4]
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+ * (rest_wavs[wav_slice_3]
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+ * (1.+z_obs)/coefs[j, 1])**5.5)
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+
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+ # Populate tau_DLA_LS
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+ for j in range(39):
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+
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+ if z_obs < 2.0:
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+ wav_slice = ((rest_wavs*(1.+z_obs) > coefs[j, 1])
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+ & (rest_wavs*(1.+z_obs)
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+ < (1+z_obs)*coefs[j, 1]))
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+
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+ tau_DLA_LS[j, wav_slice] = (coefs[j, 5]
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+ * (rest_wavs[wav_slice]
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+ * (1.+z_obs)/coefs[j, 1])**2.0)
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+
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+ else:
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+ wav_slice_1 = ((rest_wavs*(1.+z_obs) > coefs[j, 1])
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+ & (rest_wavs*(1.+z_obs) < 3.0*coefs[j, 1]))
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+
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+ wav_slice_2 = ((rest_wavs*(1.+z_obs) > 3.0*coefs[j, 1])
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+ & (rest_wavs*(1.+z_obs) < (1+z_obs)
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+ * coefs[j, 1]))
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+
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+ tau_DLA_LS[j, wav_slice_1] = (coefs[j, 5]
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+ * (rest_wavs[wav_slice_1]
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+ * (1.+z_obs)/coefs[j, 1])**2.0)
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+
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+ tau_DLA_LS[j, wav_slice_2] = (coefs[j, 6]
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+ * (rest_wavs[wav_slice_2]
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+ * (1.+z_obs)/coefs[j, 1])**3.0)
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+
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+ # Populate tau_LAF_LC
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+ if z_obs < 1.2:
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+ wav_slice = ((rest_wavs*(1.+z_obs) > 911.8)
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+ & (rest_wavs*(1.+z_obs) < 911.8*(1.+z_obs)))
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+
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+ tau_LAF_LC[wav_slice] = (0.325*((rest_wavs[wav_slice]
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+ * (1.+z_obs)/911.8)**1.2
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+ - (((1+z_obs)**-0.9)
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+ * (rest_wavs[wav_slice]
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+ * (1.+z_obs)/911.8)**2.1)))
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+
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+ elif z_obs < 4.7:
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+ wav_slice_1 = ((rest_wavs*(1.+z_obs) > 911.8)
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+ & (rest_wavs*(1.+z_obs) < 911.8*2.2))
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+
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+ wav_slice_2 = ((rest_wavs*(1.+z_obs) > 911.8*2.2)
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+ & (rest_wavs*(1.+z_obs) < 911.8*(1.+z_obs)))
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+
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+ tau_LAF_LC[wav_slice_1] = (((2.55*10**-2)*((1+z_obs)**1.6)
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+ * (rest_wavs[wav_slice_1]
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+ * (1.+z_obs)/911.8)**2.1)
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+ + (0.325*((rest_wavs[wav_slice_1]
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+ * (1.+z_obs)/911.8)**1.2))
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+ - (0.25*((rest_wavs[wav_slice_1]
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+ * (1.+z_obs)/911.8)**2.1)))
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+
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+ tau_LAF_LC[wav_slice_2] = ((2.55*10**-2)
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+ * (((1.+z_obs)**1.6)
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+ * ((rest_wavs[wav_slice_2]
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+ * (1.+z_obs)/911.8)**2.1)
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+ - ((rest_wavs[wav_slice_2]
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+ * (1.+z_obs)/911.8)**3.7)))
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+
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+ else:
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+ wav_slice_1 = ((rest_wavs*(1.+z_obs) > 911.8)
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+ & (rest_wavs*(1.+z_obs) < 911.8*2.2))
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+
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+ wav_slice_2 = ((rest_wavs*(1.+z_obs) > 911.8*2.2)
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+ & (rest_wavs*(1.+z_obs) < 911.8*5.7))
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+
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+ wav_slice_3 = ((rest_wavs*(1.+z_obs) > 911.8*5.7)
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+ & (rest_wavs*(1.+z_obs) < 911.8*(1.+z_obs)))
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+
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+ tau_LAF_LC[wav_slice_1] = (((5.22*10**-4)*((1+z_obs)**3.4)
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+ * (rest_wavs[wav_slice_1]
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+ * (1.+z_obs)/911.8)**2.1)
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+ + (0.325*(rest_wavs[wav_slice_1]
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+ * (1.+z_obs)/911.8)**1.2)
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+ - ((3.14*10**-2)*((rest_wavs[wav_slice_1]
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+ * (1.+z_obs)/911.8)**2.1)))
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+
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+ tau_LAF_LC[wav_slice_2] = (((5.22*10**-4)*((1+z_obs)**3.4)
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+ * (rest_wavs[wav_slice_2]
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+ * (1.+z_obs)/911.8)**2.1)
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+ + (0.218*((rest_wavs[wav_slice_2]
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+ * (1.+z_obs)/911.8)**2.1))
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+ - ((2.55*10**-2)*((rest_wavs[wav_slice_2]
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+ * (1.+z_obs)
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+ / 911.8)**3.7)))
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+
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+ tau_LAF_LC[wav_slice_3] = ((5.22*10**-4)
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+ * (((1+z_obs)**3.4)
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+ * (rest_wavs[wav_slice_3]
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+ * (1.+z_obs)/911.8)**2.1
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+ - (rest_wavs[wav_slice_3]
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+ * (1.+z_obs)/911.8)**5.5))
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+
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+ # Populate tau_DLA_LC
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+ if z_obs < 2.0:
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+ wav_slice = ((rest_wavs*(1.+z_obs) > 911.8)
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+ & (rest_wavs*(1.+z_obs) < 911.8*(1.+z_obs)))
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+
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+ tau_DLA_LC[wav_slice] = (0.211*((1+z_obs)**2.)
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+ - (7.66*10**-2)*(((1+z_obs)**2.3)
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+ * (rest_wavs[wav_slice]
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+ * (1.+z_obs)/911.8)**-0.3)
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+ - 0.135*((rest_wavs[wav_slice]
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+ * (1.+z_obs)/911.8)**2.0))
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+
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+ else:
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+ wav_slice_1 = ((rest_wavs*(1.+z_obs) > 911.8)
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+ & (rest_wavs*(1.+z_obs) < 911.8*3.0))
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+
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+ wav_slice_2 = ((rest_wavs*(1.+z_obs) > 911.8*3.0)
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+ & (rest_wavs*(1.+z_obs) < 911.8*(1.+z_obs)))
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+
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+ tau_DLA_LC[wav_slice_1] = (0.634 + (4.7*10**-2)*(1.+z_obs)**3.
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+ - ((1.78*10**-2)*((1.+z_obs)**3.3)
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+ * (rest_wavs[wav_slice_1]
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+ * (1.+z_obs)/911.8)**-0.3)
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+ - (0.135*(rest_wavs[wav_slice_1]
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+ * (1.+z_obs)/911.8)**2.0)
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+ - 0.291*(rest_wavs[wav_slice_1]
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+ * (1.+z_obs)/911.8)**-0.3)
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+
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+ tau_DLA_LC[wav_slice_2] = ((4.7*10**-2)*(1.+z_obs)**3.
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+ - ((1.78*10**-2)*((1.+z_obs)**3.3)
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+ * (rest_wavs[wav_slice_2]
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+ * (1.+z_obs)/911.8)**-0.3)
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+ - ((2.92*10**-2)
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+ * (rest_wavs[wav_slice_2]
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+ * (1.+z_obs)/911.8)**3.0))
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+
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+ tau_LAF_LS_sum = np.sum(tau_LAF_LS, axis=0)
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+ tau_DLA_LS_sum = np.sum(tau_DLA_LS, axis=0)
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+
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+ tau = tau_LAF_LS_sum + tau_DLA_LS_sum + tau_LAF_LC + tau_DLA_LC
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+
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+ return np.exp(-tau)
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+
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+
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+ def make_table(z_array, rest_wavs):
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+ """ Make up the igm absorption table used by bagpipes. """
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+
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+ print("BAGPIPES: Generating IGM absorption table.")
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+
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+ d_IGM_grid = np.zeros((z_array.shape[0], rest_wavs.shape[0]))
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+
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+ for i in range(z_array.shape[0]):
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+ d_IGM_grid[i, :] = get_Inoue14_trans(rest_wavs, z_array[i])
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+
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+ hdulist = fits.HDUList(hdus=[fits.PrimaryHDU(),
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+ fits.ImageHDU(name="trans", data=d_IGM_grid),
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+ fits.ImageHDU(name="wavs", data=rest_wavs),
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+ fits.ImageHDU(name="zred", data=z_array)])
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+
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+ if os.path.exists("d_igm_grid_inoue14.fits"):
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+ os.system("rm " + "d_igm_grid_inoue14.fits")
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+
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+ hdulist.writeto("d_igm_grid_inoue14.fits")
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+
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+
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+ make_table(igm_redshifts, igm_wavelengths)
chanter/utils/make_ssp_grid/ascii_files/bintoascii.py ADDED
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+ import sys
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+ import os
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+ import glob
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+
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+ bins = [f for f in sorted(glob.glob(f'CHANTER/Miles_Atlas/Chabrier_IMF/*ised'))]
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+
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+
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+ for i in bins:
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+ os.system('$bc03/ascii_ised ~/Desktop/research/' + i)
chanter/utils/make_ssp_grid/csv_to_fits.py ADDED
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+ import numpy as np
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+ from astropy.table import Table
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+ import pandas as pd
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+ import matplotlib.pyplot as plt
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+ from astropy.io import fits
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+
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+
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+ base22 = np.genfromtxt('/Users/struanstevenson/Desktop/research/CHANTER/ssp/m22_ssp.csv', delimiter=',')
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+ base32 = np.genfromtxt('/Users/struanstevenson/Desktop/research/CHANTER/ssp/m32_ssp.csv', delimiter=',')
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+ base42 = np.genfromtxt('/Users/struanstevenson/Desktop/research/CHANTER/ssp/m42_ssp.csv', delimiter=',')
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+ base52 = np.genfromtxt('/Users/struanstevenson/Desktop/research/CHANTER/ssp/m52_ssp.csv', delimiter=',')
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+ base62 = np.genfromtxt('/Users/struanstevenson/Desktop/research/CHANTER/ssp/m62_ssp.csv', delimiter=',')
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+ base72 = np.genfromtxt('/Users/struanstevenson/Desktop/research/CHANTER/ssp/m72_ssp.csv', delimiter=',')
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+ base82 = np.genfromtxt('/Users/struanstevenson/Desktop/research/CHANTER/ssp/m82_ssp.csv', delimiter=',')
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+
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+ master_base = np.array((base22, base32, base42, base52, base62, base72, base82))
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+
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+ hdul = fits.HDUList()
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+ hdul.append(fits.PrimaryHDU())
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+
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+ for img in master_base:
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+ hdul.append(fits.ImageHDU(data=img))
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+
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+ hdul.writeto('/Users/struanstevenson/Desktop/research/CHANTER/ssp/ssps.fits')
chanter/utils/make_ssp_grid/get_ssp.py ADDED
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+ import numpy as np
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+ from astropy.table import Table
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+ import pandas as pd
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+ import matplotlib.pyplot as plt
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+
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+ def get_ssp(ascii_file):
7
+
8
+
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+ ages = pd.read_table(ascii_file, sep='\s+', nrows=1, header=None, dtype='float')
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+ ages = ages.to_numpy()[0][1:]
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+ ages_df = pd.DataFrame(ages, columns=['age'])
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+
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+ waves = pd.read_table(ascii_file, sep='\s+', skiprows=6, nrows=1, header=None, dtype='float')
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+ waves = waves.drop(waves.columns[0], axis=1)
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+
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+ flux = pd.read_table(ascii_file, sep='\s+', skiprows=7, nrows=221, header=None)
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+ flux = flux.drop(flux.columns[0], axis=1)
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+ flux = flux.drop(flux.columns[-53:], axis=1)
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+ flux.columns = waves.to_numpy()[0]
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+
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+
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+ base = ages_df.join(flux)
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+
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+ return base
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+
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+ specs = ['m22', 'm32', 'm42', 'm52', 'm62', 'm72', 'm82']
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+
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+
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+ for spec in specs:
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+ df = get_ssp('/Users/struanstevenson/Desktop/research/CHANTER/ssp/ascii_files/bc2003_hr_xmiless_'+spec+'_chab_ssp.ised_ASCII')
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+ #df.to_csv('./CHANTER/ssp/'+spec+'_ssp.csv', index=False)
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+
chanter/utils/make_ssp_grid/load_fits_test.py ADDED
@@ -0,0 +1,8 @@
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+ import numpy as np
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+ from astropy.table import Table
3
+ import pandas as pd
4
+ import matplotlib.pyplot as plt
5
+ from astropy.io import fits
6
+
7
+ hdul = fits.open('output.fits')
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+ print(hdul[7].data)