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final pass at header styling & minor bug fixes
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@ajmejia
ajmejia committed Dec 3, 2024
1 parent 03cdf1d commit 74f18dc
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54 changes: 27 additions & 27 deletions python/lvmdrp/core/sky.py
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Original file line number Diff line number Diff line change
Expand Up @@ -246,9 +246,9 @@ def skymodel_pars_header(header):
skymodel_pars: dict
output dict with header keywords, values and comments
None/NAN/Null values replaced with -999
"""

# extract useful header information
sci_ra, sci_dec = header["TESCIRA"], header["TESCIDE"]
skye_ra, skye_dec = header["TESKYERA"], header["TESKYEDE"]
Expand Down Expand Up @@ -325,7 +325,7 @@ def skymodel_pars_header(header):

# Moon illumination fraction
moon_fli = m.fraction_illuminated(sun)

# altitude of sun ('altsun', -90 -- 90)
altsun, _, _ = s.altaz()

Expand Down Expand Up @@ -387,37 +387,37 @@ def skymodel_pars_header(header):


skymodel_pars = {
"HIERARCH SKYMODEL SM_H": (sm_h.to(u.km).value, "observatory height in km"),
"HIERARCH SKYMODEL SM_HMIN": ((2.0 * u.km).value, "lower height limit in km"),
"HIERARCH SKYMODEL SCI_ALT": (np.round(sci_alt.to(u.deg).value, 4), "altitude of object above horizon (deg)"),
"HIERARCH SKYMODEL SKYE_ALT": (np.round(skye_alt.to(u.deg).value, 4), "altitude of object above horizon (deg)"),
"HIERARCH SKYMODEL SKYW_ALT": (np.round(skyw_alt.to(u.deg).value, 4), "altitude of object above horizon (deg)"),
"HIERARCH SKYMODEL ALPHA": (np.round(alpha.to(u.deg).value, 4), "separation of Sun and Moon from Earth (deg)"),
"HIERARCH SKYMODEL SCI_RHO": (np.round(sci_rho.to(u.deg).value, 4), "separation of Moon and object (deg)"),
"HIERARCH SKYMODEL SKYE_RHO": (np.round(skye_rho.to(u.deg).value, 4), "separation of Moon and object (deg)"),
"HIERARCH SKYMODEL SKYW_RHO": (np.round(skyw_rho.to(u.deg).value, 4), "separation of Moon and object (deg)"),
"HIERARCH SKYMODEL MOONALT": (np.round(altmoon.to(u.deg).value, 4), "altitude of Moon above horizon (deg)"),
"HIERARCH SKYMODEL SUNALT": (np.round(altsun.to(u.deg).value, 4), "altitude of Sun above horizon (deg)"),
"HIERARCH SKYMODEL SM_H": (sm_h.to(u.km).value, "observatory height [km]"),
"HIERARCH SKYMODEL SM_HMIN": ((2.0 * u.km).value, "lower height limit [km]"),
"HIERARCH SKYMODEL SCI_ALT": (np.round(sci_alt.to(u.deg).value, 4), "altitude of object above horizon [deg]"),
"HIERARCH SKYMODEL SKYE_ALT": (np.round(skye_alt.to(u.deg).value, 4), "altitude of object above horizon [deg]"),
"HIERARCH SKYMODEL SKYW_ALT": (np.round(skyw_alt.to(u.deg).value, 4), "altitude of object above horizon [deg]"),
"HIERARCH SKYMODEL ALPHA": (np.round(alpha.to(u.deg).value, 4), "separation of Sun and Moon from Earth [deg]"),
"HIERARCH SKYMODEL SCI_RHO": (np.round(sci_rho.to(u.deg).value, 4), "separation of Moon and object [deg]"),
"HIERARCH SKYMODEL SKYE_RHO": (np.round(skye_rho.to(u.deg).value, 4), "separation of Moon and object [deg]"),
"HIERARCH SKYMODEL SKYW_RHO": (np.round(skyw_rho.to(u.deg).value, 4), "separation of Moon and object [deg]"),
"HIERARCH SKYMODEL MOONALT": (np.round(altmoon.to(u.deg).value, 4), "altitude of Moon above horizon [deg]"),
"HIERARCH SKYMODEL SUNALT": (np.round(altsun.to(u.deg).value, 4), "altitude of Sun above horizon [deg]"),
"HIERARCH SKYMODEL MOONDIST": (np.round(moondist.value, 4), "distance to Moon (mean distance=1)"),
"HIERARCH SKYMODEL PRES": ((744 * u.hPa).value, "pressure at observer altitude (hPa), set: 744"),
"HIERARCH SKYMODEL PRES": ((744 * u.hPa).value, "pressure at observer altitude, set: 744 [hPa]"),
"HIERARCH SKYMODEL SSA": (0.97, "aerosols' single scattering albedo, set: 0.97"),
"HIERARCH SKYMODEL CALCDS": ( "N", "cal double scattering of moon (Y or N)"),
"HIERARCH SKYMODEL O2COLUMN": (1.0, "relative ozone column density (1->258 DU)"),
"HIERARCH SKYMODEL CALCDS": ( "N", "cal double scattering of Moon (Y or N)"),
"HIERARCH SKYMODEL O2COLUMN": (1.0, "relative ozone column density (1->258) [DU]"),
"HIERARCH SKYMODEL MOONSCAL": (1.0, "scaling factor for scattered moonlight"),
"HIERARCH SKYMODEL SCI_LON_ECL": (np.round(sci_lon_ecl.to(u.deg).value, 5), "heliocen ecliptic longitude (deg)"),
"HIERARCH SKYMODEL SCI_LAT_ECL": (np.round(sci_lat_ecl.to(u.deg).value, 5), "ecliptic latitude (deg)"),
"HIERARCH SKYMODEL SKYE_LON_ECL": (np.round(skye_lon_ecl.to(u.deg).value, 5), "heliocen ecliptic longitude (deg)"),
"HIERARCH SKYMODEL SKYE_LAT_ECL": (np.round(skye_lat_ecl.to(u.deg).value, 5), "ecliptic latitude (deg)"),
"HIERARCH SKYMODEL SKYW_LON_ECL": (np.round(skyw_lon_ecl.to(u.deg).value, 5), "heliocen ecliptic longitude (deg)"),
"HIERARCH SKYMODEL SKYW_LAT_ECL": (np.round(skyw_lat_ecl.to(u.deg).value, 5), "ecliptic latitude (deg)"),
"HIERARCH SKYMODEL SCI_LON_ECL": (np.round(sci_lon_ecl.to(u.deg).value, 5), "heliocen ecliptic longitude [deg]"),
"HIERARCH SKYMODEL SCI_LAT_ECL": (np.round(sci_lat_ecl.to(u.deg).value, 5), "ecliptic latitude [deg]"),
"HIERARCH SKYMODEL SKYE_LON_ECL": (np.round(skye_lon_ecl.to(u.deg).value, 5), "heliocen ecliptic longitude [deg]"),
"HIERARCH SKYMODEL SKYE_LAT_ECL": (np.round(skye_lat_ecl.to(u.deg).value, 5), "ecliptic latitude [deg]"),
"HIERARCH SKYMODEL SKYW_LON_ECL": (np.round(skyw_lon_ecl.to(u.deg).value, 5), "heliocen ecliptic longitude [deg]"),
"HIERARCH SKYMODEL SKYW_LAT_ECL": (np.round(skyw_lat_ecl.to(u.deg).value, 5), "ecliptic latitude [deg]"),
"HIERARCH SKYMODEL EMIS_STR": (0.2, "grey-body emissivity"),
"HIERARCH SKYMODEL TEMP_STR": ((290.0 * u.K).value, "grey-body temperature (K)"),
"HIERARCH SKYMODEL TEMP_STR": ((290.0 * u.K).value, "grey-body temperature [K]"),
"HIERARCH SKYMODEL MSOLFLUX": (130.0, "monthly-averaged solar radio flux, set: 130"),
"HIERARCH SKYMODEL SEASON": (season, "bimonthly period (1:Dec/Jan, 6:Oct/Nov.; 0:year)"),
"HIERARCH SKYMODEL TIME": (time, "period of night (x/3 night, x=1,2,3; 0:night)"),
"HIERARCH SKYMODEL MOON_RA": (np.round(moonra.to(u.deg).value, 5), "RA of the moon (deg)"),
"HIERARCH SKYMODEL MOON_DEC": (np.round(moondec.to(u.deg).value, 5), "DEC of the moon (deg)"),
"HIERARCH SKYMODEL MOON_PHASE": (np.round(moon_phase, 2), "Phase of moon (deg; 0=new, 90=1st qt)"),
"HIERARCH SKYMODEL MOON_RA": (np.round(moonra.to(u.deg).value, 5), "RA of the Moon [deg]"),
"HIERARCH SKYMODEL MOON_DEC": (np.round(moondec.to(u.deg).value, 5), "DEC of the Moon [deg]"),
"HIERARCH SKYMODEL MOON_PHASE": (np.round(moon_phase, 2), "phase of Moon (0=new, 90=1st qt) [deg]"),
"HIERARCH SKYMODEL MOON_FLI": (np.round(moon_fli, 4), "Moon fraction lunar illumination")
}

Expand Down
20 changes: 10 additions & 10 deletions python/lvmdrp/functions/fluxCalMethod.py
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Original file line number Diff line number Diff line change
Expand Up @@ -267,7 +267,7 @@ def standard_sensitivity(stds, rss, GAIA_CACHE_DIR, ext, res, plot=False, width=
# update input file header
label = channel.upper()
rss.setHdrValue(f"STD{nn}{label}AB", mAB_std, f"Gaia AB mag in {channel}-band")
rss.setHdrValue(f"STD{nn}{label}IN", mAB_obs, f"Obs AB mag in {channel}-band")
rss.setHdrValue(f"STD{nn}{label}IN", mAB_obs, f"obs AB mag in {channel}-band")
log.info(f"AB mag in LVM_{channel}: Gaia {mAB_std:.2f}, instrumental {mAB_obs:.2f}")

if plot:
Expand Down Expand Up @@ -372,11 +372,11 @@ def science_sensitivity(rss, res_sci, ext, GAIA_CACHE_DIR, NSCI_MAX=15, r_spaxel
# update input file header
cam = channel.upper()
rss.setHdrValue(f"SCI{i+1}{cam}AB", mAB_std, f"Gaia AB mag in {channel}-band")
rss.setHdrValue(f"SCI{i+1}{cam}IN", mAB_obs, f"Obs AB mag in {channel}-band")
rss.setHdrValue(f"SCI{i+1}ID", data['source_id'], f"Field star {i+1} Gaia source ID")
rss.setHdrValue(f"SCI{i+1}FIB", scifibs['fiberid'][fib][0], f"Field star {i+1} fiber id")
rss.setHdrValue(f"SCI{i+1}RA", data['ra'], f"Field star {i+1} RA")
rss.setHdrValue(f"SCI{i+1}DE", data['dec'], f"Field star {i+1} DEC")
rss.setHdrValue(f"SCI{i+1}{cam}IN", mAB_obs, f"obs AB mag in {channel}-band")
rss.setHdrValue(f"SCI{i+1}ID", data['source_id'], f"field star {i+1} Gaia source ID")
rss.setHdrValue(f"SCI{i+1}FIB", scifibs['fiberid'][fib][0], f"field star {i+1} fiber id")
rss.setHdrValue(f"SCI{i+1}RA", data['ra'], f"field star {i+1} RA")
rss.setHdrValue(f"SCI{i+1}DE", data['dec'], f"field star {i+1} DEC")
log.info(f"AB mag in LVM_{channel}: Gaia {mAB_std:.2f}, instrumental {mAB_obs:.2f}")

# calibrate and plot against the stars for debugging:
Expand Down Expand Up @@ -461,8 +461,8 @@ def fluxcal_standard_stars(in_rss, plot=True, GAIA_CACHE_DIR=None):

label = rss._header['CCD']
channel = label.lower()
rss.setHdrValue(f"STDSENM{label}", np.nanmean(mean_std[1000:3000]), f"Mean stdstar sensitivity in {channel}")
rss.setHdrValue(f"STDSENR{label}", np.nanmean(rms_std[1000:3000]), f"Mean stdstar sensitivity rms in {channel}")
rss.setHdrValue(f"STDSENM{label}", np.nanmean(mean_std[1000:3000]), f"mean stdstar sensitivity in {channel}")
rss.setHdrValue(f"STDSENR{label}", np.nanmean(rms_std[1000:3000]), f"mean stdstar sensitivity rms in {channel}")
log.info(f"Mean stdstar sensitivity in {channel} : {np.nanmean(mean_std[1000:3000])}")

if plot:
Expand Down Expand Up @@ -537,8 +537,8 @@ def fluxcal_sci_ifu_stars(in_rss, plot=True, GAIA_CACHE_DIR=None, NSCI_MAX=15):
rms_sci_band = np.nanmean(rms_sci[1000:3000])
mean_sci_band = -999.9 if np.isnan(mean_sci_band) else mean_sci_band
rms_sci_band = -999.9 if np.isnan(rms_sci_band) else rms_sci_band
rss.setHdrValue(f"SCISENM{label}", mean_sci_band, f"Mean scistar sensitivity in {channel}")
rss.setHdrValue(f"SCISENR{label}", rms_sci_band, f"Mean scistar sensitivity rms in {channel}")
rss.setHdrValue(f"SCISENM{label}", mean_sci_band, f"mean scistar sensitivity in {channel}")
rss.setHdrValue(f"SCISENR{label}", rms_sci_band, f"mean scistar sensitivity rms in {channel}")
log.info(f"Mean scistar sensitivity in {channel} : {mean_sci_band}")

if plot:
Expand Down
18 changes: 9 additions & 9 deletions python/lvmdrp/functions/imageMethod.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2732,15 +2732,15 @@ def extract_spectra(
rss.setHdrValue("NAXIS2", data.shape[0])
rss.setHdrValue("NAXIS1", data.shape[1])
rss.setHdrValue("DISPAXIS", 1, "axis of spectral dispersion")
rss.setHdrValue(f"HIERARCH {camera.upper()} FIBER CENT_MIN", numpy.round(bn.nanmin(trace_mask._data),4), "min. fiber centroid")
rss.setHdrValue(f"HIERARCH {camera.upper()} FIBER CENT_MAX", numpy.round(bn.nanmax(trace_mask._data),4), "max. fiber centroid")
rss.setHdrValue(f"HIERARCH {camera.upper()} FIBER CENT_AVG", numpy.round(bn.nanmean(trace_mask._data),4), "avg. fiber centroid")
rss.setHdrValue(f"HIERARCH {camera.upper()} FIBER CENT_STD", numpy.round(bn.nanstd(trace_mask._data),4), "stddev. fiber centroid")
rss.setHdrValue(f"HIERARCH {camera.upper()} FIBER CENT_MIN", numpy.round(bn.nanmin(trace_mask._data),4), "min. fiber centroid [pix]")
rss.setHdrValue(f"HIERARCH {camera.upper()} FIBER CENT_MAX", numpy.round(bn.nanmax(trace_mask._data),4), "max. fiber centroid [pix]")
rss.setHdrValue(f"HIERARCH {camera.upper()} FIBER CENT_AVG", numpy.round(bn.nanmean(trace_mask._data),4), "avg. fiber centroid [pix]")
rss.setHdrValue(f"HIERARCH {camera.upper()} FIBER CENT_STD", numpy.round(bn.nanstd(trace_mask._data),4), "stddev. fiber centroid [pix]")
if method == "optimal":
rss.setHdrValue(f"HIERARCH {camera.upper()} FIBER WIDTH_MIN", numpy.round(bn.nanmin(trace_fwhm._data),4), "min. fiber width")
rss.setHdrValue(f"HIERARCH {camera.upper()} FIBER WIDTH_MAX", numpy.round(bn.nanmax(trace_fwhm._data),4), "max. fiber width")
rss.setHdrValue(f"HIERARCH {camera.upper()} FIBER WIDTH_AVG", numpy.round(bn.nanmean(trace_fwhm._data),4), "avg. fiber width")
rss.setHdrValue(f"HIERARCH {camera.upper()} FIBER WIDTH_STD", numpy.round(bn.nanstd(trace_fwhm._data),4), "stddev. fiber width")
rss.setHdrValue(f"HIERARCH {camera.upper()} FIBER WIDTH_MIN", numpy.round(bn.nanmin(trace_fwhm._data),4), "min. fiber width [pix]")
rss.setHdrValue(f"HIERARCH {camera.upper()} FIBER WIDTH_MAX", numpy.round(bn.nanmax(trace_fwhm._data),4), "max. fiber width [pix]")
rss.setHdrValue(f"HIERARCH {camera.upper()} FIBER WIDTH_AVG", numpy.round(bn.nanmean(trace_fwhm._data),4), "avg. fiber width [pix]")
rss.setHdrValue(f"HIERARCH {camera.upper()} FIBER WIDTH_STD", numpy.round(bn.nanstd(trace_fwhm._data),4), "stddev. fiber width [pix]")

rss.add_header_comment(f"{in_trace}, fiber centroids used for {camera}")
rss.add_header_comment(f"{in_fwhm}, fiber width (FWHM) used for {camera}")
Expand Down Expand Up @@ -3801,7 +3801,7 @@ def detrend_frame(
# reject cosmic rays
if reject_cr:
log.info("rejecting cosmic rays")
rdnoise = detrended_img.getHdrValue("AMP1 RDNOISE")
rdnoise = detrended_img.getHdrValue(f"{camera.upper()} AMP1 RDNOISE")
detrended_img.reject_cosmics(gain=1.0, rdnoise=rdnoise, rlim=1.3, iterations=5, fwhm_gauss=[2.75, 2.75],
replace_box=[10,2], replace_error=1e6, verbose=True, inplace=True)

Expand Down
6 changes: 3 additions & 3 deletions python/lvmdrp/functions/rssMethod.py
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Original file line number Diff line number Diff line change
Expand Up @@ -798,9 +798,9 @@ def shift_wave_skylines(in_frame: str, out_frame: str, dwave: float = 8.0, skyli
meanoffset = numpy.nan_to_num(meanoffset)
log.info(f'Applying the offsets [Angstroms] in [1,2,3] spectrographs with means: {meanoffset}')
lvmframe._wave_trace['COEFF'].data[:,0] -= fiber_offset_mod
lvmframe._header[f'HIERARCH {channel.upper()}1 WAVE SKYOFF'] = (meanoffset[0], f'avg. sky line offset in {channel}1 [angstrom]')
lvmframe._header[f'HIERARCH {channel.upper()}2 WAVE SKYOFF'] = (meanoffset[1], f'avg. sky line offset in {channel}2 [angstrom]')
lvmframe._header[f'HIERARCH {channel.upper()}3 WAVE SKYOFF'] = (meanoffset[2], f'avg. sky line offset in {channel}3 [angstrom]')
lvmframe._header[f'HIERARCH {channel.upper()}1 WAVE SKYOFF'] = (meanoffset[0], f'avg. sky line offset in {channel}1 [Angstrom]')
lvmframe._header[f'HIERARCH {channel.upper()}2 WAVE SKYOFF'] = (meanoffset[1], f'avg. sky line offset in {channel}2 [Angstrom]')
lvmframe._header[f'HIERARCH {channel.upper()}3 WAVE SKYOFF'] = (meanoffset[2], f'avg. sky line offset in {channel}3 [Angstrom]')

wave_trace = TraceMask.from_coeff_table(lvmframe._wave_trace)
lvmframe._wave = wave_trace.eval_coeffs()
Expand Down
10 changes: 4 additions & 6 deletions python/lvmdrp/functions/skyMethod.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1444,13 +1444,13 @@ def interpolate_sky( in_frame: str, out_rss: str = None, display_plots: bool = F
# TODO: add same parameters for std *fibers*

new_rss._header["HIERARCH GEOCORONAL SKYW_SH_HGHT"] = (
np.round(get_telescope_shadowheight(new_rss._header, telescope="SKYW"), 5), "height of Earth's shadow (km)"
np.round(get_telescope_shadowheight(new_rss._header, telescope="SKYW"), 5), "height of Earth's shadow [km]"
)
new_rss._header["HIERARCH GEOCORONAL SKYE_SH_HGHT"] = (
np.round(get_telescope_shadowheight(new_rss._header, telescope="SKYE"), 5), "height of Earth's shadow (km)"
np.round(get_telescope_shadowheight(new_rss._header, telescope="SKYE"), 5), "height of Earth's shadow [km]"
)
new_rss._header["HIERARCH GEOCORONAL SCI_SH_HGHT"] = (
np.round(get_telescope_shadowheight(new_rss._header, telescope="SCI"), 5), "height of Earth's shadow (km)"
np.round(get_telescope_shadowheight(new_rss._header, telescope="SCI"), 5), "height of Earth's shadow [km]"
)

# write output RSS
Expand Down Expand Up @@ -1541,8 +1541,6 @@ def combine_skies(in_rss: str, out_rss, sky_weights: Tuple[float, float] = None)

# write output sky-subtracted RSS
log.info(f"writing output RSS file '{os.path.basename(out_rss)}'")
rss.appendHeader(sky_e._header["SKYMODEL*"])
rss.appendHeader(sky_e._header["GEOCORONAL*"])
rss.setHdrValue("SKYEW", w_e, "SkyE weight for STD star sky subtraction")
rss.setHdrValue("SKYWW", w_w, "SkyW weight for STD star sky subtraction")
rss.set_sky(sky_east=sky_e._data, sky_east_error=sky_e._error,
Expand Down Expand Up @@ -1608,7 +1606,7 @@ def quick_sky_subtraction(in_cframe, out_sframe, skymethod: str = 'farlines_near
log.info(f"loading {in_cframe} for sky subtraction")

cframe = lvmCFrame.from_file(in_cframe)

# read sky table hdu
sky_hdu = prep_input_simplesky_mean(in_cframe)

Expand Down
2 changes: 1 addition & 1 deletion python/lvmdrp/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -885,7 +885,7 @@ def build_supersky(tileid: int, mjd: int, expnum: int, imagetype: str) -> fits.B
spec.extend([specid] * (nsam_e + nsam_w))
telescope.extend(["east"] * nsam_e + ["west"] * nsam_w)
sort_idx = np.argsort(sky_wave)
wave_c = fits.Column(name="wave", array=np.array(sky_wave)[sort_idx], unit="angstrom", format="E")
wave_c = fits.Column(name="wave", array=np.array(sky_wave)[sort_idx], unit="Angstrom", format="E")
sky_c = fits.Column(name="sky", array=np.array(sky)[sort_idx], unit=fsci._header["BUNIT"], format="E")
sky_error_c = fits.Column(name="sky_error", array=np.array(sky_error)[sort_idx], unit=fsci._header["BUNIT"], format="E")
fiberidx_c = fits.Column(name="fiberidx", array=np.array(fiberidx)[sort_idx], format="J")
Expand Down

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