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separately smooth the relative phase between the polarizations
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@jsdillon
jsdillon committed Jul 20, 2024
1 parent 479d295 commit 3f80a50
Showing 1 changed file with 74 additions and 14 deletions.
88 changes: 74 additions & 14 deletions notebooks/calibration_smoothing.ipynb
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"source": [
"# Calibration Smoothing\n",
"\n",
"**by Josh Dillon**, last updated July 15, 2023\n",
"**by Josh Dillon**, last updated July 19, 2023\n",
"\n",
"This notebook runs calibration smoothing to the gains coming out of [file_calibration](https://github.com/HERA-Team/hera_notebook_templates/blob/master/notebooks/file_calibration.ipynb) notebook. It removes any flags founds on by that notebook and replaces them with flags generated from [full_day_rfi](https://github.com/HERA-Team/hera_notebook_templates/blob/master/notebooks/full_day_rfi.ipynb) and [full_day_antenna_flagging](https://github.com/HERA-Team/hera_notebook_templates/blob/master/notebooks/full_day_antenna_flagging.ipynb). It also plots the results for a couple of antennas.\n",
"\n",
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"id": "c6ecd16f",
"metadata": {},
"source": [
"## Load files"
"## Load files and select reference antenna(s)"
]
},
{
Expand Down Expand Up @@ -135,36 +135,66 @@
{
"cell_type": "code",
"execution_count": null,
"id": "ee831559",
"id": "0976d9b5-b08c-4899-a866-8badc6d9173d",
"metadata": {},
"outputs": [],
"source": [
"cs = smooth_cal.CalibrationSmoother(cal_files, flag_file_list=(ant_flag_files + rfi_flag_files), ignore_calflags=True,\n",
" pick_refant=True, propagate_refant_flags=True, load_chisq=True, load_cspa=True, per_pol_refant=PER_POL_REFANT)\n",
"cs = smooth_cal.CalibrationSmoother(cal_files, flag_file_list=(ant_flag_files + rfi_flag_files),\n",
" ignore_calflags=True, pick_refant=False, load_chisq=True, load_cspa=True)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "4c2af8ac-efb8-4489-80f6-d0f30d8b62a8",
"metadata": {},
"outputs": [],
"source": [
"cs.refant = smooth_cal.pick_reference_antenna(cs.gain_grids, cs.flag_grids, cs.freqs, per_pol=True)\n",
"for pol in cs.refant:\n",
" print(f'Reference antenna {cs.refant[pol][0]} selected for smoothing {pol} gains.')\n",
"\n",
"if not PER_POL_REFANT:\n",
" # in this case, rephase both pols separately before smoothing, but also smooth the relative polarization calibration phasor\n",
" overall_refant = smooth_cal.pick_reference_antenna({ant: cs.gain_grids[ant] for ant in cs.refant.values()}, \n",
" {ant: cs.flag_grids[ant] for ant in cs.refant.values()}, \n",
" cs.freqs, per_pol=False)\n",
" print(f'Overall reference antenna {overall_refant} selected.')\n",
" other_refant = [ant for ant in cs.refant.values() if ant != overall_refant][0]\n",
"\n",
"if PER_POL_REFANT:\n",
" for pol in cs.refant:\n",
" print(f'Reference antenna {cs.refant[pol][0]} selected for {pol}.')\n",
"else:\n",
" print(f'Reference antenna {cs.refant[0]} selected for both polarizations.')"
" relative_pol_phasor = cs.gain_grids[overall_refant] * cs.gain_grids[other_refant].conj() # TODO: is this conjugation right?\n",
" relative_pol_phasor /= np.abs(relative_pol_phasor)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "482760b0",
"id": "9f459577-0ba2-4c55-a767-df9d10c7226d",
"metadata": {},
"outputs": [],
"source": [
"# duplicate a small number of abscal gains for plotting\n",
"antnums = set([ant[0] for ant in cs.ants])\n",
"flags_per_antnum = [np.sum(cs.flag_grids[ant, 'Jnn']) + np.sum(cs.flag_grids[ant, 'Jee']) for ant in antnums]\n",
"\n",
"refant_nums = [ant[0] for ant in (cs.refant.values() if PER_POL_REFANT else [cs.refant])]\n",
"refant_nums = [ant[0] for ant in cs.refant.values()]\n",
"candidate_ants = [ant for ant, nflags in zip(antnums, flags_per_antnum) if (ant not in refant_nums) and (nflags <= np.percentile(flags_per_antnum, 25))\n",
" and not np.all(cs.flag_grids[ant, 'Jee']) and not np.all(cs.flag_grids[ant, 'Jnn'])]\n",
"ants_to_plot = [func(candidate_ants) for func in (np.min, np.max)]\n",
"abscal_gains = {(ant, pol): np.array(cs.gain_grids[(ant, pol)]) for ant in ants_to_plot for pol in ['Jee', 'Jnn']}"
"abscal_gains = {}\n",
"for pol in ['Jee', 'Jnn']:\n",
" for antnum in ants_to_plot:\n",
" refant_here = (cs.refant[pol] if PER_POL_REFANT else overall_refant)\n",
" abscal_gains[antnum, pol] = cs.gain_grids[(antnum, pol)] * np.abs(cs.gain_grids[refant_here]) / cs.gain_grids[refant_here]"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "ff18e5a9-23e5-41f5-ab0b-35f09ab67404",
"metadata": {},
"outputs": [],
"source": [
"cs.rephase_to_refant(propagate_refant_flags=True)"
]
},
{
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"## Perform smoothing"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "178ce9a5-570e-4cbc-a7d0-978da71033a6",
"metadata": {},
"outputs": [],
"source": [
"if not PER_POL_REFANT:\n",
" # treat the relative_pol_phasor as if it were antenna -1\n",
" cs.gain_grids[(-1, other_refant[1])] = relative_pol_phasor\n",
" cs.flag_grids[(-1, other_refant[1])] = cs.flag_grids[overall_refant] | cs.flag_grids[other_refant]"
]
},
{
"cell_type": "code",
"execution_count": null,
Expand All @@ -186,6 +229,23 @@
" method='DPSS', fit_method='lu_solve', fix_phase_flips=True, flag_phase_flip_ints=True)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "10ff0705-f3fd-4570-b47a-e96e360d183c",
"metadata": {},
"outputs": [],
"source": [
"if not PER_POL_REFANT:\n",
" # put back in the smoothed phasor, ensuring the amplitude is 1 and that data are flagged anywhere either polarization's refant is flagged\n",
" smoothed_relative_pol_phasor = cs.gain_grids[(-1, other_refant[-1])] / np.abs(cs.gain_grids[(-1, other_refant[-1])])\n",
" for ant in cs.gain_grids:\n",
" if ant[0] >= 0 and ant[1] == other_refant[1]:\n",
" cs.gain_grids[ant] /= smoothed_relative_pol_phasor\n",
" cs.flag_grids[ant] |= (cs.flag_grids[(-1, other_refant[1])])\n",
" cs.refant = overall_refant"
]
},
{
"cell_type": "markdown",
"id": "c40160e2",
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