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knolan10 merged 1 commit into from
Jul 2, 2026
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organize redback work #13

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2 changes: 2 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
# data (catalogs, simulations, rubin alerts)
data/
docs/notebooks/tidal_disruption_event/
docs/notebooks/redback_inference

# Byte-compiled / optimized / DLL files
__pycache__/
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233 changes: 83 additions & 150 deletions docs/notebooks/Develop_Redback_Simulations.ipynb
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Expand Up @@ -4,11 +4,9 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# redback simulations\n",
"# Redback Simulations\n",
"\n",
"use redback to simulate tdes and other transients at different redshifts\n",
"\n",
"https://redback.readthedocs.io/en/latest/simulation.html#examples"
"Use [redback](https://redback.readthedocs.io/en/latest/simulation.html#examples) to simulate TDEs and other transients at different redshifts."
]
},
{
Expand All @@ -17,6 +15,13 @@
"metadata": {},
"outputs": [],
"source": [
"import warnings\n",
"# Suppress SyntaxWarnings from invalid escape sequences in redback/bilby source files\n",
"warnings.filterwarnings('ignore', category=SyntaxWarning)\n",
"# Suppress optional-dependency warnings from redback (lalsimulation, swifttools)\n",
"warnings.filterwarnings('ignore', message='.*lalsimulation.*')\n",
"warnings.filterwarnings('ignore', message='.*swifttools.*')\n",
"\n",
"import numpy as np\n",
"import pandas as pd\n",
"import os\n",
Expand All @@ -27,9 +32,7 @@
"import matplotlib \n",
"from matplotlib import rcParams\n",
"rcParams[\"font.family\"] = \"Liberation Serif\"\n",
"matplotlib.rcParams['text.usetex'] = False \n",
"\n",
"# FIXME LALsimulation not installed"
"matplotlib.rcParams['text.usetex'] = False"
]
},
{
Expand All @@ -38,9 +41,7 @@
"source": [
"## Fetch real object photometry\n",
"\n",
"https://redback.readthedocs.io/en/latest/getting_data.html\n",
"\n",
"redback has built in tools to get data from open access, otter catalogs and fink and lasair brokers"
"redback has [built in tools to get data](https://redback.readthedocs.io/en/latest/getting_data.html) from open access, otter catalogs and fink / lasair brokers"
]
},
{
Expand Down Expand Up @@ -73,7 +74,7 @@
"tdes['maxabsmag'] = pd.to_numeric(tdes['maxabsmag'], errors='coerce') \n",
" \n",
"# print brightest \n",
"brightest = tdes[['name', 'maxabsmag']].dropna().sort_values('maxabsmag').head(20) \n",
"brightest = tdes[['name', 'maxabsmag']].dropna().sort_values('maxabsmag').head(10) \n",
"print(\"Brightest TDEs by peak absolute magnitude:\") \n",
"print(brightest.to_string(index=False)) \n",
" \n",
Expand All @@ -94,7 +95,7 @@
"metadata": {},
"outputs": [],
"source": [
"# instead of filtering for OAC TDEs, just check brightest objects\n",
"# instead of filtering for OAC TDEs, just check brightest objects in general\n",
"\n",
"oac_path = os.path.join(os.path.dirname(redback.__file__), 'tables', 'OAC_metadata.csv') \n",
"df = pd.read_csv(oac_path, low_memory=False, on_bad_lines='skip')\n",
Expand All @@ -109,10 +110,12 @@
"metadata": {},
"outputs": [],
"source": [
"# we can also use Otter to query for objects\n",
"\n",
"import otter\n",
"import numpy as np\n",
"\n",
"db = otter.Otter()\n",
"db = otter.Otter(datadir='../../data/redback_sims')\n",
"\n",
"# query for confirmed TDEs with optical photometry in one step\n",
"all_transients = db.query(classification='TDE', unambiguous=True,)# has_uvoir_phot=True)\n",
Expand All @@ -132,7 +135,7 @@
"\n",
"tdes_with_z.sort(key=lambda x: x[1], reverse=True)\n",
"\n",
"print(f\"Found {len(tdes_with_z)} confirmed TDEs with UVOIR photometry\\n\")\n",
"print(f\"Found {len(tdes_with_z)} confirmed TDEs\\n\")\n",
"print(f\"{'Rank':<6} {'Name':<25} {'Redshift'}\")\n",
"print(\"-\" * 45)\n",
"for i, (name, z) in enumerate(tdes_with_z[:15], 1):\n",
Expand All @@ -145,7 +148,9 @@
"metadata": {},
"outputs": [],
"source": [
"target_object = '2025aarm'\n",
"# check for a specific transient in the results by name\n",
"\n",
"target_object = '2019cmw'\n",
"\n",
"for t in all_transients:\n",
" name = t.get('name', {}).get('default_name', str(t))\n",
Expand All @@ -158,7 +163,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"### now load photometry for selected real objects"
"### now load photometry into redback structure for selected real objects"
]
},
{
Expand All @@ -167,27 +172,9 @@
"metadata": {},
"outputs": [],
"source": [
"# FIXME redback requires to make a directory\n",
"# also can try AT2018iih (z=0.212), AT2020ysg, AT2020acka\n",
"\n",
"# load with name\n",
"name = 'AT2019cmw'\n",
"\n",
"# redback bug fix\n",
"outdir = f'tidal_disruption_event/{name}/uvoir'\n",
"os.makedirs(outdir, exist_ok=True)\n",
"\n",
"# either load from otter (tdes only right now)\n",
"data = redback.get_data.get_tidal_disruption_event_data_from_otter(transient=name)\n",
"\n",
"# # or load tdes from open access catalog\n",
"# data = redback.get_data.get_tidal_disruption_event_data_from_open_transient_catalog_data(transient=name)\n",
"\n",
"# # or load SN from OAC\n",
"# data = redback.get_data.get_supernova_data_from_open_transient_catalog_data(transient=name)\n",
"\n",
"# # or query Fink for ZTF objects\n",
"# data = redback.get_data.get_fink_data(transient=name, transient_type='supernova')"
"import importlib\n",
"import thor.utils.redback_sims\n",
"importlib.reload(thor.utils.redback_sims)"
]
},
{
Expand All @@ -196,12 +183,12 @@
"metadata": {},
"outputs": [],
"source": [
"# can query FINK and LASAIR also\n",
"#FIXME fetch more bands of data.\n",
"\n",
"name = 'ZTF25acfyeke'\n",
"# Load with name, for example AT2019cmw, AT2018iih (z=0.212), AT2020ysg, AT2020acka\n",
"name = 'AT2020qhs'\n",
"source = 'otter'\n",
"\n",
"data = redback.get_data.get_fink_data(transient=name, transient_type='tidal_disruption_event')"
"from thor.utils.redback_sims import load_data_redback_object, create_redback_transient\n",
"data = load_data_redback_object(object_name=name, data_source=source)"
]
},
{
Expand All @@ -211,21 +198,16 @@
"outputs": [],
"source": [
"# create redback transient object from loaded data\n",
"exclude_bands = ['W2', 'M2', 'W1', 'U']\n",
"bands=data['band'].unique() # utilize all bands available\n",
"#bands = [b for b in bands if b not in exclude_bands] # filter out non-optical bands\n",
"\n",
"# # from OTTER TDE (also downloads if not cached) \n",
"# transient_object = redback.tde.TDE.from_otter(name=name, data_mode=\"flux_density\") \n",
"\n",
"# # from OAC TDE \n",
"# transient_object = redback.tde.TDE.from_open_access_catalogue(name=name, data_mode=\"flux_density\", active_bands=bands)\n",
"\n",
"# # from OAC Supernova \n",
"# transient_object = redback.supernova.Supernova.from_open_access_catalogue(name=name, data_mode=\"flux_density\", active_bands=bands) \n",
" \n",
"# from Fink — same as OAC since they share the same processed file path \n",
"transient_object = redback.tde.TDE.from_open_access_catalogue(name=name, data_mode=\"flux_density\", active_bands=bands) "
"exclude_bands = ['W2', 'M2', 'W1', 'U'] # set exclude_bands = None # utilize all bands available\n",
"\n",
"transient_object = create_redback_transient(\n",
" object_name=name,\n",
" data_source=source,\n",
" data=data,\n",
" data_mode='flux_density',\n",
" exclude_bands=exclude_bands,\n",
" plot=True\n",
")"
]
},
{
Expand All @@ -236,17 +218,17 @@
"source": [
"# plot\n",
"\n",
"# the black points are bands available that havent be set as active \n",
"transient_object.plot_data(show=False, title=f\"{name} photometry\") \n",
"# fig, axes = plt.subplots(1,3, sharex=True, sharey=True, figsize=(12, 5)) \n",
"# object.plot_multiband(figure=fig, axes=axes, filters=[\"g'\", \"r'\", \"z'\"], show=False) "
"# the black points are bands available that havent been set as active\n",
"transient_object.plot_data(show=False, title=f\"{name} photometry\")\n",
"fig, axes = plt.subplots(1,3, sharex=True, sharey=True, figsize=(12, 5))\n",
"transient_object.plot_multiband(figure=fig, axes=axes, filters=[\"g\", \"r\", \"UVW1\"], show=False)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Warning: \n",
"Usage warning: \n",
"\n",
"- check if data are in AB or Vega system (redback assumes AB, throws away explicity flagged Vega from processed file)\n",
"\n",
Expand All @@ -256,31 +238,26 @@
]
},
{
"cell_type": "code",
"execution_count": null,
"cell_type": "markdown",
"metadata": {},
"outputs": [],
"source": [
"# FIXME automate data checks\n",
"\n",
"# check what bands the observations are in\n",
"print(\"Unique bands:\", transient_object.unique_bands) \n",
"print(\"Active bands:\", transient_object.active_bands) \n",
"\n",
"# count photometry points per band\n",
"from collections import Counter\n",
"all_counts = Counter(transient_object.bands)\n",
"print(\"\\nAll bands (including inactive):\")\n",
"for band, count in sorted(all_counts.items()):\n",
" active = band in transient_object.active_bands\n",
" print(f\" {band}: {count}\")"
"# fit model based on real photometry"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# fit model based on real photometry"
"### [Redback Models](https://redback.readthedocs.io/en/latest/models.html)\n",
"\n",
"tde model options:\n",
"Simple analytic fallback\n",
"Cooling envelope (Metzger 2022)\n",
"Gaussian rise + cooling envelope (Sarin and Metzger 2024)\n",
"Broken power law + cooling envelope (Sarin and Metzger 2024)\n",
"Fitted\n",
"TDEMass\n",
"Mosfit TDE"
]
},
{
Expand All @@ -289,16 +266,10 @@
"metadata": {},
"outputs": [],
"source": [
"# run inference to extract model best parameters\n",
"# print all the priors for a given model\n",
"\n",
"# tde model options:\n",
"# Simple analytic fallback\n",
"# Cooling envelope (Metzger 2022)\n",
"# Gaussian rise + cooling envelope (Sarin and Metzger 2024)\n",
"# Broken power law + cooling envelope (Sarin and Metzger 2024)\n",
"# Fitted\n",
"# TDEMass\n",
"# Mosfit TDE"
"priors = redback.priors.get_priors(model='tde_analytical')\n",
"priors"
]
},
{
Expand All @@ -307,73 +278,35 @@
"metadata": {},
"outputs": [],
"source": [
"sampler = 'dynesty'\n",
"model = 'tde_analytical'\n",
"nlive=500\n",
"outdir = f'redback_inference/{name}/{model}'\n",
"os.makedirs(outdir, exist_ok=True)\n",
"\n",
"# # By default all data is used, select bands for speed or if you only trust some of the data/physics.\n",
"# bands = [\"u\", \"r\"]\n",
"# transient_object.active_bands = bands\n",
"# Fit model for known object. \n",
"# depending on priors etc, this can take 20+ minutes to run.\n",
"\n",
"# start with default priors\n",
"priors = redback.priors.get_priors(model=model)\n",
"# Fix priors, ie if known through the metadata that was downloaded alongside the data\n",
"priors['redshift'] = 0.4030\n",
"# tighten temperature prior — TDE blackbodies are typically 10k-50k K at peak\n",
"priors['temperature_0'] = bilby.core.prior.Uniform(\n",
" minimum=10000, maximum=60000, name='temperature_0', latex_label='$T_0$ (K)')\n",
"# tighten radius prior around physically expected TDE photosphere size\n",
"priors['radius_0'] = bilby.core.prior.LogUniform(\n",
" minimum=1e13, maximum=1e16, name='radius_0', latex_label='$R_0$ (cm)')\n",
"\n",
"model_kwargs = dict(frequency=transient_object.filtered_frequencies, output_format='flux_density')\n",
"\n",
"# returns a tde result object\n",
"result = redback.fit_model(transient=transient_object, model=model, sampler=sampler,\n",
" model_kwargs=model_kwargs, prior=priors, sample='rslice', nlive=nlive, npool=4, \n",
" resume=True, outdir=outdir, label=f\"{name}_nlive{str(nlive)}\",\n",
" plot=False)\n",
"\n",
"# result.transient reconstructs from metadata with wrong path, use transient_object directly\n",
"model_func = redback.model_library.all_models_dict[model]\n",
"import bilby\n",
"import importlib\n",
"import thor.utils.redback_sims\n",
"importlib.reload(thor.utils.redback_sims)\n",
"from thor.utils.redback_sims import fit_redback_model\n",
"\n",
"prior_overrides = {\n",
" 'redshift': 0.4030,\n",
" # tighten temperature prior — TDE blackbodies are typically 10k-50k K at peak\n",
" 'temperature_0': bilby.core.prior.Uniform(\n",
" minimum=10000, maximum=60000, name='temperature_0', latex_label='$T_0$ (K)'),\n",
" # tighten radius prior around physically expected TDE photosphere size\n",
" 'radius_0': bilby.core.prior.LogUniform(\n",
" minimum=1e13, maximum=1e16, name='radius_0', latex_label='$R_0$ (cm)'),\n",
"}\n",
"\n",
"# plot results\n",
"result.plot_corner(save=False, show=True)\n",
"plt.show()\n",
"plt.close('all')\n",
"transient_object.plot_lightcurve(\n",
" model=model_func,\n",
" posterior=result.posterior,\n",
" model_kwargs=result.model_kwargs,\n",
" random_models=100,\n",
" save=False,\n",
" show=True,\n",
")\n",
"transient_object.plot_multiband_lightcurve(\n",
" model=model_func,\n",
" posterior=result.posterior,\n",
" model_kwargs=result.model_kwargs,\n",
" random_models=100,\n",
" filters=[\"ztfg\", \"ztfr\"],\n",
" save=False,\n",
" show=True,\n",
"result = fit_redback_model(\n",
" transient_object=transient_object,\n",
" object_name=name,\n",
" model='tde_analytical',\n",
" nlive=500,\n",
" prior_overrides=prior_overrides,\n",
" multiband_filters=['ztfg', 'ztfr'],\n",
")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# print all the priors for the fit model\n",
"\n",
"priors = redback.priors.get_priors(model='tde_analytical')\n",
"priors"
]
},
{
"cell_type": "code",
"execution_count": null,
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