Add derived quantities from Sharma2024

CLAUDE.md

@@ -0,0 +1,74 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+FRB is a Python package for Fast Radio Burst (FRB) calculations, observations, estimations, and analysis. It provides tools for DM (Dispersion Measure) calculations, host galaxy analysis, FRB-galaxy associations, and survey data handling.
+
+## Build and Test Commands
+
+```bash
+# Install dependencies
+pip install -r frb/requirements.txt
+pip install git+https://github.com/FRBs/ne2001.git#egg=ne2001
+pip install git+https://github.com/FRBs/astropath.git#egg=astropath
+pip install git+https://github.com/linetools/linetools#egg=linetools
+
+# Install package in development mode
+pip install -e .
+
+# Run all tests
+pytest --pyargs frb
+
+# Run specific test file
+pytest frb/tests/test_frb.py
+
+# Run with tox (specific Python version)
+tox -e 3.11-test
+
+# Run with coverage
+tox -e 3.11-test-cov
+```
+
+## Architecture
+
+### Core Classes
+
+- **`frb.frb.FRB`**: Main class representing an observed FRB event. Load by name with `FRB.by_name('FRB20121102A')`. Contains coordinates, DM, RM, redshift, and links to host galaxies.
+
+- **`frb.galaxies.frbgalaxy.FRBGalaxy`** / **`FRBHost`**: Classes for galaxies in FRB fields and confirmed host galaxies. Store photometry, redshifts, morphology, and derived properties.
+
+- **`frb.associate.frbassociate.FRBAssociate`**: Extends the astropath PATH class for probabilistic FRB-galaxy association analysis.
+
+### Key Modules
+
+- **`frb/dm/`**: Dispersion measure calculations
+  - `igm.py`: IGM DM contributions, cosmic DM estimates
+  - `host.py`: Host galaxy DM contributions
+  - `cosmic.py`: Cosmological DM calculations
+  - `prob_dmz.py`: DM-redshift probability distributions
+
+- **`frb/galaxies/`**: Host galaxy analysis
+  - `photom.py`: Photometry handling and conversions
+  - `nebular.py`: Nebular emission line analysis
+  - `eazy.py` / `cigale.py`: SED fitting interfaces
+
+- **`frb/surveys/`**: Survey data access (PanSTARRS, SDSS, DECaLS, WISE, 2MASS, etc.)
+
+- **`frb/halos/`**: Halo mass function and foreground halo DM models
+
+### Data Storage
+
+FRB and host galaxy data are stored as JSON files in `frb/data/FRBs/` and `frb/data/Galaxies/`. Access via class methods like `FRB.by_name()` or `FRBHost.by_frb()`.
+
+### Cosmology
+
+Default cosmology is Planck18, defined in `frb/defs.py` as `frb_cosmo`. All calculations use this unless explicitly overridden.
+
+### External Dependencies
+
+Critical external packages (not on PyPI):
+- `ne2001`: Galactic electron density model for ISM DM
+- `astropath`: PATH probabilistic association framework
+- `linetools`: Spectroscopic analysis utilities

frb/builds/build_hosts.py

@@ -164,6 +164,7 @@ def read_lit_table(lit_entry, coord=None):
             idx = int(np.where(match)[0])
             return lit_tbl[idx:idx+1]
         else:
+            embed(header="Multiple matches in literature table!")
             raise ValueError("More than one match in the table!!!")
     else:
         # Return
@@ -261,7 +262,7 @@ def run(host_input:pandas.core.series.Series,
         survey = survey_utils.load_survey_by_name(key, 
                                                     gal_coord, 
                                                     search_r)
-        srvy_tbl = survey.get_catalog(print_query=True)
+        srvy_tbl = survey.get_catalog()#print_query=True)
 
         if srvy_tbl is None or len(srvy_tbl) == 0:
             continue
@@ -489,6 +490,10 @@ def run(host_input:pandas.core.series.Series,
 
     # Vet all
     assert Host.vet_all()
+    #try:
+    #    assert Host.vet_all()
+    #except AssertionError as e:
+    #    embed(header='Host galaxy failed vetting! 494')
 
     # Write
     if out_path is None:

frb/data/Galaxies/20220204A/FRB20220204A_host.json

@@ -3,6 +3,20 @@
     "cosmo": "Planck18",
     "dec": 69.7222,
     "dec_FRB": 69.722503,
+    "derived": {
+        "AV_old": 1.5444,
+        "AV_old_loerr": -0.143,
+        "AV_old_ref": "Sharma2024",
+        "AV_old_uperr": 0.1565,
+        "Mtotal": 7521422760.871608,
+        "Mtotal_loerr": -1305310446.3409758,
+        "Mtotal_ref": "Sharma2024",
+        "Mtotal_uperr": 838456401.7401981,
+        "SFR_SED": 4.3058,
+        "SFR_SED_loerr": -0.8752,
+        "SFR_SED_ref": "Sharma2024",
+        "SFR_SED_uperr": 1.3978
+    },
     "offsets": {
         "ang_avg": 2.5888449308348185,
         "ang_avg_err": 1.2189686474990278,

frb/data/Galaxies/20220207C/FRB20220207C_host.json

@@ -3,6 +3,20 @@
     "cosmo": "Planck18",
     "dec": 72.88274916666666,
     "dec_FRB": 72.882327,
+    "derived": {
+        "AV_old": 0.0956,
+        "AV_old_loerr": -0.0181,
+        "AV_old_ref": "Sharma2024",
+        "AV_old_uperr": 0.0233,
+        "Mtotal": 13976550562.990356,
+        "Mtotal_loerr": -1023751341.5691204,
+        "Mtotal_ref": "Sharma2024",
+        "Mtotal_uperr": 1089520098.8770945,
+        "SFR_SED": 0.7124,
+        "SFR_SED_loerr": -0.1347,
+        "SFR_SED_ref": "Sharma2024",
+        "SFR_SED_uperr": 0.1244
+    },
     "offsets": {
         "ang_avg": 2.6272483853172286,
         "ang_avg_err": 0.5904731793305108,
@@ -12,11 +26,6 @@
         "physical_err": 0.5242639894130404
     },
     "photom": {
-        "2MASS_H": 15.089434621876995,
-        "2MASS_H_err": 0.04,
-        "2MASS_H_flux": 3.3436910716867603,
-        "2MASS_H_flux_err": 0.12318613147589151,
-        "2MASS_H_ref": "Sharma2024",
         "EBV": 0.6973,
         "Pan-STARRS_g": 13.954235698639348,
         "Pan-STARRS_g_err": 0.03,

frb/data/Galaxies/20220208A/FRB20220208A_host.json

@@ -3,6 +3,20 @@
     "cosmo": "Planck18",
     "dec": 70.042,
     "dec_FRB": 70.041042,
+    "derived": {
+        "AV_old": 0.7248,
+        "AV_old_loerr": -0.0375,
+        "AV_old_ref": "Sharma2024",
+        "AV_old_uperr": 0.0433,
+        "Mtotal": 19480495532.907654,
+        "Mtotal_loerr": -1021682479.1121788,
+        "Mtotal_ref": "Sharma2024",
+        "Mtotal_uperr": 721766508.6799965,
+        "SFR_SED": 0.6764,
+        "SFR_SED_loerr": -0.0796,
+        "SFR_SED_ref": "Sharma2024",
+        "SFR_SED_uperr": 0.073
+    },
     "offsets": {
         "ang_avg": 5.226895038582604,
         "ang_avg_err": 0.8423572215214188,
@@ -27,12 +41,7 @@
         "Pan-STARRS_z_err": 0.21,
         "Pan-STARRS_z_flux": 0.0414075477001926,
         "Pan-STARRS_z_flux_err": 0.008008929774039882,
-        "Pan-STARRS_z_ref": "Sharma2024",
-        "WIRC_J": 20.214088099135417,
-        "WIRC_J_err": 0.08,
-        "WIRC_J_flux": 0.02981019072439763,
-        "WIRC_J_flux_err": 0.0021964960250018353,
-        "WIRC_J_ref": "Sharma2024"
+        "Pan-STARRS_z_ref": "Sharma2024"
     },
     "ra": 322.57199999999995,
     "ra_FRB": 322.575125,

frb/data/Galaxies/20220307B/FRB20220307B_host.json

@@ -3,6 +3,20 @@
     "cosmo": "Planck18",
     "dec": 72.19188972222223,
     "dec_FRB": 72.192386,
+    "derived": {
+        "AV_old": 1.874,
+        "AV_old_loerr": -0.0838,
+        "AV_old_ref": "Sharma2024",
+        "AV_old_uperr": 0.0672,
+        "Mtotal": 21562544068.071934,
+        "Mtotal_loerr": -1912153185.334015,
+        "Mtotal_ref": "Sharma2024",
+        "Mtotal_uperr": 1820443566.727192,
+        "SFR_SED": 3.1663,
+        "SFR_SED_loerr": -1.0276,
+        "SFR_SED_ref": "Sharma2024",
+        "SFR_SED_uperr": 1.3512
+    },
     "offsets": {
         "ang_avg": 2.540982048954476,
         "ang_avg_err": 1.1512380152408117,
@@ -37,17 +51,7 @@
         "Pan-STARRS_z_err": 0.06,
         "Pan-STARRS_z_flux": 0.07429603274964809,
         "Pan-STARRS_z_flux_err": 0.004105750499470491,
-        "Pan-STARRS_z_ref": "Sharma2024",
-        "WIRC_H": 18.624185903942895,
-        "WIRC_H_err": 0.02,
-        "WIRC_H_flux": 0.1289215839608663,
-        "WIRC_H_flux_err": 0.0023748233391477683,
-        "WIRC_H_ref": "Sharma2024",
-        "WIRC_J": 19.18250216694357,
-        "WIRC_J_err": 0.02,
-        "WIRC_J_flux": 0.07709019203465596,
-        "WIRC_J_flux_err": 0.001420053815960377,
-        "WIRC_J_ref": "Sharma2024"
+        "Pan-STARRS_z_ref": "Sharma2024"
     },
     "ra": 350.87468666666666,
     "ra_FRB": 350.874496,

frb/data/Galaxies/20220310F/FRB20220310F_host.json

@@ -3,6 +3,20 @@
     "cosmo": "Planck18",
     "dec": 73.49095694444445,
     "dec_FRB": 73.490833,
+    "derived": {
+        "AV_old": 0.0401,
+        "AV_old_loerr": -0.027,
+        "AV_old_ref": "Sharma2024",
+        "AV_old_uperr": 0.0607,
+        "Mtotal": 14702798319.828363,
+        "Mtotal_loerr": -1854901314.8669643,
+        "Mtotal_ref": "Sharma2024",
+        "Mtotal_uperr": 2595365272.322706,
+        "SFR_SED": 0.9706,
+        "SFR_SED_loerr": -0.2879,
+        "SFR_SED_ref": "Sharma2024",
+        "SFR_SED_uperr": 0.3159
+    },
     "offsets": {
         "ang_avg": 2.1771155286258366,
         "ang_avg_err": 1.1640176640813238,
@@ -25,6 +39,10 @@
         "DECaL_z_flux": 0.028049599219039715,
         "DECaL_z_flux_err": 0.0005673137020713931,
         "EBV": 0.0254,
+        "GALEX_NUV": 22.543869802588716,
+        "GALEX_NUV_err": 0.226373971,
+        "GALEX_NUV_flux": 0.0034870010107275074,
+        "GALEX_NUV_flux_err": 0.0007270331985063052,
         "Pan-STARRS_g": 22.193716137054263,
         "Pan-STARRS_g_err": 0.1555899977684021,
         "Pan-STARRS_g_flux": 0.004814082620479617,
@@ -44,25 +62,10 @@
         "Pan-STARRS_z_flux": 0.019590731646687037,
         "Pan-STARRS_z_flux_err": 0.00018043730660203308,
         "Pan-STARRS_z_ref": "Sharma2024",
-        "WIRC_H": 20.27685233211026,
-        "WIRC_H_err": 0.23,
-        "WIRC_H_flux": 0.028135786606411944,
-        "WIRC_H_flux_err": 0.005960223939401883,
-        "WIRC_H_ref": "Sharma2024",
-        "WIRC_J": 20.198669547695637,
-        "WIRC_J_err": 0.21,
-        "WIRC_J_flux": 0.030236545732084938,
-        "WIRC_J_flux_err": 0.005848266435171848,
-        "WIRC_J_ref": "Sharma2024",
-        "WIRC_K": 20.401723512098595,
-        "WIRC_K_err": 0.3,
-        "WIRC_K_flux": 0.025079021597690106,
-        "WIRC_K_flux_err": 0.006929589753326034,
-        "WIRC_K_ref": "Sharma2024",
         "WISE_W1": 19.996196746826172,
         "WISE_W1_err": 0.23000000417232513,
         "WISE_W1_flux": 0.03643519803881645,
-        "WISE_W1_flux_err": 0.007718353066593409,
+        "WISE_W1_flux_err": 0.007718353997915983,
         "WISE_W1_ref": "Sharma2024",
         "WISE_W2": 20.477563858032227,
         "WISE_W2_err": 0.36000001430511475,

frb/data/Galaxies/20220319D/FRB20220319D_host.json

@@ -3,6 +3,20 @@
     "cosmo": "Planck18",
     "dec": 71.035875,
     "dec_FRB": 71.03526,
+    "derived": {
+        "AV_old": 0.34,
+        "AV_old_loerr": -0.01,
+        "AV_old_ref": "Sharma2024",
+        "AV_old_uperr": 0.01,
+        "Mtotal": 19787913352.337383,
+        "Mtotal_loerr": -123404260.04777144,
+        "Mtotal_ref": "Sharma2024",
+        "Mtotal_uperr": 137163262.62660217,
+        "SFR_SED": 0.4238,
+        "SFR_SED_loerr": -0.0209,
+        "SFR_SED_ref": "Sharma2024",
+        "SFR_SED_uperr": 0.0222
+    },
     "offsets": {
         "ang_avg": 9.259871760563033,
         "ang_avg_err": 0.5777504427130394,
@@ -12,21 +26,6 @@
         "physical_err": 0.13715840112809607
     },
     "photom": {
-        "2MASS_H": 11.990261074483097,
-        "2MASS_H_err": 0.02,
-        "2MASS_H_flux": 58.0624776949647,
-        "2MASS_H_flux_err": 1.0695503648218,
-        "2MASS_H_ref": "Sharma2024",
-        "2MASS_J": 11.947014523022894,
-        "2MASS_J_err": 0.02,
-        "2MASS_J_flux": 60.421873190788446,
-        "2MASS_J_flux_err": 1.1130120359990885,
-        "2MASS_J_ref": "Sharma2024",
-        "2MASS_K": 12.323423798287955,
-        "2MASS_K_err": 0.02,
-        "2MASS_K_flux": 42.71992435220384,
-        "2MASS_K_flux_err": 0.7869300878977431,
-        "2MASS_K_ref": "Sharma2024",
         "EBV": 0.6957,
         "Pan-STARRS_g": 11.159852963003852,
         "Pan-STARRS_g_err": 0.02,

frb/data/Galaxies/20220330D/FRB20220330D_host.json

@@ -3,6 +3,20 @@
     "cosmo": "Planck18",
     "dec": 70.35032222222222,
     "dec_FRB": 70.35075,
+    "derived": {
+        "AV_old": 3.8468,
+        "AV_old_loerr": -0.0242,
+        "AV_old_ref": "Sharma2024",
+        "AV_old_uperr": 0.0214,
+        "Mtotal": 49636368488.45584,
+        "Mtotal_loerr": -1121105414.4343948,
+        "Mtotal_ref": "Sharma2024",
+        "Mtotal_uperr": 1815363649.709877,
+        "SFR_SED": 2.0125,
+        "SFR_SED_loerr": -0.0749,
+        "SFR_SED_ref": "Sharma2024",
+        "SFR_SED_uperr": 0.1225
+    },
     "offsets": {
         "ang_avg": 3.468386547707636,
         "ang_avg_err": 1.373186664162618,