From 5e23a70b7938e990133c4c1dd8e02bc55dd570da Mon Sep 17 00:00:00 2001
From: Sarah Blunt <sarah.blunt.3@gmail.com>
Date: Thu, 29 Feb 2024 13:28:41 -0600
Subject: [PATCH] update notebook with latest changes

---
 docs/tutorials/ONeil-ObsPriors.ipynb | 62 +++++++++++++++-------------
 1 file changed, 33 insertions(+), 29 deletions(-)

diff --git a/docs/tutorials/ONeil-ObsPriors.ipynb b/docs/tutorials/ONeil-ObsPriors.ipynb
index ae959c59..bd7f208b 100644
--- a/docs/tutorials/ONeil-ObsPriors.ipynb
+++ b/docs/tutorials/ONeil-ObsPriors.ipynb
@@ -6,16 +6,16 @@
    "source": [
     "# Using the O'Neil (2019) Observation-based Priors\n",
     "\n",
-    "by Sarah Blunt (2020)"
+    "by Sarah Blunt (2024)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
-    "%matploltib \n",
+    "# TODO: write tutorial intro\n",
     "\n",
     "import numpy as np\n",
     "import multiprocessing as mp\n",
@@ -33,7 +33,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -41,20 +41,28 @@
     "\n",
     "# system parameters\n",
     "num_secondary_bodies = 1\n",
-    "system_mass = 1.75 # [Msol]\n",
-    "plx = 51.44 # [mas]\n",
-    "mass_err = 0.05 # [Msol]\n",
-    "plx_err = 0.12 # [mas]\n",
+    "system_mass = 1.75  # [Msol]\n",
+    "plx = 51.44  # [mas]\n",
     "\n",
     "# MCMC parameters\n",
     "num_temps = 10\n",
     "num_walkers = 50\n",
-    "num_threads = mp.cpu_count() # or a different number if you prefer\n",
+    "num_threads = mp.cpu_count()  # or a different number if you prefer\n",
     "\n",
     "\n",
     "my_driver = driver.Driver(\n",
-    "    filename, 'MCMC', num_secondary_bodies, system_mass, plx, mass_err=mass_err, plx_err=plx_err,\n",
-    "    mcmc_kwargs={'num_temps': num_temps, 'num_walkers': num_walkers, 'num_threads': num_threads}\n",
+    "    filename,\n",
+    "    \"MCMC\",\n",
+    "    num_secondary_bodies,\n",
+    "    system_mass,\n",
+    "    plx,\n",
+    "    mass_err=0,\n",
+    "    plx_err=0,\n",
+    "    mcmc_kwargs={\n",
+    "        \"num_temps\": num_temps,\n",
+    "        \"num_walkers\": num_walkers,\n",
+    "        \"num_threads\": num_threads,\n",
+    "    },\n",
     ")"
    ]
   },
@@ -92,31 +100,27 @@
    ],
    "source": [
     "# convert input sep/PA measurements to RA/decl\n",
-    "sep = np.array(my_driver.system.data_table['quant1'])\n",
-    "sep_err = np.array(my_driver.system.data_table['quant1_err'])\n",
-    "pa = np.radians(np.array(my_driver.system.data_table['quant2']))\n",
-    "pa_err = np.radians(np.array(my_driver.system.data_table['quant2_err']))\n",
+    "sep = np.array(my_driver.system.data_table[\"quant1\"])\n",
+    "sep_err = np.array(my_driver.system.data_table[\"quant1_err\"])\n",
+    "pa = np.radians(np.array(my_driver.system.data_table[\"quant2\"]))\n",
+    "pa_err = np.radians(np.array(my_driver.system.data_table[\"quant2_err\"]))\n",
     "\n",
     "\n",
-    "ra_err = np.sqrt(\n",
-    "    (np.cos(pa) * sep_err)**2 + \n",
-    "    (sep * np.sin(pa) * pa_err)**2\n",
-    ")\n",
-    "dec_err = np.sqrt(\n",
-    "    (np.sin(pa) * sep_err)**2 + \n",
-    "    (sep * np.cos(pa) * pa_err)**2\n",
-    ")\n",
+    "ra_err = np.sqrt((np.cos(pa) * sep_err) ** 2 + (sep * np.sin(pa) * pa_err) ** 2)\n",
+    "dec_err = np.sqrt((np.sin(pa) * sep_err) ** 2 + (sep * np.cos(pa) * pa_err) ** 2)\n",
     "\n",
     "\n",
-    "epochs = np.array(my_driver.system.data_table['epoch'])\n",
+    "epochs = np.array(my_driver.system.data_table[\"epoch\"])\n",
     "\n",
     "# define the `ObsPrior` object\n",
     "my_obsprior = priors.ObsPrior(ra_err, dec_err, epochs)\n",
     "\n",
+    "# TODO: change the basis\n",
+    "\n",
     "print(my_driver.system.param_idx)\n",
     "\n",
     "# set the priors on `sma`, `ecc`, `tau`, `mtot`, and `plx` to point to this object\n",
-    "for i in [0, 1, 5, 6, 7]:\n",
+    "for i in [0, 1, 5]:\n",
     "    my_driver.system.sys_priors[i] = my_obsprior\n",
     "\n",
     "my_driver.system.sys_priors"
@@ -163,15 +167,15 @@
    "source": [
     "n_pts = 10\n",
     "\n",
-    "# make an array of sample orbits to compute lnprob: maybe 1000 orbits long, drawn from uniform dists in all 5 params\n"
+    "# make an array of sample orbits to compute lnprob: maybe 1000 orbits long, drawn from uniform dists in all 5 params"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.7.6 64-bit ('python3.7': conda)",
+   "display_name": "python3.11",
    "language": "python",
-   "name": "python37664bitpython37conda5785220be34f4f6fa52b2ff37321b463"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -183,7 +187,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.6"
+   "version": "3.11.4"
   }
  },
  "nbformat": 4,