Add simple distance flow model (#114)

* Add imports * Add field LOS paths * Add basic flow model * Edit script * Add nb * Add nb * Update nb * Add some docs * Add RA reading * Add imoprts * Updates to the flow model * Update script * Bring back A2 * Update imports * Update imports * Add Carrick to ICs * Add Carrick boxsize * Add Carrick and fix minor bugs * Add Carrick box * Update script * Edit imports * Add fixed flow! * Update omega_m and add it * Update nb * Update nb * Update nb * Remove old print statements * Update params * Add thinning of chains * Add import * Add flow validation script * Add submit script * Add ksmooth * Update nb * Update params * Update script * Update string * Move where distributions are defined * Add density bias parameter * Add lognorm mean * Update scripts * Update script
2025-05-13 06:01:13 +00:00 · 2024-03-08 10:44:19 +00:00 · 2024-03-08 10:44:19 +00:00 · a65e3cb15b
commit a65e3cb15b
parent fb93f85543
14 changed files with 1762 additions and 60 deletions
--- a/scripts_independent/A2_to_hdf5.ipynb
+++ b/scripts_independent/A2_to_hdf5.ipynb
@ -0,0 +1,150 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Copyright (C) 2024 Richard Stiskalek\n",
+    "# This program is free software; you can redistribute it and/or modify it\n",
+    "# under the terms of the GNU General Public License as published by the\n",
+    "# Free Software Foundation; either version 3 of the License, or (at your\n",
+    "# option) any later version.\n",
+    "# This program is distributed in the hope that it will be useful, but\n",
+    "# WITHOUT ANY WARRANTY; without even the implied warranty of\n",
+    "# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General\n",
+    "# Public License for more details.\n",
+    "#\n",
+    "# You should have received a copy of the GNU General Public License along\n",
+    "# with this program; if not, write to the Free Software Foundation, Inc.,\n",
+    "# 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.\n",
+    "from os.path import join\n",
+    "\n",
+    "import numpy as np\n",
+    "import matplotlib.pyplot as plt\n",
+    "from h5py import File\n",
+    "\n",
+    "%matplotlib inline"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Supernovae data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "a2dir = \"/Users/richard/Data/PV/A2_paper_data/A2\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### LOSS data set"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "names = [\"z_CMB\", \"mB\", \"x1\", \"c\", \"e_mB\", \"e_x1\", \"e_c\", \"RA\", \"DEC\"]\n",
+    "dtype = [(n, np.float32) for n in names]\n",
+    "data = np.genfromtxt(join(a2dir, \"loss.csv\"), delimiter=\",\", skip_header=1,\n",
+    "                     usecols=[5 + n for n in range(len(names))])\n",
+    "\n",
+    "loss_data = np.empty(len(data), dtype=dtype)\n",
+    "for i, n in enumerate(names):\n",
+    "    loss_data[n] = data[:, i]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Foundation data set "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "names = [\"z_CMB\", \"RA\", \"DEC\", \"x1\", \"mB\", \"c\", \"peak\", \"e_peak\", \"e_x1\", \"e_mB\", \"e_c\"]\n",
+    "dtype = [(n, np.float32) for n in names]\n",
+    "data = np.genfromtxt(join(a2dir, \"foundation.csv\"), delimiter=\",\", skip_header=1,\n",
+    "                     usecols=[3 + n for n in range(len(names))])\n",
+    "\n",
+    "foundation_data = np.empty(len(data), dtype=dtype)\n",
+    "for i, n in enumerate(names):\n",
+    "    foundation_data[n] = data[:, i]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Write output as HDF5 file"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "outdir = \"/Users/richard/Downloads\"\n",
+    "fname = \"PV_compilation_Supranta2019.hdf5\"\n",
+    "\n",
+    "with File(join(outdir, fname), 'w') as f:\n",
+    "    # Write LOSS\n",
+    "    grp = f.create_group(\"LOSS\")\n",
+    "    for name in loss_data.dtype.names:\n",
+    "        grp.create_dataset(name, data=loss_data[name])\n",
+    "\n",
+    "    # Write Foundation\n",
+    "    grp = f.create_group(\"Foundation\")\n",
+    "    for name in foundation_data.dtype.names:\n",
+    "        grp.create_dataset(name, data=foundation_data[name])\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}