From 097b498da67a8caa0f31dd9ef536dd1b2bc2f2d4 Mon Sep 17 00:00:00 2001
From: rstiskalek <richard.stiskalek@protonmail.com>
Date: Sat, 1 Apr 2023 07:16:10 +0100
Subject: [PATCH] Update nb

---
 notebooks/knn.ipynb | 173 +++++++++++++++++++++++++++++++++-----------
 1 file changed, 129 insertions(+), 44 deletions(-)

diff --git a/notebooks/knn.ipynb b/notebooks/knn.ipynb
index 8ebdb6d..c99dbb6 100644
--- a/notebooks/knn.ipynb
+++ b/notebooks/knn.ipynb
@@ -2,12 +2,12 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 1,
    "id": "5a38ed25",
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2023-03-31T17:09:12.165480Z",
-     "start_time": "2023-03-31T17:09:12.116708Z"
+     "end_time": "2023-04-01T06:10:36.618752Z",
+     "start_time": "2023-04-01T06:10:10.251616Z"
     },
     "scrolled": true
    },
@@ -16,8 +16,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "The autoreload extension is already loaded. To reload it, use:\n",
-      "  %reload_ext autoreload\n"
+      "not found\n"
      ]
     }
    ],
@@ -44,12 +43,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "id": "4218b673",
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2023-03-31T17:09:13.943312Z",
-     "start_time": "2023-03-31T17:09:12.167027Z"
+     "end_time": "2023-04-01T06:10:44.171672Z",
+     "start_time": "2023-04-01T06:10:42.109733Z"
     }
    },
    "outputs": [],
@@ -59,12 +58,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": null,
    "id": "5ff7a1b6",
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2023-03-31T17:10:18.303240Z",
-     "start_time": "2023-03-31T17:10:14.674751Z"
+     "start_time": "2023-04-01T06:12:15.998Z"
     }
    },
    "outputs": [
@@ -75,36 +73,6 @@
       "\r",
       "  0%|          | 0/1 [00:00<?, ?it/s]"
      ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "float32\n",
-      "float32\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "100%|██████████| 1/1 [00:03<00:00,  3.37s/it]"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "float32\n",
-      "float32\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "\n"
-     ]
     }
    ],
    "source": [
@@ -113,18 +81,135 @@
     "\n",
     "knncdf = csiborgtools.match.kNN_CDF()\n",
     "\n",
-    "rs, cdfs_high = knncdf(knn, nneighbours=3, Rmax=155 / 0.705, rmin=0.05, rmax=40,\n",
-    "                  nsamples=int(1e6), neval=int(1e4), random_state=42)"
+    "rs, cdf = knncdf(knn, nneighbours=2, Rmax=155 / 0.705, rmin=0.01, rmax=100,\n",
+    "                  nsamples=int(1e8), neval=int(1e4), random_state=42, batch_size=int(1e7))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "2b85c1c6",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2023-04-01T06:11:13.560595Z",
+     "start_time": "2023-04-01T06:11:12.888821Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "X = knncdf.rvs_in_sphere(nsamples=int(1e7), R=1.)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "id": "3a80cb5b",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2023-04-01T06:11:15.024753Z",
+     "start_time": "2023-04-01T06:11:14.973967Z"
+    }
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Variable           Type                Data/Info\n",
+      "------------------------------------------------\n",
+      "NearestNeighbors   ABCMeta             <class 'sklearn.neighbors<...>rvised.NearestNeighbors'>\n",
+      "X                  ndarray             10000000x3: 30000000 elems, type `float32`, 120000000 bytes (114.44091796875 Mb)\n",
+      "cat                HaloCatalogue       <csiborgtools.read.make_c<...>object at 0x7fbbc6073fa0>\n",
+      "cdf                ndarray             2x9999: 19998 elems, type `float32`, 79992 bytes\n",
+      "csiborgtools       module              <module 'csiborgtools' fr<...>siborgtools/__init__.py'>\n",
+      "joblib             module              <module 'joblib' from '/m<...>ages/joblib/__init__.py'>\n",
+      "knn                NearestNeighbors    NearestNeighbors()\n",
+      "knncdf             kNN_CDF             <csiborgtools.match.knn.k<...>object at 0x7fbbc68bb5b0>\n",
+      "matplotlib         module              <module 'matplotlib' from<...>/matplotlib/__init__.py'>\n",
+      "np                 module              <module 'numpy' from '/mn<...>kages/numpy/__init__.py'>\n",
+      "plt                module              <module 'matplotlib.pyplo<...>es/matplotlib/pyplot.py'>\n",
+      "rs                 ndarray             9999: 9999 elems, type `float64`, 79992 bytes\n",
+      "sys                module              <module 'sys' (built-in)>\n",
+      "tqdm               type                <class 'tqdm.std.tqdm'>\n"
+     ]
+    }
+   ],
+   "source": [
+    "%whos"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "08321431",
+   "id": "8b9a8cf0",
    "metadata": {},
    "outputs": [],
    "source": []
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "a1825f00",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2023-04-01T06:01:29.388586Z",
+     "start_time": "2023-04-01T06:01:29.321025Z"
+    },
+    "scrolled": false
+   },
+   "outputs": [],
+   "source": [
+    "plt.figure()\n",
+    "plt.plot(rs, knncdf.peaked_cdf(cdf[0, :]))\n",
+    "\n",
+    "plt.yscale(\"log\" )\n",
+    "plt.xscale(\"log\")\n",
+    "plt.show()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "289549a0",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2023-03-31T22:55:20.690887Z",
+     "start_time": "2023-03-31T22:55:20.656550Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "mask"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7a8c5202",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2023-03-31T22:54:52.330633Z",
+     "start_time": "2023-03-31T22:54:52.299548Z"
+    }
+   },
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "46f54897",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2023-03-31T22:54:25.138813Z",
+     "start_time": "2023-03-31T22:54:25.105044Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "dist"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,