nuggt.yea_nay example

yea_nay.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import tifffile\n",
    "points = np.load(\"/media/im1/Lee/FromWG_GUItests/PVimages/spots_filtered.npy\")\n",
    "pv = tifffile.imread(\"/media/im1/Lee/FromWG_GUItests/PVimages/PV.tif\")\n",
    "syto = tifffile.imread(\"/media/im1/Lee/FromWG_GUItests/PVimages/Syto.tif\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "from nuggt.yea_nay import sort_points"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "from nuggt.utils.ngutils import green_shader, red_shader"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "http://127.0.0.1:34831/v/064fc82c720111272aeb7a90e557941c8112dfe0/\n"
     ]
    }
   ],
   "source": [
    "yea, nay = sort_points(((pv, \"PV\", red_shader),\n",
    "                       (syto, \"Syto\", green_shader)), points[:, ::-1])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(array([[  2, 746,   5],\n",
       "        [  2, 890,   6],\n",
       "        [  3, 993,   9]]), array([[  2,  34,  33],\n",
       "        [  3, 224,  30]]))"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "yea[:, ::-1], nay[:, ::-1]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Help on function stop in module neuroglancer.server:\n",
      "\n",
      "stop()\n",
      "    Stop the server, invalidating any viewer URLs.\n",
      "    \n",
      "    This allows any previously-referenced data arrays to be garbage collected if there are no other\n",
      "    references to them.\n",
      "\n"
     ]
    }
   ],
   "source": [
    "import neuroglancer\n",
    "help(neuroglancer.stop)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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