2021-07-06_Local_binary_pattern_on_images.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Local binary pattern - on artificial data\n",
    "Came from 2020-09-04_Local_binary_pattern_with_covid\n",
    "and came from 2020-09-29_Local_binary_pattern_with_covid\n",
    "and came from 2020-10-11_Local_binary_pattern_with_covid"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Loading Linux\n"
     ]
    }
   ],
   "source": [
    "import matplotlib.pyplot as plt\n",
    "import numpy as np\n",
    "import math\n",
    "from PIL import Image\n",
    "import cv2\n",
    "import skimage\n",
    "import tifffile\n",
    "import os\n",
    "import pandas as pd\n",
    "\n",
    "import platform\n",
    "if platform.system() == 'Windows':\n",
    "    fileroot = 'X:/'\n",
    "    print('Loading Windows')\n",
    "if platform.system() == 'Linux':\n",
    "    fileroot = '/home/jovyan/'\n",
    "    print('Loading Linux')\n",
    "if False:\n",
    "    fileroot = '/home/ubuntu/Documents/'\n",
    "\n",
    "colors_new=['#0072b2','#009e73','#d55e00', '#cc79a7','#f0e442','#56b4e9']\n",
    "\n",
    "import sys\n",
    "sys.path.append(fileroot+'VU_TEX/Ben_utilities/')\n",
    "import useful_functions as uf \n",
    "import time"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import matplotlib\n",
    "import matplotlib.patheffects as path_effects\n",
    "from functools import partial\n",
    "from skimage.feature import local_binary_pattern\n",
    "from importlib import reload\n",
    "from itertools import repeat\n",
    "from datetime import datetime\n",
    "from tqdm.notebook import trange"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "#reload(uf)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "pd.set_option('display.max_columns', None)  \n",
    "pd.set_option('display.expand_frame_repr', False)\n",
    "pd.set_option('max_colwidth', None)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "#This should be the folder where the LBP values for the images are output\n",
    "#Should be chosen to be a folder that already exists (but can be empty)\n",
    "directory_out_top = fileroot + 'VU_TEX/playground_Ben/2023-07-05_Thymus/2023-07-06f_LBP_values_for_image_small/'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['V11J11-099__Z4_FO3_01__A1_small.tif']"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "directory_in_imgs = fileroot + 'VU_TEX/playground_Ben/2023-07-05_Thymus/2023-07-06d_image_conversion_and_crop_to_small_version/'\n",
    "#imgs = os.listdir(directory_in_imgs)\n",
    "#imgs.remove('Thumbs.db')\n",
    "#imgs.sort(key=partial(uf.getvaluefromstringbest, variable='MS', ending='.', mydtype=int))\n",
    "imgs = ['V11J11-099__Z4_FO3_01__A1_small.tif']\n",
    "#imgs = [img for img in imgs if '.npy' in img]\n",
    "imgs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1, 2, 3, 4, 5, 6, 8, 11, 14, 19, 25, 34, 45, 59, 79]\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "15"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#this is one of the two parameters of the process\n",
    "#I normally set the highest radius in radius_list to be the highest number that is smaller than the patchsize I choose\n",
    "radius_list = [round(1.499*1.327**(float(x))) for x in range(0, 15)]\n",
    "print(radius_list); len(radius_list)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "#directory_metadata = fileroot + '0ExternalData/2022-05-10_Newcastle_University_iridium_covid_UK_CIC_dataset/'\n",
    "#filename_metadata = 'Cross_site_Technology_ROI_Summary_with_filenames.xlsx'\n",
    "#df2 = pd.read_excel(directory_metadata + filename_metadata, engine='openpyxl')\n",
    "#df2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "#df_all = pd.DataFrame(imgs, columns=['Filenames'])\n",
    "#df_all"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "#result = df_all.merge(df2, how='outer', indicator=True)\n",
    "#result[result['_merge'] != 'both']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Filenames</th>\n",
       "      <th>dims</th>\n",
       "      <th>radius</th>\n",
       "      <th>n_points</th>\n",
       "      <th>method</th>\n",
       "      <th>channel</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "      <td>uniform</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "      <td>uniform</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "      <td>uniform</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>2</td>\n",
       "      <td>13</td>\n",
       "      <td>uniform</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>2</td>\n",
       "      <td>13</td>\n",
       "      <td>uniform</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>2</td>\n",
       "      <td>13</td>\n",
       "      <td>uniform</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>3</td>\n",
       "      <td>19</td>\n",
       "      <td>uniform</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>3</td>\n",
       "      <td>19</td>\n",
       "      <td>uniform</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>3</td>\n",
       "      <td>19</td>\n",
       "      <td>uniform</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>4</td>\n",
       "      <td>26</td>\n",
       "      <td>uniform</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>4</td>\n",
       "      <td>26</td>\n",
       "      <td>uniform</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>4</td>\n",
       "      <td>26</td>\n",
       "      <td>uniform</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>5</td>\n",
       "      <td>32</td>\n",
       "      <td>uniform</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>5</td>\n",
       "      <td>32</td>\n",
       "      <td>uniform</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>5</td>\n",
       "      <td>32</td>\n",
       "      <td>uniform</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>6</td>\n",
       "      <td>38</td>\n",
       "      <td>uniform</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>6</td>\n",
       "      <td>38</td>\n",
       "      <td>uniform</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>6</td>\n",
       "      <td>38</td>\n",
       "      <td>uniform</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>8</td>\n",
       "      <td>51</td>\n",
       "      <td>uniform</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>8</td>\n",
       "      <td>51</td>\n",
       "      <td>uniform</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>8</td>\n",
       "      <td>51</td>\n",
       "      <td>uniform</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>11</td>\n",
       "      <td>70</td>\n",
       "      <td>uniform</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>11</td>\n",
       "      <td>70</td>\n",
       "      <td>uniform</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>11</td>\n",
       "      <td>70</td>\n",
       "      <td>uniform</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>14</td>\n",
       "      <td>88</td>\n",
       "      <td>uniform</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>14</td>\n",
       "      <td>88</td>\n",
       "      <td>uniform</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>14</td>\n",
       "      <td>88</td>\n",
       "      <td>uniform</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>19</td>\n",
       "      <td>120</td>\n",
       "      <td>uniform</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>19</td>\n",
       "      <td>120</td>\n",
       "      <td>uniform</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>19</td>\n",
       "      <td>120</td>\n",
       "      <td>uniform</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>25</td>\n",
       "      <td>158</td>\n",
       "      <td>uniform</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>31</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>25</td>\n",
       "      <td>158</td>\n",
       "      <td>uniform</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>25</td>\n",
       "      <td>158</td>\n",
       "      <td>uniform</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>34</td>\n",
       "      <td>214</td>\n",
       "      <td>uniform</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>34</td>\n",
       "      <td>214</td>\n",
       "      <td>uniform</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>34</td>\n",
       "      <td>214</td>\n",
       "      <td>uniform</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>45</td>\n",
       "      <td>283</td>\n",
       "      <td>uniform</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>37</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>45</td>\n",
       "      <td>283</td>\n",
       "      <td>uniform</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>38</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>45</td>\n",
       "      <td>283</td>\n",
       "      <td>uniform</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>39</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>59</td>\n",
       "      <td>371</td>\n",
       "      <td>uniform</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>40</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>59</td>\n",
       "      <td>371</td>\n",
       "      <td>uniform</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>41</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>59</td>\n",
       "      <td>371</td>\n",
       "      <td>uniform</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>79</td>\n",
       "      <td>497</td>\n",
       "      <td>uniform</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>43</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>79</td>\n",
       "      <td>497</td>\n",
       "      <td>uniform</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44</th>\n",
       "      <td>V11J11-099__Z4_FO3_01__A1_small.tif</td>\n",
       "      <td>(5539, 3739, 3)</td>\n",
       "      <td>79</td>\n",
       "      <td>497</td>\n",
       "      <td>uniform</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                              Filenames             dims  radius  n_points   method  channel\n",
       "0   V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)       1         7  uniform        0\n",
       "1   V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)       1         7  uniform        1\n",
       "2   V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)       1         7  uniform        2\n",
       "3   V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)       2        13  uniform        0\n",
       "4   V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)       2        13  uniform        1\n",
       "5   V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)       2        13  uniform        2\n",
       "6   V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)       3        19  uniform        0\n",
       "7   V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)       3        19  uniform        1\n",
       "8   V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)       3        19  uniform        2\n",
       "9   V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)       4        26  uniform        0\n",
       "10  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)       4        26  uniform        1\n",
       "11  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)       4        26  uniform        2\n",
       "12  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)       5        32  uniform        0\n",
       "13  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)       5        32  uniform        1\n",
       "14  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)       5        32  uniform        2\n",
       "15  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)       6        38  uniform        0\n",
       "16  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)       6        38  uniform        1\n",
       "17  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)       6        38  uniform        2\n",
       "18  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)       8        51  uniform        0\n",
       "19  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)       8        51  uniform        1\n",
       "20  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)       8        51  uniform        2\n",
       "21  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      11        70  uniform        0\n",
       "22  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      11        70  uniform        1\n",
       "23  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      11        70  uniform        2\n",
       "24  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      14        88  uniform        0\n",
       "25  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      14        88  uniform        1\n",
       "26  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      14        88  uniform        2\n",
       "27  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      19       120  uniform        0\n",
       "28  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      19       120  uniform        1\n",
       "29  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      19       120  uniform        2\n",
       "30  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      25       158  uniform        0\n",
       "31  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      25       158  uniform        1\n",
       "32  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      25       158  uniform        2\n",
       "33  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      34       214  uniform        0\n",
       "34  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      34       214  uniform        1\n",
       "35  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      34       214  uniform        2\n",
       "36  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      45       283  uniform        0\n",
       "37  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      45       283  uniform        1\n",
       "38  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      45       283  uniform        2\n",
       "39  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      59       371  uniform        0\n",
       "40  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      59       371  uniform        1\n",
       "41  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      59       371  uniform        2\n",
       "42  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      79       497  uniform        0\n",
       "43  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      79       497  uniform        1\n",
       "44  V11J11-099__Z4_FO3_01__A1_small.tif  (5539, 3739, 3)      79       497  uniform        2"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#This part is creating all the different conditions for LBP to run over\n",
    "#This is mostly used to run over \n",
    "\n",
    "def get_dims_tiff(filepath):\n",
    "    myimg = skimage.io.imread(filepath)\n",
    "    return myimg.shape\n",
    "\n",
    "df_all = pd.DataFrame(imgs, columns=['Filenames'])\n",
    "#df_all['dims'] = list(map(uf.get_dims_from_numpy_file, [directory_in_imgs]*len(df_all) + df_all['Filenames']))\n",
    "df_all['dims'] = list(map(get_dims_tiff, [directory_in_imgs]*len(df_all) + df_all['Filenames']))\n",
    "#df_all['dims_superpixel'] = list(map(uf.get_cropped_superpixel_dims, df_all['dims'], repeat(1)))\n",
    "\n",
    "df_all = uf.create_df_cross_for_separate_dfs(df_all,\n",
    "                                             pd.DataFrame(radius_list, columns=['radius']))\n",
    "\n",
    "#df_all['n_points'] = [int(32/5*r) for r in df_all['radius']]\n",
    "df_all['n_points'] = [math.ceil(2*math.pi*r) for r in df_all['radius']]\n",
    "df_all['method'] = ['uniform']*len(df_all)\n",
    "df_channel = pd.DataFrame([0, 1, 2], columns=['channel'])\n",
    "\n",
    "df_all = uf.create_df_cross_for_separate_dfs(df_all, df_channel)\n",
    "\n",
    "df_all.sort_values(['n_points', 'Filenames'], inplace=True)\n",
    "df_all.reset_index(drop=True, inplace=True)\n",
    "\n",
    "df_all"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "497\n",
      "<class 'numpy.uint16'>\n"
     ]
    }
   ],
   "source": [
    "def get_numpy_datatype_unsigned_int(largest_value):\n",
    "    if largest_value <= 255:\n",
    "        print('In lower 255')\n",
    "        value = np.uint8\n",
    "    elif largest_value <= 65535:\n",
    "        value = np.uint16\n",
    "    else:\n",
    "        value = 0\n",
    "    return value\n",
    "\n",
    "mymax = np.max(df_all['n_points']); print(mymax)\n",
    "mydtype = get_numpy_datatype_unsigned_int(mymax); print(mydtype)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "c605977adaa04eaaa7511e28a10b10a3",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/45 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Already exists:  /home/jovyan/VU_TEX/playground_Ben/2023-07-05_Thymus/2023-07-06f_LBP_values_for_image_small/Channel_0_METHOD_uniform_npoints_7_radius_1/V11J11-099__Z4_FO3_01__A1_small.npy\n",
      "Already exists:  /home/jovyan/VU_TEX/playground_Ben/2023-07-05_Thymus/2023-07-06f_LBP_values_for_image_small/Channel_1_METHOD_uniform_npoints_7_radius_1/V11J11-099__Z4_FO3_01__A1_small.npy\n",
      "Already exists:  /home/jovyan/VU_TEX/playground_Ben/2023-07-05_Thymus/2023-07-06f_LBP_values_for_image_small/Channel_2_METHOD_uniform_npoints_7_radius_1/V11J11-099__Z4_FO3_01__A1_small.npy\n",
      "Already exists:  /home/jovyan/VU_TEX/playground_Ben/2023-07-05_Thymus/2023-07-06f_LBP_values_for_image_small/Channel_0_METHOD_uniform_npoints_13_radius_2/V11J11-099__Z4_FO3_01__A1_small.npy\n",
      "Already exists:  /home/jovyan/VU_TEX/playground_Ben/2023-07-05_Thymus/2023-07-06f_LBP_values_for_image_small/Channel_1_METHOD_uniform_npoints_13_radius_2/V11J11-099__Z4_FO3_01__A1_small.npy\n",
      "Already exists:  /home/jovyan/VU_TEX/playground_Ben/2023-07-05_Thymus/2023-07-06f_LBP_values_for_image_small/Channel_2_METHOD_uniform_npoints_13_radius_2/V11J11-099__Z4_FO3_01__A1_small.npy\n",
      "Already exists:  /home/jovyan/VU_TEX/playground_Ben/2023-07-05_Thymus/2023-07-06f_LBP_values_for_image_small/Channel_0_METHOD_uniform_npoints_19_radius_3/V11J11-099__Z4_FO3_01__A1_small.npy\n",
      "Already exists:  /home/jovyan/VU_TEX/playground_Ben/2023-07-05_Thymus/2023-07-06f_LBP_values_for_image_small/Channel_1_METHOD_uniform_npoints_19_radius_3/V11J11-099__Z4_FO3_01__A1_small.npy\n",
      "Already exists:  /home/jovyan/VU_TEX/playground_Ben/2023-07-05_Thymus/2023-07-06f_LBP_values_for_image_small/Channel_2_METHOD_uniform_npoints_19_radius_3/V11J11-099__Z4_FO3_01__A1_small.npy\n",
      "Already exists:  /home/jovyan/VU_TEX/playground_Ben/2023-07-05_Thymus/2023-07-06f_LBP_values_for_image_small/Channel_0_METHOD_uniform_npoints_26_radius_4/V11J11-099__Z4_FO3_01__A1_small.npy\n",
      "Already exists:  /home/jovyan/VU_TEX/playground_Ben/2023-07-05_Thymus/2023-07-06f_LBP_values_for_image_small/Channel_1_METHOD_uniform_npoints_26_radius_4/V11J11-099__Z4_FO3_01__A1_small.npy\n"
     ]
    }
   ],
   "source": [
    "for i in trange(len(df_all)):\n",
    "#    print(i, '/', len(df_all))\n",
    "    filename = df_all['Filenames'][i]\n",
    "    filename_out = filename.replace('.tif', '.npy')\n",
    "#    out_dims = df_all['dims_superpixel'][i]\n",
    "    radius = df_all['radius'][i]\n",
    "    n_points = df_all['n_points'][i]\n",
    "    method = df_all['method'][i]\n",
    "    channel = df_all['channel'][i]\n",
    "\n",
    "    start = datetime.now()\n",
    "#    print(start)\n",
    "    \n",
    "    sub_directory_out = 'Channel_' + str(channel) + '_METHOD_'+ method + '_npoints_' + str(n_points) + '_radius_' + str(radius) + '/'\n",
    "#    print(directory_out_top+sub_directory_out)\n",
    "    if not os.path.exists(directory_out_top+sub_directory_out):\n",
    "        os.mkdir(directory_out_top+sub_directory_out)\n",
    "        \n",
    "    if os.path.exists(directory_out_top+sub_directory_out+filename_out):\n",
    "        print('Already exists: ', directory_out_top+sub_directory_out+filename_out)\n",
    "        continue\n",
    "    \n",
    "    img = skimage.io.imread(directory_in_imgs + filename)[:,:,channel]\n",
    "    lbp = local_binary_pattern(img, n_points, radius, method).astype(mydtype)\n",
    "    np.save(directory_out_top+sub_directory_out+filename_out, lbp)\n",
    "#    print(datetime.now() - start)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## "
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "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": "3.8.0"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}