From b8ca2a712b39db144fa6dd2730d764912bc707dc Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Tue, 5 Nov 2019 10:49:54 +0900 Subject: Created using Colaboratory --- notebooks/ImageAI_Object_Detection_Malaria.ipynb | 8654 ++++++++++++++++++++++ 1 file changed, 8654 insertions(+) create mode 100644 notebooks/ImageAI_Object_Detection_Malaria.ipynb (limited to 'notebooks/ImageAI_Object_Detection_Malaria.ipynb') diff --git a/notebooks/ImageAI_Object_Detection_Malaria.ipynb b/notebooks/ImageAI_Object_Detection_Malaria.ipynb new file mode 100644 index 0000000..3a4ad07 --- /dev/null +++ b/notebooks/ImageAI_Object_Detection_Malaria.ipynb @@ -0,0 +1,8654 @@ +{ + "nbformat": 4, + "nbformat_minor": 0, + "metadata": { + "colab": { + "name": "ImageAI - Object Detection - Malaria.ipynb", + "provenance": [], + "collapsed_sections": [], + "include_colab_link": true + }, + "kernelspec": { + "name": "python3", + "display_name": "Python 3" + }, + "accelerator": "GPU" + }, + "cells": [ + { + "cell_type": "markdown", + "metadata": { + "id": "view-in-github", + "colab_type": "text" + }, + "source": [ + "\"Open" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "2zOSN4i_lYIo", + "colab_type": "text" + }, + "source": [ + "# Malaria Detection using Object Detection Techinique (FastAI YOLOv3)" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "9Y6vpGtJlhLB", + "colab_type": "text" + }, + "source": [ + "### Download the Dataset" + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "xXaLKSfZlGWS", + "colab_type": "code", + "outputId": "3911e5b9-8f0d-45a0-96c6-deee32e4cad6", + "colab": { + "base_uri": "https://localhost:8080/", + "height": 1000 + } + }, + "source": [ + "!wget http://air.ug/downloads/plasmodium-images.zip\n", + "!unzip plasmodium-images.zip" + ], + "execution_count": 0, + "outputs": [ + { + "output_type": "stream", + "text": [ + "--2019-10-29 08:38:31-- http://air.ug/downloads/plasmodium-images.zip\n", + "Resolving air.ug (air.ug)... 34.242.164.142\n", + "Connecting to air.ug (air.ug)|34.242.164.142|:80... connected.\n", + "HTTP request sent, awaiting response... 200 OK\n", + "Length: 148185339 (141M) [application/zip]\n", + "Saving to: ‘plasmodium-images.zip’\n", + "\n", + "plasmodium-images.z 100%[===================>] 141.32M 10.4MB/s in 17s \n", + "\n", + "2019-10-29 08:38:48 (8.38 MB/s) - ‘plasmodium-images.zip’ saved [148185339/148185339]\n", + "\n", + "Archive: plasmodium-images.zip\n", + " inflating: annotation/plasmodium-0000.xml \n", + " inflating: annotation/plasmodium-0001.xml \n", + " inflating: annotation/plasmodium-0002.xml \n", + " inflating: annotation/plasmodium-0003.xml \n", + " inflating: annotation/plasmodium-0004.xml \n", + " inflating: annotation/plasmodium-0005.xml \n", + " inflating: annotation/plasmodium-0006.xml \n", + " inflating: annotation/plasmodium-0007.xml \n", + " inflating: annotation/plasmodium-0008.xml \n", + " inflating: annotation/plasmodium-0009.xml \n", + " 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+ "cell_type": "code", + "metadata": { + "id": "nJEpLerRlQPU", + "colab_type": "code", + "outputId": "33deb625-9560-4a3a-e4fa-a72ec1e302df", + "colab": { + "base_uri": "https://localhost:8080/", + "height": 1000 + } + }, + "source": [ + "import os\n", + "from xml.etree import ElementTree as ET\n", + "\n", + "path = './annotation/'\n", + "\n", + "addSize = False\n", + "replaceString = True\n", + "addFileName = True\n", + "\n", + "def fixIt(XML_File):\n", + "\ttree = ET.parse(XML_File)\n", + "\troot = tree.getroot()\n", + "\n", + "\tsize = ET.Element(\"size\")\n", + "\theight = ET.Element(\"height\")\n", + "\twidth = ET.Element(\"width\")\n", + "\n", + "\theight.text = \"750\"\n", + "\twidth.text = \"750\"\n", + "\n", + "\tsize.append(height)\n", + "\tsize.append(width)\n", + "\n", + "\troot.insert(1,size)\n", + "\n", + "\ttree.write(XML_File)\n", + "\n", + "def addname(file, xml_file):\n", + "\ttree = ET.parse(xml_file)\n", + "\troot = tree.getroot()\n", + "\n", + "\tf = ET.Element(\"filename\")\n", + "\n", + "\tf.text = file\n", + "\n", + "\troot.insert(1, f)\n", + "\n", + "\ttree.write(xml_file)\n", + "\n", + "\n", + "def replaceIt(filename, old, new):\n", + "\tf = open(filename,'r')\n", + "\tfiledata = f.read()\n", + "\tf.close()\n", + "\tnewdata = filedata.replace(old,new)\n", + "\tf = open(filename,'w')\n", + "\tf.write(newdata)\n", + "\tf.close()\n", + "\n", + "\n", + "\n", + "for filename in os.listdir(path):\n", + "\tif not filename.endswith('.xml'): continue\n", + "\tfullname = os.path.join(path, filename)\n", + "\tif addFileName:\n", + "\t\timagename = filename.replace('xml','jpg')\n", + "\t\taddname(imagename, fullname)\n", + "\tif addSize:\n", + "\t\tfixIt(fullname)\n", + "\tif replaceString:\n", + "\t\treplaceIt(fullname, \"person\", \"plasmodium\")\n", + "\tprint(\"Fixed\", fullname)\n", + "\n" + ], + "execution_count": 0, + "outputs": [ + { + "output_type": "stream", + "text": [ + "Fixed ./annotation/plasmodium-1064.xml\n", + "Fixed ./annotation/plasmodium-1248.xml\n", + "Fixed ./annotation/plasmodium-0551.xml\n", + "Fixed ./annotation/plasmodium-2616.xml\n", + "Fixed ./annotation/plasmodium-1163.xml\n", + "Fixed ./annotation/plasmodium-1551.xml\n", + "Fixed ./annotation/plasmodium-0699.xml\n", + "Fixed ./annotation/plasmodium-0276.xml\n", + "Fixed ./annotation/plasmodium-2109.xml\n", + "Fixed ./annotation/plasmodium-2667.xml\n", + "Fixed ./annotation/plasmodium-1619.xml\n", + "Fixed ./annotation/plasmodium-0892.xml\n", + "Fixed ./annotation/plasmodium-2536.xml\n", + "Fixed ./annotation/plasmodium-0037.xml\n", + "Fixed ./annotation/plasmodium-1746.xml\n", + "Fixed ./annotation/plasmodium-0238.xml\n", + "Fixed ./annotation/plasmodium-0377.xml\n", + "Fixed ./annotation/plasmodium-1928.xml\n", + "Fixed ./annotation/plasmodium-1046.xml\n", + "Fixed ./annotation/plasmodium-0790.xml\n", + "Fixed ./annotation/plasmodium-1996.xml\n", + "Fixed ./annotation/plasmodium-1301.xml\n", + "Fixed ./annotation/plasmodium-1584.xml\n", + "Fixed ./annotation/plasmodium-1999.xml\n", + "Fixed ./annotation/plasmodium-0593.xml\n", + "Fixed ./annotation/plasmodium-2541.xml\n", + "Fixed ./annotation/plasmodium-1512.xml\n", + "Fixed ./annotation/plasmodium-1610.xml\n", + "Fixed ./annotation/plasmodium-1118.xml\n", + "Fixed ./annotation/plasmodium-0149.xml\n", + "Fixed ./annotation/plasmodium-2111.xml\n", + "Fixed ./annotation/plasmodium-0441.xml\n", + "Fixed ./annotation/plasmodium-0534.xml\n", + "Fixed ./annotation/plasmodium-1877.xml\n", + "Fixed ./annotation/plasmodium-0339.xml\n", + "Fixed ./annotation/plasmodium-0973.xml\n", + "Fixed ./annotation/plasmodium-2674.xml\n", + "Fixed ./annotation/plasmodium-0745.xml\n", + "Fixed ./annotation/plasmodium-0589.xml\n", + "Fixed ./annotation/plasmodium-0030.xml\n", + "Fixed ./annotation/plasmodium-0617.xml\n", + "Fixed ./annotation/plasmodium-2300.xml\n", + "Fixed ./annotation/plasmodium-0982.xml\n", + "Fixed ./annotation/plasmodium-2657.xml\n", + "Fixed ./annotation/plasmodium-1081.xml\n", + "Fixed ./annotation/plasmodium-0914.xml\n", + "Fixed ./annotation/plasmodium-2423.xml\n", + "Fixed ./annotation/plasmodium-2192.xml\n", + "Fixed ./annotation/plasmodium-0427.xml\n", + "Fixed ./annotation/plasmodium-2360.xml\n", + "Fixed ./annotation/plasmodium-0999.xml\n", + "Fixed ./annotation/plasmodium-0814.xml\n", + "Fixed ./annotation/plasmodium-0573.xml\n", + "Fixed ./annotation/plasmodium-1893.xml\n", + "Fixed ./annotation/plasmodium-2497.xml\n", + "Fixed ./annotation/plasmodium-0762.xml\n", + "Fixed ./annotation/plasmodium-1483.xml\n", + "Fixed ./annotation/plasmodium-0053.xml\n", + "Fixed ./annotation/plasmodium-2197.xml\n", + "Fixed ./annotation/plasmodium-1728.xml\n", + "Fixed ./annotation/plasmodium-2307.xml\n", + "Fixed ./annotation/plasmodium-1067.xml\n", + "Fixed ./annotation/plasmodium-1949.xml\n", + "Fixed ./annotation/plasmodium-1549.xml\n", + "Fixed ./annotation/plasmodium-0743.xml\n", + "Fixed ./annotation/plasmodium-0212.xml\n", + "Fixed ./annotation/plasmodium-2275.xml\n", + "Fixed ./annotation/plasmodium-2308.xml\n", + "Fixed ./annotation/plasmodium-2468.xml\n", + "Fixed ./annotation/plasmodium-1898.xml\n", + "Fixed ./annotation/plasmodium-0246.xml\n", + "Fixed ./annotation/plasmodium-0521.xml\n", + "Fixed ./annotation/plasmodium-2082.xml\n", + "Fixed ./annotation/plasmodium-1822.xml\n", + "Fixed ./annotation/plasmodium-1523.xml\n", + "Fixed ./annotation/plasmodium-2567.xml\n", + "Fixed ./annotation/plasmodium-2106.xml\n", + "Fixed ./annotation/plasmodium-0857.xml\n", + "Fixed ./annotation/plasmodium-2655.xml\n", + "Fixed ./annotation/plasmodium-1223.xml\n", + "Fixed ./annotation/plasmodium-1629.xml\n", + "Fixed ./annotation/plasmodium-1666.xml\n", + "Fixed ./annotation/plasmodium-0454.xml\n", + "Fixed ./annotation/plasmodium-0041.xml\n", + "Fixed ./annotation/plasmodium-0519.xml\n", + "Fixed ./annotation/plasmodium-1432.xml\n", + "Fixed ./annotation/plasmodium-0387.xml\n", + "Fixed ./annotation/plasmodium-1912.xml\n", + "Fixed ./annotation/plasmodium-1500.xml\n", + "Fixed ./annotation/plasmodium-1057.xml\n", + "Fixed ./annotation/plasmodium-0597.xml\n", + "Fixed ./annotation/plasmodium-2191.xml\n", + "Fixed ./annotation/plasmodium-2263.xml\n", + "Fixed ./annotation/plasmodium-0292.xml\n", + "Fixed ./annotation/plasmodium-0992.xml\n", + "Fixed ./annotation/plasmodium-0288.xml\n", + "Fixed ./annotation/plasmodium-1434.xml\n", + "Fixed ./annotation/plasmodium-0038.xml\n", + "Fixed ./annotation/plasmodium-0017.xml\n", + "Fixed ./annotation/plasmodium-0031.xml\n", + "Fixed ./annotation/plasmodium-0853.xml\n", + "Fixed ./annotation/plasmodium-0763.xml\n", + "Fixed ./annotation/plasmodium-0680.xml\n", + "Fixed ./annotation/plasmodium-0200.xml\n", + "Fixed ./annotation/plasmodium-2386.xml\n", + "Fixed ./annotation/plasmodium-0217.xml\n", + "Fixed ./annotation/plasmodium-2377.xml\n", + "Fixed ./annotation/plasmodium-0206.xml\n", + "Fixed ./annotation/plasmodium-0709.xml\n", + "Fixed ./annotation/plasmodium-1385.xml\n", + "Fixed ./annotation/plasmodium-1061.xml\n", + "Fixed ./annotation/plasmodium-1238.xml\n", + "Fixed ./annotation/plasmodium-1773.xml\n", + "Fixed ./annotation/plasmodium-0682.xml\n", + "Fixed ./annotation/plasmodium-1372.xml\n", + "Fixed ./annotation/plasmodium-0253.xml\n", + "Fixed ./annotation/plasmodium-0275.xml\n", + "Fixed ./annotation/plasmodium-1667.xml\n", + "Fixed ./annotation/plasmodium-1786.xml\n", + "Fixed ./annotation/plasmodium-0809.xml\n", + "Fixed ./annotation/plasmodium-0612.xml\n", + "Fixed ./annotation/plasmodium-1650.xml\n", + "Fixed ./annotation/plasmodium-1304.xml\n", + "Fixed ./annotation/plasmodium-0866.xml\n", + "Fixed ./annotation/plasmodium-1049.xml\n", + "Fixed ./annotation/plasmodium-0436.xml\n", + "Fixed ./annotation/plasmodium-1649.xml\n", + "Fixed ./annotation/plasmodium-2566.xml\n", + "Fixed ./annotation/plasmodium-2376.xml\n", + "Fixed ./annotation/plasmodium-0610.xml\n", + "Fixed ./annotation/plasmodium-0415.xml\n", + "Fixed ./annotation/plasmodium-1299.xml\n", + "Fixed ./annotation/plasmodium-2483.xml\n", + "Fixed ./annotation/plasmodium-2323.xml\n", + "Fixed ./annotation/plasmodium-2432.xml\n", + "Fixed ./annotation/plasmodium-2650.xml\n", + "Fixed ./annotation/plasmodium-1062.xml\n", + "Fixed ./annotation/plasmodium-0890.xml\n", + "Fixed ./annotation/plasmodium-2212.xml\n", + "Fixed ./annotation/plasmodium-0325.xml\n", + "Fixed ./annotation/plasmodium-2177.xml\n", + "Fixed ./annotation/plasmodium-1848.xml\n", + "Fixed ./annotation/plasmodium-0843.xml\n", + "Fixed ./annotation/plasmodium-1244.xml\n", + "Fixed ./annotation/plasmodium-0775.xml\n", + "Fixed ./annotation/plasmodium-0738.xml\n", + "Fixed ./annotation/plasmodium-1841.xml\n", + "Fixed ./annotation/plasmodium-0780.xml\n", + "Fixed ./annotation/plasmodium-2101.xml\n", + "Fixed ./annotation/plasmodium-2479.xml\n", + "Fixed ./annotation/plasmodium-1817.xml\n", + "Fixed ./annotation/plasmodium-1350.xml\n", + "Fixed ./annotation/plasmodium-1279.xml\n", + "Fixed ./annotation/plasmodium-0450.xml\n", + "Fixed ./annotation/plasmodium-0653.xml\n", + "Fixed ./annotation/plasmodium-1413.xml\n", + "Fixed ./annotation/plasmodium-1622.xml\n", + "Fixed ./annotation/plasmodium-0097.xml\n", + "Fixed ./annotation/plasmodium-0431.xml\n", + "Fixed ./annotation/plasmodium-1277.xml\n", + "Fixed ./annotation/plasmodium-1110.xml\n", + "Fixed ./annotation/plasmodium-0310.xml\n", + "Fixed ./annotation/plasmodium-1222.xml\n", + "Fixed ./annotation/plasmodium-0278.xml\n", + "Fixed ./annotation/plasmodium-2385.xml\n", + "Fixed ./annotation/plasmodium-2347.xml\n", + "Fixed ./annotation/plasmodium-1430.xml\n", + "Fixed ./annotation/plasmodium-1661.xml\n", + "Fixed ./annotation/plasmodium-1600.xml\n", + "Fixed ./annotation/plasmodium-1821.xml\n", + "Fixed ./annotation/plasmodium-1132.xml\n", + "Fixed ./annotation/plasmodium-0783.xml\n", + "Fixed ./annotation/plasmodium-0565.xml\n", + "Fixed ./annotation/plasmodium-2118.xml\n", + "Fixed ./annotation/plasmodium-1505.xml\n", + "Fixed ./annotation/plasmodium-2564.xml\n", + "Fixed ./annotation/plasmodium-2003.xml\n", + "Fixed ./annotation/plasmodium-0394.xml\n", + "Fixed ./annotation/plasmodium-0428.xml\n", + "Fixed ./annotation/plasmodium-1048.xml\n", + "Fixed ./annotation/plasmodium-2573.xml\n", + "Fixed ./annotation/plasmodium-2487.xml\n", + "Fixed ./annotation/plasmodium-1492.xml\n", + "Fixed ./annotation/plasmodium-1341.xml\n", + "Fixed ./annotation/plasmodium-2278.xml\n", + "Fixed ./annotation/plasmodium-1636.xml\n", + "Fixed ./annotation/plasmodium-0061.xml\n", + "Fixed ./annotation/plasmodium-0563.xml\n", + "Fixed ./annotation/plasmodium-0079.xml\n", + "Fixed ./annotation/plasmodium-0559.xml\n", + "Fixed 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./annotation/plasmodium-1722.xml\n", + "Fixed ./annotation/plasmodium-0141.xml\n", + "Fixed ./annotation/plasmodium-0421.xml\n", + "Fixed ./annotation/plasmodium-2558.xml\n", + "Fixed ./annotation/plasmodium-0280.xml\n", + "Fixed ./annotation/plasmodium-1466.xml\n", + "Fixed ./annotation/plasmodium-1228.xml\n", + "Fixed ./annotation/plasmodium-2280.xml\n", + "Fixed ./annotation/plasmodium-0227.xml\n", + "Fixed ./annotation/plasmodium-2524.xml\n", + "Fixed ./annotation/plasmodium-2687.xml\n", + "Fixed ./annotation/plasmodium-0590.xml\n", + "Fixed ./annotation/plasmodium-2475.xml\n", + "Fixed ./annotation/plasmodium-1015.xml\n", + "Fixed ./annotation/plasmodium-2429.xml\n", + "Fixed ./annotation/plasmodium-1485.xml\n", + "Fixed ./annotation/plasmodium-0844.xml\n", + "Fixed ./annotation/plasmodium-1013.xml\n", + "Fixed ./annotation/plasmodium-1611.xml\n", + "Fixed ./annotation/plasmodium-0178.xml\n", + "Fixed ./annotation/plasmodium-2318.xml\n", + "Fixed ./annotation/plasmodium-1070.xml\n", + "Fixed ./annotation/plasmodium-0163.xml\n", + "Fixed ./annotation/plasmodium-2221.xml\n", + "Fixed ./annotation/plasmodium-0905.xml\n", + "Fixed ./annotation/plasmodium-0679.xml\n", + "Fixed ./annotation/plasmodium-2502.xml\n", + "Fixed ./annotation/plasmodium-0365.xml\n", + "Fixed ./annotation/plasmodium-1559.xml\n", + "Fixed ./annotation/plasmodium-2648.xml\n", + "Fixed ./annotation/plasmodium-2163.xml\n", + "Fixed ./annotation/plasmodium-0504.xml\n", + "Fixed ./annotation/plasmodium-0927.xml\n", + "Fixed ./annotation/plasmodium-0880.xml\n", + "Fixed ./annotation/plasmodium-2597.xml\n", + "Fixed ./annotation/plasmodium-0363.xml\n", + "Fixed ./annotation/plasmodium-0123.xml\n", + "Fixed ./annotation/plasmodium-1384.xml\n", + "Fixed ./annotation/plasmodium-0324.xml\n", + "Fixed ./annotation/plasmodium-0352.xml\n", + "Fixed ./annotation/plasmodium-0595.xml\n", + "Fixed ./annotation/plasmodium-0119.xml\n", + "Fixed ./annotation/plasmodium-0487.xml\n", + "Fixed ./annotation/plasmodium-2333.xml\n", + "Fixed ./annotation/plasmodium-1338.xml\n", + "Fixed ./annotation/plasmodium-1632.xml\n", + "Fixed ./annotation/plasmodium-0142.xml\n", + "Fixed ./annotation/plasmodium-0279.xml\n", + "Fixed ./annotation/plasmodium-2340.xml\n", + "Fixed ./annotation/plasmodium-1169.xml\n", + "Fixed ./annotation/plasmodium-0591.xml\n", + "Fixed ./annotation/plasmodium-0234.xml\n", + "Fixed ./annotation/plasmodium-1181.xml\n", + "Fixed ./annotation/plasmodium-1120.xml\n", + "Fixed ./annotation/plasmodium-2017.xml\n", + "Fixed ./annotation/plasmodium-0322.xml\n", + "Fixed ./annotation/plasmodium-2440.xml\n", + "Fixed ./annotation/plasmodium-0432.xml\n", + "Fixed ./annotation/plasmodium-2588.xml\n", + "Fixed ./annotation/plasmodium-0430.xml\n", + "Fixed ./annotation/plasmodium-0856.xml\n", + "Fixed ./annotation/plasmodium-2443.xml\n", + "Fixed ./annotation/plasmodium-1674.xml\n", + "Fixed ./annotation/plasmodium-1285.xml\n", + "Fixed ./annotation/plasmodium-2021.xml\n", + "Fixed ./annotation/plasmodium-2686.xml\n", + "Fixed ./annotation/plasmodium-1291.xml\n", + "Fixed ./annotation/plasmodium-0219.xml\n", + "Fixed ./annotation/plasmodium-1498.xml\n", + "Fixed ./annotation/plasmodium-0799.xml\n", + "Fixed ./annotation/plasmodium-2154.xml\n", + "Fixed ./annotation/plasmodium-0222.xml\n", + "Fixed ./annotation/plasmodium-0189.xml\n", + "Fixed ./annotation/plasmodium-0804.xml\n", + "Fixed ./annotation/plasmodium-0695.xml\n", + "Fixed ./annotation/plasmodium-0071.xml\n", + "Fixed ./annotation/plasmodium-2242.xml\n", + "Fixed ./annotation/plasmodium-0615.xml\n", + "Fixed ./annotation/plasmodium-1175.xml\n", + "Fixed ./annotation/plasmodium-1137.xml\n", + "Fixed ./annotation/plasmodium-2689.xml\n", + "Fixed ./annotation/plasmodium-1104.xml\n", + "Fixed ./annotation/plasmodium-2312.xml\n", + "Fixed ./annotation/plasmodium-0789.xml\n", + "Fixed ./annotation/plasmodium-2675.xml\n", + "Fixed ./annotation/plasmodium-0819.xml\n", + "Fixed ./annotation/plasmodium-2343.xml\n", + "Fixed ./annotation/plasmodium-1392.xml\n", + "Fixed ./annotation/plasmodium-2485.xml\n", + "Fixed ./annotation/plasmodium-0469.xml\n", + "Fixed ./annotation/plasmodium-0518.xml\n", + "Fixed ./annotation/plasmodium-1876.xml\n", + "Fixed ./annotation/plasmodium-0676.xml\n", + "Fixed ./annotation/plasmodium-0935.xml\n", + "Fixed ./annotation/plasmodium-2217.xml\n", + "Fixed ./annotation/plasmodium-2552.xml\n", + "Fixed ./annotation/plasmodium-0741.xml\n", + "Fixed ./annotation/plasmodium-1484.xml\n", + "Fixed ./annotation/plasmodium-0306.xml\n", + "Fixed ./annotation/plasmodium-2218.xml\n", + "Fixed ./annotation/plasmodium-2134.xml\n", + "Fixed ./annotation/plasmodium-1211.xml\n", + "Fixed ./annotation/plasmodium-1945.xml\n", + "Fixed ./annotation/plasmodium-1348.xml\n", + "Fixed ./annotation/plasmodium-2249.xml\n", + "Fixed ./annotation/plasmodium-0075.xml\n", + "Fixed ./annotation/plasmodium-1007.xml\n", + "Fixed ./annotation/plasmodium-2100.xml\n", + "Fixed ./annotation/plasmodium-2592.xml\n", + "Fixed ./annotation/plasmodium-1591.xml\n", + "Fixed ./annotation/plasmodium-0566.xml\n", + "Fixed ./annotation/plasmodium-2223.xml\n", + "Fixed ./annotation/plasmodium-1032.xml\n", + "Fixed ./annotation/plasmodium-0023.xml\n", + "Fixed ./annotation/plasmodium-1617.xml\n", + "Fixed ./annotation/plasmodium-0865.xml\n", + "Fixed ./annotation/plasmodium-0475.xml\n", + "Fixed ./annotation/plasmodium-1815.xml\n", + "Fixed ./annotation/plasmodium-0100.xml\n", + "Fixed ./annotation/plasmodium-0334.xml\n", + "Fixed ./annotation/plasmodium-1552.xml\n", + "Fixed ./annotation/plasmodium-0791.xml\n", + "Fixed ./annotation/plasmodium-1747.xml\n", + "Fixed ./annotation/plasmodium-1321.xml\n", + "Fixed ./annotation/plasmodium-2067.xml\n", + "Fixed ./annotation/plasmodium-1429.xml\n", + "Fixed ./annotation/plasmodium-2617.xml\n", + "Fixed ./annotation/plasmodium-2454.xml\n", + "Fixed ./annotation/plasmodium-0086.xml\n", + "Fixed ./annotation/plasmodium-0173.xml\n", + "Fixed ./annotation/plasmodium-1176.xml\n", + "Fixed ./annotation/plasmodium-1906.xml\n", + "Fixed ./annotation/plasmodium-0884.xml\n", + "Fixed ./annotation/plasmodium-1040.xml\n", + "Fixed ./annotation/plasmodium-2179.xml\n", + "Fixed ./annotation/plasmodium-0116.xml\n", + "Fixed ./annotation/plasmodium-0088.xml\n", + "Fixed ./annotation/plasmodium-0101.xml\n", + "Fixed ./annotation/plasmodium-0984.xml\n", + "Fixed ./annotation/plasmodium-0010.xml\n", + "Fixed ./annotation/plasmodium-0201.xml\n", + "Fixed ./annotation/plasmodium-1180.xml\n", + "Fixed ./annotation/plasmodium-2088.xml\n", + "Fixed ./annotation/plasmodium-1711.xml\n", + "Fixed ./annotation/plasmodium-1895.xml\n", + "Fixed ./annotation/plasmodium-2233.xml\n", + "Fixed ./annotation/plasmodium-2495.xml\n", + "Fixed ./annotation/plasmodium-0408.xml\n", + "Fixed ./annotation/plasmodium-1984.xml\n", + "Fixed ./annotation/plasmodium-0645.xml\n", + "Fixed ./annotation/plasmodium-1204.xml\n", + "Fixed ./annotation/plasmodium-1069.xml\n", + "Fixed ./annotation/plasmodium-2519.xml\n", + "Fixed ./annotation/plasmodium-1263.xml\n", + "Fixed ./annotation/plasmodium-1695.xml\n", + "Fixed ./annotation/plasmodium-1763.xml\n", + "Fixed ./annotation/plasmodium-0261.xml\n", + "Fixed ./annotation/plasmodium-0668.xml\n", + "Fixed ./annotation/plasmodium-0321.xml\n", + "Fixed ./annotation/plasmodium-1034.xml\n", + "Fixed ./annotation/plasmodium-1373.xml\n", + "Fixed ./annotation/plasmodium-0547.xml\n", + "Fixed ./annotation/plasmodium-2358.xml\n", + "Fixed ./annotation/plasmodium-0761.xml\n", + "Fixed ./annotation/plasmodium-0535.xml\n", + "Fixed ./annotation/plasmodium-1366.xml\n", + "Fixed ./annotation/plasmodium-1183.xml\n", + "Fixed ./annotation/plasmodium-0390.xml\n", + "Fixed ./annotation/plasmodium-1428.xml\n", + "Fixed ./annotation/plasmodium-0964.xml\n", + "Fixed ./annotation/plasmodium-1489.xml\n", + "Fixed ./annotation/plasmodium-0244.xml\n", + "Fixed ./annotation/plasmodium-2132.xml\n", + "Fixed ./annotation/plasmodium-0167.xml\n", + "Fixed ./annotation/plasmodium-2199.xml\n", + "Fixed ./annotation/plasmodium-2637.xml\n", + "Fixed ./annotation/plasmodium-1058.xml\n", + "Fixed ./annotation/plasmodium-0036.xml\n", + "Fixed ./annotation/plasmodium-1154.xml\n", + "Fixed ./annotation/plasmodium-1796.xml\n", + "Fixed ./annotation/plasmodium-0989.xml\n", + "Fixed ./annotation/plasmodium-2022.xml\n", + "Fixed ./annotation/plasmodium-1844.xml\n", + "Fixed ./annotation/plasmodium-1091.xml\n", + "Fixed ./annotation/plasmodium-0894.xml\n", + "Fixed ./annotation/plasmodium-0107.xml\n", + "Fixed ./annotation/plasmodium-0862.xml\n", + "Fixed ./annotation/plasmodium-1116.xml\n", + "Fixed ./annotation/plasmodium-0495.xml\n", + "Fixed ./annotation/plasmodium-1157.xml\n", + "Fixed ./annotation/plasmodium-1829.xml\n", + "Fixed ./annotation/plasmodium-1873.xml\n", + "Fixed ./annotation/plasmodium-2146.xml\n", + "Fixed ./annotation/plasmodium-0254.xml\n", + "Fixed ./annotation/plasmodium-0577.xml\n", + "Fixed ./annotation/plasmodium-2234.xml\n", + "Fixed ./annotation/plasmodium-1245.xml\n", + "Fixed ./annotation/plasmodium-1334.xml\n", + "Fixed ./annotation/plasmodium-0207.xml\n", + "Fixed ./annotation/plasmodium-2610.xml\n", + "Fixed ./annotation/plasmodium-1012.xml\n", + "Fixed ./annotation/plasmodium-2228.xml\n", + "Fixed ./annotation/plasmodium-1358.xml\n", + "Fixed ./annotation/plasmodium-0130.xml\n", + "Fixed ./annotation/plasmodium-0517.xml\n", + "Fixed ./annotation/plasmodium-0188.xml\n", + "Fixed ./annotation/plasmodium-1421.xml\n", + "Fixed ./annotation/plasmodium-0388.xml\n", + "Fixed ./annotation/plasmodium-1325.xml\n", + "Fixed ./annotation/plasmodium-0991.xml\n", + "Fixed ./annotation/plasmodium-1751.xml\n", + "Fixed ./annotation/plasmodium-1289.xml\n", + "Fixed ./annotation/plasmodium-1679.xml\n", + "Fixed ./annotation/plasmodium-1833.xml\n", + "Fixed ./annotation/plasmodium-1311.xml\n", + "Fixed ./annotation/plasmodium-1606.xml\n", + "Fixed ./annotation/plasmodium-0782.xml\n", + "Fixed ./annotation/plasmodium-1369.xml\n", + "Fixed ./annotation/plasmodium-1433.xml\n", + "Fixed ./annotation/plasmodium-2463.xml\n", + "Fixed ./annotation/plasmodium-0127.xml\n", + "Fixed ./annotation/plasmodium-1526.xml\n", + "Fixed ./annotation/plasmodium-0510.xml\n", + "Fixed ./annotation/plasmodium-1857.xml\n", + "Fixed ./annotation/plasmodium-0110.xml\n", + "Fixed ./annotation/plasmodium-0719.xml\n", + "Fixed ./annotation/plasmodium-1756.xml\n", + "Fixed ./annotation/plasmodium-1693.xml\n", + "Fixed ./annotation/plasmodium-1884.xml\n", + "Fixed ./annotation/plasmodium-1614.xml\n", + "Fixed ./annotation/plasmodium-0362.xml\n", + "Fixed ./annotation/plasmodium-1389.xml\n", + "Fixed ./annotation/plasmodium-1018.xml\n", + "Fixed ./annotation/plasmodium-0489.xml\n", + "Fixed ./annotation/plasmodium-2041.xml\n", + "Fixed ./annotation/plasmodium-2615.xml\n", + "Fixed ./annotation/plasmodium-1475.xml\n", + "Fixed ./annotation/plasmodium-2253.xml\n", + "Fixed ./annotation/plasmodium-0497.xml\n", + "Fixed ./annotation/plasmodium-1084.xml\n", + "Fixed ./annotation/plasmodium-1588.xml\n", + "Fixed ./annotation/plasmodium-2159.xml\n", + "Fixed ./annotation/plasmodium-0922.xml\n", + "Fixed ./annotation/plasmodium-1503.xml\n", + "Fixed ./annotation/plasmodium-2219.xml\n", + "Fixed ./annotation/plasmodium-1251.xml\n", + "Fixed ./annotation/plasmodium-1317.xml\n", + "Fixed ./annotation/plasmodium-2032.xml\n", + "Fixed ./annotation/plasmodium-1144.xml\n", + "Fixed ./annotation/plasmodium-2190.xml\n", + "Fixed ./annotation/plasmodium-0496.xml\n", + "Fixed ./annotation/plasmodium-1883.xml\n", + "Fixed ./annotation/plasmodium-1944.xml\n", + "Fixed ./annotation/plasmodium-0845.xml\n", + "Fixed ./annotation/plasmodium-1854.xml\n", + "Fixed ./annotation/plasmodium-2261.xml\n", + "Fixed ./annotation/plasmodium-0944.xml\n", + "Fixed ./annotation/plasmodium-1795.xml\n", + "Fixed ./annotation/plasmodium-2023.xml\n", + "Fixed ./annotation/plasmodium-1644.xml\n", + "Fixed ./annotation/plasmodium-1215.xml\n", + "Fixed ./annotation/plasmodium-1333.xml\n", + "Fixed ./annotation/plasmodium-2596.xml\n", + "Fixed ./annotation/plasmodium-1443.xml\n", + "Fixed ./annotation/plasmodium-0954.xml\n", + "Fixed ./annotation/plasmodium-1020.xml\n", + "Fixed ./annotation/plasmodium-1082.xml\n", + "Fixed ./annotation/plasmodium-2466.xml\n", + "Fixed ./annotation/plasmodium-1623.xml\n", + "Fixed ./annotation/plasmodium-2460.xml\n", + "Fixed ./annotation/plasmodium-1327.xml\n", + "Fixed ./annotation/plasmodium-0514.xml\n", + "Fixed ./annotation/plasmodium-0267.xml\n", + "Fixed ./annotation/plasmodium-1077.xml\n", + "Fixed ./annotation/plasmodium-0148.xml\n", + "Fixed ./annotation/plasmodium-2297.xml\n", + "Fixed ./annotation/plasmodium-0757.xml\n", + "Fixed ./annotation/plasmodium-1379.xml\n", + "Fixed ./annotation/plasmodium-2336.xml\n", + "Fixed ./annotation/plasmodium-0215.xml\n", + "Fixed ./annotation/plasmodium-0582.xml\n", + "Fixed ./annotation/plasmodium-2131.xml\n", + "Fixed ./annotation/plasmodium-1924.xml\n", + "Fixed ./annotation/plasmodium-1038.xml\n", + "Fixed ./annotation/plasmodium-1547.xml\n", + "Fixed ./annotation/plasmodium-0555.xml\n", + "Fixed ./annotation/plasmodium-1809.xml\n", + "Fixed ./annotation/plasmodium-0232.xml\n", + "Fixed ./annotation/plasmodium-1234.xml\n", + "Fixed ./annotation/plasmodium-0473.xml\n", + "Fixed ./annotation/plasmodium-0063.xml\n", + "Fixed ./annotation/plasmodium-0917.xml\n", + "Fixed ./annotation/plasmodium-1331.xml\n", + "Fixed ./annotation/plasmodium-1541.xml\n", + "Fixed ./annotation/plasmodium-1407.xml\n", + "Fixed ./annotation/plasmodium-1634.xml\n", + "Fixed ./annotation/plasmodium-2556.xml\n", + "Fixed ./annotation/plasmodium-2670.xml\n", + "Fixed ./annotation/plasmodium-1440.xml\n", + "Fixed ./annotation/plasmodium-0356.xml\n", + "Fixed ./annotation/plasmodium-0781.xml\n", + "Fixed ./annotation/plasmodium-1004.xml\n", + "Fixed ./annotation/plasmodium-0050.xml\n", + "Fixed ./annotation/plasmodium-0651.xml\n", + "Fixed ./annotation/plasmodium-0312.xml\n", + "Fixed ./annotation/plasmodium-2513.xml\n", + "Fixed ./annotation/plasmodium-1881.xml\n", + "Fixed ./annotation/plasmodium-0895.xml\n", + "Fixed ./annotation/plasmodium-2013.xml\n", + "Fixed ./annotation/plasmodium-0382.xml\n", + "Fixed ./annotation/plasmodium-0557.xml\n", + "Fixed ./annotation/plasmodium-0801.xml\n", + "Fixed ./annotation/plasmodium-2270.xml\n", + "Fixed ./annotation/plasmodium-0453.xml\n", + "Fixed ./annotation/plasmodium-0832.xml\n", + "Fixed ./annotation/plasmodium-2514.xml\n", + "Fixed ./annotation/plasmodium-0550.xml\n", + "Fixed ./annotation/plasmodium-0176.xml\n", + "Fixed ./annotation/plasmodium-2019.xml\n", + "Fixed ./annotation/plasmodium-2424.xml\n", + "Fixed ./annotation/plasmodium-2455.xml\n", + "Fixed ./annotation/plasmodium-1340.xml\n", + "Fixed ./annotation/plasmodium-2634.xml\n", + "Fixed ./annotation/plasmodium-2621.xml\n", + "Fixed ./annotation/plasmodium-1867.xml\n", + "Fixed ./annotation/plasmodium-0304.xml\n", + "Fixed ./annotation/plasmodium-0560.xml\n", + "Fixed ./annotation/plasmodium-1837.xml\n", + "Fixed ./annotation/plasmodium-1045.xml\n", + "Fixed ./annotation/plasmodium-1978.xml\n", + "Fixed ./annotation/plasmodium-1861.xml\n", + "Fixed ./annotation/plasmodium-1352.xml\n", + "Fixed ./annotation/plasmodium-2659.xml\n", + "Fixed ./annotation/plasmodium-1189.xml\n", + "Fixed ./annotation/plasmodium-0385.xml\n", + "Fixed ./annotation/plasmodium-0197.xml\n", + "Fixed ./annotation/plasmodium-0925.xml\n", + "Fixed ./annotation/plasmodium-2652.xml\n", + "Fixed ./annotation/plasmodium-1878.xml\n", + "Fixed ./annotation/plasmodium-1397.xml\n", + "Fixed ./annotation/plasmodium-2037.xml\n", + "Fixed ./annotation/plasmodium-0777.xml\n", + "Fixed ./annotation/plasmodium-2142.xml\n", + "Fixed ./annotation/plasmodium-1188.xml\n", + "Fixed ./annotation/plasmodium-0570.xml\n", + "Fixed ./annotation/plasmodium-0165.xml\n", + "Fixed ./annotation/plasmodium-0019.xml\n", + "Fixed ./annotation/plasmodium-1250.xml\n", + "Fixed ./annotation/plasmodium-2224.xml\n", + "Fixed ./annotation/plasmodium-0466.xml\n", + "Fixed ./annotation/plasmodium-0080.xml\n", + "Fixed ./annotation/plasmodium-0803.xml\n", + "Fixed ./annotation/plasmodium-2534.xml\n", + "Fixed ./annotation/plasmodium-0863.xml\n", + "Fixed ./annotation/plasmodium-0395.xml\n", + "Fixed ./annotation/plasmodium-1265.xml\n", + "Fixed ./annotation/plasmodium-0571.xml\n", + "Fixed ./annotation/plasmodium-1548.xml\n", + "Fixed ./annotation/plasmodium-2395.xml\n", + "Fixed ./annotation/plasmodium-0754.xml\n", + "Fixed ./annotation/plasmodium-1572.xml\n", + "Fixed ./annotation/plasmodium-1033.xml\n", + "Fixed ./annotation/plasmodium-1726.xml\n", + "Fixed ./annotation/plasmodium-0192.xml\n", + "Fixed ./annotation/plasmodium-1000.xml\n", + "Fixed ./annotation/plasmodium-2415.xml\n", + "Fixed ./annotation/plasmodium-0174.xml\n", + "Fixed ./annotation/plasmodium-2404.xml\n", + "Fixed ./annotation/plasmodium-2419.xml\n", + "Fixed ./annotation/plasmodium-0613.xml\n", + "Fixed ./annotation/plasmodium-1095.xml\n", + "Fixed ./annotation/plasmodium-0214.xml\n", + "Fixed ./annotation/plasmodium-1871.xml\n", + "Fixed ./annotation/plasmodium-2605.xml\n", + "Fixed ./annotation/plasmodium-0301.xml\n", + "Fixed ./annotation/plasmodium-0910.xml\n", + "Fixed ./annotation/plasmodium-1098.xml\n", + "Fixed ./annotation/plasmodium-0114.xml\n", + "Fixed ./annotation/plasmodium-0697.xml\n", + "Fixed ./annotation/plasmodium-1699.xml\n", + "Fixed ./annotation/plasmodium-0823.xml\n", + "Fixed ./annotation/plasmodium-1662.xml\n", + "Fixed ./annotation/plasmodium-2600.xml\n", + "Fixed ./annotation/plasmodium-1487.xml\n", + "Fixed ./annotation/plasmodium-0533.xml\n", + "Fixed ./annotation/plasmodium-2407.xml\n", + "Fixed ./annotation/plasmodium-2438.xml\n", + "Fixed ./annotation/plasmodium-2072.xml\n", + "Fixed ./annotation/plasmodium-2006.xml\n", + "Fixed ./annotation/plasmodium-1586.xml\n", + "Fixed ./annotation/plasmodium-2339.xml\n", + "Fixed ./annotation/plasmodium-0587.xml\n", + "Fixed ./annotation/plasmodium-1842.xml\n", + "Fixed ./annotation/plasmodium-2064.xml\n", + "Fixed ./annotation/plasmodium-0067.xml\n", + "Fixed ./annotation/plasmodium-1294.xml\n", + "Fixed ./annotation/plasmodium-1195.xml\n", + "Fixed ./annotation/plasmodium-0561.xml\n", + "Fixed ./annotation/plasmodium-2351.xml\n", + "Fixed ./annotation/plasmodium-0694.xml\n", + "Fixed ./annotation/plasmodium-1573.xml\n", + "Fixed ./annotation/plasmodium-1261.xml\n", + "Fixed ./annotation/plasmodium-1393.xml\n", + "Fixed ./annotation/plasmodium-2024.xml\n", + "Fixed ./annotation/plasmodium-2623.xml\n", + "Fixed ./annotation/plasmodium-2482.xml\n", + "Fixed ./annotation/plasmodium-2342.xml\n", + "Fixed ./annotation/plasmodium-1694.xml\n", + "Fixed ./annotation/plasmodium-0032.xml\n", + "Fixed ./annotation/plasmodium-1220.xml\n", + "Fixed ./annotation/plasmodium-0650.xml\n", + "Fixed ./annotation/plasmodium-1633.xml\n", + "Fixed ./annotation/plasmodium-2441.xml\n" + ], + "name": "stdout" + } + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "oQfWG04ElmIM", + "colab_type": "text" + }, + "source": [ + "### Split the files" + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "nOKAWNaMlXQE", + "colab_type": "code", + "colab": {} + }, + "source": [ + "!mv annotation annotations\n", + "\n", + "!mkdir data/\n", + "!mkdir data/train\n", + "!mkdir data/validation\n", + "\n", + "!mkdir data/train/images\n", + "!mkdir data/train/annotations\n", + "\n", + "!mkdir data/validation/images\n", + "!mkdir data/validation/annotations" + ], + "execution_count": 0, + "outputs": [] + }, + { + "cell_type": "code", + "metadata": { + "id": "YSkICBehn43J", + "colab_type": "code", + "outputId": "61187f8e-750b-4839-bc93-bfb41aa23ca6", + "colab": { + "base_uri": "https://localhost:8080/", + "height": 68 + } + }, + "source": [ + "import random \n", + "import shutil\n", + "\n", + "img = []\n", + "xml = []\n", + "\n", + "trainPathImages = './data/train/images'\n", + "trainPathAnnotation = './data/train/annotations'\n", + "\n", + "valPathImages = './data/validation/images'\n", + "valPathAnnotation = './data/validation/annotations'\n", + "\n", + "\n", + "originI = './images'\n", + "\n", + "\n", + "train_ratio = 0.8\n", + "val_ratio = 1.0 - train_ratio\n", + "\n", + "ImgCount = len(os.listdir('./images/'))\n", + "\n", + "for (dirname, dirs, files) in os.walk('./images'):\n", + " for filename in files:\n", + " if filename.endswith('.xml'):\n", + " xml.append(filename)\n", + " else:\n", + " img.append(filename)\n", + "\n", + "countForTrain = int(len(img)*train_ratio)\n", + "countForValidation = int(len(img)*val_ratio)\n", + "\n", + "\n", + "for x in range(countForTrain):\n", + " index = random.choice(range(len(img)))\n", + " fileJpg = img[index]\n", + " fileXml = fileJpg[:-4] +'.xml'\n", + "\n", + " shutil.move(os.path.join('./images/', fileJpg), os.path.join(trainPathImages, fileJpg))\n", + " shutil.move(os.path.join('./annotations/', fileXml), os.path.join(trainPathAnnotation, fileXml))\n", + "\n", + " img.remove(fileJpg)\n", + " \n", + "for x in range(countForValidation):\n", + " index = random.choice(range(len(img)))\n", + " fileJpg = img[index]\n", + " fileXml = fileJpg[:-4] +'.xml'\n", + "\n", + " shutil.move(os.path.join('./images', fileJpg), os.path.join(valPathImages, fileJpg))\n", + " shutil.move(os.path.join('./annotations', fileXml), os.path.join(valPathAnnotation, fileXml))\n", + " \n", + " img.remove(fileJpg)\n", + "\n", + "print('Total images: ', ImgCount)\n", + "print('Images in train dir:', len(os.listdir(trainPathImages)))\n", + "print('Images in validation dir:', len(os.listdir(valPathImages)))\n" + ], + "execution_count": 0, + "outputs": [ + { + "output_type": "stream", + "text": [ + "Total images: 541\n", + "Images in train dir: 2594\n", + "Images in validation dir: 108\n" + ], + "name": "stdout" + } + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "MJ-YsR_4loih", + "colab_type": "text" + }, + "source": [ + "### Install Dependencies" + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "oFgdBj1ElwN3", + "colab_type": "code", + "outputId": "36356b1f-c054-4a6c-d203-4e851de3222f", + "colab": { + "base_uri": "https://localhost:8080/", + "height": 938 + } + }, + "source": [ + "!pip3 install tensorflow-gpu==1.13.1\n", + "!pip3 install imageai --upgrade" + ], + "execution_count": 0, + "outputs": [ + { + "output_type": "stream", + "text": [ + "Collecting tensorflow-gpu==1.13.1\n", + "\u001b[?25l Downloading https://files.pythonhosted.org/packages/7b/b1/0ad4ae02e17ddd62109cd54c291e311c4b5fd09b4d0678d3d6ce4159b0f0/tensorflow_gpu-1.13.1-cp36-cp36m-manylinux1_x86_64.whl (345.2MB)\n", + "\u001b[K |████████████████████████████████| 345.2MB 50kB/s \n", + "\u001b[?25hRequirement already satisfied: termcolor>=1.1.0 in /usr/local/lib/python3.6/dist-packages (from tensorflow-gpu==1.13.1) (1.1.0)\n", + "Requirement already satisfied: grpcio>=1.8.6 in /usr/local/lib/python3.6/dist-packages (from tensorflow-gpu==1.13.1) (1.15.0)\n", + "Requirement already satisfied: numpy>=1.13.3 in /usr/local/lib/python3.6/dist-packages (from tensorflow-gpu==1.13.1) (1.17.3)\n", + "Requirement already satisfied: six>=1.10.0 in /usr/local/lib/python3.6/dist-packages (from tensorflow-gpu==1.13.1) (1.12.0)\n", + "Collecting 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/usr/local/lib/python3.6/dist-packages (from tensorboard<1.14.0,>=1.13.0->tensorflow-gpu==1.13.1) (0.16.0)\n", + "Requirement already satisfied: h5py in /usr/local/lib/python3.6/dist-packages (from keras-applications>=1.0.6->tensorflow-gpu==1.13.1) (2.8.0)\n", + "Requirement already satisfied: setuptools in /usr/local/lib/python3.6/dist-packages (from protobuf>=3.6.1->tensorflow-gpu==1.13.1) (41.4.0)\n", + "\u001b[31mERROR: tensorflow 1.15.0 has requirement tensorboard<1.16.0,>=1.15.0, but you'll have tensorboard 1.13.1 which is incompatible.\u001b[0m\n", + "\u001b[31mERROR: tensorflow 1.15.0 has requirement tensorflow-estimator==1.15.1, but you'll have tensorflow-estimator 1.13.0 which is incompatible.\u001b[0m\n", + "Installing collected packages: mock, tensorflow-estimator, tensorboard, tensorflow-gpu\n", + " Found existing installation: tensorflow-estimator 1.15.1\n", + " Uninstalling tensorflow-estimator-1.15.1:\n", + " Successfully uninstalled tensorflow-estimator-1.15.1\n", + " Found existing installation: tensorboard 1.15.0\n", + " Uninstalling tensorboard-1.15.0:\n", + " Successfully uninstalled tensorboard-1.15.0\n", + "Successfully installed mock-3.0.5 tensorboard-1.13.1 tensorflow-estimator-1.13.0 tensorflow-gpu-1.13.1\n", + "Collecting imageai\n", + "\u001b[?25l Downloading https://files.pythonhosted.org/packages/09/99/4023e191a343fb23f01ae02ac57a5ca58037c310e8d8c62f87638a3bafc7/imageai-2.1.5-py3-none-any.whl (180kB)\n", + "\u001b[K |████████████████████████████████| 184kB 3.5MB/s \n", + "\u001b[?25hRequirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.6/dist-packages (from imageai) (1.3.1)\n", + "Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.6/dist-packages (from imageai) (3.1.1)\n", + "Requirement already satisfied, skipping upgrade: h5py in /usr/local/lib/python3.6/dist-packages (from imageai) (2.8.0)\n", + "Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.6/dist-packages (from imageai) (1.17.3)\n", + "Requirement already satisfied, skipping upgrade: pillow in /usr/local/lib/python3.6/dist-packages (from imageai) (4.3.0)\n", + "Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.6/dist-packages (from matplotlib->imageai) (1.1.0)\n", + "Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.6/dist-packages (from matplotlib->imageai) (0.10.0)\n", + "Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.6/dist-packages (from matplotlib->imageai) (2.4.2)\n", + "Requirement already satisfied, skipping upgrade: python-dateutil>=2.1 in /usr/local/lib/python3.6/dist-packages (from matplotlib->imageai) (2.6.1)\n", + "Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.6/dist-packages (from h5py->imageai) (1.12.0)\n", + "Requirement already satisfied, skipping upgrade: olefile in /usr/local/lib/python3.6/dist-packages (from pillow->imageai) (0.46)\n", + "Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.6/dist-packages (from kiwisolver>=1.0.1->matplotlib->imageai) (41.4.0)\n", + "Installing collected packages: imageai\n", + "Successfully installed imageai-2.1.5\n" + ], + "name": "stdout" + } + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "79q2Feq00LIi", + "colab_type": "text" + }, + "source": [ + "### Download Pre-Trained YOLOv3 weights for transfer learning" + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "xLJXm1WE0Kuj", + "colab_type": "code", + "outputId": "abe9472b-fd96-48d4-def6-a34f25e18c0d", + "colab": { + "base_uri": "https://localhost:8080/", + "height": 343 + } + }, + "source": [ + "#https://github-production-release-asset-2e65be.s3.amazonaws.com/125932201/12701d80-b2ab-11e9-9f56-c06e1dfbec05?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20191029%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20191029T092049Z&X-Amz-Expires=300&X-Amz-Signature=2c9d2e1d5850ea3ec042f06855c545c25c5fcee848b944dce270135b8c17c4d1&X-Amz-SignedHeaders=host&actor_id=29234112&response-content-disposition=attachment%3B%20filename%3Dpretrained-yolov3.h5&response-content-type=application%2Foctet-stream\n", + "%cd data/\n", + "!wget https://github.com/OlafenwaMoses/ImageAI/releases/download/essential-v4/pretrained-yolov3.h5\n", + "%cd /content/" + ], + "execution_count": 0, + "outputs": [ + { + "output_type": "stream", + "text": [ + "/content/data\n", + "--2019-10-29 09:21:30-- https://github.com/OlafenwaMoses/ImageAI/releases/download/essential-v4/pretrained-yolov3.h5\n", + "Resolving github.com (github.com)... 140.82.114.4\n", + "Connecting to github.com (github.com)|140.82.114.4|:443... connected.\n", + "HTTP request sent, awaiting response... 302 Found\n", + "Location: https://github-production-release-asset-2e65be.s3.amazonaws.com/125932201/12701d80-b2ab-11e9-9f56-c06e1dfbec05?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20191029%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20191029T092130Z&X-Amz-Expires=300&X-Amz-Signature=0aa815cd6c7fad46b7e98ca957dd79b5d2d9fc8162a149c66a6bd939b03e680f&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dpretrained-yolov3.h5&response-content-type=application%2Foctet-stream [following]\n", + "--2019-10-29 09:21:30-- 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"pretrained-yolov3.h 100%[===================>] 237.15M 69.0MB/s in 3.4s \n", + "\n", + "2019-10-29 09:21:34 (69.0 MB/s) - ‘pretrained-yolov3.h5’ saved [248671664/248671664]\n", + "\n", + "/content\n" + ], + "name": "stdout" + } + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "ilpUdAESnPpD", + "colab_type": "text" + }, + "source": [ + "### Train Model" + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "kaqLP8sOmJ-6", + "colab_type": "code", + "outputId": "d1c77329-1b60-4b37-8967-0530eb1074b3", + "colab": { + "base_uri": "https://localhost:8080/", + "height": 445 + } + }, + "source": [ + "from imageai.Detection.Custom import DetectionModelTrainer\n", + "\n", + "trainer = DetectionModelTrainer()\n", + "trainer.setModelTypeAsYOLOv3()\n", + "trainer.setDataDirectory(data_directory=\"data\")\n", + "trainer.setTrainConfig(object_names_array=[\"plasmodium\"], batch_size=4, num_experiments=200, train_from_pretrained_model='./data/pretrained-yolov3.h5')\n", + "\n", + "trainer.trainModel()" + ], + "execution_count": 0, + "outputs": [ + { + "output_type": "stream", + "text": [ + "Generating anchor boxes for training images and annotation...\n", + "Average IOU for 9 anchors: 0.96\n", + "Anchor Boxes generated.\n", + "Detection configuration saved in data/json/detection_config.json\n", + "Training on: \t['plasmodium']\n", + "Training with Batch Size: 4\n", + "Number of Experiments: 200\n", + "Training with transfer learning from pretrained Model\n" + ], + "name": "stdout" + }, + { + "output_type": "stream", + "text": [ + "/usr/local/lib/python3.6/dist-packages/keras/callbacks.py:1335: UserWarning: `epsilon` argument is deprecated and will be removed, use `min_delta` instead.\n", + " warnings.warn('`epsilon` argument is deprecated and '\n" + ], + "name": "stderr" + }, + { + "output_type": "stream", + "text": [ + "Epoch 1/200\n", + "4632/4632 [==============================] - 6288s 1s/step - loss: 14.0821 - yolo_layer_7_loss: 12.6587 - yolo_layer_8_loss: 0.4870 - yolo_layer_9_loss: 0.9365 - val_loss: 12.0209 - val_yolo_layer_7_loss: 12.0160 - val_yolo_layer_8_loss: 0.0011 - val_yolo_layer_9_loss: 0.0038\n", + "Epoch 2/200\n", + "4632/4632 [==============================] - 6110s 1s/step - loss: 10.3765 - yolo_layer_7_loss: 10.3750 - yolo_layer_8_loss: 4.9893e-04 - yolo_layer_9_loss: 0.0011 - val_loss: 10.8461 - val_yolo_layer_7_loss: 10.8455 - val_yolo_layer_8_loss: 1.8135e-04 - val_yolo_layer_9_loss: 3.6427e-04\n", + "Epoch 3/200\n", + "4632/4632 [==============================] - 6051s 1s/step - loss: 9.8156 - yolo_layer_7_loss: 9.8152 - yolo_layer_8_loss: 1.2940e-04 - yolo_layer_9_loss: 2.0879e-04 - val_loss: 10.7831 - val_yolo_layer_7_loss: 10.7829 - val_yolo_layer_8_loss: 7.2118e-05 - val_yolo_layer_9_loss: 1.2143e-04\n", + "Epoch 4/200\n", + "4632/4632 [==============================] - 6072s 1s/step - loss: 9.4670 - yolo_layer_7_loss: 9.4668 - yolo_layer_8_loss: 6.4030e-05 - yolo_layer_9_loss: 9.0184e-05 - val_loss: 10.7459 - val_yolo_layer_7_loss: 10.7458 - val_yolo_layer_8_loss: 4.4788e-05 - val_yolo_layer_9_loss: 6.9398e-05\n", + "Epoch 5/200\n", + "4632/4632 [==============================] - 6055s 1s/step - loss: 9.2720 - yolo_layer_7_loss: 9.2719 - yolo_layer_8_loss: 4.1976e-05 - yolo_layer_9_loss: 5.5873e-05 - val_loss: 10.2132 - val_yolo_layer_7_loss: 10.2131 - val_yolo_layer_8_loss: 3.0568e-05 - val_yolo_layer_9_loss: 4.3454e-05\n", + "Epoch 6/200\n", + "4632/4632 [==============================] - 6157s 1s/step - loss: 9.1783 - yolo_layer_7_loss: 9.1783 - yolo_layer_8_loss: 3.1061e-05 - yolo_layer_9_loss: 4.0417e-05 - val_loss: 11.2590 - val_yolo_layer_7_loss: 11.2589 - val_yolo_layer_8_loss: 2.4745e-05 - val_yolo_layer_9_loss: 3.4325e-05\n", + "Epoch 7/200\n", + "2660/4632 [================>.............] - ETA: 42:20 - loss: 9.0553 - yolo_layer_7_loss: 9.0552 - yolo_layer_8_loss: 2.4331e-05 - yolo_layer_9_loss: 3.1945e-05" + ], + "name": "stdout" + } + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "7ehEilE_nRf5", + "colab_type": "text" + }, + "source": [ + "### Evaluate Model" + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "i633k48mnS1A", + "colab_type": "code", + "colab": {} + }, + "source": [ + "from imageai.Detection.Custom import DetectionModelTrainer\n", + "\n", + "trainer = DetectionModelTrainer()\n", + "trainer.setModelTypeAsYOLOv3()\n", + "trainer.setDataDirectory(data_directory=\"data\")\n", + "metrics = trainer.evaluateModel(model_path=\"data/models\", json_path=\"data/json/detection_config.json\", iou_threshold=0.5, object_threshold=0.3, nms_threshold=0.5)" + ], + "execution_count": 0, + "outputs": [] + } + ] +} \ No newline at end of file -- cgit v1.2.3