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diff --git a/notebooks/Turicreate_Obejct_Detection_Malaria_02.ipynb b/notebooks/Turicreate_Obejct_Detection_Malaria_02.ipynb new file mode 100644 index 0000000..3de73ee --- /dev/null +++ b/notebooks/Turicreate_Obejct_Detection_Malaria_02.ipynb @@ -0,0 +1,10136 @@ +{ + "nbformat": 4, + "nbformat_minor": 0, + "metadata": { + "colab": { + "name": "Turicreate - Obejct Detection - Malaria - 02.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": [ + "<a href=\"https://colab.research.google.com/github/navanchauhan/Malaria-Detection/blob/master/notebooks/Turicreate_Obejct_Detection_Malaria_02.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "uObyj04Ma_yK", + "colab_type": "text" + }, + "source": [ + "# Object Detection for Malaria using Turicreate" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "EexmbgqLbPZy", + "colab_type": "text" + }, + "source": [ + "### 1) Mount Google Drive\n", + "\n", + "The trained model is thus directly copied to your google drive" + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "9dM_OI1La9Jf", + "colab_type": "code", + "outputId": "44f04eac-f470-4546-8e8d-c98dcb06a279", + "colab": { + "base_uri": "https://localhost:8080/", + "height": 127 + } + }, + "source": [ + "from google.colab import drive\n", + "\n", + "drive.mount('/content/gdrive')" + ], + "execution_count": 0, + "outputs": [ + { + "output_type": "stream", + "text": [ + "Go to this URL in a browser: https://accounts.google.com/o/oauth2/auth?client_id=947318989803-6bn6qk8qdgf4n4g3pfee6491hc0brc4i.apps.googleusercontent.com&redirect_uri=urn%3Aietf%3Awg%3Aoauth%3A2.0%3Aoob&scope=email%20https%3A%2F%2Fwww.googleapis.com%2Fauth%2Fdocs.test%20https%3A%2F%2Fwww.googleapis.com%2Fauth%2Fdrive%20https%3A%2F%2Fwww.googleapis.com%2Fauth%2Fdrive.photos.readonly%20https%3A%2F%2Fwww.googleapis.com%2Fauth%2Fpeopleapi.readonly&response_type=code\n", + "\n", + "Enter your authorization code:\n", + "··········\n", + "Mounted at /content/gdrive\n" + ], + "name": "stdout" + } + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "8FPZWglobXOn", + "colab_type": "text" + }, + "source": [ + "### 2) Install Dependencies\n", + "\n", + "To train the model on the Colab GPU we need to install the custom version of mxnet\n", + "\n", + "\n", + "##### Make sure you have selected GPU in the runtype settings" + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "Sch_tPbJKZ9b", + "colab_type": "code", + "outputId": "948c81b5-b683-4b5e-96f0-e13215e6f90e", + "colab": { + "base_uri": "https://localhost:8080/", + "height": 1000 + } + }, + "source": [ + "!pip install turicreate\n", + "!pip uninstall -y mxnet\n", + "!pip install mxnet-cu100==1.4.0.post0" + ], + "execution_count": 0, + "outputs": [ + { + "output_type": "stream", + "text": [ + "Collecting turicreate\n", + "\u001b[?25l Downloading https://files.pythonhosted.org/packages/05/bf/d1c74d5002be47db24b13adde42e5898b1ff63cae31e582ddd908006ae37/turicreate-5.8-cp36-cp36m-manylinux1_x86_64.whl (90.7MB)\n", + "\u001b[K |████████████████████████████████| 90.7MB 116kB/s \n", + "\u001b[?25hRequirement already satisfied: prettytable==0.7.2 in /usr/local/lib/python3.6/dist-packages (from turicreate) (0.7.2)\n", + "Requirement already satisfied: six>=1.10.0 in /usr/local/lib/python3.6/dist-packages (from turicreate) (1.12.0)\n", + "Collecting mxnet<1.2.0,>=1.1.0\n", + "\u001b[?25l Downloading 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numpy>=1.15, but you'll have numpy 1.14.6 which is incompatible.\u001b[0m\n", + "\u001b[31mERROR: datascience 0.10.6 has requirement folium==0.2.1, but you'll have folium 0.8.3 which is incompatible.\u001b[0m\n", + "\u001b[31mERROR: cvxpy 1.0.25 has requirement numpy>=1.15, but you'll have numpy 1.14.6 which is incompatible.\u001b[0m\n", + "\u001b[31mERROR: blis 0.2.4 has requirement numpy>=1.15.0, but you'll have numpy 1.14.6 which is incompatible.\u001b[0m\n", + "\u001b[31mERROR: albumentations 0.1.12 has requirement imgaug<0.2.7,>=0.2.5, but you'll have imgaug 0.2.9 which is incompatible.\u001b[0m\n", + "Installing collected packages: numpy, mxnet-cu100\n", + " Found existing installation: numpy 1.16.4\n", + " Uninstalling numpy-1.16.4:\n", + " Successfully uninstalled numpy-1.16.4\n", + "Successfully installed mxnet-cu100-1.4.0.post0 numpy-1.14.6\n" + ], + "name": "stdout" + }, + { + "output_type": "display_data", + "data": { + "application/vnd.colab-display-data+json": { + "pip_warning": { + "packages": [ + "numpy" + ] + } + } + }, + "metadata": { + "tags": [] + } + } + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "69zbhy-zdip0", + "colab_type": "text" + }, + "source": [ + "Now restart the runtime." + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "XIAuyza3drzJ", + "colab_type": "text" + }, + "source": [ + "### 3) Fetch the dataset" + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "0SUgEVilK-t5", + "colab_type": "code", + "outputId": "aa26c154-3027-4fd9-829a-c3e6499574cf", + "colab": { + "base_uri": "https://localhost:8080/", + "height": 1000 + } + }, + "source": [ + "!wget http://air.ug/downloads/plasmodium-images.zip\n", + "!unzip plasmodium-images.zip\n", + "!ls images/" + ], + "execution_count": 0, + "outputs": [ + { + "output_type": "stream", + "text": [ + "--2019-11-05 00:45:29-- http://air.ug/downloads/plasmodium-images.zip\n", + "Resolving air.ug (air.ug)... 34.242.164.142\n", + "Connecting to air.ug 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"plasmodium-0898.jpg plasmodium-1799.jpg plasmodium-2700.jpg\n", + "plasmodium-0899.jpg plasmodium-1800.jpg plasmodium-2701.jpg\n", + "plasmodium-0900.jpg plasmodium-1801.jpg plasmodium-2702.jpg\n" + ], + "name": "stdout" + } + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "jeT5N_R-dyKW", + "colab_type": "text" + }, + "source": [ + "### 4) Fix issues with the dataset" + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "ckoCqc8MLQdi", + "colab_type": "code", + "outputId": "32a89913-d0d2-4696-f399-78544cb37f4d", + "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", + "replaceString = True\n", + "addFileName = True\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 replaceString:\n", + "\t\treplaceIt(fullname, \"person\", \"plasmodium\")\n", + "\tprint(\"Fixed\", fullname)\n", + "\n" + ], + "execution_count": 0, + "outputs": [ + { + "output_type": "stream", + "text": [ + "Fixed ./annotation/plasmodium-0492.xml\n", + "Fixed ./annotation/plasmodium-2168.xml\n", + "Fixed ./annotation/plasmodium-1707.xml\n", + "Fixed ./annotation/plasmodium-0149.xml\n", + "Fixed ./annotation/plasmodium-1330.xml\n", + "Fixed ./annotation/plasmodium-0485.xml\n", + "Fixed ./annotation/plasmodium-0756.xml\n", + "Fixed ./annotation/plasmodium-1670.xml\n", + "Fixed ./annotation/plasmodium-1875.xml\n", + "Fixed ./annotation/plasmodium-0108.xml\n", + "Fixed ./annotation/plasmodium-1053.xml\n", + "Fixed ./annotation/plasmodium-0659.xml\n", + "Fixed ./annotation/plasmodium-2069.xml\n", + "Fixed ./annotation/plasmodium-0153.xml\n", + "Fixed ./annotation/plasmodium-2155.xml\n", + "Fixed ./annotation/plasmodium-1284.xml\n", + "Fixed ./annotation/plasmodium-2352.xml\n", + "Fixed ./annotation/plasmodium-0261.xml\n", + "Fixed ./annotation/plasmodium-0195.xml\n", + "Fixed ./annotation/plasmodium-1939.xml\n", + "Fixed ./annotation/plasmodium-1430.xml\n", + "Fixed ./annotation/plasmodium-0935.xml\n", + "Fixed ./annotation/plasmodium-0041.xml\n", + "Fixed ./annotation/plasmodium-0605.xml\n", + "Fixed ./annotation/plasmodium-1007.xml\n", + "Fixed ./annotation/plasmodium-0783.xml\n", + "Fixed ./annotation/plasmodium-2442.xml\n", + "Fixed ./annotation/plasmodium-1742.xml\n", + "Fixed ./annotation/plasmodium-1415.xml\n", + "Fixed ./annotation/plasmodium-0619.xml\n", + "Fixed ./annotation/plasmodium-0321.xml\n", + "Fixed ./annotation/plasmodium-0021.xml\n", + "Fixed ./annotation/plasmodium-0442.xml\n", + "Fixed ./annotation/plasmodium-2011.xml\n", + "Fixed ./annotation/plasmodium-2277.xml\n", + "Fixed ./annotation/plasmodium-1044.xml\n", + "Fixed ./annotation/plasmodium-2454.xml\n", + "Fixed ./annotation/plasmodium-2469.xml\n", + "Fixed ./annotation/plasmodium-2185.xml\n", + "Fixed ./annotation/plasmodium-0703.xml\n", + "Fixed ./annotation/plasmodium-1986.xml\n", + "Fixed ./annotation/plasmodium-1647.xml\n", + "Fixed ./annotation/plasmodium-2075.xml\n", + "Fixed ./annotation/plasmodium-0658.xml\n", + "Fixed ./annotation/plasmodium-1648.xml\n", + "Fixed ./annotation/plasmodium-1826.xml\n", + "Fixed ./annotation/plasmodium-1862.xml\n", + "Fixed ./annotation/plasmodium-1108.xml\n", + "Fixed ./annotation/plasmodium-1211.xml\n", + "Fixed ./annotation/plasmodium-2427.xml\n", + "Fixed ./annotation/plasmodium-1713.xml\n", + "Fixed ./annotation/plasmodium-0803.xml\n", + "Fixed ./annotation/plasmodium-1234.xml\n", + "Fixed ./annotation/plasmodium-1709.xml\n", + "Fixed ./annotation/plasmodium-0299.xml\n", + "Fixed ./annotation/plasmodium-1273.xml\n", + "Fixed ./annotation/plasmodium-1050.xml\n", + "Fixed ./annotation/plasmodium-0718.xml\n", + "Fixed ./annotation/plasmodium-2577.xml\n", + "Fixed ./annotation/plasmodium-0636.xml\n", + "Fixed ./annotation/plasmodium-0971.xml\n", + "Fixed ./annotation/plasmodium-1142.xml\n", + "Fixed ./annotation/plasmodium-2406.xml\n", + "Fixed ./annotation/plasmodium-2568.xml\n", + "Fixed ./annotation/plasmodium-0852.xml\n", + "Fixed ./annotation/plasmodium-1463.xml\n", + "Fixed 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./annotation/plasmodium-1933.xml\n", + "Fixed ./annotation/plasmodium-0129.xml\n", + "Fixed ./annotation/plasmodium-2579.xml\n", + "Fixed ./annotation/plasmodium-1805.xml\n", + "Fixed ./annotation/plasmodium-0478.xml\n", + "Fixed ./annotation/plasmodium-2694.xml\n", + "Fixed ./annotation/plasmodium-0329.xml\n", + "Fixed ./annotation/plasmodium-2674.xml\n", + "Fixed ./annotation/plasmodium-0037.xml\n", + "Fixed ./annotation/plasmodium-1350.xml\n", + "Fixed ./annotation/plasmodium-0594.xml\n", + "Fixed ./annotation/plasmodium-0369.xml\n", + "Fixed ./annotation/plasmodium-2475.xml\n", + "Fixed ./annotation/plasmodium-2448.xml\n", + "Fixed ./annotation/plasmodium-0665.xml\n", + "Fixed ./annotation/plasmodium-0854.xml\n", + "Fixed ./annotation/plasmodium-0014.xml\n", + "Fixed ./annotation/plasmodium-1110.xml\n", + "Fixed ./annotation/plasmodium-1764.xml\n", + "Fixed ./annotation/plasmodium-2227.xml\n", + "Fixed ./annotation/plasmodium-2464.xml\n", + "Fixed ./annotation/plasmodium-0890.xml\n", + "Fixed ./annotation/plasmodium-1180.xml\n", + "Fixed ./annotation/plasmodium-1495.xml\n", + "Fixed ./annotation/plasmodium-1513.xml\n", + "Fixed ./annotation/plasmodium-1492.xml\n", + "Fixed ./annotation/plasmodium-0359.xml\n", + "Fixed ./annotation/plasmodium-0802.xml\n", + "Fixed ./annotation/plasmodium-2397.xml\n", + "Fixed ./annotation/plasmodium-2423.xml\n", + "Fixed ./annotation/plasmodium-1168.xml\n", + "Fixed ./annotation/plasmodium-0805.xml\n", + "Fixed ./annotation/plasmodium-0070.xml\n", + "Fixed ./annotation/plasmodium-1451.xml\n", + "Fixed ./annotation/plasmodium-0428.xml\n", + "Fixed ./annotation/plasmodium-1403.xml\n", + "Fixed ./annotation/plasmodium-1649.xml\n", + "Fixed ./annotation/plasmodium-2177.xml\n", + "Fixed ./annotation/plasmodium-0795.xml\n", + "Fixed ./annotation/plasmodium-1164.xml\n", + "Fixed ./annotation/plasmodium-2554.xml\n", + "Fixed ./annotation/plasmodium-2072.xml\n", + "Fixed ./annotation/plasmodium-1813.xml\n", + "Fixed ./annotation/plasmodium-2586.xml\n", + "Fixed ./annotation/plasmodium-1016.xml\n", + "Fixed ./annotation/plasmodium-1748.xml\n", + "Fixed ./annotation/plasmodium-0988.xml\n", + "Fixed ./annotation/plasmodium-1869.xml\n", + "Fixed ./annotation/plasmodium-0553.xml\n", + "Fixed ./annotation/plasmodium-0582.xml\n", + "Fixed ./annotation/plasmodium-0711.xml\n", + "Fixed ./annotation/plasmodium-2344.xml\n", + "Fixed ./annotation/plasmodium-2121.xml\n", + "Fixed ./annotation/plasmodium-2618.xml\n", + "Fixed ./annotation/plasmodium-0201.xml\n", + "Fixed ./annotation/plasmodium-1490.xml\n", + "Fixed ./annotation/plasmodium-0073.xml\n", + "Fixed ./annotation/plasmodium-2495.xml\n", + "Fixed ./annotation/plasmodium-0215.xml\n", + "Fixed ./annotation/plasmodium-1746.xml\n", + "Fixed ./annotation/plasmodium-1839.xml\n", + "Fixed ./annotation/plasmodium-1287.xml\n", + "Fixed ./annotation/plasmodium-1519.xml\n", + "Fixed ./annotation/plasmodium-2689.xml\n", + "Fixed ./annotation/plasmodium-0174.xml\n", + "Fixed ./annotation/plasmodium-0629.xml\n", + "Fixed ./annotation/plasmodium-1895.xml\n", + "Fixed ./annotation/plasmodium-2093.xml\n", + "Fixed ./annotation/plasmodium-1553.xml\n", + "Fixed ./annotation/plasmodium-2604.xml\n", + "Fixed ./annotation/plasmodium-1317.xml\n", + "Fixed ./annotation/plasmodium-1313.xml\n", + "Fixed ./annotation/plasmodium-2309.xml\n", + "Fixed ./annotation/plasmodium-0806.xml\n", + "Fixed ./annotation/plasmodium-2665.xml\n", + "Fixed ./annotation/plasmodium-0067.xml\n", + "Fixed ./annotation/plasmodium-1229.xml\n", + "Fixed ./annotation/plasmodium-2626.xml\n", + "Fixed ./annotation/plasmodium-0416.xml\n", + "Fixed ./annotation/plasmodium-1725.xml\n", + "Fixed ./annotation/plasmodium-2021.xml\n", + "Fixed ./annotation/plasmodium-2017.xml\n", + "Fixed ./annotation/plasmodium-2346.xml\n", + "Fixed ./annotation/plasmodium-0031.xml\n", + "Fixed ./annotation/plasmodium-1699.xml\n", + "Fixed ./annotation/plasmodium-0271.xml\n", + "Fixed ./annotation/plasmodium-0797.xml\n", + "Fixed ./annotation/plasmodium-0650.xml\n", + "Fixed ./annotation/plasmodium-2698.xml\n", + "Fixed ./annotation/plasmodium-2189.xml\n", + "Fixed ./annotation/plasmodium-1449.xml\n", + "Fixed ./annotation/plasmodium-0877.xml\n", + "Fixed ./annotation/plasmodium-2612.xml\n", + "Fixed ./annotation/plasmodium-1866.xml\n", + "Fixed ./annotation/plasmodium-0403.xml\n", + "Fixed ./annotation/plasmodium-1082.xml\n", + "Fixed ./annotation/plasmodium-2071.xml\n", + "Fixed ./annotation/plasmodium-1736.xml\n", + "Fixed ./annotation/plasmodium-0332.xml\n", + "Fixed ./annotation/plasmodium-2214.xml\n", + "Fixed ./annotation/plasmodium-2522.xml\n", + "Fixed ./annotation/plasmodium-1195.xml\n", + "Fixed ./annotation/plasmodium-1169.xml\n", + "Fixed ./annotation/plasmodium-0739.xml\n", + "Fixed ./annotation/plasmodium-2060.xml\n", + "Fixed ./annotation/plasmodium-0139.xml\n", + "Fixed ./annotation/plasmodium-1851.xml\n", + "Fixed ./annotation/plasmodium-1696.xml\n", + "Fixed ./annotation/plasmodium-0633.xml\n", + "Fixed ./annotation/plasmodium-2129.xml\n", + "Fixed ./annotation/plasmodium-1338.xml\n", + "Fixed ./annotation/plasmodium-1236.xml\n", + "Fixed ./annotation/plasmodium-1358.xml\n", + "Fixed ./annotation/plasmodium-1014.xml\n", + "Fixed ./annotation/plasmodium-0430.xml\n", + "Fixed ./annotation/plasmodium-1758.xml\n", + "Fixed ./annotation/plasmodium-1334.xml\n" + ], + "name": "stdout" + } + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "2u872ZKKeZ8h", + "colab_type": "text" + }, + "source": [ + "### 5) Download pregenerated csv file\n", + "\n", + "The annotations.csv file was created using RectLabel" + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "EpFSdUGALaop", + "colab_type": "code", + "outputId": "92726632-bae5-41e5-873d-397a9e47a4cc", + "colab": { + "base_uri": "https://localhost:8080/", + "height": 235 + } + }, + "source": [ + "!wget https://gist.githubusercontent.com/navanchauhan/dd91c089c743217868a00d68c9b7d3fe/raw/1b61cbc39d8a7406f2fbb2d687d34820aa063054/annotations.csv" + ], + "execution_count": 0, + "outputs": [ + { + "output_type": "stream", + "text": [ + "--2019-11-05 00:45:49-- https://gist.githubusercontent.com/navanchauhan/dd91c089c743217868a00d68c9b7d3fe/raw/1b61cbc39d8a7406f2fbb2d687d34820aa063054/annotations.csv\n", + "Resolving gist.githubusercontent.com (gist.githubusercontent.com)... 151.101.0.133, 151.101.64.133, 151.101.128.133, ...\n", + "Connecting to gist.githubusercontent.com (gist.githubusercontent.com)|151.101.0.133|:443... connected.\n", + "HTTP request sent, awaiting response... 200 OK\n", + "Length: 5091493 (4.9M) [text/plain]\n", + "Saving to: ‘annotations.csv’\n", + "\n", + "\rannotations.csv 0%[ ] 0 --.-KB/s \rannotations.csv 100%[===================>] 4.86M --.-KB/s in 0.04s \n", + "\n", + "2019-11-05 00:45:49 (137 MB/s) - ‘annotations.csv’ saved [5091493/5091493]\n", + "\n" + ], + "name": "stdout" + } + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "Qem0xslven3Y", + "colab_type": "text" + }, + "source": [ + "### 6) Change Absolute Path to Relative Path" + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "TWPJ8zVsMoEP", + "colab_type": "code", + "colab": {} + }, + "source": [ + "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", + "replaceIt(\"./annotations.csv\",\"/Users/navanchauhan/Downloads/malaria-data-object/plasmodium-images/images\",\"./images\")\n" + ], + "execution_count": 0, + "outputs": [] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "7bfuY1ISeuFN", + "colab_type": "text" + }, + "source": [ + "### 7) Train Model" + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "RLSloYzNMrQG", + "colab_type": "code", + "outputId": "2c0b2088-8da7-43a3-c01e-3f7b856f7f62", + "colab": { + "base_uri": "https://localhost:8080/", + "height": 1000 + } + }, + "source": [ + "import turicreate as tc\n", + "import sys\n", + "import os\n", + "\n", + "tc.config.set_num_gpus(-1)\n", + "\n", + "csv_file = './annotations.csv'\n", + "csv = tc.SFrame(csv_file)\n", + "\n", + "image_path = csv['path'][0]\n", + "image_folder = str(os.path.split(image_path)[0])\n", + "\n", + "data = tc.image_analysis.load_images(image_folder, recursive=False)\n", + "data = data.join(csv)\n", + "\n", + "train, val = data.random_split(0.8)\n", + "\n", + "model = tc.object_detector.create(train, max_iterations=10000)\n", + "\n", + "\n", + "model.save('plasmodium.model')\n", + "model.export_coreml('plasmodium.mlmodel')\n", + "\n", + "scores = model.evaluate(val)\n", + "print(scores)\n" + ], + "execution_count": 0, + "outputs": [ + { + "output_type": "display_data", + "data": { + "text/html": [ + "<pre>Finished parsing file /content/annotations.csv</pre>" + ], + "text/plain": [ + "Finished parsing file /content/annotations.csv" + ] + }, + "metadata": { + "tags": [] + } + }, + { + "output_type": "display_data", + "data": { + "text/html": [ + "<pre>Parsing completed. 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Parsed 2703 lines in 0.24236 secs." + ] + }, + "metadata": { + "tags": [] + } + }, + { + "output_type": "stream", + "text": [ + "WARNING: You are using MXNet 1.4.0 which may result in breaking behavior.\n", + " To fix this, please install the currently recommended version:\n", + "\n", + " pip uninstall -y mxnet && pip install mxnet==1.1.0\n", + "\n", + " If you want to use a CUDA GPU, then change 'mxnet' to 'mxnet-cu90' (adjust 'cu90' depending on your CUDA version):\n", + "\n", + "Using 'image' as feature column\n", + "Using 'annotations' as annotations column\n", + "Downloading https://docs-assets.developer.apple.com/turicreate/models/darknet.params\n", + "Download completed: /var/tmp/model_cache/darknet.params\n", + "Setting 'batch_size' to 32\n", + "Using GPU to create model (Tesla P100-PCIE-16GB)\n", + "+--------------+--------------+--------------+\n", + "| Iteration | Loss | Elapsed Time |\n", + "+--------------+--------------+--------------+\n", + "| 1 | 11.321 | 14.5 |\n", + "| 6 | 11.964 | 26.9 |\n", + "| 11 | 11.867 | 39.4 |\n", + "| 15 | 11.222 | 49.7 |\n", + "| 19 | 11.003 | 60.2 |\n", + "| 23 | 10.262 | 70.4 |\n", + "| 28 | 9.847 | 82.6 |\n", + "| 32 | 9.412 | 92.8 |\n", + "| 37 | 8.674 | 104.9 |\n", + "| 42 | 8.017 | 117.1 |\n", + "| 47 | 7.422 | 129.5 |\n", + "| 51 | 7.114 | 139.6 |\n", + "| 56 | 6.843 | 152.0 |\n", + "| 61 | 6.808 | 164.1 |\n", + "| 65 | 6.436 | 174.2 |\n", + "| 69 | 6.504 | 184.8 |\n", + "| 74 | 6.282 | 197.0 |\n", + "| 79 | 6.067 | 209.3 |\n", + "| 83 | 5.963 | 219.5 |\n", + "| 88 | 6.025 | 231.9 |\n", + "| 93 | 6.185 | 244.0 |\n", + "| 98 | 6.007 | 256.5 |\n", + "| 103 | 5.922 | 268.7 |\n", + "| 108 | 5.832 | 281.1 |\n", + "| 113 | 5.542 | 293.2 |\n", + "| 117 | 5.619 | 303.2 |\n", + "| 122 | 5.946 | 315.3 |\n", + "| 127 | 5.938 | 327.5 |\n", + "| 132 | 5.881 | 339.9 |\n", + "| 137 | 5.716 | 352.7 |\n", + "| 141 | 5.286 | 362.8 |\n", + "| 146 | 5.581 | 374.8 |\n", + "| 151 | 5.496 | 387.2 |\n", + "| 156 | 5.624 | 399.5 |\n", + "| 161 | 5.667 | 411.6 |\n", + "| 166 | 5.578 | 423.8 |\n", + "| 171 | 5.675 | 436.3 |\n", + "| 176 | 5.682 | 448.3 |\n", + "| 181 | 5.621 | 460.4 |\n", + "| 186 | 5.520 | 472.6 |\n", + "| 191 | 5.539 | 484.8 |\n", + "| 195 | 5.635 | 494.9 |\n", + "| 200 | 5.518 | 507.1 |\n", + "| 205 | 5.383 | 519.9 |\n", + "| 210 | 5.394 | 532.2 |\n", + "| 214 | 5.661 | 542.3 |\n", + "| 218 | 5.843 | 552.3 |\n", + "| 223 | 5.539 | 564.4 |\n", + "| 228 | 5.513 | 576.7 |\n", + "| 233 | 5.377 | 589.1 |\n", + "| 238 | 5.409 | 601.4 |\n", + "| 243 | 5.086 | 613.5 |\n", + "| 248 | 5.315 | 625.8 |\n", + "| 253 | 5.525 | 638.0 |\n", + "| 258 | 5.241 | 650.1 |\n", + "| 263 | 5.364 | 662.2 |\n", + "| 268 | 5.414 | 674.1 |\n", + "| 273 | 5.359 | 686.5 |\n", + "| 278 | 5.366 | 698.6 |\n", + "| 283 | 5.019 | 710.8 |\n", + "| 288 | 5.301 | 722.9 |\n", + "| 293 | 5.207 | 734.8 |\n", + "| 298 | 4.881 | 746.9 |\n", + "| 303 | 5.331 | 759.2 |\n", + "| 308 | 5.575 | 771.5 |\n", + "| 313 | 5.477 | 783.7 |\n", + "| 318 | 5.481 | 796.0 |\n", + "| 323 | 5.288 | 807.9 |\n", + "| 328 | 5.290 | 820.0 |\n", + "| 333 | 5.211 | 832.2 |\n", + "| 338 | 5.416 | 844.3 |\n", + "| 342 | 5.432 | 854.7 |\n", + "| 347 | 5.150 | 866.8 |\n", + "| 352 | 5.276 | 878.9 |\n", + "| 357 | 5.267 | 891.2 |\n", + "| 362 | 5.101 | 903.6 |\n", + "| 367 | 5.168 | 915.6 |\n", + "| 371 | 5.182 | 925.9 |\n", + "| 376 | 5.069 | 938.0 |\n", + "| 381 | 5.345 | 950.2 |\n", + "| 386 | 5.367 | 962.1 |\n", + "| 391 | 4.857 | 974.4 |\n", + "| 396 | 5.069 | 986.6 |\n", + "| 401 | 5.216 | 999.0 |\n", + "| 406 | 5.087 | 1011.3 |\n", + "| 410 | 5.050 | 1021.9 |\n", + "| 415 | 5.280 | 1034.1 |\n", + "| 420 | 5.347 | 1046.4 |\n", + "| 424 | 5.162 | 1056.5 |\n", + "| 429 | 5.069 | 1068.5 |\n", + "| 434 | 4.889 | 1080.8 |\n", + "| 439 | 5.035 | 1092.9 |\n", + "| 444 | 5.011 | 1105.3 |\n", + "| 448 | 4.905 | 1115.4 |\n", + "| 453 | 5.238 | 1127.6 |\n", + "| 458 | 5.259 | 1139.8 |\n", + "| 462 | 5.240 | 1149.9 |\n", + "| 467 | 5.046 | 1161.8 |\n", + "| 472 | 5.191 | 1174.0 |\n", + "| 477 | 5.103 | 1186.2 |\n", + "| 481 | 4.822 | 1196.3 |\n", + "| 486 | 5.067 | 1208.3 |\n", + "| 490 | 5.055 | 1218.4 |\n", + "| 495 | 5.016 | 1230.5 |\n", + "| 500 | 5.178 | 1242.7 |\n", + "| 505 | 5.261 | 1254.7 |\n", + "| 510 | 5.027 | 1267.0 |\n", + "| 515 | 5.014 | 1279.1 |\n", + "| 520 | 4.766 | 1291.4 |\n", + "| 525 | 4.762 | 1303.5 |\n", + "| 529 | 4.912 | 1313.6 |\n", + "| 534 | 5.349 | 1325.6 |\n", + "| 539 | 5.245 | 1338.0 |\n", + "| 544 | 5.019 | 1350.1 |\n", + "| 548 | 4.808 | 1360.7 |\n", + "| 553 | 4.693 | 1372.8 |\n", + "| 558 | 4.756 | 1384.9 |\n", + "| 563 | 4.790 | 1397.0 |\n", + "| 568 | 4.923 | 1409.3 |\n", + "| 573 | 5.030 | 1421.5 |\n", + "| 578 | 5.034 | 1433.8 |\n", + "| 583 | 5.111 | 1445.8 |\n", + "| 588 | 4.899 | 1458.1 |\n", + "| 593 | 5.177 | 1470.3 |\n", + "| 598 | 5.081 | 1482.5 |\n", + "| 603 | 4.922 | 1494.8 |\n", + "| 607 | 5.204 | 1504.8 |\n", + "| 611 | 5.070 | 1514.9 |\n", + "| 615 | 4.923 | 1525.2 |\n", + "| 620 | 4.796 | 1536.9 |\n", + "| 625 | 5.003 | 1549.1 |\n", + "| 630 | 4.980 | 1561.3 |\n", + "| 635 | 5.279 | 1573.6 |\n", + "| 640 | 5.200 | 1585.8 |\n", + "| 645 | 5.158 | 1598.0 |\n", + "| 650 | 5.233 | 1610.1 |\n", + "| 654 | 5.037 | 1620.3 |\n", + "| 659 | 5.218 | 1632.6 |\n", + "| 664 | 5.001 | 1644.8 |\n", + "| 669 | 4.818 | 1657.0 |\n", + "| 673 | 4.809 | 1667.1 |\n", + "| 678 | 4.772 | 1679.4 |\n", + "| 683 | 4.500 | 1691.8 |\n", + "| 688 | 4.648 | 1703.9 |\n", + "| 693 | 4.749 | 1716.2 |\n", + "| 698 | 4.911 | 1728.0 |\n", + "| 703 | 4.874 | 1740.1 |\n", + "| 708 | 5.062 | 1752.2 |\n", + "| 713 | 4.879 | 1764.5 |\n", + "| 718 | 4.925 | 1776.5 |\n", + "| 722 | 4.643 | 1786.6 |\n", + "| 727 | 4.587 | 1798.6 |\n", + "| 732 | 4.445 | 1811.0 |\n", + "| 737 | 4.766 | 1823.4 |\n", + "| 742 | 5.220 | 1835.7 |\n", + "| 747 | 5.237 | 1847.8 |\n", + "| 751 | 5.133 | 1857.8 |\n", + "| 756 | 5.017 | 1870.1 |\n", + "| 761 | 4.931 | 1882.4 |\n", + "| 766 | 4.942 | 1894.7 |\n", + "| 771 | 4.786 | 1906.9 |\n", + "| 776 | 4.912 | 1918.9 |\n", + "| 781 | 4.803 | 1931.2 |\n", + "| 786 | 4.612 | 1943.2 |\n", + "| 791 | 4.755 | 1955.5 |\n", + "| 796 | 4.678 | 1967.5 |\n", + "| 801 | 4.834 | 1979.5 |\n", + "| 806 | 4.875 | 1991.8 |\n", + "| 811 | 4.904 | 2003.8 |\n", + "| 816 | 4.807 | 2015.8 |\n", + "| 820 | 4.649 | 2026.1 |\n", + "| 825 | 4.935 | 2038.6 |\n", + "| 830 | 4.691 | 2050.5 |\n", + "| 835 | 4.697 | 2062.9 |\n", + "| 840 | 4.892 | 2075.2 |\n", + "| 845 | 4.974 | 2087.3 |\n", + "| 850 | 4.884 | 2099.6 |\n", + "| 855 | 4.801 | 2111.4 |\n", + "| 860 | 4.678 | 2123.6 |\n", + "| 865 | 4.883 | 2135.4 |\n", + "| 870 | 4.709 | 2147.7 |\n", + "| 875 | 4.780 | 2159.9 |\n", + "| 880 | 4.737 | 2172.2 |\n", + "| 885 | 4.724 | 2184.6 |\n", + "| 889 | 4.744 | 2194.9 |\n", + "| 894 | 4.909 | 2206.7 |\n", + "| 899 | 4.993 | 2218.9 |\n", + "| 904 | 4.972 | 2231.0 |\n", + "| 909 | 4.614 | 2242.8 |\n", + "| 914 | 4.739 | 2254.9 |\n", + "| 919 | 4.720 | 2267.0 |\n", + "| 924 | 4.630 | 2279.0 |\n", + "| 928 | 4.713 | 2289.0 |\n", + "| 933 | 4.643 | 2300.8 |\n", + "| 937 | 4.903 | 2310.8 |\n", + "| 942 | 4.635 | 2322.9 |\n", + "| 947 | 5.138 | 2335.0 |\n", + "| 952 | 4.815 | 2347.0 |\n", + "| 956 | 4.762 | 2357.3 |\n", + "| 960 | 4.958 | 2367.3 |\n", + "| 965 | 4.756 | 2379.4 |\n", + "| 969 | 4.838 | 2389.5 |\n", + "| 974 | 4.943 | 2401.5 |\n", + "| 979 | 4.934 | 2413.9 |\n", + "| 983 | 4.818 | 2423.9 |\n", + "| 988 | 5.022 | 2436.0 |\n", + "| 993 | 4.716 | 2448.1 |\n", + "| 998 | 4.665 | 2460.1 |\n", + "| 1002 | 4.661 | 2470.1 |\n", + "| 1007 | 4.538 | 2482.3 |\n", + "| 1012 | 4.757 | 2494.2 |\n", + "| 1017 | 4.946 | 2506.1 |\n", + "| 1022 | 5.060 | 2518.4 |\n", + "| 1026 | 4.975 | 2528.7 |\n", + "| 1031 | 4.871 | 2540.5 |\n", + "| 1035 | 5.013 | 2550.5 |\n", + "| 1040 | 4.897 | 2562.8 |\n", + "| 1044 | 4.760 | 2572.8 |\n", + "| 1049 | 4.754 | 2584.9 |\n", + "| 1054 | 4.918 | 2597.1 |\n", + "| 1059 | 4.900 | 2609.2 |\n", + "| 1064 | 5.072 | 2621.3 |\n", + "| 1068 | 4.952 | 2631.4 |\n", + "| 1072 | 4.926 | 2641.4 |\n", + "| 1077 | 4.511 | 2653.6 |\n", + "| 1082 | 4.663 | 2665.6 |\n", + "| 1087 | 4.735 | 2677.8 |\n", + "| 1092 | 4.630 | 2690.1 |\n", + "| 1097 | 4.851 | 2702.4 |\n", + "| 1102 | 4.832 | 2714.8 |\n", + "| 1107 | 4.656 | 2726.6 |\n", + "| 1112 | 4.582 | 2739.2 |\n", + "| 1117 | 4.452 | 2751.6 |\n", + "| 1121 | 4.568 | 2761.6 |\n", + "| 1126 | 4.520 | 2773.9 |\n", + "| 1131 | 4.515 | 2786.1 |\n", + "| 1136 | 4.426 | 2798.0 |\n", + "| 1141 | 4.651 | 2810.2 |\n", + "| 1146 | 4.853 | 2822.0 |\n", + "| 1151 | 4.807 | 2834.2 |\n", + "| 1156 | 4.840 | 2846.4 |\n", + "| 1160 | 4.956 | 2856.7 |\n", + "| 1165 | 4.866 | 2868.9 |\n", + "| 1170 | 4.729 | 2881.4 |\n", + "| 1175 | 4.589 | 2893.5 |\n", + "| 1180 | 4.726 | 2905.7 |\n", + "| 1185 | 4.637 | 2917.5 |\n", + "| 1190 | 4.751 | 2929.6 |\n", + "| 1195 | 4.707 | 2941.6 |\n", + "| 1200 | 4.894 | 2954.1 |\n", + "| 1205 | 4.926 | 2966.5 |\n", + "| 1210 | 4.880 | 2978.7 |\n", + "| 1215 | 4.857 | 2990.8 |\n", + "| 1220 | 4.917 | 3003.0 |\n", + "| 1225 | 4.593 | 3014.9 |\n", + "| 1229 | 4.788 | 3025.2 |\n", + "| 1234 | 4.897 | 3037.4 |\n", + "| 1239 | 4.940 | 3049.7 |\n", + "| 1244 | 4.822 | 3061.8 |\n", + "| 1249 | 4.610 | 3074.1 |\n", + "| 1254 | 4.669 | 3086.4 |\n", + "| 1259 | 4.834 | 3098.7 |\n", + "| 1264 | 4.753 | 3110.8 |\n", + "| 1268 | 4.724 | 3120.9 |\n", + "| 1273 | 4.989 | 3132.9 |\n", + "| 1278 | 4.754 | 3145.1 |\n", + "| 1283 | 4.451 | 3157.0 |\n", + "| 1288 | 4.617 | 3169.1 |\n", + "| 1293 | 4.431 | 3181.1 |\n", + "| 1297 | 4.393 | 3191.4 |\n", + "| 1302 | 4.542 | 3203.8 |\n", + "| 1307 | 4.581 | 3215.9 |\n", + "| 1312 | 4.599 | 3228.0 |\n", + "| 1317 | 4.912 | 3240.0 |\n", + "| 1322 | 4.569 | 3252.1 |\n", + "| 1327 | 4.539 | 3264.2 |\n", + "| 1332 | 4.609 | 3276.2 |\n", + "| 1337 | 4.573 | 3288.3 |\n", + "| 1342 | 4.695 | 3300.0 |\n", + "| 1347 | 4.993 | 3312.2 |\n", + "| 1351 | 4.789 | 3322.4 |\n", + "| 1356 | 4.552 | 3334.5 |\n", + "| 1361 | 4.445 | 3346.8 |\n", + "| 1365 | 4.303 | 3357.0 |\n", + "| 1370 | 4.837 | 3369.2 |\n", + "| 1374 | 4.752 | 3379.2 |\n", + "| 1378 | 4.631 | 3389.3 |\n", + "| 1383 | 4.732 | 3401.5 |\n", + "| 1388 | 4.764 | 3413.7 |\n", + "| 1393 | 4.848 | 3425.7 |\n", + "| 1398 | 4.764 | 3437.9 |\n", + "| 1403 | 4.706 | 3449.9 |\n", + "| 1408 | 4.625 | 3462.0 |\n", + "| 1413 | 4.633 | 3473.8 |\n", + "| 1418 | 4.642 | 3485.7 |\n", + "| 1423 | 4.807 | 3497.6 |\n", + "| 1428 | 4.748 | 3509.7 |\n", + "| 1433 | 4.634 | 3522.4 |\n", + "| 1438 | 4.506 | 3534.3 |\n", + "| 1443 | 4.458 | 3546.5 |\n", + "| 1448 | 4.467 | 3558.6 |\n", + "| 1453 | 4.534 | 3570.8 |\n", + "| 1458 | 4.512 | 3583.1 |\n", + "| 1463 | 4.847 | 3595.3 |\n", + "| 1468 | 4.934 | 3607.2 |\n", + "| 1473 | 4.617 | 3619.3 |\n", + "| 1478 | 4.558 | 3631.4 |\n", + "| 1483 | 4.370 | 3643.3 |\n", + "| 1488 | 4.513 | 3655.6 |\n", + "| 1493 | 4.741 | 3667.8 |\n", + "| 1498 | 4.770 | 3679.8 |\n", + "| 1502 | 4.922 | 3690.2 |\n", + "| 1507 | 4.840 | 3702.2 |\n", + "| 1512 | 4.630 | 3714.6 |\n", + "| 1517 | 4.745 | 3726.4 |\n", + "| 1522 | 4.882 | 3738.8 |\n", + "| 1527 | 4.777 | 3750.8 |\n", + "| 1532 | 4.806 | 3763.1 |\n", + "| 1537 | 4.762 | 3775.2 |\n", + "| 1542 | 4.943 | 3787.3 |\n", + "| 1547 | 4.868 | 3799.2 |\n", + "| 1552 | 4.714 | 3811.4 |\n", + "| 1557 | 4.779 | 3823.6 |\n", + "| 1562 | 4.724 | 3835.6 |\n", + "| 1567 | 4.729 | 3847.7 |\n", + "| 1571 | 4.696 | 3857.8 |\n", + "| 1576 | 4.756 | 3869.7 |\n", + "| 1581 | 4.466 | 3881.7 |\n", + "| 1586 | 4.553 | 3893.8 |\n", + "| 1591 | 4.893 | 3906.0 |\n", + "| 1595 | 4.924 | 3916.1 |\n", + "| 1600 | 4.813 | 3928.3 |\n", + "| 1605 | 4.638 | 3940.5 |\n", + "| 1609 | 4.594 | 3950.5 |\n", + "| 1614 | 4.558 | 3962.5 |\n", + "| 1619 | 4.752 | 3974.9 |\n", + "| 1624 | 4.715 | 3987.2 |\n", + "| 1628 | 4.813 | 3997.3 |\n", + "| 1633 | 4.696 | 4009.6 |\n", + "| 1638 | 4.782 | 4022.5 |\n", + "| 1643 | 4.556 | 4034.5 |\n", + "| 1648 | 4.567 | 4046.9 |\n", + "| 1653 | 4.696 | 4059.1 |\n" + ], + "name": "stdout" + } + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "_FV4qUCDfr77", + "colab_type": "text" + }, + "source": [ + "### 8) Exporting Model for Conversion\n", + "\n", + "ONNX currently does not support non maximum suppression " + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "Prxsg2pdQ0AT", + "colab_type": "code", + "colab": {} + }, + "source": [ + "model.export_coreml('plasmodium-for-onnx.mlmodel', include_non_maximum_suppression=False)" + ], + "execution_count": 0, + "outputs": [] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "VTNCsGwegDeP", + "colab_type": "text" + }, + "source": [ + "### 9) Save to Google Drive\n" + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "M3zccxx6fVt4", + "colab_type": "code", + "colab": {} + }, + "source": [ + "!cp \"./plasmodium-for-onnx.mlmodel\" \"/content/gdrive/My Drive/.\"" + ], + "execution_count": 0, + "outputs": [] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "dCy_Y5ZLh3O2", + "colab_type": "text" + }, + "source": [ + "### 10) Installing ONNX and converting model" + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "I9gf1C11yo93", + "colab_type": "code", + "outputId": "5c562a2d-c920-4fed-a04a-31c24705654c", + "colab": { + "base_uri": "https://localhost:8080/", + "height": 415 + } + }, + "source": [ + "!pip install onnx coremltools onnxmltools" + ], + "execution_count": 0, + "outputs": [ + { + "output_type": "stream", + "text": [ + "Requirement already satisfied: onnx in /usr/local/lib/python3.6/dist-packages (1.6.0)\n", + "Requirement already satisfied: coremltools in /usr/local/lib/python3.6/dist-packages (3.0b3)\n", + "Requirement already satisfied: onnxmltools in /usr/local/lib/python3.6/dist-packages (1.5.1)\n", + "Requirement already satisfied: typing-extensions>=3.6.2.1 in /usr/local/lib/python3.6/dist-packages (from onnx) (3.6.6)\n", + "Requirement already satisfied: numpy in /usr/local/lib/python3.6/dist-packages (from onnx) (1.14.6)\n", + "Requirement already satisfied: six in /usr/local/lib/python3.6/dist-packages (from onnx) (1.12.0)\n", + "Requirement already satisfied: protobuf in /usr/local/lib/python3.6/dist-packages (from onnx) (3.10.0)\n", + "Requirement already satisfied: keras2onnx in /usr/local/lib/python3.6/dist-packages (from onnxmltools) (1.6.0)\n", + "Requirement already satisfied: skl2onnx in /usr/local/lib/python3.6/dist-packages (from onnxmltools) (1.5.2)\n", + "Requirement already satisfied: onnxconverter-common>=1.5.0 in /usr/local/lib/python3.6/dist-packages (from onnxmltools) (1.6.0)\n", + "Requirement already satisfied: setuptools in /usr/local/lib/python3.6/dist-packages (from protobuf->onnx) (41.4.0)\n", + "Requirement already satisfied: fire in /usr/local/lib/python3.6/dist-packages (from keras2onnx->onnxmltools) (0.2.1)\n", + "Requirement already satisfied: requests in /usr/local/lib/python3.6/dist-packages (from keras2onnx->onnxmltools) (2.21.0)\n", + "Requirement already satisfied: scikit-learn>=0.19 in /usr/local/lib/python3.6/dist-packages (from skl2onnx->onnxmltools) (0.21.3)\n", + "Requirement already satisfied: termcolor in /usr/local/lib/python3.6/dist-packages (from fire->keras2onnx->onnxmltools) (1.1.0)\n", + "Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.6/dist-packages (from requests->keras2onnx->onnxmltools) (2019.9.11)\n", + "Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /usr/local/lib/python3.6/dist-packages (from requests->keras2onnx->onnxmltools) (3.0.4)\n", + "Requirement already satisfied: idna<2.9,>=2.5 in /usr/local/lib/python3.6/dist-packages (from requests->keras2onnx->onnxmltools) (2.8)\n", + "Requirement already satisfied: urllib3<1.25,>=1.21.1 in /usr/local/lib/python3.6/dist-packages (from requests->keras2onnx->onnxmltools) (1.24.3)\n", + "Requirement already satisfied: joblib>=0.11 in /usr/local/lib/python3.6/dist-packages (from scikit-learn>=0.19->skl2onnx->onnxmltools) (0.14.0)\n", + "Requirement already satisfied: scipy>=0.17.0 in /usr/local/lib/python3.6/dist-packages (from scikit-learn>=0.19->skl2onnx->onnxmltools) (1.3.1)\n" + ], + "name": "stdout" + } + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "HfqmoxaJ1sau", + "colab_type": "code", + "outputId": "98e95191-d67c-4f3b-fcd0-fa0f1f374fba", + "colab": { + "base_uri": "https://localhost:8080/", + "height": 171 + } + }, + "source": [ + "import onnxmltools\n", + "import coremltools" + ], + "execution_count": 0, + "outputs": [ + { + "output_type": "display_data", + "data": { + "text/html": [ + "<p style=\"color: red;\">\n", + "The default version of TensorFlow in Colab will soon switch to TensorFlow 2.x.<br>\n", + "We recommend you <a href=\"https://www.tensorflow.org/guide/migrate\" target=\"_blank\">upgrade</a> now \n", + "or ensure your notebook will continue to use TensorFlow 1.x via the <code>%tensorflow_version 1.x</code> magic:\n", + "<a href=\"https://colab.research.google.com/notebooks/tensorflow_version.ipynb\" target=\"_blank\">more info</a>.</p>\n" + ], + "text/plain": [ + "<IPython.core.display.HTML object>" + ] + }, + "metadata": { + "tags": [] + } + }, + { + "output_type": "stream", + "text": [ + "WARNING:root:TensorFlow version 1.15.0 detected. Last version known to be fully compatible is 1.13.1 .\n", + "WARNING:root:Keras version 2.2.5 detected. Last version known to be fully compatible of Keras is 2.2.4 .\n" + ], + "name": "stderr" + } + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "rKX4J5Ig17w8", + "colab_type": "code", + "colab": {} + }, + "source": [ + "input_coreml_model = 'plasmodium-for-onnx.mlmodel'\n", + "output_onnx_model = 'model.onnx'" + ], + "execution_count": 0, + "outputs": [] + }, + { + "cell_type": "code", + "metadata": { + "id": "oOAjubc92BHt", + "colab_type": "code", + "colab": {} + }, + "source": [ + "coreml_model = coremltools.utils.load_spec(input_coreml_model)\n", + "onnx_model = onnxmltools.convert_coreml(coreml_model)\n", + "onnxmltools.utils.save_model(onnx_model, output_onnx_model)\n", + "\n", + "!cp ./model.onnx \"/content/gdrive/My Drive/.\"" + ], + "execution_count": 0, + "outputs": [] + } + ] +}
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