03-Diabetic_Retinopathy_Inference_Only.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Diabetic Retinopathy Detection - Jeffery A. Brown"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Dependencies"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "nbpresent": {
     "id": "828c2e12-b1c6-4994-8f55-ce86373b6c97"
    },
    "scrolled": true,
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Using TensorFlow backend.\n"
     ]
    }
   ],
   "source": [
    "%matplotlib inline\n",
    "# %matplotlib notebook\n",
    "import matplotlib.pyplot as plt\n",
    "from mpl_toolkits.mplot3d import Axes3D    # Support 3D graphing\n",
    "\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "from pandas.plotting import table\n",
    "import math\n",
    "import random\n",
    "import shutil\n",
    "import os\n",
    "\n",
    "# from imutils import paths\n",
    "# import argparse\n",
    "# import pickle\n",
    "# import cv2\n",
    "\n",
    "from pprint import pprint\n",
    "\n",
    "# Visualization\n",
    "import graphviz\n",
    "import pydotplus\n",
    "from IPython.display import Image\n",
    "\n",
    "# Machine Learning - Data Preparation and Pre-Processing\n",
    "from sklearn.model_selection import train_test_split # Split data into training and testing samples\n",
    "from sklearn.model_selection import cross_val_score  # Score a model using k-fold or other cross validation\n",
    "\n",
    "from sklearn.preprocessing import OneHotEncoder   # Convert categorical integer features (X) to One-Hot encoded values\n",
    "from sklearn.preprocessing import LabelEncoder    # Convert categorical labeled values to categorical integer values\n",
    "from sklearn.preprocessing import LabelBinarizer  # Convert categorical labeled values to Binary encoded values\n",
    "\n",
    "from sklearn.preprocessing import StandardScaler  # Scale numerical features to standard normal distribution\n",
    "from sklearn.preprocessing import MinMaxScaler    # Scale numerical values based upon mix/max values\n",
    "\n",
    "# Machine Learning - Sci-Kit Learn - Models - Regression\n",
    "from sklearn.linear_model import LinearRegression  # TBD\n",
    "from sklearn.linear_model import Lasso             # TBD\n",
    "from sklearn.linear_model import Ridge             # TBD\n",
    "from sklearn.linear_model import ElasticNet        # TBD\n",
    "\n",
    "# Machine Learning - Sci-Kit Learn - Models - Classification\n",
    "from sklearn.linear_model import LogisticRegression   # Logistic Regression Classifier\n",
    "from sklearn import tree                              # Decision Tree Classifier\n",
    "from sklearn.ensemble import RandomForestClassifier   # Random Forest Classifier\n",
    "from sklearn import svm                               # Support Vector Machine Classifier\n",
    "from sklearn.neighbors import KNeighborsClassifier    # K-Nearest Neighbors (KNN)\n",
    "\n",
    "# Machine Learning - GridSearch for Hyper-Parameter tuning\n",
    "from sklearn.model_selection import GridSearchCV      # Grid Search\n",
    "\n",
    "# Machine Learning - Quantify Model Performance\n",
    "from sklearn.metrics import mean_squared_error    # Mean Squared Error (MSE) metric\n",
    "from sklearn.metrics import r2_score              # R-squared (Coefficient of Determination) metric\n",
    "from sklearn.metrics import confusion_matrix      # Generate a confusion matrix (actual vs. predicted counts)\n",
    "from sklearn.metrics import classification_report # Calculate metrics for prediction performance\n",
    "from sklearn.metrics import precision_score       # Calculate the precision: Tp / (Tp + Fp) => Ability to avoid false negatives\n",
    "from sklearn.metrics import recall_score          # Calculate the recall: Tp / (Tp + Fn) => Ability to find all positive samples\n",
    "from sklearn.metrics import f1_score              # Calculate the F1 score: 2*(precision*recall)/(precision+recall)\n",
    "\n",
    "# Machine Learning - Dataset Generation\n",
    "from sklearn.datasets import make_regression     # Generate linear data\n",
    "from sklearn.datasets import make_s_curve        # Generate nonlinear data\n",
    "from sklearn.datasets import make_blobs          # Generate blobs for classification\n",
    "from sklearn.datasets import make_circles        # Generate circles for classification\n",
    "from sklearn.datasets import load_iris           # Sample multi-class dataset for classification\n",
    "from sklearn.datasets import make_classification # Generate datasets for classification\n",
    "\n",
    "# Machine Learning - Keras (Tensorflow) - Models\n",
    "from keras.models import Sequential               # Sequential model serving as foundation for neural network\n",
    "# from keras.layers import Dense                    # Nodes for specifying input, hidden, and output layers\n",
    "from keras.layers.core import Activation\n",
    "from keras.layers.core import Flatten\n",
    "from keras.layers.core import Dropout\n",
    "from keras.layers.core import Dense\n",
    "\n",
    "# Machine Learning - Keras (Tensorflow) - Convolutional Neural Networks (Image Classification)\n",
    "from keras.layers.normalization import BatchNormalization\n",
    "from keras.layers.convolutional import Conv2D\n",
    "from keras.layers.convolutional import MaxPooling2D\n",
    "from keras import backend as K\n",
    "\n",
    "# Machine Learning - Keras (Tensorflow) - Optimizers\n",
    "from keras.optimizers import SGD\n",
    "from keras.optimizers import Adam\n",
    "\n",
    "# Machine Learning - Keras (Tensorflow) - Encoding\n",
    "from keras.utils import to_categorical            # One-Hot Encoder provided through Keras\n",
    "\n",
    "# Machine Learning - Keras (Tensorflow) - Other related Tools\n",
    "from keras.utils import plot_model                # Plot a neural network model\n",
    "from keras.models import load_model               # Load a saved machine learning model\n",
    "from keras.preprocessing import image             # Loads an image for application of machine learning\n",
    "from keras.preprocessing.image import img_to_array # Converts an image to a numpy array\n",
    "from keras.preprocessing.image import ImageDataGenerator\n",
    "\n",
    "# Machine Learning - Keras (Tensorflow) -  Dataset Generation\n",
    "from keras.datasets import mnist                  # Images: Handwritten digits 0-9 (28x28 grayscale, 60K train, 10K test)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Predict the Class for Official Test Images"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Load the Saved Convolutional Neural Network Model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING: Logging before flag parsing goes to stderr.\n",
      "W0907 18:40:45.327334 21972 deprecation_wrapper.py:119] From C:\\Users\\Jeff\\AppData\\Local\\conda\\conda\\envs\\PythonTF\\lib\\site-packages\\keras\\backend\\tensorflow_backend.py:517: The name tf.placeholder is deprecated. Please use tf.compat.v1.placeholder instead.\n",
      "\n",
      "W0907 18:40:45.355404 21972 deprecation_wrapper.py:119] From C:\\Users\\Jeff\\AppData\\Local\\conda\\conda\\envs\\PythonTF\\lib\\site-packages\\keras\\backend\\tensorflow_backend.py:4138: The name tf.random_uniform is deprecated. Please use tf.random.uniform instead.\n",
      "\n",
      "W0907 18:40:45.399335 21972 deprecation_wrapper.py:119] From C:\\Users\\Jeff\\AppData\\Local\\conda\\conda\\envs\\PythonTF\\lib\\site-packages\\keras\\backend\\tensorflow_backend.py:245: The name tf.get_default_graph is deprecated. Please use tf.compat.v1.get_default_graph instead.\n",
      "\n",
      "W0907 18:40:45.400335 21972 deprecation_wrapper.py:119] From C:\\Users\\Jeff\\AppData\\Local\\conda\\conda\\envs\\PythonTF\\lib\\site-packages\\keras\\backend\\tensorflow_backend.py:174: The name tf.get_default_session is deprecated. Please use tf.compat.v1.get_default_session instead.\n",
      "\n",
      "W0907 18:40:45.401282 21972 deprecation_wrapper.py:119] From C:\\Users\\Jeff\\AppData\\Local\\conda\\conda\\envs\\PythonTF\\lib\\site-packages\\keras\\backend\\tensorflow_backend.py:181: The name tf.ConfigProto is deprecated. Please use tf.compat.v1.ConfigProto instead.\n",
      "\n",
      "W0907 18:40:45.463282 21972 deprecation_wrapper.py:119] From C:\\Users\\Jeff\\AppData\\Local\\conda\\conda\\envs\\PythonTF\\lib\\site-packages\\keras\\backend\\tensorflow_backend.py:1834: The name tf.nn.fused_batch_norm is deprecated. Please use tf.compat.v1.nn.fused_batch_norm instead.\n",
      "\n",
      "W0907 18:40:45.564344 21972 deprecation_wrapper.py:119] From C:\\Users\\Jeff\\AppData\\Local\\conda\\conda\\envs\\PythonTF\\lib\\site-packages\\keras\\backend\\tensorflow_backend.py:3976: The name tf.nn.max_pool is deprecated. Please use tf.nn.max_pool2d instead.\n",
      "\n",
      "W0907 18:40:45.575336 21972 deprecation.py:506] From C:\\Users\\Jeff\\AppData\\Local\\conda\\conda\\envs\\PythonTF\\lib\\site-packages\\keras\\backend\\tensorflow_backend.py:3445: calling dropout (from tensorflow.python.ops.nn_ops) with keep_prob is deprecated and will be removed in a future version.\n",
      "Instructions for updating:\n",
      "Please use `rate` instead of `keep_prob`. Rate should be set to `rate = 1 - keep_prob`.\n",
      "W0907 18:40:47.433723 21972 deprecation_wrapper.py:119] From C:\\Users\\Jeff\\AppData\\Local\\conda\\conda\\envs\\PythonTF\\lib\\site-packages\\keras\\optimizers.py:790: The name tf.train.Optimizer is deprecated. Please use tf.compat.v1.train.Optimizer instead.\n",
      "\n",
      "W0907 18:40:47.735722 21972 deprecation.py:323] From C:\\Users\\Jeff\\AppData\\Local\\conda\\conda\\envs\\PythonTF\\lib\\site-packages\\tensorflow\\python\\ops\\math_grad.py:1250: add_dispatch_support.<locals>.wrapper (from tensorflow.python.ops.array_ops) is deprecated and will be removed in a future version.\n",
      "Instructions for updating:\n",
      "Use tf.where in 2.0, which has the same broadcast rule as np.where\n"
     ]
    }
   ],
   "source": [
    "# Load a saved model\n",
    "model = load_model(\"./saved_model.h5\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Copy the Official Test Data to a Structure Compliant with ImageDataGenerator flow_from_directory function"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Function to copy the official test data into a folder structure that\n",
    "# can be used with ImageDataGenerator and the flow_from_directory method,\n",
    "# which requires the test images to be in a *subfolder* under the main test data folder!\n",
    "# So unfortunately, since cannot change the test data folder structure I need to *copy*\n",
    "# all of the test data to another folder with proper structure\n",
    "def copy_official_test_images( a_source_dir = None, a_dest_dir = None ):\n",
    "    \n",
    "    # Basic argument checking\n",
    "    if (a_source_dir is None) or (a_dest_dir is None):\n",
    "        print(f\"Error: Source or Destination directory not specified\")\n",
    "        return False\n",
    "            \n",
    "    # Create the destination folder if it doesn't already exist\n",
    "    if not os.path.exists(a_dest_dir):\n",
    "            os.mkdir(a_dest_dir)\n",
    "\n",
    "    # Create the required subfolder in the destination folder if it doesn't already exist\n",
    "    dir_subfolder = os.path.join(a_dest_dir, \"test_subfolder\")\n",
    "    if not os.path.exists(dir_subfolder):\n",
    "            os.mkdir(dir_subfolder)\n",
    "\n",
    "    # Copy all images in the a_src_folder to the newly created dir_subfolder\n",
    "    src_files = os.listdir(a_source_dir)\n",
    "    \n",
    "    for file_name in src_files:\n",
    "        \n",
    "        full_file_name = os.path.join(a_source_dir, file_name)\n",
    "        \n",
    "        if os.path.isfile(full_file_name):\n",
    "            print(f\"Copying image {full_file_name} to {dir_subfolder}... \", end='')\n",
    "            try:\n",
    "                shutil.copy2(full_file_name, dir_subfolder)\n",
    "                print(f\"done.\")\n",
    "\n",
    "            except FileNotFoundError:\n",
    "                print(f\"error while attempting to copy.\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "# data/test_images - Source of official testing images in a single folder (used only to submit official results)\n",
    "# dir_src_test = \"../input/aptos2019-blindness-detection/test_images\"\n",
    "dir_src_test = \"./data/test_images\"\n",
    "dir_official_test = \"./official_test\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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    },
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    },
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    },
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    },
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     ]
    },
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     "name": "stdout",
     "output_type": "stream",
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     ]
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     "name": "stdout",
     "output_type": "stream",
     "text": [
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     ]
    },
    {
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     "output_type": "stream",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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     ]
    }
   ],
   "source": [
    "copy_official_test_images( dir_src_test, dir_official_test )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "1928"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Count how many test images are populated\n",
    "# test_tally_file = \"../input/aptos2019-blindness-detection/test.csv\"\n",
    "test_tally_file = \"./data/test.csv\"\n",
    "\n",
    "# Load test counts into a dataframe\n",
    "test_tally_df = pd.read_csv(test_tally_file)\n",
    "len(test_tally_df)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Configure the Image Generator for the Official Test Images"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found 1928 images belonging to 1 classes.\n"
     ]
    }
   ],
   "source": [
    "# image_dims = (2136, 3216, 3)   # Height, Width, Depth (RGB = 3, Grayscale = 1)\n",
    "image_dims = (96, 96, 3)         # Height, Width, Depth (RGB = 3, Grayscale = 1)\n",
    "\n",
    "# Create a Image Data Generator for the official testing data\n",
    "official_test_datagen = ImageDataGenerator()\n",
    "\n",
    "# Define generator batch size and step size\n",
    "official_test_n_images = len(test_tally_df)\n",
    "official_test_n_batch_size = 1\n",
    "official_test_n_step_size = official_test_n_images // official_test_n_batch_size\n",
    "\n",
    "# Associate the generator with the training images\n",
    "official_test_generator = official_test_datagen.flow_from_directory(\n",
    "    directory=dir_official_test,             # Folder containing a subfolder with official training images\n",
    "    target_size=(image_dims[1], image_dims[0]),       # (Width, Height)\n",
    "    color_mode=\"rgb\",               # Color images\n",
    "    batch_size=official_test_n_batch_size,   # Batch size\n",
    "    class_mode=None,                # Number of classes > 2, so using \"categorical\" vs \"binary\"\n",
    "    shuffle=False,                   # Shuffle the training samples randomly\n",
    "    seed=1                          # Random number seed to use for shuffle\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Predict the Classifications based upon the Images"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1928/1928 [==============================] - 74s 38ms/step\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "array([2, 3, 0, ..., 3, 0, 2], dtype=int64)"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Predict the output (using the test_generator)\n",
    "official_test_generator.reset()\n",
    "official_pred_onehot = model.predict_generator(official_test_generator,\n",
    "                             steps=len(official_test_generator),\n",
    "                             verbose=1)\n",
    "\n",
    "official_predicted_class = np.argmax(official_pred_onehot, axis=1)\n",
    "official_predicted_class"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Save the Predictions from the Official Test Data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
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       "      <td>006efc72b638</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>00836aaacf06</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>009245722fa4</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1923</td>\n",
       "      <td>ff2fd94448de</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1924</td>\n",
       "      <td>ff4c945d9b17</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1925</td>\n",
       "      <td>ff64897ac0d8</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1926</td>\n",
       "      <td>ffa73465b705</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1927</td>\n",
       "      <td>ffdc2152d455</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1928 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "           id_code  diagnosis\n",
       "0     0005cfc8afb6          2\n",
       "1     003f0afdcd15          3\n",
       "2     006efc72b638          0\n",
       "3     00836aaacf06          2\n",
       "4     009245722fa4          2\n",
       "...            ...        ...\n",
       "1923  ff2fd94448de          0\n",
       "1924  ff4c945d9b17          0\n",
       "1925  ff64897ac0d8          3\n",
       "1926  ffa73465b705          0\n",
       "1927  ffdc2152d455          2\n",
       "\n",
       "[1928 rows x 2 columns]"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
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    "# Save the prediction results to a file\n",
    "\n",
    "# Get the list of test image id codes used by the test generator to make the predictions\n",
    "official_test_id_code_list = [ (x.split(\"\\\\\"))[1].replace(\".png\",\"\") for x in official_test_generator.filenames ]\n",
    "\n",
    "# Associate the test image id codes and the preoductions in a dataframe\n",
    "official_results_df = pd.DataFrame({\"id_code\": official_test_id_code_list, \"diagnosis\": official_predicted_class})\n",
    "official_results_df.to_csv(\"./submission.csv\",index=False)\n",
    "official_results_df"
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   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
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