3. Data Augmentation.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "9990b7ea",
   "metadata": {},
   "source": [
    "# Data Augmentation process\n",
    "\n",
    "### This file has the data augmentation process. The steps performed are:\n",
    "\n",
    "1. To balance the BSD data which has a higher portion of malignant samples, data augmentation is performed on the benign samples.\n",
    "2. The augmentation techniques include flipping, random noise addition and random rotation "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6173d8e3",
   "metadata": {},
   "source": [
    "Number of images in malignant class"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "5213e016",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "313\n"
     ]
    }
   ],
   "source": [
    "import os\n",
    "\n",
    "list1 = os.listdir(\"C:/Users/Kannan-PC/Desktop/Projects/melanoma/Final Year Project/final/malignant\") \n",
    "\n",
    "number_files1 = len(list1)\n",
    "print(number_files1)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0e22a997",
   "metadata": {},
   "source": [
    "Number of images in benign class"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "43bbcdd8",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "213\n"
     ]
    }
   ],
   "source": [
    "list2 = os.listdir(\"C:/Users/Kannan-PC/Desktop/Projects/melanoma/Final Year Project/final/benign\") \n",
    "\n",
    "number_files2 = len(list2)\n",
    "print(number_files2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "c54f6af3",
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import random\n",
    "from scipy import ndarray\n",
    "import skimage as sk\n",
    "from skimage import transform\n",
    "from skimage import util\n",
    "from skimage import io"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ea6589d4",
   "metadata": {},
   "source": [
    "Defining rotation , flipping and noise functions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "8bc562c4",
   "metadata": {},
   "outputs": [],
   "source": [
    "def rotation(image_array: ndarray):\n",
    "    random_degree = random.uniform(-25, 25)\n",
    "    return sk.transform.rotate(image_array, random_degree)\n",
    "\n",
    "def noise(image_array: ndarray):\n",
    "    return sk.util.random_noise(image_array)\n",
    "\n",
    "def flip(image_array: ndarray):\n",
    "    return image_array[:, ::-1]"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2b852582",
   "metadata": {},
   "source": [
    "Defining the available transformations in a dictionary"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "95bf9a59",
   "metadata": {},
   "outputs": [],
   "source": [
    "available_transformations = {\n",
    "    'rotate': random_rotation,\n",
    "    'noise': random_noise,\n",
    "    'horizontal_flip': horizontal_flip\n",
    "}"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4aaa2287",
   "metadata": {},
   "source": [
    "Initializing the directory path and the number of images to be generated. Declare an array containing all the names of the benign images"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "536fee72",
   "metadata": {},
   "outputs": [],
   "source": [
    "folder_path = \"C:/Users/Kannan-PC/Desktop/Projects/melanoma/Final Year Project/final/benign\"\n",
    "num_files_desired = 100\n",
    "images = [os.path.join(folder_path, f) for f in os.listdir(folder_path) if os.path.isfile(os.path.join(folder_path, f))]"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8c97bd0e",
   "metadata": {},
   "source": [
    "Transforming the images till the generated images reach 100"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "id": "4c678e9b",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n",
      "Lossy conversion from float64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.\n"
     ]
    }
   ],
   "source": [
    "num_generated_files = 0\n",
    "\n",
    "while num_generated_files <= num_files_desired:\n",
    "    \n",
    "    image_path = random.choice(images)\n",
    "    image_to_transform = sk.io.imread(image_path)\n",
    "    num_transformations_to_apply = random.randint(1, len(available_transformations))\n",
    "    num_transformations = 0\n",
    "    transformed_image = None\n",
    "    \n",
    "    while num_transformations <= num_transformations_to_apply:\n",
    "        \n",
    "        key = random.choice(list(available_transformations.keys()))\n",
    "        transformed_image = available_transformations[key](image_to_transform)\n",
    "        num_transformations += 1\n",
    "\n",
    "    new_file_path = '%s/augmented_image_%s.jpg' % (folder_path, num_generated_files)\n",
    "    io.imsave(new_file_path, transformed_image)\n",
    "    num_generated_files += 1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "id": "68253905",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "314\n"
     ]
    }
   ],
   "source": [
    "list2 = os.listdir(\"C:/Users/Kannan-PC/Desktop/Projects/melanoma/Final Year Project/final/benign\") \n",
    "\n",
    "number_files2 = len(list2)\n",
    "print(number_files2)"
   ]
  }
 ],
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