preprocess_yolo_labels_4.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "v2. This time output center point of ROI instead of upper left corner.\n",
    "\n",
    "v3. Center x, y, w and h values around mean\n",
    "\n",
    "v4. Don't center around mean, but center each ROI in the middle of it's cell by default. Use mean h and w as defaults."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import matplotlib.pyplot as plt\n",
    "import matplotlib.patches as patches\n",
    "import pandas as pd\n",
    "import csv\n",
    "import pickle\n",
    "import os\n",
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "GRID_SIZE = 4\n",
    "location_data = np.zeros((GRID_SIZE,GRID_SIZE,5))\n",
    "\n",
    "for i in range(4):\n",
    "    for j in range(4):\n",
    "        location_data[i,j,:] = [0, 390, 365, 225, 335]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<Figure size 720x720 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "coords = np.arange(0, 1024, 256)\n",
    "\n",
    "fig,ax = plt.subplots(1, figsize=(10,10))\n",
    "\n",
    "rect_1 = patches.Rectangle((195,511),218,271,linewidth=1,edgecolor='r',facecolor='none')\n",
    "plt.plot(304, 646.5, marker=\"o\", color=\"r\")\n",
    "rect_2 = patches.Rectangle((612,214),109,89,linewidth=1,edgecolor='b',facecolor='none')\n",
    "plt.plot(666.5, 258.5, marker=\"o\", color=\"b\")\n",
    "rect_3 = patches.Rectangle((610,599),265,245,linewidth=1,edgecolor='g',facecolor='none')\n",
    "plt.plot(742.5, 721.5, marker=\"o\", color=\"g\")\n",
    "ax.add_patch(rect_1)\n",
    "ax.add_patch(rect_2)\n",
    "ax.add_patch(rect_3)\n",
    "plt.xticks(coords)\n",
    "plt.yticks(coords)\n",
    "for item in coords:\n",
    "    plt.axvline(item, linewidth=0.5)\n",
    "    plt.axhline(item, linewidth=0.5)\n",
    "plt.xlim(0,1024)\n",
    "plt.ylim(0,1024)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[(4.0, 10.0), (10.0, 4.0), (11.0, 11.0)]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "boxes = [\n",
    "    [195,511,218,271],\n",
    "    [612,214,109,89],\n",
    "    [610,599,265,245]\n",
    "]\n",
    "\n",
    "centers = []\n",
    "\n",
    "for box in boxes:\n",
    "    x,y,w,h = box\n",
    "    center_x = x + (w / 2)\n",
    "    center_y = y + (h / 2)\n",
    "    centers.append((center_x,center_y))\n",
    "\n",
    "pixel_locs = []    \n",
    "for center in centers:\n",
    "    x_pixel = center[0] // 64\n",
    "    y_pixel = center[1] // 64\n",
    "    \n",
    "    pixel_locs.append((x_pixel,y_pixel))\n",
    "    \n",
    "pixel_locs    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Train dir: ./stage_1_train_images\n"
     ]
    }
   ],
   "source": [
    "ROOT_DIR = \"./\"\n",
    "\n",
    "train_dicom_dir = os.path.join(ROOT_DIR, 'stage_1_train_images')\n",
    "test_dicom_dir = os.path.join(ROOT_DIR, 'stage_1_test_images')\n",
    "print(\"Train dir:\", train_dicom_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "GRID_SIZE = 4\n",
    "CELL_WIDTH = 1024 // GRID_SIZE\n",
    "\n",
    "# means to center data\n",
    "mu_x = 391.456158\n",
    "mu_y = 363.1358768\n",
    "mu_w = 220.8453815\n",
    "mu_h = 334.1743641\n",
    "mu_center_x = 501.8788487\n",
    "mu_center_y = 530.2230589\n",
    "\n",
    "\n",
    "# empty dictionary\n",
    "pneumonia_locations = {}\n",
    "used_filenames = []\n",
    "pixel_means = []\n",
    "locations = []\n",
    "\n",
    "# load table\n",
    "with open(os.path.join('./stage_1_train_labels.csv'), mode='r') as infile:\n",
    "    # open reader\n",
    "    reader = csv.reader(infile)\n",
    "    # skip header\n",
    "    next(reader, None)\n",
    "    # loop through rows\n",
    "    for rows in reader:\n",
    "        # retrieve information\n",
    "        filename = rows[0]\n",
    "        location = rows[1:5]\n",
    "        pneumonia = rows[5]\n",
    "        \n",
    "        # initialize our data\n",
    "        if filename not in used_filenames:\n",
    "            location_data = np.zeros((GRID_SIZE,GRID_SIZE,5))\n",
    "            \n",
    "            # default label to mean values\n",
    "            for i in range(4):\n",
    "                for j in range(4):\n",
    "                    y = ((i + 0.5) * CELL_WIDTH)\n",
    "                    x = ((j + 0.5) * CELL_WIDTH)\n",
    "                    location_data[i,j,:] = [0, x, y, int(mu_w), int(mu_h)]\n",
    "            \n",
    "            used_filenames.append(filename)\n",
    "            locs = np.zeros((GRID_SIZE, GRID_SIZE))\n",
    "        else:\n",
    "            location_data = pneumonia_locations[filename]\n",
    "            \n",
    "        # if row contains pneumonia add label to dictionary\n",
    "        # the dictionary will contain the presence, x, y, h, w of the pneumonia for each pixel in a 16x16 grid\n",
    "        if pneumonia == '1':\n",
    "            # extract the location and cast them to floats\n",
    "            x,y,w,h = location\n",
    "            x = float(x)\n",
    "            y = float(y)\n",
    "            w = float(w)\n",
    "            h = float(h)\n",
    "            \n",
    "            # figure out the center of the ROI\n",
    "            center_x = x + (w / 2)\n",
    "            center_y = y + (h / 2)\n",
    "            \n",
    "            # figure out which pixel is in the center\n",
    "            x_pixel = int(center_x // (1024 // GRID_SIZE))\n",
    "            y_pixel = int(center_y // (1024 // GRID_SIZE))\n",
    "            locs[y_pixel, x_pixel] = 1\n",
    "            \n",
    "            # center the data\n",
    "#             center_x = center_x - mu_center_x\n",
    "#             center_y = center_y - mu_center_y\n",
    "#             w = w - mu_w\n",
    "#             h = h - mu_h\n",
    "            \n",
    "            # write the data to our list\n",
    "            location_data[y_pixel,x_pixel,0] = 1\n",
    "            location_data[y_pixel,x_pixel,1] = center_x\n",
    "            location_data[y_pixel,x_pixel,2] = center_y\n",
    "            location_data[y_pixel,x_pixel,3] = w\n",
    "            location_data[y_pixel,x_pixel,4] = h\n",
    "        else:\n",
    "            pass\n",
    "        \n",
    "        locations.append(location_data[:,:,1:])\n",
    "        pixel_means.append(np.mean(locs))\n",
    "        pneumonia_locations[filename] = location_data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "# save our dict to disk\n",
    "with open('yolo_labels_centered_4x4_4.p', 'wb') as handle:\n",
    "    pickle.dump(pneumonia_locations, handle, protocol=pickle.HIGHEST_PROTOCOL)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "with open('yolo_labels_centered_4x4_4.p', 'rb') as handle:\n",
    "    b = pickle.load(handle)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[[  0. , 128. , 128. , 220. , 334. ],\n",
       "        [  0. , 384. , 128. , 220. , 334. ],\n",
       "        [  0. , 640. , 128. , 220. , 334. ],\n",
       "        [  0. , 896. , 128. , 220. , 334. ]],\n",
       "\n",
       "       [[  0. , 128. , 384. , 220. , 334. ],\n",
       "        [  0. , 384. , 384. , 220. , 334. ],\n",
       "        [  0. , 640. , 384. , 220. , 334. ],\n",
       "        [  0. , 896. , 384. , 220. , 334. ]],\n",
       "\n",
       "       [[  0. , 128. , 640. , 220. , 334. ],\n",
       "        [  1. , 289.5, 549.5, 225. , 529. ],\n",
       "        [  1. , 741.5, 627.5, 201. , 309. ],\n",
       "        [  0. , 896. , 640. , 220. , 334. ]],\n",
       "\n",
       "       [[  0. , 128. , 896. , 220. , 334. ],\n",
       "        [  0. , 384. , 896. , 220. , 334. ],\n",
       "        [  0. , 640. , 896. , 220. , 334. ],\n",
       "        [  0. , 896. , 896. , 220. , 334. ]]])"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pneumonia_locations[\"fffb2395-8edd-4954-8a89-ffe2fd329be3\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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