3_Cropping_Dataset.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os, shutil\n",
    "import skimage as ski\n",
    "import numpy as np\n",
    "\n",
    "from os import walk, getcwd\n",
    "from skimage import io\n",
    "from skimage import filters\n",
    "from skimage import morphology\n",
    "from skimage import measure\n",
    "from matplotlib import pyplot as plt\n",
    "%matplotlib inline\n",
    "\n",
    "\n",
    "# Retorna todos los archivos de un directorio dado\n",
    "def ls(ruta):  \n",
    "    return next(walk(ruta))[2]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Ejecutar sólo una vez, y si el dataset: data_augmentation_dataset no existe\n",
    "\n",
    "#Definimos origen y destino de datasets y nombres\n",
    "original_dataset_dir = 'split_dataset' #origen\n",
    "base_dir = 'cropped_dataset'           #destino\n",
    "os.mkdir(base_dir) #Creamos directorio dataset destino\n",
    "\n",
    "#Creamos los tres directorios train, validation y test dentro de data_augmentation_dataset\n",
    "train_dir = os.path.join(base_dir, 'train')\n",
    "os.mkdir(train_dir)\n",
    "validation_dir = os.path.join(base_dir, 'validation')\n",
    "os.mkdir(validation_dir)\n",
    "test_dir = os.path.join(base_dir, 'test')\n",
    "os.mkdir(test_dir)\n",
    "\n",
    "#Creamos las carpetas de las 4 clases dentro de la carpeta train\n",
    "train_atypical_dir = os.path.join(train_dir, 'Atypical_Lymphocyte')\n",
    "os.mkdir(train_atypical_dir)\n",
    "train_blast_dir = os.path.join(train_dir, 'Blast')\n",
    "os.mkdir(train_blast_dir)\n",
    "train_lymphocyte_dir = os.path.join(train_dir,'Lymphocyte')\n",
    "os.mkdir(train_lymphocyte_dir)\n",
    "train_variant_dir = os.path.join(train_dir,'Variant_Lymphocyte')\n",
    "os.mkdir(train_variant_dir)\n",
    "\n",
    "#Creamos las carpetas de las 4 clases dentro de la carpeta validation\n",
    "validation_atypical_dir = os.path.join(validation_dir, 'Atypical_Lymphocyte')\n",
    "os.mkdir(validation_atypical_dir)\n",
    "validation_blast_dir = os.path.join(validation_dir, 'Blast')\n",
    "os.mkdir(validation_blast_dir)\n",
    "validation_lymphocyte_dir = os.path.join(validation_dir,'Lymphocyte')\n",
    "os.mkdir(validation_lymphocyte_dir)\n",
    "validation_variant_dir = os.path.join(validation_dir,'Variant_Lymphocyte')\n",
    "os.mkdir(validation_variant_dir)\n",
    "\n",
    "#Creamos las carpetas de las 4 clases dentro de la carpeta test\n",
    "test_atypical_dir = os.path.join(test_dir, 'Atypical_Lymphocyte')\n",
    "os.mkdir(test_atypical_dir)\n",
    "test_blast_dir = os.path.join(test_dir, 'Blast')\n",
    "os.mkdir(test_blast_dir)\n",
    "test_lymphocyte_dir = os.path.join(test_dir,'Lymphocyte')\n",
    "os.mkdir(test_lymphocyte_dir)\n",
    "test_variant_dir = os.path.join(test_dir,'Variant_Lymphocyte')\n",
    "os.mkdir(test_variant_dir)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "def crop(I, width, height, c):\n",
    "    Fs = int( int(c[0]) - 0.5 * height )\n",
    "    Coli = int( int(c[1]) - 0.5 * width )\n",
    "    #Cold = int( 2400 - int(c[1])-0.5*width )\n",
    "    #Fi = int( 1800 - int(c[0]) - 0.5*height )\n",
    "    Cold = int( 600 - int(c[1])-0.5 * width )\n",
    "    Fi = int( 450 - int(c[0]) - 0.5 * height )\n",
    "    \n",
    "    print(Fs,Fi,Coli,Cold)\n",
    "    \n",
    "    # Taking in account a cell close to the borders\n",
    "    if Fs < 0:\n",
    "        Fi +=Fs\n",
    "        Fs = 0        \n",
    "    if Fi < 0:\n",
    "        Fs += Fi\n",
    "        Fi = -1801\n",
    "    if Coli < 0:\n",
    "        Cold += Coli\n",
    "        Coli = 0        \n",
    "    if Cold < 0:\n",
    "        Coli += Cold\n",
    "        Cold = -2401        \n",
    "          \n",
    "    #print(Fs,-Fi,Coli,-Cold)\n",
    "        \n",
    "    return I[Fs:-Fi, Coli:-Cold, :]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "def crop_dataset (I):\n",
    "    \n",
    "    I = ski.img_as_float(I) # Convert the image to float (64 bits)\n",
    "    G = I[:,:,1]\n",
    "    #plt.imshow(G, cmap ='gray') #It is better specify the colormap \"cmap\"\n",
    "    \n",
    "    from skimage import filters\n",
    "    G = filters.gaussian(G, sigma = 4)\n",
    "    #plt.imshow(G, cmap = 'gray')\n",
    "     \n",
    "    th = filters.threshold_minimum(G) # threshold by the isodata or minimum method of the green component \n",
    "        \n",
    "    mask = G < th # binary mas of the foreground\n",
    "    #plt.imshow(mask, cmap = 'gray')\n",
    "    \n",
    "    from skimage import morphology\n",
    "    mask2 = morphology.remove_small_objects(mask, 4000) #4000\n",
    "    #plt.imshow(mask2, cmap = 'gray')\n",
    "    \n",
    "    from skimage import measure\n",
    "    mask_label = measure.label(mask2, background = 0) #Labeling the mask\n",
    "    props = measure.regionprops(mask_label) # generate a list that contains the properties (measures) for each region\n",
    "    \n",
    "    cc = [prop.centroid for prop in props]\n",
    "     \n",
    "    for c in cc:\n",
    "        I = ski.img_as_ubyte(I)\n",
    "        #I2 = crop(1220,1230, c)\n",
    "        I2 = crop(I, 2500,2510, c)\n",
    "        #plt.imshow(I2)\n",
    "    \n",
    "    z = [int(c) for c in cc[0]] ####Añadimos z\n",
    "    \n",
    "    areas = [prop.area for prop in props]\n",
    "    #print(areas)\n",
    "    \n",
    "    c = [int(i) for i in cc[0]]\n",
    "    \n",
    "    #plt.imshow(G[300:-200,400:-600], 'gray')\n",
    "    #plt.imshow(G[100:-1,250:-100], 'gray')\n",
    "    \n",
    "    zz = int(np.round(100.8))  #####Añadimos zz\n",
    "    \n",
    "    I = ski.img_as_ubyte(I)\n",
    "    I2 = crop(I, 1500,1350, cc[0])\n",
    "    #plt.imshow(I2)\n",
    " \n",
    "    return I2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "def init_crop(orig_dir, dest_dir, archives):\n",
    "\n",
    "    for archive in archives:\n",
    "        dt_dir = os.path.join(orig_dir, archive) #origen + nombre_imagen\n",
    "        #print(dt_dir)\n",
    "        I = io.imread(dt_dir)\n",
    "        \n",
    "        I2 = crop_dataset(I)     \n",
    "               \n",
    "        destino = os.path.join(dest_dir, archive) #destino + nombre_imagen\n",
    "        io.imsave(destino,I2)\n",
    "       \n",
    "\n",
    "    return I2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [],
   "source": [
    "def init_crop_atypical(folder, orig_dir, dest_dir, archives):\n",
    "    i = 1\n",
    "    for archive in archives:\n",
    "        dt_dir = os.path.join(orig_dir, archive) #origen + nombre_imagen\n",
    "        #print(dt_dir)\n",
    "        I = io.imread(dt_dir)\n",
    "        \n",
    "        if folder == 'train' : \n",
    "            if i == 161:# or i == 161 i == 377 or i == 378:  \n",
    "                I2 = I\n",
    "            else:\n",
    "                I2 = crop_dataset(I)   \n",
    "                \n",
    "        if folder == 'validation':\n",
    "            if i == 286: # or i == 377 or i == 378:  \n",
    "                I2 = I\n",
    "            else:\n",
    "                I2 = crop_dataset(I)   \n",
    "            \n",
    "        if folder == 'test':\n",
    "            if i == 227:  \n",
    "                I2 = I\n",
    "            else:\n",
    "                I2 = crop_dataset(I)\n",
    "            \n",
    "        destino = os.path.join(dest_dir, archive) #destino + nombre_imagen\n",
    "        io.imsave(destino,I2)\n",
    "        i += 1 \n",
    "    return I2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 59,
   "metadata": {},
   "outputs": [],
   "source": [
    "def init_crop_blast(folder, orig_dir, dest_dir, archives):\n",
    "    i = 1\n",
    "    for archive in archives:\n",
    "        dt_dir = os.path.join(orig_dir, archive) #origen + nombre_imagen\n",
    "        #print(dt_dir)\n",
    "        I = io.imread(dt_dir)\n",
    "        \n",
    "        if folder == 'train' : \n",
    "            if i == 4 or i == 12 or i == 34 or i == 294 or i == 366:  \n",
    "                I2 = I\n",
    "            else:\n",
    "                I2 = crop_dataset(I)                  \n",
    "\n",
    "        if folder == 'validation':\n",
    "            if i == 63 or i == 76: # or i == 377 or i == 378:  \n",
    "                I2 = I\n",
    "            else:\n",
    "                I2 = crop_dataset(I)   \n",
    "            \n",
    "        if folder == 'test':\n",
    "            if i == 293: # or i == 260 or i == 485:  \n",
    "                I2 = I\n",
    "            else:\n",
    "                I2 = crop_dataset(I)\n",
    "            \n",
    "         \n",
    "        destino = os.path.join(dest_dir, archive) #destino + nombre_imagen\n",
    "        io.imsave(destino,I2)\n",
    "        i += 1\n",
    "    return I2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [],
   "source": [
    "def read_images(folder, subfolder):\n",
    "    \n",
    "    #origen\n",
    "    orig_dir =  os.path.join(original_dataset_dir, folder, subfolder)\n",
    "    archives = (ls(ruta = orig_dir))\n",
    "    \n",
    "    #destino\n",
    "    dest_dir = os.path.join(base_dir, folder, subfolder)\n",
    "    \n",
    "    return (orig_dir, dest_dir, archives)\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/usr/local/lib/python3.5/dist-packages/skimage/morphology/misc.py:122: UserWarning: Only one label was provided to `remove_small_objects`. Did you mean to use a boolean array?\n",
      "  warn(\"Only one label was provided to `remove_small_objects`. \"\n",
      "/usr/local/lib/python3.5/dist-packages/skimage/util/dtype.py:122: UserWarning: Possible precision loss when converting from float64 to uint8\n",
      "  .format(dtypeobj_in, dtypeobj_out))\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
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    {
     "name": "stdout",
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      "-889 -1171 -420 -1480\n",
      "-309 -591 80 -980\n",
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      "-644 -1416 -295 -1605\n",
      "-595 -1465 -337 -1563\n",
      "-241 -659 9 -909\n",
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      "-116 -784 -140 -760\n",
      "-771 -1289 -616 -1284\n",
      "-191 -709 -116 -784\n"
     ]
    }
   ],
   "source": [
    "#Leemos las imágenes originales y las copiamos en directorios train, validation y test recortadas\n",
    "#SI\n",
    "folders= ['train', 'validation', 'test']\n",
    "\n",
    "for folder in folders: \n",
    "    subfolder = 'Atypical_Lymphocyte'      \n",
    "    [orig_dir, dest_dir, archives] = read_images(folder, subfolder)\n",
    "    I = init_crop_atypical(folder, orig_dir, dest_dir, archives) #Recorte y guardamos en disco\n",
    "\n",
    "for folder in folders: \n",
    "    subfolder = 'Blast'\n",
    "    [orig_dir, dest_dir, archives] = read_images(folder, subfolder)\n",
    "    init_crop_blast(folder, orig_dir, dest_dir, archives) #Recorte y guardamos en disco"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 61,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "cropped_dataset/test/Blast\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "300"
      ]
     },
     "execution_count": 61,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dest_dir = os.path.join(base_dir, folder, subfolder)\n",
    "archives = (ls(ruta = dest_dir))\n",
    "print(dest_dir)\n",
    "len(archives)\n",
    "#plt.imshow(I)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 62,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/usr/local/lib/python3.5/dist-packages/skimage/morphology/misc.py:122: UserWarning: Only one label was provided to `remove_small_objects`. Did you mean to use a boolean array?\n",
      "  warn(\"Only one label was provided to `remove_small_objects`. \"\n",
      "/usr/local/lib/python3.5/dist-packages/skimage/util/dtype.py:122: UserWarning: Possible precision loss when converting from float64 to uint8\n",
      "  .format(dtypeobj_in, dtypeobj_out))\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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    },
    {
     "name": "stdout",
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      "-238 -662 -176 -724\n"
     ]
    }
   ],
   "source": [
    "#Leemos las imágenes originales y las copiamos en directorios train, validation y test recortadas\n",
    "#SI\n",
    "folders= ['train', 'validation', 'test']\n",
    "\n",
    "for folder in folders: \n",
    "   \n",
    "    subfolder = 'Lymphocyte'  \n",
    "    [orig_dir, dest_dir, archives] = read_images(folder, subfolder)\n",
    "    I = init_crop(orig_dir, dest_dir, archives) #Recorte y guardamos en disco\n",
    "    \n",
    "    subfolder = 'Variant_Lymphocyte'  \n",
    "    [orig_dir, dest_dir, archives] = read_images(folder, subfolder)\n",
    "    I = init_crop(orig_dir, dest_dir, archives) #Recorte y guardamos en disco"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 63,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "cropped_dataset/train/Atypical_Lymphocyte\n",
      "cropped_dataset/train/Blast\n",
      "cropped_dataset/train/Lymphocyte\n",
      "cropped_dataset/train/Variant_Lymphocyte\n",
      "1000 506 568 531\n",
      "cropped_dataset/validation/Atypical_Lymphocyte\n",
      "cropped_dataset/validation/Blast\n",
      "cropped_dataset/validation/Lymphocyte\n",
      "cropped_dataset/validation/Variant_Lymphocyte\n",
      "300 150 150 150\n",
      "cropped_dataset/test/Atypical_Lymphocyte\n",
      "cropped_dataset/test/Blast\n",
      "cropped_dataset/test/Lymphocyte\n",
      "cropped_dataset/test/Variant_Lymphocyte\n",
      "300 300 300 300\n"
     ]
    }
   ],
   "source": [
    "folders= ['train', 'validation', 'test']\n",
    "\n",
    "for folder in folders:\n",
    "    dest_dir = os.path.join(base_dir, folder, 'Atypical_Lymphocyte')\n",
    "    archives = (ls(ruta = dest_dir))\n",
    "    print(dest_dir)\n",
    "    a=len(archives)\n",
    "    \n",
    "    dest_dir = os.path.join(base_dir, folder, 'Blast')\n",
    "    archives = (ls(ruta = dest_dir))\n",
    "    print(dest_dir)\n",
    "    b=len(archives)\n",
    "    \n",
    "    dest_dir = os.path.join(base_dir, folder, 'Lymphocyte')\n",
    "    archives = (ls(ruta = dest_dir))\n",
    "    print(dest_dir)\n",
    "    c=len(archives)\n",
    "\n",
    "    dest_dir = os.path.join(base_dir, folder, 'Variant_Lymphocyte')\n",
    "    archives = (ls(ruta = dest_dir))\n",
    "    print(dest_dir)\n",
    "    d=len(archives)\n",
    "    print(a, b, c, d)"
   ]
  }
 ],
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