VGG.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Using TensorFlow backend.\n"
     ]
    }
   ],
   "source": [
    "import keras\n",
    "import tensorflow as tf\n",
    "import json, os, time, copy\n",
    "import numpy as np\n",
    "import skimage\n",
    "import seaborn as sns\n",
    "import glob\n",
    "import SimpleITK as sitk\n",
    "\n",
    "from keras.datasets import mnist\n",
    "from keras.models import Sequential\n",
    "from keras.layers import Dense, Dropout, Flatten\n",
    "from keras.layers import Conv2D, MaxPooling2D \n",
    "from keras import backend as K\n",
    "from matplotlib import pyplot as plt\n",
    "from sklearn.model_selection import train_test_split\n",
    "import imageio\n",
    "sns.set()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of source filePaths: 188\n",
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      "Processing image: 113. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_1E_25-10_30min_822_8_pre_rec.nii.gz\n",
      "Processing image: 114. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_1E_25-10_30min_822_9_pre_rec.nii.gz\n",
      "Processing image: 115. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_1E_3_842_15_pre_rec.nii.gz\n",
      "Processing image: 116. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_1E_3_842_16_pre_rec.nii.gz\n",
      "Processing image: 117. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_1E_3_842_17_pre_rec.nii.gz\n",
      "Processing image: 118. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_1E_3_842_18_pre_rec.nii.gz\n",
      "Processing image: 119. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_1E_3_842_2_pre_rec.nii.gz\n",
      "Processing image: 120. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_1E_3_842_8_pre_rec.nii.gz\n",
      "Processing image: 121. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_1E_3_842_9_pre_rec.nii.gz\n",
      "Processing image: 122. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_25Glu_10Ex30_901_4_pre_rec.nii.gz\n",
      "Processing image: 123. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_25Glu_10Ex30_901_5_pre_rec.nii.gz\n",
      "Processing image: 124. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_25Glu_10Ex30_901_6_pre_rec.nii.gz\n",
      "Processing image: 125. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_25Glu_10Ex30_901_9_pre_rec.nii.gz\n",
      "Processing image: 126. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_25Glu_10Ex30_902_1_pre_rec.nii.gz\n",
      "Processing image: 127. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_25Glu_10Ex30_902_2_pre_rec.nii.gz\n",
      "Processing image: 128. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_25Glu_10Ex30_931_10_pre_rec.nii.gz\n",
      "Processing image: 129. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_25Glu_10Ex30_931_16_pre_rec.nii.gz\n",
      "Processing image: 130. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_25Glu_10Ex30_931_17_pre_rec.nii.gz\n",
      "Processing image: 131. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_25Glu_10Ex30_931_5_pre_rec.nii.gz\n",
      "Processing image: 132. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_25Glu_10Ex30_931_6_pre_rec.nii.gz\n",
      "Processing image: 133. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_25Glu_10Ex30_931_7_pre_rec.nii.gz\n",
      "Processing image: 134. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_25Glu_10Ex30_931_8_pre_rec.nii.gz\n",
      "Processing image: 135. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_25Glu_10Ex30_931_9_pre_rec.nii.gz\n",
      "Processing image: 136. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1063_7_pre_rec.nii.gz\n",
      "Processing image: 137. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1066_10_pre_rec.nii.gz\n",
      "Processing image: 138. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1066_4_pre_rec.nii.gz\n",
      "Processing image: 139. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1066_7_pre_rec.nii.gz\n",
      "Processing image: 140. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1066_8_pre_rec.nii.gz\n",
      "Processing image: 141. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1071_10_pre_rec.nii.gz\n",
      "Processing image: 142. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1071_12_pre_rec.nii.gz\n",
      "Processing image: 143. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1071_13_pre_rec.nii.gz\n",
      "Processing image: 144. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1071_18_pre_rec.nii.gz\n",
      "Processing image: 145. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1071_19_pre_rec.nii.gz\n",
      "Processing image: 146. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1071_20_pre_rec.nii.gz\n",
      "Processing image: 147. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1071_21_pre_rec.nii.gz\n",
      "Processing image: 148. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1071_6_pre_rec.nii.gz\n",
      "Processing image: 149. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1071_8_pre_rec.nii.gz\n",
      "Processing image: 150. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1082_8_pre_rec.nii.gz\n",
      "Processing image: 151. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1084_7_pre_rec.nii.gz\n",
      "Processing image: 152. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1084_8_pre_rec.nii.gz\n",
      "Processing image: 153. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1084_9_pre_rec.nii.gz\n",
      "Processing image: 154. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1093_11_pre_rec.nii.gz\n",
      "Processing image: 155. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1093_12_pre_rec.nii.gz\n",
      "Processing image: 156. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1093_1_pre_rec.nii.gz\n",
      "Processing image: 157. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1093_5_pre_rec.nii.gz\n",
      "Processing image: 158. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1096_18_pre_rec.nii.gz\n",
      "Processing image: 159. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1096_19_pre_rec.nii.gz\n",
      "Processing image: 160. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1096_4_pre_rec.nii.gz\n",
      "Processing image: 161. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1096_5_pre_rec.nii.gz\n",
      "Processing image: 162. Filename: D:/INS-1E Source Images/Unlabeled_train\\25mM Glucose + Ex-4\\5m\\Stevens_PBC_INS1e_25mMglu+Ex-4_5min_1096_6_pre_rec.nii.gz\n",
      "Processing image: 163. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_INS_1E_765_11_pre_rec.nii.gz\n",
      "Processing image: 164. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_INS_1E_765_13_pre_rec.nii.gz\n",
      "Processing image: 165. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_INS_1E_765_3_pre_rec.nii.gz\n",
      "Processing image: 166. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_INS_1E_765_4_pre_rec.nii.gz\n",
      "Processing image: 167. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_Ins_1E_768_1_pre_rec.nii.gz\n",
      "Processing image: 168. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_Ins_1E_768_2_pre_rec.nii.gz\n",
      "Processing image: 169. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_Ins_1E_768_4_pre_rec.nii.gz\n",
      "Processing image: 170. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_INS_1E_783_10_pre_rec.nii.gz\n",
      "Processing image: 171. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_INS_1E_783_11_pre_rec.nii.gz\n",
      "Processing image: 172. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_INS_1E_783_12_pre_rec.nii.gz\n",
      "Processing image: 173. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_INS_1E_783_3_pre_rec.nii.gz\n",
      "Processing image: 174. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_INS_1E_783_4_pre_rec.nii.gz\n",
      "Processing image: 175. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_INS_1E_784_1_pre_rec.nii.gz\n",
      "Processing image: 176. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_INS_1E_784_2_pre_rec.nii.gz\n",
      "Processing image: 177. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_INS_1E_784_3_pre_rec.nii.gz\n",
      "Processing image: 178. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_INS_1E_784_4_pre_rec.nii.gz\n",
      "Processing image: 179. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_INS_1E_784_5_pre_rec.nii.gz\n",
      "Processing image: 180. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_INS_1E_784_6_pre_rec.nii.gz\n",
      "Processing image: 181. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_INS_1E_784_7_pre_rec.nii.gz\n",
      "Processing image: 182. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_INS_1E_785_1_pre_rec.nii.gz\n",
      "Processing image: 183. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_INS_1E_785_2_pre_rec.nii.gz\n",
      "Processing image: 184. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_INS_1E_785_3_pre_rec.nii.gz\n",
      "Processing image: 185. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_INS_1E_785_4_pre_rec.nii.gz\n",
      "Processing image: 186. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_INS_1E_785_5_pre_rec.nii.gz\n",
      "Processing image: 187. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_INS_1E_785_6_pre_rec.nii.gz\n",
      "Processing image: 188. Filename: D:/INS-1E Source Images/Unlabeled_train\\No treatment\\Stevens_pancreatic_INS_1E_785_7_pre_rec.nii.gz\n",
      "done uploading\n",
      "(24064, 128, 128, 3)\n"
     ]
    }
   ],
   "source": [
    "import cv2\n",
    "\n",
    "import numpy as np\n",
    "\n",
    "# Get array\n",
    "#rootdir = \"/Users/hkim20/Documents/Unlabeled_predictions/Glucose/\"\n",
    "#outdir = \"/Users/hkim20/Downloads/\"\n",
    "rootdir = \"D:/INS-1E Source Images/Unlabeled_train\"\n",
    "niiPaths = []\n",
    "fill_value = 0\n",
    "num_files=188\n",
    "imageNewArray = np.zeros((num_files*128,128,128,3))   \n",
    "\n",
    "for subdir, dirs, files in os.walk(rootdir):\n",
    "    for file in files:\n",
    "        if(file.endswith(\"nii.gz\")):\n",
    "                niiPaths.append(os.path.join(subdir, file))\n",
    "\n",
    "print(\"Number of source filePaths: \" + str(len(niiPaths)))\n",
    "#print(niiPaths)\n",
    "\n",
    "allImages = np.zeros((num_files*128, 128, 128))\n",
    "\n",
    "for fileCount, filePath in enumerate(niiPaths[:]):\n",
    "    \n",
    "    image = sitk.ReadImage(filePath) \n",
    "   # im = sitk.GetImageFromArray(image)\n",
    "    \n",
    "    print(\"Processing image: \" + str(fileCount + 1) + \". Filename: \"+ filePath)\n",
    "\n",
    "    num_dim = image.GetDimension()\n",
    "    \n",
    "    orig_pixelid = image.GetPixelIDValue()\n",
    "    orig_origin = image.GetOrigin()\n",
    "    orig_direction = image.GetDirection()\n",
    "    orig_spacing = np.array(image.GetSpacing())\n",
    "    orig_size = np.array(image.GetSize(), dtype=np.int)\n",
    "\n",
    "    \n",
    "    \n",
    "    new_size = [128,128,128] #  SimpleITK expects lists, not ndarrays\n",
    "\n",
    "    new_spacing = [sz*spc/nsz for nsz,sz,spc in zip(new_size, image.GetSize(), image.GetSpacing())]\n",
    "\n",
    "    resample_filter = sitk.ResampleImageFilter()\n",
    "\n",
    "    resampled_sitk_image = resample_filter.Execute(image,\n",
    "                                                   new_size,\n",
    "                                                   sitk.Transform(),\n",
    "                                                   sitk.sitkNearestNeighbor,\n",
    "                                                   orig_origin,\n",
    "                                                   new_spacing,\n",
    "                                                   orig_direction,\n",
    "                                                   fill_value,\n",
    "                                                   orig_pixelid)\n",
    "   \n",
    "   # resampled_sitk_image = np.expand_dims (resampled_sitk_image, axis =2)\n",
    "\n",
    "    \n",
    "\n",
    "    imageArray = sitk.GetArrayFromImage(resampled_sitk_image)\n",
    "    \n",
    "    for j in range(64):\n",
    "        allImages[64*fileCount + j] = imageArray[32+j] # middle slides    \n",
    "    \n",
    "print (\"done uploading\")\n",
    "\n",
    "for i in range(num_files*128):\n",
    "        for j in range (128):\n",
    "            for k in range (128):\n",
    "                for l in (0,1,2):\n",
    "                    imageNewArray[i][j][k][l] = allImages[i][j][k]\n",
    "\n",
    "#imageNewArray = np.expand_dims(imageNewArray, axis=3)\n",
    "print(imageNewArray.shape)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "188\n",
      "[0. 1.]\n"
     ]
    }
   ],
   "source": [
    "##@USC\n",
    "labelArray = np.zeros((num_files*128, 7))\n",
    "print(len(niiPaths))\n",
    "for fileCount, filePath in enumerate(niiPaths[:]):\n",
    "    label=np.zeros((7))\n",
    "    if \"No treatment\" in filePath:\n",
    "        label[0] = 1\n",
    "    elif \"Ex\" in filePath:\n",
    "        if \"1m\\\\\" in filePath:\n",
    "            label[1] = 1\n",
    "        elif \"5m\\\\\" in filePath:\n",
    "            label[2] = 1\n",
    "        elif \"30m\\\\\" in filePath:\n",
    "            label[3] = 1\n",
    "    else:\n",
    "        if \"1m\\\\\" in filePath:\n",
    "            label[4] = 1\n",
    "        elif \"5m\\\\\" in filePath:\n",
    "            label[5] = 1\n",
    "        elif \"30m\\\\\" in filePath:\n",
    "            label[6] = 1\n",
    "    for j in range(128):\n",
    "        labelArray[128*fileCount + j] = label\n",
    "    \n",
    "    #print(\"Saving Labels: \" + str(fileCount+1) + \". Label:\" + str(label) + \"for filepath \" + str(filePath))\n",
    "    \n",
    "print(np.unique(labelArray))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of source filePaths: 223\n",
      "Processing image: 1. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\1m\\Stevens_pancreatic_INS_1E_1_819_13_pre_rec.nii.gz\n",
      "Processing image: 2. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\1m\\Stevens_pancreatic_INS_1E_1_819_1_pre_rec.nii.gz\n",
      "Processing image: 3. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\1m\\Stevens_pancreatic_INS_1E_1_819_7_pre_rec.nii.gz\n",
      "Processing image: 4. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\1m\\Stevens_pancreatic_INS_1E_5_817_1_pre_rec.nii.gz\n",
      "Processing image: 5. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\1m\\Stevens_pancreatic_INS_1E_5_817_4_pre_rec.nii.gz\n",
      "Processing image: 6. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\1m\\Stevens_pancreatic_INS_1E_5_817_8_pre_rec.nii.gz\n",
      "Processing image: 7. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\1m\\Stevens_pancreatic_INS_25Glu_1min_930_5_pre_rec.nii.gz\n",
      "Processing image: 8. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_Ins_1E_25mM_766_15_pre_rec.nii.gz\n",
      "Processing image: 9. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_Ins_1E_25mM_766_16_pre_rec.nii.gz\n",
      "Processing image: 10. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_Ins_1E_25mM_766_17_pre_rec.nii.gz\n",
      "Processing image: 11. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_Ins_1E_25mM_766_3_pre_rec.nii.gz\n",
      "Processing image: 12. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_Ins_1E_25mM_766_4_pre_rec.nii.gz\n",
      "Processing image: 13. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_Ins_1E_25mM_766_5_pre_rec.nii.gz\n",
      "Processing image: 14. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_Ins_1E_25mM_766_6_pre_rec.nii.gz\n",
      "Processing image: 15. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_Ins_1E_25mM_766_7_pre_rec.nii.gz\n",
      "Processing image: 16. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_INS_1E_25mM_769_3_pre_rec.nii.gz\n",
      "Processing image: 17. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_INS_1E_25mM_769_4_pre_rec.nii.gz\n",
      "Processing image: 18. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_INS_1E_25mM_770_2_pre_rec.nii.gz\n",
      "Processing image: 19. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_INS_1E_25mM_770_3_pre_rec.nii.gz\n",
      "Processing image: 20. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_INS_1E_25mM_770_4_pre_rec.nii.gz\n",
      "Processing image: 21. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_INS_1E_25mM_770_5_pre_rec.nii.gz\n",
      "Processing image: 22. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_INS_1E_25mM_770_6_pre_rec.nii.gz\n",
      "Processing image: 23. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_INS_25Glu_30min_927_10_pre_rec.nii.gz\n",
      "Processing image: 24. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_INS_25Glu_30min_927_16_pre_rec.nii.gz\n",
      "Processing image: 25. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_INS_25Glu_30min_927_17_pre_rec.nii.gz\n",
      "Processing image: 26. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_INS_25Glu_30min_927_18_pre_rec.nii.gz\n",
      "Processing image: 27. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_INS_25Glu_30min_927_19_pre_rec.nii.gz\n",
      "Processing image: 28. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_INS_25Glu_30min_927_20_pre_rec.nii.gz\n",
      "Processing image: 29. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_INS_25Glu_30min_927_6_pre_rec.nii.gz\n",
      "Processing image: 30. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_INS_25Glu_30min_927_7_pre_rec.nii.gz\n",
      "Processing image: 31. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_INS_25Glu_30min_927_8_pre_rec.nii.gz\n",
      "Processing image: 32. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\30m\\Stevens_pancreatic_INS_25Glu_30min_927_9_pre_rec.nii.gz\n",
      "Processing image: 33. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1044_14_pre_rec.nii.gz\n",
      "Processing image: 34. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1044_15_pre_rec.nii.gz\n",
      "Processing image: 35. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1044_16_pre_rec.nii.gz\n",
      "Processing image: 36. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1044_5_pre_rec.nii.gz\n",
      "Processing image: 37. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1044_6_pre_rec.nii.gz\n",
      "Processing image: 38. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1044_7_pre_rec.nii.gz\n",
      "Processing image: 39. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1044_8_pre_rec.nii.gz\n",
      "Processing image: 40. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1044_9_pre_rec.nii.gz\n",
      "Processing image: 41. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1045_10_pre_rec.nii.gz\n",
      "Processing image: 42. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1045_8_pre_rec.nii.gz\n",
      "Processing image: 43. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1046_12_pre_rec.nii.gz\n",
      "Processing image: 44. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1046_14_pre_rec.nii.gz\n",
      "Processing image: 45. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1046_15_pre_rec.nii.gz\n",
      "Processing image: 46. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1046_4_pre_rec.nii.gz\n",
      "Processing image: 47. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1046_6_pre_rec.nii.gz\n",
      "Processing image: 48. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1046_7_pre_rec.nii.gz\n",
      "Processing image: 49. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1046_8_pre_rec.nii.gz\n",
      "Processing image: 50. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1060_10_pre_rec.nii.gz\n",
      "Processing image: 51. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1060_11_pre_rec.nii.gz\n",
      "Processing image: 52. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1060_12_pre_rec.nii.gz\n",
      "Processing image: 53. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1060_1_pre_rec.nii.gz\n",
      "Processing image: 54. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1060_2_pre_rec.nii.gz\n",
      "Processing image: 55. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1060_3_pre_rec.nii.gz\n",
      "Processing image: 56. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1060_8_pre_rec.nii.gz\n",
      "Processing image: 57. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1060_9_pre_rec.nii.gz\n",
      "Processing image: 58. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1091_13_pre_rec.nii.gz\n",
      "Processing image: 59. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1091_7_pre_rec.nii.gz\n",
      "Processing image: 60. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1091_8_pre_rec.nii.gz\n",
      "Processing image: 61. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1091_9_pre_rec.nii.gz\n",
      "Processing image: 62. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1092_10_pre_rec.nii.gz\n",
      "Processing image: 63. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1092_11_pre_rec.nii.gz\n",
      "Processing image: 64. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1092_1_pre_rec.nii.gz\n",
      "Processing image: 65. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1092_6_pre_rec.nii.gz\n",
      "Processing image: 66. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1092_7_pre_rec.nii.gz\n",
      "Processing image: 67. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1092_8_pre_rec.nii.gz\n",
      "Processing image: 68. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1092_9_pre_rec.nii.gz\n",
      "Processing image: 69. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1094_2_pre_rec.nii.gz\n",
      "Processing image: 70. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1094_5_pre_rec.nii.gz\n",
      "Processing image: 71. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1094_6_pre_rec.nii.gz\n",
      "Processing image: 72. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1094_9_pre_rec.nii.gz\n",
      "Processing image: 73. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1104_13_pre_rec.nii.gz\n",
      "Processing image: 74. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1104_15_pre_rec.nii.gz\n",
      "Processing image: 75. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1104_16_pre_rec.nii.gz\n",
      "Processing image: 76. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1104_17_pre_rec.nii.gz\n",
      "Processing image: 77. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1104_23_pre_rec.nii.gz\n",
      "Processing image: 78. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1104_3_pre_rec.nii.gz\n",
      "Processing image: 79. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1104_4_pre_rec.nii.gz\n",
      "Processing image: 80. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1104_5_pre_rec.nii.gz\n",
      "Processing image: 81. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1104_7_pre_rec.nii.gz\n",
      "Processing image: 82. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose\\5m\\Stevens_PBC_INS1e_25mMglu_5min_1104_9_pre_rec.nii.gz\n",
      "Processing image: 83. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Stevens_pancreatic_INS_1E_25-10_1min_821_10_pre_rec.nii.gz\n",
      "Processing image: 84. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Stevens_pancreatic_INS_1E_25-10_1min_821_11_pre_rec.nii.gz\n",
      "Processing image: 85. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Stevens_pancreatic_INS_1E_25-10_1min_821_12_pre_rec.nii.gz\n",
      "Processing image: 86. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Stevens_pancreatic_INS_1E_25-10_1min_821_4_pre_rec.nii.gz\n",
      "Processing image: 87. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Stevens_pancreatic_INS_1E_25-10_1min_821_5_pre_rec.nii.gz\n",
      "Processing image: 88. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Stevens_pancreatic_INS_1E_25-10_1min_821_6_pre_rec.nii.gz\n",
      "Processing image: 89. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Stevens_pancreatic_INS_1E_25-10_1min_821_7_pre_rec.nii.gz\n",
      "Processing image: 90. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Stevens_pancreatic_INS_1E_25-10_1min_821_8_pre_rec.nii.gz\n",
      "Processing image: 91. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Stevens_pancreatic_INS_1E_25-10_1min_821_9_pre_rec.nii.gz\n",
      "Processing image: 92. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Stevens_pancreatic_INS_1E_2_844_3_pre_rec.nii.gz\n",
      "Processing image: 93. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Stevens_pancreatic_INS_1E_2_844_4_pre_rec.nii.gz\n",
      "Processing image: 94. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Stevens_pancreatic_INS_1E_2_844_5_pre_rec.nii.gz\n",
      "Processing image: 95. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Stevens_pancreatic_INS_1E_2_844_6_pre_rec.nii.gz\n",
      "Processing image: 96. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Stevens_pancreatic_INS_1E_2_844_7_pre_rec.nii.gz\n",
      "Processing image: 97. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Stevens_pancreatic_INS_1E_Glu_Ex1_857_1_pre_rec.nii.gz\n",
      "Processing image: 98. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Stevens_pancreatic_INS_25Glu_10Ex1_908_11_pre_rec.nii.gz\n",
      "Processing image: 99. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Stevens_pancreatic_INS_25Glu_10Ex1_908_13_pre_rec.nii.gz\n",
      "Processing image: 100. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Stevens_pancreatic_INS_25Glu_10Ex1_908_15_pre_rec.nii.gz\n",
      "Processing image: 101. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Stevens_pancreatic_INS_25Glu_10Ex1_908_16_pre_rec.nii.gz\n",
      "Processing image: 102. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Stevens_pancreatic_INS_25Glu_10Ex1_908_17_pre_rec.nii.gz\n",
      "Processing image: 103. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Steven_pancreatic_iNS_1E_4_816_10_pre_rec.nii.gz\n",
      "Processing image: 104. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Steven_pancreatic_iNS_1E_4_816_11_pre_rec.nii.gz\n",
      "Processing image: 105. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Steven_pancreatic_iNS_1E_4_816_12_pre_rec.nii.gz\n",
      "Processing image: 106. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Steven_pancreatic_iNS_1E_4_816_3_pre_rec.nii.gz\n",
      "Processing image: 107. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Steven_pancreatic_iNS_1E_4_816_4_pre_rec.nii.gz\n",
      "Processing image: 108. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Steven_pancreatic_iNS_1E_4_816_5_pre_rec.nii.gz\n",
      "Processing image: 109. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Steven_pancreatic_iNS_1E_4_816_6_pre_rec.nii.gz\n",
      "Processing image: 110. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\1m\\Steven_pancreatic_iNS_1E_4_816_7_pre_rec.nii.gz\n",
      "Processing image: 111. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_1E_25-10_30min_822_3_pre_rec.nii.gz\n",
      "Processing image: 112. Filename: D:/INS-1E Source Images/Unlabeled_test\\25mM Glucose + Ex-4\\30m\\Stevens_pancreatic_INS_1E_25-10_30min_822_4_pre_rec.nii.gz\n"
     ]
    }
   ],
   "source": [
    "###FOR TESTING###\n",
    "\n",
    "# Get array\n",
    "test_rootdir = \"D:/INS-1E Source Images/Unlabeled_test\"\n",
    "test_niiPaths = []\n",
    "fill_value = 0\n",
    "num_files=223\n",
    "\n",
    "\n",
    "test_imageNewArray = np.zeros((num_files*128,128,128,3))   \n",
    "\n",
    "\n",
    "for subdir, dirs, files in os.walk(test_rootdir):\n",
    "    for file in files:\n",
    "        if(file.endswith(\"nii.gz\")):\n",
    "                test_niiPaths.append(os.path.join(subdir, file))\n",
    "\n",
    "print(\"Number of source filePaths: \" + str(len(test_niiPaths)))\n",
    "\n",
    "test_allImages = np.zeros((num_files*128, 128, 128))\n",
    "\n",
    "for fileCount, filePath in enumerate(test_niiPaths[:]):\n",
    "    \n",
    "    image = sitk.ReadImage(filePath) \n",
    "   # im = sitk.GetImageFromArray(image)\n",
    "    \n",
    "    print(\"Processing image: \" + str(fileCount + 1) + \". Filename: \"+ filePath)\n",
    "\n",
    "    num_dim = image.GetDimension()\n",
    "    \n",
    "    orig_pixelid = image.GetPixelIDValue()\n",
    "    orig_origin = image.GetOrigin()\n",
    "    orig_direction = image.GetDirection()\n",
    "    orig_spacing = np.array(image.GetSpacing())\n",
    "    orig_size = np.array(image.GetSize(), dtype=np.int)\n",
    "\n",
    "    new_size = [128,128,128] #  SimpleITK expects lists, not ndarrays\n",
    "\n",
    "    new_spacing = [sz*spc/nsz for nsz,sz,spc in zip(new_size, image.GetSize(), image.GetSpacing())]\n",
    "\n",
    "    resample_filter = sitk.ResampleImageFilter()\n",
    "\n",
    "    resampled_sitk_image = resample_filter.Execute(image,\n",
    "                                                   new_size,\n",
    "                                                   sitk.Transform(),\n",
    "                                                   sitk.sitkNearestNeighbor,\n",
    "                                                   orig_origin,\n",
    "                                                   new_spacing,\n",
    "                                                   orig_direction,\n",
    "                                                   fill_value,\n",
    "                                                   orig_pixelid)\n",
    "\n",
    "    test_imageArray = sitk.GetArrayFromImage(resampled_sitk_image)\n",
    "    \n",
    "    for j in range(64):\n",
    "        test_allImages[64*fileCount + j] = test_imageArray[32+j] # middle slides\n",
    "\n",
    "print (\"done uploading\")\n",
    "\n",
    "\n",
    "for i in range(num_files*128):\n",
    "        for j in range (128):\n",
    "            for k in range (128):\n",
    "                for l in (0,1,2):\n",
    "                    test_imageNewArray[i][j][k][l] = test_allImages[i][j][k]\n",
    "\n",
    "#imageNewArray = np.expand_dims(imageNewArray, axis=3)\n",
    "print(test_imageNewArray.shape)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'np' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-1-6f4112584d20>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0mtest_labelArray\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mzeros\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mnum_files\u001b[0m\u001b[1;33m*\u001b[0m\u001b[1;36m64\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;36m7\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m      2\u001b[0m \u001b[1;32mfor\u001b[0m \u001b[0mfileCount\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mfilePath\u001b[0m \u001b[1;32min\u001b[0m \u001b[0menumerate\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mtest_niiPaths\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      3\u001b[0m     \u001b[0mlabel\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mzeros\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;36m7\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      4\u001b[0m     \u001b[1;32mif\u001b[0m \u001b[1;34m\"No treatment\"\u001b[0m \u001b[1;32min\u001b[0m \u001b[0mfilePath\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      5\u001b[0m         \u001b[0mlabel\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;36m0\u001b[0m\u001b[1;33m]\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;36m1\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;31mNameError\u001b[0m: name 'np' is not defined"
     ]
    }
   ],
   "source": [
    "test_labelArray = np.zeros((num_files*64, 7))\n",
    "for fileCount, filePath in enumerate(test_niiPaths[:]):\n",
    "    label = np.zeros((7))\n",
    "    if \"No treatment\" in filePath:\n",
    "        label[0] = 1\n",
    "    elif \"Ex\" in filePath:\n",
    "        if \"1m\\\\\" in filePath:\n",
    "            label[1] = 1\n",
    "        elif \"5m\\\\\" in filePath:\n",
    "            label[2] = 1\n",
    "        elif \"30m\\\\\" in filePath:\n",
    "            label[3] = 1\n",
    "    else:\n",
    "        if \"1m\\\\\" in filePath:\n",
    "            label[4] = 1\n",
    "        elif \"5m\\\\\" in filePath:\n",
    "            label[5] = 1\n",
    "        elif \"30m\\\\\" in filePath:\n",
    "            label[6] = 1\n",
    "    for j in range(64):\n",
    "        test_labelArray[64*fileCount + j] = label\n",
    "    \n",
    "    #print(\"Saving Labels: \" + str(fileCount+1) + \". Label:\" + str(label) + \"for filepath \" + str(filePath))\n",
    "  \n",
    "print(len(test_labelArray))\n",
    "print(np.unique(test_labelArray))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [],
   "source": [
    "batch_size = 64\n",
    "num_classes = 7\n",
    "num_labels = 5\n",
    "epochs = 12\n",
    "\n",
    "# input image dimension\n",
    "\n",
    "img_rows, img_cols = 128, 128\n",
    "\n",
    "# the data, split between train and test sets\n",
    "\n",
    "x_train = imageNewArray\n",
    "y_train = labelArray\n",
    "\n",
    "x_test = test_imageNewArray\n",
    "y_test= test_labelArray\n",
    "\n",
    "input_shape = (img_rows, img_cols,3)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(37120, 128, 128, 3)\n",
      "(37120, 7)\n",
      "(12032, 128, 128, 3)\n",
      "(12032, 7)\n",
      "[0.]\n",
      "[0. 1.]\n",
      "[0. 0. 1. 0. 0. 0. 0.]\n"
     ]
    }
   ],
   "source": [
    "print(x_train.shape)\n",
    "print(y_train.shape)\n",
    "print(x_test.shape)\n",
    "print(y_test.shape)\n",
    "print(np.unique(y_train))\n",
    "print(np.unique(y_test))\n",
    "print(y_test[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [],
   "source": [
    "from keras import applications\n",
    "from keras.preprocessing.image import ImageDataGenerator\n",
    "from keras import optimizers\n",
    "from keras.models import Sequential, Model \n",
    "from keras.layers import Dropout, Flatten, Dense, GlobalAveragePooling2D\n",
    "from keras import backend as k \n",
    "from keras.callbacks import ModelCheckpoint, LearningRateScheduler, TensorBoard, EarlyStopping\n",
    "\n",
    "img_width, img_height = 128, 128\n",
    "train_data_dir = \"D:/INS-1E Source Images/Unlabeled_train\"\n",
    "validation_data_dir = \"D:/INS-1E Source Images/Unlabeled_test\"\n",
    "\n",
    "batch_size = 16\n",
    "epochs = 10\n",
    "\n",
    "model = applications.VGG19(weights = \"imagenet\", include_top=False, input_shape = (img_width, img_height, 3))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [],
   "source": [
    "for layer in model.layers[:5]:\n",
    "    layer.trainable = False\n",
    "x = model.output\n",
    "x = Flatten()(x)\n",
    "x = Dense(1024, activation=\"relu\")(x)\n",
    "x = Dropout(0.5)(x)\n",
    "x = Dense(1024, activation=\"relu\")(x)\n",
    "predictions = Dense(7, activation=\"softmax\")(x)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/opt/anaconda3/lib/python3.7/site-packages/ipykernel_launcher.py:1: UserWarning: Update your `Model` call to the Keras 2 API: `Model(inputs=Tensor(\"in..., outputs=Tensor(\"de...)`\n",
      "  \"\"\"Entry point for launching an IPython kernel.\n"
     ]
    }
   ],
   "source": [
    "model_final = Model(input = model.input, output = predictions)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "_________________________________________________________________\n",
      "Layer (type)                 Output Shape              Param #   \n",
      "=================================================================\n",
      "input_2 (InputLayer)         (None, 128, 128, 3)       0         \n",
      "_________________________________________________________________\n",
      "block1_conv1 (Conv2D)        (None, 128, 128, 64)      1792      \n",
      "_________________________________________________________________\n",
      "block1_conv2 (Conv2D)        (None, 128, 128, 64)      36928     \n",
      "_________________________________________________________________\n",
      "block1_pool (MaxPooling2D)   (None, 64, 64, 64)        0         \n",
      "_________________________________________________________________\n",
      "block2_conv1 (Conv2D)        (None, 64, 64, 128)       73856     \n",
      "_________________________________________________________________\n",
      "block2_conv2 (Conv2D)        (None, 64, 64, 128)       147584    \n",
      "_________________________________________________________________\n",
      "block2_pool (MaxPooling2D)   (None, 32, 32, 128)       0         \n",
      "_________________________________________________________________\n",
      "block3_conv1 (Conv2D)        (None, 32, 32, 256)       295168    \n",
      "_________________________________________________________________\n",
      "block3_conv2 (Conv2D)        (None, 32, 32, 256)       590080    \n",
      "_________________________________________________________________\n",
      "block3_conv3 (Conv2D)        (None, 32, 32, 256)       590080    \n",
      "_________________________________________________________________\n",
      "block3_conv4 (Conv2D)        (None, 32, 32, 256)       590080    \n",
      "_________________________________________________________________\n",
      "block3_pool (MaxPooling2D)   (None, 16, 16, 256)       0         \n",
      "_________________________________________________________________\n",
      "block4_conv1 (Conv2D)        (None, 16, 16, 512)       1180160   \n",
      "_________________________________________________________________\n",
      "block4_conv2 (Conv2D)        (None, 16, 16, 512)       2359808   \n",
      "_________________________________________________________________\n",
      "block4_conv3 (Conv2D)        (None, 16, 16, 512)       2359808   \n",
      "_________________________________________________________________\n",
      "block4_conv4 (Conv2D)        (None, 16, 16, 512)       2359808   \n",
      "_________________________________________________________________\n",
      "block4_pool (MaxPooling2D)   (None, 8, 8, 512)         0         \n",
      "_________________________________________________________________\n",
      "block5_conv1 (Conv2D)        (None, 8, 8, 512)         2359808   \n",
      "_________________________________________________________________\n",
      "block5_conv2 (Conv2D)        (None, 8, 8, 512)         2359808   \n",
      "_________________________________________________________________\n",
      "block5_conv3 (Conv2D)        (None, 8, 8, 512)         2359808   \n",
      "_________________________________________________________________\n",
      "block5_conv4 (Conv2D)        (None, 8, 8, 512)         2359808   \n",
      "_________________________________________________________________\n",
      "block5_pool (MaxPooling2D)   (None, 4, 4, 512)         0         \n",
      "_________________________________________________________________\n",
      "flatten_2 (Flatten)          (None, 8192)              0         \n",
      "_________________________________________________________________\n",
      "dense_4 (Dense)              (None, 1024)              8389632   \n",
      "_________________________________________________________________\n",
      "dropout_2 (Dropout)          (None, 1024)              0         \n",
      "_________________________________________________________________\n",
      "dense_5 (Dense)              (None, 1024)              1049600   \n",
      "_________________________________________________________________\n",
      "dense_6 (Dense)              (None, 7)                 7175      \n",
      "=================================================================\n",
      "Total params: 29,470,791\n",
      "Trainable params: 29,358,215\n",
      "Non-trainable params: 112,576\n",
      "_________________________________________________________________\n"
     ]
    }
   ],
   "source": [
    "model_final.summary()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [],
   "source": [
    "model_final.compile(loss = \"categorical_crossentropy\", optimizer = optimizers.SGD(lr=0.0001, momentum=0.9), metrics=[\"accuracy\"])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [],
   "source": [
    "checkpoint = ModelCheckpoint(\"vgg16_1.h5\", monitor='val_acc', verbose=1, save_best_only=True, save_weights_only=False, mode='auto', period=1)\n",
    "early = EarlyStopping(monitor='val_acc', min_delta=0, patience=10, verbose=1, mode='auto')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Train on 37120 samples, validate on 12032 samples\n",
      "Epoch 1/10\n",
      "37120/37120 [==============================] - 18213s 491ms/step - loss: 0.0000e+00 - acc: 0.4674 - val_loss: 2.1778 - val_acc: 0.0323\n",
      "\n",
      "Epoch 00001: val_acc improved from -inf to 0.03233, saving model to vgg16_1.h5\n",
      "Epoch 2/10\n",
      "37120/37120 [==============================] - 71566s 2s/step - loss: 0.0000e+00 - acc: 0.4659 - val_loss: 2.1778 - val_acc: 0.0323\n",
      "\n",
      "Epoch 00002: val_acc did not improve from 0.03233\n",
      "Epoch 3/10\n",
      "37120/37120 [==============================] - 16767s 452ms/step - loss: 0.0000e+00 - acc: 0.4731 - val_loss: 2.1778 - val_acc: 0.0323\n",
      "\n",
      "Epoch 00003: val_acc did not improve from 0.03233\n",
      "Epoch 4/10\n",
      "18144/37120 [=============>................] - ETA: 12:54:16 - loss: 0.0000e+00 - acc: 0.4660"
     ]
    }
   ],
   "source": [
    "model_final.fit(x_train, y_train,\n",
    "          epochs=epochs,\n",
    "          verbose=1,\n",
    "          validation_data=(x_test, y_test),\n",
    "          callbacks = [checkpoint, early])\n",
    "          \n",
    "score = model_final.evaluate(x_test, y_test, verbose=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "model.save_weights('D:/INS-1E Source Images/model_weights_01_09_2020.h5') \n",
    "print(\"saved\")\n",
    "\n",
    "with open('D:/INS-1E Source Images/model_architecture_01_09_2020.json', 'w') as f:\n",
    "    f.write(model.to_json())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from keras.models import model_from_json\n",
    "\n",
    "# Model reconstruction from JSON file\n",
    "with open('D:/INS-1E Source Images/model_architecture_01_09_2020.json', 'r') as f:\n",
    "    model = model_from_json(f.read())\n",
    "\n",
    "# Load weights into the new model\n",
    "model.load_weights('D:/INS-1E Source Images/model_weights_01_09_2020.h5') #change names\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# confusion matrix\n",
    "from sklearn.metrics import confusion_matrix\n",
    "\n",
    "test_labels = np.zeros((len(test_labelArray)))\n",
    "for i,label in enumerate(test_labelArray):\n",
    "    for j in range(7):\n",
    "        if label[j] == 1:\n",
    "            test_labels[i] = j\n",
    "\n",
    "print(ynew)\n",
    "print(test_labels)\n",
    "confusionArray = confusion_matrix(test_labels, ynew)\n",
    "print(confusionArray)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "print(confusionArray.shape)\n",
    "confusionFloat = np.zeros((7,7))\n",
    "for i in range(7):\n",
    "    sum = 0\n",
    "    for j in range(7):\n",
    "        sum = sum + confusionArray[i][j]\n",
    "    print(sum)\n",
    "    for k in range(7):\n",
    "        confusionFloat[i][k] = round(confusionArray[i][k]/sum, 2)\n",
    "\n",
    "print(confusionFloat)\n",
    "img = plt.imshow(confusionFloat)\n",
    "img.set_cmap('hot')\n",
    "plt.axis('off')\n",
    "plt.show()"
   ]
  }
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