Merge pull request #430 from zivy/removeUsageOfPickle

Remove the use of pickling.
InsightSoftwareConsortium · Oct 6, 2023 · e805f17 · e805f17
2 parents 66745e3 + 62f6a01
commit e805f17
Showing 1 changed file with 15 additions and 22 deletions.
diff --git a/Python/71_Trust_But_Verify.ipynb b/Python/71_Trust_But_Verify.ipynb
@@ -69,7 +69,6 @@
     "\n",
     "import hashlib\n",
     "import tempfile\n",
-    "import pickle\n",
     "\n",
     "%matplotlib notebook\n",
     "import matplotlib.pyplot as plt\n",
@@ -652,7 +651,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We next run our visualization based analysis. For large datasets this may take some time, so we save the results via pickling so that we can look at them at a later point in time.\n",
+    "We next run our visualization based analysis. For large datasets this may take some time, so we save the results so that we can look at them at a later point in time.\n",
     "\n",
     "We start with the file based approach. Notice that with this approach the display is dominated by slices from several DICOM series. After selecting our images of interest we print the associated file names."
    ]
@@ -663,19 +662,18 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "faux_image_volume_file_name = os.path.join(OUTPUT_DIR, \"faux_image_volume.pkl\")\n",
-    "faux_image_file_list_name = os.path.join(OUTPUT_DIR, \"faux_image_file_list.pkl\")\n",
+    "faux_image_volume_file_name = os.path.join(OUTPUT_DIR, \"faux_image_volume.nrrd\")\n",
+    "faux_image_file_list_name = os.path.join(OUTPUT_DIR, \"faux_image_file_list.csv\")\n",
     "faux_volume_image_files, image_file_list = visualize_files(\n",
     "    data_root_dir,\n",
     "    imageIO=\"\",\n",
     "    projection_axis=2,\n",
     "    thumbnail_size=[64, 64],\n",
     "    tile_size=[30, 20],\n",
     ")\n",
-    "with open(faux_image_volume_file_name, \"wb\") as fp:\n",
-    "    pickle.dump(faux_volume_image_files, fp)\n",
-    "with open(faux_image_file_list_name, \"wb\") as fp:\n",
-    "    pickle.dump(image_file_list, fp)"
+    "sitk.WriteImage(faux_volume_image_files, faux_image_volume_file_name, True)\n",
+    "df = pd.DataFrame(data=image_file_list, columns=[\"files\"])\n",
+    "df.to_csv(faux_image_file_list_name, index=False)"
    ]
   },
   {
@@ -684,10 +682,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "with open(faux_image_volume_file_name, \"rb\") as fp:\n",
-    "    faux_volume_image_files = pickle.load(fp)\n",
-    "with open(faux_image_file_list_name, \"rb\") as fp:\n",
-    "    image_file_list = pickle.load(fp)\n",
+    "faux_volume_image_files = sitk.ReadImage(faux_image_volume_file_name)\n",
+    "image_file_list = pd.read_csv(faux_image_file_list_name)[\"files\"].to_list()\n",
     "\n",
     "image_selection_gui = ImageSelection(\n",
     "    faux_volume_image_files,\n",
@@ -722,15 +718,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "faux_series_volume_file_name = os.path.join(OUTPUT_DIR, \"faux_series_volume.pkl\")\n",
-    "faux_series_file_list_name = os.path.join(OUTPUT_DIR, \"faux_series_file_list.pkl\")\n",
+    "faux_series_volume_file_name = os.path.join(OUTPUT_DIR, \"faux_series_volume.nrrd\")\n",
+    "faux_series_file_list_name = os.path.join(OUTPUT_DIR, \"faux_series_file_list.csv\")\n",
     "faux_volume_image_files, image_file_list = visualize_series(\n",
     "    data_root_dir, projection_axis=2, thumbnail_size=[64, 64], tile_size=[30, 20]\n",
     ")\n",
-    "with open(faux_series_volume_file_name, \"wb\") as fp:\n",
-    "    pickle.dump(faux_volume_image_files, fp)\n",
-    "with open(faux_series_file_list_name, \"wb\") as fp:\n",
-    "    pickle.dump(image_file_list, fp)"
+    "sitk.WriteImage(faux_volume_image_files, faux_series_volume_file_name, True)\n",
+    "df = pd.DataFrame(data={\"files\": image_file_list})\n",
+    "df.to_csv(faux_series_file_list_name, index=False)"
    ]
   },
   {
@@ -739,10 +734,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "with open(faux_series_volume_file_name, \"rb\") as fp:\n",
-    "    faux_volume_image_files = pickle.load(fp)\n",
-    "with open(faux_series_file_list_name, \"rb\") as fp:\n",
-    "    image_file_list = pickle.load(fp)\n",
+    "faux_volume_image_files = sitk.ReadImage(faux_series_volume_file_name)\n",
+    "image_file_list = pd.read_csv(faux_series_file_list_name)[\"files\"].apply(eval).to_list()\n",
     "\n",
     "image_selection_gui2 = ImageSelection(\n",
     "    faux_volume_image_files,\n",