kernel clear and add optional linux vs/ win paths

brickstudymasons · Oct 19, 2024 · eb6bbaf · eb6bbaf
1 parent 05b28ae
commit eb6bbaf
Showing 1 changed file with 52 additions and 16 deletions.
diff --git a/notebooks/Concatenate_volbrain_csvs_deeplesion.ipynb b/notebooks/Concatenate_volbrain_csvs_deeplesion.ipynb
@@ -18,7 +18,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 79,
+   "execution_count": null,
    "metadata": {
     "tags": []
    },
@@ -30,26 +30,31 @@
     "import zipfile\n",
     "import os\n",
     "from zipfile import ZipFile\n",
-    "import glob"
+    "import glob\n",
+    "from io import BytesIO"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 80,
+   "execution_count": null,
    "metadata": {
     "tags": []
    },
    "outputs": [],
    "source": [
-    "#navigate to zipfolders and intended folder for output\n",
-    "path_volbrain = 'Z:/VolBrain'\n",
-    "output_folder = \"Z:/VolBrain/Separate_CSV_Deeplesion\"\n"
+    "#navigate to zipfolders and intended folder for output (change to commented out if on Windows)\n",
+    "# path_volbrain = 'Z:/processed_data/VolBrain'\n",
+    "# output_folder = \"Z:/processed_data/VolBrain/Separate_CSV_Deeplesion\"\n",
+    "path_volbrain = '/mnt/data/processed_data/VolBrain'\n",
+    "output_folder = \"/mnt/data/processed_data/VolBrain/Separate_CSV_Deeplesion\""
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 81,
-   "metadata": {},
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "#create a list to store the CSV headers in\n",
@@ -58,15 +63,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 82,
+   "execution_count": null,
    "metadata": {
     "tags": []
    },
    "outputs": [],
    "source": [
     "dataframes = []\n",
-    "from io import BytesIO\n",
-    "\n",
     "\n",
     "for zip_file in glob.glob(os.path.join(path_volbrain, '*.zip')):\n",
     "    # split by underscores\n",
@@ -97,7 +100,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 84,
+   "execution_count": null,
    "metadata": {
     "tags": []
    },
@@ -110,7 +113,20 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "concat_df"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "#Now make the column names castor appropriate. Do not change the \"Participant Id\" column of course. dl stands for DeepLesion algorithm\n",
@@ -125,13 +141,33 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 86,
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "concat_df"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
    "metadata": {
     "tags": []
    },
    "outputs": [],
    "source": [
-    "concat_df.to_csv('Z:/castor_proof_files/volbrains_castor.csv')"
+    "# concat_df.to_csv('Z:/castor_proof_files/volbrains_castor.csv')\n",
+    "#(change to commented out if on Windows)\n",
+    "concat_df.to_csv('/mnt/data/castor_proof_files/volbrains_castor.csv')"
    ]
   }
  ],
@@ -151,7 +187,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.10"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,