COPDvsSCCOR2.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import matplotlib.pyplot as plt\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Dataset</th>\n",
       "      <th>File</th>\n",
       "      <th>Volume</th>\n",
       "      <th>meanF_0</th>\n",
       "      <th>medianF_0</th>\n",
       "      <th>stdF_0</th>\n",
       "      <th>maxF_0</th>\n",
       "      <th>minF_0</th>\n",
       "      <th>meanF_1</th>\n",
       "      <th>medianF_1</th>\n",
       "      <th>...</th>\n",
       "      <th>meanF_26</th>\n",
       "      <th>medianF_26</th>\n",
       "      <th>stdF_26</th>\n",
       "      <th>maxF_26</th>\n",
       "      <th>minF_26</th>\n",
       "      <th>meanF_27</th>\n",
       "      <th>medianF_27</th>\n",
       "      <th>stdF_27</th>\n",
       "      <th>maxF_27</th>\n",
       "      <th>minF_27</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>COPD</td>\n",
       "      <td>/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/T...</td>\n",
       "      <td>12876.849673</td>\n",
       "      <td>4.489312</td>\n",
       "      <td>4.405487</td>\n",
       "      <td>0.694229</td>\n",
       "      <td>6.507663</td>\n",
       "      <td>3.122153</td>\n",
       "      <td>1.688197</td>\n",
       "      <td>1.480589</td>\n",
       "      <td>...</td>\n",
       "      <td>1.136668</td>\n",
       "      <td>1.061943</td>\n",
       "      <td>0.611353</td>\n",
       "      <td>3.086398</td>\n",
       "      <td>0.201373</td>\n",
       "      <td>1.977367</td>\n",
       "      <td>1.806279</td>\n",
       "      <td>0.769858</td>\n",
       "      <td>4.308830</td>\n",
       "      <td>0.892688</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>COPD</td>\n",
       "      <td>/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/T...</td>\n",
       "      <td>10654.362069</td>\n",
       "      <td>4.652421</td>\n",
       "      <td>4.588340</td>\n",
       "      <td>0.664867</td>\n",
       "      <td>6.613097</td>\n",
       "      <td>3.268935</td>\n",
       "      <td>2.004733</td>\n",
       "      <td>1.786063</td>\n",
       "      <td>...</td>\n",
       "      <td>1.793778</td>\n",
       "      <td>1.701641</td>\n",
       "      <td>0.840154</td>\n",
       "      <td>4.271159</td>\n",
       "      <td>0.443542</td>\n",
       "      <td>2.264358</td>\n",
       "      <td>2.097129</td>\n",
       "      <td>0.837541</td>\n",
       "      <td>4.733400</td>\n",
       "      <td>0.998140</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>COPD</td>\n",
       "      <td>/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/T...</td>\n",
       "      <td>12869.886199</td>\n",
       "      <td>4.830375</td>\n",
       "      <td>4.761883</td>\n",
       "      <td>0.622473</td>\n",
       "      <td>6.628524</td>\n",
       "      <td>3.544874</td>\n",
       "      <td>1.521063</td>\n",
       "      <td>1.311622</td>\n",
       "      <td>...</td>\n",
       "      <td>1.051836</td>\n",
       "      <td>0.979868</td>\n",
       "      <td>0.576385</td>\n",
       "      <td>2.844360</td>\n",
       "      <td>0.176357</td>\n",
       "      <td>2.037571</td>\n",
       "      <td>1.854634</td>\n",
       "      <td>0.829670</td>\n",
       "      <td>4.678312</td>\n",
       "      <td>0.838808</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>COPD</td>\n",
       "      <td>/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/T...</td>\n",
       "      <td>13447.600457</td>\n",
       "      <td>4.778951</td>\n",
       "      <td>4.695040</td>\n",
       "      <td>0.726102</td>\n",
       "      <td>6.858257</td>\n",
       "      <td>3.339852</td>\n",
       "      <td>2.001859</td>\n",
       "      <td>1.775091</td>\n",
       "      <td>...</td>\n",
       "      <td>1.187279</td>\n",
       "      <td>1.107880</td>\n",
       "      <td>0.647375</td>\n",
       "      <td>3.205937</td>\n",
       "      <td>0.198243</td>\n",
       "      <td>1.947559</td>\n",
       "      <td>1.753673</td>\n",
       "      <td>0.824784</td>\n",
       "      <td>4.476933</td>\n",
       "      <td>0.790737</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>COPD</td>\n",
       "      <td>/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/I...</td>\n",
       "      <td>14111.476619</td>\n",
       "      <td>3.497660</td>\n",
       "      <td>3.361034</td>\n",
       "      <td>0.758231</td>\n",
       "      <td>5.953160</td>\n",
       "      <td>2.188663</td>\n",
       "      <td>1.448126</td>\n",
       "      <td>1.236813</td>\n",
       "      <td>...</td>\n",
       "      <td>1.275473</td>\n",
       "      <td>1.184035</td>\n",
       "      <td>0.712686</td>\n",
       "      <td>3.480566</td>\n",
       "      <td>0.218859</td>\n",
       "      <td>1.819246</td>\n",
       "      <td>1.607810</td>\n",
       "      <td>0.801722</td>\n",
       "      <td>4.267389</td>\n",
       "      <td>0.743625</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 143 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "  Dataset                                               File        Volume  \\\n",
       "0    COPD  /pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/T...  12876.849673   \n",
       "1    COPD  /pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/T...  10654.362069   \n",
       "2    COPD  /pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/T...  12869.886199   \n",
       "3    COPD  /pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/T...  13447.600457   \n",
       "4    COPD  /pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/I...  14111.476619   \n",
       "\n",
       "    meanF_0  medianF_0    stdF_0    maxF_0    minF_0   meanF_1  medianF_1  \\\n",
       "0  4.489312   4.405487  0.694229  6.507663  3.122153  1.688197   1.480589   \n",
       "1  4.652421   4.588340  0.664867  6.613097  3.268935  2.004733   1.786063   \n",
       "2  4.830375   4.761883  0.622473  6.628524  3.544874  1.521063   1.311622   \n",
       "3  4.778951   4.695040  0.726102  6.858257  3.339852  2.001859   1.775091   \n",
       "4  3.497660   3.361034  0.758231  5.953160  2.188663  1.448126   1.236813   \n",
       "\n",
       "   ...  meanF_26  medianF_26   stdF_26   maxF_26   minF_26  meanF_27  \\\n",
       "0  ...  1.136668    1.061943  0.611353  3.086398  0.201373  1.977367   \n",
       "1  ...  1.793778    1.701641  0.840154  4.271159  0.443542  2.264358   \n",
       "2  ...  1.051836    0.979868  0.576385  2.844360  0.176357  2.037571   \n",
       "3  ...  1.187279    1.107880  0.647375  3.205937  0.198243  1.947559   \n",
       "4  ...  1.275473    1.184035  0.712686  3.480566  0.218859  1.819246   \n",
       "\n",
       "   medianF_27   stdF_27   maxF_27   minF_27  \n",
       "0    1.806279  0.769858  4.308830  0.892688  \n",
       "1    2.097129  0.837541  4.733400  0.998140  \n",
       "2    1.854634  0.829670  4.678312  0.838808  \n",
       "3    1.753673  0.824784  4.476933  0.790737  \n",
       "4    1.607810  0.801722  4.267389  0.743625  \n",
       "\n",
       "[5 rows x 143 columns]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "img_df = pd.read_csv(\"fHOGSummaryCOPDSCCOR.csv\")\n",
    "img_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Test_Reproducing_Phase-1_Images/16686S/Phase-1/SuperVoxels/16686S_INSP_STD_NJC_COPD_Iso1.0mm_SuperVoxel_Param30mm_fHOG_Hist_Features.csv.gz'"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "img_df['File'][0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/17236S/Phase-2/Isotropic/17236S_INSP_SHARP_340_COL_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/17236S/Phase-2/Isotropic/17236S_INSP_SHARP_383_COL_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/15416K/Phase-2/Isotropic/15416K_INSP_SHARP_289_MSM_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/15416K/Phase-2/Isotropic/15416K_INSP_SHARP_438_MSM_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/16904C/Phase-2/Isotropic/16904C_INSP_SHARP_457_MSM_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/16904C/Phase-2/Isotropic/16904C_INSP_SHARP_324_MSM_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/19215U/Phase-2/Isotropic/19215U_INSP_SHARP_276_MSM_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/19215U/Phase-2/Isotropic/19215U_INSP_SHARP_336_MSM_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/10990R/Phase-2/Isotropic/10990R_INSP_SHARP_320_USD_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/10990R/Phase-2/Isotropic/10990R_INSP_SHARP_380_USD_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/25959C/Phase-2/Isotropic/25959C_INSP_SHARP_300_USD_LD_ASIR40_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/25959C/Phase-2/Isotropic/25959C_INSP_SHARP_360_USD_LD_ASIR40_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/25959C/Phase-2/Isotropic/25959C_INSP_SHARP_300_USD_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/25959C/Phase-2/Isotropic/25959C_INSP_SHARP_360_USD_LD_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/25959C/Phase-2/Isotropic/25959C_INSP_SHARP_360_USD_LD_ASIR100_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/25959C/Phase-2/Isotropic/25959C_INSP_SHARP_360_USD_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/23684F/Phase-2/Isotropic/23684F_INSP_SHARP_340_HAR_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/23684F/Phase-2/Isotropic/23684F_INSP_SHARP_360_HAR_LD_ASIR40_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/23684F/Phase-2/Isotropic/23684F_INSP_SHARP_360_HAR_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/23684F/Phase-2/Isotropic/23684F_INSP_SHARP_320_HAR_LD_ASIR40_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/23684F/Phase-2/Isotropic/23684F_INSP_SHARP_360_HAR_LD_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/23684F/Phase-2/Isotropic/23684F_INSP_SHARP_360_HAR_LD_ASIR100_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Test_Reproducing_Phase-1_Images/12154R/Phase-1/Isotropic/12154R_INSP_SHARP_TEM_COPD_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Test_Reproducing_Phase-1_Images/19616M/Phase-1/Isotropic/19616M_INSP_SHARP_BAY_COPD_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/16318P/Phase-2/Isotropic/16318P_INSP_SHARP_292_PIT_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/19665Z/Phase-2/Isotropic/19665Z_INSP_SHARP_350_HAR_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/19665Z/Phase-2/Isotropic/19665Z_INSP_SHARP_360_HAR_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/18132L/Phase-2/Isotropic/18132L_INSP_SHARP_357_PIT_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/22267K/Phase-2/Isotropic/22267K_INSP_SHARP_369_TXS_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/22267K/Phase-2/Isotropic/22267K_INSP_SHARP_387_TXS_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/13861V/Phase-2/Isotropic/13861V_INSP_SHARP_350_COL_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/13861V/Phase-2/Isotropic/13861V_INSP_SHARP_300_COL_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/13597E/Phase-2/Isotropic/13597E_INSP_SHARP_293_COL_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/13597E/Phase-2/Isotropic/13597E_INSP_SHARP_280_COL_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/25437Y/Phase-2/Isotropic/25437Y_INSP_SHARP_328_USD_LD_ASIR100_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/25437Y/Phase-2/Isotropic/25437Y_INSP_SHARP_328_USD_LD_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/25437Y/Phase-2/Isotropic/25437Y_INSP_SHARP_280_USD_LD_ASIR40_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/25437Y/Phase-2/Isotropic/25437Y_INSP_SHARP_280_USD_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/25437Y/Phase-2/Isotropic/25437Y_INSP_SHARP_328_USD_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/25437Y/Phase-2/Isotropic/25437Y_INSP_SHARP_328_USD_LD_ASIR40_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/20991Z/Phase-2/Isotropic/20991Z_INSP_SHARP_363_USD_LD_ASIR40_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/20991Z/Phase-2/Isotropic/20991Z_INSP_SHARP_320_USD_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/20991Z/Phase-2/Isotropic/20991Z_INSP_SHARP_363_USD_LD_ASIR100_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/20991Z/Phase-2/Isotropic/20991Z_INSP_SHARP_363_USD_LD_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/20991Z/Phase-2/Isotropic/20991Z_INSP_SHARP_320_USD_LD_ASIR40_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/20991Z/Phase-2/Isotropic/20991Z_INSP_SHARP_363_USD_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/21181V/Phase-2/Isotropic/21181V_INSP_SHARP_500_MSM_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/21181V/Phase-2/Isotropic/21181V_INSP_SHARP_279_MSM_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/10596N/Phase-2/Isotropic/10596N_INSP_SHARP_330_HAR_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/10596N/Phase-2/Isotropic/10596N_INSP_SHARP_360_HAR_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/13587B/Phase-2/Isotropic/13587B_INSP_SHARP_500_MSM_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/13587B/Phase-2/Isotropic/13587B_INSP_SHARP_277_MSM_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/11818K/Phase-2/Isotropic/11818K_INSP_SHARP_276_MSM_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/11818K/Phase-2/Isotropic/11818K_INSP_SHARP_406_MSM_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/20633Z/Phase-2/Isotropic/20633Z_INSP_SHARP_360_HAR_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/20633Z/Phase-2/Isotropic/20633Z_INSP_SHARP_320_HAR_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/21665R/Phase-2/Isotropic/21665R_INSP_SHARP_416_PIT_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/21665R/Phase-2/Isotropic/21665R_INSP_SHARP_377_PIT_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Test_Reproducing_Phase-1_Images/12770N/Phase-1/Isotropic/12770N_INSP_SHARP_NJC_COPD_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/17564J/Phase-2/Isotropic/17564J_INSP_SHARP_340_UMC_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/17564J/Phase-2/Isotropic/17564J_INSP_SHARP_320_UMC_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/13296Q/Phase-2/Isotropic/13296Q_INSP_SHARP_350_COL_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/13296Q/Phase-2/Isotropic/13296Q_INSP_SHARP_330_COL_COPD2_BSpline_Iso1.0mm.nii.gz\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/20200U/Phase-2/Isotropic/20200U_INSP_SHARP_308_PIT_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/13907T/Phase-2/Isotropic/13907T_INSP_SHARP_360_UMC_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/13907T/Phase-2/Isotropic/13907T_INSP_SHARP_330_UMC_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/24494F/Phase-2/Isotropic/24494F_INSP_SHARP_360_PIT_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/24494F/Phase-2/Isotropic/24494F_INSP_SHARP_360_PIT_LD_ASIR40_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/24494F/Phase-2/Isotropic/24494F_INSP_SHARP_312_PIT_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/24494F/Phase-2/Isotropic/24494F_INSP_SHARP_360_PIT_LD_ASIR100_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/24494F/Phase-2/Isotropic/24494F_INSP_SHARP_360_PIT_LD_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/24494F/Phase-2/Isotropic/24494F_INSP_SHARP_312_PIT_LD_ASIR40_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/25285B/Phase-2/Isotropic/25285B_INSP_SHARP_415_MSM_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/25285B/Phase-2/Isotropic/25285B_INSP_SHARP_307_MSM_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Test_Reproducing_Phase-1_Images/12817N/Phase-1/Isotropic/12817N_INSP_SHARP_BWH_COPD_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/21703Z/Phase-2/Isotropic/21703Z_INSP_SHARP_380_HAR_COPD2_BSpline_Iso1.0mm.nii.gz\n",
      "/pghbio/dbmi/batmanlab/chirayu/Data/COPDGene/Images/21703Z/Phase-2/Isotropic/21703Z_INSP_SHARP_360_HAR_COPD2_BSpline_Iso1.0mm.nii.gz\n"
     ]
    },
    {
     "ename": "KeyboardInterrupt",
     "evalue": "",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mKeyboardInterrupt\u001b[0m                         Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-5-2aa197cb00b7>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      6\u001b[0m         \u001b[0miso_img\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0miso_img\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreplace\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'_Iso1.0mm_SuperVoxel_Param30mm_fHOG_Hist_Features.csv.gz'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'_BSpline_Iso1.0mm.nii.gz'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      7\u001b[0m         \u001b[0miso_img\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0miso_img\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreplace\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'_STD_'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m'_SHARP_'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 8\u001b[0;31m         \u001b[0;32mif\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexists\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0miso_img\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      9\u001b[0m             \u001b[0mimg_list\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0miso_img\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     10\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/pylon5/ac5616p/debdas/anaconda3/envs/pylung36/lib/python3.7/genericpath.py\u001b[0m in \u001b[0;36mexists\u001b[0;34m(path)\u001b[0m\n\u001b[1;32m     17\u001b[0m     \u001b[0;34m\"\"\"Test whether a path exists.  Returns False for broken symbolic links\"\"\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     18\u001b[0m     \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 19\u001b[0;31m         \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     20\u001b[0m     \u001b[0;32mexcept\u001b[0m \u001b[0mOSError\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     21\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mKeyboardInterrupt\u001b[0m: "
     ]
    }
   ],
   "source": [
    "img_list = []\n",
    "i = 0\n",
    "for fHOG_file in img_df['File']:\n",
    "    if img_df['Dataset'][i] == 'COPD':\n",
    "        iso_img = fHOG_file.replace('/SuperVoxels/', '/Isotropic/')\n",
    "        iso_img = iso_img.replace('_Iso1.0mm_SuperVoxel_Param30mm_fHOG_Hist_Features.csv.gz', '_BSpline_Iso1.0mm.nii.gz')\n",
    "        iso_img = iso_img.replace('_STD_','_SHARP_')\n",
    "        if os.path.exists(iso_img):\n",
    "            img_list.append(iso_img)\n",
    "        else:\n",
    "            print(iso_img)\n",
    "            \n",
    "    elif img_df['Dataset'][i] == 'SCCOR':\n",
    "        iso_img = fHOG_file.replace('_Iso1.0mm_SuperVoxel_Param30mm_fHOG_Hist_Features.csv.gz', '_Iso1.0mm.nii.gz')\n",
    "        if os.path.exists(iso_img):\n",
    "            img_list.append(iso_img)\n",
    "    i += 1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "pylung36",
   "language": "python",
   "name": "pylung36"
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  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.7.7"
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 "nbformat": 4,
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