ProcessingPerformace.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import matplotlib.pyplot as plt\n",
    "import os\n",
    "import nibabel as nib\n",
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>0</th>\n",
       "      <th>1</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...</td>\n",
       "      <td>/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...</td>\n",
       "      <td>/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...</td>\n",
       "      <td>/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...</td>\n",
       "      <td>/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...</td>\n",
       "      <td>/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                   0  \\\n",
       "0  /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...   \n",
       "1  /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...   \n",
       "2  /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...   \n",
       "3  /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...   \n",
       "4  /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...   \n",
       "\n",
       "                                                   1  \n",
       "0  /pylon5/ac5616p/debdas/SCCORProcessing/nifti/1...  \n",
       "1  /pylon5/ac5616p/debdas/SCCORProcessing/nifti/1...  \n",
       "2  /pylon5/ac5616p/debdas/SCCORProcessing/nifti/1...  \n",
       "3  /pylon5/ac5616p/debdas/SCCORProcessing/nifti/1...  \n",
       "4  /pylon5/ac5616p/debdas/SCCORProcessing/nifti/1...  "
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dicom_df = pd.read_csv('/pylon5/ac5616p/debdas/SCCORProcessing/SCCOR_batch_df.csv', header=None)\n",
    "dicom_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
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      "(512, 512, 133)\n",
      "(512, 512, 133)\n",
      "(512, 512, 532)\n",
      "(888, 734, 1)\n",
      "(512, 512, 483)\n",
      "(888, 733, 1)\n",
      "(512, 512, 121)\n",
      "(512, 512, 121)\n",
      "(512, 512, 456)\n",
      "(888, 825, 1)\n",
      "(512, 512, 114)\n",
      "(512, 512, 114)\n",
      "(512, 512, 240)\n",
      "(512, 512, 60)\n",
      "(512, 512, 61)\n",
      "(512, 512, 481)\n",
      "(888, 733, 1)\n",
      "(512, 512, 130)\n",
      "(512, 512, 130)\n",
      "(512, 512, 519)\n",
      "(512, 512, 69)\n",
      "(512, 512, 545)\n",
      "(888, 733, 1)\n",
      "(512, 512, 273)\n",
      "(512, 512, 69)\n",
      "(512, 512, 132)\n",
      "(512, 512, 525)\n",
      "(888, 916, 1)\n",
      "(512, 512, 132)\n",
      "(512, 512, 137)\n",
      "(512, 512, 137)\n",
      "(888, 733, 1)\n",
      "(512, 512, 548)\n",
      "(512, 512, 548)\n",
      "(888, 734, 1)\n",
      "(512, 512, 137)\n",
      "(512, 512, 137)\n",
      "(888, 733, 1)\n",
      "(512, 512, 129)\n",
      "(512, 512, 129)\n",
      "(512, 512, 513)\n",
      "(512, 512, 537)\n",
      "(512, 512, 68)\n",
      "(888, 733, 1)\n",
      "(512, 512, 68)\n",
      "(512, 512, 269)\n",
      "(512, 512, 123)\n",
      "(888, 733, 1)\n",
      "(512, 512, 123)\n",
      "(512, 512, 489)\n",
      "(888, 733, 1)\n",
      "(512, 512, 492)\n",
      "(512, 512, 123)\n",
      "(512, 512, 123)\n",
      "(512, 512, 127)\n",
      "(512, 512, 505)\n",
      "(888, 733, 1)\n",
      "(512, 512, 127)\n",
      "(512, 512, 135)\n",
      "(512, 512, 135)\n",
      "(512, 512, 537)\n",
      "(888, 734, 1)\n",
      "(888, 733, 1)\n",
      "(512, 512, 139)\n",
      "(512, 512, 553)\n",
      "(512, 512, 139)\n",
      "(512, 512, 130)\n",
      "(512, 512, 130)\n",
      "(512, 512, 517)\n",
      "(888, 825, 1)\n",
      "(512, 512, 568)\n",
      "(888, 733, 1)\n",
      "(512, 512, 142)\n",
      "(512, 512, 142)\n",
      "(512, 512, 581)\n",
      "(512, 512, 146)\n",
      "(888, 733, 1)\n",
      "(512, 512, 146)\n",
      "(512, 512, 152)\n",
      "(512, 512, 152)\n",
      "(512, 512, 605)\n",
      "(888, 734, 1)\n",
      "(512, 512, 127)\n",
      "(512, 512, 505)\n",
      "(512, 512, 127)\n",
      "(888, 916, 1)\n",
      "(512, 512, 121)\n",
      "(512, 512, 121)\n",
      "(888, 568, 1)\n",
      "(512, 512, 481)\n",
      "(512, 512, 67)\n",
      "(512, 512, 529)\n",
      "(512, 512, 265)\n",
      "(512, 512, 67)\n",
      "(512, 512, 132)\n",
      "(512, 512, 132)\n",
      "(888, 734, 1)\n",
      "(512, 512, 525)\n",
      "(512, 512, 133)\n",
      "(512, 512, 133)\n",
      "(888, 733, 1)\n",
      "(512, 512, 529)\n",
      "(512, 512, 509)\n",
      "(512, 512, 128)\n",
      "(888, 733, 1)\n",
      "(512, 512, 128)\n",
      "(512, 512, 151)\n",
      "(512, 512, 151)\n",
      "(888, 734, 1)\n",
      "(512, 512, 602)\n",
      "(512, 512, 144)\n",
      "(512, 512, 144)\n",
      "(512, 512, 576)\n",
      "(888, 825, 1)\n",
      "(512, 512, 550)\n",
      "(888, 916, 1)\n",
      "(512, 512, 138)\n",
      "(512, 512, 138)\n",
      "(512, 512, 129)\n",
      "(512, 512, 129)\n",
      "(512, 512, 513)\n",
      "(888, 916, 1)\n",
      "(512, 512, 134)\n",
      "(512, 512, 134)\n",
      "(888, 825, 1)\n",
      "(512, 512, 535)\n",
      "(512, 512, 145)\n",
      "(512, 512, 145)\n",
      "(888, 734, 1)\n",
      "(512, 512, 577)\n",
      "(888, 733, 1)\n",
      "(512, 512, 519)\n",
      "(512, 512, 130)\n",
      "(512, 512, 130)\n",
      "(888, 825, 1)\n",
      "(512, 512, 508)\n",
      "(512, 512, 127)\n",
      "(512, 512, 127)\n",
      "(512, 512, 136)\n",
      "(512, 512, 169)\n",
      "(512, 512, 541)\n",
      "(888, 642, 1)\n",
      "(512, 512, 125)\n",
      "(512, 512, 125)\n",
      "(888, 733, 1)\n",
      "(512, 512, 500)\n",
      "(512, 512, 477)\n",
      "(512, 512, 120)\n",
      "(888, 733, 1)\n",
      "(512, 512, 120)\n",
      "(888, 916, 1)\n",
      "(512, 512, 485)\n",
      "(512, 512, 122)\n",
      "(512, 512, 122)\n",
      "(888, 734, 1)\n",
      "(512, 512, 495)\n",
      "(512, 512, 124)\n",
      "(512, 512, 124)\n",
      "(512, 512, 486)\n",
      "(888, 825, 1)\n",
      "(512, 512, 122)\n",
      "(512, 512, 122)\n",
      "(512, 512, 537)\n",
      "(512, 512, 135)\n",
      "(512, 512, 135)\n",
      "(512, 512, 147)\n",
      "(512, 512, 147)\n",
      "(888, 733, 1)\n",
      "(512, 512, 588)\n",
      "(888, 916, 1)\n",
      "(512, 512, 565)\n",
      "(512, 512, 142)\n",
      "(512, 512, 142)\n",
      "(512, 512, 152)\n",
      "(512, 512, 190)\n",
      "(512, 512, 608)\n",
      "(888, 642, 1)\n",
      "(512, 512, 120)\n",
      "(512, 512, 120)\n",
      "(512, 512, 486)\n",
      "(888, 825, 1)\n",
      "(512, 512, 528)\n",
      "(888, 733, 1)\n",
      "(512, 512, 132)\n",
      "(512, 512, 132)\n",
      "(512, 512, 550)\n",
      "(888, 734, 1)\n",
      "(512, 512, 138)\n",
      "(512, 512, 138)\n",
      "(888, 825, 1)\n",
      "(512, 512, 501)\n",
      "(512, 512, 126)\n",
      "(512, 512, 126)\n",
      "(512, 512, 61)\n",
      "(512, 512, 241)\n",
      "(888, 733, 1)\n",
      "(512, 512, 481)\n",
      "(512, 512, 61)\n",
      "(512, 512, 124)\n",
      "(512, 512, 124)\n",
      "(512, 512, 494)\n",
      "(888, 916, 1)\n",
      "(888, 642, 1)\n",
      "(512, 512, 547)\n",
      "(512, 512, 171)\n",
      "(512, 512, 137)\n",
      "(888, 733, 1)\n",
      "(512, 512, 128)\n",
      "(512, 512, 509)\n",
      "(512, 512, 128)\n",
      "(512, 512, 123)\n",
      "(512, 512, 123)\n",
      "(512, 512, 491)\n",
      "(888, 733, 1)\n",
      "(512, 512, 549)\n",
      "(512, 512, 138)\n",
      "(512, 512, 138)\n",
      "(512, 512, 15)\n",
      "(512, 512, 461)\n",
      "(888, 733, 1)\n",
      "(512, 512, 116)\n",
      "(512, 512, 116)\n",
      "(512, 512, 513)\n",
      "(888, 733, 1)\n",
      "(512, 512, 129)\n",
      "(512, 512, 129)\n",
      "(888, 734, 1)\n",
      "(512, 512, 440)\n",
      "(888, 825, 1)\n",
      "(512, 512, 110)\n",
      "(512, 512, 110)\n",
      "(888, 825, 1)\n",
      "(512, 512, 523)\n",
      "(512, 512, 131)\n",
      "(512, 512, 131)\n",
      "(888, 733, 1)\n",
      "(512, 512, 140)\n",
      "(512, 512, 140)\n",
      "(512, 512, 557)\n",
      "(512, 512, 135)\n",
      "(512, 512, 135)\n",
      "(888, 734, 1)\n",
      "(512, 512, 540)\n",
      "(512, 512, 462)\n",
      "(888, 825, 1)\n",
      "(512, 512, 116)\n",
      "(512, 512, 116)\n",
      "(888, 734, 1)\n",
      "(512, 512, 132)\n",
      "(512, 512, 525)\n",
      "(888, 916, 1)\n",
      "(512, 512, 132)\n",
      "(512, 512, 125)\n",
      "(512, 512, 125)\n",
      "(512, 512, 500)\n",
      "(888, 770, 1)\n",
      "(512, 512, 561)\n",
      "(512, 512, 141)\n",
      "(512, 512, 141)\n",
      "(888, 733, 1)\n",
      "(888, 734, 1)\n",
      "(512, 512, 589)\n",
      "(512, 512, 148)\n",
      "(512, 512, 148)\n",
      "(512, 512, 141)\n",
      "(512, 512, 141)\n",
      "(512, 512, 562)\n",
      "(888, 733, 1)\n",
      "(512, 512, 131)\n",
      "(512, 512, 131)\n",
      "(888, 733, 1)\n",
      "(512, 512, 522)\n",
      "(888, 642, 1)\n",
      "(512, 512, 566)\n",
      "(512, 512, 177)\n",
      "(512, 512, 142)\n",
      "(512, 512, 487)\n",
      "(888, 916, 1)\n",
      "(512, 512, 122)\n",
      "(512, 512, 122)\n",
      "(888, 733, 1)\n",
      "(512, 512, 119)\n",
      "(512, 512, 473)\n",
      "(512, 512, 473)\n",
      "(512, 512, 119)\n",
      "(512, 512, 129)\n",
      "(512, 512, 129)\n",
      "(888, 825, 1)\n",
      "(512, 512, 515)\n",
      "(512, 512, 520)\n",
      "(888, 734, 1)\n",
      "(512, 512, 130)\n",
      "(512, 512, 130)\n",
      "(888, 734, 1)\n",
      "(512, 512, 528)\n",
      "(512, 512, 132)\n",
      "(512, 512, 132)\n",
      "(512, 512, 480)\n",
      "(888, 825, 1)\n",
      "(512, 512, 120)\n",
      "(512, 512, 120)\n",
      "(512, 512, 126)\n",
      "(888, 733, 1)\n",
      "(512, 512, 126)\n",
      "(512, 512, 501)\n",
      "(512, 512, 139)\n",
      "(512, 512, 139)\n",
      "(512, 512, 555)\n",
      "(512, 512, 126)\n",
      "(512, 512, 126)\n",
      "(512, 512, 502)\n",
      "(512, 512, 581)\n",
      "(888, 733, 1)\n",
      "(512, 512, 146)\n",
      "(512, 512, 146)\n",
      "(512, 512, 143)\n",
      "(512, 512, 143)\n",
      "(888, 734, 1)\n",
      "(512, 512, 570)\n",
      "(512, 512, 557)\n",
      "(888, 825, 1)\n",
      "(512, 512, 140)\n",
      "(512, 512, 140)\n",
      "(512, 512, 481)\n",
      "(512, 512, 121)\n",
      "(512, 512, 121)\n",
      "(888, 733, 1)\n",
      "(512, 512, 142)\n",
      "(512, 512, 565)\n",
      "(512, 512, 142)\n",
      "(512, 512, 479)\n",
      "(888, 825, 1)\n",
      "(512, 512, 120)\n",
      "(512, 512, 120)\n",
      "(512, 512, 170)\n",
      "(512, 512, 136)\n",
      "(512, 512, 544)\n",
      "(888, 734, 1)\n",
      "(512, 512, 124)\n",
      "(512, 512, 124)\n",
      "(888, 733, 1)\n",
      "(512, 512, 510)\n",
      "(512, 512, 478)\n",
      "(888, 825, 1)\n",
      "(512, 512, 120)\n",
      "(512, 512, 120)\n",
      "(888, 734, 1)\n",
      "(512, 512, 512)\n",
      "(512, 512, 128)\n",
      "(512, 512, 128)\n",
      "(512, 512, 122)\n",
      "(888, 733, 1)\n",
      "(512, 512, 122)\n",
      "(512, 512, 485)\n",
      "(512, 512, 485)\n",
      "(512, 512, 122)\n",
      "(512, 512, 122)\n",
      "(888, 916, 1)\n",
      "(512, 512, 130)\n",
      "(888, 733, 1)\n",
      "(512, 512, 130)\n",
      "(512, 512, 517)\n",
      "(888, 825, 1)\n",
      "(512, 512, 540)\n",
      "(512, 512, 135)\n",
      "(512, 512, 135)\n",
      "(512, 512, 529)\n",
      "(512, 512, 133)\n",
      "(888, 733, 1)\n",
      "(512, 512, 133)\n",
      "(512, 512, 142)\n",
      "(512, 512, 142)\n",
      "(888, 734, 1)\n",
      "(512, 512, 566)\n",
      "(512, 512, 127)\n",
      "(512, 512, 127)\n",
      "(888, 733, 1)\n",
      "(512, 512, 507)\n",
      "(512, 512, 527)\n",
      "(888, 642, 1)\n",
      "(512, 512, 165)\n",
      "(512, 512, 132)\n",
      "(512, 512, 505)\n",
      "(512, 512, 127)\n",
      "(888, 733, 1)\n",
      "(512, 512, 127)\n",
      "(512, 512, 481)\n",
      "(512, 512, 121)\n",
      "(512, 512, 121)\n",
      "(888, 642, 1)\n",
      "(512, 512, 485)\n",
      "(512, 512, 152)\n",
      "(512, 512, 122)\n",
      "(512, 512, 122)\n",
      "(512, 512, 122)\n",
      "(888, 733, 1)\n",
      "(512, 512, 487)\n",
      "(512, 512, 109)\n",
      "(512, 512, 109)\n",
      "(888, 733, 1)\n",
      "(512, 512, 14)\n",
      "(512, 512, 433)\n",
      "(512, 512, 607)\n",
      "(888, 734, 1)\n",
      "(512, 512, 152)\n",
      "(512, 512, 152)\n",
      "(512, 512, 564)\n",
      "(888, 733, 1)\n",
      "(512, 512, 141)\n",
      "(512, 512, 141)\n",
      "(512, 512, 150)\n",
      "(888, 733, 1)\n",
      "(512, 512, 597)\n",
      "(512, 512, 150)\n",
      "(512, 512, 121)\n",
      "(512, 512, 121)\n",
      "(512, 512, 481)\n",
      "(888, 733, 1)\n",
      "(512, 512, 546)\n",
      "(888, 825, 1)\n",
      "(512, 512, 137)\n",
      "(512, 512, 137)\n",
      "(512, 512, 100)\n",
      "(512, 512, 100)\n",
      "(888, 825, 1)\n",
      "(512, 512, 400)\n",
      "(888, 916, 1)\n",
      "(512, 512, 469)\n",
      "(512, 512, 469)\n",
      "(512, 512, 118)\n",
      "(512, 512, 118)\n",
      "(512, 512, 134)\n",
      "(888, 916, 1)\n",
      "(512, 512, 533)\n",
      "(512, 512, 134)\n"
     ]
    }
   ],
   "source": [
    "success = 0\n",
    "total_cases = len(dicom_df)\n",
    "file_sizes = []\n",
    "for i in range(total_cases):\n",
    "    path = dicom_df[1][i]+'/'+dicom_df[1][i].split('/')[-1]+'.nii.gz'\n",
    "    if os.path.isfile(path):\n",
    "        success += 1\n",
    "        file_sizes.append(os.stat(path).st_size)\n",
    "        epi_img = nib.load(path)\n",
    "        epi_img_data = epi_img.get_fdata()\n",
    "        print(epi_img_data.shape)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "968\n"
     ]
    }
   ],
   "source": [
    "print(success)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
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  {
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     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "plt.hist(file_sizes, bins=100)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "kong_py35",
   "language": "python",
   "name": "kong_py35"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.5.6"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}