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| a | b/1-preprocess-brain_norm.ipynb | ||
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| 1 | { |
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| 2 | "cells": [ |
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| 3 | { |
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| 4 | "cell_type": "markdown", |
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| 5 | "metadata": {}, |
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| 6 | "source": [ |
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| 7 | "# Brain translational and rotational normalization\n", |
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| 8 | "* Zero z at the slice with max area\n", |
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| 9 | "* Use analytic minimization of moment of inertia to find orientation angle\n", |
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| 10 | "\n", |
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| 11 | "Generates:\n", |
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| 12 | "* `train_dicom_diags_norm.csv` and `test_dicom_norm.csv` with 5 new columns added: \n", |
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| 13 | " * `normz` normalized z\n", |
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| 14 | " * `xcm`, `ycm` center of mass\n", |
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| 15 | " * `theta` (rads) the CW angle the slice must be rotated to straighten it\n", |
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| 16 | " * `pct_tissue` percentage of brain tissue pixels in the radiography" |
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| 17 | ] |
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| 18 | }, |
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| 19 | { |
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| 20 | "cell_type": "code", |
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| 21 | "execution_count": 1, |
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| 22 | "metadata": {}, |
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| 23 | "outputs": [], |
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| 24 | "source": [ |
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| 25 | "stage = \"stage_2\"" |
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| 26 | ] |
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| 27 | }, |
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| 28 | { |
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| 29 | "cell_type": "code", |
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| 30 | "execution_count": 2, |
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| 31 | "metadata": {}, |
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| 32 | "outputs": [], |
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| 33 | "source": [ |
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| 34 | "import pydicom\n", |
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| 35 | "import math\n", |
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| 36 | "from pathlib import Path\n", |
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| 37 | "from fastai.vision import *\n", |
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| 38 | "from matplotlib import pyplot as plt\n", |
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| 39 | "from scipy import ndimage, misc\n", |
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| 40 | "from itertools import repeat\n", |
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| 41 | "import pandas as pd\n", |
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| 42 | "%matplotlib inline" |
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| 43 | ] |
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| 44 | }, |
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| 45 | { |
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| 46 | "cell_type": "code", |
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| 47 | "execution_count": 3, |
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| 48 | "metadata": {}, |
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| 49 | "outputs": [], |
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| 50 | "source": [ |
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| 51 | "%%capture\n", |
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| 52 | "from tqdm import tqdm_notebook as tqdm\n", |
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| 53 | "tqdm().pandas()" |
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| 54 | ] |
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| 55 | }, |
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| 56 | { |
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| 57 | "cell_type": "code", |
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| 58 | "execution_count": 4, |
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| 59 | "metadata": {}, |
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| 60 | "outputs": [], |
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| 61 | "source": [ |
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| 62 | "def dcm_to_np(dcm):\n", |
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| 63 | " ''' Dicom to numpy array\n", |
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| 64 | " :param dcm: dicom object\n", |
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| 65 | " '''\n", |
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| 66 | " rescale_slope, rescale_intercept = float(dcm.RescaleSlope), float(dcm.RescaleIntercept)\n", |
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| 67 | " t = dcm.pixel_array.astype(np.float)\n", |
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| 68 | " t = t * rescale_slope + rescale_intercept # rescale\n", |
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| 69 | " return t" |
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| 70 | ] |
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| 71 | }, |
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| 72 | { |
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| 73 | "cell_type": "code", |
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| 74 | "execution_count": 5, |
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| 75 | "metadata": {}, |
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| 76 | "outputs": [], |
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| 77 | "source": [ |
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| 78 | "def get_fid_with_max_area(dir, dfs):\n", |
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| 79 | " ''' Given a single study return the fid (fileid) with biggest brain area\n", |
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| 80 | " :param dir: datset directory\n", |
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| 81 | " :param dfs: pandas dataframe with 1 study\n", |
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| 82 | " '''\n", |
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| 83 | " brain_area_vs_z = []\n", |
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| 84 | " pcts_tissue = []\n", |
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| 85 | " max_area = 0\n", |
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| 86 | " for index, row in dfs.iterrows():\n", |
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| 87 | " fid = row['SOPInstanceUID'] # don't do this inside f'' array or jupyter bugs out\n", |
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| 88 | " try:\n", |
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| 89 | " dcm = pydicom.dcmread(f\"{dir}/{fid}.dcm\")\n", |
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| 90 | " t = dcm_to_np(dcm)\n", |
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| 91 | " except Exception as e:\n", |
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| 92 | " print(e,fid)\n", |
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| 93 | " pts = np.argwhere(np.logical_and(0 < t, t < 100)) # select only brain matter\n", |
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| 94 | " if len(pts) > max_area:\n", |
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| 95 | " max_area = len(pts)\n", |
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| 96 | " fid_max_area = row['SOPInstanceUID']\n", |
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| 97 | " brain_area_vs_z.append([float(row['ImagePositionPatient_2']), len(pts)])\n", |
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| 98 | " pcts_tissue.append(len(pts) / t.size)\n", |
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| 99 | " return fid_max_area, pcts_tissue" |
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| 100 | ] |
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| 101 | }, |
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| 102 | { |
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| 103 | "cell_type": "code", |
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| 104 | "execution_count": 6, |
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| 105 | "metadata": {}, |
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| 106 | "outputs": [], |
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| 107 | "source": [ |
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| 108 | "def get_axis(brain):\n", |
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| 109 | " ''' \n", |
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| 110 | " Get orientation axis.\n", |
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| 111 | " :param brain: numpy array (brain)\n", |
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| 112 | " :return: center of masses (xcm, ycm), coefficients (m, n) of the axis equation y=mx+n and angle (th)\n", |
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| 113 | " the brain is rotated counter-clockwise (rotate clockwise to normalize)\n", |
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| 114 | " '''\n", |
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| 115 | " pts_org = np.argwhere(np.logical_and(0 < brain, brain < 100))\n", |
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| 116 | "\n", |
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| 117 | " # Center of masses\n", |
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| 118 | " xcm = pts_org[:,1].mean()\n", |
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| 119 | " ycm = pts_org[:,0].mean()\n", |
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| 120 | "\n", |
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| 121 | " # shift brain to center\n", |
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| 122 | " xs = pts_org[:,1] - xcm\n", |
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| 123 | " ys = pts_org[:,0] - ycm\n", |
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| 124 | " \n", |
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| 125 | " # coefficients of quad eq am^2+bm+c=0\n", |
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| 126 | " a = (xs * ys).sum()\n", |
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| 127 | " b = (xs ** 2 - ys ** 2).sum()\n", |
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| 128 | " c = -a\n", |
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| 129 | "\n", |
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| 130 | " # solve for m1 (max I), m2 (min I)\n", |
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| 131 | " m1 = (-b + (b**2-4*a*c) ** (.5)) / (2 * a)\n", |
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| 132 | " m2 = (-b - (b**2-4*a*c) ** (.5)) / (2 * a)\n", |
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| 133 | " \n", |
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| 134 | " # y-ycm = m*x - m*xcm -> y = m*x - m*xcm + ycm\n", |
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| 135 | " n1 = ycm - m1 * xcm\n", |
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| 136 | " n2 = ycm - m2 * xcm\n", |
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| 137 | " \n", |
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| 138 | " th = math.atan(m2)\n", |
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| 139 | " \n", |
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| 140 | " return xcm, ycm, m2, n2, th" |
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| 141 | ] |
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| 142 | }, |
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| 143 | { |
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| 144 | "cell_type": "code", |
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| 145 | "execution_count": 7, |
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| 146 | "metadata": {}, |
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| 147 | "outputs": [], |
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| 148 | "source": [ |
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| 149 | "def norm_study(dir, group_name):\n", |
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| 150 | " ''' Normalize study given by pandas DataFrame g\n", |
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| 151 | " :param dir: dataset directory\n", |
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| 152 | " :param g: single study to normalize\n", |
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| 153 | " '''\n", |
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| 154 | " global dfg\n", |
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| 155 | " g = dfg.get_group(group_name)\n", |
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| 156 | " fid_max_area, pcts_tissue = get_fid_with_max_area(dir, g)\n", |
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| 157 | " f = f'{dir}/{fid_max_area}.dcm'\n", |
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| 158 | " try:\n", |
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| 159 | " dcm = pydicom.dcmread(str(f))\n", |
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| 160 | " except Exceptione as e:\n", |
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| 161 | " print(e,f)\n", |
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| 162 | " brain = dcm_to_np(dcm)\n", |
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| 163 | " xcm, ycm, m, n, th = get_axis(brain)\n", |
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| 164 | " eg = g.copy()\n", |
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| 165 | " z0 = g[g['SOPInstanceUID'] == fid_max_area].iloc[0]['ImagePositionPatient_2']\n", |
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| 166 | " eg['normz'] = eg['ImagePositionPatient_2'] - z0\n", |
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| 167 | " eg['xcm'] = xcm\n", |
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| 168 | " eg['ycm'] = ycm\n", |
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| 169 | " eg['theta'] = th\n", |
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| 170 | " eg['pct_tissue'] = pcts_tissue\n", |
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| 171 | " return eg" |
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| 172 | ] |
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| 173 | }, |
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| 174 | { |
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| 175 | "cell_type": "markdown", |
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| 176 | "metadata": {}, |
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| 177 | "source": [ |
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| 178 | "# Train dataset" |
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| 179 | ] |
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| 180 | }, |
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| 181 | { |
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| 182 | "cell_type": "code", |
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| 183 | "execution_count": 8, |
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| 184 | "metadata": {}, |
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| 185 | "outputs": [], |
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| 186 | "source": [ |
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| 187 | "df = pd.read_csv(f'data/{stage}_train_dicom_diags.csv')" |
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| 188 | ] |
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| 189 | }, |
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| 190 | { |
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| 191 | "cell_type": "code", |
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| 192 | "execution_count": 9, |
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| 193 | "metadata": {}, |
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| 194 | "outputs": [], |
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| 195 | "source": [ |
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| 196 | "dfg = df.groupby('SeriesInstanceUID')" |
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| 197 | ] |
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| 198 | }, |
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| 199 | { |
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| 200 | "cell_type": "code", |
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| 201 | "execution_count": 10, |
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| 202 | "metadata": {}, |
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| 203 | "outputs": [], |
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| 204 | "source": [ |
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| 205 | "group_names = list(dfg.groups.keys())\n", |
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| 206 | "#group_names = group_names[:64] # test with small subset" |
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| 207 | ] |
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| 208 | }, |
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| 209 | { |
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| 210 | "cell_type": "code", |
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| 211 | "execution_count": 11, |
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| 212 | "metadata": {}, |
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| 213 | "outputs": [ |
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| 214 | { |
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| 215 | "data": { |
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| 216 | "application/vnd.jupyter.widget-view+json": { |
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| 217 | "model_id": "4bf5a2291e32453ca38813214dbe1a11", |
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| 218 | "version_major": 2, |
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| 219 | "version_minor": 0 |
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| 220 | }, |
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| 221 | "text/plain": [ |
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| 222 | "HBox(children=(IntProgress(value=0, max=21744), HTML(value='')))" |
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| 223 | ] |
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| 224 | }, |
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| 225 | "metadata": {}, |
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| 226 | "output_type": "display_data" |
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| 227 | }, |
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| 228 | { |
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| 229 | "name": "stdout", |
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| 230 | "output_type": "stream", |
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| 231 | "text": [ |
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| 232 | "\n" |
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| 233 | ] |
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| 234 | } |
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| 235 | ], |
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| 236 | "source": [ |
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| 237 | "with ProcessPoolExecutor(max_workers=32) as e:\n", |
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| 238 | " extended_df = pd.concat(\n", |
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| 239 | " tqdm(e.map(norm_study, repeat(f'data/unzip/{stage}_train_images'), group_names), total=len(group_names)))" |
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| 240 | ] |
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| 241 | }, |
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| 242 | { |
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| 243 | "cell_type": "code", |
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| 244 | "execution_count": 12, |
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| 245 | "metadata": {}, |
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| 246 | "outputs": [ |
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| 247 | { |
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| 248 | "data": { |
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| 249 | "text/html": [ |
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| 250 | "<div>\n", |
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| 251 | "<style scoped>\n", |
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| 252 | " .dataframe tbody tr th:only-of-type {\n", |
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| 253 | " vertical-align: middle;\n", |
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| 254 | " }\n", |
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| 255 | "\n", |
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| 256 | " .dataframe tbody tr th {\n", |
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| 257 | " vertical-align: top;\n", |
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| 258 | " }\n", |
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| 259 | "\n", |
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| 260 | " .dataframe thead th {\n", |
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| 261 | " text-align: right;\n", |
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| 262 | " }\n", |
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| 263 | "</style>\n", |
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| 264 | "<table border=\"1\" class=\"dataframe\">\n", |
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| 265 | " <thead>\n", |
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| 266 | " <tr style=\"text-align: right;\">\n", |
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| 267 | " <th></th>\n", |
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| 268 | " <th>556142</th>\n", |
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| 269 | " <th>561465</th>\n", |
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| 270 | " <th>580918</th>\n", |
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| 271 | " <th>584578</th>\n", |
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| 272 | " <th>617029</th>\n", |
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| 273 | " <th>617400</th>\n", |
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| 274 | " <th>645424</th>\n", |
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| 275 | " <th>661661</th>\n", |
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| 276 | " <th>665938</th>\n", |
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| 277 | " <th>748282</th>\n", |
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| 278 | " </tr>\n", |
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| 279 | " </thead>\n", |
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| 280 | " <tbody>\n", |
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| 281 | " <tr>\n", |
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| 282 | " <th>Unnamed: 0</th>\n", |
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| 283 | " <td>556142</td>\n", |
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| 284 | " <td>561465</td>\n", |
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| 285 | " <td>580918</td>\n", |
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| 286 | " <td>584578</td>\n", |
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| 287 | " <td>617029</td>\n", |
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| 288 | " <td>617400</td>\n", |
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| 289 | " <td>645424</td>\n", |
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| 290 | " <td>661661</td>\n", |
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| 291 | " <td>665938</td>\n", |
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| 292 | " <td>748282</td>\n", |
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| 293 | " </tr>\n", |
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| 294 | " <tr>\n", |
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| 295 | " <th>BitsAllocated</th>\n", |
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| 296 | " <td>16</td>\n", |
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| 297 | " <td>16</td>\n", |
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| 298 | " <td>16</td>\n", |
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| 299 | " <td>16</td>\n", |
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| 300 | " <td>16</td>\n", |
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| 301 | " <td>16</td>\n", |
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| 302 | " <td>16</td>\n", |
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| 303 | " <td>16</td>\n", |
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| 304 | " <td>16</td>\n", |
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| 305 | " <td>16</td>\n", |
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| 306 | " </tr>\n", |
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| 307 | " <tr>\n", |
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| 308 | " <th>BitsStored</th>\n", |
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| 309 | " <td>16</td>\n", |
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| 310 | " <td>16</td>\n", |
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| 311 | " <td>16</td>\n", |
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| 312 | " <td>16</td>\n", |
||
| 313 | " <td>16</td>\n", |
||
| 314 | " <td>16</td>\n", |
||
| 315 | " <td>16</td>\n", |
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| 316 | " <td>16</td>\n", |
||
| 317 | " <td>16</td>\n", |
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| 318 | " <td>16</td>\n", |
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| 319 | " </tr>\n", |
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| 320 | " <tr>\n", |
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| 321 | " <th>Columns</th>\n", |
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| 322 | " <td>512</td>\n", |
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| 323 | " <td>512</td>\n", |
||
| 324 | " <td>512</td>\n", |
||
| 325 | " <td>512</td>\n", |
||
| 326 | " <td>512</td>\n", |
||
| 327 | " <td>512</td>\n", |
||
| 328 | " <td>512</td>\n", |
||
| 329 | " <td>512</td>\n", |
||
| 330 | " <td>512</td>\n", |
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| 331 | " <td>512</td>\n", |
||
| 332 | " </tr>\n", |
||
| 333 | " <tr>\n", |
||
| 334 | " <th>HighBit</th>\n", |
||
| 335 | " <td>15</td>\n", |
||
| 336 | " <td>15</td>\n", |
||
| 337 | " <td>15</td>\n", |
||
| 338 | " <td>15</td>\n", |
||
| 339 | " <td>15</td>\n", |
||
| 340 | " <td>15</td>\n", |
||
| 341 | " <td>15</td>\n", |
||
| 342 | " <td>15</td>\n", |
||
| 343 | " <td>15</td>\n", |
||
| 344 | " <td>15</td>\n", |
||
| 345 | " </tr>\n", |
||
| 346 | " <tr>\n", |
||
| 347 | " <th>ImageOrientationPatient_0</th>\n", |
||
| 348 | " <td>1</td>\n", |
||
| 349 | " <td>1</td>\n", |
||
| 350 | " <td>1</td>\n", |
||
| 351 | " <td>1</td>\n", |
||
| 352 | " <td>1</td>\n", |
||
| 353 | " <td>1</td>\n", |
||
| 354 | " <td>1</td>\n", |
||
| 355 | " <td>1</td>\n", |
||
| 356 | " <td>1</td>\n", |
||
| 357 | " <td>1</td>\n", |
||
| 358 | " </tr>\n", |
||
| 359 | " <tr>\n", |
||
| 360 | " <th>ImageOrientationPatient_1</th>\n", |
||
| 361 | " <td>0</td>\n", |
||
| 362 | " <td>0</td>\n", |
||
| 363 | " <td>0</td>\n", |
||
| 364 | " <td>0</td>\n", |
||
| 365 | " <td>0</td>\n", |
||
| 366 | " <td>0</td>\n", |
||
| 367 | " <td>0</td>\n", |
||
| 368 | " <td>0</td>\n", |
||
| 369 | " <td>0</td>\n", |
||
| 370 | " <td>0</td>\n", |
||
| 371 | " </tr>\n", |
||
| 372 | " <tr>\n", |
||
| 373 | " <th>ImageOrientationPatient_2</th>\n", |
||
| 374 | " <td>0</td>\n", |
||
| 375 | " <td>0</td>\n", |
||
| 376 | " <td>0</td>\n", |
||
| 377 | " <td>0</td>\n", |
||
| 378 | " <td>0</td>\n", |
||
| 379 | " <td>0</td>\n", |
||
| 380 | " <td>0</td>\n", |
||
| 381 | " <td>0</td>\n", |
||
| 382 | " <td>0</td>\n", |
||
| 383 | " <td>0</td>\n", |
||
| 384 | " </tr>\n", |
||
| 385 | " <tr>\n", |
||
| 386 | " <th>ImageOrientationPatient_3</th>\n", |
||
| 387 | " <td>0</td>\n", |
||
| 388 | " <td>0</td>\n", |
||
| 389 | " <td>0</td>\n", |
||
| 390 | " <td>0</td>\n", |
||
| 391 | " <td>0</td>\n", |
||
| 392 | " <td>0</td>\n", |
||
| 393 | " <td>0</td>\n", |
||
| 394 | " <td>0</td>\n", |
||
| 395 | " <td>0</td>\n", |
||
| 396 | " <td>0</td>\n", |
||
| 397 | " </tr>\n", |
||
| 398 | " <tr>\n", |
||
| 399 | " <th>ImageOrientationPatient_4</th>\n", |
||
| 400 | " <td>0.979925</td>\n", |
||
| 401 | " <td>0.979925</td>\n", |
||
| 402 | " <td>0.979925</td>\n", |
||
| 403 | " <td>0.979925</td>\n", |
||
| 404 | " <td>0.979925</td>\n", |
||
| 405 | " <td>0.979925</td>\n", |
||
| 406 | " <td>0.979925</td>\n", |
||
| 407 | " <td>0.979925</td>\n", |
||
| 408 | " <td>0.979925</td>\n", |
||
| 409 | " <td>0.979925</td>\n", |
||
| 410 | " </tr>\n", |
||
| 411 | " <tr>\n", |
||
| 412 | " <th>ImageOrientationPatient_5</th>\n", |
||
| 413 | " <td>-0.199368</td>\n", |
||
| 414 | " <td>-0.199368</td>\n", |
||
| 415 | " <td>-0.199368</td>\n", |
||
| 416 | " <td>-0.199368</td>\n", |
||
| 417 | " <td>-0.199368</td>\n", |
||
| 418 | " <td>-0.199368</td>\n", |
||
| 419 | " <td>-0.199368</td>\n", |
||
| 420 | " <td>-0.199368</td>\n", |
||
| 421 | " <td>-0.199368</td>\n", |
||
| 422 | " <td>-0.199368</td>\n", |
||
| 423 | " </tr>\n", |
||
| 424 | " <tr>\n", |
||
| 425 | " <th>ImagePositionPatient_0</th>\n", |
||
| 426 | " <td>-125</td>\n", |
||
| 427 | " <td>-125</td>\n", |
||
| 428 | " <td>-125</td>\n", |
||
| 429 | " <td>-125</td>\n", |
||
| 430 | " <td>-125</td>\n", |
||
| 431 | " <td>-125</td>\n", |
||
| 432 | " <td>-125</td>\n", |
||
| 433 | " <td>-125</td>\n", |
||
| 434 | " <td>-125</td>\n", |
||
| 435 | " <td>-125</td>\n", |
||
| 436 | " </tr>\n", |
||
| 437 | " <tr>\n", |
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| 438 | " <th>ImagePositionPatient_1</th>\n", |
||
| 439 | " <td>-122.491</td>\n", |
||
| 440 | " <td>-122.491</td>\n", |
||
| 441 | " <td>-122.491</td>\n", |
||
| 442 | " <td>-122.491</td>\n", |
||
| 443 | " <td>-122.491</td>\n", |
||
| 444 | " <td>-122.491</td>\n", |
||
| 445 | " <td>-122.491</td>\n", |
||
| 446 | " <td>-122.491</td>\n", |
||
| 447 | " <td>-122.491</td>\n", |
||
| 448 | " <td>-122.491</td>\n", |
||
| 449 | " </tr>\n", |
||
| 450 | " <tr>\n", |
||
| 451 | " <th>ImagePositionPatient_2</th>\n", |
||
| 452 | " <td>166.528</td>\n", |
||
| 453 | " <td>156.323</td>\n", |
||
| 454 | " <td>176.733</td>\n", |
||
| 455 | " <td>49.171</td>\n", |
||
| 456 | " <td>89.991</td>\n", |
||
| 457 | " <td>186.938</td>\n", |
||
| 458 | " <td>125.708</td>\n", |
||
| 459 | " <td>146.118</td>\n", |
||
| 460 | " <td>74.6834</td>\n", |
||
| 461 | " <td>141.016</td>\n", |
||
| 462 | " </tr>\n", |
||
| 463 | " <tr>\n", |
||
| 464 | " <th>Modality</th>\n", |
||
| 465 | " <td>CT</td>\n", |
||
| 466 | " <td>CT</td>\n", |
||
| 467 | " <td>CT</td>\n", |
||
| 468 | " <td>CT</td>\n", |
||
| 469 | " <td>CT</td>\n", |
||
| 470 | " <td>CT</td>\n", |
||
| 471 | " <td>CT</td>\n", |
||
| 472 | " <td>CT</td>\n", |
||
| 473 | " <td>CT</td>\n", |
||
| 474 | " <td>CT</td>\n", |
||
| 475 | " </tr>\n", |
||
| 476 | " <tr>\n", |
||
| 477 | " <th>PatientID</th>\n", |
||
| 478 | " <td>ID_160aea75</td>\n", |
||
| 479 | " <td>ID_160aea75</td>\n", |
||
| 480 | " <td>ID_160aea75</td>\n", |
||
| 481 | " <td>ID_160aea75</td>\n", |
||
| 482 | " <td>ID_160aea75</td>\n", |
||
| 483 | " <td>ID_160aea75</td>\n", |
||
| 484 | " <td>ID_160aea75</td>\n", |
||
| 485 | " <td>ID_160aea75</td>\n", |
||
| 486 | " <td>ID_160aea75</td>\n", |
||
| 487 | " <td>ID_160aea75</td>\n", |
||
| 488 | " </tr>\n", |
||
| 489 | " <tr>\n", |
||
| 490 | " <th>PhotometricInterpretation</th>\n", |
||
| 491 | " <td>MONOCHROME2</td>\n", |
||
| 492 | " <td>MONOCHROME2</td>\n", |
||
| 493 | " <td>MONOCHROME2</td>\n", |
||
| 494 | " <td>MONOCHROME2</td>\n", |
||
| 495 | " <td>MONOCHROME2</td>\n", |
||
| 496 | " <td>MONOCHROME2</td>\n", |
||
| 497 | " <td>MONOCHROME2</td>\n", |
||
| 498 | " <td>MONOCHROME2</td>\n", |
||
| 499 | " <td>MONOCHROME2</td>\n", |
||
| 500 | " <td>MONOCHROME2</td>\n", |
||
| 501 | " </tr>\n", |
||
| 502 | " <tr>\n", |
||
| 503 | " <th>PixelRepresentation</th>\n", |
||
| 504 | " <td>1</td>\n", |
||
| 505 | " <td>1</td>\n", |
||
| 506 | " <td>1</td>\n", |
||
| 507 | " <td>1</td>\n", |
||
| 508 | " <td>1</td>\n", |
||
| 509 | " <td>1</td>\n", |
||
| 510 | " <td>1</td>\n", |
||
| 511 | " <td>1</td>\n", |
||
| 512 | " <td>1</td>\n", |
||
| 513 | " <td>1</td>\n", |
||
| 514 | " </tr>\n", |
||
| 515 | " <tr>\n", |
||
| 516 | " <th>PixelSpacing_0</th>\n", |
||
| 517 | " <td>0.488281</td>\n", |
||
| 518 | " <td>0.488281</td>\n", |
||
| 519 | " <td>0.488281</td>\n", |
||
| 520 | " <td>0.488281</td>\n", |
||
| 521 | " <td>0.488281</td>\n", |
||
| 522 | " <td>0.488281</td>\n", |
||
| 523 | " <td>0.488281</td>\n", |
||
| 524 | " <td>0.488281</td>\n", |
||
| 525 | " <td>0.488281</td>\n", |
||
| 526 | " <td>0.488281</td>\n", |
||
| 527 | " </tr>\n", |
||
| 528 | " <tr>\n", |
||
| 529 | " <th>PixelSpacing_1</th>\n", |
||
| 530 | " <td>0.488281</td>\n", |
||
| 531 | " <td>0.488281</td>\n", |
||
| 532 | " <td>0.488281</td>\n", |
||
| 533 | " <td>0.488281</td>\n", |
||
| 534 | " <td>0.488281</td>\n", |
||
| 535 | " <td>0.488281</td>\n", |
||
| 536 | " <td>0.488281</td>\n", |
||
| 537 | " <td>0.488281</td>\n", |
||
| 538 | " <td>0.488281</td>\n", |
||
| 539 | " <td>0.488281</td>\n", |
||
| 540 | " </tr>\n", |
||
| 541 | " <tr>\n", |
||
| 542 | " <th>RescaleIntercept</th>\n", |
||
| 543 | " <td>-1024</td>\n", |
||
| 544 | " <td>-1024</td>\n", |
||
| 545 | " <td>-1024</td>\n", |
||
| 546 | " <td>-1024</td>\n", |
||
| 547 | " <td>-1024</td>\n", |
||
| 548 | " <td>-1024</td>\n", |
||
| 549 | " <td>-1024</td>\n", |
||
| 550 | " <td>-1024</td>\n", |
||
| 551 | " <td>-1024</td>\n", |
||
| 552 | " <td>-1024</td>\n", |
||
| 553 | " </tr>\n", |
||
| 554 | " <tr>\n", |
||
| 555 | " <th>RescaleSlope</th>\n", |
||
| 556 | " <td>1</td>\n", |
||
| 557 | " <td>1</td>\n", |
||
| 558 | " <td>1</td>\n", |
||
| 559 | " <td>1</td>\n", |
||
| 560 | " <td>1</td>\n", |
||
| 561 | " <td>1</td>\n", |
||
| 562 | " <td>1</td>\n", |
||
| 563 | " <td>1</td>\n", |
||
| 564 | " <td>1</td>\n", |
||
| 565 | " <td>1</td>\n", |
||
| 566 | " </tr>\n", |
||
| 567 | " <tr>\n", |
||
| 568 | " <th>Rows</th>\n", |
||
| 569 | " <td>512</td>\n", |
||
| 570 | " <td>512</td>\n", |
||
| 571 | " <td>512</td>\n", |
||
| 572 | " <td>512</td>\n", |
||
| 573 | " <td>512</td>\n", |
||
| 574 | " <td>512</td>\n", |
||
| 575 | " <td>512</td>\n", |
||
| 576 | " <td>512</td>\n", |
||
| 577 | " <td>512</td>\n", |
||
| 578 | " <td>512</td>\n", |
||
| 579 | " </tr>\n", |
||
| 580 | " <tr>\n", |
||
| 581 | " <th>SOPInstanceUID</th>\n", |
||
| 582 | " <td>ID_bcdecac1b</td>\n", |
||
| 583 | " <td>ID_beb4aacbe</td>\n", |
||
| 584 | " <td>ID_c554939b0</td>\n", |
||
| 585 | " <td>ID_c6909d6fa</td>\n", |
||
| 586 | " <td>ID_d1ad467b0</td>\n", |
||
| 587 | " <td>ID_d1d25ea8c</td>\n", |
||
| 588 | " <td>ID_db59bb95e</td>\n", |
||
| 589 | " <td>ID_e0ed751c2</td>\n", |
||
| 590 | " <td>ID_e262d76e2</td>\n", |
||
| 591 | " <td>ID_fe77ec61b</td>\n", |
||
| 592 | " </tr>\n", |
||
| 593 | " <tr>\n", |
||
| 594 | " <th>SamplesPerPixel</th>\n", |
||
| 595 | " <td>1</td>\n", |
||
| 596 | " <td>1</td>\n", |
||
| 597 | " <td>1</td>\n", |
||
| 598 | " <td>1</td>\n", |
||
| 599 | " <td>1</td>\n", |
||
| 600 | " <td>1</td>\n", |
||
| 601 | " <td>1</td>\n", |
||
| 602 | " <td>1</td>\n", |
||
| 603 | " <td>1</td>\n", |
||
| 604 | " <td>1</td>\n", |
||
| 605 | " </tr>\n", |
||
| 606 | " <tr>\n", |
||
| 607 | " <th>SeriesInstanceUID</th>\n", |
||
| 608 | " <td>ID_000a935543</td>\n", |
||
| 609 | " <td>ID_000a935543</td>\n", |
||
| 610 | " <td>ID_000a935543</td>\n", |
||
| 611 | " <td>ID_000a935543</td>\n", |
||
| 612 | " <td>ID_000a935543</td>\n", |
||
| 613 | " <td>ID_000a935543</td>\n", |
||
| 614 | " <td>ID_000a935543</td>\n", |
||
| 615 | " <td>ID_000a935543</td>\n", |
||
| 616 | " <td>ID_000a935543</td>\n", |
||
| 617 | " <td>ID_000a935543</td>\n", |
||
| 618 | " </tr>\n", |
||
| 619 | " <tr>\n", |
||
| 620 | " <th>StudyID</th>\n", |
||
| 621 | " <td>NaN</td>\n", |
||
| 622 | " <td>NaN</td>\n", |
||
| 623 | " <td>NaN</td>\n", |
||
| 624 | " <td>NaN</td>\n", |
||
| 625 | " <td>NaN</td>\n", |
||
| 626 | " <td>NaN</td>\n", |
||
| 627 | " <td>NaN</td>\n", |
||
| 628 | " <td>NaN</td>\n", |
||
| 629 | " <td>NaN</td>\n", |
||
| 630 | " <td>NaN</td>\n", |
||
| 631 | " </tr>\n", |
||
| 632 | " <tr>\n", |
||
| 633 | " <th>StudyInstanceUID</th>\n", |
||
| 634 | " <td>ID_41d976e5d3</td>\n", |
||
| 635 | " <td>ID_41d976e5d3</td>\n", |
||
| 636 | " <td>ID_41d976e5d3</td>\n", |
||
| 637 | " <td>ID_41d976e5d3</td>\n", |
||
| 638 | " <td>ID_41d976e5d3</td>\n", |
||
| 639 | " <td>ID_41d976e5d3</td>\n", |
||
| 640 | " <td>ID_41d976e5d3</td>\n", |
||
| 641 | " <td>ID_41d976e5d3</td>\n", |
||
| 642 | " <td>ID_41d976e5d3</td>\n", |
||
| 643 | " <td>ID_41d976e5d3</td>\n", |
||
| 644 | " </tr>\n", |
||
| 645 | " <tr>\n", |
||
| 646 | " <th>WindowCenter</th>\n", |
||
| 647 | " <td>30</td>\n", |
||
| 648 | " <td>30</td>\n", |
||
| 649 | " <td>30</td>\n", |
||
| 650 | " <td>30</td>\n", |
||
| 651 | " <td>30</td>\n", |
||
| 652 | " <td>30</td>\n", |
||
| 653 | " <td>30</td>\n", |
||
| 654 | " <td>30</td>\n", |
||
| 655 | " <td>30</td>\n", |
||
| 656 | " <td>30</td>\n", |
||
| 657 | " </tr>\n", |
||
| 658 | " <tr>\n", |
||
| 659 | " <th>WindowCenter_0</th>\n", |
||
| 660 | " <td>NaN</td>\n", |
||
| 661 | " <td>NaN</td>\n", |
||
| 662 | " <td>NaN</td>\n", |
||
| 663 | " <td>NaN</td>\n", |
||
| 664 | " <td>NaN</td>\n", |
||
| 665 | " <td>NaN</td>\n", |
||
| 666 | " <td>NaN</td>\n", |
||
| 667 | " <td>NaN</td>\n", |
||
| 668 | " <td>NaN</td>\n", |
||
| 669 | " <td>NaN</td>\n", |
||
| 670 | " </tr>\n", |
||
| 671 | " <tr>\n", |
||
| 672 | " <th>WindowCenter_1</th>\n", |
||
| 673 | " <td>NaN</td>\n", |
||
| 674 | " <td>NaN</td>\n", |
||
| 675 | " <td>NaN</td>\n", |
||
| 676 | " <td>NaN</td>\n", |
||
| 677 | " <td>NaN</td>\n", |
||
| 678 | " <td>NaN</td>\n", |
||
| 679 | " <td>NaN</td>\n", |
||
| 680 | " <td>NaN</td>\n", |
||
| 681 | " <td>NaN</td>\n", |
||
| 682 | " <td>NaN</td>\n", |
||
| 683 | " </tr>\n", |
||
| 684 | " <tr>\n", |
||
| 685 | " <th>WindowWidth</th>\n", |
||
| 686 | " <td>80</td>\n", |
||
| 687 | " <td>80</td>\n", |
||
| 688 | " <td>80</td>\n", |
||
| 689 | " <td>80</td>\n", |
||
| 690 | " <td>80</td>\n", |
||
| 691 | " <td>80</td>\n", |
||
| 692 | " <td>80</td>\n", |
||
| 693 | " <td>80</td>\n", |
||
| 694 | " <td>80</td>\n", |
||
| 695 | " <td>80</td>\n", |
||
| 696 | " </tr>\n", |
||
| 697 | " <tr>\n", |
||
| 698 | " <th>WindowWidth_0</th>\n", |
||
| 699 | " <td>NaN</td>\n", |
||
| 700 | " <td>NaN</td>\n", |
||
| 701 | " <td>NaN</td>\n", |
||
| 702 | " <td>NaN</td>\n", |
||
| 703 | " <td>NaN</td>\n", |
||
| 704 | " <td>NaN</td>\n", |
||
| 705 | " <td>NaN</td>\n", |
||
| 706 | " <td>NaN</td>\n", |
||
| 707 | " <td>NaN</td>\n", |
||
| 708 | " <td>NaN</td>\n", |
||
| 709 | " </tr>\n", |
||
| 710 | " <tr>\n", |
||
| 711 | " <th>WindowWidth_1</th>\n", |
||
| 712 | " <td>NaN</td>\n", |
||
| 713 | " <td>NaN</td>\n", |
||
| 714 | " <td>NaN</td>\n", |
||
| 715 | " <td>NaN</td>\n", |
||
| 716 | " <td>NaN</td>\n", |
||
| 717 | " <td>NaN</td>\n", |
||
| 718 | " <td>NaN</td>\n", |
||
| 719 | " <td>NaN</td>\n", |
||
| 720 | " <td>NaN</td>\n", |
||
| 721 | " <td>NaN</td>\n", |
||
| 722 | " </tr>\n", |
||
| 723 | " <tr>\n", |
||
| 724 | " <th>fid</th>\n", |
||
| 725 | " <td>ID_bcdecac1b</td>\n", |
||
| 726 | " <td>ID_beb4aacbe</td>\n", |
||
| 727 | " <td>ID_c554939b0</td>\n", |
||
| 728 | " <td>ID_c6909d6fa</td>\n", |
||
| 729 | " <td>ID_d1ad467b0</td>\n", |
||
| 730 | " <td>ID_d1d25ea8c</td>\n", |
||
| 731 | " <td>ID_db59bb95e</td>\n", |
||
| 732 | " <td>ID_e0ed751c2</td>\n", |
||
| 733 | " <td>ID_e262d76e2</td>\n", |
||
| 734 | " <td>ID_fe77ec61b</td>\n", |
||
| 735 | " </tr>\n", |
||
| 736 | " <tr>\n", |
||
| 737 | " <th>any</th>\n", |
||
| 738 | " <td>0</td>\n", |
||
| 739 | " <td>0</td>\n", |
||
| 740 | " <td>0</td>\n", |
||
| 741 | " <td>0</td>\n", |
||
| 742 | " <td>0</td>\n", |
||
| 743 | " <td>0</td>\n", |
||
| 744 | " <td>0</td>\n", |
||
| 745 | " <td>0</td>\n", |
||
| 746 | " <td>0</td>\n", |
||
| 747 | " <td>0</td>\n", |
||
| 748 | " </tr>\n", |
||
| 749 | " <tr>\n", |
||
| 750 | " <th>epidural</th>\n", |
||
| 751 | " <td>0</td>\n", |
||
| 752 | " <td>0</td>\n", |
||
| 753 | " <td>0</td>\n", |
||
| 754 | " <td>0</td>\n", |
||
| 755 | " <td>0</td>\n", |
||
| 756 | " <td>0</td>\n", |
||
| 757 | " <td>0</td>\n", |
||
| 758 | " <td>0</td>\n", |
||
| 759 | " <td>0</td>\n", |
||
| 760 | " <td>0</td>\n", |
||
| 761 | " </tr>\n", |
||
| 762 | " <tr>\n", |
||
| 763 | " <th>intraparenchymal</th>\n", |
||
| 764 | " <td>0</td>\n", |
||
| 765 | " <td>0</td>\n", |
||
| 766 | " <td>0</td>\n", |
||
| 767 | " <td>0</td>\n", |
||
| 768 | " <td>0</td>\n", |
||
| 769 | " <td>0</td>\n", |
||
| 770 | " <td>0</td>\n", |
||
| 771 | " <td>0</td>\n", |
||
| 772 | " <td>0</td>\n", |
||
| 773 | " <td>0</td>\n", |
||
| 774 | " </tr>\n", |
||
| 775 | " <tr>\n", |
||
| 776 | " <th>intraventricular</th>\n", |
||
| 777 | " <td>0</td>\n", |
||
| 778 | " <td>0</td>\n", |
||
| 779 | " <td>0</td>\n", |
||
| 780 | " <td>0</td>\n", |
||
| 781 | " <td>0</td>\n", |
||
| 782 | " <td>0</td>\n", |
||
| 783 | " <td>0</td>\n", |
||
| 784 | " <td>0</td>\n", |
||
| 785 | " <td>0</td>\n", |
||
| 786 | " <td>0</td>\n", |
||
| 787 | " </tr>\n", |
||
| 788 | " <tr>\n", |
||
| 789 | " <th>subarachnoid</th>\n", |
||
| 790 | " <td>0</td>\n", |
||
| 791 | " <td>0</td>\n", |
||
| 792 | " <td>0</td>\n", |
||
| 793 | " <td>0</td>\n", |
||
| 794 | " <td>0</td>\n", |
||
| 795 | " <td>0</td>\n", |
||
| 796 | " <td>0</td>\n", |
||
| 797 | " <td>0</td>\n", |
||
| 798 | " <td>0</td>\n", |
||
| 799 | " <td>0</td>\n", |
||
| 800 | " </tr>\n", |
||
| 801 | " <tr>\n", |
||
| 802 | " <th>subdural</th>\n", |
||
| 803 | " <td>0</td>\n", |
||
| 804 | " <td>0</td>\n", |
||
| 805 | " <td>0</td>\n", |
||
| 806 | " <td>0</td>\n", |
||
| 807 | " <td>0</td>\n", |
||
| 808 | " <td>0</td>\n", |
||
| 809 | " <td>0</td>\n", |
||
| 810 | " <td>0</td>\n", |
||
| 811 | " <td>0</td>\n", |
||
| 812 | " <td>0</td>\n", |
||
| 813 | " </tr>\n", |
||
| 814 | " <tr>\n", |
||
| 815 | " <th>normz</th>\n", |
||
| 816 | " <td>61.23</td>\n", |
||
| 817 | " <td>51.0251</td>\n", |
||
| 818 | " <td>71.4351</td>\n", |
||
| 819 | " <td>-56.1273</td>\n", |
||
| 820 | " <td>-15.3073</td>\n", |
||
| 821 | " <td>81.64</td>\n", |
||
| 822 | " <td>20.41</td>\n", |
||
| 823 | " <td>40.82</td>\n", |
||
| 824 | " <td>-30.6149</td>\n", |
||
| 825 | " <td>35.7176</td>\n", |
||
| 826 | " </tr>\n", |
||
| 827 | " <tr>\n", |
||
| 828 | " <th>xcm</th>\n", |
||
| 829 | " <td>249.719</td>\n", |
||
| 830 | " <td>249.719</td>\n", |
||
| 831 | " <td>249.719</td>\n", |
||
| 832 | " <td>249.719</td>\n", |
||
| 833 | " <td>249.719</td>\n", |
||
| 834 | " <td>249.719</td>\n", |
||
| 835 | " <td>249.719</td>\n", |
||
| 836 | " <td>249.719</td>\n", |
||
| 837 | " <td>249.719</td>\n", |
||
| 838 | " <td>249.719</td>\n", |
||
| 839 | " </tr>\n", |
||
| 840 | " <tr>\n", |
||
| 841 | " <th>ycm</th>\n", |
||
| 842 | " <td>249.632</td>\n", |
||
| 843 | " <td>249.632</td>\n", |
||
| 844 | " <td>249.632</td>\n", |
||
| 845 | " <td>249.632</td>\n", |
||
| 846 | " <td>249.632</td>\n", |
||
| 847 | " <td>249.632</td>\n", |
||
| 848 | " <td>249.632</td>\n", |
||
| 849 | " <td>249.632</td>\n", |
||
| 850 | " <td>249.632</td>\n", |
||
| 851 | " <td>249.632</td>\n", |
||
| 852 | " </tr>\n", |
||
| 853 | " <tr>\n", |
||
| 854 | " <th>theta</th>\n", |
||
| 855 | " <td>-0.0280377</td>\n", |
||
| 856 | " <td>-0.0280377</td>\n", |
||
| 857 | " <td>-0.0280377</td>\n", |
||
| 858 | " <td>-0.0280377</td>\n", |
||
| 859 | " <td>-0.0280377</td>\n", |
||
| 860 | " <td>-0.0280377</td>\n", |
||
| 861 | " <td>-0.0280377</td>\n", |
||
| 862 | " <td>-0.0280377</td>\n", |
||
| 863 | " <td>-0.0280377</td>\n", |
||
| 864 | " <td>-0.0280377</td>\n", |
||
| 865 | " </tr>\n", |
||
| 866 | " <tr>\n", |
||
| 867 | " <th>pct_tissue</th>\n", |
||
| 868 | " <td>0.140537</td>\n", |
||
| 869 | " <td>0.194378</td>\n", |
||
| 870 | " <td>0.0751762</td>\n", |
||
| 871 | " <td>0.170967</td>\n", |
||
| 872 | " <td>0.320599</td>\n", |
||
| 873 | " <td>0.0209999</td>\n", |
||
| 874 | " <td>0.305298</td>\n", |
||
| 875 | " <td>0.242409</td>\n", |
||
| 876 | " <td>0.247257</td>\n", |
||
| 877 | " <td>0.262268</td>\n", |
||
| 878 | " </tr>\n", |
||
| 879 | " </tbody>\n", |
||
| 880 | "</table>\n", |
||
| 881 | "</div>" |
||
| 882 | ], |
||
| 883 | "text/plain": [ |
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| 885 | "Unnamed: 0 556142 561465 580918 \n", |
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| 899 | "Modality CT CT CT \n", |
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| 900 | "PatientID ID_160aea75 ID_160aea75 ID_160aea75 \n", |
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| 901 | "PhotometricInterpretation MONOCHROME2 MONOCHROME2 MONOCHROME2 \n", |
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| 906 | "RescaleSlope 1 1 1 \n", |
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| 907 | "Rows 512 512 512 \n", |
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| 909 | "SamplesPerPixel 1 1 1 \n", |
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| 910 | "SeriesInstanceUID ID_000a935543 ID_000a935543 ID_000a935543 \n", |
||
| 911 | "StudyID NaN NaN NaN \n", |
||
| 912 | "StudyInstanceUID ID_41d976e5d3 ID_41d976e5d3 ID_41d976e5d3 \n", |
||
| 913 | "WindowCenter 30 30 30 \n", |
||
| 914 | "WindowCenter_0 NaN NaN NaN \n", |
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| 915 | "WindowCenter_1 NaN NaN NaN \n", |
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| 916 | "WindowWidth 80 80 80 \n", |
||
| 917 | "WindowWidth_0 NaN NaN NaN \n", |
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| 918 | "WindowWidth_1 NaN NaN NaN \n", |
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| 919 | "fid ID_bcdecac1b ID_beb4aacbe ID_c554939b0 \n", |
||
| 920 | "any 0 0 0 \n", |
||
| 921 | "epidural 0 0 0 \n", |
||
| 922 | "intraparenchymal 0 0 0 \n", |
||
| 923 | "intraventricular 0 0 0 \n", |
||
| 924 | "subarachnoid 0 0 0 \n", |
||
| 925 | "subdural 0 0 0 \n", |
||
| 926 | "normz 61.23 51.0251 71.4351 \n", |
||
| 927 | "xcm 249.719 249.719 249.719 \n", |
||
| 928 | "ycm 249.632 249.632 249.632 \n", |
||
| 929 | "theta -0.0280377 -0.0280377 -0.0280377 \n", |
||
| 930 | "pct_tissue 0.140537 0.194378 0.0751762 \n", |
||
| 931 | "\n", |
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| 932 | " 584578 617029 617400 \\\n", |
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| 933 | "Unnamed: 0 584578 617029 617400 \n", |
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| 939 | "ImageOrientationPatient_1 0 0 0 \n", |
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| 941 | "ImageOrientationPatient_3 0 0 0 \n", |
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| 942 | "ImageOrientationPatient_4 0.979925 0.979925 0.979925 \n", |
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| 944 | "ImagePositionPatient_0 -125 -125 -125 \n", |
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| 945 | "ImagePositionPatient_1 -122.491 -122.491 -122.491 \n", |
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| 946 | "ImagePositionPatient_2 49.171 89.991 186.938 \n", |
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| 947 | "Modality CT CT CT \n", |
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| 948 | "PatientID ID_160aea75 ID_160aea75 ID_160aea75 \n", |
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| 966 | "WindowWidth_1 NaN NaN NaN \n", |
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| 968 | "any 0 0 0 \n", |
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| 969 | "epidural 0 0 0 \n", |
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| 970 | "intraparenchymal 0 0 0 \n", |
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| 971 | "intraventricular 0 0 0 \n", |
||
| 972 | "subarachnoid 0 0 0 \n", |
||
| 973 | "subdural 0 0 0 \n", |
||
| 974 | "normz -56.1273 -15.3073 81.64 \n", |
||
| 975 | "xcm 249.719 249.719 249.719 \n", |
||
| 976 | "ycm 249.632 249.632 249.632 \n", |
||
| 977 | "theta -0.0280377 -0.0280377 -0.0280377 \n", |
||
| 978 | "pct_tissue 0.170967 0.320599 0.0209999 \n", |
||
| 979 | "\n", |
||
| 980 | " 645424 661661 665938 \\\n", |
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| 981 | "Unnamed: 0 645424 661661 665938 \n", |
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| 983 | "BitsStored 16 16 16 \n", |
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| 984 | "Columns 512 512 512 \n", |
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| 985 | "HighBit 15 15 15 \n", |
||
| 986 | "ImageOrientationPatient_0 1 1 1 \n", |
||
| 987 | "ImageOrientationPatient_1 0 0 0 \n", |
||
| 988 | "ImageOrientationPatient_2 0 0 0 \n", |
||
| 989 | "ImageOrientationPatient_3 0 0 0 \n", |
||
| 990 | "ImageOrientationPatient_4 0.979925 0.979925 0.979925 \n", |
||
| 991 | "ImageOrientationPatient_5 -0.199368 -0.199368 -0.199368 \n", |
||
| 992 | "ImagePositionPatient_0 -125 -125 -125 \n", |
||
| 993 | "ImagePositionPatient_1 -122.491 -122.491 -122.491 \n", |
||
| 994 | "ImagePositionPatient_2 125.708 146.118 74.6834 \n", |
||
| 995 | "Modality CT CT CT \n", |
||
| 996 | "PatientID ID_160aea75 ID_160aea75 ID_160aea75 \n", |
||
| 997 | "PhotometricInterpretation MONOCHROME2 MONOCHROME2 MONOCHROME2 \n", |
||
| 998 | "PixelRepresentation 1 1 1 \n", |
||
| 999 | "PixelSpacing_0 0.488281 0.488281 0.488281 \n", |
||
| 1000 | "PixelSpacing_1 0.488281 0.488281 0.488281 \n", |
||
| 1001 | "RescaleIntercept -1024 -1024 -1024 \n", |
||
| 1002 | "RescaleSlope 1 1 1 \n", |
||
| 1003 | "Rows 512 512 512 \n", |
||
| 1004 | "SOPInstanceUID ID_db59bb95e ID_e0ed751c2 ID_e262d76e2 \n", |
||
| 1005 | "SamplesPerPixel 1 1 1 \n", |
||
| 1006 | "SeriesInstanceUID ID_000a935543 ID_000a935543 ID_000a935543 \n", |
||
| 1007 | "StudyID NaN NaN NaN \n", |
||
| 1008 | "StudyInstanceUID ID_41d976e5d3 ID_41d976e5d3 ID_41d976e5d3 \n", |
||
| 1009 | "WindowCenter 30 30 30 \n", |
||
| 1010 | "WindowCenter_0 NaN NaN NaN \n", |
||
| 1011 | "WindowCenter_1 NaN NaN NaN \n", |
||
| 1012 | "WindowWidth 80 80 80 \n", |
||
| 1013 | "WindowWidth_0 NaN NaN NaN \n", |
||
| 1014 | "WindowWidth_1 NaN NaN NaN \n", |
||
| 1015 | "fid ID_db59bb95e ID_e0ed751c2 ID_e262d76e2 \n", |
||
| 1016 | "any 0 0 0 \n", |
||
| 1017 | "epidural 0 0 0 \n", |
||
| 1018 | "intraparenchymal 0 0 0 \n", |
||
| 1019 | "intraventricular 0 0 0 \n", |
||
| 1020 | "subarachnoid 0 0 0 \n", |
||
| 1021 | "subdural 0 0 0 \n", |
||
| 1022 | "normz 20.41 40.82 -30.6149 \n", |
||
| 1023 | "xcm 249.719 249.719 249.719 \n", |
||
| 1024 | "ycm 249.632 249.632 249.632 \n", |
||
| 1025 | "theta -0.0280377 -0.0280377 -0.0280377 \n", |
||
| 1026 | "pct_tissue 0.305298 0.242409 0.247257 \n", |
||
| 1027 | "\n", |
||
| 1028 | " 748282 \n", |
||
| 1029 | "Unnamed: 0 748282 \n", |
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| 1030 | "BitsAllocated 16 \n", |
||
| 1031 | "BitsStored 16 \n", |
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| 1032 | "Columns 512 \n", |
||
| 1033 | "HighBit 15 \n", |
||
| 1034 | "ImageOrientationPatient_0 1 \n", |
||
| 1035 | "ImageOrientationPatient_1 0 \n", |
||
| 1036 | "ImageOrientationPatient_2 0 \n", |
||
| 1037 | "ImageOrientationPatient_3 0 \n", |
||
| 1038 | "ImageOrientationPatient_4 0.979925 \n", |
||
| 1039 | "ImageOrientationPatient_5 -0.199368 \n", |
||
| 1040 | "ImagePositionPatient_0 -125 \n", |
||
| 1041 | "ImagePositionPatient_1 -122.491 \n", |
||
| 1042 | "ImagePositionPatient_2 141.016 \n", |
||
| 1043 | "Modality CT \n", |
||
| 1044 | "PatientID ID_160aea75 \n", |
||
| 1045 | "PhotometricInterpretation MONOCHROME2 \n", |
||
| 1046 | "PixelRepresentation 1 \n", |
||
| 1047 | "PixelSpacing_0 0.488281 \n", |
||
| 1048 | "PixelSpacing_1 0.488281 \n", |
||
| 1049 | "RescaleIntercept -1024 \n", |
||
| 1050 | "RescaleSlope 1 \n", |
||
| 1051 | "Rows 512 \n", |
||
| 1052 | "SOPInstanceUID ID_fe77ec61b \n", |
||
| 1053 | "SamplesPerPixel 1 \n", |
||
| 1054 | "SeriesInstanceUID ID_000a935543 \n", |
||
| 1055 | "StudyID NaN \n", |
||
| 1056 | "StudyInstanceUID ID_41d976e5d3 \n", |
||
| 1057 | "WindowCenter 30 \n", |
||
| 1058 | "WindowCenter_0 NaN \n", |
||
| 1059 | "WindowCenter_1 NaN \n", |
||
| 1060 | "WindowWidth 80 \n", |
||
| 1061 | "WindowWidth_0 NaN \n", |
||
| 1062 | "WindowWidth_1 NaN \n", |
||
| 1063 | "fid ID_fe77ec61b \n", |
||
| 1064 | "any 0 \n", |
||
| 1065 | "epidural 0 \n", |
||
| 1066 | "intraparenchymal 0 \n", |
||
| 1067 | "intraventricular 0 \n", |
||
| 1068 | "subarachnoid 0 \n", |
||
| 1069 | "subdural 0 \n", |
||
| 1070 | "normz 35.7176 \n", |
||
| 1071 | "xcm 249.719 \n", |
||
| 1072 | "ycm 249.632 \n", |
||
| 1073 | "theta -0.0280377 \n", |
||
| 1074 | "pct_tissue 0.262268 " |
||
| 1075 | ] |
||
| 1076 | }, |
||
| 1077 | "execution_count": 12, |
||
| 1078 | "metadata": {}, |
||
| 1079 | "output_type": "execute_result" |
||
| 1080 | } |
||
| 1081 | ], |
||
| 1082 | "source": [ |
||
| 1083 | "extended_df[90:100].T" |
||
| 1084 | ] |
||
| 1085 | }, |
||
| 1086 | { |
||
| 1087 | "cell_type": "code", |
||
| 1088 | "execution_count": 13, |
||
| 1089 | "metadata": {}, |
||
| 1090 | "outputs": [ |
||
| 1091 | { |
||
| 1092 | "data": { |
||
| 1093 | "text/plain": [ |
||
| 1094 | "752802" |
||
| 1095 | ] |
||
| 1096 | }, |
||
| 1097 | "execution_count": 13, |
||
| 1098 | "metadata": {}, |
||
| 1099 | "output_type": "execute_result" |
||
| 1100 | } |
||
| 1101 | ], |
||
| 1102 | "source": [ |
||
| 1103 | "assert len(df) == len(extended_df)\n", |
||
| 1104 | "len(df)" |
||
| 1105 | ] |
||
| 1106 | }, |
||
| 1107 | { |
||
| 1108 | "cell_type": "code", |
||
| 1109 | "execution_count": 14, |
||
| 1110 | "metadata": {}, |
||
| 1111 | "outputs": [], |
||
| 1112 | "source": [ |
||
| 1113 | "extended_df.to_csv(f'data/{stage}_train_dicom_diags_norm.csv')" |
||
| 1114 | ] |
||
| 1115 | }, |
||
| 1116 | { |
||
| 1117 | "cell_type": "code", |
||
| 1118 | "execution_count": 15, |
||
| 1119 | "metadata": {}, |
||
| 1120 | "outputs": [], |
||
| 1121 | "source": [ |
||
| 1122 | "df = pd.read_csv(f'data/{stage}_test_dicom.csv')" |
||
| 1123 | ] |
||
| 1124 | }, |
||
| 1125 | { |
||
| 1126 | "cell_type": "code", |
||
| 1127 | "execution_count": 16, |
||
| 1128 | "metadata": {}, |
||
| 1129 | "outputs": [], |
||
| 1130 | "source": [ |
||
| 1131 | "dfg = df.groupby('SeriesInstanceUID')" |
||
| 1132 | ] |
||
| 1133 | }, |
||
| 1134 | { |
||
| 1135 | "cell_type": "code", |
||
| 1136 | "execution_count": 17, |
||
| 1137 | "metadata": {}, |
||
| 1138 | "outputs": [ |
||
| 1139 | { |
||
| 1140 | "data": { |
||
| 1141 | "text/plain": [ |
||
| 1142 | "3518" |
||
| 1143 | ] |
||
| 1144 | }, |
||
| 1145 | "execution_count": 17, |
||
| 1146 | "metadata": {}, |
||
| 1147 | "output_type": "execute_result" |
||
| 1148 | } |
||
| 1149 | ], |
||
| 1150 | "source": [ |
||
| 1151 | "group_names = list(dfg.groups.keys())\n", |
||
| 1152 | "len(group_names)" |
||
| 1153 | ] |
||
| 1154 | }, |
||
| 1155 | { |
||
| 1156 | "cell_type": "code", |
||
| 1157 | "execution_count": 18, |
||
| 1158 | "metadata": {}, |
||
| 1159 | "outputs": [ |
||
| 1160 | { |
||
| 1161 | "data": { |
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| 1162 | "text/html": [ |
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| 1164 | "<style scoped>\n", |
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| 1169 | " .dataframe tbody tr th {\n", |
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| 1170 | " vertical-align: top;\n", |
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| 1171 | " }\n", |
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| 1172 | "\n", |
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| 1173 | " .dataframe thead th {\n", |
||
| 1174 | " text-align: right;\n", |
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| 1175 | " }\n", |
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| 1176 | "</style>\n", |
||
| 1177 | "<table border=\"1\" class=\"dataframe\">\n", |
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| 1178 | " <thead>\n", |
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| 1188 | " <tbody>\n", |
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| 1207 | " <td>12</td>\n", |
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| 1215 | " <td>512</td>\n", |
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| 1236 | " </tr>\n", |
||
| 1237 | " <tr>\n", |
||
| 1238 | " <th>ImageOrientationPatient_1</th>\n", |
||
| 1239 | " <td>0</td>\n", |
||
| 1240 | " <td>0</td>\n", |
||
| 1241 | " <td>0</td>\n", |
||
| 1242 | " <td>0</td>\n", |
||
| 1243 | " <td>0</td>\n", |
||
| 1244 | " </tr>\n", |
||
| 1245 | " <tr>\n", |
||
| 1246 | " <th>ImageOrientationPatient_2</th>\n", |
||
| 1247 | " <td>0</td>\n", |
||
| 1248 | " <td>0</td>\n", |
||
| 1249 | " <td>0</td>\n", |
||
| 1250 | " <td>0</td>\n", |
||
| 1251 | " <td>0</td>\n", |
||
| 1252 | " </tr>\n", |
||
| 1253 | " <tr>\n", |
||
| 1254 | " <th>ImageOrientationPatient_3</th>\n", |
||
| 1255 | " <td>0</td>\n", |
||
| 1256 | " <td>0</td>\n", |
||
| 1257 | " <td>0</td>\n", |
||
| 1258 | " <td>0</td>\n", |
||
| 1259 | " <td>0</td>\n", |
||
| 1260 | " </tr>\n", |
||
| 1261 | " <tr>\n", |
||
| 1262 | " <th>ImageOrientationPatient_4</th>\n", |
||
| 1263 | " <td>0.981627</td>\n", |
||
| 1264 | " <td>0.987688</td>\n", |
||
| 1265 | " <td>0.927184</td>\n", |
||
| 1266 | " <td>0.986286</td>\n", |
||
| 1267 | " <td>1</td>\n", |
||
| 1268 | " </tr>\n", |
||
| 1269 | " <tr>\n", |
||
| 1270 | " <th>ImageOrientationPatient_5</th>\n", |
||
| 1271 | " <td>-0.190809</td>\n", |
||
| 1272 | " <td>-0.156434</td>\n", |
||
| 1273 | " <td>-0.374607</td>\n", |
||
| 1274 | " <td>-0.165048</td>\n", |
||
| 1275 | " <td>0</td>\n", |
||
| 1276 | " </tr>\n", |
||
| 1277 | " <tr>\n", |
||
| 1278 | " <th>ImagePositionPatient_0</th>\n", |
||
| 1279 | " <td>-112</td>\n", |
||
| 1280 | " <td>-125</td>\n", |
||
| 1281 | " <td>-125</td>\n", |
||
| 1282 | " <td>-125</td>\n", |
||
| 1283 | " <td>-125</td>\n", |
||
| 1284 | " </tr>\n", |
||
| 1285 | " <tr>\n", |
||
| 1286 | " <th>ImagePositionPatient_1</th>\n", |
||
| 1287 | " <td>-9.80803</td>\n", |
||
| 1288 | " <td>-127.061</td>\n", |
||
| 1289 | " <td>-119.998</td>\n", |
||
| 1290 | " <td>-120.286</td>\n", |
||
| 1291 | " <td>-16</td>\n", |
||
| 1292 | " </tr>\n", |
||
| 1293 | " <tr>\n", |
||
| 1294 | " <th>ImagePositionPatient_2</th>\n", |
||
| 1295 | " <td>267.219</td>\n", |
||
| 1296 | " <td>197.807</td>\n", |
||
| 1297 | " <td>78.6604</td>\n", |
||
| 1298 | " <td>131.737</td>\n", |
||
| 1299 | " <td>98.2</td>\n", |
||
| 1300 | " </tr>\n", |
||
| 1301 | " <tr>\n", |
||
| 1302 | " <th>Modality</th>\n", |
||
| 1303 | " <td>CT</td>\n", |
||
| 1304 | " <td>CT</td>\n", |
||
| 1305 | " <td>CT</td>\n", |
||
| 1306 | " <td>CT</td>\n", |
||
| 1307 | " <td>CT</td>\n", |
||
| 1308 | " </tr>\n", |
||
| 1309 | " <tr>\n", |
||
| 1310 | " <th>PatientID</th>\n", |
||
| 1311 | " <td>ID_52c1ab5a</td>\n", |
||
| 1312 | " <td>ID_39e44bce</td>\n", |
||
| 1313 | " <td>ID_6f87831a</td>\n", |
||
| 1314 | " <td>ID_7a7c9c9e</td>\n", |
||
| 1315 | " <td>ID_ab5e477f</td>\n", |
||
| 1316 | " </tr>\n", |
||
| 1317 | " <tr>\n", |
||
| 1318 | " <th>PhotometricInterpretation</th>\n", |
||
| 1319 | " <td>MONOCHROME2</td>\n", |
||
| 1320 | " <td>MONOCHROME2</td>\n", |
||
| 1321 | " <td>MONOCHROME2</td>\n", |
||
| 1322 | " <td>MONOCHROME2</td>\n", |
||
| 1323 | " <td>MONOCHROME2</td>\n", |
||
| 1324 | " </tr>\n", |
||
| 1325 | " <tr>\n", |
||
| 1326 | " <th>PixelRepresentation</th>\n", |
||
| 1327 | " <td>0</td>\n", |
||
| 1328 | " <td>1</td>\n", |
||
| 1329 | " <td>1</td>\n", |
||
| 1330 | " <td>1</td>\n", |
||
| 1331 | " <td>0</td>\n", |
||
| 1332 | " </tr>\n", |
||
| 1333 | " <tr>\n", |
||
| 1334 | " <th>PixelSpacing_0</th>\n", |
||
| 1335 | " <td>0.488281</td>\n", |
||
| 1336 | " <td>0.488281</td>\n", |
||
| 1337 | " <td>0.488281</td>\n", |
||
| 1338 | " <td>0.488281</td>\n", |
||
| 1339 | " <td>0.488281</td>\n", |
||
| 1340 | " </tr>\n", |
||
| 1341 | " <tr>\n", |
||
| 1342 | " <th>PixelSpacing_1</th>\n", |
||
| 1343 | " <td>0.488281</td>\n", |
||
| 1344 | " <td>0.488281</td>\n", |
||
| 1345 | " <td>0.488281</td>\n", |
||
| 1346 | " <td>0.488281</td>\n", |
||
| 1347 | " <td>0.488281</td>\n", |
||
| 1348 | " </tr>\n", |
||
| 1349 | " <tr>\n", |
||
| 1350 | " <th>RescaleIntercept</th>\n", |
||
| 1351 | " <td>-1024</td>\n", |
||
| 1352 | " <td>-1024</td>\n", |
||
| 1353 | " <td>-1024</td>\n", |
||
| 1354 | " <td>-1024</td>\n", |
||
| 1355 | " <td>-1024</td>\n", |
||
| 1356 | " </tr>\n", |
||
| 1357 | " <tr>\n", |
||
| 1358 | " <th>RescaleSlope</th>\n", |
||
| 1359 | " <td>1</td>\n", |
||
| 1360 | " <td>1</td>\n", |
||
| 1361 | " <td>1</td>\n", |
||
| 1362 | " <td>1</td>\n", |
||
| 1363 | " <td>1</td>\n", |
||
| 1364 | " </tr>\n", |
||
| 1365 | " <tr>\n", |
||
| 1366 | " <th>Rows</th>\n", |
||
| 1367 | " <td>512</td>\n", |
||
| 1368 | " <td>512</td>\n", |
||
| 1369 | " <td>512</td>\n", |
||
| 1370 | " <td>512</td>\n", |
||
| 1371 | " <td>512</td>\n", |
||
| 1372 | " </tr>\n", |
||
| 1373 | " <tr>\n", |
||
| 1374 | " <th>SOPInstanceUID</th>\n", |
||
| 1375 | " <td>ID_000000e27</td>\n", |
||
| 1376 | " <td>ID_000009146</td>\n", |
||
| 1377 | " <td>ID_00007b8cb</td>\n", |
||
| 1378 | " <td>ID_000134952</td>\n", |
||
| 1379 | " <td>ID_000176f2a</td>\n", |
||
| 1380 | " </tr>\n", |
||
| 1381 | " <tr>\n", |
||
| 1382 | " <th>SamplesPerPixel</th>\n", |
||
| 1383 | " <td>1</td>\n", |
||
| 1384 | " <td>1</td>\n", |
||
| 1385 | " <td>1</td>\n", |
||
| 1386 | " <td>1</td>\n", |
||
| 1387 | " <td>1</td>\n", |
||
| 1388 | " </tr>\n", |
||
| 1389 | " <tr>\n", |
||
| 1390 | " <th>SeriesInstanceUID</th>\n", |
||
| 1391 | " <td>ID_4d28912ba6</td>\n", |
||
| 1392 | " <td>ID_acabdeee86</td>\n", |
||
| 1393 | " <td>ID_d00cee7f0c</td>\n", |
||
| 1394 | " <td>ID_a52a0112d5</td>\n", |
||
| 1395 | " <td>ID_f552d3b922</td>\n", |
||
| 1396 | " </tr>\n", |
||
| 1397 | " <tr>\n", |
||
| 1398 | " <th>StudyID</th>\n", |
||
| 1399 | " <td>NaN</td>\n", |
||
| 1400 | " <td>NaN</td>\n", |
||
| 1401 | " <td>NaN</td>\n", |
||
| 1402 | " <td>NaN</td>\n", |
||
| 1403 | " <td>NaN</td>\n", |
||
| 1404 | " </tr>\n", |
||
| 1405 | " <tr>\n", |
||
| 1406 | " <th>StudyInstanceUID</th>\n", |
||
| 1407 | " <td>ID_1f6d1e8aeb</td>\n", |
||
| 1408 | " <td>ID_4a8d7ec19f</td>\n", |
||
| 1409 | " <td>ID_a6ca244172</td>\n", |
||
| 1410 | " <td>ID_fa950a03af</td>\n", |
||
| 1411 | " <td>ID_965d8b3d8e</td>\n", |
||
| 1412 | " </tr>\n", |
||
| 1413 | " <tr>\n", |
||
| 1414 | " <th>WindowCenter</th>\n", |
||
| 1415 | " <td>NaN</td>\n", |
||
| 1416 | " <td>30</td>\n", |
||
| 1417 | " <td>30</td>\n", |
||
| 1418 | " <td>30</td>\n", |
||
| 1419 | " <td>NaN</td>\n", |
||
| 1420 | " </tr>\n", |
||
| 1421 | " <tr>\n", |
||
| 1422 | " <th>WindowCenter_0</th>\n", |
||
| 1423 | " <td>40</td>\n", |
||
| 1424 | " <td>NaN</td>\n", |
||
| 1425 | " <td>NaN</td>\n", |
||
| 1426 | " <td>NaN</td>\n", |
||
| 1427 | " <td>36</td>\n", |
||
| 1428 | " </tr>\n", |
||
| 1429 | " <tr>\n", |
||
| 1430 | " <th>WindowCenter_1</th>\n", |
||
| 1431 | " <td>40</td>\n", |
||
| 1432 | " <td>NaN</td>\n", |
||
| 1433 | " <td>NaN</td>\n", |
||
| 1434 | " <td>NaN</td>\n", |
||
| 1435 | " <td>36</td>\n", |
||
| 1436 | " </tr>\n", |
||
| 1437 | " <tr>\n", |
||
| 1438 | " <th>WindowWidth</th>\n", |
||
| 1439 | " <td>NaN</td>\n", |
||
| 1440 | " <td>80</td>\n", |
||
| 1441 | " <td>80</td>\n", |
||
| 1442 | " <td>80</td>\n", |
||
| 1443 | " <td>NaN</td>\n", |
||
| 1444 | " </tr>\n", |
||
| 1445 | " <tr>\n", |
||
| 1446 | " <th>WindowWidth_0</th>\n", |
||
| 1447 | " <td>80</td>\n", |
||
| 1448 | " <td>NaN</td>\n", |
||
| 1449 | " <td>NaN</td>\n", |
||
| 1450 | " <td>NaN</td>\n", |
||
| 1451 | " <td>80</td>\n", |
||
| 1452 | " </tr>\n", |
||
| 1453 | " <tr>\n", |
||
| 1454 | " <th>WindowWidth_1</th>\n", |
||
| 1455 | " <td>80</td>\n", |
||
| 1456 | " <td>NaN</td>\n", |
||
| 1457 | " <td>NaN</td>\n", |
||
| 1458 | " <td>NaN</td>\n", |
||
| 1459 | " <td>80</td>\n", |
||
| 1460 | " </tr>\n", |
||
| 1461 | " </tbody>\n", |
||
| 1462 | "</table>\n", |
||
| 1463 | "</div>" |
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| 1464 | ], |
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| 1465 | "text/plain": [ |
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| 1466 | " 0 1 2 \\\n", |
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| 1467 | "Unnamed: 0 0 1 2 \n", |
||
| 1468 | "BitsAllocated 16 16 16 \n", |
||
| 1469 | "BitsStored 12 16 16 \n", |
||
| 1470 | "Columns 512 512 512 \n", |
||
| 1471 | "HighBit 11 15 15 \n", |
||
| 1472 | "ImageOrientationPatient_0 1 1 1 \n", |
||
| 1473 | "ImageOrientationPatient_1 0 0 0 \n", |
||
| 1474 | "ImageOrientationPatient_2 0 0 0 \n", |
||
| 1475 | "ImageOrientationPatient_3 0 0 0 \n", |
||
| 1476 | "ImageOrientationPatient_4 0.981627 0.987688 0.927184 \n", |
||
| 1477 | "ImageOrientationPatient_5 -0.190809 -0.156434 -0.374607 \n", |
||
| 1478 | "ImagePositionPatient_0 -112 -125 -125 \n", |
||
| 1479 | "ImagePositionPatient_1 -9.80803 -127.061 -119.998 \n", |
||
| 1480 | "ImagePositionPatient_2 267.219 197.807 78.6604 \n", |
||
| 1481 | "Modality CT CT CT \n", |
||
| 1482 | "PatientID ID_52c1ab5a ID_39e44bce ID_6f87831a \n", |
||
| 1483 | "PhotometricInterpretation MONOCHROME2 MONOCHROME2 MONOCHROME2 \n", |
||
| 1484 | "PixelRepresentation 0 1 1 \n", |
||
| 1485 | "PixelSpacing_0 0.488281 0.488281 0.488281 \n", |
||
| 1486 | "PixelSpacing_1 0.488281 0.488281 0.488281 \n", |
||
| 1487 | "RescaleIntercept -1024 -1024 -1024 \n", |
||
| 1488 | "RescaleSlope 1 1 1 \n", |
||
| 1489 | "Rows 512 512 512 \n", |
||
| 1490 | "SOPInstanceUID ID_000000e27 ID_000009146 ID_00007b8cb \n", |
||
| 1491 | "SamplesPerPixel 1 1 1 \n", |
||
| 1492 | "SeriesInstanceUID ID_4d28912ba6 ID_acabdeee86 ID_d00cee7f0c \n", |
||
| 1493 | "StudyID NaN NaN NaN \n", |
||
| 1494 | "StudyInstanceUID ID_1f6d1e8aeb ID_4a8d7ec19f ID_a6ca244172 \n", |
||
| 1495 | "WindowCenter NaN 30 30 \n", |
||
| 1496 | "WindowCenter_0 40 NaN NaN \n", |
||
| 1497 | "WindowCenter_1 40 NaN NaN \n", |
||
| 1498 | "WindowWidth NaN 80 80 \n", |
||
| 1499 | "WindowWidth_0 80 NaN NaN \n", |
||
| 1500 | "WindowWidth_1 80 NaN NaN \n", |
||
| 1501 | "\n", |
||
| 1502 | " 3 4 \n", |
||
| 1503 | "Unnamed: 0 3 4 \n", |
||
| 1504 | "BitsAllocated 16 16 \n", |
||
| 1505 | "BitsStored 16 12 \n", |
||
| 1506 | "Columns 512 512 \n", |
||
| 1507 | "HighBit 15 11 \n", |
||
| 1508 | "ImageOrientationPatient_0 1 1 \n", |
||
| 1509 | "ImageOrientationPatient_1 0 0 \n", |
||
| 1510 | "ImageOrientationPatient_2 0 0 \n", |
||
| 1511 | "ImageOrientationPatient_3 0 0 \n", |
||
| 1512 | "ImageOrientationPatient_4 0.986286 1 \n", |
||
| 1513 | "ImageOrientationPatient_5 -0.165048 0 \n", |
||
| 1514 | "ImagePositionPatient_0 -125 -125 \n", |
||
| 1515 | "ImagePositionPatient_1 -120.286 -16 \n", |
||
| 1516 | "ImagePositionPatient_2 131.737 98.2 \n", |
||
| 1517 | "Modality CT CT \n", |
||
| 1518 | "PatientID ID_7a7c9c9e ID_ab5e477f \n", |
||
| 1519 | "PhotometricInterpretation MONOCHROME2 MONOCHROME2 \n", |
||
| 1520 | "PixelRepresentation 1 0 \n", |
||
| 1521 | "PixelSpacing_0 0.488281 0.488281 \n", |
||
| 1522 | "PixelSpacing_1 0.488281 0.488281 \n", |
||
| 1523 | "RescaleIntercept -1024 -1024 \n", |
||
| 1524 | "RescaleSlope 1 1 \n", |
||
| 1525 | "Rows 512 512 \n", |
||
| 1526 | "SOPInstanceUID ID_000134952 ID_000176f2a \n", |
||
| 1527 | "SamplesPerPixel 1 1 \n", |
||
| 1528 | "SeriesInstanceUID ID_a52a0112d5 ID_f552d3b922 \n", |
||
| 1529 | "StudyID NaN NaN \n", |
||
| 1530 | "StudyInstanceUID ID_fa950a03af ID_965d8b3d8e \n", |
||
| 1531 | "WindowCenter 30 NaN \n", |
||
| 1532 | "WindowCenter_0 NaN 36 \n", |
||
| 1533 | "WindowCenter_1 NaN 36 \n", |
||
| 1534 | "WindowWidth 80 NaN \n", |
||
| 1535 | "WindowWidth_0 NaN 80 \n", |
||
| 1536 | "WindowWidth_1 NaN 80 " |
||
| 1537 | ] |
||
| 1538 | }, |
||
| 1539 | "execution_count": 18, |
||
| 1540 | "metadata": {}, |
||
| 1541 | "output_type": "execute_result" |
||
| 1542 | } |
||
| 1543 | ], |
||
| 1544 | "source": [ |
||
| 1545 | "df.head().T" |
||
| 1546 | ] |
||
| 1547 | }, |
||
| 1548 | { |
||
| 1549 | "cell_type": "code", |
||
| 1550 | "execution_count": 19, |
||
| 1551 | "metadata": {}, |
||
| 1552 | "outputs": [ |
||
| 1553 | { |
||
| 1554 | "data": { |
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| 1555 | "application/vnd.jupyter.widget-view+json": { |
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| 1556 | "model_id": "cce4c6aa74ec4e65adc8cafc672f8ba1", |
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| 1557 | "version_major": 2, |
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| 1558 | "version_minor": 0 |
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| 1559 | }, |
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| 1560 | "text/plain": [ |
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| 1561 | "HBox(children=(IntProgress(value=0, max=3518), HTML(value='')))" |
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| 1562 | ] |
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| 1563 | }, |
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| 1564 | "metadata": {}, |
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| 1565 | "output_type": "display_data" |
||
| 1566 | }, |
||
| 1567 | { |
||
| 1568 | "name": "stdout", |
||
| 1569 | "output_type": "stream", |
||
| 1570 | "text": [ |
||
| 1571 | "\n" |
||
| 1572 | ] |
||
| 1573 | } |
||
| 1574 | ], |
||
| 1575 | "source": [ |
||
| 1576 | "with ProcessPoolExecutor(max_workers=32) as e:\n", |
||
| 1577 | " extended_df = pd.concat(tqdm(\n", |
||
| 1578 | " e.map(norm_study, repeat(f'data/unzip/{stage}_test_images'), group_names), total=len(group_names)))" |
||
| 1579 | ] |
||
| 1580 | }, |
||
| 1581 | { |
||
| 1582 | "cell_type": "code", |
||
| 1583 | "execution_count": 20, |
||
| 1584 | "metadata": {}, |
||
| 1585 | "outputs": [ |
||
| 1586 | { |
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| 1587 | "data": { |
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| 1588 | "text/html": [ |
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| 1589 | "<div>\n", |
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| 1590 | "<style scoped>\n", |
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| 1591 | " .dataframe tbody tr th:only-of-type {\n", |
||
| 1592 | " vertical-align: middle;\n", |
||
| 1593 | " }\n", |
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| 1594 | "\n", |
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| 1595 | " .dataframe tbody tr th {\n", |
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| 1596 | " vertical-align: top;\n", |
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| 1597 | " }\n", |
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| 1598 | "\n", |
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| 1599 | " .dataframe thead th {\n", |
||
| 1600 | " text-align: right;\n", |
||
| 1601 | " }\n", |
||
| 1602 | "</style>\n", |
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| 1603 | "<table border=\"1\" class=\"dataframe\">\n", |
||
| 1604 | " <thead>\n", |
||
| 1605 | " <tr style=\"text-align: right;\">\n", |
||
| 1606 | " <th></th>\n", |
||
| 1607 | " <th>13820</th>\n", |
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| 1608 | " <th>18901</th>\n", |
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| 1609 | " <th>20132</th>\n", |
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| 1610 | " <th>24764</th>\n", |
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| 1611 | " <th>36224</th>\n", |
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| 1612 | " </tr>\n", |
||
| 1613 | " </thead>\n", |
||
| 1614 | " <tbody>\n", |
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| 1615 | " <tr>\n", |
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| 1616 | " <th>Unnamed: 0</th>\n", |
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| 1617 | " <td>13820</td>\n", |
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| 1618 | " <td>18901</td>\n", |
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| 1619 | " <td>20132</td>\n", |
||
| 1620 | " <td>24764</td>\n", |
||
| 1621 | " <td>36224</td>\n", |
||
| 1622 | " </tr>\n", |
||
| 1623 | " <tr>\n", |
||
| 1624 | " <th>BitsAllocated</th>\n", |
||
| 1625 | " <td>16</td>\n", |
||
| 1626 | " <td>16</td>\n", |
||
| 1627 | " <td>16</td>\n", |
||
| 1628 | " <td>16</td>\n", |
||
| 1629 | " <td>16</td>\n", |
||
| 1630 | " </tr>\n", |
||
| 1631 | " <tr>\n", |
||
| 1632 | " <th>BitsStored</th>\n", |
||
| 1633 | " <td>12</td>\n", |
||
| 1634 | " <td>12</td>\n", |
||
| 1635 | " <td>12</td>\n", |
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| 1636 | " <td>12</td>\n", |
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| 1637 | " <td>12</td>\n", |
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| 1638 | " </tr>\n", |
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| 1639 | " <tr>\n", |
||
| 1640 | " <th>Columns</th>\n", |
||
| 1641 | " <td>512</td>\n", |
||
| 1642 | " <td>512</td>\n", |
||
| 1643 | " <td>512</td>\n", |
||
| 1644 | " <td>512</td>\n", |
||
| 1645 | " <td>512</td>\n", |
||
| 1646 | " </tr>\n", |
||
| 1647 | " <tr>\n", |
||
| 1648 | " <th>HighBit</th>\n", |
||
| 1649 | " <td>11</td>\n", |
||
| 1650 | " <td>11</td>\n", |
||
| 1651 | " <td>11</td>\n", |
||
| 1652 | " <td>11</td>\n", |
||
| 1653 | " <td>11</td>\n", |
||
| 1654 | " </tr>\n", |
||
| 1655 | " <tr>\n", |
||
| 1656 | " <th>ImageOrientationPatient_0</th>\n", |
||
| 1657 | " <td>1</td>\n", |
||
| 1658 | " <td>1</td>\n", |
||
| 1659 | " <td>1</td>\n", |
||
| 1660 | " <td>1</td>\n", |
||
| 1661 | " <td>1</td>\n", |
||
| 1662 | " </tr>\n", |
||
| 1663 | " <tr>\n", |
||
| 1664 | " <th>ImageOrientationPatient_1</th>\n", |
||
| 1665 | " <td>0</td>\n", |
||
| 1666 | " <td>0</td>\n", |
||
| 1667 | " <td>0</td>\n", |
||
| 1668 | " <td>0</td>\n", |
||
| 1669 | " <td>0</td>\n", |
||
| 1670 | " </tr>\n", |
||
| 1671 | " <tr>\n", |
||
| 1672 | " <th>ImageOrientationPatient_2</th>\n", |
||
| 1673 | " <td>0</td>\n", |
||
| 1674 | " <td>0</td>\n", |
||
| 1675 | " <td>0</td>\n", |
||
| 1676 | " <td>0</td>\n", |
||
| 1677 | " <td>0</td>\n", |
||
| 1678 | " </tr>\n", |
||
| 1679 | " <tr>\n", |
||
| 1680 | " <th>ImageOrientationPatient_3</th>\n", |
||
| 1681 | " <td>0</td>\n", |
||
| 1682 | " <td>0</td>\n", |
||
| 1683 | " <td>0</td>\n", |
||
| 1684 | " <td>0</td>\n", |
||
| 1685 | " <td>0</td>\n", |
||
| 1686 | " </tr>\n", |
||
| 1687 | " <tr>\n", |
||
| 1688 | " <th>ImageOrientationPatient_4</th>\n", |
||
| 1689 | " <td>0.939693</td>\n", |
||
| 1690 | " <td>0.939693</td>\n", |
||
| 1691 | " <td>0.939693</td>\n", |
||
| 1692 | " <td>0.939693</td>\n", |
||
| 1693 | " <td>0.939693</td>\n", |
||
| 1694 | " </tr>\n", |
||
| 1695 | " <tr>\n", |
||
| 1696 | " <th>ImageOrientationPatient_5</th>\n", |
||
| 1697 | " <td>-0.34202</td>\n", |
||
| 1698 | " <td>-0.34202</td>\n", |
||
| 1699 | " <td>-0.34202</td>\n", |
||
| 1700 | " <td>-0.34202</td>\n", |
||
| 1701 | " <td>-0.34202</td>\n", |
||
| 1702 | " </tr>\n", |
||
| 1703 | " <tr>\n", |
||
| 1704 | " <th>ImagePositionPatient_0</th>\n", |
||
| 1705 | " <td>-167</td>\n", |
||
| 1706 | " <td>-167</td>\n", |
||
| 1707 | " <td>-167</td>\n", |
||
| 1708 | " <td>-167</td>\n", |
||
| 1709 | " <td>-167</td>\n", |
||
| 1710 | " </tr>\n", |
||
| 1711 | " <tr>\n", |
||
| 1712 | " <th>ImagePositionPatient_1</th>\n", |
||
| 1713 | " <td>17.8026</td>\n", |
||
| 1714 | " <td>17.8026</td>\n", |
||
| 1715 | " <td>17.8026</td>\n", |
||
| 1716 | " <td>17.8026</td>\n", |
||
| 1717 | " <td>17.8026</td>\n", |
||
| 1718 | " </tr>\n", |
||
| 1719 | " <tr>\n", |
||
| 1720 | " <th>ImagePositionPatient_2</th>\n", |
||
| 1721 | " <td>340.091</td>\n", |
||
| 1722 | " <td>302.953</td>\n", |
||
| 1723 | " <td>324.153</td>\n", |
||
| 1724 | " <td>387.753</td>\n", |
||
| 1725 | " <td>265.891</td>\n", |
||
| 1726 | " </tr>\n", |
||
| 1727 | " <tr>\n", |
||
| 1728 | " <th>Modality</th>\n", |
||
| 1729 | " <td>CT</td>\n", |
||
| 1730 | " <td>CT</td>\n", |
||
| 1731 | " <td>CT</td>\n", |
||
| 1732 | " <td>CT</td>\n", |
||
| 1733 | " <td>CT</td>\n", |
||
| 1734 | " </tr>\n", |
||
| 1735 | " <tr>\n", |
||
| 1736 | " <th>PatientID</th>\n", |
||
| 1737 | " <td>ID_f997418a</td>\n", |
||
| 1738 | " <td>ID_f997418a</td>\n", |
||
| 1739 | " <td>ID_f997418a</td>\n", |
||
| 1740 | " <td>ID_f997418a</td>\n", |
||
| 1741 | " <td>ID_f997418a</td>\n", |
||
| 1742 | " </tr>\n", |
||
| 1743 | " <tr>\n", |
||
| 1744 | " <th>PhotometricInterpretation</th>\n", |
||
| 1745 | " <td>MONOCHROME2</td>\n", |
||
| 1746 | " <td>MONOCHROME2</td>\n", |
||
| 1747 | " <td>MONOCHROME2</td>\n", |
||
| 1748 | " <td>MONOCHROME2</td>\n", |
||
| 1749 | " <td>MONOCHROME2</td>\n", |
||
| 1750 | " </tr>\n", |
||
| 1751 | " <tr>\n", |
||
| 1752 | " <th>PixelRepresentation</th>\n", |
||
| 1753 | " <td>0</td>\n", |
||
| 1754 | " <td>0</td>\n", |
||
| 1755 | " <td>0</td>\n", |
||
| 1756 | " <td>0</td>\n", |
||
| 1757 | " <td>0</td>\n", |
||
| 1758 | " </tr>\n", |
||
| 1759 | " <tr>\n", |
||
| 1760 | " <th>PixelSpacing_0</th>\n", |
||
| 1761 | " <td>0.488281</td>\n", |
||
| 1762 | " <td>0.488281</td>\n", |
||
| 1763 | " <td>0.488281</td>\n", |
||
| 1764 | " <td>0.488281</td>\n", |
||
| 1765 | " <td>0.488281</td>\n", |
||
| 1766 | " </tr>\n", |
||
| 1767 | " <tr>\n", |
||
| 1768 | " <th>PixelSpacing_1</th>\n", |
||
| 1769 | " <td>0.488281</td>\n", |
||
| 1770 | " <td>0.488281</td>\n", |
||
| 1771 | " <td>0.488281</td>\n", |
||
| 1772 | " <td>0.488281</td>\n", |
||
| 1773 | " <td>0.488281</td>\n", |
||
| 1774 | " </tr>\n", |
||
| 1775 | " <tr>\n", |
||
| 1776 | " <th>RescaleIntercept</th>\n", |
||
| 1777 | " <td>-1024</td>\n", |
||
| 1778 | " <td>-1024</td>\n", |
||
| 1779 | " <td>-1024</td>\n", |
||
| 1780 | " <td>-1024</td>\n", |
||
| 1781 | " <td>-1024</td>\n", |
||
| 1782 | " </tr>\n", |
||
| 1783 | " <tr>\n", |
||
| 1784 | " <th>RescaleSlope</th>\n", |
||
| 1785 | " <td>1</td>\n", |
||
| 1786 | " <td>1</td>\n", |
||
| 1787 | " <td>1</td>\n", |
||
| 1788 | " <td>1</td>\n", |
||
| 1789 | " <td>1</td>\n", |
||
| 1790 | " </tr>\n", |
||
| 1791 | " <tr>\n", |
||
| 1792 | " <th>Rows</th>\n", |
||
| 1793 | " <td>512</td>\n", |
||
| 1794 | " <td>512</td>\n", |
||
| 1795 | " <td>512</td>\n", |
||
| 1796 | " <td>512</td>\n", |
||
| 1797 | " <td>512</td>\n", |
||
| 1798 | " </tr>\n", |
||
| 1799 | " <tr>\n", |
||
| 1800 | " <th>SOPInstanceUID</th>\n", |
||
| 1801 | " <td>ID_1cf8d2973</td>\n", |
||
| 1802 | " <td>ID_2775d5917</td>\n", |
||
| 1803 | " <td>ID_29fb61fbb</td>\n", |
||
| 1804 | " <td>ID_33ba827f2</td>\n", |
||
| 1805 | " <td>ID_4c1ea3745</td>\n", |
||
| 1806 | " </tr>\n", |
||
| 1807 | " <tr>\n", |
||
| 1808 | " <th>SamplesPerPixel</th>\n", |
||
| 1809 | " <td>1</td>\n", |
||
| 1810 | " <td>1</td>\n", |
||
| 1811 | " <td>1</td>\n", |
||
| 1812 | " <td>1</td>\n", |
||
| 1813 | " <td>1</td>\n", |
||
| 1814 | " </tr>\n", |
||
| 1815 | " <tr>\n", |
||
| 1816 | " <th>SeriesInstanceUID</th>\n", |
||
| 1817 | " <td>ID_0018be306d</td>\n", |
||
| 1818 | " <td>ID_0018be306d</td>\n", |
||
| 1819 | " <td>ID_0018be306d</td>\n", |
||
| 1820 | " <td>ID_0018be306d</td>\n", |
||
| 1821 | " <td>ID_0018be306d</td>\n", |
||
| 1822 | " </tr>\n", |
||
| 1823 | " <tr>\n", |
||
| 1824 | " <th>StudyID</th>\n", |
||
| 1825 | " <td>NaN</td>\n", |
||
| 1826 | " <td>NaN</td>\n", |
||
| 1827 | " <td>NaN</td>\n", |
||
| 1828 | " <td>NaN</td>\n", |
||
| 1829 | " <td>NaN</td>\n", |
||
| 1830 | " </tr>\n", |
||
| 1831 | " <tr>\n", |
||
| 1832 | " <th>StudyInstanceUID</th>\n", |
||
| 1833 | " <td>ID_16aac16e79</td>\n", |
||
| 1834 | " <td>ID_16aac16e79</td>\n", |
||
| 1835 | " <td>ID_16aac16e79</td>\n", |
||
| 1836 | " <td>ID_16aac16e79</td>\n", |
||
| 1837 | " <td>ID_16aac16e79</td>\n", |
||
| 1838 | " </tr>\n", |
||
| 1839 | " <tr>\n", |
||
| 1840 | " <th>WindowCenter</th>\n", |
||
| 1841 | " <td>NaN</td>\n", |
||
| 1842 | " <td>NaN</td>\n", |
||
| 1843 | " <td>NaN</td>\n", |
||
| 1844 | " <td>NaN</td>\n", |
||
| 1845 | " <td>NaN</td>\n", |
||
| 1846 | " </tr>\n", |
||
| 1847 | " <tr>\n", |
||
| 1848 | " <th>WindowCenter_0</th>\n", |
||
| 1849 | " <td>40</td>\n", |
||
| 1850 | " <td>40</td>\n", |
||
| 1851 | " <td>40</td>\n", |
||
| 1852 | " <td>40</td>\n", |
||
| 1853 | " <td>40</td>\n", |
||
| 1854 | " </tr>\n", |
||
| 1855 | " <tr>\n", |
||
| 1856 | " <th>WindowCenter_1</th>\n", |
||
| 1857 | " <td>40</td>\n", |
||
| 1858 | " <td>40</td>\n", |
||
| 1859 | " <td>40</td>\n", |
||
| 1860 | " <td>40</td>\n", |
||
| 1861 | " <td>40</td>\n", |
||
| 1862 | " </tr>\n", |
||
| 1863 | " <tr>\n", |
||
| 1864 | " <th>WindowWidth</th>\n", |
||
| 1865 | " <td>NaN</td>\n", |
||
| 1866 | " <td>NaN</td>\n", |
||
| 1867 | " <td>NaN</td>\n", |
||
| 1868 | " <td>NaN</td>\n", |
||
| 1869 | " <td>NaN</td>\n", |
||
| 1870 | " </tr>\n", |
||
| 1871 | " <tr>\n", |
||
| 1872 | " <th>WindowWidth_0</th>\n", |
||
| 1873 | " <td>80</td>\n", |
||
| 1874 | " <td>80</td>\n", |
||
| 1875 | " <td>80</td>\n", |
||
| 1876 | " <td>80</td>\n", |
||
| 1877 | " <td>80</td>\n", |
||
| 1878 | " </tr>\n", |
||
| 1879 | " <tr>\n", |
||
| 1880 | " <th>WindowWidth_1</th>\n", |
||
| 1881 | " <td>80</td>\n", |
||
| 1882 | " <td>80</td>\n", |
||
| 1883 | " <td>80</td>\n", |
||
| 1884 | " <td>80</td>\n", |
||
| 1885 | " <td>80</td>\n", |
||
| 1886 | " </tr>\n", |
||
| 1887 | " <tr>\n", |
||
| 1888 | " <th>normz</th>\n", |
||
| 1889 | " <td>37.1382</td>\n", |
||
| 1890 | " <td>0</td>\n", |
||
| 1891 | " <td>21.2001</td>\n", |
||
| 1892 | " <td>84.8</td>\n", |
||
| 1893 | " <td>-37.0619</td>\n", |
||
| 1894 | " </tr>\n", |
||
| 1895 | " <tr>\n", |
||
| 1896 | " <th>xcm</th>\n", |
||
| 1897 | " <td>255.127</td>\n", |
||
| 1898 | " <td>255.127</td>\n", |
||
| 1899 | " <td>255.127</td>\n", |
||
| 1900 | " <td>255.127</td>\n", |
||
| 1901 | " <td>255.127</td>\n", |
||
| 1902 | " </tr>\n", |
||
| 1903 | " <tr>\n", |
||
| 1904 | " <th>ycm</th>\n", |
||
| 1905 | " <td>241.378</td>\n", |
||
| 1906 | " <td>241.378</td>\n", |
||
| 1907 | " <td>241.378</td>\n", |
||
| 1908 | " <td>241.378</td>\n", |
||
| 1909 | " <td>241.378</td>\n", |
||
| 1910 | " </tr>\n", |
||
| 1911 | " <tr>\n", |
||
| 1912 | " <th>theta</th>\n", |
||
| 1913 | " <td>0.132157</td>\n", |
||
| 1914 | " <td>0.132157</td>\n", |
||
| 1915 | " <td>0.132157</td>\n", |
||
| 1916 | " <td>0.132157</td>\n", |
||
| 1917 | " <td>0.132157</td>\n", |
||
| 1918 | " </tr>\n", |
||
| 1919 | " <tr>\n", |
||
| 1920 | " <th>pct_tissue</th>\n", |
||
| 1921 | " <td>0.191586</td>\n", |
||
| 1922 | " <td>0.271954</td>\n", |
||
| 1923 | " <td>0.242237</td>\n", |
||
| 1924 | " <td>0.00454712</td>\n", |
||
| 1925 | " <td>0.143639</td>\n", |
||
| 1926 | " </tr>\n", |
||
| 1927 | " </tbody>\n", |
||
| 1928 | "</table>\n", |
||
| 1929 | "</div>" |
||
| 1930 | ], |
||
| 1931 | "text/plain": [ |
||
| 1932 | " 13820 18901 20132 \\\n", |
||
| 1933 | "Unnamed: 0 13820 18901 20132 \n", |
||
| 1934 | "BitsAllocated 16 16 16 \n", |
||
| 1935 | "BitsStored 12 12 12 \n", |
||
| 1936 | "Columns 512 512 512 \n", |
||
| 1937 | "HighBit 11 11 11 \n", |
||
| 1938 | "ImageOrientationPatient_0 1 1 1 \n", |
||
| 1939 | "ImageOrientationPatient_1 0 0 0 \n", |
||
| 1940 | "ImageOrientationPatient_2 0 0 0 \n", |
||
| 1941 | "ImageOrientationPatient_3 0 0 0 \n", |
||
| 1942 | "ImageOrientationPatient_4 0.939693 0.939693 0.939693 \n", |
||
| 1943 | "ImageOrientationPatient_5 -0.34202 -0.34202 -0.34202 \n", |
||
| 1944 | "ImagePositionPatient_0 -167 -167 -167 \n", |
||
| 1945 | "ImagePositionPatient_1 17.8026 17.8026 17.8026 \n", |
||
| 1946 | "ImagePositionPatient_2 340.091 302.953 324.153 \n", |
||
| 1947 | "Modality CT CT CT \n", |
||
| 1948 | "PatientID ID_f997418a ID_f997418a ID_f997418a \n", |
||
| 1949 | "PhotometricInterpretation MONOCHROME2 MONOCHROME2 MONOCHROME2 \n", |
||
| 1950 | "PixelRepresentation 0 0 0 \n", |
||
| 1951 | "PixelSpacing_0 0.488281 0.488281 0.488281 \n", |
||
| 1952 | "PixelSpacing_1 0.488281 0.488281 0.488281 \n", |
||
| 1953 | "RescaleIntercept -1024 -1024 -1024 \n", |
||
| 1954 | "RescaleSlope 1 1 1 \n", |
||
| 1955 | "Rows 512 512 512 \n", |
||
| 1956 | "SOPInstanceUID ID_1cf8d2973 ID_2775d5917 ID_29fb61fbb \n", |
||
| 1957 | "SamplesPerPixel 1 1 1 \n", |
||
| 1958 | "SeriesInstanceUID ID_0018be306d ID_0018be306d ID_0018be306d \n", |
||
| 1959 | "StudyID NaN NaN NaN \n", |
||
| 1960 | "StudyInstanceUID ID_16aac16e79 ID_16aac16e79 ID_16aac16e79 \n", |
||
| 1961 | "WindowCenter NaN NaN NaN \n", |
||
| 1962 | "WindowCenter_0 40 40 40 \n", |
||
| 1963 | "WindowCenter_1 40 40 40 \n", |
||
| 1964 | "WindowWidth NaN NaN NaN \n", |
||
| 1965 | "WindowWidth_0 80 80 80 \n", |
||
| 1966 | "WindowWidth_1 80 80 80 \n", |
||
| 1967 | "normz 37.1382 0 21.2001 \n", |
||
| 1968 | "xcm 255.127 255.127 255.127 \n", |
||
| 1969 | "ycm 241.378 241.378 241.378 \n", |
||
| 1970 | "theta 0.132157 0.132157 0.132157 \n", |
||
| 1971 | "pct_tissue 0.191586 0.271954 0.242237 \n", |
||
| 1972 | "\n", |
||
| 1973 | " 24764 36224 \n", |
||
| 1974 | "Unnamed: 0 24764 36224 \n", |
||
| 1975 | "BitsAllocated 16 16 \n", |
||
| 1976 | "BitsStored 12 12 \n", |
||
| 1977 | "Columns 512 512 \n", |
||
| 1978 | "HighBit 11 11 \n", |
||
| 1979 | "ImageOrientationPatient_0 1 1 \n", |
||
| 1980 | "ImageOrientationPatient_1 0 0 \n", |
||
| 1981 | "ImageOrientationPatient_2 0 0 \n", |
||
| 1982 | "ImageOrientationPatient_3 0 0 \n", |
||
| 1983 | "ImageOrientationPatient_4 0.939693 0.939693 \n", |
||
| 1984 | "ImageOrientationPatient_5 -0.34202 -0.34202 \n", |
||
| 1985 | "ImagePositionPatient_0 -167 -167 \n", |
||
| 1986 | "ImagePositionPatient_1 17.8026 17.8026 \n", |
||
| 1987 | "ImagePositionPatient_2 387.753 265.891 \n", |
||
| 1988 | "Modality CT CT \n", |
||
| 1989 | "PatientID ID_f997418a ID_f997418a \n", |
||
| 1990 | "PhotometricInterpretation MONOCHROME2 MONOCHROME2 \n", |
||
| 1991 | "PixelRepresentation 0 0 \n", |
||
| 1992 | "PixelSpacing_0 0.488281 0.488281 \n", |
||
| 1993 | "PixelSpacing_1 0.488281 0.488281 \n", |
||
| 1994 | "RescaleIntercept -1024 -1024 \n", |
||
| 1995 | "RescaleSlope 1 1 \n", |
||
| 1996 | "Rows 512 512 \n", |
||
| 1997 | "SOPInstanceUID ID_33ba827f2 ID_4c1ea3745 \n", |
||
| 1998 | "SamplesPerPixel 1 1 \n", |
||
| 1999 | "SeriesInstanceUID ID_0018be306d ID_0018be306d \n", |
||
| 2000 | "StudyID NaN NaN \n", |
||
| 2001 | "StudyInstanceUID ID_16aac16e79 ID_16aac16e79 \n", |
||
| 2002 | "WindowCenter NaN NaN \n", |
||
| 2003 | "WindowCenter_0 40 40 \n", |
||
| 2004 | "WindowCenter_1 40 40 \n", |
||
| 2005 | "WindowWidth NaN NaN \n", |
||
| 2006 | "WindowWidth_0 80 80 \n", |
||
| 2007 | "WindowWidth_1 80 80 \n", |
||
| 2008 | "normz 84.8 -37.0619 \n", |
||
| 2009 | "xcm 255.127 255.127 \n", |
||
| 2010 | "ycm 241.378 241.378 \n", |
||
| 2011 | "theta 0.132157 0.132157 \n", |
||
| 2012 | "pct_tissue 0.00454712 0.143639 " |
||
| 2013 | ] |
||
| 2014 | }, |
||
| 2015 | "execution_count": 20, |
||
| 2016 | "metadata": {}, |
||
| 2017 | "output_type": "execute_result" |
||
| 2018 | } |
||
| 2019 | ], |
||
| 2020 | "source": [ |
||
| 2021 | "extended_df.head().T" |
||
| 2022 | ] |
||
| 2023 | }, |
||
| 2024 | { |
||
| 2025 | "cell_type": "code", |
||
| 2026 | "execution_count": 21, |
||
| 2027 | "metadata": {}, |
||
| 2028 | "outputs": [ |
||
| 2029 | { |
||
| 2030 | "data": { |
||
| 2031 | "text/plain": [ |
||
| 2032 | "121232" |
||
| 2033 | ] |
||
| 2034 | }, |
||
| 2035 | "execution_count": 21, |
||
| 2036 | "metadata": {}, |
||
| 2037 | "output_type": "execute_result" |
||
| 2038 | } |
||
| 2039 | ], |
||
| 2040 | "source": [ |
||
| 2041 | "assert len(df) == len(extended_df)\n", |
||
| 2042 | "len(df)" |
||
| 2043 | ] |
||
| 2044 | }, |
||
| 2045 | { |
||
| 2046 | "cell_type": "code", |
||
| 2047 | "execution_count": 22, |
||
| 2048 | "metadata": {}, |
||
| 2049 | "outputs": [], |
||
| 2050 | "source": [ |
||
| 2051 | "extended_df.to_csv(f'data/{stage}_test_dicom_norm.csv')" |
||
| 2052 | ] |
||
| 2053 | } |
||
| 2054 | ], |
||
| 2055 | "metadata": { |
||
| 2056 | "kernelspec": { |
||
| 2057 | "display_name": "Python 3", |
||
| 2058 | "language": "python", |
||
| 2059 | "name": "python3" |
||
| 2060 | }, |
||
| 2061 | "language_info": { |
||
| 2062 | "codemirror_mode": { |
||
| 2063 | "name": "ipython", |
||
| 2064 | "version": 3 |
||
| 2065 | }, |
||
| 2066 | "file_extension": ".py", |
||
| 2067 | "mimetype": "text/x-python", |
||
| 2068 | "name": "python", |
||
| 2069 | "nbconvert_exporter": "python", |
||
| 2070 | "pygments_lexer": "ipython3", |
||
| 2071 | "version": "3.7.3" |
||
| 2072 | } |
||
| 2073 | }, |
||
| 2074 | "nbformat": 4, |
||
| 2075 | "nbformat_minor": 2 |
||
| 2076 | } |