added test for new morph data structure
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James McClure committed
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commit
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4 files changed
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+36
-114
@@ -2,85 +2,52 @@
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 37,
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"execution_count": 3,
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"metadata": {},
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"outputs": [],
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"source": [
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"import random\n",
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"import numpy as np\n",
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"import matplotlib.pylab as plt\n"
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"import matplotlib.pylab as plt\n",
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"import pandas as pd\n",
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"\n",
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"Nx=3\n",
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"Ny=128\n",
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"Nz=128\n",
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"dx = 1.0/(Nz-1)\n",
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"ID = np.ones(Nx*Ny*Nz,dtype='uint8')\n",
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"ID.shape = (Nz,Ny,Nx)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 38,
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"execution_count": 6,
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"metadata": {},
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"outputs": [],
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"source": [
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"for idx in range(len(D)):\n",
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" #print(idx)\n",
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" cx=D['cx'][idx] / dx\n",
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" cy=D['cy'][idx] /dx\n",
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" r=D['r'][idx] /dx\n",
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" for i in range(0,Nz):\n",
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" for j in range(0,Ny):\n",
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" if ( (cx-i)*(cx-i) + (cy-j)*(cy-j) < r*r ):\n",
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" ID[i,j,0] = 0\n",
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" ID[i,j,1] = 0\n",
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" ID[i,j,2] = 0\n",
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"\n",
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" \n",
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"ID.tofile(\"discs_3x128x128.raw\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"473.53100883248396"
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]
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},
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"execution_count": 38,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"Radius = 36\n",
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"random.seed(23)\n",
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"random.uniform(0,512)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 203,
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"metadata": {},
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"outputs": [],
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"source": [
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"cx = [312, 70, 173, 250, 100, 30, 70, 210, 200, 112, 332, 346, 452, 431, 500, 480]\n",
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"cy = [327, 64, 112, 20, 350, 450, 210, 438, 261, 500, 172, 455, 349, 60, 210, 460]\n",
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"radius = [46, 42, 49, 48, 43, 48, 64, 56, 46, 30, 86, 62, 52, 38, 59, 41]\n",
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"#for i in range(1,30):\n",
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"# cx.append(random.uniform(0,512))\n",
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"# cy.append(random.uniform(0,512))\n",
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" "
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]
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},
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{
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"cell_type": "code",
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"execution_count": 244,
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"metadata": {},
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"outputs": [],
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"source": [
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"Lid = np.ones((512,512),dtype=np.uint8)\n",
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"ID = np.ones((512,512),dtype=np.uint8)\n",
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"for i in range(len(radius)):\n",
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" Cx = cx[i]\n",
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" Cy = cy[i]\n",
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" Radius = radius[i]\n",
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" for i in range(np.int(Cx-Radius),np.int(Cx+Radius)):\n",
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" for j in range(np.int(Cy-Radius),np.int(Cy+Radius)):\n",
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" if i>1 and i<512 and j>1 and j<512:\n",
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" if ((i-Cx)*(i-Cx) + (j-Cy)*(j-Cy) < Radius*Radius):\n",
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" ID[i,j] = 0\n",
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" \n",
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"for i in range(512):\n",
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" ID[1,i] = 0\n",
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" ID[2,i] = 0\n",
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" ID[510,i] = 0\n",
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" ID[511,i] = 0"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 245,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"image/png": 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truncated
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"image/png": "iVBORw0KGgoAAAANSUhEUgAAAXcAAAEICAYAAACktLTqAAAABHNCSVQICAgIfAhkiAAAAAlwSFlzAAALEgAACxIB0t1+/AAAADh0RVh0U29mdHdhcmUAbWF0cGxvdGxpYiB2ZXJzaW9uMy4xLjEsIGh0dHA6Ly9tYXRwbG90bGliLm9yZy8QZhcZAAAaHklEQVR4nO3df7RddXnn8ffHBBBywYDgnZAbCWrEImtqOFGYWq0xVIERQ1udCavVWHFlzSypONo1QFlTmE7pSBvp4BJrnYaaVuCKKENkhpE0XmqdmaC5BEkwUgIoXIjEH6FwlWJjn/ljfy9sDufcH+ecfc7e+35ea+11z/79nL3Pee5zvvuXIgIzM6uXFw06ADMz6z0ndzOzGnJyNzOrISd3M7MacnI3M6shJ3czsxpycjfrEUnvk/T1NuNeLmlS0oJ+x2Xzk5O7WSLpDkkfKGLZEfFwRAxFxM+LWL5ZMyd3M7MacnK3npF0kaRHJT0l6T5Ja9LwF0m6WNIDkn4k6UZJx+Tme6+k76Vx/0nSdyWdkcZdLukLkj6XlrtL0qslXSJpv6RHJL0tt6yXSNokaV+K5Q+nmkKmmk0kbZR0QNJDks5K464A3gR8MjWffDINf42krZJ+nN7Tv8mt66WStkh6UtI3gFdOs22WSwpJC1P/HSm2/5vW9+W0vOvS8r4paXlu/qvTe31S0rikN+XGHS5pc3pPeyT9R0kTufHHS/qipB+k9/yhDnexVYiTu/WEpJOAC4DXR8SRwNuB76bRHwLOBX4FOB44AFyT5jsZ+BTwm8AS4CXA0qbFnwP8NXA0sBP4CtlndynwB8Cf56bdDBwEXgWsBN4G5JtaTgPuA44F/hjYJEkRcSnwd8AFqfnkAkmLgK3A9cDLgPOAT0l6bVrWNcA/prjfn7q5WAe8J72PVwL/D/hL4BhgD3BZbtpvAq9L464HviDpxWncZcBy4BXArwK/NTWTpBcBXwa+ldazBviwpLfPMVarmohw567rjiyZ7gfOAA5pGrcHWJPrXwL8E7AQ+H3ghty4I4CfAWek/suBrbnx5wCTwILUfyQQwGJgGHgGODw3/XnAWHr9PmBv07oC+Bep/w7gA7nx/xb4u6b38udkyXRBeg+vyY37I+DrbbbP8rSuhbl1XZob/3Hgtqb3efc02/sA8Ivp9YPA23PjPgBMpNenAQ83zXsJ8JeD/sy4K7ZbONt/AmbTiYi9kj5MloxfK+krwEci4jHgBOBmSf+cm+XnZMn4eOCR3HJ+KulHTYt/PPf6aeCH8dyByafT36G0rEOAfZKmpn9RfvnA95vWNTVvKycAp0l6IjdsIdmviOPS6/yyv9dmOe00v6/m/mfjkvRRsqR9PNk/iaPIfn1A0zZsen0CcHzTe1hA9ivFaszJ3XomIq4Hrpd0FFmFeyVZs8MjwPsj4v80zyNpH3BSrv9w4KUdhvAIWeV+bEQc7GD+5lukPgL8bUT8avOEqR3/ILAM+E4a/PIO1jmj1L5+EVmTyr0R8c+SDgBT/8H2ASPAt1P/stzsjwAPRcSKImKz8nKbu/WEpJMkvVXSYWTt0E+TVecAnwaukHRCmvY4SWvTuJuAcyT9kqRDgf/Mc0lrTiJiH3A78HFJR6UDua+U9CuzXMTjZO3WU24FXi3pPZIOSd3rJf1C+uXwJeBySUekYwfrO4l7Fo4k+0fyA2ChpN8nq9yn3AhcIuloSUvJjn1M+QbwZDrYfbikBZJOkfT6gmK1knByt145DPgY8EOypo+XAb+Xxl0NbAFul/QUsJ2sLZiIuBf4HWCUrAJ9iqzt/pkO43gvcChZFXuA7J/HklnOezXwrnTWySci4imyA7LrgMfS+7oyvVfIkuhQGv5ZsoOhRfgKcBvw92RNP//I85te/gCYAB4C/obsPT8DkP4JnUN2MPYhsv3zF2QHrq3GFOGHdVh5SBoCngBWRMRDg46niiT9e2BdRMz2F4vVkCt3GzhJ56SmjUXARmAXz51GaTOQtETSG1Mz1EnAR4GbBx2XDZaTu5XBWrJmj8eAFWRVp39Szt6hZAewnwK+CtxCdu2AzWNuljEzqyFX7mZmNVSK89yPPfbYWL58ecfz/+QnP2HRokW9C6hAVYm1KnFCdWKtSpxQnVirEicUE+v4+PgPI+K4liMHfYlsRNBoNKIbY2NjXc3fT1WJtSpxRlQn1qrEGVGdWKsSZ0QxsQI7ok1edbOMmVkNObmbmdWQk7uZWQ05uZuZ1ZCTu5lZDTm5m5nVkJO7mVkNObmbmdWQk7uZWQ3NmNwlXStpv6TduWF/Iuk7ku6RdLOkxblxl0jaK+k+P2HdzGwwZlO5fxY4s2nYVuCUiPiXZE+HuQQgPWpsHfDaNM+n0rMmzcysj2ZM7hHxNeDHTcNuj+ceQLyd7OG8kN2XezQinonsKTp7gTf0MF4zM5uFWd3PXdJy4NaIOKXFuC8Dn4+Iz0n6JLA9Ij6Xxm0CbouIm1rMtwHYADA8PNwYHR3t+E1MTk4yNDTU8fz9VJVYqxInVCfWqsQJ1Ym1KnFCMbGuXr16PCJWtRzZ7o5i+Q5YDuxuMfxSssd5Tf2TuAb4rdz4TcBvzLR83xWyfKoSZ0R1Yq1KnBHVibUqcUb0/66QHd/PXdJ64B3AmrQSyJ7Aviw32QjZo9OsZoaktuMm/XQvs4Hr6FRISWcCFwHvjIif5kZtAdZJOkzSiWTPw/xG92GamdlczFi5S7oBeAtwrKQJ4DKys2MOA7Yqq+C2R8S/i4h7Jd0IfBs4CHwwIn5eVPBWvOkq9E7mcVVv1h8zJveIOK/F4E3TTH8FcEU3QZmZWXd8hao9z5DEkMTO8fGOqvbZLr+IZZvZc0rxgGwbvEEk2+Z1usnGrHdcuZuZ1ZAr93msbE0jQ5Krd7MeceVuZlZDrtznobJV7HlTsbmCN+uOK/d5psyJPc9n1Jh1x8ndzKyGnNyt1FzBm3XGyd3MrIZ8QHWecPVrNr+4cq+5ujRr1OE9mPWTk7uZWQ05uZuZ1ZCTu5lZDTm5W2XU5fiBWT84uZuZ1ZCTe425yjWbv5zczcxqyMndzKyGnNytcnxgtVj5Z+g2d1YdTu5mZjXke8uYzUOdVuHTzecHrJSLk7vZPFF0s0p++U70g+dmGTOzGpoxuUu6VtJ+Sbtzw46RtFXS/env0Wm4JH1C0l5J90g6tcjgzWxmgzgY6gOwgzebyv2zwJlNwy4GtkXECmBb6gc4C1iRug3An/UmTDMzm4sZk3tEfA34cdPgtcDm9HozcG5u+F9FZjuwWNKSXgVrZnMz6OrZp1EOjmIWBz4kLQdujYhTUv8TEbE4N/5ARBwt6VbgYxHx9TR8G3BRROxoscwNZNU9w8PDjdHR0Y7fxOTkJENDQx3P30/9jHXn+HjH8y4dGeHRiYkeRtN7KxsNoDr7vyr7Hord/1P7rReqsu+hmFhXr149HhGrWo6MiBk7YDmwO9f/RNP4A+nv/wR+OTd8G9CYafmNRiO6MTY21tX8/dTPWBdBx91VGzd2NX8/ukFs025UZd8Xvf97qSr7PqKYWIEd0Savdnq2zONTzS3p7/40fAJYlptuBHisw3WYtTQZ4VPt2nATiE3pNLlvAdan1+uBW3LD35vOmjkd+IeI2NdljGZmNkczXsQk6QbgLcCxkiaAy4CPATdKOh94GHh3mvx/AWcDe4GfAr9dQMxm1kJVKvapOP3rq1gzJveIOK/NqDUtpg3gg90GZWZm3fEVqjXmysjKrCq/NKrK95axyvA/q9acJK0VV+5mZjXk5F5zPm3QbH5ycjczqyG3uVsl+NfHC9Whrd2nRRbHlfs84eYZs/nFyd3MrIac3OeZqlXv/sVh1hkndzOzGvIB1XloqhIu8wE5V+tm3XFyn8fKmOSd1M16w80yZmY15ORupamWyxKHWR04uZuZ1ZCTuwHPnXLYz1MPB7FOs/nCyd3MrIZ8toy1tLLRKORsGlfoZv3h5G4zckI2qx43y5iZ1ZCTu1lF+UC0TcfJ3cyshtzmbmYD418exXHlblZxbp6xVpzczcxqqKvkLuk/SLpX0m5JN0h6saQTJd0p6X5Jn5d0aK+CNbP68K+NYnWc3CUtBT4ErIqIU4AFwDrgSuBPI2IFcAA4vxeBmpnZ7HXbLLMQOFzSQuAIYB/wVuCmNH4zcG6X6zCzWahKJexjBP2h6GIjS7oQuAJ4GrgduBDYHhGvSuOXAbelyr553g3ABoDh4eHG6Ohox3FMTk4yNDTU8fz9VJVYqxInVCfWfsa5c3y8q/mXjozw6MREj6J5vpWNRs+WVZV9D8XEunr16vGIWNVyZER01AFHA18FjgMOAf4H8B5gb26aZcCumZbVaDSiG2NjY13N309VibUqcUZUJ9Z+xrkIuuqu2rix62W063qpKvs+ophYgR3RJq92c577GcBDEfEDAElfAn4JWCxpYUQcBEaAx7pYh5nVhJti+qubNveHgdMlHSFJwBrg28AY8K40zXrglu5CNDOzueo4uUfEnWQHTu8CdqVlfQa4CPiIpL3AS4FNPYjTzOagbA9BKUsc80lXtx+IiMuAy5oGPwi8oZvlmpXFbO5lX/bEVcR9+We7ThscX6FqZlZDvnGYzXvdVrTt5i9b9ZqPp4gqvmzvd75z5W5mVkNO7jYvDUnPdv1YRz/bu2cjf8C1k4Ov3cxr/eHkbmZWQ07uNm8MuoreOT5eyio+b6oKX9lotK3uXaVXgw+oWu2VMZlOxeREaUVx5W5mVkOu3K12ylipt5OP1VW89ZIrdzOzGnJyt1qpUtXerOwHW61anNzNzGrIyd3MrIZ8QNVqoU7NGT5N0nrBlbuZWQ05uVulDUldPwy6rOr0a8T6z8ndzKyGnNzNzGrIyd0qaz40W/jcd+uUk7uZWQ05uZuZ1ZCTu5lZDfkiJquc+dgG7QubbK5cuZuZ1ZCTu5lZDXWV3CUtlnSTpO9I2iPpX0k6RtJLine truncated
|
||||
"text/plain": [
|
||||
"<Figure size 432x288 with 1 Axes>"
|
||||
]
|
||||
@@ -94,57 +61,12 @@
|
||||
"source": [
|
||||
"plt.figure(1)\n",
|
||||
"plt.title('segmented image')\n",
|
||||
"plt.pcolormesh(ID[:,:],cmap='hot')\n",
|
||||
"plt.pcolormesh(ID[:,:,1],cmap='hot')\n",
|
||||
"plt.grid(True)\n",
|
||||
"plt.axis('equal')\n",
|
||||
"plt.show()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 246,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"Data = np.transpose(np.array([Lid,ID,ID,ID,ID,ID,ID,ID,ID,ID,ID,ID,ID,ID,ID,ID,ID,Lid]))"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 248,
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"image/png": 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truncated
|
||||
"text/plain": [
|
||||
"<Figure size 432x288 with 1 Axes>"
|
||||
]
|
||||
},
|
||||
"metadata": {
|
||||
"needs_background": "light"
|
||||
},
|
||||
"output_type": "display_data"
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"plt.figure(1)\n",
|
||||
"plt.title('segmented image')\n",
|
||||
"plt.pcolormesh(Data[:,:,9],cmap='hot')\n",
|
||||
"plt.grid(True)\n",
|
||||
"plt.axis('equal')\n",
|
||||
"plt.show()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 249,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"Data.tofile(\"discs512x512x18.raw\")"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
@@ -169,7 +91,7 @@
|
||||
"name": "python",
|
||||
"nbconvert_exporter": "python",
|
||||
"pygments_lexer": "ipython3",
|
||||
"version": "3.8.3"
|
||||
"version": "3.7.4"
|
||||
}
|
||||
},
|
||||
"nbformat": 4,
|
||||
|
||||
Reference in new issue
Block a user