Layout changes.

Auto_mesh/Fast_auto_mesh.ipynb

@@ -12,13 +12,8 @@
     "\n",
     "from frap_img import find_sigma, contour_from_tif\n",
     "\n",
-    "    \n",
-    "    \n",
-    "# find_sigma(tif[9][20], tif[10][20],0.23) # we need to play with sigma until we find a value at which all the contours are black and the rest is not\n",
     "\n",
-    "\n",
-    "\n",
-    "base_folder = 'Analysis/';\n",
+    "base_folder = '/home/user/MPIPKS/Automatic_meshing_16/Analysis/';\n",
     "tif = tifffile.imread(base_folder + 'halfFrapBig_t000000_cropped.tif')\n",
     "fig = plt.figure()\n",
     "x_mid, y_mid, z_mid, r = np.genfromtxt(base_folder + '/mid_point_and_radius.csv', delimiter=',')\n",
@@ -28,25 +23,35 @@
     "sigma = 0.23\n",
     "d = 20\n",
     "FRAP = 1\n",
-    "N = 8 # when FRAP lot of point in the midlle are created => can lead to a long time for meshing 1D. The number of points is divided by this value\n",
+    "N = 8 # when FRAP lot of points are created => can lead to a long time for meshing 1D. The number of points is divided by this value\n",
     "\n",
     "# Recommended values of precision = [best:0.0025, worst:0.05]\n",
     "lc_min = 0.032\n",
     "lc_min_selected = 0.01\n",
     "lc_min_frap = 0.02\n",
     "\n",
+    "# find_sigma(FRAP,tif[9][20], tif[10][20],0.23) # we need to play with sigma until we find a value at which all the contours are black and the rest is not\n",
     "\n",
-    "\n",
-    "\n",
-    "\n",
-    "contour_from_tif(FRAP,tif[9][20], tif[10][20],sigma,d,'workfilefast.geo', lc_min, lc_min_selected, lc_min_frap,z,number_pixel,N)\n",
+    "contour_from_tif(FRAP,tif[9][4], tif[10][4],sigma,d,'workfilefast.geo', lc_min, lc_min_selected, lc_min_frap,z,number_pixel,N)\n",
     "\n",
     "N = 14\n",
-    "# contour_from_tif(FRAP,tif[9][30], tif[10][30],sigma,d,'workfile.geo', lc_min, lc_min_selected, lc_min_frap,z,number_pixel,N)\n",
-    "\n",
-    "\n"
+    "# contour_from_tif(FRAP,tif[9][30], tif[10][30],sigma,d,'workfile.geo', lc_min, lc_min_selected, lc_min_frap,z,number_pixel,N)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "markdown",
    "metadata": {},