added example/continuous_border.ipynb

examples/continuous_border.ipynb

@@ -0,0 +1,124 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Add Continuous Borders Around Labelled Regions"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from freesurfer_surface import Surface\n",
+    "\n",
+    "SUBJECTS_DIR = '../tests/subjects'\n",
+    "surface = Surface.read_triangular(SUBJECTS_DIR + '/fabian/surf/lh.pial')\n",
+    "surface.load_annotation_file(SUBJECTS_DIR + '/fabian/label/lh.aparc.annot')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "import numpy\n",
+    "from freesurfer_surface import Label, Vertex\n",
+    "\n",
+    "def unit_vector(vector: numpy.array) -> numpy.array:\n",
+    "    return vector / numpy.linalg.norm(vector)\n",
+    "\n",
+    "def add_border_around_labelled_surface(label: Label, border_length_add_mm: float,\n",
+    "                                       border_height_mm: float, border_width_mm: float):\n",
+    "    border_chain, = surface.find_label_border_polygonal_chains(label)\n",
+    "    print('#{}/{}: {} border segments'.format(label.index, \n",
+    "                                               label.name,\n",
+    "                                               len(border_chain.vertex_indices)))\n",
+    "    for vertex_triplet_indices in border_chain.adjacent_vertex_indices(3):\n",
+    "        vertex_triplet_coords = tuple(numpy.array(surface.vertices[idx])\n",
+    "                                      for idx in vertex_triplet_indices)\n",
+    "        backward_vector = vertex_triplet_coords[0] - vertex_triplet_coords[1]\n",
+    "        forward_vector = vertex_triplet_coords[2] - vertex_triplet_coords[1]\n",
+    "        forward_vector = unit_vector(forward_vector) \\\n",
+    "                         * (numpy.linalg.norm(forward_vector) + border_length_add_mm)\n",
+    "        upward_vector = unit_vector(numpy.cross(backward_vector, forward_vector)) * border_height_mm / 2\n",
+    "        sideward_vector = unit_vector(numpy.cross(upward_vector, forward_vector)) * border_width_mm / 2\n",
+    "        base_corners = [vertex_triplet_coords[1] + v\n",
+    "                                 for v in [-upward_vector -sideward_vector,\n",
+    "                                           -upward_vector +sideward_vector,\n",
+    "                                           +upward_vector +sideward_vector,\n",
+    "                                           +upward_vector -sideward_vector]]\n",
+    "        top_corners = [v + forward_vector for v in base_corners]\n",
+    "        base_indices = [surface.add_vertex(Vertex(*coords)) for coords in base_corners]\n",
+    "        top_indices = [surface.add_vertex(Vertex(*coords)) for coords in top_corners]\n",
+    "        for surface_indices in [base_indices, top_indices]:\n",
+    "            surface.add_rectangle(surface_indices)\n",
+    "        for i in range(4):\n",
+    "            j = (i + 1) % 4\n",
+    "            surface.add_rectangle((base_indices[i], base_indices[j],\n",
+    "                                   top_indices[j], top_indices[i]))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "#17/paracentral: 167 border segments\n",
+      "#22/postcentral: 396 border segments\n",
+      "#24/precentral: 418 border segments\n"
+     ]
+    }
+   ],
+   "source": [
+    "for label in filter(lambda l: 'central' in l.name, surface.annotation.labels.values()):\n",
+    "    add_border_around_labelled_surface(label,\n",
+    "                                       border_length_add_mm=0.2,\n",
+    "                                       border_height_mm=1.5,\n",
+    "                                       border_width_mm=1.0)\n",
+    "            \n",
+    "surface.write_triangular('border.lh.pial')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "```sh\n",
+    "freeview --surface examples/precentral-border.lh.pial:annot=tests/subjects/fabian/label/lh.aparc.annot\n",
+    "```"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.7"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}