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