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@@ -29,26 +29,22 @@
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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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+ "from freesurfer_surface import PolygonalChain, 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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+ "def add_blocks_along(border_chain: PolygonalChain, length_add_mm: float,\n",
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+ " height_mm: float, width_mm: float):\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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+ " * (numpy.linalg.norm(forward_vector) + length_add_mm)\n",
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+ " upward_vector = unit_vector(numpy.cross(backward_vector, forward_vector)) * height_mm / 2\n",
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+ " sideward_vector = unit_vector(numpy.cross(upward_vector, forward_vector)) * 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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@@ -74,18 +70,22 @@
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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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+ "#8: inferiorparietal (borders: 1)\n",
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+ "#17: paracentral (borders: 1)\n",
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+ "#22: postcentral (borders: 1)\n",
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+ "#24: precentral (borders: 1)\n",
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+ "#29: superiorparietal (borders: 1)\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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+ "for label in filter(lambda l: 'central' in l.name or 'parietal' in l.name,\n",
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+ " surface.annotation.labels.values()):\n",
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+ " borders = list(surface.find_label_border_polygonal_chains(label))\n",
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+ " print('#{}: {} (borders: {})'.format(label.index, label.name, len(borders)))\n",
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+ " for border in borders:\n",
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+ " add_blocks_along(border, length_add_mm=0.2,\n",
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+ " height_mm=1.5, 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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@@ -95,7 +95,7 @@
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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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+ "freeview --surface examples/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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