From 9c7a72d370ca78b2e856373e0dba51cc30372b42 Mon Sep 17 00:00:00 2001 From: Viktor Sip Date: Mon, 27 Mar 2017 09:59:57 +0200 Subject: [PATCH] TVB surface zip file: save also vertex normals --- .../flow/surfaces_to_structural_datasets.py | 29 ++++++++++--------- 1 file changed, 16 insertions(+), 13 deletions(-) diff --git a/tvb/recon/flow/surfaces_to_structural_datasets.py b/tvb/recon/flow/surfaces_to_structural_datasets.py index 40f3e30..1497965 100644 --- a/tvb/recon/flow/surfaces_to_structural_datasets.py +++ b/tvb/recon/flow/surfaces_to_structural_datasets.py @@ -40,18 +40,31 @@ def __init__(self, vertices: np.array, triangles: np.array, region_mapping: np.a self.triangles = triangles self.region_mapping = region_mapping + self.nverts = self.vertices.shape[0] + self.ntriangs = self.triangles.shape[0] + + self.vertex_triangles = compute_vertex_triangles(self.nverts, self.ntriangs, self.triangles) + self.triangle_normals = compute_triangle_normals(self.triangles, self.vertices) + self.triangle_angles = compute_triangle_angles(self.vertices, self.ntriangs, self.triangles) + self.vertex_normals = compute_vertex_normals(self.nverts, self.vertex_triangles, self.triangles, + self.triangle_angles, self.triangle_normals, self.vertices) + self.triangle_areas = compute_triangle_areas(self.vertices, self.triangles) + def save_surf_zip(self, filename): tmpdir = tempfile.TemporaryDirectory() file_vertices = os.path.join(tmpdir.name, 'vertices.txt') file_triangles = os.path.join(tmpdir.name, 'triangles.txt') + file_normals = os.path.join(tmpdir.name, 'normals.txt') - np.savetxt(file_vertices, self.vertices, fmt='%.2f %.2f %.2f') + np.savetxt(file_vertices, self.vertices, fmt='%.6f %.6f %.6f') np.savetxt(file_triangles, self.triangles, fmt='%d %d %d') + np.savetxt(file_normals, self.vertex_normals, fmt='%.6f %.6f %.6f') with ZipFile(filename, 'w') as zip_file: zip_file.write(file_vertices, os.path.basename(file_vertices)) zip_file.write(file_triangles, os.path.basename(file_triangles)) + zip_file.write(file_normals, os.path.basename(file_normals)) def save_region_mapping_txt(self, filename): np.savetxt(filename, self.region_mapping, fmt="%d") @@ -241,19 +254,9 @@ def compute_region_params(surface: Surface, subcortical: bool=False)\ -> (np.ndarray, np.ndarray, np.ndarray, np.ndarray): verts, triangs, region_mapping = surface.vertices, surface.triangles, surface.region_mapping - nverts = verts.shape[0] - ntriangs = triangs.shape[0] - - vertex_triangles = compute_vertex_triangles(nverts, ntriangs, triangs) - triangle_normals = compute_triangle_normals(triangs, verts) - triangle_angles = compute_triangle_angles(verts, ntriangs, triangs) - vertex_normals = compute_vertex_normals(nverts, vertex_triangles, triangs, - triangle_angles, triangle_normals, verts) - triangle_areas = compute_triangle_areas(verts, triangs) - regions = np.unique(region_mapping) - areas = compute_region_areas(regions, triangle_areas, vertex_triangles, region_mapping) - orientations = compute_region_orientations(regions, vertex_normals, region_mapping) + areas = compute_region_areas(regions, surface.triangle_areas, surface.vertex_triangles, region_mapping) + orientations = compute_region_orientations(regions, surface.vertex_normals, region_mapping) centers = compute_region_centers(regions, verts, region_mapping) return regions, areas, orientations, centers