mcot.surface.grid¶
Defines many functions that take both a grid and a mesh as input.
Classes
|
Represents the intersections between a surface and a grid. |
Functions
|
Computes the shape and affine of a grid spanning the bounding box with given voxel size. |
|
Find for every point in the grid the closest point on the surface. |
|
Find for every non-zero point in the grid the closest point on the surface. |
|
Computes the intersection between surface and a grid. |
|
Computes the intersection between the surface and a grid spanning the bounding box with given voxel size. |
|
Signed distance from the surface to a grid with size shape in mm. |
bounding¶
closest_point¶
-
mcot.surface.grid.closest_point(points, grid, orientation, test_orientation=False, max_dist=inf)[source]¶ Find for every point in the grid the closest point on the surface.
- Parameters
points – (3, N) array of points in the grid in voxel coordinates
grid – (Nx, Ny, Nz) array, where all elements that are not -1 will be replaced by the index of the closest point.
orientation – (3, N) array of the hemisphere of each of these vertices (only grid vertices which are in the semi-hemisphere defined by this hemisphere will be considered
max_dist – maximum distance from the surface to consider. Points beyond this maximum are set to -1.
test_orientation – whether to test the hemisphere
closest_surface¶
-
mcot.surface.grid.closest_surface(surface, grid, affine=None, pos_inpr=None, max_dist=inf)[source]¶ Find for every non-zero point in the grid the closest point on the surface.
- Parameters
surface (Mesh2D) – target surface
grid – (Nx, Ny, Nz) array, where for all non-zero elements the closest element on the target surface will be computed
affine – (4, 4) array with the transformation from voxel space to the mm space in which the surface has been defined (default: no transformation)
pos_inpr – whether the normal of the surface vertices should point towards (True) or away (False) from the grid point (default: no such constraint)
max_dist – maximum distance from the surface to consider (in mm). Points beyond this maximum are set to -1.
- Returns
(Nx, Ny, Nz) integer array, which is -1 for all zero elements in grid and contains the indices of the closest surface vertices otherwise
intersect¶
-
mcot.surface.grid.intersect(surface, shape, affine=array([[1.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0], [0.0, 0.0, 1.0, 0.0], [0.0, 0.0, 0.0, 1.0]]))[source]¶ Computes the intersection between surface and a grid.
- Parameters
surface (Mesh2D) – 2D surface in a 3D space that intersects with the grid.
shape (tuple) – tuple of volume shape (nx, ny, nz)
affine (np.ndarray) – (4, 4) array describing the transformation from voxel space to the mm space that the surface is in
- Returns
GridSurfaceIntersection object
intersect_resolution¶
-
mcot.surface.grid.intersect_resolution(surface, resolution=1)[source]¶ Computes the intersection between the surface and a grid spanning the bounding box with given voxel size.
- Parameters
surface (Mesh2D) – 2D surface in a 3D space
resolution (float) – voxel size
- Returns
GridSurfaceIntersection object
signed_distance¶
-
mcot.surface.grid.signed_distance(surface, shape, affine=None)[source]¶ Signed distance from the surface to a grid with size shape in mm.
Calls out to workbench to do the actual calculation.
- Parameters
surface (Mesh2D) – reference surface
shape – (Nx, Ny, Nz) tuple defining the shape of the grid
affine – (4, 4) array transforming the voxel to mm coordinates (default: no transformation)
- Returns
(Nx, Ny, Nz)-array with the signed distance from the surface (negative inside the brain)