#include <EmbedSurface.hpp>

Public Member Functions
	EmbedSurface (const std::vector< std::string > &img_filenames, const std::vector< Matrix4d > &img_transform={}, const double tol_rel=-1, const double tol_abs=-1, const bool split_connected_components=false, const io::ComponentIO *component_io=nullptr, const bool record_history=false)
	Input from meshes.

const history::SurfaceHistory &	input_history () const
	With record_history: the files as read, concatenated, then what became of them on the way to the arrangement – the weld, the transform, the split into components and the concatenation as one relabel, and the simplification's own edits.

FacetSources &	facet_sources ()
	With record_history, once embedded: the input triangles each surface facet lies on.

void	simplify_surface (const double eps, const bool use_exact, const int num_threads=0, const double boundary_eps=0)
	Simplify the input surface while staying within the eps envelope.

void	remove_duplicates (const double eps)
	Merge vertices that are closer than eps.

bool	embed_surface (const bool flood_fill=false, const bool tag_from_winding_number=true, const bool provenance=false)
	Run the arrangement and tag the resulting cells.

void	consolidate ()
	Remove unreferenced vertices.

const MatrixXd &	V_emb () const

const MatrixXr &	V_emb_r () const

const MatrixXd &	V_surface () const

const MatrixXi &	T_emb () const

const MatrixSi &	T_tags () const

const MatrixXi &	F_on_surface () const

const std::vector< std::vector< size_t > > &	F_tags_surface () const
	Per row of F_on_surface(): the inputs tiling it. Empty unless embed_surface recorded it.

const std::vector< std::vector< int > > &	F_tags_surface_orientation () const

const MatrixXi &	F_surface () const

const std::vector< size_t > &	F_input () const
	Per row of F_surface(): the input it came from, SIZE_MAX for none.

void	write_surf_off (const std::string &filename) const
	Write surface as read from image.

void	write_emb_surf_off (const std::string &filename) const
	Write embedded surface.

void	write_emb_msh (const std::string &filename) const

void	write_emb_vtu (const std::string &filename) const

std::pair< Vector3d, Vector3d >	bbox_minmax () const

std::pair< Vector3d, Vector3d >	bbox_surf_minmax () const

std::vector< Eigen::Vector3d >	V_surf_to_vector () const

std::vector< std::array< size_t, 3 > >	F_surf_to_vector () const

Public Attributes
bool	m_smooth_surface = false

bool	m_perform_sanity_checks = false

int	m_num_threads = 0

Private Member Functions
void	V_surf_from_vector (const std::vector< Eigen::Vector3d > &verts)

void	F_surf_from_vector (const std::vector< std::array< size_t, 3 > > &tris)

void	tag_from_winding_number ()
	One binary tag column per input, set where that input's winding number at a tet barycenter is at least 0.5. Auto-corrects an inside-out input and warns when an input claims nothing, as the 2D EmbedCurves::tag_from_winding_number does.

void	tag_from_provenance ()
	Decide the cell tags from the arrangement's surface provenance.

void	check_tag_surface_invariant (const std::string &how) const
	Count where the tagging and the arrangement's surface disagree.

Private Attributes
bool	m_record_history = false

history::SurfaceHistory	m_input_history

FacetSources	m_facet_sources

std::vector< std::string >	m_img_filenames

std::vector< ImageData >	m_img_datas

MatrixXd	m_V_surface

MatrixXi	m_F_surface

std::vector< size_t >	m_F_input

std::vector< std::vector< size_t > >	m_F_tags_surface

std::vector< std::vector< int > >	m_F_tags_surface_orientation

std::vector< size_t >	modified_nonmanifold_v

MatrixXd	m_V_emb

MatrixXr	m_V_emb_r

MatrixXi	m_T_emb

MatrixXi	m_F_on_surface

MatrixSi	m_T_tags

std::vector< std::set< int64_t > >	m_tags

std::vector< MatrixXd >	Vs

std::vector< MatrixXi >	Fs

Detailed Description

A class for reading an image and converting it into a tet mesh.

Constructor & Destructor Documentation

◆ EmbedSurface()

wmtk::components::simwild::EmbedSurface::EmbedSurface	(	const std::vector< std::string > &	img_filenames,
		const std::vector< Matrix4d > &	img_transform = `{}`,
		const double	tol_rel = `-1`,
		const double	tol_abs = `-1`,
		const bool	split_connected_components = `false`,
		const io::ComponentIO *	component_io = `nullptr`,
		const bool	record_history = `false`
	)

Input from meshes.

Parameters

split_connected_components Treat each connected component of an input file as an input in its own right, rather than the file as a whole. What counts as "an input" is what gets its own tag column and its own winding-number evaluation, so a file holding several disjoint closed surfaces is tagged as one region with this off, and as one region per component with it on. Off by default.

Note that the inputs then outnumber the files, so input_names – which is applied by position – no longer lines up with the filenames; components past the end of that list fall back to the generic tag_N names.

Member Function Documentation

◆ check_tag_surface_invariant()

void wmtk::components::simwild::EmbedSurface::check_tag_surface_invariant ( const std::string & how ) const

private

Count where the tagging and the arrangement's surface disagree.

Everything downstream reads the surface off the tags – SimWildMesh marks a face as surface exactly when its two tets' tags differ – so a tagging is only right if it reproduces the surface the arrangement computed. Diagnostic, under DEBUG_sanity_checks.

◆ embed_surface()

bool wmtk::components::simwild::EmbedSurface::embed_surface	(	const bool	flood_fill = `false`,
		const bool	tag_from_winding_number = `true`,
		const bool	provenance = `false`
	)

Run the arrangement and tag the resulting cells.

Parameters

flood_fill	Unify the tags of each region bounded by the surface.
tag_from_winding_number	Decide each cell's tags by evaluating the winding number of every input at its centroid (the default), rather than by propagating them across the arrangement's own surface provenance. See tag_from_provenance.
provenance	Also record which inputs tile each surface face (F_tags_surface()), which the provenance tagging records anyway.

Only do a trivial rounding here. The more complex rounding is performed later on.

Cluster tags by flood-filling regions that are bounded by the surface. All tags within one region are unified by taking the tag with most occurances.

This is for several reasons not the best way to do this.

The tags should be volume-weighted so that the tag that represents the most volume should be picked.
We should not rely on geometric look-up at all, but use the information stored in m_F_tags_surface. This is more work so I took a shortcut here.

◆ F_tags_surface_orientation()

const std::vector< std::vector< int > > & wmtk::components::simwild::EmbedSurface::F_tags_surface_orientation ( ) const

inline

Parallel to F_tags_surface(): each input's direction on the row, +1 along its vertex order, -1 against, 0 where its triangles face both ways.

◆ simplify_surface()

void wmtk::components::simwild::EmbedSurface::simplify_surface	(	const double	eps,
		const bool	use_exact,
		const int	num_threads = `0`,
		const double	boundary_eps = `0`
	)

Simplify the input surface while staying within the eps envelope.

Parameters

eps	The absolute envelope thickness.
use_exact	Whether the envelope uses the exact predicate rather than the sampled one. The simwild application passes !simplify_use_sample_envelope.
boundary_eps	How the open boundary is held: 0 freezes it; positive lets it move within a tube of this radius around the input's boundary edges. See ShortestEdgeCollapse::create_mesh.

◆ tag_from_provenance()

void wmtk::components::simwild::EmbedSurface::tag_from_provenance ( )

private

Decide the cell tags from the arrangement's surface provenance.

The exact alternative to tag_from_winding_number. m_F_tags_surface says which inputs each surface face belongs to, so tags propagate combinatorially: start from a cell of the padded box, which is outside everything, and walk the tet adjacency graph toggling membership of input i whenever a face belonging to input i is crossed. Every input surface is closed, so the parity along any two paths to the same cell agrees; if it does not, the input was not closed and this throws rather than returning a tagging that depends on the traversal order.

◆ write_emb_surf_off()

void wmtk::components::simwild::EmbedSurface::write_emb_surf_off ( const std::string & filename ) const

Write embedded surface.

This writes all the vertices that exist in the volume and all triangles that are representing the embedded surface.

◆ write_surf_off()

void wmtk::components::simwild::EmbedSurface::write_surf_off ( const std::string & filename ) const

Write surface as read from image.

The surface is all the contours in the image, i.e., the surface in between voxels with different value.

The documentation for this class was generated from the following files:

components/simwild/wmtk/components/simwild/EmbedSurface.hpp
components/simwild/wmtk/components/simwild/EmbedSurface.cpp

Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ EmbedSurface()

Member Function Documentation

◆ check_tag_surface_invariant()

◆ embed_surface()

◆ F_tags_surface_orientation()

◆ simplify_surface()

◆ tag_from_provenance()

◆ write_emb_surf_off()

◆ write_surf_off()