DataSerializer - Abstract base class for format-agnostic DIC data I/O. More...

Namespaces
namespace	detail

namespace	input

namespace	log

namespace	stepsABC

Classes
struct	BaseParameters
	Base parameters structure Contains fundamental paths and settings for DIC analysis Equivalent to base_parameters struct in Matlab. More...

class	BinarySerializer

struct	CalibrationData
	Calibration data. More...

struct	CuncorrDicConfig
	Tunables mirrored onto cuncorr::SessionConfig. More...

struct	CuncorrDicInfo
	Which backend actually ran. More...

class	DataSerializer

struct	DeformationResult
	Deformation result structure Contains all computed deformation and strain measures. More...

struct	DeformData
	Deformation data. More...

struct	DeformGradient
	Deformation gradient tensor. More...

class	DelaunayTriangulation
	DelaunayTriangulation class Provides Delaunay triangulation utilities using CGAL. More...

struct	DIC2DPairResults
	DIC 2D Pair Results Equivalent to MATLAB's DIC2DpairResults. More...

struct	DIC3Dcombined
	DIC 3D Combined Results Equivalent to MATLAB's DIC3Dcombined This represents stitched results from multiple stereo pairs. More...

struct	DIC3DpairResults
	DIC 3D Pair Results (Individual stereo pair) Equivalent to MATLAB's DIC3DpairResults This represents the 3D reconstruction for a single stereo pair. More...

struct	DIC3DPPresults
	DIC 3D Post-Processing Results Equivalent to MATLAB's DIC3DPPresults. More...

struct	DICConstants
	DIC constants Global constants used throughout the DIC analysis. More...

struct	DICInfo
	DIC Info structure (parameters) Matches MATLAB ncorrInfo structure. More...

struct	DispData
	Displacement data. More...

struct	DistortionData
	Distortion data. More...

struct	DLTCalibrationData

struct	FrameDeformationResult
	Frame-based deformation result Contains deformation results for all frames. More...

class	ImageProcessor
	ImageProcessor class Provides image preprocessing operations for DIC analysis. More...

class	JsonSerializer

class	MatReader
	MatReader class Provides utilities for reading MAT files. More...

class	MatSerializer

class	MatWriter
	MatWriter class Provides utilities for writing MAT files with proper xDIC structure. More...

struct	Point3DFrame
	3D Points per frame More...

struct	Points2D
	2D Points per frame More...

struct	ProtocolFileData

struct	ProtocolInfo
	Protocol information structure Contains trial condition information from protocol MAT file. More...

struct	RBMData
	Rigid Body Motion (RBM) data. More...

class	ROIManager
	ROIManager class Manages ROI masks and seed points for DIC analysis. More...

struct	SeedPoint
	Seed point structure Stores seed points in both pixel world (pw) and subset world (sw) coordinates. More...

struct	StepAnalysisInfo
	Step Analysis parameters (for high strain analysis) More...

struct	StepAnalysisParams
	Step analysis parameters structure Contains high strain analysis settings. More...

class	StepDWorkflow
	StepDWorkflow class Implements the complete 2D DIC analysis workflow Equivalent to stepD_2DDIC.m in Matlab. More...

struct	StepParameters
	Step parameters structure for DIC analysis Contains DIC-specific parameters like radius, spacing, cutoff Equivalent to step1_parameters, step2_parameters, step1_2_parameters in Matlab. More...

struct	StrainTensor
	Strain tensor. More...

struct	SubjectTrial
	A single (subject, trial) row, e.g. More...

struct	VisData
	Visualization data container Holds filtered and processed data ready for export. More...

class	Visualization
	Visualization manager class Handles loading, filtering, and exporting DIC results. More...

Typedefs
typedef CGAL::Exact_predicates_inexact_constructions_kernel	K

typedef CGAL::Triangulation_vertex_base_with_info_2< size_t, K >	Vb

typedef CGAL::Triangulation_data_structure_2< Vb >	Tds

typedef CGAL::Delaunay_triangulation_2< K, Tds >	Delaunay

typedef K::Point_2	Point_2

Enumerations
enum class	ExportFormat { VTK , PLY , CSV }
	Visualization export formats. More...

Functions
bool	cuncorr_cuda_available ()
	True if cuNCorr was built with CUDA and a device is present at runtime.

ncorr::DIC_analysis_output	run_cuncorr_dic (const std::vector< ncorr::Image2D > &imgs, const ncorr::ROI2D &roi, const CuncorrDicConfig &cfg, CuncorrDicInfo *info=nullptr)
	Run cuNCorr in sequence mode (fixed reference = imgs[0], warm-start each frame) over the stack against the full-resolution `roi`.

std::vector< double >	computeFaceIsotropyIndex (const std::vector< int > &faces, const std::vector< Eigen::Vector3d > &vertices)
	Compute isotropy index for triangular faces.

double	computeSingleFaceIsotropyIndex (const Eigen::Vector3d &v0, const Eigen::Vector3d &v1, const Eigen::Vector3d &v2)
	Compute isotropy index for a single triangle.

int	matlab_replacebadcorr (ncorr::DIC_analysis_output &data, double level_corr_coef=1.0, double sigma_spatial=1.0, double sigma_temporal=2.0, double shrink_factor=0.9)
	Replaces badly correlated displacement data with spatiotemporally filtered values.

std::vector< cv::Mat >	matlab_imgaussfilt3 (const std::vector< cv::Mat > &volume, double sigma_spatial, double sigma_temporal)
	Applies a 3D Gaussian filter (spatial + temporal) to a volume of 2D fields.

cv::Mat	matlab_shrink_mask (const cv::Mat &mask, double factor)
	Shrinks a binary mask by a scale factor around its centroid.

FrameDeformationResult	computeTriSurfaceDeformation (const std::vector< int > &faces, const std::vector< Eigen::Vector3d > &vertices_ref, const std::vector< std::vector< Eigen::Vector3d > > &vertices_def, bool cumulative=true)
	Compute deformation and strain for triangular surface elements.

DeformationResult	computeSingleFrameDeformation (const std::vector< int > &faces, const std::vector< Eigen::Vector3d > &vertices_ref, const std::vector< Eigen::Vector3d > &vertices_cur)
	Compute deformation for a single frame.

DIC3Dcombined	stitchPairsSimple (const std::vector< DIC3DpairResults > &all_pairs)
	Simple append-based stitching for multiple stereo pairs.

DIC3Dcombined	stitchPairsGeometric (const std::vector< DIC3DpairResults > &all_pairs, const std::vector< int > &pair_order, bool pair_forced=false)
	Geometric stitching with overlap removal and boundary zipping Matches MATLAB's DIC3DsurfaceStitch.m with geometric stitching enabled.

void	setStitchRayAccel (bool enabled)
	Enable/disable the AABB-hierarchy prefilter used by the overlap-removal ray casts.

bool	stitchRayAccel ()
	Current state of the ray-cast prefilter (see setStitchRayAccel).

std::vector< int >	computeMeshBoundary (const std::vector< int > &faces, const std::vector< Eigen::Vector3d > &vertices)
	Compute boundary edges of a triangular mesh Matches MATLAB: patchBoundary(F, V)

std::vector< double >	computeEdgeLengths (const std::vector< int > &faces, const std::vector< Eigen::Vector3d > &vertices)
	Compute edge lengths for all triangles Matches MATLAB: patchEdgeLengths(F, V)

std::pair< std::vector< bool >, std::vector< bool > >	removeOverlapSurfaces (const std::vector< int > &faces1, const std::vector< int > &faces2, const std::vector< Eigen::Vector3d > &vertices1, const std::vector< Eigen::Vector3d > &vertices2, double min_gap, bool pair_forced=false)
	Remove overlapping regions from two surfaces Matches MATLAB: removeOverlapSurface_temp_2018_10_30(F1, F2, V1, V2, [], [], minGap, pairforced)

std::vector< std::vector< int > >	groupBoundaryEdges (const std::vector< int > &boundary_edges)
	Group boundary edges into connected components.

std::vector< int >	edgeListToCurve (const std::vector< int > &edges)
	Convert an unordered list of edges into an ordered curve of vertex indices.

std::vector< int >	zipBoundaryCurves (const std::vector< int > &curve1, const std::vector< int > &curve2, const std::vector< Eigen::Vector3d > &V_combined)
	Zip two boundary curves together by creating a triangle strip.

std::vector< bool >	findAllBoundaryFaces (const std::vector< int > &faces, const std::vector< int > &boundary_edges)
	Remove faces where all 3 edges are on the boundary (degenerate boundary triangles).

std::vector< std::vector< double > >	filterTime (const std::vector< std::vector< double > > &data, double freq_filt=10.0, double freq_acq=50.0)
	Apply temporal Butterworth low-pass filter to displacement data.

std::tuple< std::vector< std::vector< double > >, std::vector< std::vector< double > >, std::vector< std::vector< double > > >	filterTime3D (const std::vector< std::vector< double > > &disp_x, const std::vector< std::vector< double > > &disp_y, const std::vector< std::vector< double > > &disp_z, double freq_filt=10.0, double freq_acq=50.0)
	Apply temporal filtering to 3D displacement vectors.

std::string	trim (const std::string &s)
	Trim leading/trailing whitespace (spaces, tabs, CR, LF).

std::vector< int >	parseTrialList (const std::string &spec)
	Parse a comma/space-separated list of integer trial IDs.

std::vector< int >	readTrialsFile (const std::string &path)
	Read a trials file: one trial ID per line.

std::vector< SubjectTrial >	readSubjectTrialCsv (const std::string &path)
	Read subject_trial.csv (header "subject,trial") into rows, skipping the header line and any blank/comment lines.

int	slurmArrayTaskId ()
	Resolve SLURM_ARRAY_TASK_ID from the environment.

static nlohmann::json	points3dToJson (const Point3DFrame &pts)

static Point3DFrame	points3dFromJson (const nlohmann::json &j)

static nlohmann::json	deformGradientToJson (const DeformGradient &F)

static nlohmann::json	strainTensorToJson (const StrainTensor &E)

static nlohmann::json	deformDataToJson (const DeformData &deform)

template<typename T >
void	writePOD (std::ofstream &ofs, const T &value)

template<typename T >
void	readPOD (std::ifstream &ifs, T &value)

template<typename T >
void	writeVector (std::ofstream &ofs, const std::vector< T > &vec)

template<typename T >
void	readVector (std::ifstream &ifs, std::vector< T > &vec)

void	writeString (std::ofstream &ofs, const std::string &str)

void	readString (std::ifstream &ifs, std::string &str)

template<typename T >
void	writeVector2D (std::ofstream &ofs, const std::vector< std::vector< T > > &vec)

template<typename T >
void	readVector2D (std::ifstream &ifs, std::vector< std::vector< T > > &vec)

void	writePoints3D (std::ofstream &ofs, const Point3DFrame &pts)

void	readPoints3D (std::ifstream &ifs, Point3DFrame &pts)

void	writeDispData (std::ofstream &ofs, const DispData &disp)

void	readDispData (std::ifstream &ifs, DispData &disp)

void	writeCalibrationData (std::ofstream &ofs, const CalibrationData &calib)

void	readCalibrationData (std::ifstream &ifs, CalibrationData &calib)

void	writeDistortionData (std::ofstream &ofs, const DistortionData &dist)

void	writeStringMap (std::ofstream &ofs, const std::map< std::string, std::string > &map)

void	readDistortionData (std::ifstream &ifs, DistortionData &dist)

void	readStringMap (std::ifstream &ifs, std::map< std::string, std::string > &map)

static matvar_t *	createEmptyCharVar (const char *name=nullptr)

static std::vector< Eigen::Vector3d >	computeVertexNormals (const std::vector< int > &faces, const std::vector< Eigen::Vector3d > &vertices)

static double	rayTriangleHit (const Eigen::Vector3d &O, const Eigen::Vector3d &D, const Eigen::Vector3d &A, const Eigen::Vector3d &B, const Eigen::Vector3d &C, double eps)

static std::vector< Eigen::Vector3d >	raySetTriangleIntersect (const std::vector< Eigen::Vector3d > &origins, const std::vector< Eigen::Vector3d > &dirs, const std::vector< int > &faces, const std::vector< Eigen::Vector3d > &vertices, double eps=1e-6)

static std::vector< double >	computeRaySurfaceDistance (const std::vector< Eigen::Vector3d > &V1, const std::vector< Eigen::Vector3d > &N1, const std::vector< int > &F2, const std::vector< Eigen::Vector3d > &V2)

static double	meanFiniteEdgeLength (const std::vector< int > &faces, const std::vector< Eigen::Vector3d > &vertices)

static std::vector< int >	applyFaceMask (const std::vector< int > &F, const std::vector< bool > &CT)

static bool	removeFacesContainingVertex (const std::vector< int > &F, std::vector< bool > &CT, int v_remove)

static std::vector< int >	filterFaces (const std::vector< int > &faces, const std::vector< bool > &keep)

template<typename T >
static std::vector< T >	filterByMask (const std::vector< T > &data, const std::vector< bool > &keep)

static std::vector< std::vector< int > >	buildFaceAdjacency (const std::vector< int > &faces, size_t n_faces)
	Build face adjacency map from triangle connectivity For each face, find all faces that share at least one vertex.

static std::vector< std::array< double, 3 > >	computeFaceCentroids (const Point3DFrame &points, const std::vector< int > &faces, size_t n_faces)
	Compute face centroids from vertices and faces.

static double	computeAverageResolution (const std::vector< std::array< double, 3 > > &centroids, const std::vector< std::vector< int > > &adjacency)
	Compute average resolution (spacing) of face centroids.

static std::vector< std::vector< std::pair< int, int > > >	findKNearestByHops (const std::vector< std::vector< int > > &adjacency, int k)
	Find k-nearest neighbors for each face using BFS on adjacency graph.

static void	designButterworth4 (double Wn, std::vector< double > &b, std::vector< double > &a)
	Design 4th order Butterworth low-pass filter coefficients Equivalent to MATLAB's [B,A] = butter(4, Wn)

static std::vector< double >	filtfilt (const std::vector< double > &b, const std::vector< double > &a, const std::vector< double > &x)
	Apply zero-phase filtering (equivalent to MATLAB's filtfilt) Filters forward and backward to eliminate phase distortion.

static void	fillMissingLinear (std::vector< double > &data)
	Fill missing values (NaN) with linear interpolation Equivalent to MATLAB's fillmissing(d,'linear',1,'EndValues','nearest')

Variables
static size_t	scalar_dims [2] = {1, 1}

static bool	g_stitch_ray_bvh = false

Detailed Description

DataSerializer - Abstract base class for format-agnostic DIC data I/O.

Implementation of visualization module for DIC results.

Temporal Filtering Implementation Port of MATLAB myfilterTime.m and filtfilt.

Surface Stitching Implementation for Multi-Pair 3D Reconstruction Based on Matlab's DIC3DsurfaceStitch.m.

Strain Computation Implementation Direct port of MATLAB triSurfaceDeformation_rewrited.m.

Implementation of StepC stereovision / DLT calibration.

Implementation of MASK + Seed setup for xDIC stepsABC.

ROI and Seed Point Manager for CPPXDIC Implementation of ROI/seed loading and coordinate transformations Based on MATLAB draw_ref_roi.m, draw_ref_seed.m, and map_*.m functions.

MAT File Writer for CPPXDIC Implementation of MAT file writing in xDIC format Produces MATLAB v7.3 (HDF5) compatible output.

MAT File Reader Implementation.

Image processing utilities for CPPXDIC Implementation of saturation and filtering operations Based on MATLAB satur.m and filter_like_ben.m.

Face Isotropy Index Implementation Port of MATLAB faceIsotropyIndex.m.

Implementation of binary serialization for DIC structures.

Delaunay Triangulation Implementation using CGAL.

DataSerializer implementations for mat, bin, and json formats.

Visualization module for DIC results Exports 3D mesh data with deformation/strain fields for visualization Equivalent to MATLAB's plot_singleTrial_map and anim8_rewrited functions.

Trial / (subject, trial) selection helpers for CPPXDIC drivers.

Temporal Filtering for CPPXDIC Port of MATLAB myfilterTime.m.

Surface Stitching for Multi-Pair 3D Reconstruction.

Strain Computation for CPPXDIC Port of MATLAB triSurfaceDeformation_rewrited.m Based on Triangular Cosserat Point Elements (TCPE)

StepC: stereovision / DLT calibration.

MASK + Seed setup for the xDIC stepsABC tool.

Step D: 2D DIC Analysis Workflow for CPPXDIC Complete implementation of stepD_2DDIC from Matlab xDIC Handles the full 2D DIC analysis pipeline.

ROI and Seed Point Manager for CPPXDIC Handles ROI loading/creation and seed point management Equivalent to draw_ref_roi.m, draw_ref_seed.m, and related functions in Matlab xDIC.

Parameter structures for CPPXDIC Encapsulates parameters to avoid passing many arguments between functions Equivalent to parameter structures in Matlab stepD_2DDIC.m.

MATLAB-equivalent functions for DIC processing.

MAT File Writer for CPPXDIC Handles writing DIC results to MATLAB v7.3 (HDF5) format Produces output structure matching xDIC format.

MAT File Reader for CPPXDIC Helper functions for reading MATLAB .mat files using matio.

Image processing utilities for CPPXDIC Handles image saturation and filtering operations Equivalent to satur.m and filter_like_ben.m in Matlab xDIC.

Face Isotropy Index for CPPXDIC Port of MATLAB faceIsotropyIndex.m.

Data structures for DIC results Matches MATLAB xDIC structure format.

Delaunay Triangulation for CPPXDIC CGAL-based implementation matching MATLAB's delaunayTriangulation.

The MATLAB data structure (mat_trees.txt) is the canonical schema. This abstraction allows transparent switching between output formats (.mat, .bin, .json) via a config parameter, without changing pipeline code.

To add a new format, implement a new subclass and register it in create().

Computes triangle regularity/quality metric

Reference: Cappozzo, A., Cappello, A., Della Croce, U., & Pensalfini, F. (1997). Surface-marker cluster design criteria for 3-D bone movement reconstruction. IEEE Transactions on Biomedical Engineering, 44(12), 1165-1174.

These functions replicate specific MATLAB operations used in the xDIC pipeline, prefixed with matlab_ to clearly indicate their origin and purpose.

matlab_replacebadcorr: Equivalent of replacebadcorr() in step2_dic_finish.m
matlab_shrink_mask: Equivalent of shrink_mask.m
matlab_imgaussfilt3: Equivalent of imgaussfilt3() with 'spatial' FilterDomain

Provides interactive (OpenCV highgui) and non-interactive (file/config based) setup of the reference MASK (polygon ROI) and Seed point(s) used to initialise DIC tracking.

This mirrors the MATLAB MultiDIC interactive helpers draw_ref_roi.m and draw_ref_seed.m (polygon ROI via roipoly + seed point picking) but exposes a headless path so the exact same binary runs on a cluster node with no display.

The mask/seed data structures and any persistence to/from the cppxdic MAT format are delegated to cppxdic::ROIManager so this tool does not duplicate ROI/seed logic.

C++ port of MATLAB MultiDIC main_script/stepC_stereovision_calibration.m and the helpers it calls:

generate_cylindrical_calibration_object_coordinate_file.m
STEP1_CalcDLTparameters_rewrited.m (per-camera DLT11 parameter fit)
the DLT reconstruction-error computation

The 11-parameter DLT fit itself reuses the existing Utils::DLT11Calibration helper (src/utils.cpp) so no new linear-algebra path is introduced. Eigen is used for the stereo triangulation least-squares solve, consistent with the rest of the repo.

Reference: Solav, Dana, et al. "Bone pose estimation in the presence of soft tissue artifact using triangular cosserat point elements." Annals of biomedical engineering 44.4 (2016): 1181-1190.

Implements Butterworth low-pass filtering for smoothing displacement time series

Small, header-only utilities shared by the gen_subject_trial generator and the trial-level experiment runner (single trial, SLURM array over a trial list, SLURM array over a subject_trial.csv). Kept self-contained so new targets can include just this header without pulling in the full pipeline.

See matlab_functions.h for documentation.

GUI drawing code is guarded by XDIC_STEPSABC_GUI so the translation unit compiles and links on a headless cluster node where no highgui window backend is available. When GUI support is disabled, runGui() returns a clean error.

Ported from MATLAB MultiDIC stepC_stereovision_calibration.m. The 11-parameter DLT fit reuses Utils::DLT11Calibration; the stereo triangulation uses Eigen (consistent with the rest of the repo).

Typedef Documentation

◆ Delaunay

typedef CGAL::Delaunay_triangulation_2<K, Tds> cppxdic::Delaunay

Definition at line 20 of file delaunay_triangulation.cpp.

◆ K

typedef CGAL::Exact_predicates_inexact_constructions_kernel cppxdic::K

Definition at line 17 of file delaunay_triangulation.cpp.

◆ Point_2

typedef K::Point_2 cppxdic::Point_2

Definition at line 21 of file delaunay_triangulation.cpp.

◆ Tds

typedef CGAL::Triangulation_data_structure_2<Vb> cppxdic::Tds

Definition at line 19 of file delaunay_triangulation.cpp.

◆ Vb

typedef CGAL::Triangulation_vertex_base_with_info_2<size_t, K> cppxdic::Vb

Definition at line 18 of file delaunay_triangulation.cpp.

Enumeration Type Documentation

◆ ExportFormat

enum class cppxdic::ExportFormat

strong

Visualization export formats.

Enumerator
VTK
PLY
CSV

Definition at line 22 of file visualization.h.

Function Documentation

◆ applyFaceMask()

static std::vector< int > cppxdic::applyFaceMask	(	const std::vector< int > &	F,
		const std::vector< bool > &	CT
	)

static

Definition at line 593 of file surface_stitching.cpp.

◆ buildFaceAdjacency()

static std::vector< std::vector< int > > cppxdic::buildFaceAdjacency	(	const std::vector< int > &	faces,
		size_t	n_faces
	)

static

Build face adjacency map from triangle connectivity For each face, find all faces that share at least one vertex.

Parameters

faces	Flattened triangle indices (size = n_faces * 3)
n_faces	Number of faces

Returns: Adjacency list: adj[face_idx] = vector of adjacent face indices

Definition at line 110 of file visualization.cpp.

◆ computeAverageResolution()

static double cppxdic::computeAverageResolution	(	const std::vector< std::array< double, 3 > > &	centroids,
		const std::vector< std::vector< int > > &	adjacency
	)

static

Compute average resolution (spacing) of face centroids.

Parameters

centroids	Face centroid positions
adjacency	Face adjacency list

Returns: Average distance between adjacent face centroids

Definition at line 182 of file visualization.cpp.

◆ computeEdgeLengths()

std::vector< double > cppxdic::computeEdgeLengths	(	const std::vector< int > &	faces,
		const std::vector< Eigen::Vector3d > &	vertices
	)

Compute edge lengths for all triangles Matches MATLAB: patchEdgeLengths(F, V)

Definition at line 263 of file surface_stitching.cpp.

◆ computeFaceCentroids()

static std::vector< std::array< double, 3 > > cppxdic::computeFaceCentroids	(	const Point3DFrame &	points,
		const std::vector< int > &	faces,
		size_t	n_faces
	)

static

Compute face centroids from vertices and faces.

Parameters

points	3D points for the current frame
faces	Flattened triangle indices
n_faces	Number of faces

Returns: Vector of centroids (x, y, z) for each face

Definition at line 156 of file visualization.cpp.

◆ computeFaceIsotropyIndex()

std::vector< double > cppxdic::computeFaceIsotropyIndex	(	const std::vector< int > &	faces,
		const std::vector< Eigen::Vector3d > &	vertices
	)

Compute isotropy index for triangular faces.

The isotropy index measures the "regularity" of a triangle:

Value of 1.0: Perfectly equilateral triangle (most regular)
Value of 0.0: Degenerate triangle (vertices aligned on a line)
NaN: Triangle has NaN vertices

Algorithm:

Compute cluster position model: X = [x1-xa, x2-xa, x3-xa] where xa is centroid
Compute covariance-like matrix: K = X*X'/3
Compute eigenvalues of K
Isotropy index = 2*λ2 / (λ2 + λ3) where λ2 < λ3 are sorted eigenvalues

Parameters

faces	Triangle connectivity (3*nFaces flattened: [v0,v1,v2, v0,v1,v2, ...])
vertices	3D vertex positions (nVertices x 3)

Returns: Isotropy index for each face (nFaces values)

Definition at line 64 of file face_isotropy.cpp.

◆ computeMeshBoundary()

std::vector< int > cppxdic::computeMeshBoundary	(	const std::vector< int > &	faces,
		const std::vector< Eigen::Vector3d > &	vertices
	)

Compute boundary edges of a triangular mesh Matches MATLAB: patchBoundary(F, V)

Parameters

faces	Triangle faces (flat array: [v0,v1,v2, v0,v1,v2, ...])
vertices	Vertex positions

Returns: Boundary edges as pairs [v0,v1, v0,v1, ...]

Definition at line 218 of file surface_stitching.cpp.

◆ computeRaySurfaceDistance()

static std::vector< double > cppxdic::computeRaySurfaceDistance	(	const std::vector< Eigen::Vector3d > &	V1,
		const std::vector< Eigen::Vector3d > &	N1,
		const std::vector< int > &	F2,
		const std::vector< Eigen::Vector3d > &	V2
	)

static

Definition at line 568 of file surface_stitching.cpp.

◆ computeSingleFaceIsotropyIndex()

double cppxdic::computeSingleFaceIsotropyIndex	(	const Eigen::Vector3d &	v0,
		const Eigen::Vector3d &	v1,
		const Eigen::Vector3d &	v2
	)

Compute isotropy index for a single triangle.

Parameters

v0	First vertex position
v1	Second vertex position
v2	Third vertex position

Returns: Isotropy index (0 to 1, or NaN if degenerate)

Definition at line 12 of file face_isotropy.cpp.

◆ computeSingleFrameDeformation()

DeformationResult cppxdic::computeSingleFrameDeformation	(	const std::vector< int > &	faces,
		const std::vector< Eigen::Vector3d > &	vertices_ref,
		const std::vector< Eigen::Vector3d > &	vertices_cur
	)

Compute deformation for a single frame.

Parameters

faces	Triangle connectivity
vertices_ref	Reference vertices
vertices_cur	Current (deformed) vertices

Returns: Deformation result for single frame

Definition at line 14 of file strain_computation.cpp.

◆ computeTriSurfaceDeformation()

FrameDeformationResult cppxdic::computeTriSurfaceDeformation	(	const std::vector< int > &	faces,
		const std::vector< Eigen::Vector3d > &	vertices_ref,
		const std::vector< std::vector< Eigen::Vector3d > > &	vertices_def,
		bool	cumulative = `true`
	)

Compute deformation and strain for triangular surface elements.

Parameters

faces	Triangle connectivity (Nx3, each row is [v1, v2, v3])
vertices_ref	Reference vertex positions (Mx3)
vertices_def	Deformed vertex positions for each frame (vector of Mx3)
cumulative	If true, use first frame as reference; if false, use previous frame

Returns: Frame-based deformation results

Definition at line 319 of file strain_computation.cpp.

◆ computeVertexNormals()

static std::vector< Eigen::Vector3d > cppxdic::computeVertexNormals	(	const std::vector< int > &	faces,
		const std::vector< Eigen::Vector3d > &	vertices
	)

static

Definition at line 298 of file surface_stitching.cpp.

◆ createEmptyCharVar()

static matvar_t * cppxdic::createEmptyCharVar ( const char * name = nullptr )

static

Definition at line 25 of file mat_writer.cpp.

◆ cuncorr_cuda_available()

bool cppxdic::cuncorr_cuda_available ( )

True if cuNCorr was built with CUDA and a device is present at runtime.

Definition at line 47 of file cuncorr_dic.cpp.

◆ deformDataToJson()

static nlohmann::json cppxdic::deformDataToJson ( const DeformData & deform )

static

Definition at line 368 of file data_serializer.cpp.

◆ deformGradientToJson()

static nlohmann::json cppxdic::deformGradientToJson ( const DeformGradient & F )

static

Definition at line 350 of file data_serializer.cpp.

◆ designButterworth4()

static void cppxdic::designButterworth4	(	double	Wn,
		std::vector< double > &	b,
		std::vector< double > &	a
	)

static

Design 4th order Butterworth low-pass filter coefficients Equivalent to MATLAB's [B,A] = butter(4, Wn)

Parameters

Wn	Normalized cutoff frequency (0 to 1, where 1 = Nyquist)
b	Output numerator coefficients (size 5 for 4th order)
a	Output denominator coefficients (size 5 for 4th order)

Definition at line 830 of file visualization.cpp.

◆ edgeListToCurve()

std::vector< int > cppxdic::edgeListToCurve ( const std::vector< int > & edges )

Convert an unordered list of edges into an ordered curve of vertex indices.

Matches MATLAB: edgeListToCurve(E)

Parameters

edges Edge pairs [v0,v1, v0,v1, ...]

Returns: Ordered list of vertex indices forming the curve

Definition at line 933 of file surface_stitching.cpp.

◆ fillMissingLinear()

static void cppxdic::fillMissingLinear ( std::vector< double > & data )

static

Fill missing values (NaN) with linear interpolation Equivalent to MATLAB's fillmissing(d,'linear',1,'EndValues','nearest')

Definition at line 952 of file visualization.cpp.

◆ filterByMask()

template<typename T >

static std::vector< T > cppxdic::filterByMask	(	const std::vector< T > &	data,
		const std::vector< bool > &	keep
	)

static

Definition at line 1065 of file surface_stitching.cpp.

◆ filterFaces()

static std::vector< int > cppxdic::filterFaces	(	const std::vector< int > &	faces,
		const std::vector< bool > &	keep
	)

static

Definition at line 1049 of file surface_stitching.cpp.

◆ filterTime()

std::vector< std::vector< double > > cppxdic::filterTime	(	const std::vector< std::vector< double > > &	data,
		double	freq_filt = `10.0`,
		double	freq_acq = `50.0`
	)

Apply temporal Butterworth low-pass filter to displacement data.

Parameters

data	Input data (nPoints x nFrames) - each column is a time series
freq_filt	Filter cutoff frequency (Hz)
freq_acq	Acquisition/sampling frequency (Hz)
nPoints	Number of spatial points
nFrames	Number of time frames

Returns: Filtered data (same dimensions as input)

Algorithm:

4th order Butterworth low-pass filter
Zero-phase filtering using forward-backward pass (filtfilt)
Boundary padding to reduce edge effects
Preserves NaN values (only filters valid data)

Definition at line 17 of file temporal_filter.cpp.

◆ filterTime3D()

std::tuple< std::vector< std::vector< double > >, std::vector< std::vector< double > >, std::vector< std::vector< double > > > cppxdic::filterTime3D	(	const std::vector< std::vector< double > > &	disp_x,
		const std::vector< std::vector< double > > &	disp_y,
		const std::vector< std::vector< double > > &	disp_z,
		double	freq_filt = `10.0`,
		double	freq_acq = `50.0`
	)

Apply temporal filtering to 3D displacement vectors.

Parameters

disp_x	X-component displacement (nPoints x nFrames)
disp_y	Y-component displacement (nPoints x nFrames)
disp_z	Z-component displacement (nPoints x nFrames)
freq_filt	Filter cutoff frequency (Hz)
freq_acq	Acquisition/sampling frequency (Hz)

Returns: Tuple of (filtered_x, filtered_y, filtered_z)

Definition at line 89 of file temporal_filter.cpp.

◆ filtfilt()

static std::vector< double > cppxdic::filtfilt	(	const std::vector< double > &	b,
		const std::vector< double > &	a,
		const std::vector< double > &	x
	)

static

Apply zero-phase filtering (equivalent to MATLAB's filtfilt) Filters forward and backward to eliminate phase distortion.

Parameters

b	Numerator coefficients
a	Denominator coefficients
x	Input signal

Returns: Filtered signal

Definition at line 885 of file visualization.cpp.

◆ findAllBoundaryFaces()

std::vector< bool > cppxdic::findAllBoundaryFaces	(	const std::vector< int > &	faces,
		const std::vector< int > &	boundary_edges
	)

Remove faces where all 3 edges are on the boundary (degenerate boundary triangles).

Matches MATLAB DIC3DsurfaceStitch lines 127-160.

Parameters

faces	Triangle faces (flat: [v0,v1,v2, ...])
boundary_edges	Boundary edge pairs [v0,v1, ...]

Returns: Boolean mask per face: true = keep, false = remove

Definition at line 972 of file surface_stitching.cpp.

◆ findKNearestByHops()

static std::vector< std::vector< std::pair< int, int > > > cppxdic::findKNearestByHops	(	const std::vector< std::vector< int > > &	adjacency,
		int	k
	)

static

Find k-nearest neighbors for each face using BFS on adjacency graph.

Parameters

adjacency	Face adjacency list
k	Number of neighbors to find

Returns: For each face: vector of (neighbor_idx, distance_in_hops)

Definition at line 208 of file visualization.cpp.

◆ groupBoundaryEdges()

std::vector< std::vector< int > > cppxdic::groupBoundaryEdges ( const std::vector< int > & boundary_edges )

Group boundary edges into connected components.

Matches MATLAB: tesgroup(E)

Parameters

boundary_edges Boundary edges as pairs [v0,v1, v0,v1, ...]

Returns: Vector of groups, each group is a list of edge indices

Definition at line 888 of file surface_stitching.cpp.

◆ matlab_imgaussfilt3()

std::vector< cv::Mat > cppxdic::matlab_imgaussfilt3	(	const std::vector< cv::Mat > &	volume,
		double	sigma_spatial,
		double	sigma_temporal
	)

Applies a 3D Gaussian filter (spatial + temporal) to a volume of 2D fields.

Equivalent to MATLAB imgaussfilt3(volume, sigma, 'FilterDomain', 'spatial', 'padding', 'replicate').

Uses separable filtering: 2D spatial Gaussian per frame, then 1D temporal Gaussian per pixel.

Parameters

volume	Input 3D data as vector of CV_64F Mats (H x W each)
sigma_spatial	Gaussian sigma for spatial (x,y) dimensions
sigma_temporal	Gaussian sigma for temporal (frame) dimension

Returns: Filtered volume (same dimensions)

Definition at line 84 of file matlab_functions.cpp.

◆ matlab_replacebadcorr()

int cppxdic::matlab_replacebadcorr	(	ncorr::DIC_analysis_output &	data,
		double	level_corr_coef = `1.0`,
		double	sigma_spatial = `1.0`,
		double	sigma_temporal = `2.0`,
		double	shrink_factor = `0.9`
	)

Replaces badly correlated displacement data with spatiotemporally filtered values.

Equivalent to MATLAB replacebadcorr() in step2_dic_finish.m.

Algorithm:

Stack displacement fields into 3D volumes (H x W x Nframe)
Identify bad correlation mask: corrcoef > level_corr_coef
Apply 3D Gaussian filter (sigma_spatial, sigma_temporal) with replicate padding
Shrink the valid mask by shrink_factor to avoid border artifacts
Replace only bad-corr points within shrunk mask with filtered values
Repeat filtering + replacement (double pass) for smoother results

Parameters

data	DIC analysis output (modified in-place)
level_corr_coef	Correlation coefficient threshold (MATLAB default: 1.0)
sigma_spatial	Spatial Gaussian sigma (MATLAB default: 1.0)
sigma_temporal	Temporal Gaussian sigma (MATLAB default: 2.0)
shrink_factor	Mask shrink factor to avoid border effects (MATLAB default: 0.9)

Returns: Number of replaced subsets across all frames

Definition at line 163 of file matlab_functions.cpp.

◆ matlab_shrink_mask()

cv::Mat cppxdic::matlab_shrink_mask	(	const cv::Mat &	mask,
		double	factor
	)

Shrinks a binary mask by a scale factor around its centroid.

Equivalent to MATLAB shrink_mask.m:

Find boundary of mask
Compute centroid
Scale polygon by factor around centroid
Fill scaled polygon

Parameters

mask	Input binary mask (CV_8U, nonzero = valid)
factor	Scale factor (0.9 = shrink to 90%)

Returns: Shrunk binary mask (CV_8U)

Definition at line 21 of file matlab_functions.cpp.

◆ meanFiniteEdgeLength()

static double cppxdic::meanFiniteEdgeLength	(	const std::vector< int > &	faces,
		const std::vector< Eigen::Vector3d > &	vertices
	)

static

Definition at line 583 of file surface_stitching.cpp.

◆ parseTrialList()

std::vector< int > cppxdic::parseTrialList ( const std::string & spec )

inline

Parse a comma/space-separated list of integer trial IDs.

Accepts e.g. "7,12,25" or "7 12 25" or "7, 12 , 25".

Definition at line 42 of file trial_selection.h.

◆ points3dFromJson()

static Point3DFrame cppxdic::points3dFromJson ( const nlohmann::json & j )

static

Definition at line 244 of file data_serializer.cpp.

◆ points3dToJson()

static nlohmann::json cppxdic::points3dToJson ( const Point3DFrame & pts )

static

Definition at line 235 of file data_serializer.cpp.

◆ raySetTriangleIntersect()

static std::vector< Eigen::Vector3d > cppxdic::raySetTriangleIntersect	(	const std::vector< Eigen::Vector3d > &	origins,
		const std::vector< Eigen::Vector3d > &	dirs,
		const std::vector< int > &	faces,
		const std::vector< Eigen::Vector3d > &	vertices,
		double	eps = `1e-6`
	)

static

Definition at line 512 of file surface_stitching.cpp.

◆ rayTriangleHit()

static double cppxdic::rayTriangleHit	(	const Eigen::Vector3d &	O,
		const Eigen::Vector3d &	D,
		const Eigen::Vector3d &	A,
		const Eigen::Vector3d &	B,
		const Eigen::Vector3d &	C,
		double	eps
	)

static

Definition at line 328 of file surface_stitching.cpp.

◆ readCalibrationData()

void cppxdic::readCalibrationData	(	std::ifstream &	ifs,
		CalibrationData &	calib
	)

Definition at line 125 of file dic_structures.cpp.

◆ readDispData()

void cppxdic::readDispData	(	std::ifstream &	ifs,
		DispData &	disp
	)

Definition at line 96 of file dic_structures.cpp.

◆ readDistortionData()

void cppxdic::readDistortionData	(	std::ifstream &	ifs,
		DistortionData &	dist
	)

Definition at line 186 of file dic_structures.cpp.

◆ readPOD()

template<typename T >

void cppxdic::readPOD	(	std::ifstream &	ifs,
		T &	value
	)

Definition at line 20 of file dic_structures.cpp.

◆ readPoints3D()

void cppxdic::readPoints3D	(	std::ifstream &	ifs,
		Point3DFrame &	pts
	)

Definition at line 85 of file dic_structures.cpp.

◆ readString()

void cppxdic::readString	(	std::ifstream &	ifs,
		std::string &	str
	)

Definition at line 51 of file dic_structures.cpp.

◆ readStringMap()

void cppxdic::readStringMap	(	std::ifstream &	ifs,
		std::map< std::string, std::string > &	map
	)

Definition at line 214 of file dic_structures.cpp.

◆ readSubjectTrialCsv()

std::vector< SubjectTrial > cppxdic::readSubjectTrialCsv ( const std::string & path )

inline

Read subject_trial.csv (header "subject,trial") into rows, skipping the header line and any blank/comment lines.

Each data line must contain at least two comma-separated fields: subject, trial.

Definition at line 83 of file trial_selection.h.

◆ readTrialsFile()

std::vector< int > cppxdic::readTrialsFile ( const std::string & path )

inline

Read a trials file: one trial ID per line.

Blank lines and lines whose first non-whitespace character is '#' are ignored.

Definition at line 63 of file trial_selection.h.

◆ readVector()

template<typename T >

void cppxdic::readVector	(	std::ifstream &	ifs,
		std::vector< T > &	vec
	)

Definition at line 34 of file dic_structures.cpp.

◆ readVector2D()

template<typename T >

void cppxdic::readVector2D	(	std::ifstream &	ifs,
		std::vector< std::vector< T > > &	vec
	)

Definition at line 70 of file dic_structures.cpp.

◆ removeFacesContainingVertex()

static bool cppxdic::removeFacesContainingVertex	(	const std::vector< int > &	F,
		std::vector< bool > &	CT,
		int	v_remove
	)

static

Definition at line 610 of file surface_stitching.cpp.

◆ removeOverlapSurfaces()

std::pair< std::vector< bool >, std::vector< bool > > cppxdic::removeOverlapSurfaces	(	const std::vector< int > &	faces1,
		const std::vector< int > &	faces2,
		const std::vector< Eigen::Vector3d > &	vertices1,
		const std::vector< Eigen::Vector3d > &	vertices2,
		double	min_gap,
		bool	pair_forced = `false`
	)

Remove overlapping regions from two surfaces Matches MATLAB: removeOverlapSurface_temp_2018_10_30(F1, F2, V1, V2, [], [], minGap, pairforced)

Parameters

faces1	First surface faces
faces2	Second surface faces
vertices1	First surface vertices
vertices2	Second surface vertices
min_gap	Minimum gap threshold for overlap detection

Returns: Pair of boolean masks (keep face 1, keep face 2)

Definition at line 642 of file surface_stitching.cpp.

◆ run_cuncorr_dic()

ncorr::DIC_analysis_output cppxdic::run_cuncorr_dic	(	const std::vector< ncorr::Image2D > &	imgs,
		const ncorr::ROI2D &	roi,
		const CuncorrDicConfig &	cfg,
		CuncorrDicInfo *	info = `nullptr`
	)

Run cuNCorr in sequence mode (fixed reference = imgs[0], warm-start each frame) over the stack against the full-resolution roi.

Returns a raw Lagrangian, pixel-unit DIC_analysis_output on the reduced grid (one Disp2D per current frame).

Exceptions

std::invalid_argument if fewer than 2 images.

Definition at line 53 of file cuncorr_dic.cpp.

◆ setStitchRayAccel()

void cppxdic::setStitchRayAccel ( bool enabled )

Enable/disable the AABB-hierarchy prefilter used by the overlap-removal ray casts.

Off by default. The prefilter is exact (a ray that hits a triangle also hits its padded bounding box, so nothing is pruned that could have been hit) and only changes how many triangles are tested per ray: O(log F) box tests instead of O(F) triangle tests. On rigs with many pairs the brute-force path is the dominant cost of Step E.

Process-wide, set once from Config::step_e_ray_bvh before stitching.

Definition at line 372 of file surface_stitching.cpp.

◆ slurmArrayTaskId()

int cppxdic::slurmArrayTaskId ( )

inline

Resolve SLURM_ARRAY_TASK_ID from the environment.

Returns: the task id, or -1 if the variable is unset/empty.

Definition at line 120 of file trial_selection.h.

◆ stitchPairsGeometric()

DIC3Dcombined cppxdic::stitchPairsGeometric	(	const std::vector< DIC3DpairResults > &	all_pairs,
		const std::vector< int > &	pair_order,
		bool	pair_forced = `false`
	)

Geometric stitching with overlap removal and boundary zipping Matches MATLAB's DIC3DsurfaceStitch.m with geometric stitching enabled.

Parameters

all_pairs	Vector of DIC3DpairResults structures, one per stereo pair
pair_order	Order in which to stitch pairs (1-indexed, matching MATLAB pairIndList)

Returns: Stitched DIC3Dcombined structure with overlaps removed

Definition at line 1077 of file surface_stitching.cpp.

◆ stitchPairsSimple()

DIC3Dcombined cppxdic::stitchPairsSimple ( const std::vector< DIC3DpairResults > & all_pairs )

Simple append-based stitching for multiple stereo pairs.

Simple append-based stitching (no geometric overlap removal) Equivalent to Matlab lines 450-479 (when pairIndList is empty)

Concatenates all pairs together with proper index offsetting. Does not perform geometric overlap removal.

Parameters

all_pairs Vector of DIC3DpairResults structures, one per stereo pair

Returns: Stitched DIC3Dcombined structure with all pairs combined

Definition at line 25 of file surface_stitching.cpp.

◆ stitchRayAccel()

bool cppxdic::stitchRayAccel ( )

Current state of the ray-cast prefilter (see setStitchRayAccel).

Definition at line 373 of file surface_stitching.cpp.

◆ strainTensorToJson()

static nlohmann::json cppxdic::strainTensorToJson ( const StrainTensor & E )

static

Definition at line 359 of file data_serializer.cpp.

◆ trim()

std::string cppxdic::trim ( const std::string & s )

inline

Trim leading/trailing whitespace (spaces, tabs, CR, LF).

Definition at line 30 of file trial_selection.h.

◆ writeCalibrationData()

void cppxdic::writeCalibrationData	(	std::ofstream &	ofs,
		const CalibrationData &	calib
	)

Definition at line 101 of file dic_structures.cpp.

◆ writeDispData()

void cppxdic::writeDispData	(	std::ofstream &	ofs,
		const DispData &	disp
	)

Definition at line 91 of file dic_structures.cpp.

◆ writeDistortionData()

void cppxdic::writeDistortionData	(	std::ofstream &	ofs,
		const DistortionData &	dist
	)

Definition at line 153 of file dic_structures.cpp.

◆ writePOD()

template<typename T >

void cppxdic::writePOD	(	std::ofstream &	ofs,
		const T &	value
	)

Definition at line 15 of file dic_structures.cpp.

◆ writePoints3D()

void cppxdic::writePoints3D	(	std::ofstream &	ofs,
		const Point3DFrame &	pts
	)

Definition at line 79 of file dic_structures.cpp.

◆ writeString()

void cppxdic::writeString	(	std::ofstream &	ofs,
		const std::string &	str
	)

Definition at line 43 of file dic_structures.cpp.

◆ writeStringMap()

void cppxdic::writeStringMap	(	std::ofstream &	ofs,
		const std::map< std::string, std::string > &	map
	)

Definition at line 177 of file dic_structures.cpp.

◆ writeVector()

template<typename T >

void cppxdic::writeVector	(	std::ofstream &	ofs,
		const std::vector< T > &	vec
	)

Definition at line 25 of file dic_structures.cpp.

◆ writeVector2D()

template<typename T >

void cppxdic::writeVector2D	(	std::ofstream &	ofs,
		const std::vector< std::vector< T > > &	vec
	)

Definition at line 61 of file dic_structures.cpp.

◆ zipBoundaryCurves()

std::vector< int > cppxdic::zipBoundaryCurves	(	const std::vector< int > &	curve1,
		const std::vector< int > &	curve2,
		const std::vector< Eigen::Vector3d > &	V_combined
	)

Zip two boundary curves together by creating a triangle strip.

Simplified equivalent of MATLAB's delaunayZip. Uses greedy advancing-front: picks the shorter diagonal at each step.

Parameters

curve1	Ordered vertex indices of boundary curve 1
curve2	Ordered vertex indices of boundary curve 2 (already offset for combined mesh)
V_combined	Combined vertex positions [V1; V2]

Returns: New faces (flat array) connecting the two curves

Definition at line 999 of file surface_stitching.cpp.

Variable Documentation

◆ g_stitch_ray_bvh

bool cppxdic::g_stitch_ray_bvh = false

static

Definition at line 370 of file surface_stitching.cpp.

◆ scalar_dims

size_t cppxdic::scalar_dims[2] = {1, 1}

static

Definition at line 20 of file mat_writer.cpp.

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Detailed Description

Typedef Documentation

◆ Delaunay

◆ K

◆ Point_2

◆ Tds

◆ Vb

Enumeration Type Documentation

◆ ExportFormat

Function Documentation

◆ applyFaceMask()

◆ buildFaceAdjacency()

◆ computeAverageResolution()

◆ computeEdgeLengths()

◆ computeFaceCentroids()

◆ computeFaceIsotropyIndex()

◆ computeMeshBoundary()

◆ computeRaySurfaceDistance()

◆ computeSingleFaceIsotropyIndex()

◆ computeSingleFrameDeformation()

◆ computeTriSurfaceDeformation()

◆ computeVertexNormals()

◆ createEmptyCharVar()

◆ cuncorr_cuda_available()

◆ deformDataToJson()

◆ deformGradientToJson()

◆ designButterworth4()

◆ edgeListToCurve()

◆ fillMissingLinear()

◆ filterByMask()

◆ filterFaces()

◆ filterTime()

◆ filterTime3D()

◆ filtfilt()

◆ findAllBoundaryFaces()

◆ findKNearestByHops()

◆ groupBoundaryEdges()

◆ matlab_imgaussfilt3()

◆ matlab_replacebadcorr()

◆ matlab_shrink_mask()

◆ meanFiniteEdgeLength()

◆ parseTrialList()

◆ points3dFromJson()

◆ points3dToJson()

◆ raySetTriangleIntersect()

◆ rayTriangleHit()

◆ readCalibrationData()

◆ readDispData()

◆ readDistortionData()

◆ readPOD()

◆ readPoints3D()

◆ readString()

◆ readStringMap()

◆ readSubjectTrialCsv()

◆ readTrialsFile()

◆ readVector()

◆ readVector2D()

◆ removeFacesContainingVertex()

◆ removeOverlapSurfaces()

◆ run_cuncorr_dic()

◆ setStitchRayAccel()

◆ slurmArrayTaskId()

◆ stitchPairsGeometric()

◆ stitchPairsSimple()

◆ stitchRayAccel()

◆ strainTensorToJson()

◆ trim()

◆ writeCalibrationData()

◆ writeDispData()

◆ writeDistortionData()

◆ writePOD()

◆ writePoints3D()

◆ writeString()

◆ writeStringMap()