CortidQCT.h File Reference

This file contains the C API definition. More...

#include <stddef.h>

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Classes
struct	CQCT_VoxelVolumeSize
	VoxelVolume size. More...
struct	CQCT_VoxelVolumeVoxelSize
	VoxelVolume voxel size. More...
struct	CQCT_BarycentricPoint_t
	Barycentric point type. More...
struct	CQCT_Ray_t
	Ray type. More...
struct	CQCT_RayMeshIntersection

Typedefs
Custom Color To Label Map
typedef struct CQCT_ColorToLabelMap_t *	CQCT_ColorToLabelMap
	ColorToLabelMap handle type.

Functions
ColorToLabelMap object type
CQCT_EXTERN CQCT_ColorToLabelMap	CQCT_createColorToLabelMap ()
	Creates a default color to label map.
CQCT_EXTERN int	CQCT_colorToLabelMapLoadFromFile (CQCT_ColorToLabelMap map, const char *filename, CQCT_Error *error)
	Loads the mapping from YAML file.
CQCT_EXTERN size_t	CQCT_colorToLabelMapEntryCount (CQCT_ColorToLabelMap map)
	Returns number of entries of the map.
CQCT_EXTERN size_t	CQCT_colorToLabelMapCopyEntries (CQCT_ColorToLabelMap map, unsigned int **bufferPtr)
	Copies the entries of the map into the given buffer. More...
CQCT_EXTERN void	CQCT_colorToLabelMapSetEntries (CQCT_ColorToLabelMap map, size_t count, const unsigned int *entries)
	Sets the entries of the mapping.
MeshFitter object type
CQCT_EXTERN CQCT_MeshFitter	CQCT_createMeshFitter (const char *filename, CQCT_Error *error)
	Creates a mesh fitter given the configuration file.
CQCT_EXTERN CQCT_MeshFitterResult	CQCT_meshFitterFit (CQCT_MeshFitter meshFitter, CQCT_VoxelVolume volume)
	Fits the reference mesh to the given voxel volume.
CQCT_EXTERN int	CQCT_meshFitterFitOneIteration (CQCT_MeshFitter meshFitter, CQCT_MeshFitterState state, CQCT_Error *error)
	Runs one iteration of the fitting algorithm.
CQCT_EXTERN int	CQCT_meshFitterVolumeSamplingStep (CQCT_MeshFitter meshFitter, CQCT_MeshFitterState state, CQCT_Error *error)
	Runs the volume sampling step.
CQCT_EXTERN int	CQCT_meshFitterOptimalDisplacementStep (CQCT_MeshFitter meshFitter, CQCT_MeshFitterState state, CQCT_Error *error)
	Runs the displacement optimization step.
CQCT_EXTERN int	CQCT_meshFitterOptimalDeformationStep (CQCT_MeshFitter meshFitter, CQCT_MeshFitterState state, CQCT_Error *error)
	Runs the deformation optimization step.
CQCT_EXTERN int	CQCT_meshFitterLogLikelihoodStep (CQCT_MeshFitter meshFitter, CQCT_MeshFitterState state, CQCT_Error *error)
	Runs the log likelihood computation step.
CQCT_EXTERN int	CQCT_meshFitterConvergenceTestStep (CQCT_MeshFitter meshFitter, CQCT_MeshFitterState state, CQCT_Error *error)
	Runs the convergence testing step.

Generic Functions / Object Type
typedef void *	Id
	Generic 'object' type.
CQCT_EXTERN Id	CQCT_retain (Id obj)
	Retains an object, i.e. increments its retain count.
CQCT_EXTERN void	CQCT_release (Id obj)
CQCT_EXTERN Id	CQCT_autorelease (Id obj)
CQCT_EXTERN void	CQCT_autoreleasePoolPush ()
	Adds a new autorelease pool to the stack.
CQCT_EXTERN void	CQCT_autoreleasePoolPop ()

Error type
enum	CQCT_ErrorId {   CQCT_ErrorId_Unknown, CQCT_ErrorId_InvalidArgument, CQCT_ErrorId_OutOfRange, CQCT_ErrorId_Unknown,   CQCT_ErrorId_InvalidArgument }
	Error types/Ids.
typedef struct CQCT_Error_t *	CQCT_Error
	Error type.
CQCT_EXTERN CQCT_Error	CQCT_createError (enum CQCT_ErrorId id, const char *message)
	Creates an error object.
CQCT_EXTERN enum CQCT_ErrorId	CQCT_errorType (CQCT_Error error)
	Returns the error id.
CQCT_EXTERN const char *	CQCT_errorMessage (CQCT_Error error)
	Returns the error message.

VoxelVolume type
typedef struct CQCT_VoxelVolume_t *	CQCT_VoxelVolume
	Voxel volume handle type.
CQCT_EXTERN CQCT_VoxelVolume	CQCT_createVoxelVolume ()
	Creates an empty voxel volume.
CQCT_EXTERN int	CQCT_voxelVolumeLoadFromFile (CQCT_VoxelVolume volume, const char *filename, CQCT_Error *error)
	Loads the voxel volume from file.
CQCT_EXTERN CQCT_VoxelVolumeSize	CQCT_voxelVolumeSize (CQCT_VoxelVolume volume)
	Returns the size of the voxel volume.
CQCT_EXTERN CQCT_VoxelVolumeVoxelSize	CQCT_voxelVolumeVoxelSize (CQCT_VoxelVolume volume)
	Returns the size of a voxel.
CQCT_EXTERN size_t	CQCT_voxelVolumeCopyVoxels (CQCT_VoxelVolume volume, float **buffer)
	Copies the voxel data to the given buffer.

Mesh type
typedef struct CQCT_Mesh_t *	CQCT_Mesh
	Mesh handle type.
typedef struct CQCT_BarycentricPoint_t	CQCT_BarycentricPoint
typedef struct CQCT_Ray_t	CQCT_Ray
typedef struct CQCT_RayMeshIntersection	CQCT_RayMeshIntersection
CQCT_EXTERN CQCT_Mesh	CQCT_createMesh ()
	Creates an empty mesh.
CQCT_EXTERN CQCT_Mesh	CQCT_createMeshAndAllocateMemory (size_t nVertices, size_t nTriangles, CQCT_Error *error)
	Creates an mesh and reserve space for vertices and indices. More...
CQCT_EXTERN CQCT_Mesh	CQCT_meshFromFile (const char *filename, CQCT_Error *error)
	Creates and loads a mesh from file. More...
CQCT_EXTERN CQCT_Mesh	CQCT_meshFromFileWithCustomMapping (const char *filename, CQCT_ColorToLabelMap map, CQCT_Error *error)
	Creates and loads a mesh from file using the given custom color to label mapping. More...
CQCT_EXTERN CQCT_Mesh	CQCT_meshAndLabelsFromFile (const char *meshFilename, const char *labelFilename, CQCT_Error *error)
	Creates and loads a mesh from a mesh and a label file. More...
CQCT_EXTERN int	CQCT_loadMesh (CQCT_Mesh mesh, const char *filename, CQCT_Error *error)
	Loads a mesh from file.
CQCT_EXTERN int	CQCT_loadMeshWithCustomMapping (CQCT_Mesh mesh, const char *filename, CQCT_ColorToLabelMap map, CQCT_Error *error)
	Loads a mesh from file using a custom color to label map.
CQCT_EXTERN int	CQCT_loadMeshAndLabels (CQCT_Mesh mesh, const char *meshFilename, const char *labelFilename, CQCT_Error *error)
	Loads a mesh from mesh and label file.
CQCT_EXTERN int	CQCT_meshAndLabelsWriteToFile (CQCT_Mesh mesh, const char *meshFilename, const char *labelsFilename, CQCT_Error *error)
	Writes mesh and labels to seperate files.
CQCT_EXTERN size_t	CQCT_meshVertexCount (CQCT_Mesh mesh)
	Return number of vertices of the given mesh.
CQCT_EXTERN size_t	CQCT_meshTriangleCount (CQCT_Mesh mesh)
	Return number of triangles of the given mesh.
CQCT_EXTERN size_t	CQCT_meshCopyVertices (CQCT_Mesh mesh, float **bufferPtr)
	Copies the mesh's vertices into the given buffer. More...
CQCT_EXTERN void	CQCT_meshSetVertices (CQCT_Mesh mesh, float const *buffer)
	Copies the vertices from the given buffer into the mesh data structure. More...
CQCT_EXTERN size_t	CQCT_meshCopyVertexNormals (CQCT_Mesh mesh, float **bufferPtr)
	Copies the mesh's per-vertex normals into the given buffer. More...
CQCT_EXTERN void	CQCT_meshSetVertexNormals (CQCT_Mesh mesh, float const *buffer)
	Copies the per-vertex normals from the given buffer into the mesh data structure. More...
CQCT_EXTERN size_t	CQCT_meshCopyTriangles (CQCT_Mesh mesh, ptrdiff_t **bufferPtr)
	Copies the mesh's indices into the given buffer. More...
CQCT_EXTERN void	CQCT_meshSetTriangles (CQCT_Mesh mesh, ptrdiff_t const *buffer)
	Copies the triangle indices from the given buffer into the mesh data structure. More...
CQCT_EXTERN size_t	CQCT_meshCopyLabels (CQCT_Mesh mesh, unsigned int **bufferPtr)
	Copies the mesh's labels into the given buffer. More...
CQCT_EXTERN void	CQCT_meshSetLabels (CQCT_Mesh mesh, unsigned int const *buffer)
	Copies the vertex labels from the given buffer into the mesh data structure. More...
CQCT_EXTERN int	CQCT_meshBarycentricToCartesian (CQCT_Mesh mesh, CQCT_BarycentricPoint const *barycentricPtr, size_t nPoints, float **bufferPtr, CQCT_Error *error)
	Converts the given list of barycentric points in cartesian coordinates. More...
CQCT_EXTERN int	CQCT_meshBarycentricInterpolation (CQCT_Mesh mesh, CQCT_BarycentricPoint const *barycentricPtr, size_t nPoints, float const *attributePtr, size_t attributeDimensions, float **bufferPtr, CQCT_Error *error)
	Interpolates attribute values given at mesh vertices at arbitrary points on the surface of the mesh. More...
CQCT_EXTERN size_t	CQCT_meshRayIntersections (CQCT_Mesh mesh, CQCT_Ray *raysPtr, size_t nRays, CQCT_RayMeshIntersection **intersectionsOutPtr)
	Computes the intersection of a set of rays with the mesh. More...
CQCT_EXTERN void	CQCT_meshUpsample (CQCT_Mesh mesh, size_t nTimes)
	Upsamples the given mesh nTimes without touchting the original vertices. More...
CQCT_EXTERN void	CQCT_meshUpdatePerVertexNormals (CQCT_Mesh mesh)
	Re-computes per-vertex normals. More...

MeshFitterState object type
typedef struct CQCT_MeshFitter_t *	CQCT_MeshFitter
	Mesh fitter handle type.
typedef struct CQCT_MeshFitterState_t *	CQCT_MeshFitterState
	Mesh fitter state handle type.
typedef CQCT_MeshFitterState	CQCT_MeshFitterResult
	Mesh fitter result object.
CQCT_EXTERN CQCT_MeshFitterState	CQCT_createMeshFitterState (CQCT_MeshFitter fitter, CQCT_VoxelVolume volume)
	Creates an MeshFitter optimization state object.
CQCT_EXTERN CQCT_Mesh	CQCT_meshFitterResultReferenceMesh (CQCT_MeshFitterResult result)
	Returns the result reference mesh.
CQCT_EXTERN CQCT_Mesh	CQCT_meshFitterResultMesh (CQCT_MeshFitterResult result)
	Returns the result mesh.
CQCT_EXTERN size_t	CQCT_meshFitterResultCopyDisplacementVector (CQCT_MeshFitterResult result, float **buffer)
	Copies the displacement vector.
CQCT_EXTERN void	CQCT_meshFitterResultSetDisplacementVector (CQCT_MeshFitterResult result, float const *buffer)
	Sets the displacement vector.
CQCT_EXTERN size_t	CQCT_meshFitterResultCopyWeights (CQCT_MeshFitterResult result, float **buffer)
	Copies the weight vector.
CQCT_EXTERN void	CQCT_meshFitterResultSetWeights (CQCT_MeshFitterResult result, float const *buffer)
	Sets the weight vector.
CQCT_EXTERN size_t	CQCT_meshFitterResultCopyVertexNormals (CQCT_MeshFitterResult result, float **buffer) __attribute__((deprecated("Use normals stored in deformedMesh instead.")))
CQCT_EXTERN size_t	CQCT_meshFitterResultVolumeSamplingPositionsCount (CQCT_MeshFitterResult result)
	Returns the number of volume sampling positions.
CQCT_EXTERN size_t	CQCT_meshFitterResultCopyVolumeSamplingPositions (CQCT_MeshFitterResult result, float **buffer)
	Copies the volume sampling positions.
CQCT_EXTERN size_t	CQCT_meshFitterResultCopyVolumeSamples (CQCT_MeshFitterResult result, float **buffer)
	Copies the volume samples.
CQCT_EXTERN float	CQCT_meshFitterResultMinimumDisplacementNorm (CQCT_MeshFitterResult result)
	Returns the minimum norm of the displacement vector.
CQCT_EXTERN float	CQCT_meshFitterResultLogLikelihood (CQCT_MeshFitterResult result)
	Returns the current log likelihood of the model given the input volume.
CQCT_EXTERN float	CQCT_meshFitterResultCopyPerVertexLogLikelihood (CQCT_MeshFitterResult result, float **buffer)
CQCT_EXTERN void	CQCT_meshFitterResultSetLogLikelihood (CQCT_MeshFitterResult result, float ll)
	Sets the current log likelihood of the model given the input volume.
CQCT_EXTERN float	CQCT_meshFitterResultEffectiveSigmaS (CQCT_MeshFitterResult result)
	Returns the current effective sigmaS (after applying decay)
CQCT_EXTERN size_t	CQCT_meshFitterResultIterationCount (CQCT_MeshFitterResult result)
	Returns the iteration count.
CQCT_EXTERN void	CQCT_meshFitterResultSetIterationCount (CQCT_MeshFitterResult result, size_t count)
	Sets the iteration count.
CQCT_EXTERN int	CQCT_meshFitterResultHasConverged (CQCT_MeshFitterResult result)
	Returns whether the optimization has converged.
CQCT_EXTERN void	CQCT_meshFitterResultSetHasConverged (CQCT_MeshFitterResult result, int converged)
	Sets whether the optimization has converged.
CQCT_EXTERN int	CQCT_meshFitterResultSuccess (CQCT_MeshFitterResult result)
	Returns whether the optimization was successfull.
CQCT_EXTERN void	CQCT_meshFitterResultSetSuccess (CQCT_MeshFitterResult result, int success)
	Sets whether the optimization was successfull.
CQCT_EXTERN size_t	CQCT_meshFitterResultNonDecreasingCount (CQCT_MeshFitterResult result)
	Returns the current non decreasing count.
CQCT_EXTERN void	CQCT_meshFitterResultSetNonDecreasingCount (CQCT_MeshFitterResult result, size_t count)
	Sets the current non decreasing count.
CQCT_EXTERN size_t	CQCT_meshFitterStateCopyModelSamplingPositions (CQCT_MeshFitterState state, float **buffer)
	Copies the model sampling positions.

Detailed Description

This file contains the C API definition.

Author

Stefan Reinhold

Copyright

Copyright (C) 2018 Stefan Reinhold – All Rights Reserved. You may use, distribute and modify this code under the terms of the AFL 3.0 license; see LICENSE for full license details.