Package gov.nih.mipav.model.algorithms

Class SIFT3D

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.SIFT3D

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class SIFT3D
extends AlgorithmBase

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	SIFT3D.Affine
(package private) class	SIFT3D.CL_data
(package private) class	SIFT3D.Cvec
(package private) class	SIFT3D.Gauss_filter
(package private) class	SIFT3D.GSS_filters
(package private) class	SIFT3D.Hist
private static enum	SIFT3D.im_format
(package private) class	SIFT3D.Image
(package private) static enum	SIFT3D.interp_type
(package private) class	SIFT3D.Kernels
(package private) class	SIFT3D.Keypoint
(package private) class	SIFT3D.Keypoint_store
(package private) class	SIFT3D.Mat_rm
private static enum	SIFT3D.Mat_rm_type
(package private) class	SIFT3D.Mesh
(package private) class	SIFT3D.Pyramid
(package private) class	SIFT3D.Ransac
(package private) class	SIFT3D.Reg_SIFT3D
(package private) class	SIFT3D.Sep_FIR_filter
(package private) class	SIFT3D.SIFT_cl_kernels
(package private) class	SIFT3D.SIFT3D_Descriptor
(package private) class	SIFT3D.SIFT3D_Descriptor_store
(package private) class	SIFT3D.SIFT3DC
(package private) class	SIFT3D.Slab
(package private) class	SIFT3D.Svec
(package private) class	SIFT3D.Tform
(package private) static enum	SIFT3D.tform_type
(package private) class	SIFT3D.Tps
(package private) class	SIFT3D.Tri

Nested classes/interfaces inherited from class java.lang.Thread

Thread.Builder, Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
private final double	bary_eps
private final double	corner_thresh_default
private boolean	CUBOID_EXTREMA
private final double	DBL_EPSILON
private int	DESC_NUM_TOTAL_HIST
private int	DESC_NUMEL
private final double	desc_rad_fctr
private final double	desc_sig_fctr
private String	ext_gz
private String	fileDir
private final double	FLT_EPSILON
private final double	gr
private int	HIST_NUMEL
private boolean	ICOS_HIST
private int	ICOS_NFACES
private int	ICOS_NVERT
private int	IM_NDIMS
private ModelImage	inputImage	This image is to registered to the reference image.
private final double	max_eig_ratio
private int	NBINS_AZ
private int	NBINS_PO
private int	NHIST_PER_DIM
private final int	num_kp_levels_default
private final String	opt_corner_thresh
private final String	opt_num_kp_levels
private final String	opt_peak_thresh
private final String	opt_sigma_n
private final String	opt_sigma0
private final double	ori_grad_thresh
private final double	ori_rad_fctr
private final double	ori_sig_fctr
private final double	peak_thresh_default
private ModelImage	refImage	The inputImage will be registered to this reference image.
private final int	REJECT
private double	SIFT3D_AZ_MAX_F
private final int	SIFT3D_DUPLICATE_SLICES
private double	SIFT3D_err_thresh_default
private final int	SIFT3D_FAILURE
private final int	SIFT3D_FALSE
private final int	SIFT3D_FILE_DOES_NOT_EXIST
private double	SIFT3D_GAUSS_WIDTH_FCTR
private final int	SIFT3D_HELP
private final int	SIFT3D_INCONSISTENT_AXES
private double	SIFT3D_MATCH_MAX_DIST
private double	SIFT3D_nn_thresh_default
private int	SIFT3D_num_iter_default
private boolean	SIFT3D_ORI_SOLID_ANGLE_WEIGHT
private double	SIFT3D_PO_MAX_F
private boolean	SIFT3D_RANSAC_REFINE
private final int	SIFT3D_SINGULAR
private final int	SIFT3D_SUCCESS
private final int	SIFT3D_TRUE
private final int	SIFT3D_UNEVEN_SPACING
private final int	SIFT3D_UNSUPPORTED_FILE_TYPE
private final int	SIFT3D_VERSION
private final int	SIFT3D_WRAPPER_NOT_COMPILED
private final double	sigma_n_default
private final double	sigma0_default
private final double	trunc_thresh
private boolean	useOCL
private ModelImage	warpedImage

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

destFlag, destImage, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, srcImage, threadStopped

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors

Constructor	Description
SIFT3D()	SIFT3D - default constructor.
SIFT3D(ModelImage imageA, ModelImage imageB, double SIFT3D_nn_thresh_default, double SIFT3D_err_thresh_default, int SIFT3D_num_iter_default, boolean useOCL, double SIFT3D_GAUSS_WIDTH_FCTR, double SIFT3D_MATCH_MAX_DIST, boolean ICOS_HIST, boolean SIFT3D_RANSAC_REFINE, boolean CUBOID_EXTREMA, boolean SIFT3D_ORI_SOLID_ANGLE_WEIGHT)

Method Summary

Modifier and Type	Method	Description
private int	_SIFT3D_extract_descriptors(SIFT3D.SIFT3DC sift3d, SIFT3D.Pyramid gpyr, SIFT3D.Keypoint_store kp, SIFT3D.SIFT3D_Descriptor_store desc)
private int	Affine_set_mat(SIFT3D.Mat_rm mat, SIFT3D.Affine affine)
private void	apply_Affine_xyz(SIFT3D.Affine affine, double x_in, double y_in, double z_in, double[] x_out, double[] y_out, double[] z_out)
private int	apply_Sep_FIR_filter(SIFT3D.Image src, SIFT3D.Image dst, SIFT3D.Sep_FIR_filter f, double unit)
private int	assign_eig_ori(SIFT3D.Image im, SIFT3D.Cvec vcenter, double sigma, SIFT3D.Mat_rm R, double[] conf)
private int	assign_orientation_thresh(SIFT3D.Image im, SIFT3D.Cvec vcenter, double sigma, double thresh, SIFT3D.Mat_rm R)
private int	assign_orientations(SIFT3D.SIFT3DC sift3d, SIFT3D.Keypoint_store kp)
private int	build_dog(SIFT3D.SIFT3DC sift3d)
private int	build_gpyr(SIFT3D.SIFT3DC sift3d)
private int	cart2bary(SIFT3D.Cvec cart, SIFT3D.Tri tri, SIFT3D.Cvec bary, double[] k)
private void	cleanup_Affine(SIFT3D.Affine aff)
private void	cleanup_Gauss_filter(SIFT3D.Gauss_filter gauss)
private void	cleanup_GSS_filters(SIFT3D.GSS_filters gss)
private void	cleanup_Keypoint_store(SIFT3D.Keypoint_store kp)
private void	cleanup_Mat_rm(SIFT3D.Mat_rm mat)
private void	cleanup_Mesh(SIFT3D.Mesh mesh)
private void	cleanup_Pyramid(SIFT3D.Pyramid pyr)
private void	cleanup_Reg_SIFT3D(SIFT3D.Reg_SIFT3D reg)
private void	cleanup_Sep_FIR_filter(SIFT3D.Sep_FIR_filter f)
private void	cleanup_SIFT3D(SIFT3D.SIFT3DC sift3d)
private void	cleanup_SIFT3D_Descriptor_store(SIFT3D.SIFT3D_Descriptor_store desc)
private void	cleanup_Slab(SIFT3D.Slab slab)
private boolean	CMP_CUBE_GT(SIFT3D.Image im, int x, int y, int z, int IGNORESELF, double val)
private boolean	CMP_CUBE_LT(SIFT3D.Image im, int x, int y, int z, int IGNORESELF, double val)
private boolean	CMP_CUR_GT(SIFT3D.Image im, int x, int y, int z, double val)
private boolean	CMP_CUR_LT(SIFT3D.Image im, int x, int y, int z, double val)
private boolean	CMP_NEXT_GT(SIFT3D.Image im, int x, int y, int z, double val)
private boolean	CMP_NEXT_LT(SIFT3D.Image im, int x, int y, int z, double val)
private boolean	CMP_PREV_GT(SIFT3D.Image im, int x, int y, int z, double val)
private boolean	CMP_PREV_LT(SIFT3D.Image im, int x, int y, int z, double val)
private int	convert_Mat_rm(SIFT3D.Mat_rm in, SIFT3D.Mat_rm out, SIFT3D.Mat_rm_type type)
private int	convolve_sep(SIFT3D.Image src, SIFT3D.Image dst, SIFT3D.Sep_FIR_filter f, int dim, double unit)
private int	convolve_sep_gen(SIFT3D.Image src, SIFT3D.Image dst, SIFT3D.Sep_FIR_filter f, int dim, double unit)
private int	convolve_sep_sym(SIFT3D.Image src, SIFT3D.Image dst, SIFT3D.Sep_FIR_filter f, int dim, double unit)
private int	copy_Affine(SIFT3D.Affine src, SIFT3D.Affine dst)
(package private) int	copy_Keypoint(SIFT3D.Keypoint src, SIFT3D.Keypoint dst)
private int	copy_Mat_rm(SIFT3D.Mat_rm src, SIFT3D.Mat_rm dst)
private int	Cvec_to_sbins(SIFT3D.Cvec vd, SIFT3D.Svec bins)
private int	detect_extrema(SIFT3D.SIFT3DC sift3d, SIFT3D.Keypoint_store kp)
private int	eigen_Mat_rm(SIFT3D.Mat_rm A, SIFT3D.Mat_rm Q, SIFT3D.Mat_rm L)
private int	extract_descrip(SIFT3D.SIFT3DC sift3d, SIFT3D.Image im, SIFT3D.Keypoint key, SIFT3D.SIFT3D_Descriptor desc)
private int	find_tform_ransac(SIFT3D.Ransac ran, SIFT3D.Mat_rm src, SIFT3D.Mat_rm ref, SIFT3D.Affine tform)
private double	fmodf(double in1, double in2)
ModelImage	getResultImage()
private void	hist_zero(SIFT3D.Hist hist)
private int	icos_hist_bin(SIFT3D.SIFT3DC sift3d, SIFT3D.Cvec x, SIFT3D.Cvec bary, int[] bin)
private int	im_copy_data(SIFT3D.Image src, SIFT3D.Image dst)
private int	im_copy_dims(SIFT3D.Image src, SIFT3D.Image dst)
private void	im_default_stride(SIFT3D.Image im)
private int	im_downsample_2x(SIFT3D.Image src, SIFT3D.Image dst)
private void	im_free(SIFT3D.Image im)
private void	IM_GET_GRAD_ISO(SIFT3D.Image im, int x, int y, int z, int c, SIFT3D.Cvec vd)
private int	im_inv_transform(SIFT3D.Affine tform, SIFT3D.Image src, SIFT3D.interp_type interp, int resize, SIFT3D.Image dst)
private double	im_max_abs(SIFT3D.Image im)
private int	im_permute(SIFT3D.Image src, int dim1, int dim2, SIFT3D.Image dst)
private int	im_resize(SIFT3D.Image im)
private void	im_scale(SIFT3D.Image im)
private int	im_subtract(SIFT3D.Image src1, SIFT3D.Image src2, SIFT3D.Image dst)
private void	im_zero(SIFT3D.Image im)
private int	im2mm(SIFT3D.Mat_rm im, double[] units, SIFT3D.Mat_rm mm)
private int	init_Affine(SIFT3D.Affine affine, int dim)
private int	init_cl_SIFT3D(SIFT3D.SIFT3DC sift3d)
private int	init_Gauss_filter(SIFT3D.Gauss_filter gauss, double sigma, int dim)
(package private) int	init_Gauss_incremental_filter(SIFT3D.Gauss_filter gauss, double s_cur, double s_next, int dim)
private int	init_geometry(SIFT3D.SIFT3DC sift3d)
private void	init_GSS_filters(SIFT3D.GSS_filters gss)
private void	init_im(SIFT3D.Image im)
private int	init_Keypoint(SIFT3D.Keypoint key)
private void	init_Keypoint_store(SIFT3D.Keypoint_store kp)
private int	init_Mat_rm(SIFT3D.Mat_rm mat, int num_rows, int num_cols, SIFT3D.Mat_rm_type type, int set_zero)
private int	init_Mat_rm_p(SIFT3D.Mat_rm mat, double[][] p, int num_rows, int num_cols, SIFT3D.Mat_rm_type type, int set_zero)
private void	init_Mesh(SIFT3D.Mesh mesh)
private void	init_Pyramid(SIFT3D.Pyramid pyr)
private void	init_Ransac(SIFT3D.Ransac ran)
private int	init_Reg_SIFT3D(SIFT3D.Reg_SIFT3D reg)
private int	init_Sep_FIR_filter(SIFT3D.Sep_FIR_filter f, int dim, int width, double[] kernel, int symmetric)
private int	init_SIFT3D(SIFT3D.SIFT3DC sift3d)
private void	init_SIFT3D_Descriptor_store(SIFT3D.SIFT3D_Descriptor_store desc)
private void	init_Slab(SIFT3D.Slab slab)
private double	lanczos(double x, double a)
private double	log2(double x)
private int	make_affine_matrix(SIFT3D.Mat_rm pts_in, int dim, SIFT3D.Mat_rm mat_out)
(package private) int	make_gss(SIFT3D.GSS_filters gss, SIFT3D.Pyramid pyr)
private int	match_desc(SIFT3D.SIFT3D_Descriptor desc, SIFT3D.SIFT3D_Descriptor_store store, double nn_thresh)
private int	mm2im(double[] src_units, double[] ref_units, SIFT3D.Affine aff)
private int[]	n_choose_k(int n, int k, int[] status_out)
private void	normalize_desc(SIFT3D.SIFT3D_Descriptor desc)
private int[]	ransac(SIFT3D.Mat_rm src, SIFT3D.Mat_rm ref, SIFT3D.Ransac ran, SIFT3D.Affine tform, int[] cset, int[] len, int[] status_out)
private void	refine_Hist(SIFT3D.Hist hist)
private int	register_SIFT3D(SIFT3D.Reg_SIFT3D reg, SIFT3D.Affine tform)
private double	resample_lanczos2(SIFT3D.Image im, double x, double y, double z, int c)
private double	resample_linear(SIFT3D.Image in, double x, double y, double z, int c)
private int	resize_Keypoint_store(SIFT3D.Keypoint_store kp, int num)
private int	resize_Mat_rm(SIFT3D.Mat_rm mat)
(package private) int	resize_Pyramid(SIFT3D.Image im, int first_level, int num_kp_levels, int num_levels, int first_octave, int num_octaves, SIFT3D.Pyramid pyr)
private int	resize_SIFT3D(SIFT3D.SIFT3DC sift3d, int num_kp_levels)
private int	resize_SIFT3D_Descriptor_store(SIFT3D.SIFT3D_Descriptor_store desc, int num)
void	runAlgorithm()	Actually runs the algorithm.
private void	SAMP_AND_ACC(SIFT3D.Image src, SIFT3D.Image dst, double tap, double[] coords, int x, int y, int z, int c, int dim)
private int	set_corner_thresh_SIFT3D(SIFT3D.SIFT3DC sift3d, double corner_thresh)
private int	set_im_Reg_SIFT3D(SIFT3D.Reg_SIFT3D reg, SIFT3D.Image im, double[] units, SIFT3D.SIFT3D_Descriptor_store desc)
private int	set_im_SIFT3D(SIFT3D.SIFT3DC sift3d, SIFT3D.Image im)
private int	set_num_kp_levels_SIFT3D(SIFT3D.SIFT3DC sift3d, int num_kp_levels)
private int	set_peak_thresh_SIFT3D(SIFT3D.SIFT3DC sift3d, double peak_thresh)
private int	set_ref_Reg_SIFT3D(SIFT3D.Reg_SIFT3D reg, SIFT3D.Image ref)
private int	set_scales_Pyramid(double sigma0, double sigma_n, SIFT3D.Pyramid pyr)
private int	set_scales_SIFT3D(SIFT3D.SIFT3DC sift3d, double sigma0, double sigma_n)
private int	set_sigma_n_SIFT3D(SIFT3D.SIFT3DC sift3d, double sigma_n)
private int	set_sigma0_SIFT3D(SIFT3D.SIFT3DC sift3d, double sigma0)
private int	set_src_Reg_SIFT3D(SIFT3D.Reg_SIFT3D reg, SIFT3D.Image src)
private void	SIFT3D_CVEC_CROSS(SIFT3D.Cvec in1, SIFT3D.Cvec in2, SIFT3D.Cvec out)
private double	SIFT3D_CVEC_DOT(SIFT3D.Cvec in1, SIFT3D.Cvec in2)
private double	SIFT3D_CVEC_L2_NORM(SIFT3D.Cvec cvec)
private double	SIFT3D_CVEC_L2_NORM_SQ(SIFT3D.Cvec cvec)
private void	SIFT3D_CVEC_MINUS(SIFT3D.Cvec ca, SIFT3D.Cvec cb, SIFT3D.Cvec cc)
private void	SIFT3D_CVEC_PLUS(SIFT3D.Cvec ca, SIFT3D.Cvec cb, SIFT3D.Cvec cc)
private void	SIFT3D_CVEC_SCALE(SIFT3D.Cvec cvec, double a)
private void	SIFT3D_CVEC_TO_SVEC(SIFT3D.Cvec cvec, SIFT3D.Svec svec)
private void	SIFT3D_desc_acc_interp(SIFT3D.SIFT3DC sift3d, SIFT3D.Cvec vbins, SIFT3D.Cvec grad, SIFT3D.SIFT3D_Descriptor desc)
private int	SIFT3D_detect_keypoints(SIFT3D.SIFT3DC sift3d, SIFT3D.Image im, SIFT3D.Keypoint_store kp)
private int	SIFT3D_extract_descriptors(SIFT3D.SIFT3DC sift3d, SIFT3D.Keypoint_store kp, SIFT3D.SIFT3D_Descriptor_store desc)
private SIFT3D.Gauss_filter	SIFT3D_GAUSS_GET(SIFT3D.GSS_filters gss, int s)
private int	SIFT3D_have_gpyr(SIFT3D.SIFT3DC sift3d)
private boolean	SIFT3D_IM_CONTAINS_CVEC(SIFT3D.Image im, SIFT3D.Cvec cvec)
private void	SIFT3D_IM_GET_GRAD(SIFT3D.Image im, int x, int y, int z, int c, SIFT3D.Cvec vd)
private int	SIFT3D_matches_to_Mat_rm(SIFT3D.SIFT3D_Descriptor_store d1, SIFT3D.SIFT3D_Descriptor_store d2, int[] matches, SIFT3D.Mat_rm match1, SIFT3D.Mat_rm match2)
private void	SIFT3D_MUL_MAT_RM_CVEC(SIFT3D.Mat_rm mat, SIFT3D.Cvec v_in, SIFT3D.Cvec v_out)
private int[]	SIFT3D_nn_match(SIFT3D.SIFT3D_Descriptor_store d1, SIFT3D.SIFT3D_Descriptor_store d2, double nn_thresh, int[] status_out)
private SIFT3D.Image	SIFT3D_PYR_IM_GET(SIFT3D.Pyramid pyr, int o, int s)
private int	SIFT3D_PYR_LAST_LEVEL(SIFT3D.Pyramid pyr)
private int	SIFT3D_PYR_LAST_OCTAVE(SIFT3D.Pyramid pyr)
private void	SIFT3D_RESIZE_SLAB(SIFT3D.Slab slab, int num_new)
(package private) int	solve_Mat_rm(SIFT3D.Mat_rm A, SIFT3D.Mat_rm B, double limit, SIFT3D.Mat_rm X)
(package private) int	solve_Mat_rm_ls(SIFT3D.Mat_rm A, SIFT3D.Mat_rm B, SIFT3D.Mat_rm X)
private int	solve_system(SIFT3D.Mat_rm src, SIFT3D.Mat_rm ref, SIFT3D.Affine tform)
private double	tform_err_sq(SIFT3D.Affine tform, SIFT3D.Mat_rm src, SIFT3D.Mat_rm ref, int i)
private int	transpose_Mat_rm(SIFT3D.Mat_rm src, SIFT3D.Mat_rm dst)
private int	verify_keys(SIFT3D.Keypoint_store kp, SIFT3D.Image im)
private int	write_Affine(String path, SIFT3D.Affine affine)
private int	write_Mat_rm(String path, SIFT3D.Mat_rm mat)
private int	zero_Mat_rm(SIFT3D.Mat_rm mat)

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, finalize, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, getSrcImage, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setSrcImage, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Thread

activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, isVirtual, join, join, join, join, ofPlatform, ofVirtual, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, sleep, start, startVirtualThread, stop, suspend, threadId, toString, yield

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details

inputImage

private ModelImage inputImage

This image is to registered to the reference image.

refImage

private ModelImage refImage

The inputImage will be registered to this reference image.

warpedImage

private ModelImage warpedImage

SIFT3D_nn_thresh_default

private double SIFT3D_nn_thresh_default

SIFT3D_err_thresh_default

private double SIFT3D_err_thresh_default

SIFT3D_num_iter_default

private int SIFT3D_num_iter_default

useOCL

private boolean useOCL

SIFT3D_GAUSS_WIDTH_FCTR

private double SIFT3D_GAUSS_WIDTH_FCTR

SIFT3D_MATCH_MAX_DIST

private double SIFT3D_MATCH_MAX_DIST

ICOS_HIST

private boolean ICOS_HIST

SIFT3D_RANSAC_REFINE

private boolean SIFT3D_RANSAC_REFINE

CUBOID_EXTREMA

private boolean CUBOID_EXTREMA

SIFT3D_ORI_SOLID_ANGLE_WEIGHT

private boolean SIFT3D_ORI_SOLID_ANGLE_WEIGHT

fileDir

private String fileDir

ext_gz

private String ext_gz

SIFT3D_SINGULAR

private final int SIFT3D_SINGULAR

See Also:

• Constant Field Values

SIFT3D_SUCCESS

private final int SIFT3D_SUCCESS

See Also:

• Constant Field Values

SIFT3D_FAILURE

private final int SIFT3D_FAILURE

See Also:

• Constant Field Values

SIFT3D_HELP

private final int SIFT3D_HELP

See Also:

• Constant Field Values

SIFT3D_VERSION

private final int SIFT3D_VERSION

See Also:

• Constant Field Values

SIFT3D_FILE_DOES_NOT_EXIST

private final int SIFT3D_FILE_DOES_NOT_EXIST

See Also:

• Constant Field Values

SIFT3D_UNSUPPORTED_FILE_TYPE

private final int SIFT3D_UNSUPPORTED_FILE_TYPE

See Also:

• Constant Field Values

SIFT3D_WRAPPER_NOT_COMPILED

private final int SIFT3D_WRAPPER_NOT_COMPILED

See Also:

• Constant Field Values

SIFT3D_UNEVEN_SPACING

private final int SIFT3D_UNEVEN_SPACING

See Also:

• Constant Field Values

SIFT3D_INCONSISTENT_AXES

private final int SIFT3D_INCONSISTENT_AXES

See Also:

• Constant Field Values

SIFT3D_DUPLICATE_SLICES

private final int SIFT3D_DUPLICATE_SLICES

See Also:

• Constant Field Values

SIFT3D_TRUE

private final int SIFT3D_TRUE

See Also:

• Constant Field Values

SIFT3D_FALSE

private final int SIFT3D_FALSE

See Also:

• Constant Field Values

NBINS_AZ

private int NBINS_AZ

NBINS_PO

private int NBINS_PO

NHIST_PER_DIM

private int NHIST_PER_DIM

IM_NDIMS

private int IM_NDIMS

ICOS_NFACES

private int ICOS_NFACES

ICOS_NVERT

private int ICOS_NVERT

SIFT3D_AZ_MAX_F

private double SIFT3D_AZ_MAX_F

SIFT3D_PO_MAX_F

private double SIFT3D_PO_MAX_F

HIST_NUMEL

private int HIST_NUMEL

DESC_NUM_TOTAL_HIST

private int DESC_NUM_TOTAL_HIST

DESC_NUMEL

private int DESC_NUMEL

REJECT

private final int REJECT

See Also:

• Constant Field Values

peak_thresh_default

private final double peak_thresh_default

See Also:

• Constant Field Values

num_kp_levels_default

private final int num_kp_levels_default

See Also:

• Constant Field Values

corner_thresh_default

private final double corner_thresh_default

See Also:

• Constant Field Values

sigma_n_default

private final double sigma_n_default

See Also:

• Constant Field Values

sigma0_default

private final double sigma0_default

See Also:

• Constant Field Values

opt_peak_thresh

private final String opt_peak_thresh

See Also:

• Constant Field Values

opt_corner_thresh

private final String opt_corner_thresh

See Also:

• Constant Field Values

opt_num_kp_levels

private final String opt_num_kp_levels

See Also:

• Constant Field Values

opt_sigma_n

private final String opt_sigma_n

See Also:

• Constant Field Values

opt_sigma0

private final String opt_sigma0

See Also:

• Constant Field Values

max_eig_ratio

private final double max_eig_ratio

See Also:

• Constant Field Values

ori_grad_thresh

private final double ori_grad_thresh

See Also:

• Constant Field Values

FLT_EPSILON

private final double FLT_EPSILON

See Also:

• Constant Field Values

DBL_EPSILON

private final double DBL_EPSILON

See Also:

• Constant Field Values

bary_eps

private final double bary_eps

See Also:

• Constant Field Values

ori_sig_fctr

private final double ori_sig_fctr

See Also:

• Constant Field Values

ori_rad_fctr

private final double ori_rad_fctr

See Also:

• Constant Field Values

desc_sig_fctr

private final double desc_sig_fctr

See Also:

• Constant Field Values

desc_rad_fctr

private final double desc_rad_fctr

See Also:

• Constant Field Values

trunc_thresh

private final double trunc_thresh

gr

private final double gr

Constructor Details

SIFT3D

public SIFT3D()

SIFT3D - default constructor.

SIFT3D

public SIFT3D(ModelImage imageA,
 ModelImage imageB,
 double SIFT3D_nn_thresh_default,
 double SIFT3D_err_thresh_default,
 int SIFT3D_num_iter_default,
 boolean useOCL,
 double SIFT3D_GAUSS_WIDTH_FCTR,
 double SIFT3D_MATCH_MAX_DIST,
 boolean ICOS_HIST,
 boolean SIFT3D_RANSAC_REFINE,
 boolean CUBOID_EXTREMA,
 boolean SIFT3D_ORI_SOLID_ANGLE_WEIGHT)

Parameters:

imageA - Reference image (register input image to reference image).

imageB - Input image (register input image to reference image).

SIFT3D_nn_thresh_default -

SIFT3D_err_thresh_default -

SIFT3D_num_iter_default -

useOCL -

SIFT3D_GAUSS_WIDTH_FCTR -

Method Details

runAlgorithm

public void runAlgorithm()

Description copied from class: AlgorithmBase

Actually runs the algorithm. Implemented by inheriting algorithms.

Specified by:

runAlgorithm in class AlgorithmBase

init_im

private void init_im(SIFT3D.Image im)

init_Affine

private int init_Affine(SIFT3D.Affine affine,
 int dim)

init_Mat_rm

private int init_Mat_rm(SIFT3D.Mat_rm mat,
 int num_rows,
 int num_cols,
 SIFT3D.Mat_rm_type type,
 int set_zero)

resize_Mat_rm

private int resize_Mat_rm(SIFT3D.Mat_rm mat)

cleanup_Mat_rm

private void cleanup_Mat_rm(SIFT3D.Mat_rm mat)

zero_Mat_rm

private int zero_Mat_rm(SIFT3D.Mat_rm mat)

cleanup_Affine

private void cleanup_Affine(SIFT3D.Affine aff)

init_Reg_SIFT3D

private int init_Reg_SIFT3D(SIFT3D.Reg_SIFT3D reg)

init_SIFT3D_Descriptor_store

private void init_SIFT3D_Descriptor_store(SIFT3D.SIFT3D_Descriptor_store desc)

init_Ransac

private void init_Ransac(SIFT3D.Ransac ran)

init_SIFT3D

private int init_SIFT3D(SIFT3D.SIFT3DC sift3d)

init_Pyramid

private void init_Pyramid(SIFT3D.Pyramid pyr)

init_GSS_filters

private void init_GSS_filters(SIFT3D.GSS_filters gss)

init_geometry

private int init_geometry(SIFT3D.SIFT3DC sift3d)

init_Mat_rm_p

private int init_Mat_rm_p(SIFT3D.Mat_rm mat,
 double[][] p,
 int num_rows,
 int num_cols,
 SIFT3D.Mat_rm_type type,
 int set_zero)

init_Mesh

private void init_Mesh(SIFT3D.Mesh mesh)

SIFT3D_CVEC_L2_NORM

private double SIFT3D_CVEC_L2_NORM(SIFT3D.Cvec cvec)

SIFT3D_CVEC_SCALE

private void SIFT3D_CVEC_SCALE(SIFT3D.Cvec cvec,
 double a)

SIFT3D_CVEC_MINUS

private void SIFT3D_CVEC_MINUS(SIFT3D.Cvec ca,
 SIFT3D.Cvec cb,
 SIFT3D.Cvec cc)

SIFT3D_CVEC_PLUS

private void SIFT3D_CVEC_PLUS(SIFT3D.Cvec ca,
 SIFT3D.Cvec cb,
 SIFT3D.Cvec cc)

SIFT3D_CVEC_CROSS

private void SIFT3D_CVEC_CROSS(SIFT3D.Cvec in1,
 SIFT3D.Cvec in2,
 SIFT3D.Cvec out)

SIFT3D_CVEC_DOT

private double SIFT3D_CVEC_DOT(SIFT3D.Cvec in1,
 SIFT3D.Cvec in2)

init_cl_SIFT3D

private int init_cl_SIFT3D(SIFT3D.SIFT3DC sift3d)

set_sigma_n_SIFT3D

private int set_sigma_n_SIFT3D(SIFT3D.SIFT3DC sift3d,
 double sigma_n)

set_scales_SIFT3D

private int set_scales_SIFT3D(SIFT3D.SIFT3DC sift3d,
 double sigma0,
 double sigma_n)

set_scales_Pyramid

private int set_scales_Pyramid(double sigma0,
 double sigma_n,
 SIFT3D.Pyramid pyr)

SIFT3D_PYR_IM_GET

private SIFT3D.Image SIFT3D_PYR_IM_GET(SIFT3D.Pyramid pyr,
 int o,
 int s)

SIFT3D_PYR_LAST_OCTAVE

private int SIFT3D_PYR_LAST_OCTAVE(SIFT3D.Pyramid pyr)

SIFT3D_PYR_LAST_LEVEL

private int SIFT3D_PYR_LAST_LEVEL(SIFT3D.Pyramid pyr)

make_gss

int make_gss(SIFT3D.GSS_filters gss,
 SIFT3D.Pyramid pyr)

cleanup_GSS_filters

private void cleanup_GSS_filters(SIFT3D.GSS_filters gss)

cleanup_Gauss_filter

private void cleanup_Gauss_filter(SIFT3D.Gauss_filter gauss)

cleanup_Sep_FIR_filter

private void cleanup_Sep_FIR_filter(SIFT3D.Sep_FIR_filter f)

SIFT3D_GAUSS_GET

private SIFT3D.Gauss_filter SIFT3D_GAUSS_GET(SIFT3D.GSS_filters gss,
 int s)

init_Gauss_incremental_filter

int init_Gauss_incremental_filter(SIFT3D.Gauss_filter gauss,
 double s_cur,
 double s_next,
 int dim)

init_Gauss_filter

private int init_Gauss_filter(SIFT3D.Gauss_filter gauss,
 double sigma,
 int dim)

init_Sep_FIR_filter

private int init_Sep_FIR_filter(SIFT3D.Sep_FIR_filter f,
 int dim,
 int width,
 double[] kernel,
 int symmetric)

set_sigma0_SIFT3D

private int set_sigma0_SIFT3D(SIFT3D.SIFT3DC sift3d,
 double sigma0)

set_peak_thresh_SIFT3D

private int set_peak_thresh_SIFT3D(SIFT3D.SIFT3DC sift3d,
 double peak_thresh)

set_corner_thresh_SIFT3D

private int set_corner_thresh_SIFT3D(SIFT3D.SIFT3DC sift3d,
 double corner_thresh)

set_num_kp_levels_SIFT3D

private int set_num_kp_levels_SIFT3D(SIFT3D.SIFT3DC sift3d,
 int num_kp_levels)

resize_SIFT3D

private int resize_SIFT3D(SIFT3D.SIFT3DC sift3d,
 int num_kp_levels)

log2

private double log2(double x)

resize_Pyramid

int resize_Pyramid(SIFT3D.Image im,
 int first_level,
 int num_kp_levels,
 int num_levels,
 int first_octave,
 int num_octaves,
 SIFT3D.Pyramid pyr)

im_free

private void im_free(SIFT3D.Image im)

im_default_stride

private void im_default_stride(SIFT3D.Image im)

im_resize

private int im_resize(SIFT3D.Image im)

cleanup_Reg_SIFT3D

private void cleanup_Reg_SIFT3D(SIFT3D.Reg_SIFT3D reg)

cleanup_SIFT3D_Descriptor_store

private void cleanup_SIFT3D_Descriptor_store(SIFT3D.SIFT3D_Descriptor_store desc)

cleanup_SIFT3D

private void cleanup_SIFT3D(SIFT3D.SIFT3DC sift3d)

cleanup_Pyramid

private void cleanup_Pyramid(SIFT3D.Pyramid pyr)

cleanup_Mesh

private void cleanup_Mesh(SIFT3D.Mesh mesh)

register_SIFT3D

private int register_SIFT3D(SIFT3D.Reg_SIFT3D reg,
 SIFT3D.Affine tform)

SIFT3D_nn_match

private int[] SIFT3D_nn_match(SIFT3D.SIFT3D_Descriptor_store d1,
 SIFT3D.SIFT3D_Descriptor_store d2,
 double nn_thresh,
 int[] status_out)

match_desc

private int match_desc(SIFT3D.SIFT3D_Descriptor desc,
 SIFT3D.SIFT3D_Descriptor_store store,
 double nn_thresh)

SIFT3D_matches_to_Mat_rm

private int SIFT3D_matches_to_Mat_rm(SIFT3D.SIFT3D_Descriptor_store d1,
 SIFT3D.SIFT3D_Descriptor_store d2,
 int[] matches,
 SIFT3D.Mat_rm match1,
 SIFT3D.Mat_rm match2)

im2mm

private int im2mm(SIFT3D.Mat_rm im,
 double[] units,
 SIFT3D.Mat_rm mm)

copy_Mat_rm

private int copy_Mat_rm(SIFT3D.Mat_rm src,
 SIFT3D.Mat_rm dst)

find_tform_ransac

private int find_tform_ransac(SIFT3D.Ransac ran,
 SIFT3D.Mat_rm src,
 SIFT3D.Mat_rm ref,
 SIFT3D.Affine tform)

ransac

private int[] ransac(SIFT3D.Mat_rm src,
 SIFT3D.Mat_rm ref,
 SIFT3D.Ransac ran,
 SIFT3D.Affine tform,
 int[] cset,
 int[] len,
 int[] status_out)

n_choose_k

private int[] n_choose_k(int n,
 int k,
 int[] status_out)

solve_system

private int solve_system(SIFT3D.Mat_rm src,
 SIFT3D.Mat_rm ref,
 SIFT3D.Affine tform)

make_affine_matrix

private int make_affine_matrix(SIFT3D.Mat_rm pts_in,
 int dim,
 SIFT3D.Mat_rm mat_out)

solve_Mat_rm

int solve_Mat_rm(SIFT3D.Mat_rm A,
 SIFT3D.Mat_rm B,
 double limit,
 SIFT3D.Mat_rm X)

transpose_Mat_rm

private int transpose_Mat_rm(SIFT3D.Mat_rm src,
 SIFT3D.Mat_rm dst)

solve_Mat_rm_ls

int solve_Mat_rm_ls(SIFT3D.Mat_rm A,
 SIFT3D.Mat_rm B,
 SIFT3D.Mat_rm X)

Affine_set_mat

private int Affine_set_mat(SIFT3D.Mat_rm mat,
 SIFT3D.Affine affine)

convert_Mat_rm

private int convert_Mat_rm(SIFT3D.Mat_rm in,
 SIFT3D.Mat_rm out,
 SIFT3D.Mat_rm_type type)

tform_err_sq

private double tform_err_sq(SIFT3D.Affine tform,
 SIFT3D.Mat_rm src,
 SIFT3D.Mat_rm ref,
 int i)

apply_Affine_xyz

private void apply_Affine_xyz(SIFT3D.Affine affine,
 double x_in,
 double y_in,
 double z_in,
 double[] x_out,
 double[] y_out,
 double[] z_out)

copy_Affine

private int copy_Affine(SIFT3D.Affine src,
 SIFT3D.Affine dst)

mm2im

private int mm2im(double[] src_units,
 double[] ref_units,
 SIFT3D.Affine aff)

write_Affine

private int write_Affine(String path,
 SIFT3D.Affine affine)

write_Mat_rm

private int write_Mat_rm(String path,
 SIFT3D.Mat_rm mat)

im_inv_transform

private int im_inv_transform(SIFT3D.Affine tform,
 SIFT3D.Image src,
 SIFT3D.interp_type interp,
 int resize,
 SIFT3D.Image dst)

im_copy_dims

private int im_copy_dims(SIFT3D.Image src,
 SIFT3D.Image dst)

resample_linear

private double resample_linear(SIFT3D.Image in,
 double x,
 double y,
 double z,
 int c)

resample_lanczos2

private double resample_lanczos2(SIFT3D.Image im,
 double x,
 double y,
 double z,
 int c)

lanczos

private double lanczos(double x,
 double a)

getResultImage

public ModelImage getResultImage()

set_src_Reg_SIFT3D

private int set_src_Reg_SIFT3D(SIFT3D.Reg_SIFT3D reg,
 SIFT3D.Image src)

set_ref_Reg_SIFT3D

private int set_ref_Reg_SIFT3D(SIFT3D.Reg_SIFT3D reg,
 SIFT3D.Image ref)

set_im_Reg_SIFT3D

private int set_im_Reg_SIFT3D(SIFT3D.Reg_SIFT3D reg,
 SIFT3D.Image im,
 double[] units,
 SIFT3D.SIFT3D_Descriptor_store desc)

init_Keypoint_store

private void init_Keypoint_store(SIFT3D.Keypoint_store kp)

init_Slab

private void init_Slab(SIFT3D.Slab slab)

cleanup_Keypoint_store

private void cleanup_Keypoint_store(SIFT3D.Keypoint_store kp)

cleanup_Slab

private void cleanup_Slab(SIFT3D.Slab slab)

SIFT3D_detect_keypoints

private int SIFT3D_detect_keypoints(SIFT3D.SIFT3DC sift3d,
 SIFT3D.Image im,
 SIFT3D.Keypoint_store kp)

set_im_SIFT3D

private int set_im_SIFT3D(SIFT3D.SIFT3DC sift3d,
 SIFT3D.Image im)

im_copy_data

private int im_copy_data(SIFT3D.Image src,
 SIFT3D.Image dst)

im_max_abs

private double im_max_abs(SIFT3D.Image im)

im_scale

private void im_scale(SIFT3D.Image im)

build_gpyr

private int build_gpyr(SIFT3D.SIFT3DC sift3d)

apply_Sep_FIR_filter

private int apply_Sep_FIR_filter(SIFT3D.Image src,
 SIFT3D.Image dst,
 SIFT3D.Sep_FIR_filter f,
 double unit)

im_permute

private int im_permute(SIFT3D.Image src,
 int dim1,
 int dim2,
 SIFT3D.Image dst)

convolve_sep

private int convolve_sep(SIFT3D.Image src,
 SIFT3D.Image dst,
 SIFT3D.Sep_FIR_filter f,
 int dim,
 double unit)

convolve_sep_sym

private int convolve_sep_sym(SIFT3D.Image src,
 SIFT3D.Image dst,
 SIFT3D.Sep_FIR_filter f,
 int dim,
 double unit)

convolve_sep_gen

private int convolve_sep_gen(SIFT3D.Image src,
 SIFT3D.Image dst,
 SIFT3D.Sep_FIR_filter f,
 int dim,
 double unit)

SAMP_AND_ACC

private void SAMP_AND_ACC(SIFT3D.Image src,
 SIFT3D.Image dst,
 double tap,
 double[] coords,
 int x,
 int y,
 int z,
 int c,
 int dim)

im_zero

private void im_zero(SIFT3D.Image im)

im_downsample_2x

private int im_downsample_2x(SIFT3D.Image src,
 SIFT3D.Image dst)

build_dog

private int build_dog(SIFT3D.SIFT3DC sift3d)

im_subtract

private int im_subtract(SIFT3D.Image src1,
 SIFT3D.Image src2,
 SIFT3D.Image dst)

detect_extrema

private int detect_extrema(SIFT3D.SIFT3DC sift3d,
 SIFT3D.Keypoint_store kp)

CMP_PREV_GT

private boolean CMP_PREV_GT(SIFT3D.Image im,
 int x,
 int y,
 int z,
 double val)

CMP_PREV_LT

private boolean CMP_PREV_LT(SIFT3D.Image im,
 int x,
 int y,
 int z,
 double val)

CMP_CUR_GT

private boolean CMP_CUR_GT(SIFT3D.Image im,
 int x,
 int y,
 int z,
 double val)

CMP_CUR_LT

private boolean CMP_CUR_LT(SIFT3D.Image im,
 int x,
 int y,
 int z,
 double val)

CMP_NEXT_GT

private boolean CMP_NEXT_GT(SIFT3D.Image im,
 int x,
 int y,
 int z,
 double val)

CMP_NEXT_LT

private boolean CMP_NEXT_LT(SIFT3D.Image im,
 int x,
 int y,
 int z,
 double val)

CMP_CUBE_GT

private boolean CMP_CUBE_GT(SIFT3D.Image im,
 int x,
 int y,
 int z,
 int IGNORESELF,
 double val)

CMP_CUBE_LT

private boolean CMP_CUBE_LT(SIFT3D.Image im,
 int x,
 int y,
 int z,
 int IGNORESELF,
 double val)

resize_Keypoint_store

private int resize_Keypoint_store(SIFT3D.Keypoint_store kp,
 int num)

SIFT3D_RESIZE_SLAB

private void SIFT3D_RESIZE_SLAB(SIFT3D.Slab slab,
 int num_new)

init_Keypoint

private int init_Keypoint(SIFT3D.Keypoint key)

assign_orientations

private int assign_orientations(SIFT3D.SIFT3DC sift3d,
 SIFT3D.Keypoint_store kp)

copy_Keypoint

int copy_Keypoint(SIFT3D.Keypoint src,
 SIFT3D.Keypoint dst)

assign_orientation_thresh

private int assign_orientation_thresh(SIFT3D.Image im,
 SIFT3D.Cvec vcenter,
 double sigma,
 double thresh,
 SIFT3D.Mat_rm R)

assign_eig_ori

private int assign_eig_ori(SIFT3D.Image im,
 SIFT3D.Cvec vcenter,
 double sigma,
 SIFT3D.Mat_rm R,
 double[] conf)

SIFT3D_IM_CONTAINS_CVEC

private boolean SIFT3D_IM_CONTAINS_CVEC(SIFT3D.Image im,
 SIFT3D.Cvec cvec)

SIFT3D_CVEC_L2_NORM_SQ

private double SIFT3D_CVEC_L2_NORM_SQ(SIFT3D.Cvec cvec)

IM_GET_GRAD_ISO

private void IM_GET_GRAD_ISO(SIFT3D.Image im,
 int x,
 int y,
 int z,
 int c,
 SIFT3D.Cvec vd)

SIFT3D_IM_GET_GRAD

private void SIFT3D_IM_GET_GRAD(SIFT3D.Image im,
 int x,
 int y,
 int z,
 int c,
 SIFT3D.Cvec vd)

eigen_Mat_rm

private int eigen_Mat_rm(SIFT3D.Mat_rm A,
 SIFT3D.Mat_rm Q,
 SIFT3D.Mat_rm L)

SIFT3D_extract_descriptors

private int SIFT3D_extract_descriptors(SIFT3D.SIFT3DC sift3d,
 SIFT3D.Keypoint_store kp,
 SIFT3D.SIFT3D_Descriptor_store desc)

verify_keys

private int verify_keys(SIFT3D.Keypoint_store kp,
 SIFT3D.Image im)

SIFT3D_have_gpyr

private int SIFT3D_have_gpyr(SIFT3D.SIFT3DC sift3d)

_SIFT3D_extract_descriptors

private int _SIFT3D_extract_descriptors(SIFT3D.SIFT3DC sift3d,
 SIFT3D.Pyramid gpyr,
 SIFT3D.Keypoint_store kp,
 SIFT3D.SIFT3D_Descriptor_store desc)

resize_SIFT3D_Descriptor_store

private int resize_SIFT3D_Descriptor_store(SIFT3D.SIFT3D_Descriptor_store desc,
 int num)

extract_descrip

private int extract_descrip(SIFT3D.SIFT3DC sift3d,
 SIFT3D.Image im,
 SIFT3D.Keypoint key,
 SIFT3D.SIFT3D_Descriptor desc)

hist_zero

private void hist_zero(SIFT3D.Hist hist)

SIFT3D_MUL_MAT_RM_CVEC

private void SIFT3D_MUL_MAT_RM_CVEC(SIFT3D.Mat_rm mat,
 SIFT3D.Cvec v_in,
 SIFT3D.Cvec v_out)

SIFT3D_desc_acc_interp

private void SIFT3D_desc_acc_interp(SIFT3D.SIFT3DC sift3d,
 SIFT3D.Cvec vbins,
 SIFT3D.Cvec grad,
 SIFT3D.SIFT3D_Descriptor desc)

icos_hist_bin

private int icos_hist_bin(SIFT3D.SIFT3DC sift3d,
 SIFT3D.Cvec x,
 SIFT3D.Cvec bary,
 int[] bin)

cart2bary

private int cart2bary(SIFT3D.Cvec cart,
 SIFT3D.Tri tri,
 SIFT3D.Cvec bary,
 double[] k)

Cvec_to_sbins

private int Cvec_to_sbins(SIFT3D.Cvec vd,
 SIFT3D.Svec bins)

SIFT3D_CVEC_TO_SVEC

private void SIFT3D_CVEC_TO_SVEC(SIFT3D.Cvec cvec,
 SIFT3D.Svec svec)

fmodf

private double fmodf(double in1,
 double in2)

refine_Hist

private void refine_Hist(SIFT3D.Hist hist)

normalize_desc

private void normalize_desc(SIFT3D.SIFT3D_Descriptor desc)