java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.SIFT3D

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.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 class`	`SIFT3D.im_format`
`(package private) class`	`SIFT3D.Image`
`(package private) static class`	`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 class`	`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 class`	`SIFT3D.tform_type`
`(package private) class`	`SIFT3D.Tps`
`(package private) class`	`SIFT3D.Tri`

Nested classes/interfaces inherited from class java.lang.Thread
java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields
Modifier and Type	Field	Description
`private double`	`bary_eps`
`private double`	`corner_thresh_default`
`private boolean`	`CUBOID_EXTREMA`
`private double`	`DBL_EPSILON`
`private int`	`DESC_NUM_TOTAL_HIST`
`private int`	`DESC_NUMEL`
`private double`	`desc_rad_fctr`
`private double`	`desc_sig_fctr`
`private java.lang.String`	`ext_gz`
`private java.lang.String`	`fileDir`
`private double`	`FLT_EPSILON`
`private 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 double`	`max_eig_ratio`
`private int`	`NBINS_AZ`
`private int`	`NBINS_PO`
`private int`	`NHIST_PER_DIM`
`private int`	`num_kp_levels_default`
`private java.lang.String`	`opt_corner_thresh`
`private java.lang.String`	`opt_num_kp_levels`
`private java.lang.String`	`opt_peak_thresh`
`private java.lang.String`	`opt_sigma_n`
`private java.lang.String`	`opt_sigma0`
`private double`	`ori_grad_thresh`
`private double`	`ori_rad_fctr`
`private double`	`ori_sig_fctr`
`private double`	`peak_thresh_default`
`private ModelImage`	`refImage`	The inputImage will be registered to this reference image.
`private int`	`REJECT`
`private double`	`SIFT3D_AZ_MAX_F`
`private int`	`SIFT3D_DUPLICATE_SLICES`
`private double`	`SIFT3D_err_thresh_default`
`private int`	`SIFT3D_FAILURE`
`private int`	`SIFT3D_FALSE`
`private int`	`SIFT3D_FILE_DOES_NOT_EXIST`
`private double`	`SIFT3D_GAUSS_WIDTH_FCTR`
`private int`	`SIFT3D_HELP`
`private 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 int`	`SIFT3D_SINGULAR`
`private int`	`SIFT3D_SUCCESS`
`private int`	`SIFT3D_TRUE`
`private int`	`SIFT3D_UNEVEN_SPACING`
`private int`	`SIFT3D_UNSUPPORTED_FILE_TYPE`
`private int`	`SIFT3D_VERSION`
`private int`	`SIFT3D_WRAPPER_NOT_COMPILED`
`private double`	`sigma_n_default`
`private double`	`sigma0_default`
`private 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

All Methods Instance Methods Concrete Methods
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(java.lang.String path, SIFT3D.Affine affine)`
`private int`	`write_Mat_rm(java.lang.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, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, suspend, toString, yield

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

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 java.lang.String fileDir
```

ext_gz
```
private java.lang.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 java.lang.String opt_peak_thresh

See Also:: Constant Field Values

opt_corner_thresh

private final java.lang.String opt_corner_thresh

See Also:: Constant Field Values

opt_num_kp_levels

private final java.lang.String opt_num_kp_levels

See Also:: Constant Field Values

opt_sigma_n

private final java.lang.String opt_sigma_n

See Also:: Constant Field Values

opt_sigma0

private final java.lang.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 Detail

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 Detail

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(java.lang.String path,
                         SIFT3D.Affine affine)

write_Mat_rm

private int write_Mat_rm(java.lang.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)

Class SIFT3D

Nested Class Summary

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

Field Summary

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

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

inputImage

refImage

warpedImage

SIFT3D_nn_thresh_default

SIFT3D_err_thresh_default

SIFT3D_num_iter_default

useOCL

SIFT3D_GAUSS_WIDTH_FCTR

SIFT3D_MATCH_MAX_DIST

ICOS_HIST

SIFT3D_RANSAC_REFINE

CUBOID_EXTREMA

SIFT3D_ORI_SOLID_ANGLE_WEIGHT

fileDir

ext_gz

SIFT3D_SINGULAR

SIFT3D_SUCCESS

SIFT3D_FAILURE

SIFT3D_HELP

SIFT3D_VERSION

SIFT3D_FILE_DOES_NOT_EXIST

SIFT3D_UNSUPPORTED_FILE_TYPE

SIFT3D_WRAPPER_NOT_COMPILED

SIFT3D_UNEVEN_SPACING

SIFT3D_INCONSISTENT_AXES

SIFT3D_DUPLICATE_SLICES

SIFT3D_TRUE

SIFT3D_FALSE

NBINS_AZ

NBINS_PO

NHIST_PER_DIM

IM_NDIMS

ICOS_NFACES

ICOS_NVERT

SIFT3D_AZ_MAX_F

SIFT3D_PO_MAX_F

HIST_NUMEL

DESC_NUM_TOTAL_HIST

DESC_NUMEL

REJECT

peak_thresh_default

num_kp_levels_default

corner_thresh_default

sigma_n_default

sigma0_default

opt_peak_thresh

opt_corner_thresh

opt_num_kp_levels

opt_sigma_n

opt_sigma0

max_eig_ratio

ori_grad_thresh

FLT_EPSILON

DBL_EPSILON

bary_eps

ori_sig_fctr

ori_rad_fctr

desc_sig_fctr

desc_rad_fctr

trunc_thresh

gr

Constructor Detail

SIFT3D

SIFT3D

Method Detail

runAlgorithm

init_im

init_Affine