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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class SIFT
extends AlgorithmBase
```
Copyright (C) 2007-11, Andrea Vedaldi and Brian Fulkerson Copyright (C) 2012-13, The VLFeat Team All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`(package private) class`	`SIFT.FitMosaicModel`
`private class`	`SIFT.ikeysComparator`
`(package private) class`	`SIFT.VlFileMeta`
`(package private) class`	`SIFT.VlPgmImage`
`(package private) class`	`SIFT.VlSiftFilt`	------------------------------------------------------------------
`(package private) class`	`SIFT.VlSiftKeypoint`

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 java.lang.String`	`descriptorarg`
`private double`	`edge_thresh`
`private int`	`EOF`
`private double`	`EXPN_MAX`
`private int`	`EXPN_SZ`
`private double[]`	`expn_tab`
`private java.lang.String[]`	`fileDir`
`private java.lang.String[]`	`fileName`
`private int`	`fileNum`
`private boolean`	`force_orientations`
`private java.lang.String`	`framesarg`
`private java.lang.String`	`gssarg`
`private double`	`magnif`
`private java.lang.String`	`metaarg`
`private boolean`	`mosaic`
`private int`	`NBO`
`private int`	`NBP`
`private double`	`norm_thresh`
`private int`	`O`
`private int`	`omin`
`private java.lang.String`	`outarg`
`private double`	`peak_thresh`
`private java.lang.String`	`read_framesarg`
`private boolean`	`readFrames`
`private int`	`S`
`private boolean`	`verbose`
`private double`	`VL_EPSILON_D`
`private float`	`VL_EPSILON_F`
`private int`	`VL_ERR_ALLOC`
`private int`	`VL_ERR_BAD_ARG`
`private int`	`VL_ERR_EOF`
`private int`	`VL_ERR_IO`
`private int`	`VL_ERR_OK`
`private int`	`VL_ERR_OVERFLOW`
`private int`	`VL_ERR_PGM_INV_DATA`
`private int`	`VL_ERR_PGM_INV_HEAD`
`private int`	`VL_ERR_PGM_INV_META`
`private int`	`VL_ERR_PGM_IO`
`private int`	`VL_PAD_BY_CONTINUITY`
`private int`	`VL_PAD_BY_ZERO`
`private int`	`VL_PAD_MASK`
`private int`	`VL_PROT_ASCII`
`private int`	`VL_PROT_BINARY`
`private int`	`VL_PROT_NONE`
`private int`	`VL_PROT_UNKNOWN`
`private boolean`	`VL_SIFT_BILINEAR_ORIENTATIONS`
`private int`	`VL_TRANSPOSE`
`private double`	`window_size`
`private boolean`	`writeDescriptor`
`private boolean`	`writeFrames`
`private boolean`	`writeGss`
`private boolean`	`writeMeta`

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
`SIFT()`	SIFT - default constructor.
SIFT(java.lang.String[] fileDir, java.lang.String[] fileName, boolean mosaic, boolean verbose, java.lang.String outarg, java.lang.String framesarg, java.lang.String descriptorarg, java.lang.String metaarg, java.lang.String read_framesarg, java.lang.String gssarg, int O, int S, int omin, double edge_thresh, double peak_thresh, double norm_thresh, double magnif, double window_size, boolean force_orientations, boolean writeFrames, boolean readFrames, boolean writeDescriptor, boolean writeMeta, boolean writeGss)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`_vl_sift_smooth(SIFT.VlSiftFilt self, float[] outputImage, int output_index, float[] tempImage, float[] inputImage, int input_index, int width, int height, double sigma)`	------------------------------------------------------------------
`private void`	`copy_and_downsample(float[] dst, int dstIndex, float[] src, int srcIndex, int width, int height, int d)`	------------------------------------------------------------------
`private void`	`copy_and_upsample_rows(float[] dst, int dstIndex, float[] src, int srcIndex, int width, int height)`	------------------------------------------------------------------
`private void`	`fast_expn_init()`
`private int`	`findNeighbor(double x, int[] X, int K)`
`private double`	`log2(double x)`
`private float`	`normalize_histogram(float[] buf, int begin, int end)`	------------------------------------------------------------------
`private void`	`PRNFO(java.lang.String name, SIFT.VlFileMeta fm)`
`private void`	`randomize(int[] arr)`
`private double`	`readAsciiDouble(java.io.RandomAccessFile f, int[] err)`
`private int`	`readAsciiInt(java.io.RandomAccessFile f)`
`private int`	`remove_blanks(java.io.RandomAccessFile f, int[] err)`	------------------------------------------------------------------
`private int`	`remove_line(java.io.RandomAccessFile f)`	------------------------------------------------------------------
`void`	`runAlgorithm()`	Actually runs the algorithm.
`private int`	`save_gss(SIFT.VlSiftFilt filt, SIFT.VlFileMeta fm, java.lang.String basename, boolean verbose)`
`private void`	`update_gradient(SIFT.VlSiftFilt f)`	------------------------------------------------------------------
`private void`	`vl_file_meta_close(SIFT.VlFileMeta self)`
`private int`	`vl_file_meta_get_double(int protocol, java.io.RandomAccessFile file, double[] x)`
`private java.io.RandomAccessFile`	`vl_file_meta_open(SIFT.VlFileMeta self, java.lang.String basename, java.lang.String mode, int[] error)`
`private int`	`vl_file_meta_parse(SIFT.VlFileMeta self, java.lang.String optarg)`
`private int`	`vl_file_meta_put_double(int protocol, java.io.RandomAccessFile file, double x)`
`private int`	`vl_file_meta_put_uint8(int protocol, java.io.RandomAccessFile file, byte x)`
`private void`	`vl_imconvcol_vf(float[] dst, int dst_index, int dst_stride, float[] src, int src_index, int src_width, int src_height, int src_stride, float[] filt, int filt_begin, int filt_end, int step, int flags)`
`private double[]`	`vl_imwbackwardmx(int[] X_pt, int[] Y_pt, double[] I_pt, double[][] iwXp_pt, double[][] iwYp_pt, int M, int N)`
`private float[]`	`vl_imwbackwardmx(int[] X_pt, int[] Y_pt, float[] I_pt, double[][] iwXp_pt, double[][] iwYp_pt, int M, int N)`
`private float`	`vl_mod_2pi_f(float x)`
`(package private) int`	`vl_pgm_extract_data(java.io.RandomAccessFile f, SIFT.VlPgmImage im, int[] data)`
`private int`	`vl_pgm_extract_head(java.io.RandomAccessFile f, SIFT.VlPgmImage im)`	------------------------------------------------------------------
`private int`	`vl_pgm_get_bpp(SIFT.VlPgmImage im)`
`private int`	`vl_pgm_get_npixels(SIFT.VlPgmImage im)`
`private int`	`vl_pgm_insert(java.io.RandomAccessFile f, SIFT.VlPgmImage im, byte[] data)`
`private int`	`VL_SHIFT_LEFT(int x, int n)`
`private void`	`vl_sift_calc_keypoint_descriptor(SIFT.VlSiftFilt f, float[] descr, SIFT.VlSiftKeypoint k, double angle0)`	------------------------------------------------------------------
`private int`	`vl_sift_calc_keypoint_orientations(SIFT.VlSiftFilt f, double[] angles, SIFT.VlSiftKeypoint k)`	------------------------------------------------------------------
`private void`	`vl_sift_delete(SIFT.VlSiftFilt f)`	------------------------------------------------------------------
`private void`	`vl_sift_detect(SIFT.VlSiftFilt f)`	------------------------------------------------------------------
`private float[]`	`vl_sift_get_octave(SIFT.VlSiftFilt f, int s, int[] octave_index)`	------------------------------------------------------------------
`private void`	`vl_sift_keypoint_init(SIFT.VlSiftFilt f, SIFT.VlSiftKeypoint k, double x, double y, double sigma)`	------------------------------------------------------------------
`(package private) SIFT.VlSiftFilt`	`vl_sift_new(int width, int height, int noctaves, int nlevels, int o_min)`
`private int`	`vl_sift_process_first_octave(SIFT.VlSiftFilt f, float[] im)`
`private int`	`vl_sift_process_next_octave(SIFT.VlSiftFilt f)`	------------------------------------------------------------------
`private java.lang.String`	`vl_string_basename(java.lang.String destination, int destinationSize, java.lang.String source, int maxNumStrippedExtensions, int[] num)`	------------------------------------------------------------------
`private java.lang.String`	`vl_string_copy_sub(java.lang.String destination, int destinationSize, java.lang.String source, int beginning, int end, int[] num)`	------------------------------------------------------------------
`private java.lang.String`	`vl_string_parse_protocol(java.lang.String string, int[] protocol)`	------------------------------------------------------------------
`private java.lang.String`	`vl_string_protocol_name(int protocol)`	------------------------------------------------------------------
`private java.lang.String`	`vl_string_replace_wildcard(java.lang.String destination, int destinationSize, java.lang.String source, java.lang.String wildcardChar, java.lang.String escapeChar, java.lang.String replacement, int[] num)`	------------------------------------------------------------------

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
  - VL_ERR_OK
```
private final int VL_ERR_OK
```
    See Also:
    
    Constant Field Values
  - VL_ERR_OVERFLOW
```
private final int VL_ERR_OVERFLOW
```
    See Also:
    
    Constant Field Values
    
    VL_ERR_ALLOC
    
    private final int VL_ERR_ALLOC
    
    See Also:
    
    Constant Field Values
    
    VL_ERR_BAD_ARG
    
    private final int VL_ERR_BAD_ARG
    
    See Also:
    
    Constant Field Values
    
    VL_ERR_IO
    
    private final int VL_ERR_IO
    
    See Also:
    
    Constant Field Values
    
    VL_ERR_EOF
    
    private final int VL_ERR_EOF
    
    See Also:
    
    Constant Field Values
    
    VL_PROT_UNKNOWN
    
    private final int VL_PROT_UNKNOWN
    
    See Also:
    
    Constant Field Values
    
    VL_PROT_NONE
    
    private final int VL_PROT_NONE
    
    See Also:
    
    Constant Field Values
    
    VL_PROT_ASCII
    
    private final int VL_PROT_ASCII
    
    See Also:
    
    Constant Field Values
    
    VL_PROT_BINARY
    
    private final int VL_PROT_BINARY
    
    See Also:
    
    Constant Field Values
    
    VL_ERR_PGM_INV_HEAD
    
    private final int VL_ERR_PGM_INV_HEAD
    
    See Also:
    
    Constant Field Values
    
    VL_ERR_PGM_INV_META
    
    private final int VL_ERR_PGM_INV_META
    
    See Also:
    
    Constant Field Values
    
    VL_ERR_PGM_INV_DATA
    
    private final int VL_ERR_PGM_INV_DATA
    
    See Also:
    
    Constant Field Values
    
    VL_ERR_PGM_IO
    
    private final int VL_ERR_PGM_IO
    
    See Also:
    
    Constant Field Values
    
    EOF
    
    private final int EOF
    
    See Also:
    
    Constant Field Values
    
    fileDir
    
    private java.lang.String[] fileDir
    
    fileName
    
    private java.lang.String[] fileName
    
    fileNum
    
    private int fileNum
    
    mosaic
    
    private boolean mosaic
    
    verbose
    
    private boolean verbose
    
    outarg
    
    private java.lang.String outarg
    
    framesarg
    
    private java.lang.String framesarg
    
    descriptorarg
    
    private java.lang.String descriptorarg
    
    metaarg
    
    private java.lang.String metaarg
    
    read_framesarg
    
    private java.lang.String read_framesarg
    
    gssarg
    
    private java.lang.String gssarg
    
    O
    
    private int O
    
    S
    
    private int S
    
    omin
    
    private int omin
    
    edge_thresh
    
    private double edge_thresh
    
    peak_thresh
    
    private double peak_thresh
    
    norm_thresh
    
    private double norm_thresh
    
    magnif
    
    private double magnif
    
    window_size
    
    private double window_size
    
    force_orientations
    
    private boolean force_orientations
    
    writeFrames
    
    private boolean writeFrames
    
    readFrames
    
    private boolean readFrames
    
    writeDescriptor
    
    private boolean writeDescriptor
    
    writeMeta
    
    private boolean writeMeta
    
    writeGss
    
    private boolean writeGss
    
    NBO
    
    private int NBO
    
    NBP
    
    private int NBP
    
    EXPN_SZ
    
    private int EXPN_SZ
    
    EXPN_MAX
    
    private double EXPN_MAX
    
    expn_tab
    
    private double[] expn_tab
    
    VL_PAD_BY_ZERO
    
    private int VL_PAD_BY_ZERO
    
    VL_PAD_BY_CONTINUITY
    
    private int VL_PAD_BY_CONTINUITY
    
    VL_PAD_MASK
    
    private int VL_PAD_MASK
    
    VL_TRANSPOSE
    
    private int VL_TRANSPOSE
    
    VL_EPSILON_F
    
    private float VL_EPSILON_F
    
    VL_EPSILON_D
    
    private double VL_EPSILON_D
    
    VL_SIFT_BILINEAR_ORIENTATIONS
    
    private boolean VL_SIFT_BILINEAR_ORIENTATIONS
    
    Constructor Detail
    
    SIFT
    
    public SIFT()
    
    SIFT - default constructor.
    
    SIFT
    
    public SIFT(java.lang.String[] fileDir, java.lang.String[] fileName, boolean mosaic, boolean verbose, java.lang.String outarg, java.lang.String framesarg, java.lang.String descriptorarg, java.lang.String metaarg, java.lang.String read_framesarg, java.lang.String gssarg, int O, int S, int omin, double edge_thresh, double peak_thresh, double norm_thresh, double magnif, double window_size, boolean force_orientations, boolean writeFrames, boolean readFrames, boolean writeDescriptor, boolean writeMeta, boolean writeGss)
    
    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
    
    vl_imwbackwardmx
    
    private float[] vl_imwbackwardmx(int[] X_pt, int[] Y_pt, float[] I_pt, double[][] iwXp_pt, double[][] iwYp_pt, int M, int N)
    
    findNeighbor
    
    private int findNeighbor(double x, int[] X, int K)
    
    vl_imwbackwardmx
    
    private double[] vl_imwbackwardmx(int[] X_pt, int[] Y_pt, double[] I_pt, double[][] iwXp_pt, double[][] iwYp_pt, int M, int N)
    
    randomize
    
    private void randomize(int[] arr)
    
    vl_file_meta_open
    
    private java.io.RandomAccessFile vl_file_meta_open(SIFT.VlFileMeta self, java.lang.String basename, java.lang.String mode, int[] error)
    
    Parameters:
    
    self - File meta information.
    
    basename - Basename.
    
    mode - Opening mode (as in @c fopen).
    
    Returns:
    
    error code. The error may be either either ::VL_ERR_OVERFLOW if the file name is too long or to ::VL_ERR_IO if the file cannot be opened.
    
    vl_file_meta_close
    
    private void vl_file_meta_close(SIFT.VlFileMeta self)
    
    Parameters:
    
    self - File meta information.
    
    vl_file_meta_parse
    
    private int vl_file_meta_parse(SIFT.VlFileMeta self, java.lang.String optarg)
    
    Parameters:
    
    optarg - argument to parse.
    
    self - structure to initalize. The function parses the string @a optarg to fill the structure @a self. @a optarg is supposed to be composed of two parts: a file protocol specification and a file pattern. Then the function: - Sets VlFileMeta::active to true. - Sets VlFileMeta::protocol to the file protocol id (if any). - Sets VlFileMeta::pattern to the file pattern (if any).
    
    Returns:
    
    error code. The funciton may fail either because the file protocol is not recognized (::VL_ERR_BAD_ARG) or because the file pattern is too long to be stored (::VL_ERR_OVERFLOW).
    
    vl_string_parse_protocol
    
    private java.lang.String vl_string_parse_protocol(java.lang.String string, int[] protocol)
    
    ------------------------------------------------------------------
    
    Parameters:
    
    string - string.
    
    protocol - protocol code (output).
    
    Returns:
    
    pointer to the first character after the protocol prefix. The function extracts the prefix of the string @a string terminated by the first occurrence of the @c :// substring (if any). It then matches the suffix terminated by @c :// to the supported @ref vl-stringop-file-protocols protocols. If @c protocol is not
    
    vl_string_protocol_name
    
    private java.lang.String vl_string_protocol_name(int protocol)
    
    ------------------------------------------------------------------
    
    Parameters:
    
    protocol - protocol code.
    
    Returns:
    
    pointer protocol name string. The function returns a pointer to a string containing the name of the protocol @a protocol (see the @a vl-file-protocols protocols list). If the protocol is unknown the function returns the empty string.
    
    PRNFO
    
    private void PRNFO(java.lang.String name, SIFT.VlFileMeta fm)
    
    vl_string_basename
    
    private java.lang.String vl_string_basename(java.lang.String destination, int destinationSize, java.lang.String source, int maxNumStrippedExtensions, int[] num)
    
    ------------------------------------------------------------------
    
    Parameters:
    
    destination - destination buffer.
    
    destinationSize - size of destination buffer.
    
    source - input string.
    
    maxNumStrippedExtensions - maximum number of extensions to strip.
    
    Returns:
    
    length of the destination string. The function removes the leading path and up to @c maxNumStrippedExtensions trailing extensions from the string @a source and writes the result to the buffer @a destination. The leading path is the longest suffix that ends with either the
    
    vl_string_copy_sub
    
    private java.lang.String vl_string_copy_sub(java.lang.String destination, int destinationSize, java.lang.String source, int beginning, int end, int[] num)
    
    ------------------------------------------------------------------
    
    Parameters:
    
    destination - output buffer.
    
    destinationSize - size of output buffer.
    
    beginning - start of the substring.
    
    end - end of the substring.
    
    Returns:
    
    length of the destination string. The function copies the substring from at @a beginning to @a end (not included) to the buffer @a destination of size @a destinationSize. If, however, the null character is found before
    
    vl_pgm_extract_head
    
    private int vl_pgm_extract_head(java.io.RandomAccessFile f, SIFT.VlPgmImage im)
    
    ------------------------------------------------------------------
    
    Parameters:
    
    f - input file.
    
    im - image structure to fill.
    
    Returns:
    
    error code. The function extracts from the file @a f the meta-data section of an image encoded in PGM format. The function fills the structure ::VlPgmImage accordingly. The error may be either ::VL_ERR_PGM_INV_HEAD or ::VL_ERR_PGM_INV_META depending whether the error occurred in decoding the header or meta section of the PGM file.
    
    remove_line
    
    private int remove_line(java.io.RandomAccessFile f)
    
    ------------------------------------------------------------------
    
    Parameters:
    
    f - file to strip.
    
    Returns:
    
    number of characters removed.
    
    remove_blanks
    
    private int remove_blanks(java.io.RandomAccessFile f, int[] err)
    
    ------------------------------------------------------------------
    
    Parameters:
    
    f - file to strip.
    
    Returns:
    
    number of characters removed.
    
    readAsciiInt
    
    private int readAsciiInt(java.io.RandomAccessFile f)
    
    readAsciiDouble
    
    private double readAsciiDouble(java.io.RandomAccessFile f, int[] err)
    
    vl_pgm_get_npixels
    
    private int vl_pgm_get_npixels(SIFT.VlPgmImage im)
    
    vl_pgm_get_bpp
    
    private int vl_pgm_get_bpp(SIFT.VlPgmImage im)
    
    vl_pgm_extract_data
    
    int vl_pgm_extract_data(java.io.RandomAccessFile f, SIFT.VlPgmImage im, int[] data)
    
    vl_string_replace_wildcard
    
    private java.lang.String vl_string_replace_wildcard(java.lang.String destination, int destinationSize, java.lang.String source, java.lang.String wildcardChar, java.lang.String escapeChar, java.lang.String replacement, int[] num)
    
    ------------------------------------------------------------------
    
    Parameters:
    
    destination - output buffer.
    
    destinationSize - size of the output buffer.
    
    source - input string.
    
    wildcardChar - wildcard character.
    
    escapeChar - escape character.
    
    replacement - replacement string. The function replaces the occurrence of the specified wildcard character @a wildcardChar by the string @a replacement. The result is written to the buffer @a destination of size @a destinationSize. Wildcard characters may be escaped by preceding them by the @a esc character. More in general, anything following an occurrence of @a esc character is copied verbatim. To disable the escape characters simply set @a esc to 0.
    
    Returns:
    
    length of the result.
    
    vl_file_meta_get_double
    
    private int vl_file_meta_get_double(int protocol, java.io.RandomAccessFile file, double[] x)
    
    Parameters:
    
    self - File meta information.
    
    x - Datum read.
    
    Returns:
    
    error code. The function returns ::VL_ERR_EOF if the end-of-file is reached and ::VL_ERR_BAD_ARG if the file is malformed.
    
    log2
    
    private double log2(double x)
    
    VL_SHIFT_LEFT
    
    private int VL_SHIFT_LEFT(int x, int n)
    
    Parameters:
    
    x - value.
    
    n - number of shift positions.
    
    Returns:
    
    fast_expn_init
    
    private void fast_expn_init()
    
    vl_sift_new
    
    SIFT.VlSiftFilt vl_sift_new(int width, int height, int noctaves, int nlevels, int o_min)
    
    copy_and_upsample_rows
    
    private void copy_and_upsample_rows(float[] dst, int dstIndex, float[] src, int srcIndex, int width, int height)
    
    ------------------------------------------------------------------
    
    Parameters:
    
    f - SIFT filter.
    
    im - image data. The function starts processing a new image by computing its Gaussian scale space at the lower octave. It also empties the internal keypoint buffer.
    
    copy_and_downsample
    
    private void copy_and_downsample(float[] dst, int dstIndex, float[] src, int srcIndex, int width, int height, int d)
    
    ------------------------------------------------------------------
    
    Parameters:
    
    dst - output imgae buffer.
    
    src - input image buffer.
    
    width - input image width.
    
    height - input image height.
    
    d - octaves (non negative). The function downsamples the image @a d times, reducing it to @c 1/2^d of its original size. The parameters @a width and @a height are the size of the input image. The destination image @a dst is assumed to be floor(width/2^d) pixels wide and floor(height/2^d) pixels high.
    
    vl_imconvcol_vf
    
    private void vl_imconvcol_vf(float[] dst, int dst_index, int dst_stride, float[] src, int src_index, int src_width, int src_height, int src_stride, float[] filt, int filt_begin, int filt_end, int step, int flags)
    
    _vl_sift_smooth
    
    private void _vl_sift_smooth(SIFT.VlSiftFilt self, float[] outputImage, int output_index, float[] tempImage, float[] inputImage, int input_index, int width, int height, double sigma)
    
    ------------------------------------------------------------------
    
    Parameters:
    
    self - SIFT filter.
    
    outputImage - output imgae buffer.
    
    tempImage - temporary image buffer.
    
    inputImage - input image buffer.
    
    width - input image width.
    
    height - input image height.
    
    sigma - smoothing.
    
    vl_sift_process_first_octave
    
    private int vl_sift_process_first_octave(SIFT.VlSiftFilt f, float[] im)
    
    vl_sift_get_octave
    
    private float[] vl_sift_get_octave(SIFT.VlSiftFilt f, int s, int[] octave_index)
    
    ------------------------------------------------------------------
    
    Parameters:
    
    f - SIFT filter.
    
    s - level index. The level index @a s ranges in the interval s_min = -1 and s_max = S + 2, where @c S is the number of levels per octave.
    
    Returns:
    
    pointer to the octave data for level @a s.
    
    vl_sift_process_next_octave
    
    private int vl_sift_process_next_octave(SIFT.VlSiftFilt f)
    
    ------------------------------------------------------------------
    
    Parameters:
    
    f - SIFT filter. The function computes the next octave of the Gaussian scale space. Notice that this clears the record of any feature detected in the previous octave.
    
    Returns:
    
    error code. The function returns the error ::VL_ERR_EOF when there are no more octaves to process.
    
    save_gss
    
    private int save_gss(SIFT.VlSiftFilt filt, SIFT.VlFileMeta fm, java.lang.String basename, boolean verbose)
    
    vl_pgm_insert
    
    private int vl_pgm_insert(java.io.RandomAccessFile f, SIFT.VlPgmImage im, byte[] data)
    
    vl_sift_detect
    
    private void vl_sift_detect(SIFT.VlSiftFilt f)
    
    ------------------------------------------------------------------
    
    Parameters:
    
    f - SIFT filter.
    
    vl_sift_keypoint_init
    
    private void vl_sift_keypoint_init(SIFT.VlSiftFilt f, SIFT.VlSiftKeypoint k, double x, double y, double sigma)
    
    ------------------------------------------------------------------
    
    Parameters:
    
    f - SIFT filter.
    
    k - SIFT keypoint (output).
    
    x - x coordinate of the keypoint center.
    
    y - y coordinate of the keypoint center.
    
    sigma - keypoint scale. The function initializes a keypoint structure @a k from the location @a x and @a y and the scale @a sigma of the keypoint. The keypoint structure maps the keypoint to an octave and scale level of the discretized Gaussian scale space, which is required for instance to compute the keypoint SIFT descriptor.
    
    vl_sift_calc_keypoint_orientations
    
    private int vl_sift_calc_keypoint_orientations(SIFT.VlSiftFilt f, double[] angles, SIFT.VlSiftKeypoint k)
    
    ------------------------------------------------------------------
    
    Parameters:
    
    f - SIFT filter.
    
    angles - orientations (output).
    
    k - keypoint. The function computes the orientation(s) of the keypoint @a k. The function returns the number of orientations found (up to four). The orientations themselves are written to the vector @a angles.
    
    Returns:
    
    number of orientations found.
    
    update_gradient
    
    private void update_gradient(SIFT.VlSiftFilt f)
    
    ------------------------------------------------------------------
    
    Parameters:
    
    f - SIFT filter. The function makes sure that the gradient buffer is up-to-date with the current GSS data.
    
    vl_mod_2pi_f
    
    private float vl_mod_2pi_f(float x)
    
    vl_sift_calc_keypoint_descriptor
    
    private void vl_sift_calc_keypoint_descriptor(SIFT.VlSiftFilt f, float[] descr, SIFT.VlSiftKeypoint k, double angle0)
    
    ------------------------------------------------------------------
    
    Parameters:
    
    f - SIFT filter.
    
    descr - SIFT descriptor (output)
    
    k - keypoint.
    
    angle0 - keypoint direction. The function computes the SIFT descriptor of the keypoint @a k of orientation @a angle0. The function fills the buffer @a descr which must be large enough to hold the descriptor. The function assumes that the keypoint is on the current octave. If not, it does not do anything.
    
    normalize_histogram
    
    private float normalize_histogram(float[] buf, int begin, int end)
    
    ------------------------------------------------------------------
    
    Parameters:
    
    begin - begin of histogram.
    
    end - end of histogram.
    
    vl_file_meta_put_double
    
    private int vl_file_meta_put_double(int protocol, java.io.RandomAccessFile file, double x)
    
    Parameters:
    
    self - File meta information.
    
    x - Datum to write.
    
    Returns:
    
    error code. The function returns ::VL_ERR_ALLOC if the datum cannot be written.
    
    vl_file_meta_put_uint8
    
    private int vl_file_meta_put_uint8(int protocol, java.io.RandomAccessFile file, byte x)
    
    Parameters:
    
    self - File meta information.
    
    x - Datum to write.
    
    Returns:
    
    error code. The function returns ::VL_ERR_ALLOC if the datum cannot be written.
    
    vl_sift_delete
    
    private void vl_sift_delete(SIFT.VlSiftFilt f)
    
    ------------------------------------------------------------------
    
    Parameters:
    
    dst - destination 8-byte buffer.
    
    src - source 8-byte bufffer.
    
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Class SIFT

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

VL_ERR_OK

VL_ERR_OVERFLOW

VL_ERR_ALLOC

VL_ERR_BAD_ARG

VL_ERR_IO

VL_ERR_EOF

VL_PROT_UNKNOWN

VL_PROT_NONE

VL_PROT_ASCII

VL_PROT_BINARY

VL_ERR_PGM_INV_HEAD

VL_ERR_PGM_INV_META

VL_ERR_PGM_INV_DATA

VL_ERR_PGM_IO

EOF

fileDir

fileName

fileNum

mosaic

verbose

outarg

framesarg

descriptorarg

metaarg

read_framesarg

gssarg

O

S

omin

edge_thresh

peak_thresh

norm_thresh

magnif

window_size

force_orientations

writeFrames

readFrames

writeDescriptor

writeMeta

writeGss

NBO

NBP

EXPN_SZ

EXPN_MAX

expn_tab

VL_PAD_BY_ZERO

VL_PAD_BY_CONTINUITY

VL_PAD_MASK

VL_TRANSPOSE

VL_EPSILON_F

VL_EPSILON_D

VL_SIFT_BILINEAR_ORIENTATIONS

Constructor Detail

SIFT

SIFT

Method Detail

runAlgorithm

vl_imwbackwardmx

findNeighbor

vl_imwbackwardmx

randomize

vl_file_meta_open

vl_file_meta_close

vl_file_meta_parse

vl_string_parse_protocol

vl_string_protocol_name

PRNFO

vl_string_basename