diff --git a/Testing/Utilities/itkScaleInvariantFeatureImageFilterHistTest.cxx b/Testing/Utilities/itkScaleInvariantFeatureImageFilterHistTest.cxx
deleted file mode 100644
index f8ebb3addf9941a3e16d1a42206c77ab70d1d10d..0000000000000000000000000000000000000000
--- a/Testing/Utilities/itkScaleInvariantFeatureImageFilterHistTest.cxx
+++ /dev/null
@@ -1,419 +0,0 @@
-/*=========================================================================
-Program: ITK nSIFT Implemention - Command Line Wrapper
-Module: $RCSfile: testnD.cxx,v $
-Language: C++
-Date: $Date: 2007/11/25 15:51:48 $
-Version: $Revision: 1.0 $
-Copyright (c) 2005,2006,2007 Warren Cheung
-All rights reserved.
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-* Redistributions of source code must retain the above copyright notice,
-this list of conditions and the following disclaimer.
-* 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.
-* The name of the Insight Consortium, nor the names of any consortium members,
-nor of any contributors, may be used to endorse or promote products derived
-from this software without specific prior written permission.
-* Modified source versions must be plainly marked as such, and must not be
-misrepresented as being the original software.
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER 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 AUTHORS 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.
-=========================================================================*/
-
-#define VERBOSE
-//#define DEBUG
-//#define DEBUG_VERBOSE
-
-//#define SIFT_FEATURE
-//#define REORIENT
-
-#define GENERATE_KEYS
-//#define SUBSAMPLE
-#define CROP
-//#define DO_DOUBLE
-
-#include "itkScaleInvariantFeatureImageFilter.h"
-#include "itkImageSeriesReader.h"
-#include "itkNumericSeriesFileNames.h"
-#include "itkPointSetToImageFilter.h"
-#include "itkImageFileWriter.h"
-#include <getopt.h>
-
-int itk2DScaleInvariantFeatureImageFilterHist( int argc, char *argv[] )
-{
- // Command Line Arguments
- unsigned int ARG_IMG1=2;
- unsigned int ARG_IMG2=3;
-
- const unsigned int Dimension = 2;
-
- // Default scale is 1.0
- double test_scale = 1.0;
- float test_rotate = 0.0; // 0 degrees
- double test_crop = 0.5;
- // float test_rotate = 0.0874; // 5 degrees
- //float test_rotate = 0.1748; // 10 degrees
- int series_start = 1;
- int series_end = 9;
- int series_inc = 1;
-
- int mode = 'i'; /* defaults to comparing 2 images */;
- int rotate_middle=0; /* defaults to rotating around the origin */
-
-#define OPT_SCALE 'x'
-#define OPT_ROTATE 'r'
-#define OPT_DIM 'd'
-#define OPT_CROP 'c'
-#define OPT_SERIES_START 's'
-#define OPT_SERIES_END 'e'
-#define OPT_SERIES_INC 'i'
-
- /* new Getopt code */
- while(1) {
- static struct option long_options[] =
- {
- /* These options set a flag. */
- {"synthetic", 0, &mode, 's'},
- {"image", 0, &mode, 'i'},
- {"rotate-mid", 0, &rotate_middle, 1},
- /* These options don't set a flag.
- We distinguish them by their indices. */
- {"scale", required_argument, 0, OPT_SCALE},
- {"rotate", required_argument, 0, OPT_ROTATE},
- {"crop", required_argument, 0, OPT_CROP},
- {"series-start", required_argument, 0, OPT_SERIES_START},
- {"series-end", required_argument, 0, OPT_SERIES_END},
- {"series-inc", required_argument, 0, OPT_SERIES_INC},
- // {"dimension", required_argument, 0, OPT_DIM},
- {0, 0, 0, 0}
- };
-
- int optindex;
- int val = getopt_long(argc, argv, "", long_options, &optindex);
-
- if (val == -1)
- break;
-
- switch(val) {
- case OPT_SCALE:
- test_scale = atof(optarg);
- break;
- case OPT_ROTATE:
- if (atof(optarg) >= 0.0 && atof(optarg) <= 360.0)
- test_rotate = atof(optarg) * PI * 2.0 / 360.0;
- break;
- case OPT_CROP:
- if (atof(optarg) <= 1.0) {
- test_crop = atof(optarg);
- }
- break;
- case OPT_SERIES_START:
- series_start = atoi(optarg);
- break;
- case OPT_SERIES_END:
- series_end = atoi(optarg);
- break;
- case OPT_SERIES_INC:
- series_inc = atoi(optarg);
- break;
- /*
- case OPT_DIM:
- Dimension = atoi(optarg);
- break;
- */
- }
- }
-
- ARG_IMG1 = optind;
- ARG_IMG2 = optind+1;
-
- typedef float PixelType;
- typedef itk::Image< PixelType, Dimension > FixedImageType;
- typedef itk::ScaleInvariantFeatureImageFilter<FixedImageType, Dimension> SiftFilterType;
- typedef itk::Image<unsigned char, Dimension> OutputImageType;
-
- typedef itk::ImageSource< FixedImageType > ImageSourceType;
-
- ImageSourceType::Pointer fixedImageReader, fixedImageReader2;
-
- typedef itk::PointSetToImageFilter<SiftFilterType::PointSetType, OutputImageType> PointSetFilterType;
-
- if( static_cast<unsigned int>(argc) <= ARG_IMG1 || (mode == 'i' && static_cast<unsigned int>(argc) <= ARG_IMG2))
- {
- std::cerr << "Incorrect number of parameters " << std::endl;
- std::cerr << std::endl;
- std::cerr << "siftkeys program ( ";
- std::cerr << Dimension << "D ";
-#ifdef SIFT_FEATURE
- std::cerr << "sift-feature ";
-#else
- std::cerr << "histogram-feature ";
-#endif
-#ifdef REORIENT
- std::cerr << "reoriented ";
-#endif
- std::cerr << ")" << std::endl;
-
- std::cerr << "Usage: \n";
- std::cerr << argv[0] << " [options] ImageFile [ImageFile2]\n";
- std::cerr << "This program takes an input image file(s) and generates scale invariant features." << std::endl;
- std::cerr << std::endl;
- std::cerr << "Image Processing Options (Choose ONE):" << std::endl;
- std::cerr << "--image" << std::endl;
- std::cerr << " compare ImageFile and ImageFile2" << std::endl;
- std::cerr << "\nOR\n" << std::endl;
- std::cerr << "--synthetic" << std::endl;
- std::cerr << " compare ImageFile to synthetically generated version" << std::endl;
- std::cerr << "Synthetic Image Options:" << std::endl;
- std::cerr << "--rotate value" << std::endl;
- std::cerr << " rotate synthetic image on first axis by value degrees" << std::endl;
- std::cerr << "--rotate-middle" << std::endl;
- std::cerr << " centre of rotation at the centre of image (defaults to origin)" << std::endl;
- std::cerr << "--scale value" << std::endl;
- std::cerr << " scale all axes of synthetic image by value" << std::endl;
- std::cerr << "--tmp directory" << std::endl;
- std::cerr << " temporary directory" << std::endl;
- std::cerr << std::endl;
- return 1;
- }
-
- std::cerr << "Dimension = " << Dimension << "\n";
- std::cerr << "Test Scale = " << test_scale << "\n";
- std::cerr << "Test Rotate = " << test_rotate << "\n";
- std::cerr << "Image Crop Ratio (first 3D) = " << test_crop << "\n";
- std::cerr << "Mode = " << (char) mode << "\n";
- std::cerr << "ImageFile1 = " << argv[optind] << "\n";
- if (Dimension == 4) {
- std::cerr << "Image Series Start = " << series_start << "\n";
- std::cerr << "Image Series End = " << series_end << "\n";
- std::cerr << "Image Series Inc = " << series_inc << "\n";
- }
-
-#ifdef SIFT_FEATURE
- std::cerr << "SIFT Feature\n" << std::endl;
-#else
- std::cerr << "Histogram Feature\n" << std::endl;
-#endif
-
-#ifdef REORIENT
- std::cerr << "Reorientation enabled\n" << std::endl;
-#endif
-
- if (Dimension == 4) {
- /* Assume fileseries reader */
- typedef itk::ImageSeriesReader< FixedImageType > FixedImageReaderType;
- FixedImageReaderType::Pointer tmpImageReader = FixedImageReaderType::New();
-
- typedef itk::NumericSeriesFileNames NameGeneratorType;
- NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
-
- nameGenerator->SetSeriesFormat( argv[ARG_IMG1] );
- nameGenerator->SetStartIndex( series_start );
- nameGenerator->SetEndIndex( series_end );
- nameGenerator->SetIncrementIndex( series_inc );
-
- tmpImageReader->SetFileNames( nameGenerator->GetFileNames() );
-
- fixedImageReader = tmpImageReader;
- } else {
- typedef itk::ImageFileReader< FixedImageType > FixedImageReaderType;
- FixedImageReaderType::Pointer tmpImageReader = FixedImageReaderType::New();
- tmpImageReader = FixedImageReaderType::New();
-
- tmpImageReader->SetFileName( argv[ARG_IMG1] );
- fixedImageReader=tmpImageReader;
- }
- fixedImageReader->Update();
-
- typedef itk::ScalableAffineTransform< double, Dimension > ScaleType;
-#ifdef CROP
- ScaleType::Pointer no_transform = ScaleType::New();
- no_transform->SetIdentity();
-
- SiftFilterType::ResampleFilterType::Pointer cropper = SiftFilterType::ResampleFilterType::New();
- cropper->SetInput(fixedImageReader->GetOutput());
- FixedImageType::SizeType cropsize =
- fixedImageReader->GetOutput()->GetLargestPossibleRegion().GetSize();
- for (unsigned int k = 0; k < Dimension; ++k) {
- if (k < 4)
- cropsize[k] = (int) (cropsize[k] * test_crop);
- }
- cropper->SetSize( cropsize );
- cropper->SetOutputSpacing(fixedImageReader->GetOutput()->GetSpacing());
- cropper->SetTransform(no_transform);
- cropper->Update();
- FixedImageType::Pointer fixedImage = cropper->GetOutput();
-#else
- FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput();
-#endif
-
- SiftFilterType::PointSetTypePointer keypoints1, keypoints2;
- PointSetFilterType::Pointer pointSet1 = PointSetFilterType::New();
- PointSetFilterType::Pointer pointSet2 = PointSetFilterType::New();
-
- SiftFilterType siftFilter1, siftFilter2;
-
-#ifdef DEBUG
- siftFilter1.writeImage(fixedImage, "tmp0.png");
- std::cout << std::endl << "Starting SIFT Feature Extraction...\n";
-#endif
-
- keypoints1 = siftFilter1.getSiftFeatures(fixedImage);
-
- pointSet1->SetInput(keypoints1);
- pointSet1->SetOutsideValue(0);
- pointSet1->SetInsideValue(255);
- pointSet1->SetSize(fixedImageReader->GetOutput()->GetLargestPossibleRegion().GetSize());
-
- typedef itk::ImageFileWriter<OutputImageType> WriterType;
-
- WriterType::Pointer writer = WriterType::New();
- writer->SetFileName("tmp0_keys.png");
- writer->SetInput(pointSet1->GetOutput());
- writer->Update();
-
- typedef itk::ScalableAffineTransform< double, Dimension > TestTransformType;
- TestTransformType::Pointer inv_test_transform;
-
- // Synthetic test image
- if (mode=='s') {
- std::cerr << std::endl << "Synthetic image mode\n";
- TestTransformType::Pointer test_transform = TestTransformType::New();
-
- inv_test_transform = TestTransformType::New();
-
- TestTransformType::InputPointType translate_vector;
-
- test_transform->SetIdentity();
- test_transform->Scale( 1.0 / test_scale);
- if (rotate_middle) {
- std::cerr << "Rotation centred at middle of image." << std::endl;
- /* Cycle through each dimension and shift by half*/
- FixedImageType::SizeType size =
- fixedImage->GetLargestPossibleRegion().GetSize();
- for (unsigned int k = 0; k < Dimension; ++k)
- translate_vector[k] = size[k]/2.0;
- test_transform->SetCenter( translate_vector);
- } else {
- std::cerr << "Rotation centred at origin." << std::endl;
- }
-#if 0
- if (rotate_middle) {
- std::cerr << "Rotation centred at middle of image." << std::endl;
- /* Cycle through each dimension and shift by half*/
- FixedImageType::SizeType size =
- fixedImage->GetLargestPossibleRegion().GetSize();
- for (unsigned int k = 0; k < Dimension; ++k)
- translate_vector[k] = size[k]/2.0;
- test_transform->Translate( translate_vector);
- } else {
- std::cerr << "Rotation centred at origin." << std::endl;
- }
-#endif
-
- test_transform->Rotate(0,1,test_rotate);
-
-#if 0
- if (rotate_middle) {
- /* Cycle through each dimension and shift back*/
- for (unsigned int k = 0; k < Dimension; ++k)
- translate_vector[k] = -translate_vector[k];
- test_transform->Translate( translate_vector);
- }
-#endif
-
- test_transform->GetInverse(inv_test_transform);
-
- {
- FixedImageType::Pointer scaledImage;
-
- SiftFilterType::ResampleFilterType::Pointer scaler = SiftFilterType::ResampleFilterType::New();
- scaler->SetInput(fixedImage);
- FixedImageType::SizeType size =
- fixedImage->GetLargestPossibleRegion().GetSize();
- for (unsigned int k = 0; k < Dimension; ++k)
- size[k] = (unsigned int) floor(size[k] * test_scale);
- scaler->SetSize( size );
- scaler->SetOutputSpacing(fixedImage->GetSpacing());
- scaler->SetTransform(test_transform);
- scaler->Update();
- scaledImage = scaler->GetOutput();
-
-#ifdef DEBUG
- siftFilter2.writeImage(scaledImage, "tmp1.png");
- std::cout << std::endl;
-#endif
- keypoints2 = siftFilter2.getSiftFeatures(scaledImage);
- }
-
- std::cerr << "Test Image Scale: " << test_scale << std::endl;
- // std::cerr << "Test Translate: " << test_translate << std::endl;
- std::cerr << "Test Image Rotate: " << test_rotate << std::endl;
- } else if (mode == 'i') {
- std::cerr << std::endl << "Image Comparison mode\n";
- inv_test_transform = NULL;
-
- if (Dimension == 4) {
- typedef itk::ImageSeriesReader< FixedImageType > FixedImageReaderType;
- FixedImageReaderType::Pointer tmpImageReader = FixedImageReaderType::New();
- tmpImageReader = FixedImageReaderType::New();
-
- typedef itk::NumericSeriesFileNames NameGeneratorType;
- NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
-
- nameGenerator->SetSeriesFormat( argv[ARG_IMG2] );
- nameGenerator->SetStartIndex( series_start );
- nameGenerator->SetEndIndex( series_end );
- nameGenerator->SetIncrementIndex( series_inc );
-
- tmpImageReader->SetFileNames( nameGenerator->GetFileNames() );
- fixedImageReader2 = tmpImageReader;
- } else {
- typedef itk::ImageFileReader< FixedImageType > FixedImageReaderType;
- FixedImageReaderType::Pointer tmpImageReader = FixedImageReaderType::New();
- tmpImageReader = FixedImageReaderType::New();
-
- tmpImageReader->SetFileName( argv[ARG_IMG2] );
- fixedImageReader2 = tmpImageReader;
- }
- fixedImageReader2->Update();
-
-#ifdef CROP
- SiftFilterType::ResampleFilterType::Pointer cropper2 = SiftFilterType::ResampleFilterType::New();
- cropper2->SetInput(fixedImageReader2->GetOutput());
- FixedImageType::SizeType cropsize2 =
- fixedImageReader2->GetOutput()->GetLargestPossibleRegion().GetSize();
- for (unsigned int k = 0; k < Dimension; ++k) {
- if (k < 4)
- cropsize2[k] /= 2;
- }
- cropper2->SetSize( cropsize2 );
- cropper2->SetOutputSpacing(fixedImageReader2->GetOutput()->GetSpacing());
- cropper2->SetTransform(no_transform);
- cropper2->Update();
- FixedImageType::Pointer fixedImage2 = cropper2->GetOutput();
-#else
- FixedImageType::Pointer fixedImage2 = fixedImageReader2->GetOutput();
-#endif
-
- keypoints2 = siftFilter2.getSiftFeatures(fixedImage2);
- }
-
- std::cerr << std::endl << "Matching Keypoints\n";
- siftFilter2.MatchKeypointsPos(keypoints1, keypoints2, inv_test_transform);
-#ifdef GENERATE_KEYS
- siftFilter2.MatchKeypointsFeatures(keypoints1, keypoints2, inv_test_transform);
-#endif
- return 0;
-
-}
diff --git a/Testing/Utilities/itkScaleInvariantFeatureImageFilterRHistTest.cxx b/Testing/Utilities/itkScaleInvariantFeatureImageFilterRHistTest.cxx
deleted file mode 100644
index 68d2e7b41494bbbc63f75ba156a369e83351bf3b..0000000000000000000000000000000000000000
--- a/Testing/Utilities/itkScaleInvariantFeatureImageFilterRHistTest.cxx
+++ /dev/null
@@ -1,419 +0,0 @@
-/*=========================================================================
-Program: ITK nSIFT Implemention - Command Line Wrapper
-Module: $RCSfile: testnD.cxx,v $
-Language: C++
-Date: $Date: 2007/11/25 15:51:48 $
-Version: $Revision: 1.0 $
-Copyright (c) 2005,2006,2007 Warren Cheung
-All rights reserved.
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-* Redistributions of source code must retain the above copyright notice,
-this list of conditions and the following disclaimer.
-* 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.
-* The name of the Insight Consortium, nor the names of any consortium members,
-nor of any contributors, may be used to endorse or promote products derived
-from this software without specific prior written permission.
-* Modified source versions must be plainly marked as such, and must not be
-misrepresented as being the original software.
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER 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 AUTHORS 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.
-=========================================================================*/
-
-#define VERBOSE
-//#define DEBUG
-//#define DEBUG_VERBOSE
-
-//#define SIFT_FEATURE
-#define REORIENT
-
-#define GENERATE_KEYS
-//#define SUBSAMPLE
-#define CROP
-//#define DO_DOUBLE
-
-#include "itkScaleInvariantFeatureImageFilter.h"
-#include "itkImageSeriesReader.h"
-#include "itkNumericSeriesFileNames.h"
-#include "itkPointSetToImageFilter.h"
-#include "itkImageFileWriter.h"
-#include <getopt.h>
-
-int itk2DScaleInvariantFeatureImageFilterRHist( int argc, char *argv[] )
-{
- // Command Line Arguments
- unsigned int ARG_IMG1=2;
- unsigned int ARG_IMG2=3;
-
- const unsigned int Dimension = 2;
-
- // Default scale is 1.0
- double test_scale = 1.0;
- float test_rotate = 0.0; // 0 degrees
- double test_crop = 0.5;
- // float test_rotate = 0.0874; // 5 degrees
- //float test_rotate = 0.1748; // 10 degrees
- int series_start = 1;
- int series_end = 9;
- int series_inc = 1;
-
- int mode = 'i'; /* defaults to comparing 2 images */;
- int rotate_middle=0; /* defaults to rotating around the origin */
-
-#define OPT_SCALE 'x'
-#define OPT_ROTATE 'r'
-#define OPT_DIM 'd'
-#define OPT_CROP 'c'
-#define OPT_SERIES_START 's'
-#define OPT_SERIES_END 'e'
-#define OPT_SERIES_INC 'i'
-
- /* new Getopt code */
- while(1) {
- static struct option long_options[] =
- {
- /* These options set a flag. */
- {"synthetic", 0, &mode, 's'},
- {"image", 0, &mode, 'i'},
- {"rotate-mid", 0, &rotate_middle, 1},
- /* These options don't set a flag.
- We distinguish them by their indices. */
- {"scale", required_argument, 0, OPT_SCALE},
- {"rotate", required_argument, 0, OPT_ROTATE},
- {"crop", required_argument, 0, OPT_CROP},
- {"series-start", required_argument, 0, OPT_SERIES_START},
- {"series-end", required_argument, 0, OPT_SERIES_END},
- {"series-inc", required_argument, 0, OPT_SERIES_INC},
- // {"dimension", required_argument, 0, OPT_DIM},
- {0, 0, 0, 0}
- };
-
- int optindex;
- int val = getopt_long(argc, argv, "", long_options, &optindex);
-
- if (val == -1)
- break;
-
- switch(val) {
- case OPT_SCALE:
- test_scale = atof(optarg);
- break;
- case OPT_ROTATE:
- if (atof(optarg) >= 0.0 && atof(optarg) <= 360.0)
- test_rotate = atof(optarg) * PI * 2.0 / 360.0;
- break;
- case OPT_CROP:
- if (atof(optarg) <= 1.0) {
- test_crop = atof(optarg);
- }
- break;
- case OPT_SERIES_START:
- series_start = atoi(optarg);
- break;
- case OPT_SERIES_END:
- series_end = atoi(optarg);
- break;
- case OPT_SERIES_INC:
- series_inc = atoi(optarg);
- break;
- /*
- case OPT_DIM:
- Dimension = atoi(optarg);
- break;
- */
- }
- }
-
- ARG_IMG1 = optind;
- ARG_IMG2 = optind+1;
-
- typedef float PixelType;
- typedef itk::Image< PixelType, Dimension > FixedImageType;
- typedef itk::ScaleInvariantFeatureImageFilter<FixedImageType, Dimension> SiftFilterType;
- typedef itk::Image<unsigned char, Dimension> OutputImageType;
-
- typedef itk::ImageSource< FixedImageType > ImageSourceType;
-
- ImageSourceType::Pointer fixedImageReader, fixedImageReader2;
-
- typedef itk::PointSetToImageFilter<SiftFilterType::PointSetType, OutputImageType> PointSetFilterType;
-
- if( static_cast<unsigned int>(argc) <= ARG_IMG1 || (mode == 'i' && static_cast<unsigned int>(argc) <= ARG_IMG2))
- {
- std::cerr << "Incorrect number of parameters " << std::endl;
- std::cerr << std::endl;
- std::cerr << "siftkeys program ( ";
- std::cerr << Dimension << "D ";
-#ifdef SIFT_FEATURE
- std::cerr << "sift-feature ";
-#else
- std::cerr << "histogram-feature ";
-#endif
-#ifdef REORIENT
- std::cerr << "reoriented ";
-#endif
- std::cerr << ")" << std::endl;
-
- std::cerr << "Usage: \n";
- std::cerr << argv[0] << " [options] ImageFile [ImageFile2]\n";
- std::cerr << "This program takes an input image file(s) and generates scale invariant features." << std::endl;
- std::cerr << std::endl;
- std::cerr << "Image Processing Options (Choose ONE):" << std::endl;
- std::cerr << "--image" << std::endl;
- std::cerr << " compare ImageFile and ImageFile2" << std::endl;
- std::cerr << "\nOR\n" << std::endl;
- std::cerr << "--synthetic" << std::endl;
- std::cerr << " compare ImageFile to synthetically generated version" << std::endl;
- std::cerr << "Synthetic Image Options:" << std::endl;
- std::cerr << "--rotate value" << std::endl;
- std::cerr << " rotate synthetic image on first axis by value degrees" << std::endl;
- std::cerr << "--rotate-middle" << std::endl;
- std::cerr << " centre of rotation at the centre of image (defaults to origin)" << std::endl;
- std::cerr << "--scale value" << std::endl;
- std::cerr << " scale all axes of synthetic image by value" << std::endl;
- std::cerr << "--tmp directory" << std::endl;
- std::cerr << " temporary directory" << std::endl;
- std::cerr << std::endl;
- return 1;
- }
-
- std::cerr << "Dimension = " << Dimension << "\n";
- std::cerr << "Test Scale = " << test_scale << "\n";
- std::cerr << "Test Rotate = " << test_rotate << "\n";
- std::cerr << "Image Crop Ratio (first 3D) = " << test_crop << "\n";
- std::cerr << "Mode = " << (char) mode << "\n";
- std::cerr << "ImageFile1 = " << argv[optind] << "\n";
- if (Dimension == 4) {
- std::cerr << "Image Series Start = " << series_start << "\n";
- std::cerr << "Image Series End = " << series_end << "\n";
- std::cerr << "Image Series Inc = " << series_inc << "\n";
- }
-
-#ifdef SIFT_FEATURE
- std::cerr << "SIFT Feature\n" << std::endl;
-#else
- std::cerr << "Histogram Feature\n" << std::endl;
-#endif
-
-#ifdef REORIENT
- std::cerr << "Reorientation enabled\n" << std::endl;
-#endif
-
- if (Dimension == 4) {
- /* Assume fileseries reader */
- typedef itk::ImageSeriesReader< FixedImageType > FixedImageReaderType;
- FixedImageReaderType::Pointer tmpImageReader = FixedImageReaderType::New();
-
- typedef itk::NumericSeriesFileNames NameGeneratorType;
- NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
-
- nameGenerator->SetSeriesFormat( argv[ARG_IMG1] );
- nameGenerator->SetStartIndex( series_start );
- nameGenerator->SetEndIndex( series_end );
- nameGenerator->SetIncrementIndex( series_inc );
-
- tmpImageReader->SetFileNames( nameGenerator->GetFileNames() );
-
- fixedImageReader = tmpImageReader;
- } else {
- typedef itk::ImageFileReader< FixedImageType > FixedImageReaderType;
- FixedImageReaderType::Pointer tmpImageReader = FixedImageReaderType::New();
- tmpImageReader = FixedImageReaderType::New();
-
- tmpImageReader->SetFileName( argv[ARG_IMG1] );
- fixedImageReader=tmpImageReader;
- }
- fixedImageReader->Update();
-
- typedef itk::ScalableAffineTransform< double, Dimension > ScaleType;
-#ifdef CROP
- ScaleType::Pointer no_transform = ScaleType::New();
- no_transform->SetIdentity();
-
- SiftFilterType::ResampleFilterType::Pointer cropper = SiftFilterType::ResampleFilterType::New();
- cropper->SetInput(fixedImageReader->GetOutput());
- FixedImageType::SizeType cropsize =
- fixedImageReader->GetOutput()->GetLargestPossibleRegion().GetSize();
- for (unsigned int k = 0; k < Dimension; ++k) {
- if (k < 4)
- cropsize[k] = (int) (cropsize[k] * test_crop);
- }
- cropper->SetSize( cropsize );
- cropper->SetOutputSpacing(fixedImageReader->GetOutput()->GetSpacing());
- cropper->SetTransform(no_transform);
- cropper->Update();
- FixedImageType::Pointer fixedImage = cropper->GetOutput();
-#else
- FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput();
-#endif
-
- SiftFilterType::PointSetTypePointer keypoints1, keypoints2;
- PointSetFilterType::Pointer pointSet1 = PointSetFilterType::New();
- PointSetFilterType::Pointer pointSet2 = PointSetFilterType::New();
-
- SiftFilterType siftFilter1, siftFilter2;
-
-#ifdef DEBUG
- siftFilter1.writeImage(fixedImage, "tmp0.png");
- std::cout << std::endl << "Starting SIFT Feature Extraction...\n";
-#endif
-
- keypoints1 = siftFilter1.getSiftFeatures(fixedImage);
-
- pointSet1->SetInput(keypoints1);
- pointSet1->SetOutsideValue(0);
- pointSet1->SetInsideValue(255);
- pointSet1->SetSize(fixedImageReader->GetOutput()->GetLargestPossibleRegion().GetSize());
-
- typedef itk::ImageFileWriter<OutputImageType> WriterType;
-
- WriterType::Pointer writer = WriterType::New();
- writer->SetFileName("tmp0_keys.png");
- writer->SetInput(pointSet1->GetOutput());
- writer->Update();
-
- typedef itk::ScalableAffineTransform< double, Dimension > TestTransformType;
- TestTransformType::Pointer inv_test_transform;
-
- // Synthetic test image
- if (mode=='s') {
- std::cerr << std::endl << "Synthetic image mode\n";
- TestTransformType::Pointer test_transform = TestTransformType::New();
-
- inv_test_transform = TestTransformType::New();
-
- TestTransformType::InputPointType translate_vector;
-
- test_transform->SetIdentity();
- test_transform->Scale( 1.0 / test_scale);
- if (rotate_middle) {
- std::cerr << "Rotation centred at middle of image." << std::endl;
- /* Cycle through each dimension and shift by half*/
- FixedImageType::SizeType size =
- fixedImage->GetLargestPossibleRegion().GetSize();
- for (unsigned int k = 0; k < Dimension; ++k)
- translate_vector[k] = size[k]/2.0;
- test_transform->SetCenter( translate_vector);
- } else {
- std::cerr << "Rotation centred at origin." << std::endl;
- }
-#if 0
- if (rotate_middle) {
- std::cerr << "Rotation centred at middle of image." << std::endl;
- /* Cycle through each dimension and shift by half*/
- FixedImageType::SizeType size =
- fixedImage->GetLargestPossibleRegion().GetSize();
- for (unsigned int k = 0; k < Dimension; ++k)
- translate_vector[k] = size[k]/2.0;
- test_transform->Translate( translate_vector);
- } else {
- std::cerr << "Rotation centred at origin." << std::endl;
- }
-#endif
-
- test_transform->Rotate(0,1,test_rotate);
-
-#if 0
- if (rotate_middle) {
- /* Cycle through each dimension and shift back*/
- for (unsigned int k = 0; k < Dimension; ++k)
- translate_vector[k] = -translate_vector[k];
- test_transform->Translate( translate_vector);
- }
-#endif
-
- test_transform->GetInverse(inv_test_transform);
-
- {
- FixedImageType::Pointer scaledImage;
-
- SiftFilterType::ResampleFilterType::Pointer scaler = SiftFilterType::ResampleFilterType::New();
- scaler->SetInput(fixedImage);
- FixedImageType::SizeType size =
- fixedImage->GetLargestPossibleRegion().GetSize();
- for (unsigned int k = 0; k < Dimension; ++k)
- size[k] = (unsigned int) floor(size[k] * test_scale);
- scaler->SetSize( size );
- scaler->SetOutputSpacing(fixedImage->GetSpacing());
- scaler->SetTransform(test_transform);
- scaler->Update();
- scaledImage = scaler->GetOutput();
-
-#ifdef DEBUG
- siftFilter2.writeImage(scaledImage, "tmp1.png");
- std::cout << std::endl;
-#endif
- keypoints2 = siftFilter2.getSiftFeatures(scaledImage);
- }
-
- std::cerr << "Test Image Scale: " << test_scale << std::endl;
- // std::cerr << "Test Translate: " << test_translate << std::endl;
- std::cerr << "Test Image Rotate: " << test_rotate << std::endl;
- } else if (mode == 'i') {
- std::cerr << std::endl << "Image Comparison mode\n";
- inv_test_transform = NULL;
-
- if (Dimension == 4) {
- typedef itk::ImageSeriesReader< FixedImageType > FixedImageReaderType;
- FixedImageReaderType::Pointer tmpImageReader = FixedImageReaderType::New();
- tmpImageReader = FixedImageReaderType::New();
-
- typedef itk::NumericSeriesFileNames NameGeneratorType;
- NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
-
- nameGenerator->SetSeriesFormat( argv[ARG_IMG2] );
- nameGenerator->SetStartIndex( series_start );
- nameGenerator->SetEndIndex( series_end );
- nameGenerator->SetIncrementIndex( series_inc );
-
- tmpImageReader->SetFileNames( nameGenerator->GetFileNames() );
- fixedImageReader2 = tmpImageReader;
- } else {
- typedef itk::ImageFileReader< FixedImageType > FixedImageReaderType;
- FixedImageReaderType::Pointer tmpImageReader = FixedImageReaderType::New();
- tmpImageReader = FixedImageReaderType::New();
-
- tmpImageReader->SetFileName( argv[ARG_IMG2] );
- fixedImageReader2 = tmpImageReader;
- }
- fixedImageReader2->Update();
-
-#ifdef CROP
- SiftFilterType::ResampleFilterType::Pointer cropper2 = SiftFilterType::ResampleFilterType::New();
- cropper2->SetInput(fixedImageReader2->GetOutput());
- FixedImageType::SizeType cropsize2 =
- fixedImageReader2->GetOutput()->GetLargestPossibleRegion().GetSize();
- for (unsigned int k = 0; k < Dimension; ++k) {
- if (k < 4)
- cropsize2[k] /= 2;
- }
- cropper2->SetSize( cropsize2 );
- cropper2->SetOutputSpacing(fixedImageReader2->GetOutput()->GetSpacing());
- cropper2->SetTransform(no_transform);
- cropper2->Update();
- FixedImageType::Pointer fixedImage2 = cropper2->GetOutput();
-#else
- FixedImageType::Pointer fixedImage2 = fixedImageReader2->GetOutput();
-#endif
-
- keypoints2 = siftFilter2.getSiftFeatures(fixedImage2);
- }
-
- std::cerr << std::endl << "Matching Keypoints\n";
- siftFilter2.MatchKeypointsPos(keypoints1, keypoints2, inv_test_transform);
-#ifdef GENERATE_KEYS
- siftFilter2.MatchKeypointsFeatures(keypoints1, keypoints2, inv_test_transform);
-#endif
- return 0;
-
-}