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register.cxx
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register.cxx
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/*=========================================================================
Program: Atamai Image Registration and Segmentation
Module: register.cxx
This software is distributed WITHOUT ANY WARRANTY; without even the
implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
=========================================================================*/
// Image registration is done first on a blurred, low-resolution version of
// the image before being done on the full resolution image, and is also
// done first with no interpolation before being done with linear interpolation.
// This multi-stage approach increases the robustness and often the speed of
// the registration.
#include <vtkSmartPointer.h>
#include <vtkImageReslice.h>
#include <vtkImageResize.h>
#include <vtkImageBSplineCoefficients.h>
#include <vtkImageBSplineInterpolator.h>
#include <vtkImageSincInterpolator.h>
#include <vtkImageHistogramStatistics.h>
#include <vtkImageThreshold.h>
#include <vtkImageCast.h>
#include <vtkROIStencilSource.h>
#include <vtkImageData.h>
#include <vtkPointData.h>
#include <vtkMatrix4x4.h>
#include <vtkTransform.h>
#include <vtkDoubleArray.h>
#include <vtkIntArray.h>
#include <vtkIdTypeArray.h>
#include <vtkStringArray.h>
#include <vtkMath.h>
#include <vtkCommand.h>
#include <vtkMultiThreader.h>
#include <vtkMINCImageReader.h>
#include <vtkMINCImageWriter.h>
#include <vtkMNITransformReader.h>
#include <vtkMNITransformWriter.h>
#include <vtkDICOMImageReader.h>
#include <vtkRenderer.h>
#include <vtkCamera.h>
#include <vtkRenderWindow.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkInteractorStyleImage.h>
#include <vtkImageSlice.h>
#include <vtkImageStack.h>
#include <vtkImageResliceMapper.h>
#include <vtkImageProperty.h>
#include <vtkWindowToImageFilter.h>
#include <vtkPNGWriter.h>
#include <vtkTIFFWriter.h>
#include <vtkJPEGWriter.h>
#include <vtkTimerLog.h>
#include <vtkVersion.h>
#include <vtksys/SystemTools.hxx>
#include "AIRSConfig.h"
#include "vtkITKXFMReader.h"
#include "vtkITKXFMWriter.h"
#include "vtkImageRegistration.h"
#include "vtkLabelInterpolator.h"
// optional readers
#ifdef AIRS_USE_DICOM
#define AIRS_USE_NIFTI
#include <vtkNIFTIReader.h>
#include <vtkNIFTIWriter.h>
#include <vtkDICOMReader.h>
#include <vtkDICOMSorter.h>
#include <vtkDICOMMRGenerator.h>
#include <vtkDICOMCTGenerator.h>
#include <vtkDICOMWriter.h>
#include <vtkDICOMMetaData.h>
#include <vtkGlobFileNames.h>
#endif
#include <vector>
#include <string>
// A macro to assist VTK 5 backwards compatibility
#if VTK_MAJOR_VERSION >= 6
#define SET_INPUT_DATA SetInputData
#define SET_STENCIL_DATA SetStencilData
#else
#define SET_INPUT_DATA SetInput
#define SET_STENCIL_DATA SetStencil
#endif
// Check for vtkImageReslice::SetOutputScalarType()
#if VTK_MAJOR_VERSION > 6 || (VTK_MAJOR_VERSION == 6 && VTK_MINOR_VERSION >= 2)
#define VTK_RESLICE_HAS_OUTPUT_SCALAR_TYPE
#endif
#if VTK_MAJOR_VERSION > 7 || (VTK_MAJOR_VERSION == 7 && VTK_MINOR_VERSION >= 0)
#define USE_SMP_THREADED_IMAGE_ALGORITHM
#endif
// parallel processing
enum { MultiThread = 1, ThreadPool = 2 };
// coord systems
enum { NativeCoords, DICOMCoords, NIFTICoords };
// file types
enum { DICOMImage, NIFTIImage, MINCImage,
LastImageType = MINCImage,
MNITransform, ITKTransform, CSVTransform, TXTTransform,
LastTransformType = TXTTransform };
// internal methods for reading images, these methods read the image
// into the specified data object and also provide a matrix for converting
// the data coordinates into patient coordinates.
namespace {
void ComputeRange(vtkImageData *image, double range[2], double fill[2]);
// set the interpolator as requested
void SetInterpolator(vtkImageReslice *reslice, int interpolator)
{
vtkSmartPointer<vtkImageBSplineInterpolator> bsplineInterpolator =
vtkSmartPointer<vtkImageBSplineInterpolator>::New();
vtkSmartPointer<vtkImageSincInterpolator> sincInterpolator =
vtkSmartPointer<vtkImageSincInterpolator>::New();
sincInterpolator->SetWindowFunctionToBlackman();
vtkSmartPointer<vtkLabelInterpolator> labelInterpolator =
vtkSmartPointer<vtkLabelInterpolator>::New();
switch (interpolator)
{
case vtkImageRegistration::Nearest:
reslice->SetInterpolationModeToNearestNeighbor();
break;
case vtkImageRegistration::Linear:
reslice->SetInterpolationModeToLinear();
break;
case vtkImageRegistration::Cubic:
reslice->SetInterpolationModeToCubic();
break;
case vtkImageRegistration::BSpline:
reslice->SetInterpolator(bsplineInterpolator);
break;
case vtkImageRegistration::Sinc:
reslice->SetInterpolator(sincInterpolator);
break;
case vtkImageRegistration::ASinc:
sincInterpolator->AntialiasingOn();
reslice->SetInterpolator(sincInterpolator);
break;
case vtkImageRegistration::Label:
reslice->SetInterpolator(labelInterpolator);
break;
}
}
// use file extension to guess file type
int GuessFileType(const char *filename)
{
size_t n = strlen(filename);
if (n > 4 && strcmp(&filename[n-4], ".txt") == 0)
{
int ftype = TXTTransform;
ifstream infile(filename);
if (infile.good())
{
char firstline[32];
memset(firstline, '\0', 32);
infile.getline(firstline, 32);
if (strncmp(firstline, "#Insight Transform File V1.0", 28) == 0)
{
ftype = ITKTransform;
}
}
infile.close();
return ftype;
}
if (n > 4 && strcmp(&filename[n-4], ".xfm") == 0)
{
return MNITransform;
}
if (n > 4 && strcmp(&filename[n-4], ".tfm") == 0)
{
return ITKTransform;
}
if (n > 4 && strcmp(&filename[n-4], ".mat") == 0)
{
return TXTTransform;
}
if (n > 4 && strcmp(&filename[n-4], ".csv") == 0)
{
return CSVTransform;
}
if (n > 4 && strcmp(&filename[n-4], ".mnc") == 0)
{
return MINCImage;
}
if ((n > 4 && strcmp(&filename[n-4], ".nii") == 0) ||
(n > 7 && strcmp(&filename[n-7], ".nii.gz") == 0) ||
(n > 4 && strcmp(&filename[n-4], ".hdr") == 0) ||
(n > 4 && strcmp(&filename[n-4], ".img") == 0) ||
(n > 7 && strcmp(&filename[n-7], ".img.gz") == 0))
{
return NIFTIImage;
}
return DICOMImage;
}
#ifdef AIRS_USE_DICOM
vtkDICOMReader *ReadDICOMImage(
vtkImageData *data, vtkMatrix4x4 *matrix, const char *directoryName,
int coordSystem)
{
vtkDICOMReader *reader = vtkDICOMReader::New();
bool singleFile = true;
if (vtksys::SystemTools::FileIsDirectory(directoryName))
{
// get all the DICOM files in the directory
singleFile = false;
std::string dirString = directoryName;
vtksys::SystemTools::ConvertToUnixSlashes(dirString);
vtkSmartPointer<vtkGlobFileNames> glob =
vtkSmartPointer<vtkGlobFileNames>::New();
glob->SetDirectory(dirString.c_str());
glob->AddFileNames("*");
// sort the files
vtkSmartPointer<vtkDICOMSorter> sorter =
vtkSmartPointer<vtkDICOMSorter>::New();
sorter->SetInputFileNames(glob->GetFileNames());
sorter->Update();
if (sorter->GetNumberOfSeries() == 0)
{
fprintf(stderr, "Folder contains no DICOM files: %s\n", directoryName);
exit(1);
}
else if (sorter->GetNumberOfSeries() > 1)
{
fprintf(stderr, "Folder contains more than one DICOM series: %s\n",
directoryName);
exit(1);
}
reader->SetFileNames(sorter->GetFileNamesForSeries(0));
}
else
{
// was given a single file instead of a directory
reader->SetFileName(directoryName);
}
if (coordSystem == NIFTICoords)
{
reader->SetMemoryRowOrderToBottomUp();
}
else
{
reader->SetMemoryRowOrderToFileNative();
}
reader->UpdateInformation();
if (reader->GetErrorCode())
{
exit(1);
}
if (!singleFile)
{
// when reading images, only read 1st component if the
// image has multiple components or multiple time points
vtkIntArray *fileArray = reader->GetFileIndexArray();
// create a filtered list of files
vtkSmartPointer<vtkStringArray> fileNames =
vtkSmartPointer<vtkStringArray>::New();
vtkIdType n = fileArray->GetNumberOfTuples();
for (vtkIdType i = 0; i < n; i++)
{
std::string newFileName =
reader->GetFileNames()->GetValue(fileArray->GetComponent(i, 0));
bool alreadyThere = false;
vtkIdType m = fileNames->GetNumberOfTuples();
for (vtkIdType j = 0; j < m; j++)
{
if (newFileName == fileNames->GetValue(j))
{
alreadyThere = true;
break;
}
}
if (!alreadyThere)
{
fileNames->InsertNextValue(newFileName);
}
}
reader->SetFileNames(fileNames);
}
reader->SetDesiredTimeIndex(0);
reader->Update();
if (reader->GetErrorCode())
{
exit(1);
}
vtkImageData *image = reader->GetOutput();
// get the data
data->CopyStructure(image);
data->GetPointData()->PassData(image->GetPointData());
// get the matrix
matrix->DeepCopy(reader->GetPatientMatrix());
return reader;
}
void WriteDICOMImage(
vtkImageReader2 *sourceReader, vtkImageReader2 *targetReader,
vtkImageData *data, vtkMatrix4x4 *matrix, const char *directoryName,
int vtkNotUsed(coordSystem))
{
if (vtksys::SystemTools::FileExists(directoryName))
{
if (!vtksys::SystemTools::FileIsDirectory(directoryName))
{
fprintf(stderr, "option -o must give a DICOM directory, not a file.\n");
exit(1);
}
}
else if (!vtksys::SystemTools::MakeDirectory(directoryName))
{
fprintf(stderr, "Cannot create directory: %s\n", directoryName);
exit(1);
}
// get the meta data
vtkDICOMReader *reader = vtkDICOMReader::SafeDownCast(targetReader);
vtkDICOMReader *reader2 = vtkDICOMReader::SafeDownCast(sourceReader);
vtkSmartPointer<vtkDICOMMetaData> meta =
vtkSmartPointer<vtkDICOMMetaData>::New();
if (reader)
{
// copy the bulk of the meta data from the target image
meta->DeepCopy(reader->GetMetaData());
meta->SetAttributeValue(DC::SeriesNumber,
meta->GetAttributeValue(DC::SeriesNumber).AsUnsignedInt() + 1000);
std::string seriesDescription =
meta->GetAttributeValue(DC::SeriesDescription).AsString() + " REG";
if (seriesDescription.size() < 64)
{
meta->SetAttributeValue(DC::SeriesDescription, seriesDescription);
}
}
if (reader2)
{
// set the frame of reference from the source image
meta->SetAttributeValue(DC::FrameOfReferenceUID,
reader2->GetMetaData()->GetAttributeValue(
DC::FrameOfReferenceUID));
}
// make the generator
vtkSmartPointer<vtkDICOMMRGenerator> mrgenerator =
vtkSmartPointer<vtkDICOMMRGenerator>::New();
vtkSmartPointer<vtkDICOMCTGenerator> ctgenerator =
vtkSmartPointer<vtkDICOMCTGenerator>::New();
vtkDICOMGenerator *generator = 0;
if (reader)
{
std::string SOPClass =
meta->GetAttributeValue(DC::SOPClassUID).AsString();
if (SOPClass == "1.2.840.10008.5.1.4.1.1.2" ||
SOPClass == "1.2.840.10008.5.1.4.1.1.2.1" ||
SOPClass == "1.2.840.10008.5.1.4.1.1.2.2")
{
generator = ctgenerator;
}
else if (SOPClass == "1.2.840.10008.5.1.4.1.1.4" ||
SOPClass == "1.2.840.10008.5.1.4.1.1.4.1" ||
SOPClass == "1.2.840.10008.5.1.4.1.1.4.4")
{
generator = mrgenerator;
}
}
// prepare the writer to write the image
vtkSmartPointer<vtkDICOMWriter> writer =
vtkSmartPointer<vtkDICOMWriter>::New();
if (generator)
{
writer->SetGenerator(generator);
}
writer->SetMetaData(meta);
writer->SetFilePrefix(directoryName);
writer->SetFilePattern("%s/IM-0001-%04.4d.dcm");
writer->TimeAsVectorOn();
if (reader)
{
if (reader->GetTimeDimension() > 1)
{
writer->SetTimeDimension(reader->GetTimeDimension());
writer->SetTimeSpacing(reader->GetTimeSpacing());
}
if (reader->GetRescaleSlope() > 0)
{
writer->SetRescaleSlope(reader->GetRescaleSlope());
writer->SetRescaleIntercept(reader->GetRescaleIntercept());
}
writer->SetMemoryRowOrder(reader->GetMemoryRowOrder());
}
writer->SET_INPUT_DATA(data);
writer->SetPatientMatrix(matrix);
writer->Write();
}
#else
vtkDICOMImageReader *ReadDICOMImage(
vtkImageData *data, vtkMatrix4x4 *matrix, const char *directoryName,
int coordSystem)
{
// read the image
vtkDICOMImageReader *reader = vtkDICOMImageReader::New();
reader->SetDirectoryName(directoryName);
reader->Update();
if (reader->GetErrorCode())
{
exit(1);
}
vtkSmartPointer<vtkImageData> image = reader->GetOutput();
if (coordSystem != NIFTICoords)
{
// the reader flips the image and reverses the ordering, so undo these
vtkSmartPointer<vtkImageReslice> flip =
vtkSmartPointer<vtkImageReslice>::New();
flip->SetInputConnection(reader->GetOutputPort());
flip->SetResliceAxesDirectionCosines(
1,0,0, 0,-1,0, 0,0,-1);
flip->Update();
image = flip->GetOutput();
}
// get the data
data->CopyStructure(image);
data->GetPointData()->PassData(image->GetPointData());
data->SetOrigin(0,0,0);
// generate the matrix
float *position = reader->GetImagePositionPatient();
float *orientation = reader->GetImageOrientationPatient();
float *xdir = &orientation[0];
float *ydir = &orientation[3];
float zdir[3];
vtkMath::Cross(xdir, ydir, zdir);
for (int i = 0; i < 3; i++)
{
matrix->Element[i][0] = xdir[i];
matrix->Element[i][1] = ydir[i];
matrix->Element[i][2] = zdir[i];
matrix->Element[i][3] = position[i];
}
matrix->Element[3][0] = 0;
matrix->Element[3][1] = 0;
matrix->Element[3][2] = 0;
matrix->Element[3][3] = 1;
if (coordSystem == NIFTICoords)
{
double spacing[3], origin[3];
int extent[6];
image->GetSpacing(spacing);
image->GetOrigin(origin);
image->GetExtent(extent);
// account fo the y and z flips
double point[4];
point[0] = origin[0] + spacing[0]*extent[0];
point[1] = origin[1] + spacing[1]*extent[3];
point[2] = origin[2] + spacing[2]*extent[5];
point[3] = 1.0;
matrix->MultiplyPoint(point, point);
for (int j = 0; j < 3; j++)
{
matrix->Element[j][1] = -matrix->Element[j][1];
matrix->Element[j][2] = -matrix->Element[j][2];
matrix->Element[j][3] = point[j];
}
// do the DICOM to NIFTI coord conversion
for (int k = 0; k < 4; k++)
{
matrix->Element[0][k] = -matrix->Element[0][k];
matrix->Element[1][k] = -matrix->Element[1][k];
}
}
matrix->Modified();
return reader;
}
#endif
vtkMINCImageReader *ReadMINCImage(
vtkImageData *data, vtkMatrix4x4 *matrix, const char *fileName,
int coordSystem)
{
// read the image
vtkMINCImageReader *reader = vtkMINCImageReader::New();
reader->SetFileName(fileName);
reader->Update();
if (reader->GetErrorCode())
{
exit(1);
}
vtkSmartPointer<vtkImageData> image = reader->GetOutput();
if (coordSystem == DICOMCoords)
{
double spacing[3];
reader->GetOutput()->GetSpacing(spacing);
spacing[0] = fabs(spacing[0]);
spacing[1] = fabs(spacing[1]);
spacing[2] = fabs(spacing[2]);
// flip the image rows into a DICOM-style ordering
vtkSmartPointer<vtkImageReslice> flip =
vtkSmartPointer<vtkImageReslice>::New();
flip->SetInputConnection(reader->GetOutputPort());
flip->SetResliceAxesDirectionCosines(
-1,0,0, 0,-1,0, 0,0,1);
flip->SetOutputSpacing(spacing);
flip->Update();
image = flip->GetOutput();
}
// get the data
data->CopyStructure(image);
data->GetPointData()->PassData(image->GetPointData());
if (coordSystem == DICOMCoords)
{
// generate the matrix, but modify to use DICOM coords
static double xyFlipMatrix[16] =
{ -1, 0, 0, 0, 0, -1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1 };
// correct for the flip that was done earlier
vtkMatrix4x4::Multiply4x4(*reader->GetDirectionCosines()->Element,
xyFlipMatrix, *matrix->Element);
// do the left/right, up/down dicom-to-minc transformation
vtkMatrix4x4::Multiply4x4(xyFlipMatrix, *matrix->Element, *matrix->Element);
matrix->Modified();
}
else
{
matrix->DeepCopy(reader->GetDirectionCosines());
}
return reader;
}
void WriteMINCImage(
vtkImageReader2 *vtkNotUsed(sourceReader),
vtkImageReader2 *vtkNotUsed(targetReader),
vtkImageData *data, vtkMatrix4x4 *vtkNotUsed(matrix), const char *fileName,
int vtkNotUsed(coordSystem))
{
fprintf(stderr, "Writing MINC images is not supported yet, "
"the output file will have incorrect information\n");
vtkSmartPointer<vtkMINCImageWriter> writer =
vtkSmartPointer<vtkMINCImageWriter>::New();
writer->SetFileName(fileName);
writer->SET_INPUT_DATA(data);
// the input matrix must be converted
//writer->SetDirectionCosines(matrix);
writer->Write();
}
#ifdef AIRS_USE_NIFTI
vtkNIFTIReader *ReadNIFTIImage(
vtkImageData *data, vtkMatrix4x4 *matrix, const char *fileName,
int coordSystem)
{
// read the image
vtkNIFTIReader *reader = vtkNIFTIReader::New();
reader->SetFileName(fileName);
reader->Update();
if (reader->GetErrorCode())
{
exit(1);
}
vtkSmartPointer<vtkImageData> image = reader->GetOutput();
if (coordSystem == DICOMCoords)
{
double spacing[3];
reader->GetOutput()->GetSpacing(spacing);
spacing[0] = fabs(spacing[0]);
spacing[1] = fabs(spacing[1]);
spacing[2] = fabs(spacing[2]);
// flip the image rows into a DICOM-style ordering
vtkSmartPointer<vtkImageReslice> flip =
vtkSmartPointer<vtkImageReslice>::New();
flip->SetInputConnection(reader->GetOutputPort());
flip->SetResliceAxesDirectionCosines(
-1,0,0, 0,-1,0, 0,0,1);
flip->SetOutputSpacing(spacing);
flip->Update();
image = flip->GetOutput();
}
// get the data
data->CopyStructure(image);
data->GetPointData()->PassData(image->GetPointData());
// get the SForm or QForm matrix if present
static double nMatrix[16] =
{ 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1 };
if (reader->GetQFormMatrix())
{
vtkMatrix4x4::DeepCopy(nMatrix, reader->GetQFormMatrix());
}
else if (reader->GetSFormMatrix())
{
vtkMatrix4x4::DeepCopy(nMatrix, reader->GetSFormMatrix());
}
if (coordSystem == DICOMCoords)
{
// generate the matrix, but modify to use DICOM coords
static double xyFlipMatrix[16] =
{ -1, 0, 0, 0, 0, -1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1 };
// correct for the flip that was done earlier
vtkMatrix4x4::Multiply4x4(nMatrix, xyFlipMatrix, *matrix->Element);
// do the left/right, up/down dicom-to-minc transformation
vtkMatrix4x4::Multiply4x4(xyFlipMatrix, *matrix->Element, *matrix->Element);
matrix->Modified();
}
else
{
matrix->DeepCopy(nMatrix);
}
return reader;
}
void WriteNIFTIImage(
vtkImageReader2 *sourceReader, vtkImageReader2 *targetReader,
vtkImageData *data, vtkMatrix4x4 *matrix, const char *fileName,
int vtkNotUsed(coordSystem))
{
vtkNIFTIReader *sreader = vtkNIFTIReader::SafeDownCast(sourceReader);
vtkNIFTIReader *treader = vtkNIFTIReader::SafeDownCast(targetReader);
vtkSmartPointer<vtkNIFTIWriter> writer =
vtkSmartPointer<vtkNIFTIWriter>::New();
if (treader)
{
writer->SetNIFTIHeader(treader->GetNIFTIHeader());
if (treader->GetTimeDimension() > 1)
{
writer->SetTimeDimension(treader->GetTimeDimension());
writer->SetTimeSpacing(treader->GetTimeSpacing());
}
}
if (sreader)
{
if (sreader->GetQFac() < 0)
{
writer->SetQFac(-1.0);
}
}
writer->SET_INPUT_DATA(data);
writer->SetQFormMatrix(matrix);
writer->SetSFormMatrix(matrix);
writer->SetFileName(fileName);
writer->Write();
}
#endif /* AIRS_USE_NIFTI */
vtkImageReader2 *ReadImage(
vtkImageData *image, vtkMatrix4x4 *matrix, double vrange[2],
const char *filename, int coordSystem, int interpolator)
{
int t = GuessFileType(filename);
vtkImageReader2 *reader = 0;
if (t == MINCImage)
{
reader = ReadMINCImage(image, matrix, filename, coordSystem);
}
else if (t == NIFTIImage)
{
#ifdef AIRS_USE_NIFTI
reader = ReadNIFTIImage(image, matrix, filename, coordSystem);
#else
fprintf(stderr, "NIFTI files are not supported.\n");
exit(1);
#endif
}
else
{
reader = ReadDICOMImage(image, matrix, filename, coordSystem);
}
// compute the range of values present (between 1st and 99th percentile)
double fill[2];
ComputeRange(image, vrange, fill);
// if a pad value was detected, threshold to get rid of it
if (fill[1] != 0)
{
vtkSmartPointer<vtkImageThreshold> thresh =
vtkSmartPointer<vtkImageThreshold>::New();
thresh->SET_INPUT_DATA(image);
thresh->ReplaceInOff();
thresh->ReplaceOutOn();
thresh->SetOutValue(vrange[0]);
if (fill[0] > vrange[1])
{
thresh->ThresholdByLower(fill[0] - fill[1]);
}
else
{
thresh->ThresholdByUpper(fill[0] + fill[1]);
}
thresh->Update();
image->CopyStructure(thresh->GetOutput());
image->GetPointData()->PassData(thresh->GetOutput()->GetPointData());
}
// ---------
// use vtkImageReslice to eliminate any shear caused by CT tilted gantry
// use sinc interpolation here unless NN or LA requested
if (interpolator != vtkImageRegistration::Nearest &&
interpolator != vtkImageRegistration::Label)
{
interpolator = vtkImageRegistration::Sinc;
}
// get the directions from the patient matrix
vtkSmartPointer<vtkMatrix4x4> pmat =
vtkSmartPointer<vtkMatrix4x4>::New();
pmat->DeepCopy(matrix);
double xvec[4] = { 1.0, 0.0, 0.0, 0.0 };
double yvec[4] = { 0.0, 1.0, 0.0, 0.0 };
pmat->MultiplyPoint(xvec, xvec);
pmat->MultiplyPoint(yvec, yvec);
// create a matrix with z orthogonal to x and y
double normal[3];
vtkMath::Cross(xvec, yvec, normal);
matrix->SetElement(0, 2, normal[0]);
matrix->SetElement(1, 2, normal[1]);
matrix->SetElement(2, 2, normal[2]);
// compute the shear matrix
vtkSmartPointer<vtkMatrix4x4> rmat =
vtkSmartPointer<vtkMatrix4x4>::New();
pmat->Invert();
vtkMatrix4x4::Multiply4x4(pmat, matrix, rmat);
// get the parameters that characterize the shear
double zdn = rmat->GetElement(2, 2);
double xshear = rmat->GetElement(0, 2)/zdn;
double yshear = rmat->GetElement(1, 2)/zdn;
if (fabs(zdn - 1.0) < 1e-3 && fabs(xshear) < 1e-3)
{
// pure gantry tilt shear matrix will have only one element that
// is different from the identity matrix, so enforce this exactly:
xshear = 0;
zdn = 1.0;
rmat->Identity();
rmat->SetElement(1, 2, yshear);
}
// if shear is not insignificant, resample on an orthogonal grid
if (fabs(xshear) > 1e-3 || fabs(yshear) > 1e-3)
{
double origin[3], spacing[3];
int extent[6];
image->GetOrigin(origin);
image->GetSpacing(spacing);
image->GetExtent(extent);
// adjust the spacing if necessary
spacing[2] *= zdn;
origin[2] *= zdn;
// adjust the origin to centre the new volume on the old trapezoid
origin[0] -= xshear*0.5*spacing[2]*(extent[5] - extent[4]);
origin[1] -= yshear*0.5*spacing[2]*(extent[5] - extent[4]);
vtkSmartPointer<vtkImageReslice> reslice =
vtkSmartPointer<vtkImageReslice>::New();
reslice->SetResliceAxes(rmat);
reslice->SET_INPUT_DATA(image);
reslice->SetOutputOrigin(origin);
reslice->SetOutputSpacing(spacing);
reslice->SetOutputExtent(extent);
reslice->SetBackgroundLevel(vrange[0]);
SetInterpolator(reslice, interpolator);
reslice->Update();
image->CopyStructure(reslice->GetOutput());
image->GetPointData()->PassData(reslice->GetOutput()->GetPointData());
}
return reader;
}
int CoordSystem(const char *filename)
{
int t = GuessFileType(filename);
if (t == MINCImage || t == NIFTIImage)
{
return NIFTICoords;
}
return DICOMCoords;
}
void WriteImage(
vtkImageReader2 *sourceReader, vtkImageReader2 *targetReader,
vtkImageData *image, vtkMatrix4x4 *matrix,
const char *filename, int coordSystem, int interpolator)
{
#ifdef AIRS_USE_DICOM
// check if tilted-gantry images must be produced
vtkSmartPointer<vtkImageReslice> reslice =
vtkSmartPointer<vtkImageReslice>::New();
// use sinc interpolation here unless NN or LA requested
if (interpolator != vtkImageRegistration::Nearest &&
interpolator != vtkImageRegistration::Label)
{
interpolator = vtkImageRegistration::Sinc;
}
vtkDICOMReader *reader = vtkDICOMReader::SafeDownCast(sourceReader);
if (reader)
{
// get the directions from the patient matrix
vtkSmartPointer<vtkMatrix4x4> pmat =
vtkSmartPointer<vtkMatrix4x4>::New();
pmat->DeepCopy(reader->GetPatientMatrix());
// compute the shear matrix
vtkSmartPointer<vtkMatrix4x4> rmat =
vtkSmartPointer<vtkMatrix4x4>::New();
rmat->DeepCopy(matrix);
rmat->Invert();
vtkMatrix4x4::Multiply4x4(rmat, pmat, rmat);
// get the parameters that characterize the shear
double zdn = rmat->GetElement(2, 2);
double xshear = rmat->GetElement(0, 2)/zdn;
double yshear = rmat->GetElement(1, 2)/zdn;
if (fabs(zdn - 1.0) < 1e-3 && fabs(xshear) < 1e-3)
{
// pure gantry tilt shear matrix will have only one element that
// is different from the identity matrix, so enforce this exactly:
xshear = 0;
zdn = 1.0;
rmat->Identity();
rmat->SetElement(1, 2, yshear);
}
// if shear is not insignificant, resample on an orthogonal grid
if (fabs(xshear) > 1e-3 || fabs(yshear) > 1e-3)
{
double origin[3], spacing[3];
int extent[6];
image->GetOrigin(origin);
image->GetSpacing(spacing);
image->GetExtent(extent);
// adjust the spacing if necessary
spacing[2] *= zdn;
origin[2] *= zdn;
// adjust the origin to keep everything centered
origin[0] -= xshear*0.5*spacing[2]*(extent[5] - extent[4]);
origin[1] -= yshear*0.5*spacing[2]*(extent[5] - extent[4]);
reslice->SetResliceAxes(rmat);
reslice->SET_INPUT_DATA(image);
reslice->SetOutputOrigin(origin);
reslice->SetOutputSpacing(spacing);
reslice->SetOutputExtent(extent);
SetInterpolator(reslice, interpolator);
reslice->Update();
image = reslice->GetOutput();
matrix = reader->GetPatientMatrix();
}
}
#endif
int t = GuessFileType(filename);
if (t == MINCImage)
{
WriteMINCImage(
sourceReader, targetReader, image, matrix, filename, coordSystem);
}
else if (t == NIFTIImage)
{
#ifdef AIRS_USE_NIFTI
WriteNIFTIImage(
sourceReader, targetReader, image, matrix, filename, coordSystem);
#else
fprintf(stderr, "NIFTI files are not supported.\n");
exit(1);
#endif
}
else
{
#ifdef AIRS_USE_DICOM
WriteDICOMImage(
sourceReader, targetReader, image, matrix, filename, coordSystem);
#else
fprintf(stderr, "Writing DICOM files is not supported.\n");
exit(1);
#endif
}
}
// Write a csv file that can be used to plot the convergence of the
// registration. The first column is the function evaluation count,
// the second column is the cost, the fourth is the metric value,
// and the remainder of the columns are the parameters.
void WriteReport(vtkImageRegistration *reg, const char *fname)
{
vtkDoubleArray *costArray = reg->GetCostValues();
vtkDoubleArray *metricArray = reg->GetMetricValues();
vtkDoubleArray *paramArray = reg->GetParameterValues();
FILE *f = fopen(fname, "w");
if (!f)
{
fprintf(stderr, "Unable to open output file %s\n", fname);
return;
}
// get the number of free parameters
int dof = paramArray->GetNumberOfComponents();
// get the parameter names
const char **pnames = 0;
if (reg->GetTransformDimensionality() == 2)
{
static const char *p[] = {
"tx", "ty", "r", "s", "a", "q"
};
pnames = p;
}
else
{
static const char *p[] = {
"tx", "ty", "tz", "rx", "ry", "rz", "s", "a", "b", "qx", "qy", "qz"
};
pnames = p;
}
// print the header
fprintf(f, "\"%s\",\"%s\",\"%s\"", "feval", "cost", "metric");
for (int k = 0; k < dof; k++)
{
fprintf(f, ",\"%s\"", pnames[k]);
}
fprintf(f, "\n");