static void doSeparate(Options& opts, StringVector& args) {
if (!opts.GetBool("--separate")) {
return;
}
ImageIO<DisplacementFieldType> io;
DisplacementFieldType::Pointer input = io.ReadImage(args[0]);
for (int i = 0; i < DisplacementFieldType::PixelType::Length; i++) {
ImageIO<RealImage> realIO;
RealImage::Pointer output = realIO.NewImageS<DisplacementFieldType>(input);
RealImage::PixelType* oBuf = output->GetBufferPointer();
itk::ImageRegionConstIteratorWithIndex<DisplacementFieldType> iter(input, input->GetBufferedRegion());
int j = 0;
for (iter.GoToBegin(); !iter.IsAtEnd(); ++iter, j++) {
DisplacementFieldType::PixelType p = iter.Get();
oBuf[j] = p[i];
}
realIO.WriteImage(args[i+1], output);
}
end();
}
// draw gaussian like line
void runExpr1(StringVector &args) {
if (args.size() < 2) {
cout << "--expr1 [output-real-image] [bending-height]" << endl;
return;
}
float bendingHeight = atof(args[1].c_str());
int bandWidth = 12;
ImageIO<RealImage2> io;
RealImage2::Pointer canvas = io.NewImageT(300, 200, 1);
for (int x = 25; x < 275; x++) {
double xx = (x - 150) * 0.1;
double y = 150 - bendingHeight * exp(-xx*xx/100);
RealImage2::IndexType realIdx;
for (int j = y; j >= y - bandWidth; j--) {
realIdx[0] = x;
realIdx[1] = j;
canvas->SetPixel(realIdx, 1);
}
}
io.WriteImage(args[0], canvas);
}
/// utility function
void zeroCrossing(Options& parser, StringVector& args) {
if (args.size() < 2) {
cout << "--zercorssing requires [srcimg] [dstimg]" << endl;
return;
}
string srcImg = args[0];
string dstImg = args[1];
ImageProcessing proc;
LabelImage::Pointer label = labelIO.ReadImage(args[0].c_str());
LabelImage::Pointer zeroCross = proc.ZeroCrossing(label);
labelIO.WriteImage(args[1].c_str(), zeroCross);
return;
}
/// create a new image which has the same attributes with the reference image
///
int runPointMarks(pi::Options& opts, pi::StringVector& args) {
vtkPolyDataReader* reader = vtkPolyDataReader::New();
reader->SetFileName(args[0].c_str());
reader->Update();
vtkPolyData*pd = reader->GetOutput();
// load an image
ImageIO<RealImage> imageIO;
RealImage::Pointer refImage = imageIO.ReadImage(args[1].c_str());
// create an empty image
ImageIO<LabelImage> labelIO;
LabelImage::Pointer markImage = labelIO.NewImageS<RealImage>(refImage);
markImage->FillBuffer(0);
// point flipping
for (int i = 0; i < pd->GetNumberOfPoints(); i++) {
RealImage::PointType p;
pd->GetPoint(i, p.GetDataPointer());
p[0] = -p[0];
p[1] = -p[1];
pd->GetPoints()->SetPoint(i, p.GetDataPointer());
// point to index
RealImage::IndexType idx;
refImage->TransformPhysicalPointToIndex(p, idx);
// mark image
markImage->SetPixel(idx, 255);
}
labelIO.WriteImage(args[2], markImage);
return EXIT_SUCCESS;
}
int main(int argc, char* argv[]) {
CSimpleOpt::SOption specs[] = {
{ 9, "--seeConfig", SO_NONE },
{ 1000, "--json", SO_REQ_SEP },
{ 1001, "--config", SO_REQ_SEP },
{ 1002, "--run", SO_NONE },
{ 1, "-w", SO_NONE },
{ 8, "-d", SO_NONE },
{ 2, "-o", SO_REQ_SEP },
{ 3, "--mean", SO_NONE },
{ 4, "--srcidx", SO_REQ_SEP },
{ 7, "--dstidx", SO_REQ_SEP },
{ 6, "--noTrace", SO_NONE },
{ 10, "--markTrace", SO_NONE },
{ 23, "--markOutput", SO_NONE },
{ 11, "--srcsubj", SO_REQ_SEP },
{ 12, "--inputimage", SO_REQ_SEP },
{ 13, "--inputlabel", SO_REQ_SEP },
{ 14, "--normalize", SO_NONE },
{ 15, "--magnitude", SO_NONE },
{ 16, "--distancemap", SO_NONE },
{ 17, "--createmask", SO_NONE },
{ 18, "--rescaletoshort", SO_NONE },
{ 19, "--mask", SO_REQ_SEP },
{ 20, "--align", SO_NONE },
{ 21, "--warp", SO_NONE },
{ 22, "--norigidalign", SO_NONE },
{ 24, "--onlyrigidalign", SO_NONE },
{ 25, "--showpoints", SO_NONE },
{ 26, "--eval", SO_NONE },
{ 27, "--histo", SO_NONE },
{ 28, "--nbin", SO_NONE },
{ 29, "--rmin", SO_NONE },
{ 30, "--rmax", SO_NONE },
{ 31, "--removeborder", SO_NONE },
{ 32, "--size", SO_REQ_SEP },
{ 33, "--traceWarp", SO_NONE },
{ 34, "--interval", SO_REQ_SEP },
{ 35, "--zerocrossing", SO_NONE },
{ 36, "--meanwarp", SO_NONE },
{ 41, "--magnitude2", SO_NONE },
{ 42, "--vector2mat", SO_NONE },
// Experiment #1
{ 37, "--expr1", SO_NONE },
{ 39, "--expr2", SO_NONE },
{ 40, "--bspline2d", SO_NONE },
{ 43, "--particleExpr", SO_NONE },
// Image Processing
{ 100, "--doGaussian", SO_REQ_SEP },
{ 101, "--doBlur2", SO_NONE },
{ 102, "--ellipse", SO_NONE },
{ 103, "--affineReg", SO_NONE },
{ 104, "--gradhist", SO_NONE },
{ 105, "--testgradreg", SO_NONE },
{ 106, "--gradmag", SO_NONE },
{ 107, "--transform2", SO_NONE },
{ 108, "--boundingbox", SO_NONE },
{ 109, "--crop", SO_REQ_SEP },
{ 110, "--slice", SO_NONE },
{ 111, "--padding", SO_REQ_SEP },
{ 112, "--deform", SO_NONE },
{ 113, "--testdisplacementfield", SO_NONE },
{ 114, "--distmap2contour", SO_NONE },
// Test Main
{ 200, "--newuoa", SO_NONE },
{ 201, "--boost", SO_NONE },
{ 202, "--testconfig", SO_NONE },
// Particle Tools
{ 300, "--coverlabel", SO_NONE },
{ 301, "--p2mat", SO_NONE },
// Options Test
{ 400, "--testjson", SO_NONE },
// PatchCompare
{ 500, "--demons", SO_NONE },
{ 501, "--makeGradientPatch", SO_NONE },
{ 502, "--opticalFlow", SO_NONE },
{ 503, "--patchtest", SO_NONE },
SO_END_OF_OPTIONS
};
cout << argv[0] << " version compiled at " << __TIMESTAMP__ << endl;
Options parser;
parser.ParseOptions(argc, argv, specs);
StringVector& args = parser.GetStringVector("args");
string output = parser.GetString("-o", "");
ParticleSystemSolver solver;
ParticleSystem& system = solver.m_System;
Options& options = solver.m_Options;
srcIdx = atoi(parser.GetString("--srcidx", "1").c_str());
dstIdx = atoi(parser.GetString("--dstidx", "0").c_str());
if (parser.GetBool("--run")) {
executeParticleRunner(parser, args);
return 0;
} else if (parser.GetBool("--demons")) {
executeDemonsRunner(parser, args);
} else if (parser.GetBool("--expr1")) {
runExpr1(args);
} else if (parser.GetBool("--expr2")) {
runExpr2(args);
} else if (parser.GetBool("--bspline2d")) {
runBspline2D(args);
} else if (parser.GetBool("--vector2mat")) {
runVector2Mat(args);
} else if (parser.GetBool("--particleExpr")) {
runParticleExperiments(args);
} else if (parser.GetBool("--seeConfig")) {
solver.LoadConfig(args[0].c_str());
cout << "Option Contents:\n\n" << options << endl;
if (args.size() > 1) {
solver.SaveConfig(args[1].c_str());
}
} else if (parser.GetBool("-w", false)) {
if (args.size() < 1 || output == "") {
cout << "warping requires [config.txt] -o [outputimage]" << endl;
return 0;
}
// load data
solver.LoadConfig(args[0].c_str());
// bspline resampling
ParticleBSpline particleTransform;
particleTransform.SetReferenceImage(solver.m_System[0].GetLabel());
int srcIdx = atoi(parser.GetString("--srcidx", "1").c_str());
int dstIdx = atoi(parser.GetString("--dstidx", "0").c_str());
if (parser.GetBool("--mean")) {
system.ComputeXMeanSubject();
particleTransform.EstimateTransform(system.GetMeanSubject(), system[srcIdx]);
} else {
cout << "warping from " << srcIdx << " to " << dstIdx << endl;
particleTransform.EstimateTransform(system[dstIdx], system[srcIdx]);
}
string input = parser.GetString("--inputimage", "");
string label = parser.GetString("--inputlabel", "");
cout << parser << endl;
bool doingSomething = false;
if (label != "") {
// write image
ImageIO<LabelImage> io;
LabelImage::Pointer outputImage = particleTransform.WarpLabel(io.ReadImage(label.c_str()));
io.WriteImage(output.c_str(), outputImage);
doingSomething = true;
}
if (input != "") {
ImageIO<RealImage> io;
RealImage::Pointer outputImage = particleTransform.WarpImage(io.ReadImage(input.c_str()));
io.WriteImage(output.c_str(), outputImage);
doingSomething = true;
}
if (!doingSomething) {
cout << "-w requires --inputimage or --inputlabel to warp" << endl;
}
} else if (parser.GetBool("--warp")) {
if (args.size() < 2) {
cout << "--warp requires [output.txt] --inputimage|inputlabel [source-image] --reference [reference] [warped-output-image]" << endl;
return 0;
}
PRINT_IDX();
string outputName = args[1];
string inputImage, inputLabel, refImageName;
parser.GetStringTo("--inputimage", inputImage);
parser.GetStringTo("--inputlabel", inputLabel);
parser.GetStringTo("--reference", refImageName);
solver.LoadConfig(args[0].c_str());
if (system.size() < 2) {
cout << "system is not loaded successfully" << endl;
return 0;
}
if (inputImage != "") {
RealImage::Pointer refImage;
// warp from srcidx to dstidx
if (refImageName != "") {
refImage = realIO.ReadImage(refImageName.c_str());
}
RealImage::Pointer output = warp_image<RealImage>(system[dstIdx], system[srcIdx], realIO.ReadImage(inputImage.c_str()), refImage, false, parser.GetBool("--norigidalign"), parser.GetBool("--onlyrigidalign"));
realIO.WriteImage(outputName.c_str(), output);
}
if (inputLabel != "") {
LabelImage::Pointer refImage;
// warp from srcidx to dstidx
if (refImageName != "") {
refImage = labelIO.ReadImage(refImageName.c_str());
}
LabelImage::Pointer output = warp_image<LabelImage>(system[dstIdx], system[srcIdx], labelIO.ReadImage(inputLabel.c_str()), refImage, true, parser.GetBool("--norigidalign"), parser.GetBool("--onlyrigidalign"));
labelIO.WriteImage(outputName.c_str(), output);
}
} else if (parser.GetBool("--meanwarp")) {
if (args.size() < 2) {
cout << "--meanwarp requires [output.txt] --inputimage|--inputlabel [source-image] [warped-output-image]" << endl;
return 0;
}
PRINT_IDX();
string outputName = args[1];
string inputImage, inputLabel, refImageName;
parser.GetStringTo("--inputimage", inputImage);
parser.GetStringTo("--inputlabel", inputLabel);
parser.GetStringTo("--reference", refImageName);
solver.LoadConfig(args[0].c_str());
ParticleSubject meanSubj = system.ComputeXMeanSubject();
if (system.size() < 2) {
cout << "system is not loaded successfully" << endl;
return 0;
}
if (inputImage != "") {
RealImage::Pointer refImage;
// warp from srcidx to dstidx
if (refImageName != "") {
refImage = realIO.ReadImage(refImageName.c_str());
}
RealImage::Pointer output = warp_image<RealImage>(meanSubj, system[srcIdx], realIO.ReadImage(inputImage.c_str()), refImage, false, parser.GetBool("--norigidalign"), parser.GetBool("--onlyrigidalign"));
realIO.WriteImage(outputName.c_str(), output);
}
if (inputLabel != "") {
LabelImage::Pointer refImage;
// warp from srcidx to dstidx
if (refImageName != "") {
refImage = labelIO.ReadImage(refImageName.c_str());
}
LabelImage::Pointer output = warp_image<LabelImage>(meanSubj, system[srcIdx], labelIO.ReadImage(inputLabel.c_str()), refImage, true, parser.GetBool("--norigidalign"), parser.GetBool("--onlyrigidalign"));
labelIO.WriteImage(outputName.c_str(), output);
}
} else if (parser.GetBool("--markTrace")) {
if (args.size() < 2) {
cout << "--meanwarp requires [output.txt] [reference-image] [output-image] --srcidx [point-index] --srcsubj [subject-index]" << endl;
return 0;
}
ifstream in(args[0].c_str());
ParticleTrace trace;
trace.Read(in);
in.close();
cout << trace << endl;
int srcIdx = atoi(parser.GetString("--srcidx", "-1").c_str());
int srcSubj = atoi(parser.GetString("--srcsubj", "-1").c_str());
ImageIO<LabelImage> io;
LabelImage::Pointer ref = io.ReadImage(args[1].c_str());
LabelImage::Pointer canvas = io.NewImage(ref);
for (int i = 0; i < trace.system.size(); i++) {
if (srcSubj == -1 || srcSubj == i) {
for (int j = 0; j < trace.system[i].timeSeries.size(); j++) {
for (int k = 0; k <= trace.system[i].maxIdx; k++) {
if (srcIdx == -1 || srcIdx == k) {
Particle& p = trace.system[i].timeSeries[j][k];
IntIndex idx;
fordim (l) {
idx[l] = p.x[l] + 0.5;
}
(*canvas)[idx] = j;
}
}
}
}
}
} else if (parser.GetBool("--markOutput")) {
// perform B-spline registration for 2D image
void runBspline2D(StringVector& args) {
typedef itk::BSplineTransform<double, 2, 3> TransformType;
typedef itk::LBFGSOptimizer OptimizerType;
typedef itk::MeanSquaresImageToImageMetric<RealImage2, RealImage2> MetricType;
typedef itk:: LinearInterpolateImageFunction<RealImage2, double> InterpolatorType;
typedef itk::ImageRegistrationMethod<RealImage2, RealImage2> RegistrationType;
MetricType::Pointer metric = MetricType::New();
OptimizerType::Pointer optimizer = OptimizerType::New();
InterpolatorType::Pointer interpolator = InterpolatorType::New();
RegistrationType::Pointer registration = RegistrationType::New();
// The old registration framework has problems with multi-threading
// For now, we set the number of threads to 1
registration->SetNumberOfThreads(1);
registration->SetMetric( metric );
registration->SetOptimizer( optimizer );
registration->SetInterpolator( interpolator );
TransformType::Pointer transform = TransformType::New();
registration->SetTransform( transform );
ImageIO<RealImage2> io;
// Create the synthetic images
RealImage2::Pointer fixedImage = io.ReadImage(args[0]);
RealImage2::Pointer movingImage = io.ReadImage(args[1]);
// Setup the registration
registration->SetFixedImage( fixedImage );
registration->SetMovingImage( movingImage);
RealImage2::RegionType fixedRegion = fixedImage->GetBufferedRegion();
registration->SetFixedImageRegion( fixedRegion );
TransformType::PhysicalDimensionsType fixedPhysicalDimensions;
TransformType::MeshSizeType meshSize;
for( unsigned int i=0; i < 2; i++ )
{
fixedPhysicalDimensions[i] = fixedImage->GetSpacing()[i] *
static_cast<double>(
fixedImage->GetLargestPossibleRegion().GetSize()[i] - 1 );
}
unsigned int numberOfGridNodesInOneDimension = 18;
meshSize.Fill( numberOfGridNodesInOneDimension - 3 );
transform->SetTransformDomainOrigin( fixedImage->GetOrigin() );
transform->SetTransformDomainPhysicalDimensions( fixedPhysicalDimensions );
transform->SetTransformDomainMeshSize( meshSize );
transform->SetTransformDomainDirection( fixedImage->GetDirection() );
typedef TransformType::ParametersType ParametersType;
const unsigned int numberOfParameters =
transform->GetNumberOfParameters();
ParametersType parameters( numberOfParameters );
parameters.Fill( 0.0 );
transform->SetParameters( parameters );
// We now pass the parameters of the current transform as the initial
// parameters to be used when the registration process starts.
registration->SetInitialTransformParameters( transform->GetParameters() );
std::cout << "Intial Parameters = " << std::endl;
std::cout << transform->GetParameters() << std::endl;
// Next we set the parameters of the LBFGS Optimizer.
optimizer->SetGradientConvergenceTolerance( 0.005 );
optimizer->SetLineSearchAccuracy( 0.9 );
optimizer->SetDefaultStepLength( .1 );
optimizer->TraceOn();
optimizer->SetMaximumNumberOfFunctionEvaluations( 1000 );
std::cout << std::endl << "Starting Registration" << std::endl;
try
{
registration->Update();
std::cout << "Optimizer stop condition = "
<< registration->GetOptimizer()->GetStopConditionDescription()
<< std::endl;
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
return;
}
OptimizerType::ParametersType finalParameters =
registration->GetLastTransformParameters();
std::cout << "Last Transform Parameters" << std::endl;
std::cout << finalParameters << std::endl;
transform->SetParameters( finalParameters );
typedef itk::ResampleImageFilter<RealImage2, RealImage2> ResampleFilterType;
ResampleFilterType::Pointer resample = ResampleFilterType::New();
resample->SetTransform( transform );
resample->SetInput( movingImage );
resample->SetSize( fixedImage->GetLargestPossibleRegion().GetSize() );
resample->SetOutputOrigin( fixedImage->GetOrigin() );
resample->SetOutputSpacing( fixedImage->GetSpacing() );
resample->SetOutputDirection( fixedImage->GetDirection() );
resample->SetDefaultPixelValue( 100 );
resample->Update();
io.WriteImage(args[2], resample->GetOutput());
}