SimpleITK/Advisory Review Board

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< SimpleITK
Revision as of 03:04, 3 September 2010 by Danmueller (talk | contribs) (Added regsitration enum approach)
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  • Harvey Cline, Kitware Inc.
  • Raghu Machiraju, The State University of Ohio
  • John Galeotti, CMU
  • Hans Johnson, University of Iowa
  • Fabrice de Chaumont, Pasteur Institute
  • New students in the UNC CISMM project (taylorr@cs.unc.edu)
  • Jesus Caban, NLM-NIH

ARB Prototype Code

Gaussian Blur

  • Open an image
  • Filter the image with a Gaussian blur using sigma = 2
  • Write the image back out

Procedural

// Read the image
Image::Pointer im = ImageFileReader::Execute("sample/path/to/image.jpg");

// Apply Gaussian with sigma = 2
im = GaussianFilter::Execute(im, 2);

// Write out the image
ImageFileWriter::Execute(im, "sample/path/to/output.png");

Filter Blocks

// Read the image
ImageFileReader reader;
reader.SetFilename( "sample/path/to/image.jpg" );
Image::Pointer im = reader.execute();

// Apply Gaussian with sigma = 2
Gaussian filter;
filter.SetSigma( 2 );
im = filter.execute( im );

// Write out the image
ImageFileWriter writer;
writer.SetFilename( "sample/path/to/output.png" );
writer.execute( im );

Pipelined

// Read the image
ImageFileReader reader;
reader.SetFilename( "sample/path/to/image.jpg" );

// Apply Gaussian with sigma = 2
Gaussian filter;
filter.SetSigma( 2 );
filter.SetInput( reader.getOutput() );

// Write out the image
ImageFileWriter writer;
writer.SetFilename( "sample/path/to/output.png" );
writer.SetInput( filter->GetOutput() );

// Execute the pipieline
writer.Update();

Image Registration

  • Open two images (one fixed, one moving)
  • Register the moving image to the fixed image using affine registration
  • Resample the moving image using the computed transform
  • Write the resampled image out

Procedural

// Open the fixed and moving images
Image::Pointer fixedImage = ImageFileReader::Execute( "path/to/fixed.jpg" );
Image::Pointer movingImage = ImageFileReader::Execute( "path/to/moving.jpg" );

// Register the moving image to the fixed image
AffineTransform::Pointer transform AffineRegistrator::Execute( fixedImage, movingImage );

// Resample the moving image
movingImage = ImageResampler::Execute( movingImage, transform );

// Write out the resampled image
ImageFileWriter::Ececute( movingImage, "path/to/output.png" );

Filter blocks

// Open the fixed and moving images
ImageFileReader reader;
reader.SetFilename( "path/to/fixed.jpg" );
Image::Pointer fixedImage = reader.execute();
reader.SetFilename( "path/to/moving.jpg" );
Image::Pointer movingImage = reader.execute();

// Register the moving image to the fixed image
AffineRegistrator registrator;
registrator.SetFixedImage( fixedImage );
registrator.SetMovingImage( movingImage );
AffineTransform transform;
transform = registrator.execute();

// Resample the moving image
Resampler resampler;
resampler.SetTransform( transform );
movingImage = resampler.execute( movingImage );

// Write out the resampled image
ImageFileWriter writer;
writer.SetFilename( "path/to/output.png" );
writer.ececute( movingImage );

Pipeline

// Open the fixed and moving images
ImageFileReader reader1;
ImageFileReader reader2;
reader1.SetFilename( "path/to/fixed.jpg" );
reader2.SetFilename( "path/to/moving.jpg" );

// Register the moving image to the fixed image
AffineRegistrator registrator;
registrator.SetFixedImage( reader1.GetOutput() );
registrator.SetMovingImage( reader2.GetOutput() );

// Resample the moving image
Resampler resampler;
resampler.SetInput( reader2.GetOutput() );
resampler.SetTransform( registrator.GetOutput() );

// Write out the resampled image
ImageFileWriter writer;
writer.SetFilename( "path/to/output.png" );
writer.SetInput( movingImage );

// Execute the pipeline
writer.Update();

Enum approach

// NOTE: Language = C#
// Create metric
itk::simple::simpleMetric metric;
metric.setType( itk::simple::MattesMutualInformation );
metric.setParameterInt( "NumberOfHistogramBins", 30 );
metric.setParameterInt( "NumberOfSpatialSamples", 1000 );

// Create interpolator
itk::simple::simpleInterpolator interpolator;
interpolator.setType( itk::simple::LanczosWindowedSincInterpolation );

// Create transform
itk::simple::simpleTransform transform;
transform.setType( itk::simple::AffineTransform );

// Create optimizer
itk::simple::simpleOptimizer optimizer;
optimizer.setType( itk::simple::RegularStepGradientDescentOptimizer );
optimizer.setParameterInt( "NumberOfIterations", 100 );
optimizer.setParameterDouble( "MinimumStepLength", 0.005 );
optimizer.setParameterDouble( "MaximumStepLength", 1.0 );
optimizer.setParameterBoolean( "Maximize", true );

// Registration
itk::simple::simpleRegistration registration;
registration.setMetric( metric );
registration.setInterpolator( interpolator );
registration.setTransform( transform );
registration.setOptimizer( optimizer );

Level Set

Region Growing

Watershed

QuadEdgeMesh