SimpleITK/Advisory Review Board: Difference between revisions

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= Board Members =
* Harvey Cline, Kitware Inc.
* Harvey Cline, Kitware Inc.
* Raghu Machiraju, The State University of Ohio
* Raghu Machiraju, The Ohio State University
* John Galeotti, CMU
* John Galeotti, CMU
* Hans Johnson, University of Iowa
* Hans Johnson, University of Iowa
Line 6: Line 8:
* New students in the UNC CISMM project (taylorr@cs.unc.edu)
* New students in the UNC CISMM project (taylorr@cs.unc.edu)
* Jesus Caban, NLM-NIH
* Jesus Caban, NLM-NIH
* Manuel Grizzonet, Orfeo Toolbox, CNES - France
* Julien Michel, Orfeo Toolbox, CNES - France


= ARB Prototype Code =
= Prototype Code for Discussions =
 
== Gaussian Blur ==
* Open an image
* Filter the image with a Gaussian blur using sigma = 2
* Write the image back out
 
==== Procedural ====
<pre style="display: inline-block;">
// 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");
</pre>
 
==== Filter Blocks ====
<pre style="display: inline-block;">
// 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 );
</pre>
 
==== Pipelined ====
<pre style="display: inline-block;">
// 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();
</pre>
 
== 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 ====
<pre style="display: inline-block;">
// 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" );
</pre>
 
==== Filter blocks ====
<pre style="display: inline-block;">
// 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 );
</pre>
 
==== Pipeline ====
<pre style="display: inline-block;">
// 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();
</pre>
 
==== Enum approach ====
<pre>
// 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 );
registration.setFixedImage( fixedImage );
registration.setMovingImage( movingImage );
</pre>
 
== Level Set ==
 
== Region Growing ==
 
== Watershed ==


== QuadEdgeMesh ==
* [[ITK_Release_4/SimpleITK/Advisory Review Board/Prototype Code Discussions|Prototype Code Discussions]]

Latest revision as of 17:51, 13 February 2013

Board Members

  • Harvey Cline, Kitware Inc.
  • Raghu Machiraju, The Ohio State University
  • 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
  • Manuel Grizzonet, Orfeo Toolbox, CNES - France
  • Julien Michel, Orfeo Toolbox, CNES - France

Prototype Code for Discussions