ITK  5.2.0
Insight Toolkit
Examples/Filtering/MinMaxCurvatureFlowImageFilter.cxx
/*=========================================================================
*
* Copyright NumFOCUS
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
// Software Guide : BeginCommandLineArgs
// INPUTS: {BrainProtonDensitySlice.png}
// OUTPUTS: {MinMaxCurvatureFlowImageFilterOutput.png}
// ARGUMENTS: 10 0.125 1
// Software Guide : EndCommandLineArgs
// Software Guide : BeginLatex
//
//
// \begin{figure}
// \center
// \includegraphics[width=0.5\textwidth]{MinMaxCurvatureFlowFunctionDiagram}
// \itkcaption[MinMaxCurvatureFlow computation]{Elements involved in the
// computation of min-max curvature flow.}
// \label{fig:MinMaxCurvatureFlowFunctionDiagram}
// \end{figure}
//
// The MinMax curvature flow filter applies a variant of the curvature flow
// algorithm where diffusion is turned on or off depending of the scale of
// the noise that one wants to remove. The evolution speed is switched
// between
// $\min(\kappa,0)$ and $\max(\kappa,0)$ such that:
//
// \begin{equation}
// I_t = F |\nabla I|
// \end{equation}
//
// where $F$ is defined as
//
// \begin{equation}
// F = \left\{ \begin{array} {r@{\quad:\quad}l}
// \max(\kappa,0) & \mbox{Average} < Threshold \\ \min(\kappa,0) &
// \mbox{Average} \ge Threshold
// \end{array} \right.
// \end{equation}
//
// The $Average$ is the average intensity computed over a neighborhood of a
// user-specified radius of the pixel. The choice of the radius governs the
// scale of the noise to be removed. The $Threshold$ is calculated as the
// average of pixel intensities along the direction perpendicular to the
// gradient at the \emph{extrema} of the local neighborhood.
//
// A speed of $F = max(\kappa,0)$ will cause small dark regions in a
// predominantly light region to shrink. Conversely, a speed of $F =
// min(\kappa,0)$, will cause light regions in a predominantly dark region to
// shrink. Comparison between the neighborhood average and the threshold is
// used to select the the right speed function to use. This switching
// prevents the unwanted diffusion of the simple curvature flow method.
//
// Figure~\ref{fig:MinMaxCurvatureFlowFunctionDiagram} shows the main
// elements involved in the computation. The set of square pixels represent
// the neighborhood over which the average intensity is being computed. The
// gray pixels are those lying close to the direction perpendicular to the
// gradient. The pixels which intersect the neighborhood bounds are used to
// compute the threshold value in the equation above. The integer radius of
// the neighborhood is selected by the user.
//
// \index{itk::MinMax\-Curvature\-Flow\-Image\-Filter}
//
// Software Guide : EndLatex
#include "itkImage.h"
// Software Guide : BeginLatex
//
// The first step required to use the
// \doxygen{MinMaxCurvatureFlowImageFilter} is to include its header file.
//
// \index{itk::MinMax\-Curvature\-Flow\-Image\-Filter!header}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// Software Guide : EndCodeSnippet
int
main(int argc, char * argv[])
{
if (argc < 6)
{
std::cerr << "Usage: " << std::endl;
std::cerr << argv[0] << " inputImageFile outputImageFile ";
std::cerr << "numberOfIterations timeStep stencilRadius" << std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginLatex
//
// Types should be selected based on the pixel types required for the
// input and output images. The input and output image types are
// instantiated.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using InputPixelType = float;
using OutputPixelType = float;
using InputImageType = itk::Image<InputPixelType, 2>;
using OutputImageType = itk::Image<OutputPixelType, 2>;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The \doxygen{MinMaxCurvatureFlowImageFilter} type is now instantiated
// using both the input image and the output image types. The filter is
// then created using the \code{New()} method.
//
// \index{itk::MinMax\-Curvature\-Flow\-Image\-Filter!instantiation}
// \index{itk::MinMax\-Curvature\-Flow\-Image\-Filter!New()}
// \index{itk::MinMax\-Curvature\-Flow\-Image\-Filter!Pointer}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using FilterType =
FilterType::Pointer filter = FilterType::New();
// Software Guide : EndCodeSnippet
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(argv[1]);
// Software Guide : BeginLatex
//
// The input image can be obtained from the output of another filter. Here,
// an image reader is used as source.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
filter->SetInput(reader->GetOutput());
// Software Guide : EndCodeSnippet
const unsigned int numberOfIterations = std::stoi(argv[3]);
const double timeStep = std::stod(argv[4]);
using RadiusType = FilterType::RadiusValueType;
const RadiusType radius = atol(argv[5]);
// Software Guide : BeginLatex
//
// The \doxygen{MinMaxCurvatureFlowImageFilter} requires the two normal
// parameters of the CurvatureFlow image, the number of iterations to be
// performed and the time step used in the computation of the level set
// evolution. In addition, the radius of the neighborhood is also
// required. This last parameter is passed using the
// \code{SetStencilRadius()} method. Note that the radius is provided as an
// integer number since it is referring to a number of pixels from the
// center to the border of the neighborhood. Then the filter can be
// executed by invoking \code{Update()}.
//
// \index{itk::MinMax\-Curvature\-Flow\-Image\-Filter!Update()}
// \index{itk::MinMax\-Curvature\-Flow\-Image\-Filter!SetTimeStep()}
// \index{itk::MinMax\-Curvature\-Flow\-Image\-Filter!SetNumberOfIterations()}
// \index{SetTimeStep()!itk::MinMax\-Curvature\-Flow\-Image\-Filter}
// \index{SetNumberOfIterations()!itk::MinMax\-Curvature\-Flow\-Image\-Filter}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
filter->SetTimeStep(timeStep);
filter->SetNumberOfIterations(numberOfIterations);
filter->SetStencilRadius(radius);
filter->Update();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Typical values for the time step are $0.125$ in $2D$ images and
// $0.0625$ in $3D$ images. The number of iterations can be usually around
// $10$, more iterations will result in further smoothing and will
// increase the computing time linearly. The radius of the stencil can be
// typically $1$. The \emph{edge-preserving} characteristic is not perfect
// on this filter. Some degradation will occur on the edges and will
// increase as the number of iterations is increased.
//
// Software Guide : EndLatex
// Software Guide : BeginLatex
//
// If the output of this filter has been connected to other filters down
// the pipeline, updating any of the downstream filters will
// trigger the execution of this one. For example, a writer filter can
// be used after the curvature flow filter.
//
// Software Guide : EndLatex
using WritePixelType = unsigned char;
using WriteImageType = itk::Image<WritePixelType, 2>;
using RescaleFilterType =
RescaleFilterType::Pointer rescaler = RescaleFilterType::New();
rescaler->SetOutputMinimum(0);
rescaler->SetOutputMaximum(255);
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(argv[2]);
// Software Guide : BeginCodeSnippet
rescaler->SetInput(filter->GetOutput());
writer->SetInput(rescaler->GetOutput());
writer->Update();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// \begin{figure}
// \center
// \includegraphics[width=0.44\textwidth]{BrainProtonDensitySlice}
// \includegraphics[width=0.44\textwidth]{MinMaxCurvatureFlowImageFilterOutput}
// \itkcaption[MinMaxCurvatureFlowImageFilter output]{Effect of the
// MinMaxCurvatureFlowImageFilter on a slice from a MRI proton density image
// of the brain.}
// \label{fig:MinMaxCurvatureFlowImageFilterInputOutput}
// \end{figure}
//
// Figure \ref{fig:MinMaxCurvatureFlowImageFilterInputOutput} illustrates
// the effect of this filter on a MRI proton density image of the
// brain. In this example the filter was run with a time step of $0.125$,
// $10$ iterations and a radius of $1$. The figure shows how homogeneous
// regions are smoothed and edges are preserved. Notice also, that the
// result in the figure has sharper edges than the same example using
// simple curvature flow in Figure
// \ref{fig:CurvatureFlowImageFilterInputOutput}.
//
// \relatedClasses
// \begin{itemize}
// \item \doxygen{CurvatureFlowImageFilter}
// \end{itemize}
//
//
// Software Guide : EndLatex
return EXIT_SUCCESS;
}
itk::MinMaxCurvatureFlowImageFilter
Denoise an image using min/max curvature flow.
Definition: itkMinMaxCurvatureFlowImageFilter.h:83
itkImageFileReader.h
itkImage.h
itk::ImageFileReader
Data source that reads image data from a single file.
Definition: itkImageFileReader.h:75
itk::ImageFileWriter
Writes image data to a single file.
Definition: itkImageFileWriter.h:87
itkMinMaxCurvatureFlowImageFilter.h
itkRescaleIntensityImageFilter.h
itkImageFileWriter.h
itk::RescaleIntensityImageFilter
Applies a linear transformation to the intensity levels of the input Image.
Definition: itkRescaleIntensityImageFilter.h:154
itk::Image
Templated n-dimensional image class.
Definition: itkImage.h:86