Documentation/4.0/Modules/GradientAnisotropicDiffusion

Return to the Slicer 4.0 Documentation

Gallery of New Features

Introduction and Acknowledgements

MyModule: Put the name of the module here	This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from National Centers for Biomedical Computing. Contact: millerjv at ge.crd	NA-MIC
		ITK

Module Description

Runs gradient anisotropic diffusion on a volume.

Anisotropic diffusion methods reduce noise (or unwanted detail) in images while preserving specific image features, like edges. For many applications, there is an assumption that light-dark transitions (edges) are interesting. Standard isotropic diffusion methods move and blur light-dark boundaries. Anisotropic diffusion methods are formulated to specifically preserve edges. The conductance term for this implementation is a function of the gradient magnitude of the image at each point, reducing the strength of diffusion at edges.

The numerical implementation of this equation is similar to that described in the Perona-Malik paper, but uses a more robust technique for gradient magnitude estimation and has been generalized to N-dimensions.

references giving more details on the algorithm.

Use Cases

Most frequently used for these scenarios:

• Use Case 1:
• Use Case 2:

Tutorials

Links to tutorials that use this module

Panels and their use

GradientAnisotropicDiffusion  [--returnparameterfile
                              <std::string>]
                              [--processinformationaddress
                              <std::string>] [--xml] [--echo]
                              [--timeStep <double>] [--iterations
                              <int>] [--conductance <double>]
                              [--] [--version] [-h] <std::string>
                              <std::string>


Where: 

   --returnparameterfile <std::string>
     Filename in which to write simple return parameters (int, float,
     int-vector, etc.) as opposed to bulk return parameters (image,
     geometry, transform, measurement, table).

   --processinformationaddress <std::string>
     Address of a structure to store process information (progress, abort,
     etc.). (default: 0)

   --xml
     Produce xml description of command line arguments (default: 0)

   --echo
     Echo the command line arguments (default: 0)

   --timeStep <double>
     The time step depends on the dimensionality of the image. In Slicer3
     the images are 3D and the default (.0625) time step will provide a
     stable solution. (default: 0.0625)

   --iterations <int>
     The more iterations, the more smoothing. Each iteration takes the same
     amount of time. If it takes 10 seconds for one iteration, then it will
     take 100 seconds for 10 iterations. Note that the conductance controls
     how much each iteration smooths across edges. (default: 5)

   --conductance <double>
     Conductance controls the sensitivity of the conductance term. As a
     general rule, the lower the value, the more strongly the filter
     preserves edges. A high value will cause diffusion (smoothing) across
     edges. Note that the number of iterations controls how much smoothing
     is done within regions bounded by edges. (default: 1)

   --,  --ignore_rest
     Ignores the rest of the labeled arguments following this flag.

   --version
     Displays version information and exits.

   -h,  --help
     Displays usage information and exits.

   <std::string>
     (required)  Input volume to be filtered

   <std::string>
     (required)  Output filtered

A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:

Input panel1: First input Second input Parameters panel: First parameter Second parameter Output panel: First output Second output Viewing panel:	GradientAnisotropicDiffusion
Input panel2: First input Second input Parameters panel: First parameter Second parameter Output panel: First output Second output Viewing panel:	Name of panel 2

Similar Modules

• Point to other modules that have similar functionality

References

Publications related to this module go here. Links to pdfs would be useful. For extensions: link to the source code repository and additional documentation

Information for Developers

Module Type & Category

Type: Interactive or CLI

Category: Base or (Filtering, Registration, etc.)

Notes from the Developer(s)

Algorithms used, library classes depended upon, use cases, etc.

Dependencies

Other modules or packages that are required for this module's use.

Tests

On the Slicer4 Dashboard, these tests verify that the module is working on various platforms:

• MyModuleTest1 MyModuleTest1.cxx
• MyModuleTest2 MyModuleTest2.cxx

Source code & documentation

Links to the module's source code:

Source code:

• file.cxx
• file.h

Doxygen documentation:

• class1