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Description:

itkthickness3d 6.0.0

An ITK module to compute 3D thickness

Overview
This is a module for the Insight Toolkit (ITK) that
provides filters that compute the skeleton and thickness transforms of a 3D
image.
ITK currently comes without a hands-on solution for 3D thickness evaluation.
This contribution implements several filters based on the Euclidean distance
transform and binary skeleton to fill this blank.

Binary thinning
Provides a 1 pixel-thin wire skeleton using an efficient curve thinning algorithm.
The thinning algorithm used in this module comes from the
Insight Journal article:
Homann H.
Implementation of a 3D thinning algorithm
The Insight Journal - 2007 July - December.
https://hdl.handle.net/1926/1292
https://insight-journal.org/browse/publication/181

Medial thickness
The idea behind the medial thickness as implemented in this module is
twice the shortest distance to the outter shell along the medial axis
of the object (i.e. diameter of the local maximal fitting sphere).
This definition provides an unbiased method for thickness evaluation compared
to the local thickness transform since this last one will result in a higher
number of points for thick parts. The skeletonization insure a minimal set of
measurements to fully describe the object.

Filters

itk::BinaryThinningImageFilter3D<TInputImage, TOutputImage>: Compute the 3D skeleton
of the input image.
itk::MedialThicknessImageFilter3D<TInputImage, TOutputImage>: 2x the
distance
to the outside along the medial axis.

Installation

Python
Binary Python packages are
available for Linux, macOS, and Windows. They can be installed with:
python -m pip install --upgrade pip
python -m pip install itk-thickness3d

C++
You need to build ITK
from source to use this module.
In the newer versions of ITK, this module is available as a
Remote module in the
ITK source code. Build it with the CMake option: Module_Thickness3D, this
can be switched on with a CMake graphical interface ccmake or directly
from the command line with: -DModule_Thickness3D:BOOL=ON
For older ITK versions, add it manually as an External or Remote module to
the ITK source code:
External:
cd ${itk_src}/Modules/External
git clone https://github.com/InsightSoftwareConsortium/ITKThickness3D
Remote:
Create a file in ${itk_src}/Modules/Remote called
Thickness3D.remote.cmake (see
this GitHub gist)
with the the following contents:
itk_fetch_module(Thickness3D
"Tools for 3D thickness measurement"
GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKThickness3D.git
GIT_TAG <replace with the latest stable commit tag>
)

Usage
Python
Once ITK imported, you can use the itk.MedialThicknessImageFilter3D just as
any other ITK methods:
skeleton = itk.BinaryThinningImageFilter3D.New(image)
Here is a simple python script that reads an image, applies the medial
thickness filter and writes the resulting image in a file:
import itk

input_filename = sys.argv[1]
output_filename = sys.argv[2]

image = itk.imread(input_filename)
thickness_map = itk.MedialThicknessImageFilter3D.New(image)

itk.imwrite(thickness_map, output_filename)

License
This software is distributed under the Apache 2.0 license. Please see the
LICENSE file for details.