A module for the Insight Toolkit (ITK) that provides a generic, modular, and extensible architecture for lesion sizing algorithms in medical images as well as a reference algorithm for lung solid lesion segmentation in CT images.

License: Other

TeX 13.48% C++ 76.32% CMake 9.84% Python 0.24% C 0.12%

itk insight-toolkit itk-module computed-tomography segmentation lung-cancer

lesionsizingtoolkit's Introduction

The Lesion Sizing Toolkit (LSTK)

Linux	macOS	Windows

Overview

This is a module for the Insight Toolkit (ITK) that provides a generic, modular, and extensible architecture for lesion sizing algorithms in medical images as well as a reference algorithm for lung solid lesion segmentation in CT images.

For more information, see the Insight Journal article:

Liu X., Helba B., Krishnan K., Reynolds P., McCormick M., Turner W., Ibáñez L., Yankelevitz D., Avila R.
Fostering Open Science in Lung Cancer Lesion Sizing with ITK module LSTK
The Insight Journal. January-December. 2012.
https://hdl.handle.net/10380/3369
https://www.insight-journal.org/browse/publication/869

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-lesionsizingtoolkit

Data

The project has extensively used the CT lesion data assembled by NIST for the Biochange 2008 Pilot Study. The data collection can be obtained via ftp from here.

The team participated in the Volcano'09 Challenge benchmark.

The project has also been used on the BioChange 2011 study. The clinical data used here was chosen from the publicly available Reference Image Database to Evaluate Therapy Response (RIDER) database and from the NIST-generated CT phantom series. 96 pairs of clinical datasets are present. Datasets have slice thickness varying from 0.63 to 2.5 mm. Kitware's results on the Biochange2011 challenge may be found here.

License

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

Acknowledgements

This work was supported by the Optical Society of America (OSA), the Air Force Research Laboratory (AFRL), and the National Library of Medicine (NLM).

lesionsizingtoolkit's People

Contributors

Stargazers

Watchers

Forkers

cpatrick midasplatform luisibanez kanowl jhlegarreta devhliu dzenanz thewtex lhn0610 gunnups mseng10 joonvan

lesionsizingtoolkit's Issues

Add CI

Add Continuous Integration to the module.

Refactor the module

As @dzenanz pointed in #20 , the module needs to be refactored. Some classes seem to be specialized versions of classes that exist in the toolkit (Canny detection filters, morphological filters, etc.), but it should be investigated whether better inheritance can be achieved.

Some minor issues related to the refactoring, or which could be done while refactoring are:

Separate the class header from the implementation (e.g. see itk::DescoteauxSheetnessImageFilter).
Provide Set / Get methods using ITK macros for all ivars.
Provide some default values for ivars (e.g. see itk::DescoteauxSheetnessImageFilter).
Provide the implementation for the PrintSelf method in cases which is missing or incomplete.
Prefer initialization lists over assignment.

BUG: itkGrayscaleImageSegmentationVolumeEstimatorTest1 test fails

When LesionSizingToolkit is compiled against any version of ITK and ctest is ran in the build directory, itkGrayscaleImageSegmentationVolumeEstimatorTest1 fails with the following error:

Source of issue:

The function FloatAlmostEqual is comparing 1e-1 (0.1%) against the percent error in the volume estimation, with epsilon = 1e-6. If we are asserting the percent error is less than .1%, would we want to compare the percent error against 0.0%, with epsilon = 1e-1? If not, would this be an error in the estimator?

Trouble installing itk-lesionsizingtoolkit

I input the following code -
!pip install itk
!python -m pip install --upgrade pip
!python -m pip install itk-lesionsizingtoolkit

and I am getting the following error-
ERROR: Could not find a version that satisfies the requirement itk-lesionsizingtoolkit (from versions: none)
ERROR: No matching distribution found for itk-lesionsizingtoolkit

Is there a reason I am still not able to install?

Unable to successfully compile LesionSizingToolkit module

I am unable to successfully compile the LesionSizingToolkit module using ITK 5.12. I am building the module in tree by enabling the Module_LesionSizingToolkit option, setting LSTK_USE_VTK=ON. I have tried VTK 9.0.1 and VTK 7.1.1. I am using Ubuntu 20.04.2.

I receive the following errors:
`[ 80%] Building CXX object Modules/Remote/LesionSizingToolkit/Examples/CMakeFiles/LesionSegmentation.dir/LesionSegmentation.cxx.o

In file included from /home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentation.cxx:40:

/home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentationCLI.h: In member function ‘double* LesionSegmentationCLI::GetROI()’:
/home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentationCLI.h:128:37: error: ‘__gnu_cxx::__alloc_traits<std::allocator<itk::SpatialObjectPoint<3> >, itk::SpatialObjectPoint<3> >::value_type’ {aka ‘class itk::SpatialObjectPoint<3>’} has no member named ‘GetPosition’
128 | this->ROI[2 * i] = seeds[0].GetPosition()[i] - this->GetValueAsFloat("MaximumRadius");
| ^~~~~~~~~~~
/home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentationCLI.h:129:41: error: ‘__gnu_cxx::__alloc_traits<std::allocator<itk::SpatialObjectPoint<3> >, itk::SpatialObjectPoint<3> >::value_type’ {aka ‘class itk::SpatialObjectPoint<3>’} has no member named ‘GetPosition’
129 | this->ROI[2 * i + 1] = seeds[0].GetPosition()[i] + this->GetValueAsFloat("MaximumRadius");
| ^~~~~~~~~~~
/home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentationCLI.h: In member function ‘LesionSegmentationCLI::LandmarkPointListType LesionSegmentationCLI::GetSeeds()’:
/home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentationCLI.h:255:16: error: ‘__gnu_cxx::__alloc_traits<std::allocator<itk::SpatialObjectPoint<3> >, itk::SpatialObjectPoint<3> >::value_type’ {aka ‘class itk::SpatialObjectPoint<3>’} has no member named ‘SetPosition’
255 | seeds[i].SetPosition(sx, sy, sz);
| ^~~~~~~~~~~
In file included from /usr/include/dirent.h:245,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentationCLI.h:17,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentation.cxx:40:
/home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentation.cxx: In function ‘itk::Image<short int, 3>::Pointer GetImage(std::string, bool)’:
/home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentation.cxx:154:14: error: conversion from ‘long int’ to ‘itk::Image<short int, 3>::Pointer’ {aka ‘itk::SmartPointer<itk::Image<short int, 3> >’} is ambiguous
154 | return NULL;
| ^~~~
In file included from /home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkExceptionObject.h:25,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkMacro.h:1272,
from /home/artit/src/InsightToolkit-5.1.2/Modules/IO/ImageBase/include/itkImageFileReaderException.h:22,
from /home/artit/src/InsightToolkit-5.1.2/Modules/IO/ImageBase/include/itkImageFileReader.h:20,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentation.cxx:1:
/home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkSmartPointer.h:99:3: note: candidate: ‘itk::SmartPointer::SmartPointer(itk::SmartPointer::ObjectType*) [with TObjectType = itk::Image<short int, 3>; itk::SmartPointer::ObjectType = itk::Image<short int, 3>]’
99 | SmartPointer(ObjectType * p) noexcept
| ^~~~~~~~~~~~
/home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkSmartPointer.h:71:13: note: candidate: ‘constexpr itk::SmartPointer::SmartPointer(std::nullptr_t) [with TObjectType = itk::Image<short int, 3>; std::nullptr_t = std::nullptr_t]’
71 | constexpr SmartPointer(std::nullptr_t p) noexcept
| ^~~~~~~~~~~~
In file included from /usr/include/dirent.h:245,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentationCLI.h:17,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentation.cxx:40:
/home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentation.cxx:175:12: error: conversion from ‘long int’ to ‘itk::Image<short int, 3>::Pointer’ {aka ‘itk::SmartPointer<itk::Image<short int, 3> >’} is ambiguous
175 | return NULL;
| ^~~~
In file included from /home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkExceptionObject.h:25,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkMacro.h:1272,
from /home/artit/src/InsightToolkit-5.1.2/Modules/IO/ImageBase/include/itkImageFileReaderException.h:22,
from /home/artit/src/InsightToolkit-5.1.2/Modules/IO/ImageBase/include/itkImageFileReader.h:20,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentation.cxx:1:
/home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkSmartPointer.h:99:3: note: candidate: ‘itk::SmartPointer::SmartPointer(itk::SmartPointer::ObjectType*) [with TObjectType = itk::Image<short int, 3>; itk::SmartPointer::ObjectType = itk::Image<short int, 3>]’
99 | SmartPointer(ObjectType * p) noexcept
| ^~~~~~~~~~~~
/home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkSmartPointer.h:71:13: note: candidate: ‘constexpr itk::SmartPointer::SmartPointer(std::nullptr_t) [with TObjectType = itk::Image<short int, 3>; std::nullptr_t = std::nullptr_t]’
71 | constexpr SmartPointer(std::nullptr_t p) noexcept
| ^~~~~~~~~~~~
In file included from /usr/include/dirent.h:245,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentationCLI.h:17,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentation.cxx:40:
/home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentation.cxx:178:10: error: conversion from ‘long int’ to ‘itk::Image<short int, 3>::Pointer’ {aka ‘itk::SmartPointer<itk::Image<short int, 3> >’} is ambiguous
178 | return NULL;
| ^~~~
In file included from /home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkExceptionObject.h:25,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkMacro.h:1272,
from /home/artit/src/InsightToolkit-5.1.2/Modules/IO/ImageBase/include/itkImageFileReaderException.h:22,
from /home/artit/src/InsightToolkit-5.1.2/Modules/IO/ImageBase/include/itkImageFileReader.h:20,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentation.cxx:1:
/home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkSmartPointer.h:99:3: note: candidate: ‘itk::SmartPointer::SmartPointer(itk::SmartPointer::ObjectType*) [with TObjectType = itk::Image<short int, 3>; itk::SmartPointer::ObjectType = itk::Image<short int, 3>]’
99 | SmartPointer(ObjectType * p) noexcept
| ^~~~~~~~~~~~
/home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkSmartPointer.h:71:13: note: candidate: ‘constexpr itk::SmartPointer::SmartPointer(std::nullptr_t) [with TObjectType = itk::Image<short int, 3>; std::nullptr_t = std::nullptr_t]’
71 | constexpr SmartPointer(std::nullptr_t p) noexcept
| ^~~~~~~~~~~~
make[2]: *** [Modules/Remote/LesionSizingToolkit/Examples/CMakeFiles/LesionSegmentation.dir/build.make:63: Modules/Remote/LesionSizingToolkit/Examples/CMakeFiles/LesionSegmentation.dir/LesionSegmentation.cxx.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:15615: Modules/Remote/LesionSizingToolkit/Examples/CMakeFiles/LesionSegmentation.dir/all] Error 2
make: *** [Makefile:152: all] Error 2`

EDIT: I tried ITK 4.13.3 with VTK 7.1 and it compiled successfully. So the problem seems to be with the latest versions of ITK.

Compiler error concerning ITK_THREAD_RETURN_VALUE

There seems to be a compiler error involving the ITK_THREAD_RETURN_VALUE define:

Error C2065 'ITK_THREAD_RETURN_VALUE': undeclared identifier itkCannyEdgeDetectionImageFilter2  
\lesionsizingtoolkit\include\itkCannyEdgeDetectionRecursiveGaussianImageFilter.hxx 305

@dzenanz could you please cast some light on this?

Also missing to use the ProgressTransformer class instead of ProgressReporter.

Add license file.

The license file is missing from this module.

According to the LST wiki, BSD applies, but ITK uses Apache. Which one should be used?

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