ENH: Add CI.

.circleci/config.yml

@@ -0,0 +1,63 @@
+version: 2
+jobs:
+  build-and-test:
+    working_directory: /LesionSizingToolkit-build
+    docker:
+      - image: insighttoolkit/module-ci:latest
+    steps:
+      - checkout:
+          path: /LesionSizingToolkit
+      - run:
+          name: Fetch CTest driver script
+          command: |
+            curl -L https://raw.githubusercontent.com/InsightSoftwareConsortium/ITK/dashboard/itk_common.cmake -O
+      - run:
+          name: Configure CTest script
+          command: |
+            SHASNIP=$(echo $CIRCLE_SHA1 | cut -c1-7)
+            cat > dashboard.cmake << EOF
+            set(CTEST_SITE "CircleCI")
+            set(CTEST_BUILD_NAME "External-LesionSizingToolkit-${CIRCLE_BRANCH}-${CIRCLE_BUILD_NUM}-${SHASNIP}")
+            set(CTEST_BUILD_CONFIGURATION "MinSizeRel")
+            set(CTEST_CMAKE_GENERATOR "Unix Makefiles")
+            set(CTEST_BUILD_FLAGS: "-j5")
+            set(CTEST_SOURCE_DIRECTORY /LesionSizingToolkit)
+            set(CTEST_BINARY_DIRECTORY /LesionSizingToolkit-build)
+            set(dashboard_model Experimental)
+            set(dashboard_no_clean 1)
+            set(dashboard_cache "
+            ITK_DIR:PATH=/ITK-build
+            BUILD_TESTING:BOOL=ON
+            ")
+            include(\${CTEST_SCRIPT_DIRECTORY}/itk_common.cmake)
+            EOF
+      - run:
+          name: Build and Test
+          no_output_timeout: 1.0h
+          command: |
+            ctest -j 2 -VV -S dashboard.cmake
+  package:
+    working_directory: ~/LesionSizingToolkit
+    machine: true
+    steps:
+      - checkout
+      - run:
+          name: Fetch build script
+          command: |
+            curl -L https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKPythonPackage/master/scripts/dockcross-manylinux-download-cache-and-build-module-wheels.sh -O
+            chmod u+x dockcross-manylinux-download-cache-and-build-module-wheels.sh
+      - run:
+          name: Build Python packages
+          no_output_timeout: 1.0h
+          command: |
+            ./dockcross-manylinux-download-cache-and-build-module-wheels.sh
+      - store_artifacts:
+          path: dist
+          destination: dist
+
+workflows:
+    version: 2
+    build-test-package:
+      jobs:
+        - build-and-test
+        - package

.travis.yml

@@ -0,0 +1,15 @@
+sudo: true
+language: cpp
+os:
+- osx
+compiler:
+- gcc
+cache:
+  directories:
+  - "$HOME/Library/Caches/Homebrew"
+script:
+- curl -L https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKPythonPackage/master/scripts/macpython-download-cache-and-build-module-wheels.sh -O
+- chmod u+x macpython-download-cache-and-build-module-wheels.sh
+- ./macpython-download-cache-and-build-module-wheels.sh
+- tar -zcvf dist.tar.gz dist/
+- curl --upload-file dist.tar.gz https://transfer.sh/dist.tar.gz

CTestConfig.cmake

@@ -1,13 +1,7 @@
-## This file should be placed in the root directory of your project.
-## Then modify the CMakeLists.txt file in the root directory of your
-## project to incorporate the testing dashboard.
-## # The following are required to uses Dart and the Cdash dashboard
-##   ENABLE_TESTING()
-##   INCLUDE(CTest)
-set(CTEST_PROJECT_NAME "LesionSizing")
-set(CTEST_NIGHTLY_START_TIME "2:00:00 UTC")
+set(CTEST_PROJECT_NAME "ITK")
+set(CTEST_NIGHTLY_START_TIME "1:00:00 UTC")
 
 set(CTEST_DROP_METHOD "http")
-set(CTEST_DROP_SITE "my.cdash.org")
-set(CTEST_DROP_LOCATION "/submit.php?project=LesionSizingToolkit")
+set(CTEST_DROP_SITE "open.cdash.org")
+set(CTEST_DROP_LOCATION "/submit.php?project=Insight")
 set(CTEST_DROP_SITE_CDASH TRUE)

README.rst

@@ -1,6 +1,21 @@
 The Lesion Sizing Toolkit (LSTK)
 ================================
 
+.. |CircleCI| image:: https://circleci.com/gh/InsightSoftwareConsortium/LesionSizingToolkit.svg?style=shield
+    :target: https://circleci.com/gh/InsightSoftwareConsortium/LesionSizingToolkit
+
+.. |TravisCI| image:: https://travis-ci.org/InsightSoftwareConsortium/LesionSizingToolkit.svg?branch=master
+    :target: https://travis-ci.org/InsightSoftwareConsortium/LesionSizingToolkit
+
+.. |AppVeyor| image:: https://img.shields.io/appveyor/ci/InsightSoftwareConsortium/lesionsizingtoolkit.svg
+    :target: https://ci.appveyor.com/project/InsightSoftwareConsortium/lesionsizingtoolkit
+
+=========== =========== ===========
+   Linux      macOS       Windows
+=========== =========== ===========
+|CircleCI|  |TravisCI|  |AppVeyor|
+=========== =========== ===========
+
 Overview
 --------
 
@@ -17,6 +32,18 @@ For more information, see the `Insight Journal article <http://hdl.handle.net/10
   http://hdl.handle.net/10380/3369
   http://www.insight-journal.org/browse/publication/869
 
+Installation
+------------
+
+Python
+^^^^^^
+
+Binary `Python packages <https://pypi.python.org/pypi/itk-lesionsizingtoolkit>`_
+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

appveyor.yml

@@ -0,0 +1,21 @@
+branches:
+ only:
+  - master
+
+version: "0.0.1.{build}"
+
+install:
+
+  - curl -L https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKPythonPackage/master/scripts/windows-download-cache-and-build-module-wheels.ps1 -O
+  - ps: .\windows-download-cache-and-build-module-wheels.ps1
+
+build: off
+
+test: off
+
+artifacts:
+
+  # pushing entire folder as a zip archive
+  - path: dist\*
+
+deploy: off

itk-module.cmake

@@ -1,32 +1,27 @@
-set(DOCUMENTATION "This module contains a collection of classes for performing
-measurement of lesions. Its clinical motivation is the study of cancerous lung
-lesions. However, the functionalities developed here are usable in a wider
-range of applications. The Lesion Sizing Toolkit is built upon ITK and adds to
-it specific classes for computing image features that are then combined into a
-detection and measurement layer.")
+# the top-level README is used for describing this module, just
+# re-used it for documentation here
+get_filename_component(MY_CURRENT_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
+file(READ "${MY_CURRENT_DIR}/README.rst" DOCUMENTATION)
 
+# itk_module() defines the module dependencies in LesionSizingToolkit
+# The testing module in LesionSizingToolkit depends on ITKTestKernel
+# By convention those modules outside of ITK are not prefixed with
+# ITK.
+
+# define the dependencies of the include module and the tests
 itk_module(LesionSizingToolkit
- DEPENDS
-   ITKImageFeature
-   ITKLevelSets
-   ITKStatistics
-   ITKIOSpatialObjects
-   ITKRegionGrowing
-   ITKLabelVoting
-   ITKMathematicalMorphology
-   ITKIOBruker
-   ITKIOGDCM
-   ITKIOMeta
-   ITKIOMINC
-   ITKIOGE
-   ITKIOBioRad
-   ITKIOHDF5
-   ITKIOLSM
-   ITKIOMRC
-   ITKIOStimulate
-   ITKVtkGlue
-   ITKTestKernel #to handle IO in src
- EXCLUDE_FROM_DEFAULT
- DESCRIPTION
-   "${DOCUMENTATION}"
+  DEPENDS
+    ITKImageFeature
+    ITKLevelSets
+    ITKStatistics
+    ITKRegionGrowing
+    ITKLabelVoting
+    ITKMathematicalMorphology
+    ITKImageIO
+    ITKVtkGlue
+  TEST_DEPENDS
+    ITKTestKernel
+  EXCLUDE_FROM_DEFAULT
+  DESCRIPTION
+    "${DOCUMENTATION}"
 )

setup.py

@@ -0,0 +1,56 @@
+# -*- coding: utf-8 -*-
+from __future__ import print_function
+from os import sys
+
+try:
+    from skbuild import setup
+except ImportError:
+    print('scikit-build is required to build from source.', file=sys.stderr)
+    print('Please run:', file=sys.stderr)
+    print('', file=sys.stderr)
+    print('  python -m pip install scikit-build')
+    sys.exit(1)
+
+setup(
+    name='lesionsizingtoolkit',
+    version='0.0.1',
+    author='Xiao Xiao Liu',
+    author_email='[email protected]',
+    packages=['itk'],
+    package_dir={'itk': 'itk'},
+    download_url=r'https://github.com/InsightSoftwareConsortium/LesionSizingToolkit',
+    description=r'A generic and extensible ITK module for lesion segmentation',
+    long_description='LesionSizingToolkit (LSTK) 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.\n'
+                     'Please refer to:'
+                     '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”, '
+                     'Insight Journal, http://hdl.handle.net/10380/3369, 2012.',
+    classifiers=[
+        "License :: OSI Approved :: BSD 2-Clause \"Simplified\" License",
+        "Programming Language :: Python",
+        "Programming Language :: C++",
+        "Development Status :: 4 - Beta",
+        "Intended Audience :: Developers",
+        "Intended Audience :: Education",
+        "Intended Audience :: Healthcare Industry",
+        "Intended Audience :: Science/Research",
+        "Topic :: Scientific/Engineering",
+        "Topic :: Scientific/Engineering :: Medical Science Apps.",
+        "Topic :: Scientific/Engineering :: Information Analysis",
+        "Topic :: Software Development :: Libraries",
+        "Operating System :: Android",
+        "Operating System :: Microsoft :: Windows",
+        "Operating System :: POSIX",
+        "Operating System :: Unix",
+        "Operating System :: MacOS"
+        ],
+    license='BSD',
+    keywords='ITK InsightToolkit',
+    url=r'https://itk.org/',
+    install_requires=[
+        r'itk'
+    ]
+    )

wrapping/CMakeLists.txt

@@ -0,0 +1,48 @@
+itk_wrap_module(LesionSizingToolkit)
+
+set(WRAPPER_SUBMODULE_ORDER
+   itkBinaryThresholdFeatureGenerator
+   itkCannyEdgeDetectionRecursiveGaussianImageFilter
+   itkCannyEdgesDistanceAdvectionFieldFeatureGenerator
+   itkCannyEdgesDistanceFeatureGenerator
+   itkCannyEdgesFeatureGenerator
+   itkConfidenceConnectedSegmentationModule
+   itkConnectedreoldSegmentationModule
+   itkDescoteauxeetnessFeatureGenerator
+   itkDescoteauxeetnessImageFilter
+   itkFastMaringAndGeodesicActiveContourLevelSetSegmentationModule
+   itkFastMaringAndapeDetectionLevelSetSegmentationModule
+   itkFastMaringSegmentationModule
+   itkFeatureAggregator
+   itkFeatureGenerator
+   itkFrangiTubularnessFeatureGenerator
+   itkFrangiTubularnessImageFilter
+   itkGeodesicActiveContourLevelSetSegmentationModule
+   itkGradientMagnitudeSigmoidFeatureGenerator
+   itkGrayscaleImageSegmentationVolumeEstimator
+   itkIsotropicResampler
+   itkIsotropicResamplerImageFilter
+   itkLandmarksReader
+   itkLesionSegmentationImageFilter8
+   itkLesionSegmentationMeod
+   itkLocalStructureImageFilter
+   itkLungWallFeatureGenerator
+   itkMaximumFeatureAggregator
+   itkMinimumFeatureAggregator
+   itkMorologicalOpenningFeatureGenerator
+   itkRegionCompetitionImageFilter
+   itkRegionGrowingSegmentationModule
+   itkSatoLocalStructureFeatureGenerator
+   itkSatoVesselnessFeatureGenerator
+   itkSatoVesselnessSigmoidFeatureGenerator
+   itkSegmentationModule
+   itkSegmentationVolumeEstimator
+   itkapeDetectionLevelSetSegmentationModule
+   itkSigmoidFeatureGenerator
+   itkSingleaseLevelSetSegmentationModule
+   itkVesselEancingDiffusion3DImageFilter
+   itkVotingBinaroleFillFloodingImageFilter
+   itkWeitedSumFeatureAggregator)
+
+itk_auto_load_submodules()
+itk_end_wrap_module()

wrapping/itkBinaryThresholdFeatureGenerator.wrap

@@ -0,0 +1,5 @@
+itk_wrap_class("itk::BinaryThresholdFeatureGenerator" POINTER)
+  foreach(d ${ITK_WRAP_IMAGE_DIMS})
+    itk_wrap_template(${d} ${d})
+  endforeach()
+itk_end_wrap_class()

wrapping/itkCannyEdgeDetectionRecursiveGaussianImageFilter.wrap

@@ -0,0 +1,3 @@
+itk_wrap_class("itk::CannyEdgeDetectionRecursiveGaussianImageFilter" POINTER)
+  itk_wrap_image_filter("${WRAP_ITK_SCALAR}" 2+)
+itk_end_wrap_class()

wrapping/itkCannyEdgesDistanceAdvectionFieldFeatureGenerator.wrap

@@ -0,0 +1,5 @@
+itk_wrap_class("itk::CannyEdgesDistanceAdvectionFieldFeatureGenerator" POINTER)
+  foreach(d ${ITK_WRAP_IMAGE_DIMS})
+    itk_wrap_template(${d} ${d})
+  endforeach()
+itk_end_wrap_class()

wrapping/itkCannyEdgesDistanceFeatureGenerator.wrap

@@ -0,0 +1,5 @@
+itk_wrap_class("itk::CannyEdgesDistanceFeatureGenerator" POINTER)
+  foreach(d ${ITK_WRAP_IMAGE_DIMS})
+    itk_wrap_template(${d} ${d})
+  endforeach()
+itk_end_wrap_class()

wrapping/itkCannyEdgesFeatureGenerator.wrap

@@ -0,0 +1,5 @@
+itk_wrap_class("itk::CannyEdgesFeatureGenerator" POINTER)
+  foreach(d ${ITK_WRAP_IMAGE_DIMS})
+    itk_wrap_template(${d} ${d})
+  endforeach()
+itk_end_wrap_class()

wrapping/itkConfidenceConnectedSegmentationModule.wrap

@@ -0,0 +1,5 @@
+itk_wrap_class("itk::ConfidenceConnectedSegmentationModule" POINTER)
+  foreach(d ${ITK_WRAP_IMAGE_DIMS})
+    itk_wrap_template(${d} ${d})
+  endforeach()
+itk_end_wrap_class()

wrapping/itkConnectedThresholdSegmentationModule.wrap

@@ -0,0 +1,5 @@
+itk_wrap_class("itk::ConnectedThresholdSegmentationModule" POINTER)
+  foreach(d ${ITK_WRAP_IMAGE_DIMS})
+    itk_wrap_template(${d} ${d})
+  endforeach()
+itk_end_wrap_class()

wrapping/itkDescoteauxSheetnessFeatureGenerator.wrap

@@ -0,0 +1,5 @@
+itk_wrap_class("itk::DescoteauxSheetnessFeatureGenerator" POINTER)
+  foreach(d ${ITK_WRAP_IMAGE_DIMS})
+    itk_wrap_template(${d} ${d})
+  endforeach()
+itk_end_wrap_class()

wrapping/itkDescoteauxSheetnessImageFilter.wrap

@@ -0,0 +1,3 @@
+itk_wrap_class("itk::DescoteauxSheetnessImageFilter" POINTER)
+  itk_wrap_image_filter("${WRAP_ITK_SCALAR}" 2+)
+itk_end_wrap_class()

wrapping/itkFastMarchingAndGeodesicActiveContourLevelSetSegmentationModule.wrap

@@ -0,0 +1,5 @@
+itk_wrap_class("itk::FastMarchingAndGeodesicActiveContourLevelSetSegmentationModule" POINTER)
+  foreach(d ${ITK_WRAP_IMAGE_DIMS})
+    itk_wrap_template(${d} ${d})
+  endforeach()
+itk_end_wrap_class()

wrapping/itkFastMarchingAndShapeDetectionLevelSetSegmentationModule.wrap

@@ -0,0 +1,5 @@
+itk_wrap_class("itk::FastMarchingAndShapeDetectionLevelSetSegmentationModule" POINTER)
+  foreach(d ${ITK_WRAP_IMAGE_DIMS})
+    itk_wrap_template(${d} ${d})
+  endforeach()
+itk_end_wrap_class()

wrapping/itkFastMarchingSegmentationModule.wrap

@@ -0,0 +1,5 @@
+itk_wrap_class("itk::FastMarchingSegmentationModule" POINTER)
+  foreach(d ${ITK_WRAP_IMAGE_DIMS})
+    itk_wrap_template(${d} ${d})
+  endforeach()
+itk_end_wrap_class()

wrapping/itkFeatureAggregator.wrap

@@ -0,0 +1,5 @@
+itk_wrap_class("itk::FeatureAggregator" POINTER_WITH_SUPERCLASS)
+  foreach(d ${ITK_WRAP_IMAGE_DIMS})
+    itk_wrap_template(${d} ${d})
+  endforeach()
+itk_end_wrap_class()