<commit_before>cmake_minimum_required(VERSION 2.8.7)

set(EXTENSION_NAME carma)
set(EXTENSION_HOMEPAGE "http://www.carmacenter.org")
set(EXTENSION_CATEGORY "CARMA")
set(EXTENSION_STATUS "Beta")
set(EXTENSION_ICONURL "https://github.com/carma-center/carma_slicer_extension/raw/master/carma-logo-128.png")
set(EXTENSION_CONTRIBUTORS "<NAME> (CARMA), <NAME> (CARMA), <NAME> (CARMA), <NAME> (CARMA), <NAME> (CARMA)")
set(EXTENSION_DESCRIPTION "The CARMA extension includes modules for the Utah Afib DBP")
set(EXTENSION_SCREENSHOTURLS "http://wiki.na-mic.org/Wiki/images/d/d1/Carma_afib_inhomogeneity_correction.png http://wiki.na-mic.org/Wiki/images/7/7a/Carma_afib_auto_scar.png")

#-----------------------------------------------------------------------------
if(NOT Slicer_SOURCE_DIR)
  find_package(Slicer REQUIRED)
  include(${Slicer_USE_FILE})
endif()

set(cli_module_target_libraries
  ${ITK_LIBRARIES}
)



#-----------------------------------------------------------------------------
# Inhomogeneity Correction Module
#-----------------------------------------------------------------------------

#-----------------------------------------------------------------------------
set(MODULE_NAME "Inhomogeneity Correction") # Do not use 'project()'
set(MODULE_FILE_NAME "CarmaInhomogeneityCorrection")

#-----------------------------------------------------------------------------
set(MODULE_HOMEPAGE "http://wiki.na-mic.org/Wiki/index.php/DBP3:Utah:SlicerModuleInhomogeneity")
set(MODULE_CATEGORY "CARMA")
set(MODULE_STATUS "Beta")
set(MODULE_CONTRIBUTORS "<NAME> (CARMA), <NAME> (CARMA), <NAME> (CARMA), <NAME> (CARMA), <NAME> (CARMA)")
set(MODULE_DESCRIPTION "Inhomogeneity Correction for the CARMA Afib project.  This algorithm corrects specific types of intensity inhomogeneity.  Under the assumption that the LA blood pool should exhibit uniform intensity with Gaussian noise, we estimate localized intensity variation in the LA by fitting a second-order polynomial to intensity values only within the LA endocardium.  Intensity in the immediately adjacent LA wall is then normalized with respect to this model.")
set(MODULE_ICONURL "http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Extensions/Testing/carma_inhomogeneity_correction/carma_inhomogeneity_correction.png?revision=19437&view=co")
set(MODULE_SCREENSHOTURLS "http://wiki.slicer.org/slicerWiki/images/a/ab/Slicer-r19441-inhomogeneity_correction-screenshot.png http://wiki.slicer.org/slicerWiki/images/1/1e/Slicer-r19441-inhomogeneity_correction-screenshot-2.png")
set(MODULE_ACKNOWLEDGEMENTS "This work was supported by ...")
set(MODULE_MAJOR_VERSION 0)
set(MODULE_MINOR_VERSION 1)
set(MODULE_PATCH_VERSION 0)



#-----------------------------------------------------------------------------
# Configure XML description
configure_file(
  ${MODULE_FILE_NAME}.xml.in
  ${CMAKE_CURRENT_BINARY_DIR}/${MODULE_FILE_NAME}.xml
  @ONLY
  )


#-----------------------------------------------------------------------------
slicerMacroBuildCLI(
  NAME ${MODULE_FILE_NAME}
  #LOGO_HEADER ${Slicer_SOURCE_DIR}/Resources/NAMICLogo.h
  TARGET_LIBRARIES ${cli_module_target_libraries}
  INCLUDE_DIRECTORIES ${cli_module_include_directories}
  ADDITIONAL_SRCS ${cli_module_SRCS}
  #EXECUTABLE_ONLY
  )


#-----------------------------------------------------------------------------
# Automatic Left Atrial Scar Module
#-----------------------------------------------------------------------------


#-----------------------------------------------------------------------------
set(MODULE_NAME "Automatic Left Atrial Scar") # Do not use 'project()'
set(MODULE_FILE_NAME "CarmaAutomaticLeftAtrialScar")

#-----------------------------------------------------------------------------
set(MODULE_HOMEPAGE "http://www.slicer.org/slicerWiki/index.php/Documentation/Snapshot/Developers/Tutorials/ExtensionWriting")
set(MODULE_CATEGORY "CARMA")
set(MODULE_STATUS "Beta")
set(MODULE_CONTRIBUTORS "<NAME> (CARMA), <NAME> (CARMA), <NAME> (CARMA), <NAME> (CARMA)")
set(MODULE_DESCRIPTION "Determine Left Atrial Scar Automatically given the wall segmentation, in a post-ablation LGE-MRI. For details see: Perry, D. et al. "Automatic classification of scar tissue...", Proceedings of SPIE Medical Imaging: Computer Aided Diagnosis, Feb 2012.")
set(MODULE_ICONURL "http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Extensions/Testing/CarmaAutomaticLeftAtrialScar/CarmaAutomaticLeftAtrialScar.png?revision=19437&view=co")
set(MODULE_SCREENSHOTURLS "http://wiki.slicer.org/slicerWiki/images/a/ab/Slicer-r19441-CarmaAutomaticLeftAtrialScar-screenshot.png http://wiki.slicer.org/slicerWiki/images/1/1e/Slicer-r19441-CarmaAutomaticLeftAtrialScar-screenshot-2.png")
set(MODULE_ACKNOWLEDGEMENTS "This work was supported by ...")
set(MODULE_MAJOR_VERSION 0)
set(MODULE_MINOR_VERSION 1)
set(MODULE_PATCH_VERSION 0)

#-----------------------------------------------------------------------------
# Configure XML description
configure_file(
  ${MODULE_FILE_NAME}.xml.in
  ${CMAKE_CURRENT_BINARY_DIR}/${MODULE_FILE_NAME}.xml
  @ONLY
  )


#-----------------------------------------------------------------------------
slicerMacroBuildCLI(
  NAME ${MODULE_FILE_NAME}
  #LOGO_HEADER ${Slicer_SOURCE_DIR}/Resources/NAMICLogo.h
  TARGET_LIBRARIES ${cli_module_target_libraries}
  INCLUDE_DIRECTORIES ${cli_module_include_directories}
  ADDITIONAL_SRCS ${cli_module_SRCS}
  #EXECUTABLE_ONLY
  )

#-----------------------------------------------------------------------------
if(BUILD_TESTING)
  add_subdirectory(Testing)
endif()

#-----------------------------------------------------------------------------
if(NOT Slicer_SOURCE_DIR)
  include(${Slicer_EXTENSION_CPACK})
endif()
<commit_msg>Updated description of inhomogeneity correction filter.<commit_after>cmake_minimum_required(VERSION 2.8.7)

set(EXTENSION_NAME carma)
set(EXTENSION_HOMEPAGE "http://www.carmacenter.org")
set(EXTENSION_CATEGORY "CARMA")
set(EXTENSION_STATUS "Beta")
set(EXTENSION_ICONURL "https://github.com/carma-center/carma_slicer_extension/raw/master/carma-logo-128.png")
set(EXTENSION_CONTRIBUTORS "<NAME> (CARMA), <NAME> (CARMA), <NAME> (CARMA), <NAME> (CARMA), <NAME> (CARMA)")
set(EXTENSION_DESCRIPTION "The CARMA extension includes modules for the Utah Afib DBP")
set(EXTENSION_SCREENSHOTURLS "http://wiki.na-mic.org/Wiki/images/d/d1/Carma_afib_inhomogeneity_correction.png http://wiki.na-mic.org/Wiki/images/7/7a/Carma_afib_auto_scar.png")

#-----------------------------------------------------------------------------
if(NOT Slicer_SOURCE_DIR)
  find_package(Slicer REQUIRED)
  include(${Slicer_USE_FILE})
endif()

set(cli_module_target_libraries
  ${ITK_LIBRARIES}
)



#-----------------------------------------------------------------------------
# Inhomogeneity Correction Module
#-----------------------------------------------------------------------------

#-----------------------------------------------------------------------------
set(MODULE_NAME "Inhomogeneity Correction") # Do not use 'project()'
set(MODULE_FILE_NAME "CarmaInhomogeneityCorrection")

#-----------------------------------------------------------------------------
set(MODULE_HOMEPAGE "http://wiki.na-mic.org/Wiki/index.php/DBP3:Utah:SlicerModuleInhomogeneity")
set(MODULE_CATEGORY "CARMA")
set(MODULE_STATUS "Beta")
set(MODULE_CONTRIBUTORS "<NAME> (CARMA), <NAME> (CARMA), <NAME> (CARMA), <NAME> (CARMA), <NAME> (CARMA)")
set(MODULE_DESCRIPTION "Inhomogeneity Correction for the CARMA Afib project.  This algorithm corrects specific types of intensity inhomogeneity.  Under the assumption that the LA blood pool should exhibit uniform intensity with Gaussian noise, we estimate localized intensity variation in the LA by fitting a second-order polynomial to intensity values only within the LA endocardium.  Intensity in the immediately adjacent LA wall is then normalized with respect to this model.  In contrast to the N4ITK MRI Bias correction filter, this filter makes certain assumptions about the MRI (e.g. blood pool uniformity), so it can correct the image in different ways.")
set(MODULE_ICONURL "http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Extensions/Testing/carma_inhomogeneity_correction/carma_inhomogeneity_correction.png?revision=19437&view=co")
set(MODULE_SCREENSHOTURLS "http://wiki.slicer.org/slicerWiki/images/a/ab/Slicer-r19441-inhomogeneity_correction-screenshot.png http://wiki.slicer.org/slicerWiki/images/1/1e/Slicer-r19441-inhomogeneity_correction-screenshot-2.png")
set(MODULE_ACKNOWLEDGEMENTS "This work was supported by ...")
set(MODULE_MAJOR_VERSION 0)
set(MODULE_MINOR_VERSION 1)
set(MODULE_PATCH_VERSION 0)



#-----------------------------------------------------------------------------
# Configure XML description
configure_file(
  ${MODULE_FILE_NAME}.xml.in
  ${CMAKE_CURRENT_BINARY_DIR}/${MODULE_FILE_NAME}.xml
  @ONLY
  )


#-----------------------------------------------------------------------------
slicerMacroBuildCLI(
  NAME ${MODULE_FILE_NAME}
  #LOGO_HEADER ${Slicer_SOURCE_DIR}/Resources/NAMICLogo.h
  TARGET_LIBRARIES ${cli_module_target_libraries}
  INCLUDE_DIRECTORIES ${cli_module_include_directories}
  ADDITIONAL_SRCS ${cli_module_SRCS}
  #EXECUTABLE_ONLY
  )


#-----------------------------------------------------------------------------
# Automatic Left Atrial Scar Module
#-----------------------------------------------------------------------------


#-----------------------------------------------------------------------------
set(MODULE_NAME "Automatic Left Atrial Scar") # Do not use 'project()'
set(MODULE_FILE_NAME "CarmaAutomaticLeftAtrialScar")

#-----------------------------------------------------------------------------
set(MODULE_HOMEPAGE "http://www.slicer.org/slicerWiki/index.php/Documentation/Snapshot/Developers/Tutorials/ExtensionWriting")
set(MODULE_CATEGORY "CARMA")
set(MODULE_STATUS "Beta")
set(MODULE_CONTRIBUTORS "<NAME> (CARMA), <NAME> (CARMA), <NAME> (CARMA), <NAME> (CARMA)")
set(MODULE_DESCRIPTION "Determine Left Atrial Scar Automatically given the wall segmentation, in a post-ablation LGE-MRI. For details see: <NAME>. et al. "Automatic classification of scar tissue...", Proceedings of SPIE Medical Imaging: Computer Aided Diagnosis, Feb 2012.")
set(MODULE_ICONURL "http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Extensions/Testing/CarmaAutomaticLeftAtrialScar/CarmaAutomaticLeftAtrialScar.png?revision=19437&view=co")
set(MODULE_SCREENSHOTURLS "http://wiki.slicer.org/slicerWiki/images/a/ab/Slicer-r19441-CarmaAutomaticLeftAtrialScar-screenshot.png http://wiki.slicer.org/slicerWiki/images/1/1e/Slicer-r19441-CarmaAutomaticLeftAtrialScar-screenshot-2.png")
set(MODULE_ACKNOWLEDGEMENTS "This work was supported by ...")
set(MODULE_MAJOR_VERSION 0)
set(MODULE_MINOR_VERSION 1)
set(MODULE_PATCH_VERSION 0)

#-----------------------------------------------------------------------------
# Configure XML description
configure_file(
  ${MODULE_FILE_NAME}.xml.in
  ${CMAKE_CURRENT_BINARY_DIR}/${MODULE_FILE_NAME}.xml
  @ONLY
  )


#-----------------------------------------------------------------------------
slicerMacroBuildCLI(
  NAME ${MODULE_FILE_NAME}
  #LOGO_HEADER ${Slicer_SOURCE_DIR}/Resources/NAMICLogo.h
  TARGET_LIBRARIES ${cli_module_target_libraries}
  INCLUDE_DIRECTORIES ${cli_module_include_directories}
  ADDITIONAL_SRCS ${cli_module_SRCS}
  #EXECUTABLE_ONLY
  )

#-----------------------------------------------------------------------------
if(BUILD_TESTING)
  add_subdirectory(Testing)
endif()

#-----------------------------------------------------------------------------
if(NOT Slicer_SOURCE_DIR)
  include(${Slicer_EXTENSION_CPACK})
endif()

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