Merge topic 'UpdateToVXL2.0.0'

1f56f37 COMP: Many of the remotes require updates for ITKv5
e7db79d Merge branch 'upstream-vnl' into UpdateToVXL2.0.0
d83514c VNL 2018-11-04 (ea3a2cc9)
60c11f4 ENH: Provide mechanism for changing git remote url
ff285c3 STYLE: Remove unused include headers
135f08e ENH: Update to require VXL 2.0.0 or later
0249113 BUG: Do not override user selection settings
093da0c ENH: Adding a few more clang tidy checks.
d8744c0 ENH: Add scripts to assist with migrations

Author: hjmjohnson

CMake/ITKModuleRemote.cmake

@@ -45,6 +45,31 @@ endfunction()
 # Helper to perform a git update.  Checks the current Git revision against the
 # desired revision and only performs a fetch and checkout if needed.
 function(_git_update git_executable git_repository git_tag module_dir)
+  # Verify that remote url are the same
+  execute_process(
+    COMMAND "${git_executable}" config --get remote.origin.url
+    WORKING_DIRECTORY "${module_dir}"
+    RESULT_VARIABLE error_code
+    OUTPUT_VARIABLE remote_origin_url
+    OUTPUT_STRIP_TRAILING_WHITESPACE
+  )
+  if ( NOT "${remote_origin_url}" STREQUAL "${git_repository}")
+    message(WARNING "Remote URL changed from ${git_repository} to ${remote_origin_url}")
+    execute_process(
+      COMMAND "${git_executable}" remote rename origin old_origin
+      WORKING_DIRECTORY "${module_dir}"
+      RESULT_VARIABLE error_code
+      OUTPUT_VARIABLE ignored
+      OUTPUT_STRIP_TRAILING_WHITESPACE
+    )
+    execute_process(
+      COMMAND "${git_executable}" remote add origin "${git_repository}"
+      WORKING_DIRECTORY "${module_dir}"
+      RESULT_VARIABLE error_code
+      OUTPUT_VARIABLE ignored
+      OUTPUT_STRIP_TRAILING_WHITESPACE
+    )
+  endif()
   execute_process(
     COMMAND "${git_executable}" rev-parse --verify "${git_tag}"
     WORKING_DIRECTORY "${module_dir}"

Examples/Segmentation/GeodesicActiveContourShapePriorLevelSetImageFilter.cxx

@@ -124,7 +124,6 @@
 #include "itkEuler2DTransform.h"
 #include "itkOnePlusOneEvolutionaryOptimizer.h"
 #include "itkNormalVariateGenerator.h"
-#include "vnl/vnl_sample.h"
 #include "itkNumericSeriesFileNames.h"
 // Software Guide : EndCodeSnippet
 

Modules/Core/Transform/include/itkKernelTransform.h

@@ -28,7 +28,6 @@
 #include "vnl/vnl_vector.h"
 #include "vnl/vnl_vector_fixed.h"
 #include "vnl/algo/vnl_svd.h"
-#include "vnl/vnl_sample.h"
 
 namespace itk
 {

Modules/Core/Transform/test/itkTransformsSetParametersTest.cxx

@@ -35,6 +35,7 @@
 #include "itkThinPlateSplineKernelTransform.h"
 #include "itkVolumeSplineKernelTransform.h"
 #include "itkIntTypes.h"
+#include <vnl/vnl_sample.h>
 
 
 // Generic Kernel Transform Tester

Modules/Remote/AnalyzeObjectMapIO.remote.cmake

@@ -1,5 +1,5 @@
 itk_fetch_module(AnalyzeObjectMapIO
   "AnalyzeObjectMapIO plugin for ITK. From Insight Journal article with handle: https://hdl.handle.net/1926/593"
   GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/itkAnalyzeObjectMap.git
-  GIT_TAG c58f513b6e81fb0a09a712720a4a92f3ec12cf08
+  GIT_TAG 54c3e2dbf0b4259aabe6c430df75171469d7bfee
   )

Modules/Remote/AnisotropicDiffusionLBR.remote.cmake

@@ -20,5 +20,5 @@ itk_fetch_module(AnisotropicDiffusionLBR
     http://insight-journal.org/browse/publication/953
   "
   GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKAnisotropicDiffusionLBR.git
-  GIT_TAG 1a6e25e407331c1d8c88be1a93ce44a5ba0628a2
+  GIT_TAG d9f3746456ebd1c7116083492803995fba59c5a6
   )

Modules/Remote/BoneMorphometry.remote.cmake

@@ -7,5 +7,5 @@ itk_fetch_module(BoneMorphometry
   http://hdl.handle.net/10380/3588
   "
   GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKBoneMorphometry.git
-  GIT_TAG 5d152b584e311c89af926c82d5ca268d27f50976
+  GIT_TAG f6b7a1427cc7f4e597a3032e4c49e8f7892e7fca
 )

Modules/Remote/DVMeshNoise.remote.cmake

@@ -6,5 +6,5 @@ itk_fetch_module(DVMeshNoise
   http://hdl.handle.net/10380/3567
   "
   GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/DVMeshNoise
-  GIT_TAG ed83b8291bcbc2d2718f198f1422182c8d7f4d11
+  GIT_TAG 80d7815221173b20fcea75aabd973afb72c1e294
   )

Modules/Remote/IOFDF.remote.cmake

@@ -1,5 +1,5 @@
 itk_fetch_module(IOFDF
   "FDFImageIO plugin for ITK. Authors Gleen Pierce/Nick Tustison/Kent Williams"
   GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/itkFDFImageIO.git
-  GIT_TAG d87a7f1bed73addb1351152b6d82af41d4924a68
+  GIT_TAG f6b4a00c610c9876987492fccc763a57f497448e
   )

Modules/Remote/IOTransformDCMTK.remote.cmake

@@ -4,5 +4,5 @@ itk_fetch_module(IOTransformDCMTK
   files. See http://www.insight-journal.org/browse/publication/923
              https://hdl.handle.net/10380/3468"
   GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKIOTransformDCMTK.git
-  GIT_TAG 8be6a9e561b6a506121ec936bfe332b3917a9bf3
+  GIT_TAG 6ffd7d9e1d4db35f093045a28da7045eda305fab
   )