COMP: Many of the remotes require updates for ITKv5

hjmjohnson · hjmjohnson · commit 1f56f37d48c4 · 2018-11-05T10:35:50.000-06:00
There have been many updates to the remote modules
to make them compatible with ITKv5.

These are the branches that need to be merged into
their respective branches to allow buiding against
VXL 2.0.0 with deprecated code turned off.

Change-Id: Ie453496d3d0b4e3018b29cbed4a821afb5914fd4
diff --git a/Modules/Remote/AnalyzeObjectMapIO.remote.cmake b/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
   )
diff --git a/Modules/Remote/AnisotropicDiffusionLBR.remote.cmake b/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
   )
diff --git a/Modules/Remote/BoneMorphometry.remote.cmake b/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
 )
diff --git a/Modules/Remote/DVMeshNoise.remote.cmake b/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
   )
diff --git a/Modules/Remote/IOFDF.remote.cmake b/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
   )
diff --git a/Modules/Remote/IOTransformDCMTK.remote.cmake b/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
   )
diff --git a/Modules/Remote/IsotropicWavelets.remote.cmake b/Modules/Remote/IsotropicWavelets.remote.cmake
@@ -9,5 +9,5 @@ Cerdan, P.H. \"Steerable Isotropic Wavelets for Multiscale and Phase Analysis\".
 "
   # Upstream repository was transfered from phcerdan to InsightSoftwareConsortium
   GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKIsotropicWavelets.git
-  GIT_TAG 80fefd47f5177d29328b0106bd2ff53fa84b0396
+  GIT_TAG 3f88e669f759cfb62d7ae6d5fc839974f24f480c
 )
diff --git a/Modules/Remote/LabelErodeDilate.remote.cmake b/Modules/Remote/LabelErodeDilate.remote.cmake
@@ -8,5 +8,5 @@ itk_fetch_module(LabelErodeDilate
   https://hdl.handle.net/10380/3399"
   #UPSTREAM_GIT_REPOSITORY
   GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/LabelErodeDilate.git
-  GIT_TAG fc148f9e30cae0653d901934b2ca70f66fdce7dc
+  GIT_TAG 009e0456007885550d23057fbe16fc33e511198b
   )
diff --git a/Modules/Remote/LesionSizingToolkit.remote.cmake b/Modules/Remote/LesionSizingToolkit.remote.cmake
@@ -1,5 +1,5 @@
 itk_fetch_module(LesionSizingToolkit
   "Framework for determining the sizes of lesions in medical images."
-  GIT_REPOSITORY https://github.com/InsightSoftwareConsortium/LesionSizingToolkit.git
-  GIT_TAG 46f56c74257a16a2130cfea48815a5ed4466ad04
+  GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/LesionSizingToolkit.git
+  GIT_TAG e119ec370555dc586e10e4f9f83776ad04988b1e
   )
diff --git a/Modules/Remote/MinimalPathExtraction.remote.cmake b/Modules/Remote/MinimalPathExtraction.remote.cmake
@@ -3,5 +3,5 @@ itk_fetch_module(MinimalPathExtraction
  "http://www.insight-journal.org/browse/publication/213
 "
   GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKMinimalPathExtraction.git
-  GIT_TAG a98dd704928d074422db3ffc1ff6b9d898d115d1
+  GIT_TAG 72b9dc1c9556f4f9562bab39f7fc38381a8f0129
   )
diff --git a/Modules/Remote/MorphologicalContourInterpolation.remote.cmake b/Modules/Remote/MorphologicalContourInterpolation.remote.cmake
@@ -14,5 +14,5 @@ IEEE Trans Biomed Eng. 2008 Aug;55(8):2022-38. doi: 10.1109/TBME.2008.921158.
 This work is supported by NIH grant R01 EB014346
 'Continued development and maintenance of the ITK-SNAP 3D image segmentation software'."
   GIT_REPOSITORY ${git_protocol}://github.com/KitwareMedical/ITKMorphologicalContourInterpolation.git
-  GIT_TAG f8f13f647199ff5eddc2513654cd99c9da23e59f
+  GIT_TAG cc87ca170e775e8d2838014a59fb7c77b9d606d7
   )
diff --git a/Modules/Remote/ParabolicMorphology.remote.cmake b/Modules/Remote/ParabolicMorphology.remote.cmake
@@ -5,5 +5,5 @@ itk_fetch_module(ParabolicMorphology
   http://www.insight-journal.org/browse/publication/228
   https://hdl.handle.net/1926/1370"
   GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKParabolicMorphology.git
-  GIT_TAG aefcb19a65a2b1b743aebbc314bc2ab8171df553
+  GIT_TAG 4717f4d54dcef796a2bb4305ebde95aa3c6e78ef
   )
diff --git a/Modules/Remote/PerformanceBenchmarking.remote.cmake b/Modules/Remote/PerformanceBenchmarking.remote.cmake
@@ -15,5 +15,5 @@ For more information, see::
   http://insight-journal.org/browse/publication/972
 "
   GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKPerformanceBenchmarking.git
-  GIT_TAG 0a7dd27e66bff1f1f46ebc02a50530d4f73439f4
+  GIT_TAG 2c2fc8cbe7f3283f2d595c11771fd145cf753e7d
   )
diff --git a/Modules/Remote/PolarTransform.remote.cmake b/Modules/Remote/PolarTransform.remote.cmake
@@ -11,5 +11,5 @@ For more information, see the Insight Journal article:
   http://insight-journal.org/browse/publication/130
   "
   GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKPolarTransform.git
-  GIT_TAG 77c7c8c6a65a490cdde395c659ff6b1a85921f06
+  GIT_TAG cf1b0a6b98e61e8ab7a504969eb534d1d6df319c
   )
diff --git a/Modules/Remote/PrincipalComponentsAnalysis.remote.cmake b/Modules/Remote/PrincipalComponentsAnalysis.remote.cmake
@@ -8,5 +8,5 @@ A more detailed description can be found in the Insight Journal article:
     August, 2013.
 "
   GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKPrincipalComponentsAnalysis.git
-  GIT_TAG 87fc36675b0153014085fd5aef5b61b8ef33e464
+  GIT_TAG 1089415ddea672469ead745e1898454a8c4d7414
   )
diff --git a/Modules/Remote/SCIFIO.remote.cmake b/Modules/Remote/SCIFIO.remote.cmake
@@ -1,5 +1,5 @@
 itk_fetch_module(SCIFIO
   "SCIFIO (Bioformats) ImageIO plugin for ITK"
   GIT_REPOSITORY ${git_protocol}://github.com/scifio/scifio-imageio.git
-  GIT_TAG b54a227a6311f5ea18fd844fa428a0e1cbc89637
+  GIT_TAG f27bc5552c68ec11bb22e48e082a8e492d4489af
   )
diff --git a/Modules/Remote/SmoothingRecursiveYvvGaussianFilter.remote.cmake b/Modules/Remote/SmoothingRecursiveYvvGaussianFilter.remote.cmake
@@ -3,5 +3,5 @@ itk_fetch_module(SmoothingRecursiveYvvGaussianFilter
   "GPU and CPU Young & Van Vliet Recursive Gaussian Smoothing Filter: https://hdl.handle.net/10380/3425"
   #UPSTREAM_REPO GIT_REPOSITORY ${git_protocol}://github.com/Inria-Asclepios/SmoothingRecursiveYvvGaussianFilter
   GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/SmoothingRecursiveYvvGaussianFilter.git
-  GIT_TAG 7e5946aa49017541076d4a707527ccaf99b1a6ec
+  GIT_TAG f515ba80ca971027f5e3aafef4278d0b0f69d698
   )
diff --git a/Modules/Remote/SphinxExamples.remote.cmake b/Modules/Remote/SphinxExamples.remote.cmake
@@ -2,5 +2,5 @@
 itk_fetch_module(SphinxExamples
   "This module builds the examples found at https://itk.org/ITKExamples/"
   GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKExamples.git
-  GIT_TAG 8b51e34b1ae60f962b028f844371dd1263bf0db4
+  GIT_TAG 0c5fa04069cb0565930aff14d919fffca05d2d92
   )
diff --git a/Modules/Remote/SplitComponents.remote.cmake b/Modules/Remote/SplitComponents.remote.cmake
@@ -5,5 +5,5 @@ itk::SplitComponentsImageFilter.  This filter generates component images from an
 itk::Image of, for example, itk::Vector, itk::CovariantVector, or
 itk::SymmetricSecondRankTensor. https://hdl.handle.net/10380/3230"
   GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKSplitComponents.git
-  GIT_TAG 137c093eabdeec2cf956d684d93ab434f3d794c9
+  GIT_TAG 9349567031960e08a3ff20119c2a776e8368598c
   )
diff --git a/Modules/Remote/Strain.remote.cmake b/Modules/Remote/Strain.remote.cmake
@@ -12,5 +12,5 @@ For more information, see:
   http://insight-journal.org/browse/publication/984
 "
   GIT_REPOSITORY ${git_protocol}://github.com/KitwareMedical/ITKStrain.git
-  GIT_TAG 40ee311babddc0075b12f08314b5a75ab8319059
+  GIT_TAG f6981e61cd6c951708254a0650c990f946dd2d4f
   )
diff --git a/Modules/Remote/SubdivisionQuadEdgeMeshFilter.remote.cmake b/Modules/Remote/SubdivisionQuadEdgeMeshFilter.remote.cmake
@@ -7,5 +7,5 @@ See the following Insight Journal's publication:
   http://www.insight-journal.org/browse/publication/831
   https://hdl.handle.net/10380/3307"
   GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/itkSubdivisionQuadEdgeMeshFilter
-  GIT_TAG 1fb2019cafe4df67405ea574eea103bd8b715dcc
+  GIT_TAG ac103579dc5d0d0a9a4f09d07fad7df2be37c21d
   )
diff --git a/Modules/Remote/TextureFeatures.remote.cmake b/Modules/Remote/TextureFeatures.remote.cmake
@@ -13,5 +13,5 @@ For more information, see:
   http://insight-journal.org/browse/publication/985
 "
   GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKTextureFeatures.git
-  GIT_TAG 1f2fec8be121afd6e9827db01717cbcd35cbef79
+  GIT_TAG 087a0964835f08831e3e88948918ecd234fec2ea
   )
diff --git a/Modules/Remote/TwoProjectionRegistration.remote.cmake b/Modules/Remote/TwoProjectionRegistration.remote.cmake
@@ -18,5 +18,5 @@ Wu, J. \"ITK-Based Implementation of Two-Projection 2D/3D Registration Method wi
   December, 2010.
 "
   GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKTwoProjectionRegistration.git
-  GIT_TAG 0456876332e49b89c561101be2c8d5b595583111
+  GIT_TAG 922e785e996964e1afad9370ff53c5fd9c222942
   )
diff --git a/Modules/Remote/VariationalRegistration.remote.cmake b/Modules/Remote/VariationalRegistration.remote.cmake
@@ -5,5 +5,5 @@
 itk_fetch_module(VariationalRegistration
   "A module to perform variational image registration. https://hdl.handle.net/10380/3460"
   GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKVariationalRegistration.git
-  GIT_TAG 33acbe7cedb9a0873a1f7abcd4e9b1319b02a238
+  GIT_TAG b28eb7114929d40e70035a85477ac014110799f2
   )
diff --git a/Utilities/ITKv5Preparation/update_remote_hash.sh b/Utilities/ITKv5Preparation/update_remote_hash.sh
@@ -31,16 +31,28 @@ echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 echo ""
 remoteCache=${remoteFile//.remote.cmake}
 
+if [[ ! -d ${remoteCache} ]]; then
+  export git_protocol=https
+  clone_url=$(eval "echo $(cat ${remoteFile} | grep GIT_REPOSITORY |tail -1 |awk '{print $2}')")
+  echo clone_url
+  git clone ${clone_url} ${remoteCache}
+  pushd  ${remoteCache}
+    git submodule init
+    git submodule update --recursive
+  popd
+fi
+
 pushd ${remoteCache}
 git fetch origin
 git rebase origin/master
 HEAD_HASH=$(git rev-parse --verify HEAD)
-sed -i "" "s/GIT_TAG .*/GIT_TAG ${HEAD_HASH}/g" ${remoteFile}
+sed -i "" "s/GIT_TAG .*/GIT_TAG ${HEAD_HASH}/g" ../${remoteFile}
 MASTER_HASH=$(git rev-parse --verify origin/master)
 if [[ "${HEAD_HASH}" != "${MASTER_HASH}" ]]; then
     CURR_BRANCH=$(git rev-parse --abbrev-ref HEAD)
     if [[ "${CURR_BRANCH}" != "${branchName}" ]]; then
       git checkout ${HEAD_HASH} -b ${branchName};
+      git submodule update --recursive
     fi
     git push --set-upstream origin ${branchName};
     hub pull-request -m "ENH: C++11 updates warning fixes

Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`itk_fetch_module(AnalyzeObjectMapIO`
`2`	`2`	`"AnalyzeObjectMapIO plugin for ITK. From Insight Journal article with handle: https://hdl.handle.net/1926/593"`
`3`	`3`	`GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/itkAnalyzeObjectMap.git`
`4`		`- GIT_TAG c58f513b6e81fb0a09a712720a4a92f3ec12cf08`
	`4`	`+ GIT_TAG 54c3e2dbf0b4259aabe6c430df75171469d7bfee`
`5`	`5`	`)`
Original file line number	Diff line number	Diff line change
`@@ -20,5 +20,5 @@ itk_fetch_module(AnisotropicDiffusionLBR`
`20`	`20`	`http://insight-journal.org/browse/publication/953`
`21`	`21`	`"`
`22`	`22`	`GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKAnisotropicDiffusionLBR.git`
`23`		`- GIT_TAG 1a6e25e407331c1d8c88be1a93ce44a5ba0628a2`
	`23`	`+ GIT_TAG d9f3746456ebd1c7116083492803995fba59c5a6`
`24`	`24`	`)`
Original file line number	Diff line number	Diff line change
`@@ -7,5 +7,5 @@ itk_fetch_module(BoneMorphometry`
`7`	`7`	`http://hdl.handle.net/10380/3588`
`8`	`8`	`"`
`9`	`9`	`GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKBoneMorphometry.git`
`10`		`- GIT_TAG 5d152b584e311c89af926c82d5ca268d27f50976`
	`10`	`+ GIT_TAG f6b7a1427cc7f4e597a3032e4c49e8f7892e7fca`
`11`	`11`	`)`
Original file line number	Diff line number	Diff line change
`@@ -6,5 +6,5 @@ itk_fetch_module(DVMeshNoise`
`6`	`6`	`http://hdl.handle.net/10380/3567`
`7`	`7`	`"`
`8`	`8`	`GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/DVMeshNoise`
`9`		`- GIT_TAG ed83b8291bcbc2d2718f198f1422182c8d7f4d11`
	`9`	`+ GIT_TAG 80d7815221173b20fcea75aabd973afb72c1e294`
`10`	`10`	`)`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`itk_fetch_module(IOFDF`
`2`	`2`	`"FDFImageIO plugin for ITK. Authors Gleen Pierce/Nick Tustison/Kent Williams"`
`3`	`3`	`GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/itkFDFImageIO.git`
`4`		`- GIT_TAG d87a7f1bed73addb1351152b6d82af41d4924a68`
	`4`	`+ GIT_TAG f6b4a00c610c9876987492fccc763a57f497448e`
`5`	`5`	`)`
Original file line number	Diff line number	Diff line change
`@@ -4,5 +4,5 @@ itk_fetch_module(IOTransformDCMTK`
`4`	`4`	`files. See http://www.insight-journal.org/browse/publication/923`
`5`	`5`	`https://hdl.handle.net/10380/3468"`
`6`	`6`	`GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKIOTransformDCMTK.git`
`7`		`- GIT_TAG 8be6a9e561b6a506121ec936bfe332b3917a9bf3`
	`7`	`+ GIT_TAG 6ffd7d9e1d4db35f093045a28da7045eda305fab`
`8`	`8`	`)`
Original file line number	Diff line number	Diff line change
`@@ -9,5 +9,5 @@ Cerdan, P.H. \"Steerable Isotropic Wavelets for Multiscale and Phase Analysis\".`
`9`	`9`	`"`
`10`	`10`	`# Upstream repository was transfered from phcerdan to InsightSoftwareConsortium`
`11`	`11`	`GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKIsotropicWavelets.git`
`12`		`- GIT_TAG 80fefd47f5177d29328b0106bd2ff53fa84b0396`
	`12`	`+ GIT_TAG 3f88e669f759cfb62d7ae6d5fc839974f24f480c`
`13`	`13`	`)`
Original file line number	Diff line number	Diff line change
`@@ -8,5 +8,5 @@ itk_fetch_module(LabelErodeDilate`
`8`	`8`	`https://hdl.handle.net/10380/3399"`
`9`	`9`	`#UPSTREAM_GIT_REPOSITORY`
`10`	`10`	`GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/LabelErodeDilate.git`
`11`		`- GIT_TAG fc148f9e30cae0653d901934b2ca70f66fdce7dc`
	`11`	`+ GIT_TAG 009e0456007885550d23057fbe16fc33e511198b`
`12`	`12`	`)`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`itk_fetch_module(LesionSizingToolkit`
`2`	`2`	`"Framework for determining the sizes of lesions in medical images."`
`3`		`- GIT_REPOSITORY https://github.com/InsightSoftwareConsortium/LesionSizingToolkit.git`
`4`		`- GIT_TAG 46f56c74257a16a2130cfea48815a5ed4466ad04`
	`3`	`+ GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/LesionSizingToolkit.git`
	`4`	`+ GIT_TAG e119ec370555dc586e10e4f9f83776ad04988b1e`
`5`	`5`	`)`
Original file line number	Diff line number	Diff line change
`@@ -3,5 +3,5 @@ itk_fetch_module(MinimalPathExtraction`
`3`	`3`	`"http://www.insight-journal.org/browse/publication/213`
`4`	`4`	`"`
`5`	`5`	`GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKMinimalPathExtraction.git`
`6`		`- GIT_TAG a98dd704928d074422db3ffc1ff6b9d898d115d1`
	`6`	`+ GIT_TAG 72b9dc1c9556f4f9562bab39f7fc38381a8f0129`
`7`	`7`	`)`