Skip to content

Commit

Permalink
Squashed old master commits:
Browse files Browse the repository at this point in the history 
commit 0cd691698dafce4df971ddfa1be8192ff8942544
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 11 16:29:56 2016 +0000

    Squashed commit of the following:

    commit 6a4d43a3e25d3b9cbe3418a5762afdb8cfe11661
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Mon Jan 11 16:19:02 2016 +0000

        mod: Update Documentation with removed reference of "release" branch

    commit d439ce6ab3ed2fd1ac5ddd29616596a74a96553c
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Mon Jan 11 16:08:51 2016 +0000

        mod: Update Documentation with corrected auto-generated pages and minor edits

    commit 04c3f5259a9ded49e0a72f7abe4135803530b124
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Mon Jan 11 16:06:52 2016 +0000

        fix: Generation of commands help pages, Synopsis included again [Applications]

    commit ab95439fa8e59695b0a9dda57274d2452b4dbd8c
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Mon Jan 11 15:41:32 2016 +0000

        mod: Update ThirdParty modules with corrected module paths in README

    commit bccfbf74201f81ad2a051881eab76ecfbaadfa6b
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Mon Jan 11 15:39:16 2016 +0000

        mod: Update Documentation with added auto-generated .rst files

    commit 785d68aeb011f52c9b5e89780cb4800b0d8fff31
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Mon Jan 11 15:38:58 2016 +0000

        doc: Fix/enhance help output to .rst conversion [Applications]

    commit 9d3167060cf8596c191b6c846ab5347f36fdb705
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Mon Jan 11 15:38:33 2016 +0000

        cmake: Add BUILD_DOCUMENTATION_SOURCES option to disable auto-generation of .rst files

    commit 18e612b27d0b459cb22e4c575dfb185f1ad7ad86
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 21:50:22 2016 +0000

        doc: Group items by year [ChangeLog]

    commit bae3730bd4c7a2d51a95acc3430486b4885d1cde
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 21:21:29 2016 +0000

        mod: Update Documentation with statistical FFD reference and keywords

    commit 0cd0605568e6411d808b9c5d88bb1784a42dfd11
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 19:04:18 2016 +0000

        doc: Change 1.0.0rc1 to 1.0rc1 [ChangeLog]

    commit f49e781def20560eb98f3c2080e3e2e65e6f6af8
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 08:27:40 2016 +0000

        doc: Change version and comment on release status [ChangeLog]

    commit fab0893d26fc6b33c4ad02742ff03204362a1cca
    Merge: 2436941 1764bb4
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 08:24:32 2016 +0000

        Merge CMake BASIS Modules with PROJECT_RELEASE version including 'rc' prefix.

        Commit '1764bb4929c28edb93079c5b060c5f329c77d7e8'

    commit 2436941143dba13984f142274087e4da9313e9a4
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 08:23:59 2016 +0000

        cmake: Change project version to 1.0.0rc1

    commit aa71313605278602bc48094488883383e29c1f5f
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 08:23:49 2016 +0000

        doc: Fix transformation format exclude list when NIfTI not available [Applications]

    commit a24787eb8ba761bda750635cee4665300ff394fb
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 08:23:22 2016 +0000

        doc: Insert space in module description [PointSet]

    commit 3e17a10378c4abafe5ede83e1f01644056a4518e
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 08:23:00 2016 +0000

        enh: Support full version string with "rc", "alpha", "beta" ... prefix [Common]

    commit 1764bb4929c28edb93079c5b060c5f329c77d7e8
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 08:20:32 2016 +0000

        enh: Append "rc", "beta", "alpha", ... prefix to PROJECT_RELEASE version when given

    commit 9e3749063b8b68d095be8925572087c5760b87e6
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 08:06:32 2016 +0000

        doc: Fix exlusion list of output transformation formats without NIfTI module [Applications]

    commit 6f5ef00086b3ca46b317875f776ee42135eb6e29
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 08:04:20 2016 +0000

        fix: Conversion of FFD to FSL warp without -target [Applications]

    commit eac608470308adfbf8f9aa15c83087ba540ea960
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 07:56:14 2016 +0000

        fix: Conversion between homogeneous MIRTK transformations, Nifty Reg, and FreeSurfer .xfm [Applications]

    commit 695fa7d4a800294c86ebb23d9ea3a37d55b05136
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 07:22:33 2016 +0000

        add: Transformation conversion commands [Applications]

    commit 3236dbb7d35256054626a59e98a8c90d2f703beb
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 03:15:52 2016 +0000

        mod: Update external packages with fixed links to online documentation

    commit 03783216d0420abcf0af1dba47718f9280056711
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 03:13:36 2016 +0000

        mod: Update external packages with updated README

    commit 09b35f72f733ce032c56b1f0981e89f3752175c3
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 03:02:17 2016 +0000

        cmake: Fix indentation

    commit f3d57588a27ed4ef8089b1c1e820724fb838907b
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 02:54:38 2016 +0000

        mod: Update Documentation with corrected download  and installation instructions

    commit f5307d4407089df9baf2d40b887a5ef8ced2d434
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 02:27:05 2016 +0000

        mod: Update Documentation with change from "external module" to "external package"

    commit b3ed089582413594b005e884ba789049b2235b92
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 02:14:40 2016 +0000

        add: Exernal package template files

    commit f096eaeb634b4474da2fc79c6402b57c3fb37b35
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 01:56:18 2016 +0000

        mod: Move external modules from External to Packages directory

    commit 0d01009621b970c4c33d82ef4e36e7158357b0e4
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 01:51:38 2016 +0000

        doc: Update release date in ChangeLog

    commit d254bfffba2af3fa1a357acf1c4b8a94699e5fb0
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 01:49:10 2016 +0000

        cmake: Split Tools.cmake into separate files for each function

    commit 822d14bbfc8141e741f54c505308a792547dd884
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 01:48:52 2016 +0000

        doc: Fix help output of info command [Applications]

    commit a8a492924dc2b3acf29b4203b1b34c1dc1382345
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 01:42:21 2016 +0000

        cmake: Rename Config folder to CMake

    commit 45a516a2b42b4b3b4374f5e37bbcd0b516d75a67
    Merge: 921094c a10a06c
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 01:28:49 2016 +0000

        Merge CMake BASIS Modules with TOPLEVEL_PROJECT_DOC_DIR.

        Commit 'a10a06cfd5048d8709b895cfbb1bf4b086ba1c2c'

    commit 921094caec92e2b8715af1de619566fd2c17d965
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 01:28:14 2016 +0000

        mod: Update Documentation with commands help

    commit e874e9fbcb3a078f9cb83e4200e9f6014b005f10
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 01:26:32 2016 +0000

        mod: Update external modules

    commit 4dfc578222968d969085fd3ee01b952124e4680b
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 01:25:30 2016 +0000

        enh: Auto-reformat command help output using reStructuredText [Applications, Documentation]

    commit a10a06cfd5048d8709b895cfbb1bf4b086ba1c2c
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 01:23:59 2016 +0000

        #541 Define TOPLEVEL_PROJECT_*_DIR variables

    commit 534d51661df64066ae6295285dbda7444a65f958
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 01:21:59 2016 +0000

        doc: Extend/fix help output of commands [Applications]

    commit a7dc7d48cb452234cde11c377de6e31101518dfc
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 23:29:02 2016 +0000

        add: Commands to compute vector field logarithmic/exponential map [Applications]

    commit 289bb9fbd2ed1fc2a15f9f43db6b02ee5dbb68c2
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 20:11:35 2016 +0000

        add: extract-connected-components [Applications]

    commit 0530b54cdc89bbd13c1fc025a97c496d2a8df767
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 20:11:17 2016 +0000

        enh: Remove "Total" from verbose output of extract-connected-points [Applications]

    commit 501ba7b5473c37fa04765f651f6731d1c9903791
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 20:10:49 2016 +0000

        enh: Rename extract-roi to extract-image-region [Applications]

    commit b9cf3e0d3fa259eea5025b4bf804bc07a2b5ae1f
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 20:10:23 2016 +0000

        doc: Add missing connectivity argument to help [Applications]

    commit 4a4b583cc946f2a547b6557f938941577e5783c7
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 20:09:49 2016 +0000

        add: Connected image components filter [Image]

    commit c96142903555bb5caf6a7013ee331d637828a389
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 20:09:30 2016 +0000

        fix: BaseImage::IsBoundary(idx) [Image]

    commit c6998f264eab021993e3c8f3315d6500da7f8a86
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 16:30:54 2016 +0000

        enh: Rename blur-image to smooth-image [Applications]

    commit d0eff7d8295df22ef448db00db4b7df06a5862f4
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 16:30:15 2016 +0000

        add: Point set commands [Applications]

    commit 882bde96706bf17bd0eb0d0840b2bf88c03454b6
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 16:08:42 2016 +0000

        enh: Extend info command to work for VTK point set files [Applications]

    commit cd8d1918ebc3204141f4dc40d006cfd908ad3681
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 16:07:56 2016 +0000

        fix: Add "help" mirtk command to Bash completion function

    commit e9c73ddd0506df1a92b69848260cb4e9c0f1e34c
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 16:07:37 2016 +0000

        cmake: Support commands written in Python or Bash

    commit eeb57bc18eeb1f7a92d3acededbc0ba2d3117f6f
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 16:07:13 2016 +0000

        enh: Add isalnum and isdigit to mirtk namespace [Common]

    commit fef0a7baea5884ad1150f4e9360b692d1e2e9ecb
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 15:31:49 2016 +0000

        doc: Add README to Templates/ directory

    commit c7d8dba45a07a00639e4e6eec16fb98a538904f7
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 15:24:33 2016 +0000

        enh: Add ImageReader::TryNew [Image]

    commit 31e8c5133fb036f4e4c35cee3adbdb2cdff23596
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 15:24:17 2016 +0000

        cmake: Add missing dependency on FLANN libraries [PointSet]

    commit 4f56d284cb6187ebee8f3f09f7bb91d012d72cbd
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 15:23:18 2016 +0000

        fix: Temporarily disable warning triggered by unused private field in MCR [Common]

    commit 5ad0a4992aa228dadd59fa74ca3c682cf0083228
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 11:39:01 2016 +0000

        enh: Include mirtkVtk.h in mirtkPointSetUtils.h [PointSet]

    commit fe7434b9573a30faa865cb7a86bf8196c0e66291
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 15:33:58 2016 +0000

        fix: concatenate-images [Applications]

    commit 50c4ee4ebcb8944aa0a0b4aa2ae68bb888f98e1c
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 15:14:14 2016 +0000

        cmake: Add missing build targets [Applications]

    commit f5ea8b238fea9c67450db31e8441edf313c27f35
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 15:13:50 2016 +0000

        add: extract-roi [Applications]

    commit cc443bc7a9435208a601eb5de40f2c2ae499b228
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 15:12:02 2016 +0000

        add: concatenate-images and rename compose-dofs [Applications]

    commit 47ceb004f76e56ea9c8251e596133c5f3ccec524
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 15:11:33 2016 +0000

        enh: Rename SortIndice functor to improve readability when used [Common]

    commit 42bbb56f60c4f1544a157750a7650822bd378790
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 15:10:56 2016 +0000

        fixup: reflect-image [Applications]

    commit 41bd42cf40eb932f8de04d3b73ad5a9f90816b71
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 15:05:39 2016 +0000

        add: reflect-image command [Applications]

    commit fa329d0c40cc978f47c6e976aa0e697d4980aef7
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 15:05:07 2016 +0000

        enh: Change argument type of BaseImage::FlipXY et al. to bool [Image]

    commit ae0650774faa548e098bf3c42ed807018927565a
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 15:04:14 2016 +0000

        enh: Add SortIndices functor [Common]

    commit 0bf3a93e540da66b360d0bc3c04bf1e9f026e107
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 12:33:51 2016 +0000

        fixup: Previously added commands [Applications]

    commit 0f4fd6eb553d7431765eb502a7cb81c2e5a583f3
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 12:19:08 2016 +0000

        add: More applications and clean up CMakeLists.txt [Applications]

    commit b61ae6e784b2b6f1b0a40643adb24fe1d048177d
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 12:18:45 2016 +0000

        cmake: Auto-add IO libraries when LibImage is (optional) dependency

    commit c20eea0775412a3a6735db372368cfbc5921f6b4
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 12:18:17 2016 +0000

        enh: Rename enumeration to shorter name [Image]

    commit d23841bbcc47b54ea9315ba5dd56d23312f636fa
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 10:48:58 2016 +0000

        mod: Update Deformable module with fixed ToString/FromString functions

    commit 06d25cd76e884c534064488739dc935f9911990b
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 10:48:06 2016 +0000

        add: More commands [Applications]

    commit 51f5a8413e62883de3d9898600efa505f6fdb719
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 10:47:36 2016 +0000

        enh: Enable Bash completion of file/directory arguments

    commit 96f3d6d44c4bb6862d9b57ecfb2192ecade4e30f
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 10:46:44 2016 +0000

        add: Erosion and dilation image filters [Image]

    commit 20c3553d659da52cddc787b69784f64f9024cb04
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 10:46:14 2016 +0000

        fix: Move ConnectivityType from NeighborhoodOffsets to mirtk namespace [Image]

    commit ddd7f889d0c3b5dc35d386a635035ebcd9fc2330
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 10:45:20 2016 +0000

        enh: Add pointer to first image attributes to VoxelFunction

        The pointer is set by ForEachVoxelBody, i.e., by the [Parallel]ForEachVoxel template functions. It gives voxel functions access to the common attributes of the processed images.

    commit a355ea338acbf696371efce62b2f16551d029622
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 10:43:44 2016 +0000

        enh: Add ImageAttributes::_i2w and ImageAttributes:_w2i pointers [Image]

        The private image attributes structure of an image has pointers to the pre-computed homogeneous coordinate transformation matrices stored as private members of the same image instance. This allows the use of a reference to this ImageAttributes structure to transform world/voxel coordinates without having to recompute the transformation matrix.

    commit 57867e2e2477f03924b96572ba55d74e3c191c34
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 10:40:57 2016 +0000

        enh: Make enum ToString/FromString explicit template specializations

    commit b2c6a342657628ea84d88123a85105e63563a6a8
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 10:38:45 2016 +0000

        fix: Splitting of .nii.gz file name extension [Common]

    commit bdd7248112b0123481632912bd942a753670ce59
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 08:51:18 2016 +0000

        cmake: Remove second basis_project_begin call

    commit e3a595752b6db6dde669ceb54a68cfa7b5a07c6f
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 23:06:18 2016 +0000

        add: City Block distance transform [Image]

    commit b31ae79c9c8a01654dc2739897a9b7b1ab678cc8
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 21:12:39 2016 +0000

        add: More image manipulation commands [Applications]

    commit bd08c5c5861703bfd24f6ad444a7d8d427064f56
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 21:12:14 2016 +0000

        enh: Add PARSE_ARGUMENTS helper [Common]

    commit 0aba79fcc0ebeb040142fb7efb975f92b1f1e8db
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 21:11:58 2016 +0000

        enh: Ignore case when parsing interpolation/extrapolation mode name [Image]

    commit 583f770fa7a8c743d435776b565133f4a10b3411
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 19:49:21 2016 +0000

        fix: Help of extract-surface command [Applications]

    commit 7ad3bdc8e57762b15cca4606c66d97fbd0c72189
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 19:46:22 2016 +0000

        enh: Rename commands and add some more [Applications]

    commit d241cbcda12762cce427b5bed222610611c09c99
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 17:37:11 2016 +0000

        add: dofjacobian command [Applications]

    commit f7525aa3ded0f2e64e9e455b9aded2bbe17a82ad
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 17:37:00 2016 +0000

        add: matchpoints command [Applications]

    commit 9a0ea65dd0697bd3709311c81d964f2c07e586c4
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 17:36:47 2016 +0000

        add: overlap command [Applications]

    commit bfda2c0781e6cf73e81bdf917754bbd80d9ffc42
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 17:36:36 2016 +0000

        add: splitbrain command [Applications]

    commit a049092499d7c3e79a5b527bf5e3cfcbd130cb3c
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 17:13:28 2016 +0000

        add: detectedges command [Applications]

    commit ba4c9a43fdf4c45d465c34ad0543a0275c732901
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 17:08:32 2016 +0000

        add: downsample command [Applications]

    commit 13eac486fa19cc770a8fab69665650f6b0f1e3d9
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 17:02:59 2016 +0000

        add: calculate command [Applications]

    commit 9637b576ccaf3435ea1d4b212664d1870c8db3e7
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 17:02:45 2016 +0000

        cmake: Fix installation of Bash completions script [Applications]

    commit 8746e8c4a78cc11ed42146a5ca01c5d315e05abe
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 17:02:10 2016 +0000

        doc: Correct copyright notice [Applications]

    commit 5ca5e9b97adf3d36c61b0b4a5c96e866ad20b4e5
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 17:01:53 2016 +0000

        fix: Use of MIRTK_Registration_WITH_PointSet in register.cc [Applications]

    commit d04afeedafd2103ac77cfd91acd711164bd8d77a
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 15:55:06 2016 +0000

        mod: Update external modules with fixed tools

    commit f741a60d6a290b3234c3f62429f95b8fb34292a3
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 15:53:41 2016 +0000

        fix: Build of executables and add info tool for both images and transformations [Applications]

    commit 63532b76b25650bb664e16b598d956376f3153e6
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 15:52:27 2016 +0000

        add: Wrapper script for MIRTK command execution [Applications]

    commit d6d9e912c53608666be3befee06703adc1e648f6
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 15:51:28 2016 +0000

        enh: Require explicit include of mirtkOptions.h in main source file [Common]

    commit 90fbef492817323f0fa8b07079eb5e55dd5abf4a
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 15:50:58 2016 +0000

        cmake: Use mirtk_add_library [LBFGS]

    commit 36d6559c61ce3f41866ce3bb8aa49bc056ac7e2c
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 15:50:35 2016 +0000

        add: NiftiImageInfo struct of read NIfTI-1 image header entries [NIfTI]

    commit 969c01e7fb0b4b08de7fed2fcee994177727ff05
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 01:11:03 2016 +0000

        add: Various transformation tools [Applications]

    commit 976a9a04e65fd137b0d1450dc76a7f874059e3ec
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 01:10:29 2016 +0000

        enh: Add Transformation::CheckHeader [Transformation]

    commit ede0ae82449669bf4d47df1c811db141f71da6a5
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 23:56:07 2016 +0000

        enh: Import isupper and islower in mirtk namespace [Common]

    commit 74bab924ed21d0e9d6de4d9d8417db848d6befa1
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 20:17:31 2016 +0000

        mod: Update VolumetricMapping module with volumemap tool

    commit dc2b51bb754a4b31028309c2ba24286a6c62e54e
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 20:11:35 2016 +0000

        mod: Update Deformable module and add missing EnergyMeasure enum values

    commit 2affb649832eacb1e73f34f9e40c0dd627d4a63a
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 19:50:57 2016 +0000

        add: average tool [Applications]

    commit 6d118c3882998a4ad516cbff3866dc4cd4203a5c
    Merge: 39b076b f8d8187
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 19:32:57 2016 +0000

        Merge CMake BASIS Modules with basis_use_module

        Commit 'f8d8187838a420874424cc7a3f2ced7583712024'

    commit f8d8187838a420874424cc7a3f2ced7583712024
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 19:31:55 2016 +0000

        #540 Add basis_use_module macro

    commit 8f4649249c7cc77eaa86c3fa257b932b1b795b00
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 19:31:32 2016 +0000

        #526 Fix addition of empty CODE_DIRS to PROJECT_SUBDIRS

    commit 39b076b34e76820c9d591e0966a8a9d6aa1c9755
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 19:29:46 2016 +0000

        fix: Remove obsolete STL includes [Registration]

    commit c1031428e57a486fa6b2c6be5ff88b1f62d473fa
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 19:29:21 2016 +0000

        enh: Move registration tools to Applications folder

    commit be9634f391edcf660c5298e2f8151528ae847824
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 18:33:44 2016 +0000

        cmake: Declare EXTERNAL_MODULES

    commit e94cd7643711e2173ff2e2e023cce7f8d773bbfc
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 18:32:08 2016 +0000

        mod: Update Deformable module

    commit 7f6e019aa1f9885d61c2e7f19fffa87ed1bdc070
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 18:31:27 2016 +0000

        enh: Use STL container type aliases in mirtk namespace and get rid of std::

    commit b61caac442e2496db17bad5b5c68f6d5b6ad7cad
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 18:31:04 2016 +0000

        fix: Definition of OrderedMap [Common]

    commit 5ad11155306f72cdebbdfa488ae42c4de63fc718
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 16:20:43 2016 +0000

        mod: Update external modules

        The modules now make use of the STL type aliases in the mirtk namespace.

    commit d39ae3ca3eb23efc00d720ba51cdd9cf45511474
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 16:00:10 2016 +0000

        fixup: Use mirtk_add_executable

    commit babb5fc4d805aea9e4825fc61b9fd9a7abefdf9f
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 15:58:30 2016 +0000

        fixup: Merge of CMake BASIS modules

    commit aa7f3492d9f9c5b77ea7257900a93fb7bae6ce5d
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 15:56:36 2016 +0000

        enh: Add STL container type aliases [Common]

commit 63b71c98620247ad856ef99709d6e527329330a4
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Sun Jan 10 08:37:38 2016 +0000

    merge: Squash changes on develop branch into master for release of 1.0rc1

    commit f49e781def20560eb98f3c2080e3e2e65e6f6af8
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 08:27:40 2016 +0000

        doc: Change version and comment on release status [ChangeLog]

    commit fab0893d26fc6b33c4ad02742ff03204362a1cca
    Merge: 2436941 1764bb4
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 08:24:32 2016 +0000

        Merge CMake BASIS Modules with PROJECT_RELEASE version including 'rc' prefix.

        Commit '1764bb4929c28edb93079c5b060c5f329c77d7e8'

    commit 2436941143dba13984f142274087e4da9313e9a4
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 08:23:59 2016 +0000

        cmake: Change project version to 1.0.0rc1

    commit aa71313605278602bc48094488883383e29c1f5f
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 08:23:49 2016 +0000

        doc: Fix transformation format exclude list when NIfTI not available [Applications]

    commit a24787eb8ba761bda750635cee4665300ff394fb
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 08:23:22 2016 +0000

        doc: Insert space in module description [PointSet]

    commit 3e17a10378c4abafe5ede83e1f01644056a4518e
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 08:23:00 2016 +0000

        enh: Support full version string with "rc", "alpha", "beta" ... prefix [Common]

    commit 1764bb4929c28edb93079c5b060c5f329c77d7e8
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 08:20:32 2016 +0000

        enh: Append "rc", "beta", "alpha", ... prefix to PROJECT_RELEASE version when given

    commit 9e3749063b8b68d095be8925572087c5760b87e6
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 08:06:32 2016 +0000

        doc: Fix exlusion list of output transformation formats without NIfTI module [Applications]

    commit 6f5ef00086b3ca46b317875f776ee42135eb6e29
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 08:04:20 2016 +0000

        fix: Conversion of FFD to FSL warp without -target [Applications]

    commit eac608470308adfbf8f9aa15c83087ba540ea960
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 07:56:14 2016 +0000

        fix: Conversion between homogeneous MIRTK transformations, Nifty Reg, and FreeSurfer .xfm [Applications]

    commit 695fa7d4a800294c86ebb23d9ea3a37d55b05136
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 07:22:33 2016 +0000

        add: Transformation conversion commands [Applications]

    commit 3236dbb7d35256054626a59e98a8c90d2f703beb
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 03:15:52 2016 +0000

        mod: Update external packages with fixed links to online documentation

    commit 03783216d0420abcf0af1dba47718f9280056711
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 03:13:36 2016 +0000

        mod: Update external packages with updated README

    commit 09b35f72f733ce032c56b1f0981e89f3752175c3
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 03:02:17 2016 +0000

        cmake: Fix indentation

    commit f3d57588a27ed4ef8089b1c1e820724fb838907b
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 02:54:38 2016 +0000

        mod: Update Documentation with corrected download  and installation instructions

    commit f5307d4407089df9baf2d40b887a5ef8ced2d434
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 02:27:05 2016 +0000

        mod: Update Documentation with change from "external module" to "external package"

    commit b3ed089582413594b005e884ba789049b2235b92
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 02:14:40 2016 +0000

        add: Exernal package template files

    commit f096eaeb634b4474da2fc79c6402b57c3fb37b35
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 01:56:18 2016 +0000

        mod: Move external modules from External to Packages directory

    commit 0d01009621b970c4c33d82ef4e36e7158357b0e4
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 01:51:38 2016 +0000

        doc: Update release date in ChangeLog

    commit d254bfffba2af3fa1a357acf1c4b8a94699e5fb0
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 01:49:10 2016 +0000

        cmake: Split Tools.cmake into separate files for each function

    commit 822d14bbfc8141e741f54c505308a792547dd884
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 01:48:52 2016 +0000

        doc: Fix help output of info command [Applications]

    commit a8a492924dc2b3acf29b4203b1b34c1dc1382345
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 01:42:21 2016 +0000

        cmake: Rename Config folder to CMake

    commit 45a516a2b42b4b3b4374f5e37bbcd0b516d75a67
    Merge: 921094c a10a06c
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 01:28:49 2016 +0000

        Merge CMake BASIS Modules with TOPLEVEL_PROJECT_DOC_DIR.

        Commit 'a10a06cfd5048d8709b895cfbb1bf4b086ba1c2c'

    commit 921094caec92e2b8715af1de619566fd2c17d965
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 01:28:14 2016 +0000

        mod: Update Documentation with commands help

    commit e874e9fbcb3a078f9cb83e4200e9f6014b005f10
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 01:26:32 2016 +0000

        mod: Update external modules

    commit 4dfc578222968d969085fd3ee01b952124e4680b
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 01:25:30 2016 +0000

        enh: Auto-reformat command help output using reStructuredText [Applications, Documentation]

    commit a10a06cfd5048d8709b895cfbb1bf4b086ba1c2c
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 01:23:59 2016 +0000

        #541 Define TOPLEVEL_PROJECT_*_DIR variables

    commit 534d51661df64066ae6295285dbda7444a65f958
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Sun Jan 10 01:21:59 2016 +0000

        doc: Extend/fix help output of commands [Applications]

    commit a7dc7d48cb452234cde11c377de6e31101518dfc
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 23:29:02 2016 +0000

        add: Commands to compute vector field logarithmic/exponential map [Applications]

    commit 289bb9fbd2ed1fc2a15f9f43db6b02ee5dbb68c2
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 20:11:35 2016 +0000

        add: extract-connected-components [Applications]

    commit 0530b54cdc89bbd13c1fc025a97c496d2a8df767
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 20:11:17 2016 +0000

        enh: Remove "Total" from verbose output of extract-connected-points [Applications]

    commit 501ba7b5473c37fa04765f651f6731d1c9903791
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 20:10:49 2016 +0000

        enh: Rename extract-roi to extract-image-region [Applications]

    commit b9cf3e0d3fa259eea5025b4bf804bc07a2b5ae1f
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 20:10:23 2016 +0000

        doc: Add missing connectivity argument to help [Applications]

    commit 4a4b583cc946f2a547b6557f938941577e5783c7
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 20:09:49 2016 +0000

        add: Connected image components filter [Image]

    commit c96142903555bb5caf6a7013ee331d637828a389
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 20:09:30 2016 +0000

        fix: BaseImage::IsBoundary(idx) [Image]

    commit c6998f264eab021993e3c8f3315d6500da7f8a86
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 16:30:54 2016 +0000

        enh: Rename blur-image to smooth-image [Applications]

    commit d0eff7d8295df22ef448db00db4b7df06a5862f4
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 16:30:15 2016 +0000

        add: Point set commands [Applications]

    commit 882bde96706bf17bd0eb0d0840b2bf88c03454b6
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 16:08:42 2016 +0000

        enh: Extend info command to work for VTK point set files [Applications]

    commit cd8d1918ebc3204141f4dc40d006cfd908ad3681
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 16:07:56 2016 +0000

        fix: Add "help" mirtk command to Bash completion function

    commit e9c73ddd0506df1a92b69848260cb4e9c0f1e34c
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 16:07:37 2016 +0000

        cmake: Support commands written in Python or Bash

    commit eeb57bc18eeb1f7a92d3acededbc0ba2d3117f6f
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 16:07:13 2016 +0000

        enh: Add isalnum and isdigit to mirtk namespace [Common]

    commit fef0a7baea5884ad1150f4e9360b692d1e2e9ecb
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 15:31:49 2016 +0000

        doc: Add README to Templates/ directory

    commit c7d8dba45a07a00639e4e6eec16fb98a538904f7
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 15:24:33 2016 +0000

        enh: Add ImageReader::TryNew [Image]

    commit 31e8c5133fb036f4e4c35cee3adbdb2cdff23596
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 15:24:17 2016 +0000

        cmake: Add missing dependency on FLANN libraries [PointSet]

    commit 4f56d284cb6187ebee8f3f09f7bb91d012d72cbd
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 15:23:18 2016 +0000

        fix: Temporarily disable warning triggered by unused private field in MCR [Common]

    commit 5ad0a4992aa228dadd59fa74ca3c682cf0083228
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Fri Jan 8 11:39:01 2016 +0000

        enh: Include mirtkVtk.h in mirtkPointSetUtils.h [PointSet]

    commit fe7434b9573a30faa865cb7a86bf8196c0e66291
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 15:33:58 2016 +0000

        fix: concatenate-images [Applications]

    commit 50c4ee4ebcb8944aa0a0b4aa2ae68bb888f98e1c
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 15:14:14 2016 +0000

        cmake: Add missing build targets [Applications]

    commit f5ea8b238fea9c67450db31e8441edf313c27f35
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 15:13:50 2016 +0000

        add: extract-roi [Applications]

    commit cc443bc7a9435208a601eb5de40f2c2ae499b228
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 15:12:02 2016 +0000

        add: concatenate-images and rename compose-dofs [Applications]

    commit 47ceb004f76e56ea9c8251e596133c5f3ccec524
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 15:11:33 2016 +0000

        enh: Rename SortIndice functor to improve readability when used [Common]

    commit 42bbb56f60c4f1544a157750a7650822bd378790
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 15:10:56 2016 +0000

        fixup: reflect-image [Applications]

    commit 41bd42cf40eb932f8de04d3b73ad5a9f90816b71
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 15:05:39 2016 +0000

        add: reflect-image command [Applications]

    commit fa329d0c40cc978f47c6e976aa0e697d4980aef7
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 15:05:07 2016 +0000

        enh: Change argument type of BaseImage::FlipXY et al. to bool [Image]

    commit ae0650774faa548e098bf3c42ed807018927565a
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 15:04:14 2016 +0000

        enh: Add SortIndices functor [Common]

    commit 0bf3a93e540da66b360d0bc3c04bf1e9f026e107
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 12:33:51 2016 +0000

        fixup: Previously added commands [Applications]

    commit 0f4fd6eb553d7431765eb502a7cb81c2e5a583f3
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 12:19:08 2016 +0000

        add: More applications and clean up CMakeLists.txt [Applications]

    commit b61ae6e784b2b6f1b0a40643adb24fe1d048177d
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 12:18:45 2016 +0000

        cmake: Auto-add IO libraries when LibImage is (optional) dependency

    commit c20eea0775412a3a6735db372368cfbc5921f6b4
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 12:18:17 2016 +0000

        enh: Rename enumeration to shorter name [Image]

    commit d23841bbcc47b54ea9315ba5dd56d23312f636fa
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 10:48:58 2016 +0000

        mod: Update Deformable module with fixed ToString/FromString functions

    commit 06d25cd76e884c534064488739dc935f9911990b
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 10:48:06 2016 +0000

        add: More commands [Applications]

    commit 51f5a8413e62883de3d9898600efa505f6fdb719
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 10:47:36 2016 +0000

        enh: Enable Bash completion of file/directory arguments

    commit 96f3d6d44c4bb6862d9b57ecfb2192ecade4e30f
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 10:46:44 2016 +0000

        add: Erosion and dilation image filters [Image]

    commit 20c3553d659da52cddc787b69784f64f9024cb04
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 10:46:14 2016 +0000

        fix: Move ConnectivityType from NeighborhoodOffsets to mirtk namespace [Image]

    commit ddd7f889d0c3b5dc35d386a635035ebcd9fc2330
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 10:45:20 2016 +0000

        enh: Add pointer to first image attributes to VoxelFunction

        The pointer is set by ForEachVoxelBody, i.e., by the [Parallel]ForEachVoxel template functions. It gives voxel functions access to the common attributes of the processed images.

    commit a355ea338acbf696371efce62b2f16551d029622
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 10:43:44 2016 +0000

        enh: Add ImageAttributes::_i2w and ImageAttributes:_w2i pointers [Image]

        The private image attributes structure of an image has pointers to the pre-computed homogeneous coordinate transformation matrices stored as private members of the same image instance. This allows the use of a reference to this ImageAttributes structure to transform world/voxel coordinates without having to recompute the transformation matrix.

    commit 57867e2e2477f03924b96572ba55d74e3c191c34
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 10:40:57 2016 +0000

        enh: Make enum ToString/FromString explicit template specializations

    commit b2c6a342657628ea84d88123a85105e63563a6a8
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 10:38:45 2016 +0000

        fix: Splitting of .nii.gz file name extension [Common]

    commit bdd7248112b0123481632912bd942a753670ce59
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Thu Jan 7 08:51:18 2016 +0000

        cmake: Remove second basis_project_begin call

    commit e3a595752b6db6dde669ceb54a68cfa7b5a07c6f
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 23:06:18 2016 +0000

        add: City Block distance transform [Image]

    commit b31ae79c9c8a01654dc2739897a9b7b1ab678cc8
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 21:12:39 2016 +0000

        add: More image manipulation commands [Applications]

    commit bd08c5c5861703bfd24f6ad444a7d8d427064f56
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 21:12:14 2016 +0000

        enh: Add PARSE_ARGUMENTS helper [Common]

    commit 0aba79fcc0ebeb040142fb7efb975f92b1f1e8db
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 21:11:58 2016 +0000

        enh: Ignore case when parsing interpolation/extrapolation mode name [Image]

    commit 583f770fa7a8c743d435776b565133f4a10b3411
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 19:49:21 2016 +0000

        fix: Help of extract-surface command [Applications]

    commit 7ad3bdc8e57762b15cca4606c66d97fbd0c72189
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 19:46:22 2016 +0000

        enh: Rename commands and add some more [Applications]

    commit d241cbcda12762cce427b5bed222610611c09c99
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 17:37:11 2016 +0000

        add: dofjacobian command [Applications]

    commit f7525aa3ded0f2e64e9e455b9aded2bbe17a82ad
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 17:37:00 2016 +0000

        add: matchpoints command [Applications]

    commit 9a0ea65dd0697bd3709311c81d964f2c07e586c4
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 17:36:47 2016 +0000

        add: overlap command [Applications]

    commit bfda2c0781e6cf73e81bdf917754bbd80d9ffc42
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 17:36:36 2016 +0000

        add: splitbrain command [Applications]

    commit a049092499d7c3e79a5b527bf5e3cfcbd130cb3c
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 17:13:28 2016 +0000

        add: detectedges command [Applications]

    commit ba4c9a43fdf4c45d465c34ad0543a0275c732901
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 17:08:32 2016 +0000

        add: downsample command [Applications]

    commit 13eac486fa19cc770a8fab69665650f6b0f1e3d9
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 17:02:59 2016 +0000

        add: calculate command [Applications]

    commit 9637b576ccaf3435ea1d4b212664d1870c8db3e7
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 17:02:45 2016 +0000

        cmake: Fix installation of Bash completions script [Applications]

    commit 8746e8c4a78cc11ed42146a5ca01c5d315e05abe
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 17:02:10 2016 +0000

        doc: Correct copyright notice [Applications]

    commit 5ca5e9b97adf3d36c61b0b4a5c96e866ad20b4e5
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 17:01:53 2016 +0000

        fix: Use of MIRTK_Registration_WITH_PointSet in register.cc [Applications]

    commit d04afeedafd2103ac77cfd91acd711164bd8d77a
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 15:55:06 2016 +0000

        mod: Update external modules with fixed tools

    commit f741a60d6a290b3234c3f62429f95b8fb34292a3
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 15:53:41 2016 +0000

        fix: Build of executables and add info tool for both images and transformations [Applications]

    commit 63532b76b25650bb664e16b598d956376f3153e6
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 15:52:27 2016 +0000

        add: Wrapper script for MIRTK command execution [Applications]

    commit d6d9e912c53608666be3befee06703adc1e648f6
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 15:51:28 2016 +0000

        enh: Require explicit include of mirtkOptions.h in main source file [Common]

    commit 90fbef492817323f0fa8b07079eb5e55dd5abf4a
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 15:50:58 2016 +0000

        cmake: Use mirtk_add_library [LBFGS]

    commit 36d6559c61ce3f41866ce3bb8aa49bc056ac7e2c
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 15:50:35 2016 +0000

        add: NiftiImageInfo struct of read NIfTI-1 image header entries [NIfTI]

    commit 969c01e7fb0b4b08de7fed2fcee994177727ff05
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 01:11:03 2016 +0000

        add: Various transformation tools [Applications]

    commit 976a9a04e65fd137b0d1450dc76a7f874059e3ec
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Wed Jan 6 01:10:29 2016 +0000

        enh: Add Transformation::CheckHeader [Transformation]

    commit ede0ae82449669bf4d47df1c811db141f71da6a5
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 23:56:07 2016 +0000

        enh: Import isupper and islower in mirtk namespace [Common]

    commit 74bab924ed21d0e9d6de4d9d8417db848d6befa1
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 20:17:31 2016 +0000

        mod: Update VolumetricMapping module with volumemap tool

    commit dc2b51bb754a4b31028309c2ba24286a6c62e54e
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 20:11:35 2016 +0000

        mod: Update Deformable module and add missing EnergyMeasure enum values

    commit 2affb649832eacb1e73f34f9e40c0dd627d4a63a
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 19:50:57 2016 +0000

        add: average tool [Applications]

    commit 6d118c3882998a4ad516cbff3866dc4cd4203a5c
    Merge: 39b076b f8d8187
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 19:32:57 2016 +0000

        Merge CMake BASIS Modules with basis_use_module

        Commit 'f8d8187838a420874424cc7a3f2ced7583712024'

    commit f8d8187838a420874424cc7a3f2ced7583712024
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 19:31:55 2016 +0000

        #540 Add basis_use_module macro

    commit 8f4649249c7cc77eaa86c3fa257b932b1b795b00
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 19:31:32 2016 +0000

        #526 Fix addition of empty CODE_DIRS to PROJECT_SUBDIRS

    commit 39b076b34e76820c9d591e0966a8a9d6aa1c9755
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 19:29:46 2016 +0000

        fix: Remove obsolete STL includes [Registration]

    commit c1031428e57a486fa6b2c6be5ff88b1f62d473fa
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 19:29:21 2016 +0000

        enh: Move registration tools to Applications folder

    commit be9634f391edcf660c5298e2f8151528ae847824
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 18:33:44 2016 +0000

        cmake: Declare EXTERNAL_MODULES

    commit e94cd7643711e2173ff2e2e023cce7f8d773bbfc
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 18:32:08 2016 +0000

        mod: Update Deformable module

    commit 7f6e019aa1f9885d61c2e7f19fffa87ed1bdc070
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 18:31:27 2016 +0000

        enh: Use STL container type aliases in mirtk namespace and get rid of std::

    commit b61caac442e2496db17bad5b5c68f6d5b6ad7cad
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 18:31:04 2016 +0000

        fix: Definition of OrderedMap [Common]

    commit 5ad11155306f72cdebbdfa488ae42c4de63fc718
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 16:20:43 2016 +0000

        mod: Update external modules

        The modules now make use of the STL type aliases in the mirtk namespace.

    commit d39ae3ca3eb23efc00d720ba51cdd9cf45511474
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 16:00:10 2016 +0000

        fixup: Use mirtk_add_executable

    commit babb5fc4d805aea9e4825fc61b9fd9a7abefdf9f
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 15:58:30 2016 +0000

        fixup: Merge of CMake BASIS modules

    commit aa7f3492d9f9c5b77ea7257900a93fb7bae6ce5d
    Author: Andreas Schuh <andreas.schuh.84@gmail.com>
    Date:   Tue Jan 5 15:56:36 2016 +0000

        enh: Add STL container type aliases [Common]

commit 1da487ff549ded616f4cdac3ee52c1d6c7b6868f
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Tue Jan 5 16:00:10 2016 +0000

    fixup: Use mirtk_add_executable

commit 16143f6683cb4b786b4b3b5baa3eb2dcfc28a4ae
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Tue Jan 5 15:58:30 2016 +0000

    fixup: Merge of CMake BASIS modules

commit 7fe0289559fb091cdf1cbd1aed4717099ed8878c
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Tue Jan 5 15:56:36 2016 +0000

    enh: Add STL container type aliases [Common]

commit 184bbf9ed5356afd8e84f259dad2a1b3b6fcaee1
Merge: 676a8e4 9491efa
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Tue Jan 5 15:34:51 2016 +0000

    Merge branch 'master' of https://github.com/MIRTK/MIRTK

commit 676a8e4b08a7f13d99d74f656dc7073dac5f5d56
Merge: ee1ad8b d439071
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Tue Jan 5 15:34:32 2016 +0000

    mod: Update CMake BASIS modules with SOVERSION basis_project option

commit ee1ad8b4a852e0af686fd377726b74b2ea537285
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Tue Jan 5 15:30:19 2016 +0000

    cmake: Set SOVERSION of core modules to "0" (i.e., unstable)

commit d7b8bd8d029057a84e494b388d3ff84d280cf52f
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Tue Jan 5 15:29:44 2016 +0000

    mod: Update external modules

commit ab02288b90dc4eeee9773f14eb43b4a2a8dfb42f
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Tue Jan 5 15:21:58 2016 +0000

    cmake: Use mirtk_add_library

commit 583e45fc9c3fada1a59cad4218e6ffed3db7dac9
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Tue Jan 5 15:21:00 2016 +0000

    enh: Move mirtkRegistrationUtils.h functions to Common and PointSet [Registration]

commit 58a8d40429a77a37310df5392089056ef6b7298a
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Tue Jan 5 02:33:35 2016 +0000

    Squashed 'Config/Basis/' changes from c598d34..86ffc3b

    86ffc3b #505 Derive DEPENDS_*_DIR from <PKG>_EXECUTABLE path
    97124a8 #505 FindPythonInterp sets PythonInterp_DIR
    2cf09b2 #505 FindSphinx no longer caches Sphinx_DIR and always sets it

    git-subtree-dir: Config/Basis
    git-subtree-split: 86ffc3b297877b9ea36b4d85974009cd186ab7b2

commit d439071b1b7c667f6571bd694b2941a29a8351ad
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Tue Jan 5 15:25:17 2016 +0000

    #539 Set SOVERSION to major version by default, add option to basis_project

commit 9491efa302f7a6dc8dbecd7ef007f46fb7d725e0
Merge: 2d1bc1c 39f5f61
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Tue Jan 5 02:33:35 2016 +0000

    Merge CMake BASIS Modules with improved DEPENDS_*_DIR settings.

    Commit '39f5f610309b14a2cb585a3ef6a4783eac73e572'

commit 39f5f610309b14a2cb585a3ef6a4783eac73e572
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Tue Jan 5 02:33:35 2016 +0000

    Squashed 'Config/Basis/' changes from c598d34..86ffc3b

    86ffc3b #505 Derive DEPENDS_*_DIR from <PKG>_EXECUTABLE path
    97124a8 #505 FindPythonInterp sets PythonInterp_DIR
    2cf09b2 #505 FindSphinx no longer caches Sphinx_DIR and always sets it

    git-subtree-dir: Config/Basis
    git-subtree-split: 86ffc3b297877b9ea36b4d85974009cd186ab7b2

commit 86ffc3b297877b9ea36b4d85974009cd186ab7b2
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Tue Jan 5 02:31:41 2016 +0000

    #505 Derive DEPENDS_*_DIR from <PKG>_EXECUTABLE path

commit 97124a84984dd7bef8898a4a5a26e0833e4b15bb
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Tue Jan 5 02:31:18 2016 +0000

    #505 FindPythonInterp sets PythonInterp_DIR

commit 2cf09b2383666aa4293f1026759e20eff82b7479
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Tue Jan 5 02:30:57 2016 +0000

    #505 FindSphinx no longer caches Sphinx_DIR and always sets it

commit 2d1bc1c7b2c3e8218e156a65d6dd394dd2a17fba
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Tue Jan 5 02:29:12 2016 +0000

    mod: Documentation with explicit basis_find_package calls

commit 9a059a89b20a86de56eb87a3b31af51ef395b4f7
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Tue Jan 5 02:25:47 2016 +0000

    cmake: Find Boost header files only, no libraries [Numerics,PointSet,Transformation]

commit fb54a87088f88c697162163a72a10cc2f6cbc935
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Tue Jan 5 02:25:16 2016 +0000

    fix: Temporarily disable "-Wunused-local-typedefs" when including FLANN [PointSet]

commit e27301f9702986737e016350d33bd616eb776209
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 19:50:24 2016 +0000

    Squashed 'Config/Basis/' changes from 2bafc36..c598d34

    c598d34 #535 Add NO_STANDARD_INPUT option to basis_add_doxygen_doc
    17772b4 #531 Use system installation of Sphinx Doxylink extension
    9d18ce7 #534 Add PREDEFINED option to basis_add_doxygen_doc
    eb131e5 #506 Add BASIS_SPHINX_EXTENSION_PATH only when set
    24fac81 #532 Re-include package use file when additional components found
    c72457f #526 Add TOOLS_DEPENDS et al. options

    git-subtree-dir: Config/Basis
    git-subtree-split: c598d34758209f4add6f48e48f9925cf4ea9b44c

commit 59a7704ed3b8adb8c1635bd50c372d395f121fa0
Merge: f669f2f e27301f
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 19:50:24 2016 +0000

    Merge CMake BASIS Modules with MIRTK documentation support.

    Commit 'e27301f9702986737e016350d33bd616eb776209'

commit c598d34758209f4add6f48e48f9925cf4ea9b44c
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 19:49:16 2016 +0000

    #535 Add NO_STANDARD_INPUT option to basis_add_doxygen_doc

commit 17772b49e6cfa3788644ab576c4e7161bf7795b2
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 19:48:07 2016 +0000

    #531 Use system installation of Sphinx Doxylink extension

    When BASIS_SPHINX_EXTENSIONS_PATH is not set.

commit 9d18ce76d4c24cd8e8a2f7212156df7826d3d8aa
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 19:47:00 2016 +0000

    #534 Add PREDEFINED option to basis_add_doxygen_doc

commit eb131e5c73d58f2e1a26a9190d645d8184dcfe29
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 19:45:18 2016 +0000

    #506 Add BASIS_SPHINX_EXTENSION_PATH only when set

commit 24fac81b6d49eeb3c05b9c138511187171dd0163
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 19:44:51 2016 +0000

    #532 Re-include package use file when additional components found

commit c72457f1ef662ff89eca702ab6ee3d4d1a8f8926
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 19:44:18 2016 +0000

    #526 Add TOOLS_DEPENDS et al. options

commit f669f2ff93d11e3b449f71a133915a121de5af93
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 19:31:19 2016 +0000

    doc: Shorten paragraph

commit 2f2fe872116230050da783a66b3854dd14d4d4ec
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 19:30:48 2016 +0000

    doc: Shorten paragraph

commit 0fed3a229499e0e42cc40ecc5c9a9e87c17dc9df
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 19:29:15 2016 +0000

    doc: Refer user to online documentation [README]

commit c5d44d2b9a4a59f63cb08d6687ec29440d59b1a8
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 19:20:28 2016 +0000

    mod: Update submodules

commit 35f1ba8c55f572497d07de249ae958638bf44953
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 19:15:10 2016 +0000

    add: ChangeLog file

commit e513ac157c8677ac56c0564a3d921dc3bda6612e
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 19:15:02 2016 +0000

    fixup: Renaming of ThirdParty modules

commit bea6ce829bf0d4bf453ae38737c6374661f7336a
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 19:14:34 2016 +0000

    fix: Use CMAKE_CONFIGURATION_TYPES only when set

commit 39f667604179dafdad51efde51b96298e324ab29
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 19:14:11 2016 +0000

    enh: Remove "ThirdParty" prefix from NIfTI and LBFGS module names

commit 22a91c4943e23e98c5982e9745487d9bfdc0ec09
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 19:13:43 2016 +0000

    fix: In-source documentation errors

commit 215e97014f47e392721f7962046f265f682c762a
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 13:24:40 2016 +0000

    mod: Move external and third-party modules to top-level subdirectory

commit 4a319704313c5e912006b8161e0cbd670f9776d2
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 09:38:36 2016 +0000

    doc: Remove description of deleted Applications module [README]

commit e194829474ae7db29f6db6a42dedb776544500de
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 09:35:14 2016 +0000

    doc: Update CMake GUI screenshot [INSTALL]

commit 8aac1d3cc38ce7dadf11a8f46a5b2d6f2a1915a7
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 09:31:55 2016 +0000

    doc: Update installation instructions [INSTALL]

commit 856221c92f5018c8ae0e8bc4bd76a9512e385979
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 09:16:29 2016 +0000

    Squashed 'Config/Basis/' changes from 49c7d61..2bafc36

    2bafc36 #527 Add PROJECT_EXTERNAL_MODULES

    git-subtree-dir: Config/Basis
    git-subtree-split: 2bafc364d6992fe3b1333df5fa33fcea7c942427

commit 0e773810116541215e48d349f15b5ddc68a90445
Merge: 97f714f 856221c
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 09:16:29 2016 +0000

    mod: Merge CMake BASIS Modules with new EXTERNAL_MODULES option.

    Commit '856221c92f5018c8ae0e8bc4bd76a9512e385979'

commit 2bafc364d6992fe3b1333df5fa33fcea7c942427
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 09:14:05 2016 +0000

    #527 Add PROJECT_EXTERNAL_MODULES

commit 85df191f737c316e3caf2ce4eec9215e0ac87c74
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 07:55:05 2016 +0000

    Squashed 'Config/Basis/' changes from 6d6310e..49c7d61

    49c7d61 #526 Add PROJECT_TOOLS_DIRS with BUILD_APPLICATIONS option

    git-subtree-dir: Config/Basis
    git-subtree-split: 49c7d61a23d48a3f8750c8e4b5862e7e5ef0c44b

commit 97f714f89a740c3d70c33a9d28b8dd40bd723f80
Merge: fe63e0c 85df191
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 07:55:05 2016 +0000

    Merge CMake BASIS Modules with optional project tools support.

    Commit '85df191f737c316e3caf2ce4eec9215e0ac87c74'

commit 49c7d61a23d48a3f8750c8e4b5862e7e5ef0c44b
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 07:52:02 2016 +0000

    #526 Add PROJECT_TOOLS_DIRS with BUILD_APPLICATIONS option

    Also only add project subdirectories when they contain a CMakeLists.txt file.

commit fe63e0c8ec68a8ccb9bbc7ca0f1de77ab3d86013
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 07:45:53 2016 +0000

    enh: Remove Applications module, build tools as part of each module

commit a02476a83dd2ed7b9992db59e037e90c668a46ed
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 06:59:35 2016 +0000

    mod: Make VolumetricMapping an external module

commit 8f57554a6e07e01b3f41d5a13fd2b5030b685f4d
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 06:52:29 2016 +0000

    mod: Make Deformable an external module

commit a9ce375121d19b570fc0ea875df1c60a7357e179
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 06:36:24 2016 +0000

    mod: Add Documentation module

commit 5b00b42d11bec107d2e11742a7c60805a009713a
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 06:35:52 2016 +0000

    fix: Add CMake GUI screenshot in Config/ directory [INSTALL]

commit db147727a4e451d03fbb2ad1953b0eb773d083ac
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Mon Jan 4 06:34:55 2016 +0000

    del: Remove Documentation files from top-level project

commit 1543c529eb66f085866f1b700f6de70bf55797a1
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Sun Jan 3 22:29:20 2016 +0000

    doc: Grammer correction and remove note to prefer MIRTK tools [README]

commit 1e7d39de9c721490a6e8a4b0149f16437ed70214
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Sun Jan 3 22:23:57 2016 +0000

    Squashed 'Config/Basis/' content from commit 6d6310e

    git-subtree-dir: Config/Basis
    git-subtree-split: 6d6310edebdb1d3e321b2deaf49c1bcd18354a1a

commit 59184b0b45996fef9370da705472d57e2bf4fab9
Merge: b76b2d8 1e7d39d
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Sun Jan 3 22:23:57 2016 +0000

    Merge commit '1e7d39de9c721490a6e8a4b0149f16437ed70214' as 'Config/Basis'

commit b76b2d86a009faec80fe23485c57c9a1a0976dc8
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Thu Dec 17 22:45:59 2015 +0000

    add: Initial import of refactored (M)IRTK source files

commit 6d6310edebdb1d3e321b2deaf49c1bcd18354a1a
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Sun Jan 3 19:54:17 2016 +0000

    #521 Fix warning about invalid interpret version info

commit 8cde910e69544bd3ee6c8b2a3dc45bd9939db20d
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Sun Jan 3 19:53:39 2016 +0000

    #525 Do not warn about missing CTestConfig.cmake file

commit ff9e184f3bb6b471cba2fe60046a05ce8e72609f
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Sun Jan 3 15:58:33 2016 +0000

    #504 Consider WITH_<PKG>_DEFAULT set in Depends.cmake

commit 7a7000225e211e065e9d2488b574ca32add627ce
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Sun Jan 3 15:57:59 2016 +0000

    #505 Hide DEPENDS_<PKG>_DIR variables when dependency found

commit 224b48291aaf8696cae89889e6f970c89705055d
Author: Andreas Schuh <andreas.schuh.84@gmail.com>
Date:   Sun Jan 3 15:57:14 2016 +0000

    #326 Add DE…
  • Loading branch information
@schuhschuh
schuhschuh committed Jan 11, 2016
1 parent 13f0726 commit 555dad9
Show file tree
Hide file tree
Showing 748 changed files with 329,420 additions and 0 deletions.
148 changes: 148 additions & 0 deletions Applications/CMakeLists.txt
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,148 @@
# ============================================================================
# Medical Image Registration ToolKit (MIRTK)
#
# Copyright 2013-2015 Imperial College London
# Copyright 2013-2015 Andreas Schuh
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# ============================================================================

##############################################################################
# @file CMakeLists.txt
# @brief Build configuration of (core) MIRTK Applications.
##############################################################################

# ----------------------------------------------------------------------------
# Include optional dependencies (cf. Config/Depends.cmake)
if (MODULE_PointSet)
basis_use_package(VTK)
if (FLANN_FOUND)
basis_use_package(FLANN)
else ()
set(FLANN_LIBRARY)
endif ()
if (MATLAB_FOUND)
basis_use_package(MATLAB)
else ()
set(MATLAB_mwmclmcrrt_LIBRARY)
endif ()
endif ()

## NOTE: OPTIONAL dependencies on MIRTK IO modules added by mirtk_add_executable
## automatically when list of dependencies includes LibImage.

# Generic file info tool
mirtk_add_executable(info DEPENDS LibImage OPTIONAL LibTransformation LibPointSet ${VTK_LIBRARIES})

# ----------------------------------------------------------------------------
# Image tools
if (MODULE_Image)

macro(add_image_command cmd)
mirtk_add_executable(${cmd} DEPENDS LibImage ${ARGN})
endmacro()

add_image_command(average-images OPTIONAL LibTransformation)
add_image_command(calculate OPTIONAL ${VTK_LIBRARIES})
add_image_command(calculate-distance-map)
add_image_command(calculate-exponential-map)
add_image_command(calculate-lie-bracket)
add_image_command(calculate-logarithmic-map)
add_image_command(close-image)
add_image_command(convert-image)
add_image_command(cut-brain)
add_image_command(detect-edges)
add_image_command(dilate-image)
add_image_command(downsample-image)
add_image_command(edit-image OPTIONAL LibTransformation)
add_image_command(erode-image)
add_image_command(evaluate-overlap)
add_image_command(extract-connected-components)
add_image_command(extract-image-region)
add_image_command(flip-image)
add_image_command(concatenate-images)
add_image_command(open-image)
add_image_command(reflect-image)
add_image_command(resample-image)
add_image_command(smooth-image)
add_image_command(transform-image LibTransformation)

endif ()

# ----------------------------------------------------------------------------
# Registration tools
if (MODULE_Registration)

macro(add_registration_command cmd)
mirtk_add_executable(${cmd} DEPENDS LibRegistration ${ARGN})
endmacro()

add_registration_command(register LibImage OPTIONAL LibLBFGS LibPointSet LibDeformable)

endif ()

# ----------------------------------------------------------------------------
# Transformation tools
if (MODULE_Transformation)

macro(add_transformation_command cmd)
mirtk_add_executable(${cmd} DEPENDS LibTransformation ${ARGN})
endmacro()

add_transformation_command(average-dofs LibImage)
add_transformation_command(concatenate-dofs LibImage)
add_transformation_command(convert-dof LibImage)
add_transformation_command(convert-dof2csv LibImage)
add_transformation_command(convert-dof2velo LibImage)
add_transformation_command(edit-dof)
add_transformation_command(evaluate-dof LibImage)
add_transformation_command(evaluate-jacobian LibImage)
add_transformation_command(init-dof LibImage OPTIONAL LibPointSet)
add_transformation_command(invert-dof)

endif ()

# ----------------------------------------------------------------------------
# Point set tools
if (MODULE_PointSet)

macro(add_pointset_command cmd)
mirtk_add_executable(${cmd} DEPENDS LibPointSet ${VTK_LIBRARIES} ${ARGN})
endmacro()

add_pointset_command(calculate-surface-attributes)
add_pointset_command(calculate-surface-spectrum)
add_pointset_command(convert-mris) # requires Python VTK modules and FreeSurfer installation
add_pointset_command(convert-pointset LibImage)
add_pointset_command(copy-pointset-attributes)
add_pointset_command(decimate-surface)
add_pointset_command(delete-pointset-attributes)
add_pointset_command(evaluate-distance)
add_pointset_command(evaluate-distortion)
add_pointset_command(evaluate-surface-overlap ${FLANN_LIBRARY})
add_pointset_command(extract-connected-points)
add_pointset_command(extract-pointset-surface LibImage)
add_pointset_command(extract-surface LibImage)
add_pointset_command(match-points LibTransformation)
add_pointset_command(offset-surface)
add_pointset_command("project-onto-surface")
add_pointset_command(transform-points LibImage LibTransformation)
add_pointset_command(remesh)
add_pointset_command(smooth-surface)

if (MATLAB_FOUND)
add_pointset_command(convert-pointset-to-mat ${MATLAB_mwmclmcrrt_LIBRARY})
add_pointset_command(copy-pointset-attributes-from-mat ${MATLAB_mwmclmcrrt_LIBRARY})
endif ()

endif ()
Loading

0 comments on commit 555dad9

Please sign in to comment.