-DOC: update year in copyright message


git-svn-id: https://svn.bigr.nl/elastix/trunkpublic@4505 4d348492-3962-11de-aa85-65a2020054a3
ENH: adapt to latest itk 

cherry-picked from the performance branch


git-svn-id: https://svn.bigr.nl/elastix/trunkpublic@4506 4d348492-3962-11de-aa85-65a2020054a3
BUG: catch exceptions

ENH: check for dimension


git-svn-id: https://svn.bigr.nl/elastix/trunkpublic@4548 4d348492-3962-11de-aa85-65a2020054a3
ENH: generalizing elxInvertTransform for multiple dimensions


git-svn-id: https://svn.bigr.nl/elastix/trunkpublic@4549 4d348492-3962-11de-aa85-65a2020054a3
COMP: forgot to change cmake list


git-svn-id: https://svn.bigr.nl/elastix/trunkpublic@4556 4d348492-3962-11de-aa85-65a2020054a3
COMP: include in raycast interpolators


git-svn-id: https://svn.bigr.nl/elastix/trunkpublic@4557 4d348492-3962-11de-aa85-65a2020054a3
-BUG: The UseRandomSampleRegion option is ignored in the following case: 1) MultiMetricMultiResolutionRegistration, AND 2) Using more than one metric, AND 3) Using only one sampler (RandomCoordinate), AND 4) Using AdaptiveStochasticGradientDescent, AND 5) Using AutomaticParameterEstimation. The bug was caused because the SampleGradients function failed to turn on the UseRandomSampleRegion after turning it off, because it assumed that each sampler was different, while they actually all point to the same instance. Bug reported by Valerio Fortunati. 



git-svn-id: https://svn.bigr.nl/elastix/trunkpublic@4562 4d348492-3962-11de-aa85-65a2020054a3
-BUG: reported by Floris Berendsen. HowToCombineTransforms was always written as "Compose" in the TransformParameter file, even when it should be "Add". This bug was introduced in revision r3224.



git-svn-id: https://svn.bigr.nl/elastix/trunkpublic@4572 4d348492-3962-11de-aa85-65a2020054a3
ENH: merging selected commits from the performance branch

revisions: 4460-4504, 4523, 4525, 4544
This is intended to make the performance branch and the trunk very much alike.


PERF: Jacobian and moving image gradient product in one function
ENH: pre-allocated jacobians not needed anymore

ENH: replace elx::Timer with itk::TimeProbe
Probably has better (platform-independent) implementation, perhaps better precision, moves maintance burden to ITK.
Completely removed elx::Timer.
ENH: add ConvertSecondsToDHMS convenience function to elx::BaseComponent, so that every component can use it.

ENH: removed code duplication from elastix.h and transformix.h
ENH: use std::copy for copying parameters
ENH: added a showProgress boolean to the resampler base, currently used for the OpenCL resampler
STYLE: minor


git-svn-id: https://svn.bigr.nl/elastix/trunkpublic@4587 4d348492-3962-11de-aa85-65a2020054a3
DOC: license issues

In preparation of a move to a new Apache 2.0 license checked current licensing


git-svn-id: https://svn.bigr.nl/elastix/trunkpublic@4588 4d348492-3962-11de-aa85-65a2020054a3
ENH: add a tools directory

First tool is a python script to replace the copyright notice in files.


git-svn-id: https://svn.bigr.nl/elastix/trunkpublic@4589 4d348492-3962-11de-aa85-65a2020054a3
DOC: add copyright notice and license files

in preparation of a move to the apache 2.0 LICENSE


git-svn-id: https://svn.bigr.nl/elastix/trunkpublic@4590 4d348492-3962-11de-aa85-65a2020054a3
ENH: creating CMake directory and moving CMake related files

ENH: moved uncrustify files to tools


git-svn-id: https://svn.bigr.nl/elastix/trunkpublic@4591 4d348492-3962-11de-aa85-65a2020054a3
ENH: moved runelastix etc to tools


git-svn-id: https://svn.bigr.nl/elastix/trunkpublic@4592 4d348492-3962-11de-aa85-65a2020054a3
BUG: from imperfect merge



git-svn-id: https://svn.bigr.nl/elastix/trunkpublic@4593 4d348492-3962-11de-aa85-65a2020054a3
DOC: add missing copyright notice


git-svn-id: https://svn.bigr.nl/elastix/trunkpublic@4594 4d348492-3962-11de-aa85-65a2020054a3
ENH: moving parameter files to Data directory


git-svn-id: https://svn.bigr.nl/elastix/trunkpublic@4595 4d348492-3962-11de-aa85-65a2020054a3
BUG: CTestConfig.cmake should be in the root directory

Otherwise there will be errors when submitting nightly build results to the cdash dashboard


git-svn-id: https://svn.bigr.nl/elastix/trunkpublic@4599 4d348492-3962-11de-aa85-65a2020054a3
ENH: Extend AffineDTI to 2D image.
Parameter setting is 
(Scales angle shearX shearY scaleX scaleY translateX translateY)
example:(Scales 100 100000000 100000000 100 100 1 1)
and AutomaticScalesEstimation should be turned off.
(AutomaticScalesEstimation "false" ) 

git-svn-id: https://svn.bigr.nl/elastix/trunkpublic@4603 4d348492-3962-11de-aa85-65a2020054a3
STYLE: minor cleanups


git-svn-id: https://svn.bigr.nl/elastix/trunkpublic@4604 4d348492-3962-11de-aa85-65a2020054a3