ENH:  Adding winsorization and rescaling.

git-svn-id: https://advants.svn.sourceforge.net/svnroot/advants@1108 fd2da0a4-d968-48df-9cb5-d8c496287cbf
BUG:  Handling file specification on the command line

git-svn-id: https://advants.svn.sourceforge.net/svnroot/advants@1109 fd2da0a4-d968-48df-9cb5-d8c496287cbf
ENH: Added more complete notes on using svn and git together.

git-svn-id: https://advants.svn.sourceforge.net/svnroot/advants@1110 fd2da0a4-d968-48df-9cb5-d8c496287cbf
COMP: Fix compiler error

itkPICSLAdvancedNormalizationToolKit.hxx:291:64: error: default
arguments cannot be added to an out-of-line definition of a member of a
class template

git-svn-id: https://advants.svn.sourceforge.net/svnroot/advants@1111 fd2da0a4-d968-48df-9cb5-d8c496287cbf
COMP:  Fixed clang compilation issues

The clang compiler is more stringent than most.

ANTS/Examples/../ImageRegistration/ANTS_affine_registration2.h:728:6: error: redefinition of 'GetAffineTransformFromImage'
ANTS/Examples/../ImageRegistration/ANTS_affine_registration2.h:701:43: error: call to function 'ShrinkImageToScale' that is neither visible in the template definition nor found by argument-dependent lookup
ANTS/Examples/../Utilities/itkDiReCTImageFilter953.hxx:1133:25: error: default arguments cannot be added to an out-of-line definition of a member of a class template
ANTS/Examples/../Utilities/itkDiReCTImageFilter953.hxx:1182:25: error: default arguments cannot be added to an out-of-line definition of a member of a class template

git-svn-id: https://advants.svn.sourceforge.net/svnroot/advants@1112 fd2da0a4-d968-48df-9cb5-d8c496287cbf
COMP:  First attempt at adding SuperBuild

This add the superbuild system that has been
refined to accomplish several goals.  It is
more fully featured than is needed for the
simplest of ANTS superbuild systems.

The reason is that it very closely parallels
the superbuild system requirements that allow
this project to be added to the Slicer package,
and has been shown extensible and useful for the BRAINSTools
spharm-pdm and other packages.

Every attempt has been made to make this a generic
infrastructure that can be dropped on top of an existing
package, and with minimal editing add the superbuild system.

The differences from the BRAINSTools implementation include the
folowing:

1) Change LOCAL_PROJECT_NAME from "BRAINSTools" to "ANTS"
2) Remove custom BRAINSTools dependancy generation.

git-svn-id: https://advants.svn.sourceforge.net/svnroot/advants@1113 fd2da0a4-d968-48df-9cb5-d8c496287cbf
STYLE: Converted cmake directives to lower case

CMake documentation now uses lower case lettering
for it's directives.  This patch set makes
cmake directives consistent with documentation.

git-svn-id: https://advants.svn.sourceforge.net/svnroot/advants@1114 fd2da0a4-d968-48df-9cb5-d8c496287cbf
STYLE: Made whitespace consistent

Replaced seemingly random tabs with consistent spaces.
Removed end of line white-space.
Removed execute mode on source code files.
Added execute mode on shell files.

git-svn-id: https://advants.svn.sourceforge.net/svnroot/advants@1115 fd2da0a4-d968-48df-9cb5-d8c496287cbf
ENH: Remove BRAINS References.

git-svn-id: https://advants.svn.sourceforge.net/svnroot/advants@1116 fd2da0a4-d968-48df-9cb5-d8c496287cbf
ENH: Fixed pathing to output directory.

git-svn-id: https://advants.svn.sourceforge.net/svnroot/advants@1117 fd2da0a4-d968-48df-9cb5-d8c496287cbf
BUG:  Restored HSV and Jet colormaps.

git-svn-id: https://advants.svn.sourceforge.net/svnroot/advants@1118 fd2da0a4-d968-48df-9cb5-d8c496287cbf
ENH: cc image metric update 

git-svn-id: https://advants.svn.sourceforge.net/svnroot/advants@1119 fd2da0a4-d968-48df-9cb5-d8c496287cbf
BUG: need proper affie transform 

git-svn-id: https://advants.svn.sourceforge.net/svnroot/advants@1120 fd2da0a4-d968-48df-9cb5-d8c496287cbf
BUG: need to downsample currently due to shortcomings of composite transform

git-svn-id: https://advants.svn.sourceforge.net/svnroot/advants@1121 fd2da0a4-d968-48df-9cb5-d8c496287cbf
ENH: enable projection of the warp along a direction 

git-svn-id: https://advants.svn.sourceforge.net/svnroot/advants@1122 fd2da0a4-d968-48df-9cb5-d8c496287cbf
ENH: writing out eigenvalues, also updating optimization with proper gradient (rather than greedy) formulation

git-svn-id: https://advants.svn.sourceforge.net/svnroot/advants@1123 fd2da0a4-d968-48df-9cb5-d8c496287cbf
ENH: writing out eigenvalues, also updating optimization with proper gradient (rather than greedy) formulation

git-svn-id: https://advants.svn.sourceforge.net/svnroot/advants@1124 fd2da0a4-d968-48df-9cb5-d8c496287cbf
ENH: 2 - further refactoring toward a pure gradient based optimization 

git-svn-id: https://advants.svn.sourceforge.net/svnroot/advants@1125 fd2da0a4-d968-48df-9cb5-d8c496287cbf
BUG:  Fixed compilation warnings.

git-svn-id: https://advants.svn.sourceforge.net/svnroot/advants@1126 fd2da0a4-d968-48df-9cb5-d8c496287cbf
WIP: some additional algorithms for sccan and change to input options

git-svn-id: https://advants.svn.sourceforge.net/svnroot/advants@1127 fd2da0a4-d968-48df-9cb5-d8c496287cbf