Added reorient2std interface
Merge pull request #455 from hanke/master

OrderedDict is not in Python < 2.7...
ENH:  Reorganize and expand the features from ANTS

The Advanced Normalization Toolkit is a nice set
of tools that allow for registration of medical
image registration.  The "Normalization" tools available
contain both intensity normalization tools (i.e. N4) and
spatial normalizaiton tools (i.e. antsRegistration).

This effort attempts to make a more maintainable set of
nipye wrapping that closely follow the ANTS development.
The primary reason for this re-organization is to allow
the nipype interface for ANTS to very closely match the
on-going development of the ANTS tools themselves.

The guidelines used for this effort are as follows:

1) Where ever possible, nipype should mirror the command
   line options.  This rule is sometimes violated because
   the command line tool option is a key work in nipype
   (i.e. "input"), or to make nipype consistent across
   tools.
2) One nipype wrap program per python file.  This makes it easier
   to find the appropriate file and to know what has been wrapped
   from the command line tools.  It also closely matches the
   paradigm used for SEM wrapped programs, and it opens the door
   for more consistent maintenance of the tools from the ANTS
   original source code tree because there is a one-to-one mapping
   between wrapper and function.  The tools have too many permutations
   of use to have them all globbed together.

3) python file name should match program name as closely as possible .  That includes case sensitivity.
ENH: Make name match program.

for i in *.py; do
    echo "$i          $(grep _cmd $i)               $(grep ${i//.py/}InputSpec\( $i)"
done

PYTHON FILE                          SHELL PROGRAM NAME                         NIPYPE WRAPPED NAME
===================================  =========================================  =====================================================================
ANTS.py                              _cmd = 'ANTS'                              class ANTSInputSpec(ANTSCommandInputSpec):
Atropos.py                           _cmd = 'Atropos'                           class AtroposInputSpec(ANTSCommandInputSpec):
AverageAffineTransform.py            _cmd = 'AverageAffineTransform'            class AverageAffineTransformInputSpec(ANTSCommandInputSpec):
AverageImages.py                     _cmd = 'AverageImages'                     class AverageImagesInputSpec(ANTSCommandInputSpec):
MultiplyImages.py                    _cmd = 'MultiplyImages'                    class MultiplyImagesInputSpec(ANTSCommandInputSpec):
N4BiasFieldCorrection.py             _cmd = 'N4BiasFieldCorrection'             class N4BiasFieldCorrectionInputSpec(ANTSCommandInputSpec):
WarpImageMultiTransform.py           _cmd = 'WarpImageMultiTransform'           class WarpImageMultiTransformInputSpec(ANTSCommandInputSpec):
WarpTimeSeriesImageMultiTransform.py _cmd = 'WarpTimeSeriesImageMultiTransform' class WarpTimeSeriesImageMultiTransformInputSpec(ANTSCommandInputSpec):
antsApplyTransforms.py               _cmd = 'antsApplyTransforms'               class antsApplyTransformsInputSpec(ANTSCommandInputSpec):
antsIntroduction.py                  _cmd = 'antsIntroduction.sh'               class antsIntroductionInputSpec(ANTSCommandInputSpec):
antsRegistration.py                  _cmd = 'antsRegistration'                  class antsRegistrationInputSpec(CommandLineInputSpec):
buildtemplateparallel.py             _cmd = 'buildtemplateparallel.sh'          class buildtemplateparallelInputSpec(ANTSCommandInputSpec):

* This is only here for backwards compatibility,  the antsApplyTransforms.py provides a more complete interface
alternateInterfaceApplyTransforms.py _cmd = 'antsApplyTransforms'

* These are entire workflow 'pipelets'
antsRegiatrationBuildTemplate.py
ANTSBuildTemplate.py

* These are infrastructure files
base.py
__init__.py
setup.py
Moved examples from to common folder.
moved workflows where they belong
Imports cleanup
Moved ANTS test to a doctest
ANTS clean up and better Bool support.
antsRegistration cleanup
Cleanup of ApplyTransforms
AverageAffineTransform cleanup.
Cleanup of AverageImages.
Further cleanup
Cleanup and package rearangement.
Further cleanup, reverted input names changes in ApplyTrasforms, renamed
antsRegistration.
Updated workflow after renaming.
Partial revert "Further cleanup, reverted input names changes in ApplyTrasforms, renamed"

This reverts commit da3a4b8eeacce7ecdcf61010b4367f7a9d272521.
Rename ApplyTransforms, dont import depracated interfaces
BUG: Fix spelling and naming

During testing, some of the variable names were found
to be misspelled or incoherent meaningg.
ENH: Start to fix template building with new antsRegistration.