ENH: Adding libminc and updating MINC IO support.

Added libminc library inside Modules/ThirdParty/MINC to compile withing ITK.
Also rewrote MINC IO from Modules/Nonunit/Review/  to work correctly,
also added extensive testing to the module.

ENH: Modified UseITK.cmake to include automatic MINCIO initialization

BUG: MINC2 Metadata reading and writing is now supported and compatible with ITK standard

BUG: Dimension order and step sign is now preserved

BUG: Run uncrustify on all source code to satisfy ITK style requirements

BUG: Fixed error with wrong order of dimensions

BUG: Reduced number of tests

BUG: Fixed error in interslice normalization when reading floating point volumes
     in libminc, so updated GIT TAG

BUG: Made libminc to compile statically always and with itk_ prefix to avoid
     potential conflict with already installed libminc

BUG: Fixed a bug in underlying libminc library, updated GIT tag

BUG: Fixed a bug while reading vector images or time-series with zero time step

ENH: Updated to latest version of libminc

ENH: Making more tests

BUG: Fixed logical error when reading files with global normalization

BUG: Added tests for 4D Dti data and Labels

BUG: Forgot to change libminc git id

BUG: Reduced number of tests

BUG: Updated to latest version of libminc

BUG: Fixed a bug in libminc which affected building MINC2 module

BUG: Addded ability to store floating point data in a MINC2 volume with integer data type

BUG: Updated to latest version of libminc

BUG: Re-enabled test for rounding errors in case of storing floating point data in storage with integer data type

BUG: Fix warnings about unused or uninitialized values.  Add brackets for style consistency.

BUG: Fix uninitialized variable warnings and remove README

ENH: Added IO adapter for MINC style transformations (.xfm files)

ENH: Updated to latest version of libminc and fixed the way libmind is called to make .xfm files

BUG: Fixed errors in building on MacOSX

BUG: Fixed build on Windows

BUG: Second attempt to fix build on Windows

BUG: Suppressed CRT SECURE Warnings on Windows, fixed typo

BUG: Removed more warnings in Windows build

BUG: Fixed integer overflow in libminc

ENH: Rebased to the latest master

BUG: Trying to make build possible

BUG: Fixed bug while building with GCC

ENH: Rebased to current master

BUG: Updated copyright notice

Change-Id: Ie9ed4151dca83d5854cc713536a9594dc520c15a
BUG: Return of NaN by DiffusionTensor3D::GetFractionalAnisotropy

As reported here:
https://itk.icts.uiowa.edu/jira/browse/ITK-3030

There are cases where the computed anisotropy
is NaN because of taking the square root of a
negative value.  This patch returns zero for FA
if it would be NaN.

This sensible solution was reviewed by several DWI processing
experts, and consider this approach to be a good couse of action.

It is suspected that the problem enters here

 anisotropy = 3.0 * isp - trace * trace;

when precision errors make the right side of the minus sign slightly larger
than the left. In this case the true anisotropy is going to be close to zero.

Change-Id: I2f9b47998f8dcefbca9ab27f315574617191ca6c
ENH: Remove names inputs specialized comparison

With the addition of constant time access to the PrimaryInputs, this
former optimization to make the PrimaryInput the first element in the
map is no longer beneficial. Additionally, with the feature of setting
the name of the primary input, it may not always be beneficial. Also,
for the filters with just one input or output, this offered no
benefit.

Change-Id: I71ee3ce035e3ce9e933153a0ab0f8715c08aec78
PERF: Use ImageAlgorithm::Copy in JoinSeries filter

Change-Id: I012177638fe023c4a73ae590f6ba92cb18ad9f0e
ENH: JPEG IO now writes and reads spacing, similar to the TIFF IO (ITK-3023)

Change-Id: I5f40e226040233672eed3dcdec1a5b9007899574
COMP: Distance maps filters cannot wrap 1D.

itkContourDirectedMeanDistanceImageFilter, itkContourMeanDistanceImageFilter
itkDirectedHausdorffDistanceImageFilter, and itkHausdorffDistanceImageFilter
cannot wrap 1D because of eventual issues in BinaryContourImageFilter.
Use the same wrapping types as its component filter, SignedMaurerDistanceMapImageFilter.

Change-Id: I85aecc8aec084f96c085eb123fda385b55754388
DOC: Remove reference to MeanDistanceImageFilter.

This class does not appear to exist.

Change-Id: Ie9c6f710271ed5b2c3cc42935fca4bb6ffc4fa2e
STYLE: Fix KWStyle errors.

Change-Id: I2448157817368d9c8fa6265fd8ec4fd45d0b5d54
PERF: Change default index i/o prefix to just "_"

Renamed default index i/os' prefix from "IndexedDataObject" to just "_"
followed by the index number.

There are two motivation for this: 1) The prior approach required each
comparison done in the named map to compare 17 chars to get to the
number, which is inefficient. 2) With the introduction on the global
variable of these name, shortening the name reduces the ( by a small
amount ) the foot print of the variable.

Change-Id: Ifb9e2fb627f11e001f58090af88b71debb421c98
Merge topic 'MINC_IO_Modules32'

bd5eca1 ENH: Adding libminc and updating MINC IO support.
Merge topic 'JoinSeriesUseImageAlgorithmCopy'

1a2f2c2 PERF: Use ImageAlgorithm::Copy in JoinSeries filter
ENH: wrapping itkMaskFeaturePointSelectionFilter itkBlockMatchingImageFilter

Change-Id: I45d9b067c47f5a148049adec00806de1102b0dc1
Merge topic 'KWStyleError'

7cae097 STYLE: Fix KWStyle errors.
Merge topic 'wrappingErrors'

8cf08ea DOC: Remove reference to MeanDistanceImageFilter.
ef172b6 COMP: Distance maps filters cannot wrap 1D.
PERF: Use ImageAlgorithm::Copy in CastImageFilter

Overload and "specialize" the ThreadedGenerateData method to use this
optimized procedure instead of the standard functor
implementation. This results in a ~5-25X performance increase when
compared to ITKv4.3.2, when combined with the optimized copy
method. However, this does remove incremental progress reporting.

Change-Id: I8a2af5c4ec4726967bf6a0cdccaa5f2a4e82d156
Merge topic 'NamedInputsCompatibility_NoSpecializedCompare'

1a677ab ENH: Remove names inputs specialized comparison
Merge topic 'GlobalForNamesIndexedInputs'

cea64f0 PERF: Change default index i/o prefix to just "_"
Merge topic 'pythonwrapping'

a12e27c ENH: wrapping itkMaskFeaturePointSelectionFilter itkBlockMatchingImageFilter
Merge topic 'ITK-3023'

b7c7107 ENH: JPEG IO now writes and reads spacing, similar to the TIFF IO (ITK-3023)
Merge topic 'CastImageFilterToImageAlgorithmCopy'

22fa569 PERF: Use ImageAlgorithm::Copy in CastImageFilter