BUG: LabelGeometry cropped images with non-unit spacing incorrectly

The itkLabelGeometryImageFilter previously cropped object images
incorrectly when the input image had non-unit spacing.  This was
corrected by simply including spacing in the resampler.  This patch
also includes a rewritten test that is simpler and clearer.  The test
now includes image regression tests.  It also includes feature values
regression tests by writing and reading the features values as CSV
files.  It tests both 2D images and 3D volumes.

Change-Id: I6767489993b30c187ae41b3a6c904bc3dd68d67e
COMP: Prevent ITK_USE_64BITS_IDS with Wrapping on Windows.

GCCXML generates interfaces where itk::SizeValueType becomes
unsigned long.  This causes problems on Windows where unsigned long
is only 32 bits.

Change-Id: I4239b6c6c648c01d9d7c8a95725e14bd2314fc74
COMP: Fix scanf conversion specification to %u

Use %u for unsigned int conversion specification. This patch addresses
the following warning:

tkVTKImageIO.cxx(303): warning #181: argument is incompatible with
corresponding format string conversion
        sscanf(line, "%*s %*s %s %d", pixelType, &numComp)

Change-Id: Iba92a5e7fd65e9301666b061067378ed6834fba0
COMP: Fix scanf conversion specification for id types

In a reader just used for a test, scanf was used with a %ld ( signed
long ) conversion specification, while the argument was an unsigned
identifier type. This id type could be 32 or 63 bits, long or long
long. There is currently no macro in ITK to assist with the conversion
specification similar to PRIu64 from inttypes.h. So at a trade off of
not supporting 64-bit integers on windows ( for just a test), the
unsigned long type is used with the consistent %ul conversion
specifier.

Change-Id: I3a24ca1e0fa655a1ac33f957b58e4aaa139868a2
COMP: Fix ambiguous specialization of GDCM Element

To disable certain combinations of template arguments to GDCM's
Element class, ambiguous declarations where added with no
definition. These combintations are causing compilations warnings such
as:

gdcmElement.h(611): warning #889: this partial specialization would
have made the instantiation of class "gdcm::Element<4096, 218367>"
ambiguous
  template <int TVM> class Element<VR::OB, TVM>;

While simply removing ambiguous declarations, would remove the
warnings this would not preserve the authors original intent to
prevent instantiation. To achieve a additional class was added with a
concept like check, to prevent instantiation.

Change-Id: I01c7d3f663a2e97804a465fb460d964542c6bf2d
BUG: Making 2D Minc IO work properly

ENH: Bumped libminc version

Change-Id: Ie736c9114db5a68879fe7548019bd7014e0ab386
Merge topic 'MINC_2D_FIX'

864bd20 BUG: Making 2D Minc IO work properly
Merge topic 'FixVTKscanfWarning'

65a8674 COMP: Fix scanf conversion specification to %u
BUG: Remove extraneous print statement in tiffio

Change-Id: Idde8550e9b81cc5b0092d99b0f8216991c1d72d6
BUG: Incorrect va_arg type used in TIFF and LSM

This patch addresses tests failure on big endian systems and windows
debug builds.

A uint16 was used where a uint32 was expected. The checking of where
the different types are expected has been added. This changes the
type that is passed to the ReadRawByteFromTag method.

Additionally, access to the private TIFFField data structure was being
made. This has been changed to access via custom macros to use the
correct interface for TIFFv3 and TIFFv4.

Change-Id: I297942ec22af3433d57110c35b63dcca4800e11d
ENH: Use Tiff version dependent field type enable LSM

LSMImageIO was naively dependent on the ITK tiff library, when only
the return type of TIFFFieldWithTag changed between tiff library
versions. All dependencies of LSM and SYSTEM_TIFF have been removed.

Change-Id: Ibf4fc743e49de7d514b1410df28be1fc3e28d4d5
BUG: JPEG2000 bool type in C is now unsigned char

JPEG2000 is a compiled C library interfaced to a C++ library. When
compiling the C library the "bool" type is defined as a int yet in C++
it's a intrinsic bool type, which is 1 byte. While it's not guaranteed
that a bool is the same size, alignment etc as a unsigned
char. In practice its working better until the openjpeg library can be
updated.

Change-Id: I3780812dd60fc23873e5853b35df0f3e3ae5f9dc
Merge topic 'VSWrap'

07dfd5b COMP: Prevent ITK_USE_64BITS_IDS with Wrapping on Windows.
Merge topic 'RemoveExtraneousPrintInTiff'

e59b0c9 BUG: Remove extraneous print statement in tiffio
Merge topic 'FixLSMSystemTIFF'

88f0b8d BUG: Incorrect va_arg type used in TIFF and LSM
Merge topic 'FixVTKscanfWarning'

c14a1fb COMP: Fix scanf conversion specification for id types
Merge topic 'FixJPEG2000booltype'

a7eee65 BUG: JPEG2000 bool type in C is now unsigned char
BUG: add a test to demonstrate ThreadedIteratorPartitioner bug

Change-Id: Ic9eb9b2026bef51756c87340bb113a49438c3c81
BUG: Fix written other magic number in FreeSurferBinaryMeshIO

Change-Id: Ice8af8cc334f4bf8340786a34407c7efc5e5a7b6
Merge topic 'FixFreeSerferBinaryMeshIOBigEndian'

fef5070 BUG: Fix written other magic number in FreeSurferBinaryMeshIO