BUG:  Masks need to be warped.

Change-Id: Idb52f47fb4bbe0e0e876f74badd36487a4cf62a4
Merge topic 'BSplineSyNMasking'

4e0a9b3 BUG:  Masks need to be warped.
COMP: Added missing header <functional> in itkAnchorCloseImageFilter.h

Fixes VC11 complaint about undefined std::greater in
itkAnchorCloseImageFilter.h

Change-Id: Iba0fb1125386cd59c96ca934391408c8c03d45e5
Merge branch 'itkAnchorCloseImageFilter_VC11_Comp_Fix_release' into release
BUG: Warn on directories

The script only processes files. Directories are ignored. Prior to this
patch, the script exited if a directory was found.

Change-Id: I9286d17af1a8cc92cfdebe9de3d09303c690b1aa
Merge topic 'WhatModulesError'

fb8cba8 BUG: Warn on directories
Merge branch 'release'
BUG: using InputPixelType to hold label count can overflow.

The member variable m_TotalLabelCount is set to the maximum
pixel value in the input images, plus one. For any unsigned pixel
type if the maximum input value equals
itk::NumericTraits<InputPixelType>::max(), then the TotalLabelCount
gets set to zero, and zero-length tables end up causing memory errors
and crashes.

Change-Id: Icabc62f7917105cdf35524ab0c68fda5895ae0a4
Merge topic 'LabelVotingSizeVarBug'

5f5c64e BUG: using InputPixelType to hold label count can overflow.
COMP: Incomplete variable name change.

USE_WRAP_ITK changed to ITK_WRAPPING.

Change-Id: I21f85534dfcfcf3132348b3d7c0d78744da27535
DOC: Modify ContourMeanDistanceImageFilter comments.

Author: v.fortunati@erasmusmc.nl
There is was an error in line 34. Max is replaced with mean as in the definition of the directed mean distance filter.

Change-Id: Icd7ffe394ad17ff662ee1054d82f07517279b894
Merge topic 'EditDoxygen_ContourMeanDistanceImageFilter_1358167836'

7f80d3e DOC: Modify ContourMeanDistanceImageFilter comments.
STYLE: Fix errors detected by KWStyleCodeTest.

Change-Id: I83260b49569ae8adc80da830b6d309489c4e1950
KWSys 2013-01-14 (6fa1c99f)

Extract upstream KWSys using the following shell commands.

$ git archive --prefix=upstream-kwsys/ 6fa1c99f | tar x
$ git shortlog --no-merges --abbrev=8 --format='%h %s' 3b17de34..6fa1c99f
Brad King (6):
      fea37696 Process: Remove support for Windows 98
      01e15c22 Remove KWSys Registry
      cb5f835f SystemTools: Fix MakeDirectory with colon in path
      1643507a IOStream: Fix check for compiler 'long long' support
      34177aec SystemTools: Fix MakeDirectory after recent cleanup
      84827cc1 Process: Avoid argv[0]==NULL from parsing empty command line

Riku Voipio (1):
      8ce09af5 CPU: Add Aarch64 support

Rolf Eike Beer (45):
      f376ec32 SystemInformation: fix typos
      bfee5174 SystemInformation: sum up all caches found in /proc/cpuinfo
      5690d711 SystemInformation: fix value extraction from /proc/cpuinfo
      36295981 SystemInformation: PA-RISC chips are from HP
      72e9d02e SystemInformation: try harder to find a useful processor name
      b39de34c SystemInformation: try harder to find the CPU family
      933eb822 SystemInformation: extract CPU stepping information from /proc/cpuinfo, too
      4da9894d SystemInformation: Clean up QuerySolarisInfo()
      01392358 SystemInformation: don't attribute i386 Solaris systems to Sun
      3db65ac1 SystemInformation: wrap the call to CPUID in a function
      61bd9b42 SystemInformation: use the __cpuid compiler intrinsic if present
      5932e7c0 SystemInformation: query memory size on Cygwin using sysconf()
      ea5612ed SystemInformation: count memory with _SC_PAGESIZE and _SC_PHYS_PAGES
      3aca6642 SystemInformation: query memory size, CPU count, and CPU speed on BSD
      3572c54d SystemInformation: count CPUs on HP-UX
      e6771b34 SystemInformation: determine CPU type on HP-UX
      640210e5 SystemInformation: use /proc/cpuinfo only when present
      5bdcfd10 SystemInformation: query total memory on AIX
      de69d547 SystemInformation: use intrinsic for RDTSC if supported
      9808d4e7 SystemInformation: get CPU speed on Windows when RDTSC fails
      f4c625b5 tests: avoid truncation of testSystemInformation output in CDash
      03d6fbe5 SystemInformation: get x86 CPU features from /proc/cpuinfo
      f8e917c1 SystemInformation: remove the #define CPUID_INSTRUCTION
      59c4b5c5 SystemInformation: split Windows code out of QueryMemory()
      200ee91f SystemInformation: split HP-UX code out of QueryMemory()
      88217703 SystemInformation: split Linux code out of QueryMemory()
      9e317872 SystemInformation: split AIX code out of QueryMemory()
      349cee5b SystemInformation: remove useless zeroing from QueryMemory()
      7271926e SystemInformation: split Cygwin code out of QueryMemory()
      6da78ad1 SystemInformation: make QueryMemory() return bool
      182179e9 Haiku no longer defines __BEOS__
      297758a5 SystemInformation: fix conversion warning
      79ef34ef SystemInformation: fix calling kwsysProcess_WaitForData()
      f1068caf SystemInformation: speed up copying process data
      e041cd66 SystemInformation: factor out QueryMemoryBySysconf()
      ea850fa0 SystemInformation: factor out QueryProcessorBySysconf()
      57f06d49 SystemInformation: count processors with sysconf() on Solaris
      7dfc27d5 SystemInformation: check CPU vendor and SSE support on OpenBSD
      494d9d7a SystemInformation: get stepping code on Intel Macs
      608d6b47 SystemInformation: determine processor features on Intel Macs
      c6057a06 SystemInformation: fix "Multi-character character constant"
      5a27bd4f SystemInformation: make IsHyperThreadingSupported() return bool
      342c0ad2 SystemInformation: query memory size with sysconf() on Solaris
      f0b857c1 SystemInformation: cache result of IsHyperThreadingSupported()
      ab0c2a09 SystemInformation: try using assembler with BorlandC

Sean McBride (2):
      5e17bfde Process: Dereference NULL++ instead of NULL to force crash
      86a78cb7 SystemTools: Add check for empty strings to prevent integer underflow

Stephen Kelly (1):
      247b8a3c SystemTools: Rename MakeCnidentifier() to MakeCidentifier()

Change-Id: I3021b3d968a728e65e8062349f068d7c1c0820e0
Merge branch 'upstream-kwsys' into update-kwsys

Change-Id: I47f4e19c800b2acb290a5ee23221ac33586bc2bb
Merge topic 'update-kwsys'

93c6fd7 Merge branch 'upstream-kwsys' into update-kwsys
32a533d KWSys 2013-01-14 (6fa1c99f)
Merge topic 'KWStyleTestErrors'

69fa532 STYLE: Fix errors detected by KWStyleCodeTest.
COMP: Fix TIFF on big endian systems

This is similar to the fix I submitted April 24, 2012 (367953).
Basically on big endian systems you need to check if
WORDS_BIGENDIAN is defined, not its value.

This fix was overwritten when libtiff 4.0.3 was pulled in. Also,
libtiff 4.0.3 contained a second instance of this error.

The original full description is here:
     http://lists.debian.org/debian-med/2012/04/msg00070.html
ENH: Add unit test to itkThresholdImageFilterTest

Issue #2991

Change-Id: Ibdc58c387002729a7fd025cb68f49cc5633dfe67
ENH: Add MaskingValue to MaskImageFilter

Closes #2993

Change-Id: I75d8c8d3a68cc86eb67af570dc57021b4f85a9ac