ENH: Preparing point set metrics for use with registration.

Change-Id: I53e4c1b052b98377e88c5e0351f2fda12963851a
ENH: Move to latest remote module tag

Several code cleanups and compiler warnings were addressed
in the remote repository.

Change-Id: I31784ce897bcdd7c6f3dcc9488f7695cd2cb0d90
BUG: TestingExtractSliceImageFilter lacked test.

In this patch we add a unit test for the itkTestingExtractSliceImageFilter
class.

NOTE: The unit test uncovered a bug in SetExtractionRegion. The
dimension of the output size and index were being exceeded, causing a
crash on Windows systems.

This class is critical, given that it is used as part of the testing
infrastructure for the rest of the toolkit.

Change-Id: I0b5a80f88f22ccd754c1a6f433a2b0a57475f69a
COMP: Remove vcl_time and vcl_clock

These vcl methods were initialliy use because not al systems provided
a consistent interface. Now, clock_t, time_t, clock() and time() are
well supported. The complex logic in the vcl interface is no longer
needed.

Change-Id: I40975e30605bde1db389b4c7bec342d9f7ae5405
COMP: Update PCRE to 8.35

Will fix some more warnings under Windows for the Python Wrappings.

Change-Id: I99a5b4cd27eb8e391f9175f5c16d3b4aeae516e3
Merge topic 'Remove_vcl_time_vcl_clock'

1f19aa00 COMP: Remove vcl_time and vcl_clock
BUG: Match behavior of SimpleFastMutexLock on different platforms (#ITK-3248)

The WinAPI and the pthread implementation behaved differently regaring recursive locking.

The WinAPI implementation used "InitializeCriticalSection" and "EnterCriticalSection" which let the thread holding the mutex call EnterCriticalSection again without blocking:
http://msdn.microsoft.com/en-us/library/windows/desktop/ms682608%28v=vs.85%29.aspx

In contrast the pthread implementation used pthread_mutex_init and pthread_mutex_lock whose behavior concerning this matter was dependent on the initialization parameters of the mutex. The default (which was used in ITK) doesn't allow recursive locking:
http://pubs.opengroup.org/onlinepubs/7908799/xsh/pthread_mutex_lock.html

I suggest to adapt the pthread implementation because it seems to me that the current behavior of the WinAPI implementation is the one expected by most users.

Change-Id: Ic75fab3eedd1b457c531668b7786501a139426ba
Merge topic 'PCRE8.35'

39d326e3 COMP: Update PCRE to 8.35
ENH: Add RegularStep gradient optimizer to ITKv4

We probably do not need this optimizer technically; however, having such
an optimizer is the preliminary step to convert "ImageRegistration1"
example to ITKv4.

Using ordinary GradientDescentOptimizerv4 does not provide convergence
for the example 1. Also, the results generated by other v4 optimizers
(e.g. GradientDescentLineSearchOptimizerv4) show a very fast
convergence, and they are not suitable for graphical interpretation of
the registration process that is necessary for the educational purposes.

Change-Id: I547f58f776952aebaa7d36ac2dd1540406617268
COMP: Fix egregious -Wcast-qual warnings

Fix a handful of C-style casts that are throwing out 'const' for no
particular reason. (Also rewrite one that really does need to cast away
const to use a const_cast.)
Merge topic 'itkTestingExtractSliceImageFilter_CodeCoverage'

cba75dac BUG: TestingExtractSliceImageFilter lacked test.
Merge topic '3248-platform-dependent-mutex'

f8d8c7b9 BUG: Match behavior of SimpleFastMutexLock on different platforms (#ITK-3248)
KWSys 2014-04-14 (1979c02d)

Extract upstream KWSys using the following shell commands.

$ git archive --prefix=upstream-kwsys/ 1979c02d | tar x
$ git shortlog --no-merges --abbrev=8 --format='%h %s' dd873734..1979c02d
Brad King (2):
      39f98b5d Encoding: Add self-assignment check to CommandLineArguments
      1979c02d hashtable: Poison operator= on internal node type

Gerhard Grimm (1):
      fa86f1ba SystemInformation: Fix HP-UX PA-RISC processor detection

Jiri Malak (1):
      36982798 SystemTools: add Watcom single Quote processing

Rolf Eike Beer (3):
      a8aa1014 SystemInformation: Fix HP-UX Intel processor detection
      a99a9235 set the compile flags for older HP compilers to fix compilation
      8b085635 MD5: avoid casting back and forth between size_t and int

Change-Id: I2338cfae50b9703cfed4d11d5d68e3cabfcd6ce1
Merge branch 'upstream-kwsys' into update-kwsys

Change-Id: Ie3d680fab007e4bf590156be6cd7c0e710bce549
Merge topic 'PointSetRegTesting'

ec931404 ENH: Preparing point set metrics for use with registration.
Merge topic 'update-kwsys'

f806ba5c Merge branch 'upstream-kwsys' into update-kwsys
76b71d65 KWSys 2014-04-14 (1979c02d)
STYLE: Improve testing of member Get/Set functions

Increase code coverage by testing that the Get/Set
member functions are used.

Change-Id: I00df2b32c87c22998ab4cca3773c3d70dfe618c5
COMP: SigmoidTransferFunction conversion from double.

For

  /scratch/dashboards/Linux-x86_64-gcc4.1/ITK/Modules/Numerics/NeuralNetworks/include/itkSigmoidTransferFunction.hxx:53:
  warning: converting to 'unsigned char' from 'double'

Change-Id: I77bb29d9b807ed120728cd4d103c57613f7fc37c
BUG: BoxImageFilter GenerateInputRequestRegion public -> protected.

Change-Id: I3a4fc69ef6350601068132e90b4b1babf92a29e1
DOC: KernelImageFilter does not reimplement GenerateInputRequestedRegion.

Change-Id: I239ed2453e9060476d538a2617b4e8a5d845b9e7