ENH: Add Remote module group description to Doxygen.

Change-Id: Ic70edec4c163ae0f06a42c3aff6b8ea0f1c7c8be
ENH: remove VersorTransformOptimizerv4 from ITKv4

The recently added RegularStepGradientDescentOptimizerv4 can be used
form both vector and versor transforms optimization. Therefore, the
versor optimzer can be considered as a duplicated class and can be
removed form ITK.

Change-Id: I2705f21fdb4667fa31bcabf5e18b1567d75ca961
ENH: Turn off DCMTK Logger messages by default

Reading DICOM Image files will sometimes generate thousands of
DCMTK warnings, even though all the DICOM tags needed to extract
Image data and metadata are read correctly.

This patch turns off the DCMTK logger except for fatal errors.
New Set/GetLogLevel are added to control DCMTK logging. A user
might well want to turn on more verbose output from DCMTK while
debugging.

Change-Id: I152aa446b7620b8268f74436e968c21e54b59101
STYLE: dynamic_cast to pointer does not throw

Not need for try catch block when operator can't throw. dynamic_cast
may throw for conversion to a reference type, not a pointer.

Change-Id: Ifa9baa9a30a9a0b23b2e9bfc84481c89831a016c
Merge topic 'UpdateVersorOptDocs'

9b0df1ab ENH: remove VersorTransformOptimizerv4 from ITKv4
COMP: Fix "unused-local-typedefs" warnings

These were easy removals of unused typedefs.

Change-Id: I1cc1f3abae12b007e56eaa163da846bf9b8f5037
Merge topic 'fix-unused-typedef-warnings'

ee63f94b COMP: Fix "unused-local-typedefs" warnings
Merge topic 'DynamicCastDoesNotThrow'

627c2f14 STYLE: dynamic_cast to pointer does not throw
Merge topic 'SILENCE_DCMTK_WARNINGS'

934940b8 ENH: Turn off DCMTK Logger messages by default
DOC: Corrected documentation for threshold boundaries.

Previously, the documentation for itkThresholdImageFilter was
incorrect for the ThresholdAbove, ThresholdBelow, and ThresholdBetween
options because they incorrectly stated the handling of pixels in the
image equal to the threshold value itself.  The previous comments
stated that pixels equal to the threshold value will be changed to the
outsideValue.  But according to the code, the true handling of pixels
equal to the threshold value is that they are not affected by the
threshold.  The documentation has now been corrected.

The corresponding test was enhanced to add explicit testing of the
threshold value, and the new tests pass, further indicating that the
new documentation is correct.  The test was also extended to handle
cases where the inputValue is not 0 for generality and to make the
code clearer.

Change-Id: I3fc7f36a532e7b64b03d9591e31057e7d1cc745d
COMP: fixed license test command in UpdateDoubleConversionFromGoogle.sh

The script commands to check that the DoubleConversion license
hasn't changed since the last update from the upstream Google
repository were apparently untested, and did not work.

I replaced them with bash commands that did what was intended.

Change-Id: I36a13daf2cd72e7fc27a0adb15331b652e482349
COMP: Fix GCC warning about unused typedef in ConceptChecking

New in GCC 4.8 is a warning about when a local typedef is not
used. The most frequent offender of this incidental warning is the
concept checking used. This patch uses an approach suggested by Brad
King which uses the type as a template argument, to an instantiated
empty class.

Change-Id: Icc2c89e377639f829e0c1fbed4468c92eae813d5
COMP: Adding itkMacro.h for ITK_NULLPTR definition

Error detected by ITK's header test.

Change-Id: Ia3ff7792b2bf18bf38e36fbc1e89dcba508768aa
Merge topic 'FIX_DOUBLECONVERSION_UPDATESCRIPT'

00e18c24 COMP: fixed license test command in UpdateDoubleConversionFromGoogle.sh
Merge topic 'FixMissingHeaderForITK_NULLPTR'

e2927dab COMP: Adding itkMacro.h for ITK_NULLPTR definition
BUG: Missing parentheses for logic comparison

Change-Id: I308c6a5e4d41b230715d68de6cfa766c719bb80a
warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses]
  if ( !TInputImage::ImageDimension == TOutputImage::ImageDimension )
       ^                            ~~
STYLE: Refactor swig call and code cleanup

1) Removed the CSWIG_IGNORE_WARNINGS variable in ConfigureWrapping.cmake, it was used nowhere
2) add_definitions(-DSWIG_GLOBAL) in ConfigureWrapping was removed.
Following the git logs and the swig changelog (https://github.com/swig/swig/blob/master/CHANGES):
  - in 2003 the -DSWIG_GLOBAL flag was replaced by -runtime
  - in 2004, the -runtime flag was deprecated (from the logs):
    SWIG modules now exchange their pointer type information
    via the Guile interpreter.  It is no longer necessary to build a
    runtime library or to use -noruntime and -runtime etc.

3) In Python/CMakeLists.txt, remove the ITK_WRAP_PYTHON_AUTODOC variable, we are using swig 3.0.0
4) In Python/CMakeLists.txt, add a new itk_setup_swig_python macro. The macro sets up the call to
swig. The custom command was set up at two places (for the modules and submodules); it is better
if we have only one place for this.
5) Comments added to the flags passed to swig.
6) set(lib ${WRAPPER_LIBRARY_NAME}Python) was called twice
7) Removed some commented out code

8) Python/module_ext.i.in: removed #include <cstddef> workaround for old swig
9) SwigInterface/CMakeLists.txt: ensure we use swig 3.0.0
10) TypedefMacros.cmake: set(WRAPPER_LIBRARY_SWIG_INPUTS ) was called twice

Change-Id: Iae75e29c84957de474a2e61d56d25e9ee020c859
STYLE: Explicitly declare virtual (cont. of 1c8609)

This is an extension of previous work in
commit 0d61aa0798ee3f1c577e108b727a078005a641f7
commit 10757725be9cbe68ab2903c9cd4b76b738070e63
commit 1c86090118e0679ccac22a05c7e77a77fb0f6b83,
on May 6th, 2014.

The clang-modernize methods only work on code that is compiled, so cmake was
reconfigured to include other options (i.e. Review, ITKv3 compatibility, FFT, FFTWW)
to increase the convered code.

clang-modernize -p ITK-newclang/ -include ITK/Modules/ -exclude ITK/Modules/ThirdParty -add-override -override-macros
clang-modernize -p ITK-newclang/ -include ITK/Modules/ -exclude ITK/Modules/ThirdParty -use-nullptr

Change-Id: I348adc6829ac29ff31e5023e491fa82ff1aa4656
Merge topic 'FixUnUsedTypedefInConceptChecking'

8329f687 COMP: Fix GCC warning about unused typedef in ConceptChecking
Merge topic 'AddMoreOverride'

e00caf9c STYLE: Explicitly declare virtual (cont. of 1c8609)