BUG: Missing Modified() call

While reviewing differences between the bounded and unbounded
itkLBFGSOptimizer.cxx
itkLBFGSBOptimizer.cxx

The missing call to "Modified()" was identified.

Change-Id: I0bd0526a047fab3f8cb79d4a5b35c81385bd3b0f
BUG: Do not throw exception in Probes with mis-matched Stop

With the model of a stop watch as the expected behavior, hitting the
stop button multiple times has not effect.

Change-Id: Id1ade7e5e8a70ed9c9a08b5af48a7730399f7ab0
BUG: Fixes itkBoxSpatialObject part of issue ITK-3153

the bug manifests when the translation or transform is larger then the box size.

Change-Id: I86211f25aa94eb02f98214a0a26fdd743461fa53
BUG: Fixes itkImageMaskSpatialObject part of issue ITK-3153

Added ComputeLocalBoundingBox method to itkImageMaskSpatialObject
Added a 2D and 3D test of this method.

Change-Id: Ie7681aaf5af3f91fa7c7c6432d40dd0473443399
BUG: Fix for the WrapITK.pth destination path

Added a regex to remove the \n character at the end of the site_packages path found by cmake.
On OS X this would result in a wrong path for the WrapITK.pth file, so that the python linking was broken.
Note that I was not able to find out what changed since ITK 4.4.2, perhaps a change in cmake or python 2.7.6 ?

Change-Id: Ic5f985538058e625aea46d936fe0aa55b7d1ba2e
BUG: Make all specializations NumericTrails::SetLength re-zero contents

The ITK container types' specializations of NumericTrails::SetLength
all unconditionally fill the passed object with zeros. This commit makes
that behavior consistent across all scalar and container types.

Change-Id: I267128ea4d6597b65051ec555409642058d650d2
BUG: Tiff compression was broken and untested

A user reported receiving the error:
JPEGLib: Bogus input colorspace.
while trying to use JPEG compression witk TIFFImagio.

This was not covered and apparently never tested.

This patch fixes the erro and adds tests for each compresion option
for grayscales and RGB imagaes.

Also, a Warning message is substitued for a Debug message if LZW
compression is selected.

Change-Id: Iba27f4e553a427755b9a1bf2f2aa435a120242e5
BUG: Remove unused itkAffineTransformXX.txt content links.

These interfere with the content link backup script.

Change-Id: Iec8b369d936b7ab4b8be857b04afd699f066c56c
BUG: initialize m_SmallBlock ivar in ctor; fixes garbage read

fixes clang ubsan error in itkGPUReductionTest test:
Modules/Core/GPUCommon/include/itkGPUReduction.hxx:225:20: runtime error: load of value 170, which is not a valid value for type 'bool'

Initialized a couple of other ivars while I was there.

Change-Id: I95b193876386cc7ca42f0807d2a8e9b75e76a6e1