BUG: Remove unused itkAffineTransformXX.txt content links.

These interfere with the content link backup script.

Change-Id: Iec8b369d936b7ab4b8be857b04afd699f066c56c
COMP: Updated libminc, hopefully reducing number of warnings

Change-Id: I4ce46ecdb736382babea8f4f4a82940a30d3329c
Merge topic 'unused-content-links'

a58465b BUG: Remove unused itkAffineTransformXX.txt content links.
Merge topic 'LIBMINC_UPDATE_TOO_SOON'

8f8a8ec COMP: Updated libminc, hopefully reducing number of warnings
COMP: Fix compiler warnings with ITK_USE_SYSTEM_VXL

Commit 41793b40 attempted to solve an unused variable warning by forking
VXL. The warning was still triggered when ITK_USE_SYSTEM_VXL was enabled.

This reverts the fork of VXL and solves the warning when using system VXL
too.

Change-Id: I61db91d3269818a4819541dc5ec6a25d273f3dd2
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
ENH: Removed non-work TCL Examples

Wrapping for Tcl has not worked for a very long time. This tests are
outdated and not useful.

Change-Id: Iff82aba2d03155e0db1a010fd850315ae59a715e
Merge topic 'Bug_TIFFImageIO_Compression'

13331ca BUG: Tiff compression was broken and untested
ENH: Add SetJPEGQuality method

Adds Set/GetJPEGQuality to expose control of the compression quality of
the JPEG compression.

Adds three regression tests for quality settings: 1, 50, 100.

Change-Id: Ia47a86ce0c2bc2f042cf0973713b2dbc81d1ec9f
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
ENH: 3048, 3224: Refactor *SampleFilters to fix multiple issues

Updated MeanSampleFilter and WeightedMeanSampleFilter to use Kahan
summation (implemented by CompensatedSummation) for additional numerical
accuracy, resolving bug #3048.

Code was refactored for a more logical layout and to have more correct
variable types. This fixes a warning in GCC4.7, resolving bug #3224.

Commit c6d83112 made Sample frequency values be integers, so the internal
variables holding frequency totals are no longer explicitly double, and
were changed to use the proper typedefs.

If WeightedMeanSampleFilter is called with a custom weighting function
that always returns 0, the filter will now throw an exception, whereas
previously it would complete without performing the division step of
mean calculation.

Change-Id: I1d245fe15f25bbcebf6bebdea6d5d784c8e464dc
ENH: Re-enable the array-bounds warnings for GCC 4.7

The issue causing these warnings was fixed by 585eeee0, and the
warning is quite useful.

Change-Id: Ib6659ef734d3a47e7c77086e70d37bffbb56e92b
Merge topic 'VNL-Diag-Warning'

0cfabd0 COMP: Fix compiler warnings with ITK_USE_SYSTEM_VXL
Merge topic 'TIFFImageIO_JPEGQuality'

c8c3e21 ENH: Add SetJPEGQuality method
Merge topic 'WeightedCovar-Warning'

b9ffd0b ENH: Re-enable the array-bounds warnings for GCC 4.7
585eeee ENH: 3048, 3224: Refactor *SampleFilters to fix multiple issues
6db723f BUG: Make all specializations NumericTrails::SetLength re-zero contents
Merge topic 'RemoveTclExamples'

7d11ae7 ENH: Removed non-work TCL Examples
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: Fixes itkBoxSpatialObject part of issue ITK-3153

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

Change-Id: I86211f25aa94eb02f98214a0a26fdd743461fa53
DOC: Add missing const in Doxygen GetConstReferenceMacro

Change-Id: Id13ad11b0dc98fa07c62369d5d5fdddf6cf33e3e
BUG: Correctly re-throw exception to restore AbortEvent, ProcessAborted

The abort exception was incorrectly being re-thrown as pointer to an
exception instead of re-throwing the exception by using the "throw"
keyword without an argument. The AbortEvent was never emitted before
now it is. Other cases of incorrect exceptions re-throws were grep and
corrected.

Change-Id: I7f858640739d49612d9f009f00f6a0a2548088af