BUG: restore gnu aligned attribute

The test for detecting gnu aligned attribute was always generating the
following compilation error:

Modules/Core/Common/CMake/itkCheckHasGNUAttributeAligned.cxx:27:
error: 'foo<T>::foo() [with T = int]' is private

This feature is now restored.
ENH: Add SCIFIOImageIO.

This package provides an ITK ImageIO plugin that uses SCIFIO
to read and write supported life sciences file formats.

The SCIFIO ImageIO plugin was developed by Gaetan Lehmann, Mark Hiner,
Curtis Rueden, Melissa Linkert and Matt McCormick. Development of this
module was funded in part by the [FARSIGHT
project](http://farsight-toolkit.org/), as well as the [Open Microscopy
Environment](http://openmicroscopy.org/).

Special thanks to Alex Gouaillard, Sebastien Barre, Luis Ibanez and
Jim Miller for fixes and suggestions.

For further details, including usage instructions, see the [Bio-Formats
ITK page](http://openmicroscopy.org/site/support/bio-formats/users/itk).

Please [direct any questions to the OME
team](http://www.openmicroscopy.org/site/community).

To build the module, set

  Fetch_SCIFIO to ON in the ITK CMake configuration.

Change-Id: Idafa221438f1faec75f48e7ec04fc7b435e80f24
PERF: Store indexed outputs in array for constant time access

Add vector of iterators into the named outputs in the
ProcessObject. This will provide direct constant time access to the
outputs of filters with out doing string comparisons or lookups into a
map.

Wrote tests to improve coverage of the inputs operations.

Change-Id: If62aa34cbb7a46a7df2c17614f6d3c23508ccfbb
Merge topic 'SCIFIORemote'

d3c9e57 ENH: Add SCIFIOImageIO.
Merge topic 'ProcessObjectIndexNamedOutputs'

4cc805f PERF: Store indexed outputs in array for constant time access
Merge topic 'ResotreGNUAttribueAligned'

2f96c57 BUG: restore gnu aligned attribute
COMP: GCC_XML compilation error with type_traits

This patch addresses a WrapITK compilation error with gcc_xml like the
following:

In file included from
/home/kevin/kitware/ITK/Modules/Core/Common/include/itkImageAlgorithm.h:25,
                 from
                 /home/kevin/kitware/ITK/Modules/Filtering/ImageFilterBase/include/itkCastImageFilter.h:24,
                 from
                 /home/kevin/kitware/ITK/Modules/Filtering/ImageFilterBase/include/itkBoxImageFilter.h:23,
                 from
                 /home/kevin/kitware/ITK/Modules/Filtering/ImageStatistics/include/itkAdaptiveHistogramEqualizationImageFilter.h:22,
                 from
                 /home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKImageStatistics/itkAdaptiveHistogramEqualizationImageFilter.cxx:22:
/usr/lib/gcc/x86_64-redhat-linux/4.7.2/../../../../include/c++/4.7.2/tr1/type_traits:208:
error: a function call cannot appear in a constant-expression
/usr/lib/gcc/x86_64-redhat-linux/4.7.2/../../../../include/c++/4.7.2/tr1/type_traits:208:
error: template argument 2 is invalid

There is no logical reason why including ImageAlgorithm in both the h
and hxx files should have caused this error.

Change-Id: Idb12acc6c9cda0c552fb57b60141393bdfe972e0
Merge topic 'FixGCCXMLImageAlgorithm'

d43e679 COMP: GCC_XML compilation error with type_traits
BUG: Include SCIFIO in the auto-registered factories if the module is enabled.

include(${ITK_USE_FILE})

will also register the SCIFIO module if it was enabled.  The bump in the
remote repository add the factory registration code to
tikSCIFIOImageIOFactory.cxx.

Change-Id: I7816b6cfd6c8570dfa7cd0461c1d8718faadb487
BUG: Visual Studio itkClampImageFilterTest failures.

Visual Studio has a false failure in due to imprecise integer to double
conversion. It causes the comparison (dInValue > expectedMax) on line 98 to pass
when it should fail.

Change-Id: I817d9eabd32d1adf72dc393d464e99b2219cc0c6
BUG: ITK unable to detect number of threads under Unix in recent glibc.

_SC_NPROCESSORS_ONLN is defined in unistd.h. It appears this used to be implicitly defined by stdlib by glibc but this is no longer the case.

Change-Id: I442c2df910c7e00235ec0bc84eac669714ea8f23
STYLE: itkClampImageFilter.hxx in the wrong module.

ImageFilterBase -> ImageIntensity where itkClampImageFilter.h lives.

Change-Id: I1158274883fd1e1e9da585416b00483008622c19
Merge topic 'SCIFIOUseITK'

6959c0a BUG: Include SCIFIO in the auto-registered factories if the module is enabled.
Merge topic 'ClampVS'

d01aab0 BUG: Visual Studio itkClampImageFilterTest failures.
Merge topic 'ClampLocation'

c8a24ba STYLE: itkClampImageFilter.hxx in the wrong module.
COMP: Missing return error after exception

VS 2010 complains when a function that throws an exception does not
return a value. Some other VS compilers may warn rather than error.

Typical error:
error C4716: 'itk::Transform<double,3,3>::TransformVector' : must
return a value

Change-Id: Iddff1d5899dcb3d35587e96ee10b3446981cd462
Merge topic 'ReturnAfterException'

2aa44c2 COMP: Missing return error after exception
Merge topic 'pthreads_unistd'

d2af490 BUG: ITK unable to detect number of threads under Unix in recent glibc.
BUG: Add unsigned int concept check to LabelVoting filter

COMP: Don't instantiate LabelVoting with signed integer in WrapITK

Fix a potential use of negative index when a negative label was set on
input.

WrapITK instantiates this filter with signed integers. The patch
addressed the following warnings:

ITK/Modules/Segmentation/LabelVoting/include/itkLabelVotingImageFilter.hxx:116:
warning: comparison between signed and unsigned integer expressions

ITK/Modules/Segmentation/LabelVoting/include/itkLabelVotingImageFilter.hxx:132:
warning: comparison between signed and unsigned integer expressions

Change-Id: Iefa08693a557d7f0ab9feca245685c581cea7c0f
COMP: Disable conversion warning for std::copy in ImageAlgorithm

Include xutility header in itkWin32Header before most other places,
and place the MSVC warning suppression around it.

Change-Id: Ie157d99d1611d11076da2a03ca9efb1982eda302