BUG: ImageSeriesWriter + GDCMImageIO loses info

When directional cosines are copied from 3D volume to 2D slices by
ImageSeriesWriter, only the upper-left 2x2 matrix can be copied, due to the
dimension of m_Direction matrix.

Then GDCMImageIO sets zeros in the missing values of the first 2 lines of the
matrix.

This is not a problem if the directional cosines matrix is the identity matrix,
otherwise DICOM tag (0020,0037) Image Orientation (Patient) of the output
DICOM files is not valid.

ITK-281

Change-Id: I44bac496fb1132abb85a5f9d66bd7ad469c774b2
BUG: VS11 Debug mode assertions fixes

Commit 04a394ca166aadd38ae7b6642f9617781127caaf increased performance
of array data copying by using std::fill_n instead of for loops.

It seems that in VS2012 Runtime Library, Microsoft decided to check if the
pointer to the first element is null when debug assertions are turned on.

This patch simply checks to see if that pointer is null and if so,
skip the std::fill_n.

Change-Id: I64b3269d305cb81fe95dd9aee163586b341b14f1
BUG: VS10/11 debug assertions for null pointer for std::copy

In VS10 and 11, the Runtime Library checks for a null pointer to the
input array when when the number of elements to copy is zero and raises
an exception.

This patch checks if the array has a null pointer, and if so, skips the
std::copy.

Change-Id: I1ad106d7c2903bcc7b59f0c128ce8cb591404294
BUG: Wrong classpath separator on Windows

Updated the SCIFIO remote commit that is checked out. This new commit
contains logic to select the correct path separator on Windows and
OSX/Linux.

Previously this was hard-coded to the OSX path separator, which would
cause the itk-bridge-pipes jar to not be found.

Also includes cquammen's fixes for the ImageInfo test and reading
newlines on Windows.

Change-Id: I4c4a864443fedbe6439c18e8a18469c8560a9541
BUG: Remove non-existant GeSignaHDx data references.

This helps with the script to create releases tarballs.

Change-Id: Ied052b65a7fad6b3fa9d9cf5139f5ca1a073f53c
BUG: disable aligned attribute for GCC 4.1

ITK usage is causing internal compilation segfault on the version of
gcc.
BUG: Prevent signed integer overflow in vnl urand_

Use bit shifting instead of power of 2 loop, to prevent signed integer
overflow.

Change-Id: I7369dba8e0d073de4213cfc646e81dda462b9955
BUG: enable return value optimzation for VS debug mode

The GetPixel methods require return value optimization to disable a
copy constructor so that the return and used VariableLengthVectors are
internally a reference to the VectorImage's data.

This patch resolve outstanding Interpolator test failures on Visual
Studio debug builds.

Change-Id: I188f589abdcbb230a8217f8850550b6bd50aceed
BUG: fix gradient recusive gaussian in VS debug

This is another case there we are relying on return value optimization
with VectorImages.

Change-Id: I6d8d84939b80a6d82a255b75e105fe6dd0395705
BUG: in NthElementAdaptor pass by reference to modify argument

Change-Id: I54d9b264216857ebd3b2ba7ac6d302e9ebdd56f8
BUG: Assert unchanged pixels only for non-PALETTE_COLOR images

Change-Id: I1781cf8cdcaf26a54311bf1bd7e2338230465e70
COMP: host platform source dir check

Fix issue ITK-3164: When cross-compiling
from a linux host to a windows target,
the source directory length check should
check for the host platform instead of the
target platform.

Change-Id: I0825f201cc0b577b3c51ba3d6f71b214ef60d2b0
ENH: ExternalData: Do not re-stage staged object files

The ExternalData_LINK_CONTENT option tells ExternalData to convert real
data files it finds into content links and to "stage" the original
content in a ".ExternalData_<algo>_<hash>" file.  However, after a data
object has been staged it is possible that a user-provided pattern in
the "REGEX:" option will later match the staged object file.  We must
not process staged object files even when a user pattern matches them.

Fix the implementation to not match a staged object file as a normal
data file for conversion.

Change-Id: Ie21b90aa8a8ffac76c8efa1565453bb29c331527
Merge topic 'ExternalData-no-re-stage'

a894c07 ENH: ExternalData: Do not re-stage staged object files
Merge branch 'release'

Change-Id: I65a8d0c4024ad2bfbe39caa7b04ee6c4d20effbb
ENH: fix std::string usage
Merge branch 'release'

Change-Id: I4fe034418656c6a21e6728a8db9dbc4cef2205fe