BUG: GDCMImageIO ignores ImagePositionPatient

GDCMImage I/O fails to retain a user provided Image Position Patient
(0x0020, 0x0032). Prior to ITKv4, GDCMImageIO would keep the Image
Posiiton Patient tag if it was specified by the user in ITK's meta
data dictionary. This patch restores that behaviour. A new test
verifies that when provided, Image Position Patient is stored in the
dicom header. If Image Position Patient is not in the meta dictionary
for the image, the IPP is created from the image's origin.

Also, GDCM2 will not write IPP unless the modality is one of CT, MR or
RT. The test sets the modality to CT.

The patch is based on a fix suggested by Alberto Rey (bertorey at
gmail.com) on April 15, 2011.

Change-Id: Ic833627254421929ff54e3bf7004ba5b46347492
COMP: Build with ITK_USE_SYSTEM_TIFF. #2967

A method in the ITKIOTIFF Module must be excluded when ITK_USE_SYSTEM_TIFF is on
that requires the non-installed headers, particularly tif_def.h, that come with
libtiff.  This method is for custom tags and is not used in the TIFF IO, but it
is used by the ITKIOLSM Modules, so ITKIOLSM must not attempt to build in that
case.

For this patch to work as-intended, a fresh rebuild is required.

The unnecessary dependencies of ITKDeprecated and ITKReview on ITKIOLSM are
removed, and the dependencies of ITKTestKernel and ITKIntegratedTest are made
conditional.

Change-Id: Ic70dc6e58caebaa131a0990433651275da695c7a
STYLE: Made use of .hxx guards consistent

Occasionally there is a need to manually perform explicit instantiation for a project.
A .cxx file is created with the template instantiations where the .hxx files are #include'd,
and add_definitions(-DITK_MANUAL_INSTANTIATION -DITK_TEMPLATE_TXX) is added.
This is very help for identifying which types are used in an algorithm.

This patch is to consistently use only the ITK_MANUAL_INSTANTIATION instead
of an mix of ITK_MANUAL_INSTANTIATION and ITK_TEMPLATE_TXX that are performing
essentially the same task.

Change-Id: I4be7b0ff95e5ced5e1c93b1ccd00d74793ccba02
PERF: Replacing iterator copy with optimized ImageAgotithm::Copy

Change-Id: I5334a280ce5afc8c209dd187c93b02a1319b472c
BUG: Prevent segfault when logger not set for PatchedBasedDenoising

By default the m_Logger was not initialized and would cause a segfault
if not explicitly set. This was used for the non-standard convention
of printing debug information. This has been changed to use the
standard itkDebugMacro for these messages.

Change-Id: I5265ae0d3815c2fa4b90eb4b450c6d4ea530ae43
Merge topic 'BUG_GDCMImageIO_ImagePositionPatient'

160f179 BUG: GDCMImageIO ignores ImagePositionPatient
Merge topic 'ImageCopyForLevelSetFunctions'

145628b PERF: Replacing iterator copy with optimized ImageAgotithm::Copy
KWSys 2012-11-05 (df32fa6f)

Extract upstream KWSys using the following shell commands.

$ git archive --prefix=upstream-kwsys/ df32fa6f | tar x
$ git shortlog --no-merges --abbrev=8 --format='%h %s' b7a97ac3..df32fa6f
Brad King (4):
      b90f28e3 SystemInformation: Use kwsys_ios:: for string streams
      b7c42507 SystemInformation: No backtrace on LSB < 4.1
      2c46f562 SystemInformation: Fix sw_vers output processing
      df32fa6f SystemInformation: Compute FQDN only on specific platforms

Change-Id: Iaab8539c8585107bb0f9ad0bd0e7e1891312dcd2
Merge branch 'upstream-kwsys' into update-KWSys

Change-Id: Ic6532690e9292f34cab91872226f59f415c502b5
Merge topic 'update-KWSys'

7404819 Merge branch 'upstream-kwsys' into update-KWSys
2b5fb9f KWSys 2012-11-05 (df32fa6f)
Merge topic 'RemoveITK_MANUAL_INSTANTIATION'

110576c STYLE: Made use of .hxx guards consistent
Merge topic 'SystemTIFF2967'

e203cab COMP: Build with ITK_USE_SYSTEM_TIFF. #2967
Merge topic 'FixPatchBasedDenoisingLogging'

4ac88d0 BUG: Prevent segfault when logger not set for PatchedBasedDenoising