ENH: updating to libtif 4.0.3

The following procedure was followed for updating the library.

Downloaded latest tar ball from:
http://www.remotesensing.org/libtiff/

cd Modules/ThirdParty/TIFF/src/itktiff
copies files from
       tiff-4.0.3/libtiff/*
       to
       ./

git checkout tif_config.h.in
git clean -f ./
sed -i '' 's/\t/  /g' $(find ./ -type f)
sed -i '' 's/ *$//' $(find ./ -type f)

The the following include were changed to ITK's:

-#include "jpeglib.h"
-#include "jerror.h"
+#include "itk_jpeg.h"

-#include "zlib.h"
+#include "itk_zlib.h"

-#include "tiffconf.h"
+#include "tif_config.h"

Change-Id: Ifc2297cf1933664d9b45d5118cf489be6af5e958
BUG: Prevent MetaIO vessel tube from getting stuck in while loop

On some platform, the reader got stuck in the while loop. For some
reason, it seems the "eof()" method isn't working as expected while
the "good()" one is.

This patch has been done while working on Slicer issue #2734
See http://na-mic.org/Mantis/view.php?id=2734

Suggested-by: Matt McCormick <matt.mccormick@kitware.com>
BUG: Fix compilation ofswig external project

There were two fixes applied here. First installation was happening
twice dues to the additional swig-install target. Second the prefix
path was the same as the installtion. The errors occured with highly
parallel builds.

Change-Id: I5a8125f522f2b14b61a6023f910694bfcf2d1050
Merge remote-tracking branch 'jcfr-github/fix-metaio-vessel-tube-reader-stuck-while-loop-3.20' into release-3.20

Change-Id: Ie51188c69225a1f1cc8610b277b0f0be5b4fbed2
COMP: Fix 1D wrapping of itkImageToVTKImageFilter.

Wrapping this filter in 1D requires that itkVTKImageImport/itkVTKImageExport also be wrapped in 1D.

Change-Id: Ie3bc9e8b48a4a2c07ef8501e6af5a9a1900a4545
Merge branch 'release-3.20' into release

Change-Id: I7ba4ff946726fc77a19a8d46feea01d7d1bb19a5
Merge branch 'release'

Change-Id: I70d70325843dff8465a4702cf37648920c8605ed
BUG: Add test for MetaIO vessel tube from getting stuck in while loop

On some platform, the reader got stuck in the while loop. For some
reason, it seems the "eof()" method isn't working as expected while
the "good()" one is.

This patch has been done while working on Slicer issue #2734
See http://na-mic.org/Mantis/view.php?id=2734

Suggested-by: Matt McCormick <matt.mccormick@kitware.com>

Change-Id: Id80b18568f848da228c44cbc24fead1ebf05820f
Merge topic 'UpdateTolibtiff4.0.3'

54c790a ENH: updating to libtif 4.0.3
BUG: Orientation vector in FiniteCylinderFunction

As per suggestion in ITK Ticket the vector normalization
was not being performed properly.

https://itk.icts.uiowa.edu/jira/browse/ITK-2576

I don't know what was intended in the original code, but it was not
normalizing the the orientation vector properly.

Change-Id: I91c065a683c0be0eaf7e595420345bda76ca3b56
Merge topic 'FiniteCylinderFunctionOrientationFix'

512d84b BUG: Orientation vector in FiniteCylinderFunction
Merge topic 'ITKVTK1DWrap'

50767c8 COMP: Fix 1D wrapping of itkImageToVTKImageFilter.
Merge topic 'FixWrapITKSWIGexternal'

2898da0 BUG: Fix compilation ofswig external project
ENH: added suport for buffered region in GPU image

1. In GPUImageDataManager, two arrays for the buffered region are added:
m_BufferedRegionIndex and m_BufferedRegionSize, for the starting index
and size of the buffered region respectively.

2. In GPUKernelManager, a new method SetKernelArgWithImageAndBufferedRegion
is added to pass to the GPU kernel the image buffer together with the
the starting index and size of the GPU buffered region.

3. In an OpenCl program -- GPUNeighborhoodOperatorImageFilter.cl, the code
is changed to reflect the buffered region information. The main change
is about the indices in the input image:

inputBufferIndex = outputBufferIndex + outStartIndex - inStartIndex

where outputBufferIndex is the relative index in the output buffered
region, outStartIndex is the starting index of that region, and similar
for inputBufferIndex and inStartIndex.

4. In the calling program, GPUNeighborhoodOperatorImageFilter, the passing
of parameters is simplified by automatically passing buffered region
information.

Change-Id: Ic56e35ded7ea51b39bee650070757e42a818e6d0
Merge topic 'GPUBufferedRegion'

5b6373f ENH: added suport for buffered region in GPU image
Merge topic 'fix-metaio-vessel-tube-reader-stuck-while-loop'

72bdf98 BUG: Add test for MetaIO vessel tube from getting stuck in while loop
MetaIO: Prevent vessel tube from getting stuck in while loop

On some platforms, the reader got stuck in the while loop. For some
reason, it seems the "eof()" method isn't working as expected while
the "good()" one is.

This patch has been done while working on Slicer issue #2734
See http://na-mic.org/Mantis/view.php?id=2734

Suggested-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>