BUG: TestingExtractSliceImageFilterTest v3 direction strategy.

The DirectionCollapseToStrategy is different with v3 compatibility on per
the constructor.

Change-Id: I929f1a64d95958e0c280a3290ef6169dd519714e
STYLE: Remove duplicated TestingExtractSliceImageFilter doxygen.

Change-Id: I3f2b6c296032bb2b21da275e5bc85b5003c600a8
DOC: Fix description of SpatialObject::GetBoundingBox()

Change-Id: I0bbc0e3a9711651b1e0ef98544c44d94b2726f65
DOC: Improved comments and reorganized code for IsolatedConnected

Added documentation to the AddSeed1() and AddSeed2() methods.
Updated the deprecated SetSeed1() and SetSeed2() method documentation
to point to these instead of to AddSeed(), which does not exist.  Also
reorganized the code to emphasize these Add methods.
Wrapped the deprecated SetSeed1(), SetSeed2(), SetUpperValueLimit(),
and GetUpperValueLimit() methods in
ITK_FUTURE_LEGACY_REMOVE preprocessor directives.
Updated the IsolatedConnected test to wrap calls to SetSeed1(),
SetSeed2(), SetUpperValueLimit(), and GetUpperValueLimit() with
ITK_FUTURE_LEGACY_REMOVE preprocessor directives.
IsolatedConnected example also updated to avoid use of deprecated
methods.

Change-Id: Icf934b3eb9273d4b334a48b268784c32f1c6d806
ENH: New test for itkLogSigmoidTransferFunction

New test for the itk::Statistics::LogSigmoidTransferFunction class.
Compiles fine under VS2010 (64 bit), Windows 7.

Change-Id: I45120122546c3d5f39bfe9a3fa68f03e7264dce1
COMP: std::abs integral overloads not always provided

Some older C++ compilers do not provide integral overloads for
std::abs.

For example, on Visual Studio 9, vcl_abs works for long long while
std::abs does not provide a long long overload.

To accomodate this compiler, the patch uses vcl_abs.

Change-Id: I6749e452699b1ca999eb3c6464fb17605ebaa682
Merge topic 'AbsOverload'

e09e598a COMP: std::abs integral overloads not always provided
COMP: Update AnalyzeObjectMapIO replacing deprecated

The Begin() iterators were replaced with GoToBegin() for
future ITKv4 compliance.

Change-Id: I74a86eeaa721b16775b1ab3bc3d2798e778130fd
DOC: Fixed documentation regarding multi-threading

Multithreading was fixed in 2011 in preparation for
using MI for BRAINSTools testing and for inclusion into
Slicer.  It was fixed in patch set f542d0c75848ccb8bf35130a896da2fdb1a10d2c,
but the comment was overlooked.

Change-Id: I7cb2648159a7abfc75f14953c821e499ba26d5f1
COMP: Use latex formula for HoughTransform doxygen.

The std:: prefix causes a warning:

  Generating docs for compound
  itk:/.../ITK/Modules/Filtering/ImageFeature/include/itkHoughTransform2DLinesImageFilter.h:34:
  warning: explicit link request to 'cos(Teta)' could not be resolved

Use a better LaTeX formula.

Change-Id: I39c6e98dabcbd5e4606a755114f67084ca942ecf
COMP: SigmoidTransferFunction members Alpha, Beta real type.

For:

  /scratch/dashboards/Linux-x86_64-gcc4.1/ITK/Modules/Numerics/NeuralNetworks/include/itkSigmoidTransferFunction.hxx:33:
  warning: converting to 'unsigned char' from 'double'

Change-Id: I8c965d785d7bac8474ff24c402a36efb1d103274
STYLE: Fix SigmoidTransformFunction template argument names.

Change-Id: I418d256612a86a65b6e3aaa86e92e470d4ba72ab
Merge topic 'RemoveOutdatedComment'

3991bae5 DOC: Fixed documentation regarding multi-threading
Merge topic 'UpdateAnalyzeObjectIO'

4d3b91ff COMP: Update AnalyzeObjectMapIO replacing deprecated
Merge topic 'LogSigmoidTransferFunctionTestBranch'

4c20fa85 ENH: New test for itkLogSigmoidTransferFunction
Merge topic 'IsolatedConnectedSeedDocumentation'

e142b842 DOC: Improved comments and reorganized code for IsolatedConnected
Merge topic 'testing-extract-doxygen'

5144b613 STYLE: Remove duplicated TestingExtractSliceImageFilter doxygen.
Merge topic 'testing-compatibility'

808c9684 BUG: TestingExtractSliceImageFilterTest v3 direction strategy.
BUG: incorrect loop var increment

Change-Id: Id339d230d6c2962f7bce59d2a074e3d1bc6ab261
STYLE: Remove unused compile all code for Python Wrapping

This code is commented out since very long time, so not tested with recent python versions.
Anyway the compileall.py file is now a module by itself so this would need some fixes.
If it's not used and not tested, we should just remove it.

If we need to byte-compile the python files one day for whatever reason,
writing some lines to do it from scratch should not be too difficult.

Change-Id: I876213993ecee932ee87d1ef98618cf8b7407aa9