COMP: Fix the writing of .idx files

The previous change to the print function broke the wrapping build.
This should fix the writing of the .idx files.

Fixed also imports of stringIO, we can even do it without six, see:
http://python3porting.com/stdlib.html

Use also from __future__ import unicode_literals, so that StrinIO
works on both Python 2 and 3

Fix also a problem in igenerator.py with the .h file creation, the \n
was misplaced.

Change-Id: Ia7f57f0bcfc1e21bc63370ffa0373c73db4c4943
Merge topic 'sigmoid-style'

3fe754fb STYLE: Fix template statements in SigmoidTransformFunction.
Merge topic 'metadataobject-copy'

75b18386 BUG: Add missing private copy constructors to MetaDataObject.
f5874d04 BUG: Remove public MetaDataObject constructors.
b34f4026 ENH: Add MetaDataObject Print specialization for common types.
c3e4cfba ENH: Add unit test for MetaDataObject.
a5a4fd97 STYLE: Clean up MetaDataObject.
73cd2040 STYLE: Clean up MetaDataObjectBase.
Merge topic 'FixPythonWrapping4'

419625e9 COMP: Fix the writing of .idx files
COMP: Fix python print import for .pth file creation

Fixes the following error:
CMake Error at Wrapping/install_wrapitk_compatibility.cmake:3 (file):
  file called with unknown argument
  "/tmp/imichka-insighttoolkit-QtOS/itk-build/Wrapping/Generators/Python/det_spp.py",
  line 2 from __future__ import print_functionSyntaxError: from __future__
  imports must occur at the beginning of the file"".

Change-Id: I7163eb556074c4e8d403254ce7e83986e959c7b6
COMP: Fix print import statement in itkExtras.py

Will fix the following error in the tests:

Traceback (most recent call last):
  File "/home/kevin/kitware/ITK/Wrapping/Generators/Python/Tests/CurvatureFlowImageFilter.py", line 24, in <module>
    import itk
  File "/home/kevin/kitware/ITK_Build/Wrapping/Generators/Python/itk.py", line 24, in <module>
    import itkExtras
  File "/home/kevin/kitware/ITK_Build/Wrapping/Generators/Python/itkExtras.py", line 28
    from __future__ import print_function
SyntaxError: from __future__ imports must occur at the beginning of the file
itkTestDriver: Process exited with return value: 1

Change-Id: I3880862f1fd85f05dd9e85d347bd5e33498275ec
ENH: Enable observed events to modify observers

There is no way to know if an object is executing an event, and it
wasn't safe to modify the observers when an event was being executed.

This patch is inspired by the ModifiedList implementation in the VTK
SubjectHelper class. It allows for recursive execution of events
and modification of the observers during execution.

The Command list items are saved on the stack recursively. Given that
it's not expected to utilize a large number of Observers with ITK, nor
is it expected to be common practice to delete Observers during event
execution, this method was chosen because it does not utilize any
dynamic memory allocation which causes reduce performance. This was
done at the expense of stack space. Additionally, when an observer is
deleted the search time is O(n^2), but it's safe.

Change-Id: Ia2068044454806b2cf018ba881126b65b152ac3c
Merge topic 'EnhanceDirectionCosDocumentation'

e4c851f3 DOC: Improved Image Representation
PERF: Minimize redundant function calls

The highest percentage of time in the MattesMutualInformation
filter was spent evaluating if specialized work needed to
be done for displacment fields.

In a minimalistic test case, prior to this change the registration
took 846 seconds, after this change, registration took 309 seconds.

bin/BRAINSFit   \
  "--costMetric" "MMI"  \
  "--failureExitCode" "-1"   \
  "--numberOfIterations" "1"  \
  "--numberOfHistogramBins" "50"  \
  "--splineGridSize" "7,5,6"  \
  "--numberOfSamples" "14000"   \
  "--minimumStepLength" "0.1"  \
  "--initializeTransformMode" "useCenterOfHeadAlign"  \
  "--transformType" "BSpline"  \
  "--fixedVolume"  "BRAINSTools-build/ExternalData/TestData/test.nii.gz"  \
  "--movingVolume" "BRAINSTools-build/ExternalData/TestData/rotation.rescale.rigid.nii.gz"  \
  "--outputVolume" "BRAINSTools-build/BRAINSFit/TestSuite/BRAINSFitTest_BSplineScaleRotationRescaleHeadMasks.test.nii.gz"  \
  "--outputTransform" "BRAINSTools-build/BRAINSFit/TestSuite/BRAINSFitTest_BSplineScaleRotationRescaleHeadMasks.h5"  \
  "--maxBSplineDisplacement" "7.3"

Change-Id: I3782e78cae99acfe577a40444882688ae5b76472
PERF: Pull loop termination constants out of loop

When evaluating loops, loop termination criteria that
are accessed via member functions should not be
used at every iteration.  Common static loop iteration
termination values are stored locally and reused.

Change-Id: Ia847f411640cce6921b28ac2a2da448c40ebe24c
ENH: Refactoring the CompositeTransform class

Prefer initialization to assignment (i.e. use class constructors
rather than resize variables).

Add const correctness, and use const references to temporary
local variables rather than copy constructing them.

Change-Id: I79a0dd7e3e22d3e5866b13b343c7f14296293606
Merge topic 'EnableObserverModifyObservers'

f7307e26 ENH: Enable observed events to modify observers
4c4e6266 ENH: Explicitly specify internal linkage for internal observer objects
ENH: [SG]et optimizable params ITKv4 registration

Currently the only way the initialize the registration configuration is
to set up an initial moving transform. Inside the registration filter,
this initial transform is added to a composite transform along with the
output optimizable transform, and this composite transform is used for
metric evaluation at each iteration.

In this case, we also need to use a composite transform after the
regsitration process to concatenate the initial moving transform and
the output of the registration filter to create the final transform for
the resampler.

Doing all above is a lot of work that is not necessary in many cases.

In this patch new APIs are added to the ITKv4 registration framework
that allow us to directly initialize the output optimizable transform.

The new API is called "InitializeOptimizableParametersFromTransform",
and it provides a new option for iniatialization of the registration framework.
This feature lets us to initialize the optimizable registration transform
directly in a same way as we used to do in ITKv3.

Change-Id: I49a1ee0fd88e289bbc266ea61e68d6d0968fd761
Merge topic 'FixPrintImport'

ccc97cc3 COMP: Fix python print import for .pth file creation
Merge topic 'FixPythonTestPrintImports'

69f406fb COMP: Fix print import statement in itkExtras.py
Merge topic 'ImproveRegistrationInitialization'

9c1a5212 ENH: [SG]et optimizable params ITKv4 registration
Merge topic 'PerfMattesRegistration'

73835b81 ENH: Refactoring the CompositeTransform class
cafef89d PERF: Pull loop termination constants out of loop
304448f1 PERF: Minimize redundant function calls
ENH: remove VersorTransformOptimizerv4 from ITKv4

The recently added RegularStepGradientDescentOptimizerv4 can be used
form both vector and versor transforms optimization. Therefore, the
versor optimzer can be considered as a duplicated class and can be
removed form ITK.

Change-Id: I2705f21fdb4667fa31bcabf5e18b1567d75ca961
BUG: Catch exception in DeleteEvent

If an exception was thrown by a DeleteEvent Observer the reference
counting for the object wouldn't occur and a SmartPointer destructor
would thrown an exception. This would lead to a memory leak, program
termination or other undefined behavior.

Change-Id: Ib0dda1d8abc510999523db6e2eee5281e3a18056
STYLE: Explicitly declare virtual for derived class member functions

Class member functions derived from parent class with virtual functions
of the same name are implicitly virtual.  This patch set uses a macro
for the c++11 override keyword to indicate that this function was
intended to be overridden in this derived class.

Ensuring that functions signatures are described as virtual is not
strictly needed, but it facilitates maintenance by being consistent.
Approximately 1/2 of the toolkit had the explicit virtual designation and 1/2
relied on implicit behavior.

The ITK_OVERRIDE define allows for non-c++11 compilers to continue to work.

Change-Id: Iba5c2970f2bad4f7f664b92a4420d217546bb22f