STYLE: Make ordering of includes consistent

Following the 3D Slicer includes ordering rules for compatibility.

TubeTK
Boost
ITK
MetaIO
VCL/VNL
VTK
C standard library
C++ standard library

Change-Id: I9be273981021f93b0835b48d2b4b740431d85c61
Merge topic 'CleanupIncludes'

48a3e8d STYLE: Make ordering of includes consistent
BUG: Bump SEM for ParameterSerializer bug.

Was not writing valid JSON files.

Change-Id: I5e29882e37bc7b1f37ae3fec7dd128ebf842b022
BUG: Fix RidgeFeatureVectorGenerator control reaches end of non-void function

Change-Id: Ic9db38be57ca84b95ce9095df36d76c8350cfe5f
BUG: Fix MetaTubeParams overloaded virtual function

Change-Id: Ic3614a47f9869719cfba4e36d45a58b038519eb7
BUG: Fix NJetFeatureVectorGenerator uninitialized value

Change-Id: Ibc2f8c06bc0e26a293a0306ff0937934208902e1
Merge topic 'RidgeFeatureVectorGeneratorReturnType'

3e093f0 BUG: Fix RidgeFeatureVectorGenerator control reaches end of non-void function
Merge topic 'MetaTubeParamsOverloadedVirtualFunction'

4614a61 BUG: Fix MetaTubeParams overloaded virtual function
Merge topic 'NJetFeatureVectorGeneratorUninitialized'

e023edb BUG: Fix NJetFeatureVectorGenerator uninitialized value
BUG: Update CropImage test parameter archives.

The XML file describing parameters was changed in

  3f7b2ce340562a9fc182e010810588c7bbfbb3eb

and the corresponding test parameter archives are updated for the
change in the group name "Crop filter" -> "Crop Filter".

This fixes CropImage-Test5-Compare and CropImage-Test6-Compare.

Change-Id: Ia4ce3af64bd8dd9a71b9f6ce9699e977b6e2e4dc
Merge topic 'ParameterSerializerBug'

73fc498 BUG: Bump SEM for ParameterSerializer bug.
BUG: TubeTransform fix shadowed global declaration

Change-Id: I64105ab5affbd02f1ad5098b2ad5944daabbbad6
Merge topic 'TubeTransformShadowedGlobalDeclaration'

442c04e BUG: TubeTransform fix shadowed global declaration
Merge topic 'CropImageTests'

d42aa8f BUG: Update CropImage test parameter archives.
STYLE: Closing parenthesis and test indentations on cmakelists.txt files

Change-Id: I1b1aa778ff1446037f5d0769bbc968a246b23b4e
BUG: Address window error on declaraction/definition mismatch

Change-Id: I298916e74683ea8680a6789543c8f2d116cbae4d
COMP: Function did not call return in all paths - now throws exception

Change-Id: If3a63eaac8dfb84121595dd607124856744473e2
COMP: Conversion warnings involving templated vars in tubeMatrixMath

Change-Id: I50c621f6484d3f72ce4fe546848d33879eec2dc2
ENH: Add class to record optimization parameter progression.

When set to observe a SingleValuedNonLinearOptimizer, it will record
the parameters, the cost function value, and the cost function derivative
at every iteration, then save the result to an HDF5 file.  An HDF5 file
is used so it can be easily read and examined in Python while retaining
and binary precision and compression.

Change-Id: I7737cd6951c32b7f2efe0d6393469fbc8c458037
ENH: Add MetricType typedef to itkImageToTubeRigidRegistration.

Change-Id: If97c79d425babc8fa57e2045f9b02f496f9b3e99