COMP: Incomplete variable name change.

USE_WRAP_ITK changed to ITK_WRAPPING.

Change-Id: I21f85534dfcfcf3132348b3d7c0d78744da27535
ENH: Add unit test to itkThresholdImageFilterTest

Issue #2991

Change-Id: Ibdc58c387002729a7fd025cb68f49cc5633dfe67
ENH: Add MaskingValue to MaskImageFilter

Closes #2993

Change-Id: I75d8c8d3a68cc86eb67af570dc57021b4f85a9ac
DOC: Modify MattesMutualInformationImageToImageMetric comments.

Author: dr.tim.allman@gmail.com
The value 50 was not showing up in the generated document. It also states more clearly what Mattes et al state.

Change-Id: I2546755a072147c1f62d75e61889c6779ab79aba
BUG: GradientVectorFlow should calculate timestep based on image dimension

This GVF implementation seems to be based on eqns 15 and 16 this paper:
http://www.iacl.ece.jhu.edu/pubs/p084j.pdf

In the paper, the timestep to guarantee GVF covergence is:

dt <= (dx * dy)/(4 * mu) (note in this ITK implementation, dx and dy are assumed to be 1)

This above equation was derived from the Courant-Friedrichs-Lewy (CFL) restriction as mentioned
in the paper. However, this equation makes the assumption that one is dealing with 2D
images only.

According to the explanation on Wikipedia, the CFL restriction typically has CMax = 1 for 1D
case for time-marching solution. However, with the Laplacian operator, the timefront actually
expands in 2 dimensions (forwards and backwards), so here CMax = 2.

With the 2D case, the front expands in 4 directions.
With the 3D case, the front expands in 8 directions.
etc...

Thus, the timestep calculated appears (dy * dy)/(2*Dim * Mu)

Change-Id: I153ca6c52db11d36b5988c1844ea3901ee972200
STYLE: GradientVectorFlow - Add const correctness

Add const correctness to ITK iterator over the B and C images

Change-Id: I84f33af341b1adf4716e26906119ec46875d5d24
STYLE: GradientVectorFlow

* Move definition of variables from top of sections to where they are first initialized
* Replace a misleading naming of internalIt to laplacianIt

Change-Id: I3913d51bd609701b30ed079e3fa700c91fe3ac31
COMP: Update DCMTK version to incorporate new fixes.

In particular there was a fix to allow compiling with CLang
we needed.  The rest of the new commits are innocuous with
respect to how ITK uses DCMTK.

WARNING: DCMTK is not turned on by default. Set
Module_ITKDCMTK:BOOL=ON to test this patch.

Change-Id: I6815f5c8f66563f09a3eaaefd6ac9e3b127a92ab
DOC: Modify MaskImageFilter comments.

Change-Id: Iffe420a39b19d2e7810f452010c3ebc80112bfa6
Author: fedorov@bwh.harvard.edu
PERF: GradientVectorFlow - Remove redundant initializations

Remove redundant intializations of the m_IntermediateImage

Change-Id: Icfa83dd854c0c89c40fb3223eeb235b7a480e23e
PERF: Provide better default config for patch-based denoiser

Change the defaults for the patch-based denoiser to provide a faster
default configuration.  The new default does not do kernel bandwidth
estimation, and only performs one iteration of denoising.  Also, the
default configuration now provides a default sampling strategy of
sampling all the patches within 25 pixels of the current patch.

In addition, there have been some name changes to make the parameter
names more consistent and understandable.  A migration guide has been
created to document these API changes.

Change-Id: I4b98823bde5ecca27a993f41d3a05ffb8b1861a8
Merge topic 'GradientVectorFlowTimestepBug'

c1d5a81 PERF: GradientVectorFlow - Remove redundant initializations
c4ac89b STYLE: GradientVectorFlow
7c0df24 STYLE: GradientVectorFlow - Add const correctness
c5ee0b0 BUG: GradientVectorFlow should calculate timestep based on image dimension
Merge topic 'EditDoxygen_MattesMutualInformationImageToImageMetric_1358954219'

399699f DOC: Modify MattesMutualInformationImageToImageMetric comments.
Merge topic 'EditDoxygen_MaskImageFilter_1359056992'

03d0d91 DOC: Modify MaskImageFilter comments.
Merge topic 'FixITK_WRAPPING'

f50b940 COMP: Incomplete variable name change.
Merge topic '2993-add-maskingvalue'

eef8e73 ENH: Add MaskingValue to MaskImageFilter
Merge topic '2991-threshold-inside'

27a9820 ENH: Add unit test to itkThresholdImageFilterTest
Merge topic 'BetterDenoisingDefaultsAndNames'

45fc5a9 PERF: Provide better default config for patch-based denoiser
Merge topic 'UPDATE_DCMTK_8f6a4060'

b9c473e COMP: Update DCMTK version to incorporate new fixes.