COMP: Remove compiler warnings.

More regex patterns to remove.
COMP: Set graduated testing options

BRAINSTools_MAX_TEST_LEVEL adjusts how agressive the test suite is
so that long running tests or incomplete tests can easily be
silenced
1 - Run the absolute minimum very fast tests (These should always pass before any code commit)
3 - Run fast tests on continous builds (These need immediate attention if they begin to fail)
5 - Run moderate nightly tests (These need immediate attention if they begin to fail)
7 - Run long running extensive test that are a burden to normal development (perhaps test 1x per week)
8 - Run tests that fail due to incomplete test building, these are good ideas for test that we don't have time to make robust)
9 - Run silly tests that don't have much untility
set(BRAINSTools_MAX_TEST_LEVEL 3 CACHE STRING "Testing level for managing test burden")
Update README

Added Markdown headings and information about testing levels
ENH: Remove DeformationField parameter from GenericTransformImage

See https://www.icts.uiowa.edu/jira/browse/PREDICTIMG-1667

The GenericTransformImage template function isn't used that many
places. In most it's clear that either a DeformationField or
a Transform is passed in. A few places in BRAINSCut it looks like
both are passed in, but in practice only one or the other is
actually defined.

The way GenericTransformImage was actually written, if both a
transform and a displacement field are passed in, the transform
is ignored.  So I felt justified in enforcing that at the
point of call.  If needed, a DisplaceFieldTransform is created
and the Displacement Image is passed in.

The biggest 'hidden' change this brings about is that the
DisplacementField type is defined as
itk::Image<itk::Vector<float,3>,3> but the transform parameter
type is double, so I changed type DisplacementField type so it
was compatible with the Transform type.
Merge pull request #32 from Chaircrusher/GenericTransformImage

ENH: Remove DeformationField parameter from GenericTransformImage
COMP: Testing dependancy was missing

The parent dependancy test was turned off by
default, so the child test needed to also be
turned off.
ENH: Pushing ITK, NIPYPE, SimpleITK forward

Many performance improvements have been worked on in ITK.  Pushing other
tools forward as well in preparation for new build/run of autoworkup for
TRACKHD.
ENH: Remove ApplyWarp that is superceeded by BRAINSResample.
ENH: Add better exception catching and reporting.
COMP: Remove #if 0 clauses

I also removed 3 header files whose entire contents
were inside #if 0, and weren't being included anywhere
Merge pull request #37 from Chaircrusher/Rm_If_0

COMP: Remove #if 0 clauses
COMP: compare Z spacing reported in DICOM to measured difference between slices
COMP: modularize
BUG: fix bugs in test and DWI file comparison program
DOC: added comments
ENH: Check for missing gradients in Siemens files
BUG: fixed problem with directions in NRRD file.

Trim off trailing ISOTROPIC volumes
BUG: got origin wrong for Siemens Mosaic images
ENH: add the python script for testing new version

Before moving to a new version of DWIConvert, use this script to make
sure that it converts DICOM datasets at least as well as the current
production version.
BUG: Check script
BUG: Philips Multiframe Deinterleave fix
BUG: Accomodate Signa HDx scanners