Also modified Arduino device for handling roll-only data

VRPN Streaming Arduino added to client / server code

Switch to sjh/vrpn to allow for quick changes to the
Arduino vrpn server/client

This prevents linker errors in Windows from finding multiple
copies of the vrpn base classes.

ENH: Add translation offset due to angulation

See merge request !177

Custom camera controller

See merge request !176

Enh changes from cameranavigation

See merge request !174

STYLE: Uncrustify configuration

See merge request !171

Enforces license header and the rest of configuration options. To enable it,
manually run SetupForDevelopment.sh and enable uncrustify during configure.
Also provided is default configuration file to be consulted when a new
option is needed. This file has explanations for all the options.

Also, some source code files have been modified to prevent ugly auto-reformatting.

BUG: Extra character at end of a line

See merge request !172

Add bone drilling feature

See merge request !170

Tags tetrahedra that are removed from the drill process
and communicated to the tetrahedraRenderDelegate

Adds erosion feature to the bone through a collision handling step

Co-authored by Mohit Tyagi <mohit.tyagi@kitware.com>

Add interactive picking feature

See merge request !167

Thus CH generates the dynamic projection constraints based on the collision data.

Move the Linear Projection Constraints (LPC) from the nonlinear system to CG solver for simplicity.
LPC are only used in CG.

Add api to create interaction pair by objects of CD, CH.
This will allow for configuring the CD and CH by the user.

Adds a sphere to mesh collision detection.
The radius of the sphere is small to use for picking.

Refactor geometry transforms 2

See merge request !169

An array of texture coordinates was added to the surface mesh read
by AssimpIO even if there were no texture coordinates found.

- Geometry class does not have a position, orientation, scaling combination
anymore, but a rigid transformation (translation + rotation) as well as a
separate uniform scaling.
- The value of that transformation can be changed using setTranslation(),
setRotation(), and setScaling().
- scale(), translate(), and rotate() are utility functions which behavior
vary based on the parameter TransformType: ConcatenateToTransform, the
default value, will concatenate transformations to the rigid transform and
signals that the transform has been modified; ApplyToData directly enforces
the transformation given to the internal data of the geometry, and signals
that the data has been modified (useful to enforce offsets at the beginning
of the simulation to avoid concatenating that offset continuously).
- A new base class AnalyticalGeomerty is created for Capsule, Plane, Cube
and Sphere. It wraps the common attributes to those geometries: a position
and an orientation axis. The values of those properties after the transform
is applied are also stored to avoid redundant computations.
- Subclasses of AnalyticalGeometry often show properties related to size:
width, radius, length, etc. Those have their post-transform sibling also.
- The Plane has a Normal API which simply wraps the AnalyticalGeometry
orientation axis.
- The mesh base class also keeps track of a post-transform value for the
vertex positions.
- Those internal data properties can be set with regular setting methods,
which also signals that the internal data has been modified.
- Get methods for those properties have a behavior which vary based on
the parameter DataType: PostTransform is the default value, and it will
return the post transform data, computing it by applying the transform if
it was not yet done.
- CollisionDetection classes are updated to use that post-transform data
- RenderDelegates are updated to update their internal data only when
the geometry data has been modified (use VTK sources and transform filter),
as well as the rigid transform when that one has been modified also.
- Maps, Controllers, and tests are updated to use the correct API:
set translation and rotation and not position/orientation.
- Update Geometry and Plane test to take into account the change of API:
getRotation is now returning a Mat3d instead of a quaternion for less
operations, and getNormal will return a normalized vector even if the one
set was not normalized. Use `isApprox` to allow for low variability.
- Update API in sandbox example
- Got rid of the vertexDisplacements variable in the Mesh class, difference
between the vertexPosition and the initialVertexPositions: it was requiring
additional bookeeping which was not necessary

Co-Authored-by: Sreekanth Arikatla <sreekanth.arikatla@kitware.com>
Signed-off-by: Alexis Girault <alexis.girault@kitware.com>

COMP: using size_t more consistently and other warnings on MSVC/Windows

Closes #8

See merge request !168

ENH: Added and documented logging system. Cleaned up code from initial implementation.

See merge request !100

Co-Authored-by: Alexis Girault <alexis.girault@kitware.com>

ENH: Materials and texture manager

See merge request !159

Co-Authored-by: Alexis Girault <alexis.girault@kitware.com>

Virtual coupling object

See merge request !150