- 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>

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

/*=========================================================================

   Library: iMSTK

   Copyright (c) Kitware, Inc. & Center for Modeling, Simulation,
   & Imaging in Medicine, Rensselaer Polytechnic Institute.

   Licensed under the Apache License, Version 2.0 (the "License");
   you may not use this file except in compliance with the License.
   You may obtain a copy of the License at

      http://www.apache.org/licenses/LICENSE-2.0.txt

   Unless required by applicable law or agreed to in writing, software
   distributed under the License is distributed on an "AS IS" BASIS,
   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   See the License for the specific language governing permissions and
   limitations under the License.

=========================================================================*/

Update Geometry and Sphere to have scaling and
radius respectively > 0;

convert tabs to 4 spaces

- Fix workflow for PBD in SceneManager.cpp. Add/modify related functions for
PbdObject/PbdRigidObject/VirtualCoupleingPBDObject. It should work for the
most general case where collision/physics/visual meshes are different from
each other.
- Add LineMesh class and LineMeshRenderDelegate. Add support for LineMesh
class in imstkGeometry, imstkMesh, imstkRenderDelegate.

- Fix a bug for computeBoundingBox() in imstkMesh.
- Fix a bug for applying mapping in TetraTriangleMap.
- Fix a bug for computing the center of tetra in TetraTriangleMap.

Style enforcement and add comments over the entire code

Enforce consistency with braces

Use Geometry::Type instead of GeometryType.
Use GeometryMap::Type instead of GeometryMapType

1) Clean up print methods
2) Put initialize, print, clear, getVolume on top
3) Add missing overrides
4) Replace extractSurfaceMesh by computeAttachedSurfaceMesh
5) Define Mesh::print
6) Use Mesh::clear in subclasses

Adds a function to check if a geometry is a mesh.
Adds printing to geometry class
Stylistic changes in extract mesh class

Adds comments to the classes and their functions in geometry module

Adds Tetra-Triangular mesh map.
TODO: Code check and add tests

Adds geometry map base class and isometriMap

Signed-off-by: Sreekanth Arikatla <sreekanth.arikatla@kitware.com>

Also make Geometry class polymorphic by making its
destructor virtual.

Conflict existed within VTK.

This base class was needed for storing position and
orientation of the geometries. Those global transformation
can also be applied to discrete geometries, therefore
Geometry and AnalyticalGeometry classes were merged.

Use config based on https://gist.github.com/mkroman/1372117

Also remove headers in cmake files

Uses a dummy implementation of imstkScene to test
a module execution in multithreading.

Adding project name (iMSTK)

Skeleton of CMake architecture and of first few classes.