Use configuration path for examples in order to locate
configurations files.

Modify AVMNidus, FEMSimulator and Shaders examples.

Small fixes all over the place.

Refactor VRPN Server/Client API + VTKViewer window management

**VRPN:** Allows for the following workflow :
1) Create a VRPNDeviceClient by specifying its URL (name@ipadress)
and its type (see `DeviceType` class). The subclass VRPNForceDevice
is setting the style to `PHANTOM_OMNI` by default for now.
2) Create a VRPNDeviceServer
3) Call `VRPNDeviceServer::addDeviceClient()` to add the client created
on step 1). This will analyse the IP, name, and type of the device
client to instantiate a VRPN device connection. The added devices are
then stored in three std:map so the `mainloop()` can be called during
the execution.

Updated their use in `FEMSimulator` and `LaparoscopicCamera` examples.

**VTKViewer**: implementing `setVtkRenderWindow`
- This calls `VTKRenderer::setRenderWindow`. Needed to use a
vtkRenderWindow from another instance (example : for a QT
application, use QVTKWidget renderwindow)
- Rename `VTKViewer::getRenderWindow` to `getVtkRenderWindow`
- Use internal functions in `getVtkCamera` and `getVtkRenderer`

See merge request !72

- This calls `VTKRenderer::setRenderWindow`. Needed to use a
vtkRenderWindow from another instance (example : for a QT
application, use QVTKWidget renderwindow)
- Rename `VTKViewer::getRenderWindow` to `getVtkRenderWindow`
- Use internal functions in `getVtkCamera` and `getVtkRenderer`

Allows for the following workflow :
1) Create a `VRPNDeviceClient` by specifying its URL (name@ipadress)
and its type (see `DeviceType` class). The subclass `VRPNForceDevice`
is setting the style to `PHANTOM_OMNI` by default for now.
2) Create a `VRPNDeviceServer`
3) Call `VRPNDeviceServer::addDeviceClient()` to add the client created
on step 1). This will analyse the IP, name, and type of the device
client to instantiate a VRPN device connection. The added devices are
then stored in three `std:map` so the `mainloop()` can be called during
the execution.

Updated their use in `FEMSimulator` and `LaparoscopicCamera` examples.

ENH: Multiple enhancements all over.

Many are formating changes and others are
bug fixes as well as some refactoring.

See merge request !75

Many are formating changes and others are
bug fixes as well as some refactoring.

ENH: Rename the library - Fix missing names

from SimMedTK to iMSTK.

Modify the license notice in each file.
Add LICENSE file.

See merge request !74

from SimMedTK to iMSTK.

Modify the license notice in each file.
Add LICENSE file.

ENH: Rename the library

from SimMedTK to iMSTK.

Modify the license notice in each file.
Add LICENSE file.

See merge request !73

from SimMedTK to iMSTK.

Modify the license notice in each file.
Add LICENSE file.

Ricardo Ortiz authored 9 years ago and Kitware Robot committed 9 years ago

4e92d9c1 ENH: Improve support for data reading
9e97b77f ENH: Integration of Assembler.
e5c39a98 ENH: Merge collision context branch.
d2f84191 ENH: Cherry-picked from Ricardo's commit
fe72dc5a ENH: Clean up the code and update examples.
6d66149e ENH: Refactor the FEMSimulator example to use
af2c34df ENH: UpdateFEMSimulator example to use the new
14ce80ff ENH: Clean and refactor the penalty method.
...

Acked-by: Kitware Robot <kwrobot@kitware.com>
Merge-request: !71

by examples and unit tests.

Implement missing methods and logic.

Revert some changes and make it build, run FEMSimulator example

CollisionContext/CMakeLists.txt was contributed by Sreekanth.

Cherry-picked from Ricardo's edits to MeshMap related
classes in addCollisionContext branch

BUG: Fix compilation errors all over the place

ENH: Adds code to find islands

Adds code to find and list members of islands

WIP: Adds code to do stage-2 assembly

ENH: Change the mesh representation of scene objects

Adds three mesh representations for discrete geometry
for each scene object. Also adds mesh maps

Conflicts:
	Assembler/Assembler.h
	Collision/MeshToMeshCollision.h
	CollisionContext/CollisionContext.cpp
	CollisionContext/CollisionContext.h
	Core/AnalyticalGeometry.h
	Core/SceneObject.cpp
	Core/SceneObject.h
	Mesh/MeshMap.cpp
	Mesh/MeshMap.h
	Mesh/MeshMapAffine.cpp
	Mesh/MeshMapAffine.h
	Mesh/MeshMapTetToSurface.h
	SceneModels/UnitTests/VegaFEMDeformableSceneObjectSpec.cpp

iMSTK time stepping method.

classes.

Add an alias for a matrix map.
Create a templated method in the MeshModel and IOMesh to automatically
cast the underlying mesh.

Create an interpolate() method in the VegaVolumetricMesh class to
interpolate surface of the underlying volumetric mesh with an external
surface mesh and clean up the interface.

Create a computeGravity() method in the VegaVolumetricMesh class
to compute gravity forces.

Refactor getVelocity() method in DeformableSceneObject and add a
variable to hold the gravity vector.

Refactor SceneObject. Add SceneModelRenderDelegate render delegate to
take care of renderign operations for this model. Create visual,
physics and collision model variables.

Remove render delegates from the StaticSceneObject, this is now handled
by it base class.

Add storage for the gravity force in VegaFEMDeformableSceneObject and
initialized properly. Compute internal force by multiplying K*positions
instead of calling the vega function.

Refactor DefaultSimulator, VegaFEMModelSimulator. This class will be
marked obsolete soon.

This will be the main render delegate since only models are allowed to
be render and this one covers most cases.

in the Scene objects.

DefaultSimulator.

* Remove custom renderers
* Remove local storage for vertices
* Documenting

Small format changes all over the place.

Use the model from SceneObject to laod meshes.

and their tests. Streamline and refactor
time integrators and their tests.

initialized from Vega matrices. The ode rhs
now considers damping only if the coefficients are
positive, non zero. It also accumulates contact forces
if any. The updateAttachedMesh in the VegaVolumetricMesh
class now takes an Eigen vector to do the update.

to just NewtonMethod. Update the solve routine
so it always goes into the armijo loop, subsequent
function norms are computed there. If the user wants
to disable the armijo updated then it should set the
armijoMax in the base class. The armijo function now
takes an extra parameter, the old function evaluation
norm.

in favor of their own "GenerateCompressedRowMajorFormat" routine.

Refactor ObjectSimulator.

classes. Also create a SimulationManager in charge of
running the simulation.

file and add forward declarations.