diff --git a/Examples/Physiology/Fluid.hpp b/Examples/Physiology/Fluid.hpp
index 46fba29180145bd1a7c16691adc8eb5c8b3fe4f7..708548d2afe2e3b9adaf5391403d3c10e40114a8 100644
--- a/Examples/Physiology/Fluid.hpp
+++ b/Examples/Physiology/Fluid.hpp
@@ -103,10 +103,6 @@ generateFluid(const std::shared_ptr<Scene>& scene, const double particleRadius)
auto surfMeshShell = std::dynamic_pointer_cast<SurfaceMesh>(MeshIO::read(iMSTK_DATA_ROOT "/cylinder/cylinder_small_shell.stl"));
auto tetMesh = std::dynamic_pointer_cast<TetrahedralMesh>(MeshIO::read(iMSTK_DATA_ROOT "/cylinder/cylinder_small.vtk"));
- //surfMesh->rotate(Vec3d(1, 0, 0), PI / 5, Geometry::TransformType::ConcatenateToTransform);
- //surfMeshShell->rotate(Vec3d(1, 0, 0), PI / 5, Geometry::TransformType::ConcatenateToTransform);
- //tetMesh->rotate(Vec3d(1, 0, 0), PI / 5, Geometry::TransformType::ConcatenateToTransform);
-
// set tetrahedral mesh used when writing VTUs
sphModel->setGeometryMesh(tetMesh);
@@ -131,7 +127,6 @@ generateFluid(const std::shared_ptr<Scene>& scene, const double particleRadius)
selectionFilter->setInputPoints(uniformMesh);
selectionFilter->update();
auto enclosedFluidPoints = selectionFilter->getOutputPoints();
- //auto enclosedFluidPoints = GeometryUtils::getEnclosedPoints(surfMesh, uniformMesh, false);
particles = enclosedFluidPoints->getInitialVertexPositions();
@@ -139,7 +134,6 @@ generateFluid(const std::shared_ptr<Scene>& scene, const double particleRadius)
selectionFilter->setInputPoints(uniformMesh_wall);
selectionFilter->update();
auto enclosedWallPoints = selectionFilter->getOutputPoints();
- //auto enclosedWallPoints = GeometryUtils::getEnclosedPoints(surfMeshShell, uniformMesh_wall, false);
StdVectorOfVec3d wallParticles = enclosedWallPoints->getInitialVertexPositions();
@@ -196,7 +190,6 @@ generateFluid(const std::shared_ptr<Scene>& scene, const double particleRadius)
selectionFilter->setInputPoints(uniformMesh);
selectionFilter->update();
auto enclosedFluidPoints = selectionFilter->getOutputPoints();
- //auto enclosedFluidPoints = GeometryUtils::getEnclosedPoints(surfMesh, uniformMesh, false);
particles = enclosedFluidPoints->getInitialVertexPositions();
@@ -204,7 +197,6 @@ generateFluid(const std::shared_ptr<Scene>& scene, const double particleRadius)
selectionFilter->setInputPoints(uniformMesh_wall);
selectionFilter->update();
auto enclosedWallPoints = selectionFilter->getOutputPoints();
- //auto enclosedWallPoints = GeometryUtils::getEnclosedPoints(surfMeshShell, uniformMesh_wall, false);
StdVectorOfVec3d wallParticles = enclosedWallPoints->getInitialVertexPositions();
@@ -233,7 +225,6 @@ generateFluid(const std::shared_ptr<Scene>& scene, const double particleRadius)
speedOfSound = 300;
}
-
else if (SCENE_ID == 3)
{
// bifurcation flow
@@ -265,7 +256,6 @@ generateFluid(const std::shared_ptr<Scene>& scene, const double particleRadius)
selectionFilter->setInputPoints(uniformMesh);
selectionFilter->update();
auto enclosedFluidPoints = selectionFilter->getOutputPoints();
- //auto enclosedFluidPoints = GeometryUtils::getEnclosedPoints(surfMesh, uniformMesh, false);
particles = enclosedFluidPoints->getInitialVertexPositions();
@@ -273,7 +263,6 @@ generateFluid(const std::shared_ptr<Scene>& scene, const double particleRadius)
selectionFilter->setInputPoints(uniformMesh_wall);
selectionFilter->update();
auto enclosedWallPoints = selectionFilter->getOutputPoints();
- //auto enclosedWallPoints = GeometryUtils::getEnclosedPoints(surfMeshShell, uniformMesh_wall, false);
StdVectorOfVec3d wallParticles = enclosedWallPoints->getInitialVertexPositions();
@@ -312,10 +301,6 @@ generateFluid(const std::shared_ptr<Scene>& scene, const double particleRadius)
auto surfMeshShell = std::dynamic_pointer_cast<SurfaceMesh>(MeshIO::read(iMSTK_DATA_ROOT "/cylinder/cylinder_small_shell_cut_ellipse.stl"));
auto tetMesh = std::dynamic_pointer_cast<TetrahedralMesh>(MeshIO::read(iMSTK_DATA_ROOT "/cylinder/cylinder_small.vtk"));
- //surfMesh->rotate(Vec3d(1, 0, 0), PI / 5, Geometry::TransformType::ConcatenateToTransform);
- //surfMeshShell->rotate(Vec3d(1, 0, 0), PI / 5, Geometry::TransformType::ConcatenateToTransform);
- //tetMesh->rotate(Vec3d(1, 0, 0), PI / 5, Geometry::TransformType::ConcatenateToTransform);
-
// set tetrahedral mesh used when writing VTUs
sphModel->setGeometryMesh(tetMesh);
@@ -340,7 +325,6 @@ generateFluid(const std::shared_ptr<Scene>& scene, const double particleRadius)
selectionFilter->setInputPoints(uniformMesh);
selectionFilter->update();
auto enclosedFluidPoints = selectionFilter->getOutputPoints();
- //auto enclosedFluidPoints = GeometryUtils::getEnclosedPoints(surfMesh, uniformMesh, false);
particles = enclosedFluidPoints->getInitialVertexPositions();
@@ -348,7 +332,6 @@ generateFluid(const std::shared_ptr<Scene>& scene, const double particleRadius)
selectionFilter->setInputPoints(uniformMesh_wall);
selectionFilter->update();
auto enclosedWallPoints = selectionFilter->getOutputPoints();
- //auto enclosedWallPoints = GeometryUtils::getEnclosedPoints(surfMeshShell, uniformMesh_wall, false);
StdVectorOfVec3d wallParticles = enclosedWallPoints->getInitialVertexPositions();
@@ -381,7 +364,6 @@ generateFluid(const std::shared_ptr<Scene>& scene, const double particleRadius)
auto sphHemorrhageModel = std::make_shared<SPHHemorrhage>(hemorrhagePlaneCenter, hemorrhagePlaneRadius, hemorrhagePlaneArea, hemorrhagePlaneOutwardNormal);
sphModel->setHemorrhageModel(sphHemorrhageModel);
}
-
else if (SCENE_ID == 5)
{
// femoral artery flow with leak
@@ -389,10 +371,6 @@ generateFluid(const std::shared_ptr<Scene>& scene, const double particleRadius)
auto surfMeshShell = std::dynamic_pointer_cast<SurfaceMesh>(MeshIO::read(iMSTK_DATA_ROOT "/femoral/femoral_artery_shell.stl"));
auto tetMesh = std::dynamic_pointer_cast<TetrahedralMesh>(MeshIO::read(iMSTK_DATA_ROOT "/femoral/femoral_artery.vtk"));
- //surfMesh->rotate(Vec3d(1, 0, 0), PI / 5, Geometry::TransformType::ConcatenateToTransform);
- //surfMeshShell->rotate(Vec3d(1, 0, 0), PI / 5, Geometry::TransformType::ConcatenateToTransform);
- //tetMesh->rotate(Vec3d(1, 0, 0), PI / 5, Geometry::TransformType::ConcatenateToTransform);
-
// set tetrahedral mesh used when writing VTUs
sphModel->setGeometryMesh(tetMesh);
@@ -417,7 +395,6 @@ generateFluid(const std::shared_ptr<Scene>& scene, const double particleRadius)
selectionFilter->setInputPoints(uniformMesh);
selectionFilter->update();
auto enclosedFluidPoints = selectionFilter->getOutputPoints();
- //auto enclosedFluidPoints = GeometryUtils::getEnclosedPoints(surfMesh, uniformMesh, false);
particles = enclosedFluidPoints->getInitialVertexPositions();
@@ -425,7 +402,6 @@ generateFluid(const std::shared_ptr<Scene>& scene, const double particleRadius)
selectionFilter->setInputPoints(uniformMesh_wall);
selectionFilter->update();
auto enclosedWallPoints = selectionFilter->getOutputPoints();
- //auto enclosedWallPoints = GeometryUtils::getEnclosedPoints(surfMeshShell, uniformMesh_wall, false);
StdVectorOfVec3d wallParticles = enclosedWallPoints->getInitialVertexPositions();
@@ -449,15 +425,27 @@ generateFluid(const std::shared_ptr<Scene>& scene, const double particleRadius)
StdVectorOfVec3d outletNormals{ Vec3d(1, 0, 0) };
std::vector<std::pair<Vec3d, Vec3d>> outletCoords{ std::make_pair(outletMinCoord, outletMaxCoord) };
- auto sphBoundaryConditions = std::make_shared<SPHBoundaryConditions>(inletCoords, outletCoords, fluidCoords, inletNormal, outletNormals, inletRadius, inletCenterPoint, inletFlowRate, particles, wallParticles);
+ auto sphBoundaryConditions = std::make_shared<SPHBoundaryConditions>(inletCoords,
+ outletCoords,
+ fluidCoords,
+ inletNormal,
+ outletNormals,
+ inletRadius,
+ inletCenterPoint,
+ inletFlowRate,
+ particles,
+ wallParticles);
sphModel->setBoundaryConditions(sphBoundaryConditions);
const Vec3d hemorrhagePlaneCenter(0.57, -0.16, -0.12);
- const double hemorrhagePlaneRadius = 0.4;
- //const double hemorrhagePlaneArea = 0.018;
- const double hemorrhagePlaneArea = 0.158;
- //const double hemorrhagePlaneArea = 0.3152;
+ const double hemorrhagePlaneRadius = 0.4;
+ const double hemorrhagePlaneArea = 0.158;
const Vec3d hemorrhagePlaneNormal(0.31, -0.14, -0.94);
- auto sphHemorrhageModel = std::make_shared<SPHHemorrhage>(hemorrhagePlaneCenter, hemorrhagePlaneRadius, hemorrhagePlaneArea, hemorrhagePlaneNormal);
+ auto sphHemorrhageModel = std::make_shared<SPHHemorrhage>(
+ hemorrhagePlaneCenter,
+ hemorrhagePlaneRadius,
+ hemorrhagePlaneArea,
+ hemorrhagePlaneNormal);
+
sphModel->setHemorrhageModel(sphHemorrhageModel);
sphModel->setInitialVelocities(particles.size(), Vec3d(0.1, 0, 0));
diff --git a/Examples/Physiology/PhysiologyExample.hpp b/Examples/Physiology/PhysiologyExample.hpp
index 8d5e1ace1392a3441f1a498b4302539e8c3b5e3b..8ab484474a67116a796912a05ac9315a1afd90d6 100644
--- a/Examples/Physiology/PhysiologyExample.hpp
+++ b/Examples/Physiology/PhysiologyExample.hpp
@@ -29,7 +29,6 @@
#include "imstkLight.h"
#include "imstkPhysiologyModel.h"
#include "imstkPhysiologyObject.h"
-//#include "imstkPlane.h"
#include "imstkPointSet.h"
#include "imstkObjectInteractionFactory.h"
#include "imstkScene.h"
@@ -39,7 +38,6 @@
#include "imstkSPHObject.h"
#include "imstkSPHPhysiologyInteraction.h"
#include "imstkTaskGraph.h"
-//#include "imstkVTKTextStatusManager.h"
#include "imstkVTKViewer.h"
#include "imstkMouseSceneControl.h"
#include "imstkKeyboardSceneControl.h"
@@ -51,18 +49,25 @@ using namespace imstk;
static std::shared_ptr<PhysiologyObject>
makePhysiologyObject()
{
- // configure model
- auto physiologyParams = std::make_shared<PhysiologyModelConfig>();
+ // configuration for the Physiology model
+ imstkNew<PhysiologyModelConfig> physiologyParams;
- // Create a physics model
- auto physiologyModel = std::make_shared<PhysiologyModel>();
+ // Set the base physiology state to available preset
+ physiologyParams->m_basePatient = PatientPhysiology::StandardMale;
+
+ // Create a Physiology model
+ imstkNew<PhysiologyModel> physiologyModel;
physiologyModel->configure(physiologyParams);
- // Setup hemorrhage action
- auto hemorrhageAction = std::make_shared<HemorrhageAction>(HemorrhageAction::Type::External, "VascularCompartment::RightLeg");
+ // Create an external hemorrhage on the right leg
+ imstkNew<HemorrhageAction> hemorrhageAction(HemorrhageAction::Type::External,
+ "VascularCompartment::RightLeg");
+
+
+ // Add a hemorrhage action to the model
physiologyModel->addAction("Hemorrhage", hemorrhageAction);
- auto physiologyObj = std::make_shared<PhysiologyObject>("Pulse");
+ imstkNew<PhysiologyObject> physiologyObj("Human physiology");
physiologyObj->setDynamicalModel(physiologyModel);
return physiologyObj;
@@ -129,7 +134,7 @@ main(int argc, char* argv[])
scene->getCollisionGraph()->addInteraction(interactionPair);
// configure camera
- (SCENE_ID == 5) ? scene->getActiveCamera()->setPosition(0, 1.0, 4.0) : scene->getActiveCamera()->setPosition(0, 1.0, 5.0);
+ (SCENE_ID == 5) ? scene->getActiveCamera()->setPosition(0, 1.0, 4.0) : scene->getActiveCamera()->setPosition(0, 1.0, 7.0);
// configure light (white)
auto whiteLight = std::make_shared<DirectionalLight>("whiteLight");
@@ -137,7 +142,7 @@ main(int argc, char* argv[])
whiteLight->setIntensity(7);
scene->addLight(whiteLight);
- // Setup some scalars
+ //Setup some scalars
std::shared_ptr<PointSet> fluidGeometry = std::dynamic_pointer_cast<PointSet>(fluidObj->getPhysicsGeometry());
std::shared_ptr<StdVectorOfReal> scalarsPtr = std::make_shared<StdVectorOfReal>(fluidGeometry->getNumVertices());
std::fill_n(scalarsPtr->data(), scalarsPtr->size(), 0.0);
@@ -167,18 +172,21 @@ main(int argc, char* argv[])
}, "PrintTotalTime");
taskGraph->insertAfter(fluidObj->getDynamicalSPHModel()->getMoveParticlesNode(), printTotalTime);
- std::shared_ptr<TaskNode> writeSPHStateToCSV = std::make_shared<TaskNode>([&]() {
+ std::shared_ptr<TaskNode> writeSPHStateToCSV = std::make_shared<TaskNode>([&]()
+ {
fluidObj->getDynamicalSPHModel()->writeStateToCSV();
}, "WriteStateToCSV");
taskGraph->insertAfter(fluidObj->getDynamicalSPHModel()->getMoveParticlesNode(), writeSPHStateToCSV);
- std::shared_ptr<TaskNode> writeSPHStateToVtk = std::make_shared<TaskNode>([&]() {
+ std::shared_ptr<TaskNode> writeSPHStateToVtk = std::make_shared<TaskNode>([&]()
+ {
fluidObj->getDynamicalSPHModel()->writeStateToVtk();
}, "WriteStateToVtk");
taskGraph->insertAfter(fluidObj->getDynamicalSPHModel()->getMoveParticlesNode(), writeSPHStateToVtk);
// This node colors the fluid points based on their type
- std::shared_ptr<TaskNode> computeVelocityScalars = std::make_shared<TaskNode>([&]() {
+ std::shared_ptr<TaskNode> computeVelocityScalars = std::make_shared<TaskNode>([&]()
+ {
const std::shared_ptr<SPHBoundaryConditions> sphBoundaryConditions = sphModel->getBoundaryConditions();
StdVectorOfReal& scalars = *scalarsPtr;
for (size_t i = 0; i < sphModel->getCurrentState()->getNumParticles(); i++)
@@ -204,30 +212,35 @@ main(int argc, char* argv[])
taskGraph->insertAfter(fluidObj->getUpdateGeometryNode(), computeVelocityScalars);
};
- // Setup a viewer to render in its own thread
- imstkNew<VTKViewer> viewer("Viewer");
- viewer->setActiveScene(scene);
-
- // Setup a scene manager to advance the scene in its own thread
- imstkNew<SceneManager> sceneManager("Scene Manager");
- sceneManager->setActiveScene(scene);
- viewer->addChildThread(sceneManager); // SceneManager will start/stop with viewer
- connect<Event>(sceneManager, EventType::PostUpdate, displayColors);
-
- // Add mouse and keyboard controls to the viewer
+ // Run the simulation
{
- imstkNew<MouseSceneControl> mouseControl(viewer->getMouseDevice());
- mouseControl->setSceneManager(sceneManager);
- viewer->addControl(mouseControl);
+ // Setup a viewer to render in its own thread
+ imstkNew<VTKViewer> viewer("Viewer");
+ viewer->setActiveScene(scene);
- imstkNew<KeyboardSceneControl> keyControl(viewer->getKeyboardDevice());
- keyControl->setSceneManager(sceneManager);
- keyControl->setViewer(viewer);
- }
+ // Setup a scene manager to advance the scene in its own thread
+ imstkNew<SceneManager> sceneManager("Scene Manager");
+ sceneManager->setActiveScene(scene);
+ viewer->addChildThread(sceneManager); // SceneManager will start/stop with viewer
+ connect<Event>(sceneManager, EventType::PostUpdate, displayColors);
- // Start viewer running, scene as paused
- sceneManager->requestStatus(ThreadStatus::Running);
- viewer->start();
+ // Add mouse and keyboard controls to the viewer
+ {
+ imstkNew<MouseSceneControl> mouseControl(viewer->getMouseDevice());
+ mouseControl->setSceneManager(sceneManager);
+ viewer->addControl(mouseControl);
+
+ imstkNew<KeyboardSceneControl> keyControl(viewer->getKeyboardDevice());
+ keyControl->setSceneManager(sceneManager);
+ keyControl->setViewer(viewer);
+ viewer->addControl(keyControl);
+ }
+
+ // Start viewer running, scene as paused
+ sceneManager->requestStatus(ThreadStatus::Paused);
+ viewer->start();
+
+ }
return 0;
}
diff --git a/Source/GeometryMappers/imstkTetraTriangleMap.cpp b/Source/GeometryMappers/imstkTetraTriangleMap.cpp
index ffbc0e6e4f2db1ab4ab46e537471d48a41cabe9b..cef134ef0ce7e8e0084e808b3d074e3cf9b22507 100644
--- a/Source/GeometryMappers/imstkTetraTriangleMap.cpp
+++ b/Source/GeometryMappers/imstkTetraTriangleMap.cpp
@@ -141,7 +141,7 @@ TetraTriangleMap::isValid() const
{
auto meshMaster = static_cast<TetrahedralMesh*>(m_master.get());
#if defined(DEBUG) || defined(_DEBUG) || !defined(NDEBUG)
- CHECK(dynamic_cast<TetrahedralMesh*>(m_master.get()) == nullptr) << "Fail to cast from geometry to mesh";
+ CHECK(dynamic_cast<TetrahedralMesh*>(m_master.get())) << "Fail to cast from geometry to mesh";
#endif
auto totalElementsMaster = meshMaster->getNumTetrahedra();