diff --git a/CMake/External/CMakeLists.txt b/CMake/External/CMakeLists.txt
index 420a1b2c2de92d174342a1c6fbc772b537424064..415e69095cc8d696a1f4b4e32ff6fb15f5fa0b2e 100644
--- a/CMake/External/CMakeLists.txt
+++ b/CMake/External/CMakeLists.txt
@@ -100,14 +100,12 @@ ExternalProject_Add( ${PROJECT_NAME}
-D${PROJECT_NAME}_ENABLE_AUDIO:BOOL=${${PROJECT_NAME}_ENABLE_AUDIO}
-D${PROJECT_NAME}_USE_VRPN:BOOL=${${PROJECT_NAME}_USE_VRPN}
-D${PROJECT_NAME}_COLOR_OUTPUT:BOOL=${${PROJECT_NAME}_COLOR_OUTPUT}
- -D${PROJECT_NAME}_USE_Pulse:BOOL=${${PROJECT_NAME}_USE_Pulse}
# External Libraries
-DEigen3_DIR:PATH=${Eigen3_DIR}
-Dglm_DIR:PATH=${glm_DIR}
-DGTest_DIR:PATH=${GTest_DIR}
-DVegaFEM_DIR:PATH=${VegaFEM_DIR}
-DVTK_DIR:PATH=${VTK_DIR}
- -DPulse_DIR:PATH=${Pulse_DIR}
# I don't think this is needed by the inner build
# -DPHYSX_CONFIGURATION:STRING=${${PROJECT_NAME}_PHYSX_CONFIGURATION}
DEPENDS ${${PROJECT_NAME}_DEPENDENCIES}
diff --git a/CMake/External/External_Pulse.cmake b/CMake/External/External_Pulse.cmake
deleted file mode 100644
index e3120b29408617d9f69e1f1b7a3d071d5bd86fc3..0000000000000000000000000000000000000000
--- a/CMake/External/External_Pulse.cmake
+++ /dev/null
@@ -1,22 +0,0 @@
-#-----------------------------------------------------------------------------
-# Add Pulse External Project
-#-----------------------------------------------------------------------------
-
-include(imstkAddExternalProject)
-imstk_add_external_project( Pulse
- GIT_REPOSITORY https://gitlab.kitware.com/physiology/engine.git
- GIT_TAG f4d501c2f7cc091dc053a96ab5a56f79b7528c4f
- GIT_SHALLOW TRUE
- #URL https://gitlab.kitware.com/physiology/engine/-/archive/3.x/archive.zip
- #URL_HASH 4189591a6859df46920bbc35f160eef23fc33ffd
- CMAKE_CACHE_ARGS
- -DPulse_SLAVE_BUILD:BOOL=ON
- -DPulse_JAVA_API:BOOL=OFF
- -DPulse_PYTHON_API:BOOL=OFF
- INSTALL_COMMAND $(SKIP_STEP_COMMAND)
-)
-
-if(NOT USE_SYSTEM_Pulse)
- set(Pulse_DIR ${CMAKE_INSTALL_PREFIX}/lib/cmake/Pulse-3.0)
- #message(STATUS "Pulse_DIR : ${Pulse_DIR}")
-endif()
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 0c88c8a53bb29c94a23e6f79f12fe3809adfd39f..1e9703ff803a526c4c31d11ec612a55d3c957637 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -137,11 +137,6 @@ if(${PROJECT_NAME}_SUPERBUILD)
option(${PROJECT_NAME}_USE_Vulkan "Use the custom Vulkan renderer." OFF)
option(${PROJECT_NAME}_USE_OpenHaptics "Use OpenHaptic Support." OFF)
- option(${PROJECT_NAME}_USE_Pulse "Use Pulse Physiology engine." OFF)
- if(${PROJECT_NAME}_USE_Pulse)
- imstk_define_dependency(Pulse)
- endif()
-
imstk_define_dependency(Assimp)
imstk_define_dependency(Eigen3)
imstk_define_dependency(g3log)
@@ -249,13 +244,6 @@ set(PHYSX_RELEASE_TYPES "RELEASE;CHECKED;PROFILE" CACHE INTERNAL "List of availa
set_property(CACHE PHYSX_CONFIGURATION PROPERTY STRINGS ${PHYSX_RELEASE_TYPES})
find_package(PhysX REQUIRED)
-if(${PROJECT_NAME}_USE_Pulse)
- add_definitions( -DiMSTK_USE_Pulse )
- find_package( Pulse REQUIRED )
-else()
- remove_definitions( -DiMSTK_USE_Pulse )
-endif()
-
# SCCD
find_package( SCCD REQUIRED )
@@ -404,7 +392,6 @@ add_subdirectory(Source/CollisionHandling)
add_subdirectory(Source/Scene)
add_subdirectory(Source/SimulationManager)
add_subdirectory(Source/apiUtilities)
-add_subdirectory(Source/Pulse)
add_subdirectory(Source/Filtering)
add_subdirectory(Source/FilteringCore)
diff --git a/Source/DynamicalModels/ObjectModels/imstkRigidBodyModel2.cpp b/Source/DynamicalModels/ObjectModels/imstkRigidBodyModel2.cpp
index da78db3bbf3d389fe7b7618868bf5b9e6dc17674..08b81d1b15919ce7d66fabe98bcb065f0cf4e935 100644
--- a/Source/DynamicalModels/ObjectModels/imstkRigidBodyModel2.cpp
+++ b/Source/DynamicalModels/ObjectModels/imstkRigidBodyModel2.cpp
@@ -171,16 +171,16 @@ RigidBodyModel2::computeTentativeVelocities()
// Sum gravity to the forces
ParallelUtils::parallelFor(forces.size(), [&forces, &fG](const int& i)
- {
- forces[i] += fG;
+ {
+ forces[i] += fG;
}, forces.size() > m_maxBodiesParallel);
// Compute the desired velocites, later we will solve for the proper velocities,
// adjusted for the constraints
ParallelUtils::parallelFor(tentativeVelocities.size(), [&](const size_t& i)
- {
- tentativeVelocities[i] += forces[i] * invMasses[i] * dt;
- tentativeAngularVelocities[i] += invInteriaTensors[i] * torques[i] * dt;
+ {
+ tentativeVelocities[i] += forces[i] * invMasses[i] * dt;
+ tentativeAngularVelocities[i] += invInteriaTensors[i] * torques[i] * dt;
}, tentativeVelocities.size() > m_maxBodiesParallel);
}
@@ -359,33 +359,33 @@ RigidBodyModel2::integrate()
StdVectorOfVec3d& torques = getCurrentState()->getTorques();
ParallelUtils::parallelFor(positions.size(), [&](const size_t& i)
+ {
+ if (!isStatic[i])
{
- if (!isStatic[i])
+ velocities[i] += forces[i] * invMasses[i] * dt;
+ velocities[i] *= velocityDamping;
+ angularVelocities[i] += invInteriaTensors[i] * torques[i] * dt;
+ angularVelocities[i] *= angularVelocityDamping;
+ positions[i] += velocities[i] * dt;
{
- velocities[i] += forces[i] * invMasses[i] * dt;
- velocities[i] *= velocityDamping;
- angularVelocities[i] += invInteriaTensors[i] * torques[i] * dt;
- angularVelocities[i] *= angularVelocityDamping;
- positions[i] += velocities[i] * dt;
- {
- const Quatd q = Quatd(0.0,
+ const Quatd q = Quatd(0.0,
angularVelocities[i][0],
angularVelocities[i][1],
angularVelocities[i][2]) * orientations[i];
- orientations[i].x() += q.x() * dt;
- orientations[i].y() += q.y() * dt;
- orientations[i].z() += q.z() * dt;
- orientations[i].w() += q.w() * dt;
- orientations[i].normalize();
- }
+ orientations[i].x() += q.x() * dt;
+ orientations[i].y() += q.y() * dt;
+ orientations[i].z() += q.z() * dt;
+ orientations[i].w() += q.w() * dt;
+ orientations[i].normalize();
}
+ }
- // Reset
- m_bodies[i]->m_prevForce = forces[i];
- forces[i] = Vec3d(0.0, 0.0, 0.0);
- torques[i] = Vec3d(0.0, 0.0, 0.0);
- tentativeVelocities[i] = velocities[i];
- tentativeAngularVelocities[i] = angularVelocities[i];
+ // Reset
+ m_bodies[i]->m_prevForce = forces[i];
+ forces[i] = Vec3d(0.0, 0.0, 0.0);
+ torques[i] = Vec3d(0.0, 0.0, 0.0);
+ tentativeVelocities[i] = velocities[i];
+ tentativeAngularVelocities[i] = angularVelocities[i];
}, positions.size() > m_maxBodiesParallel);
}
diff --git a/Source/DynamicalModels/ObjectModels/imstkSPHHemorrhage.cpp b/Source/DynamicalModels/ObjectModels/imstkSPHHemorrhage.cpp
deleted file mode 100644
index 44522b8cfcf21e1eeff270b3405499ea149d29ad..0000000000000000000000000000000000000000
--- a/Source/DynamicalModels/ObjectModels/imstkSPHHemorrhage.cpp
+++ /dev/null
@@ -1,53 +0,0 @@
-/*=========================================================================
-
-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.
-
-=========================================================================*/
-
-#include "imstkSPHHemorrhage.h"
-
-namespace imstk
-{
-SPHHemorrhage::SPHHemorrhage(const Vec3d& center, const double radius, const double area, const Vec3d& normal) :
- m_area(area), m_center(center), m_normal(normal.normalized()), m_radius(radius)
-{
-}
-
-bool
-SPHHemorrhage::pointCrossedHemorrhagePlane(const Vec3d& oldPosition, const Vec3d& newPosition)
-{
- // todo - loop through points that are near hemorrhage plane instead of all points
- const double dist = m_normal.dot(newPosition - m_center);
-
- if (m_normal.dot(oldPosition - m_center) < 0 && dist > 0)
- {
- // particle has crossed plane in the correct direction
- // however, we still need to determine if the particle is in the domain of the hemorrhage area
- // project point onto plane
- const Vec3d pointOnPlane = newPosition - dist * m_normal;
- // check if point is farther than radius from center point
- const double distFromCenter = (pointOnPlane - m_center).norm();
-
- if (distFromCenter <= m_radius)
- {
- return true;
- }
- }
- return false;
-}
-} // end namespace imstk
diff --git a/Source/DynamicalModels/ObjectModels/imstkSPHHemorrhage.h b/Source/DynamicalModels/ObjectModels/imstkSPHHemorrhage.h
deleted file mode 100644
index a924aa971ae4125596ef5f8a4701b5c590b6bb8a..0000000000000000000000000000000000000000
--- a/Source/DynamicalModels/ObjectModels/imstkSPHHemorrhage.h
+++ /dev/null
@@ -1,70 +0,0 @@
-/*=========================================================================
-
- 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.
-
-=========================================================================*/
-
-#pragma once
-
-#include "imstkMath.h"
-
-namespace imstk
-{
-///
-/// \class SPHHemorrhage
-/// \brief Class that holds methods and members for hemorrhage model
-///
-class SPHHemorrhage
-{
-public:
- // constructor
- SPHHemorrhage(const Vec3d& center, const double radius, const double area, const Vec3d& normal);
-
- ///
- /// \brief Determine if fluid particle crossed the hemorrhage plane
- ///
- bool pointCrossedHemorrhagePlane(const Vec3d& oldPosition, const Vec3d& newPosition);
-
- ///
- /// \brief Get the outward normal to the hemorrhage plane
- ///
- const Vec3d getNormal() { return m_normal; }
-
- ///
- /// \brief Get the area of the hemorrhage plane
- ///
- const double getHemorrhagePlaneArea() { return m_area; }
-
- ///
- /// \brief Get the rate of hemorrhage from SPH
- ///
- const double getHemorrhageRate() { return m_hemorrhageRate; }
-
- ///
- /// \brief Set the rate of hemorrhage from SPH
- ///
- void setHemorrhageRate(const double hemorrhageRate) { m_hemorrhageRate = hemorrhageRate; }
-
-private:
- double m_area; ///> cross-sectional area of hemorrhage plane
- Vec3d m_center; ///> hemorrhage plane center
- double m_hemorrhageRate = 0; ///> rate of hemorrhage
- Vec3d m_normal; ///> outward unit normal of hemorrhage plane
- double m_radius; ///> hemorrhage plane radius
-};
-} // end namespace imstk
diff --git a/Source/DynamicalModels/ObjectModels/imstkSPHModel.cpp b/Source/DynamicalModels/ObjectModels/imstkSPHModel.cpp
index c3eb5af92d85c0c512e4c90edf01841a066e52b7..282e3a6da357df73d8332c1ec632c7c997b7d354 100644
--- a/Source/DynamicalModels/ObjectModels/imstkSPHModel.cpp
+++ b/Source/DynamicalModels/ObjectModels/imstkSPHModel.cpp
@@ -198,11 +198,6 @@ SPHModel::initialize()
m_pointSetGeometry->setVertexAttribute("Normals", m_currentState->getNormals());
m_pointSetGeometry->setVertexAttribute("Accels", m_currentState->getAccelerations());
- if (m_geomUnstructuredGrid)
- {
- m_minIndices.resize(m_geomUnstructuredGrid->getNumVertices());
- }
-
return true;
}
@@ -769,29 +764,7 @@ SPHModel::moveParticles(const Real timestep)
m_sphBoundaryConditions->getBufferIndices().push_back(p);
}
}
-
- if (m_SPHHemorrhage && m_SPHHemorrhage->pointCrossedHemorrhagePlane(oldPosition, newPosition))
- {
- averageVelThroughHemorrhage += m_SPHHemorrhage->getNormal() * fullStepVelocities[p].dot(m_SPHHemorrhage->getNormal());
- numParticlesAcrossHemorrhagePlane++;
- }
- }
-
- if (m_SPHHemorrhage)
- {
- if (numParticlesAcrossHemorrhagePlane > 0)
- {
- averageVelThroughHemorrhage /= numParticlesAcrossHemorrhagePlane;
- }
- else
- {
- averageVelThroughHemorrhage = m_prevAvgVelThroughHemorrhage;
- }
- m_prevAvgVelThroughHemorrhage = averageVelThroughHemorrhage;
- const double hemorrhageFlowRate = averageVelThroughHemorrhage.norm() * m_SPHHemorrhage->getHemorrhagePlaneArea();
- m_SPHHemorrhage->setHemorrhageRate(hemorrhageFlowRate);
}
- m_totalTime += m_dt;
m_timeStepCount++;
}
@@ -844,52 +817,4 @@ SPHModel::findNearestParticleToVertex(const VecDataArray<double, 3>& points, con
m_minIndices[i] = minIndex;
}
}
-
-void
-SPHModel::writeStateToVtk()
-{
- if (!m_geomUnstructuredGrid)
- {
- return;
- }
-
- if (m_vtkPreviousTime <= m_vtkTimeModulo && m_totalTime >= m_vtkTimeModulo)
- {
- LOG(INFO) << "Writing VTK at time: " << m_totalTime;
- const VecDataArray<double, 3>& particleVelocities = *getCurrentState()->getFullStepVelocities();
- const DataArray<double>& particleDensities = *getCurrentState()->getDensities();
-
- std::shared_ptr<VecDataArray<double, 3>> velocityPtr = std::make_shared<VecDataArray<double, 3>>();
- VecDataArray<double, 3>& velocity = *velocityPtr;
- std::shared_ptr<DataArray<double>> pressurePtr = std::make_shared<DataArray<double>>();
- DataArray<double>& pressure = *pressurePtr;
- std::shared_ptr<DataArray<double>> densityPtr = std::make_shared<DataArray<double>>();
- DataArray<double>& density = *densityPtr;
-
- velocity.reserve(static_cast<int>(m_geomUnstructuredGrid->getNumVertices()));
- pressure.reserve(static_cast<int>(m_geomUnstructuredGrid->getNumVertices()));
- density.reserve(static_cast<int>(m_geomUnstructuredGrid->getNumVertices()));
-
- std::vector<std::vector<size_t>> result;
- m_neighborSearcher->getNeighbors(result, *m_geomUnstructuredGrid->getInitialVertexPositions(), *getCurrentState()->getPositions());
- findNearestParticleToVertex(*m_geomUnstructuredGrid->getInitialVertexPositions(), result);
-
- for (auto i : m_minIndices)
- {
- velocity.push_back(particleVelocities[i]);
- density.push_back(particleDensities[i]);
- pressure.push_back(particlePressure(particleDensities[i]));
- }
- m_geomUnstructuredGrid->setVertexAttribute("velocity", velocityPtr);
- m_geomUnstructuredGrid->setVertexAttribute("pressure", pressurePtr);
- m_geomUnstructuredGrid->setVertexAttribute("density", densityPtr);
-
- VTKMeshIO vtkWriter;
- std::string filePath = std::string("sph_output_") + std::to_string(m_totalTime) + std::string(".vtu");
- vtkWriter.write(m_geomUnstructuredGrid, filePath, MeshFileType::VTU);
-
- m_vtkTimeModulo += m_writeToOutputModulo;
- m_vtkPreviousTime = m_totalTime;
- }
-}
} // end namespace imstk
diff --git a/Source/DynamicalModels/ObjectModels/imstkSPHModel.h b/Source/DynamicalModels/ObjectModels/imstkSPHModel.h
index 08ab7455c37567f148792f661c4d1ae0bf4402f1..9181d1ebc32b09b845b5c58fc1a5ed09a9c52383 100644
--- a/Source/DynamicalModels/ObjectModels/imstkSPHModel.h
+++ b/Source/DynamicalModels/ObjectModels/imstkSPHModel.h
@@ -26,8 +26,6 @@
#include "imstkSPHKernels.h"
#include "imstkNeighborSearch.h"
#include "imstkSPHBoundaryConditions.h"
-#include "imstkSPHHemorrhage.h"
-#include "imstkTetrahedralMesh.h"
namespace imstk
{
@@ -157,19 +155,11 @@ public:
/// \brief Write the state to external file
/// \todo move this out of this class
///
- void setWriteToOutputModulo(const double modulo) { m_writeToOutputModulo = modulo; }
- double getTotalTime() const { return m_totalTime; }
- int getTimeStepCount() const { return m_timeStepCount; }
- void writeStateToVtk();
- void setGeometryMesh(std::shared_ptr<TetrahedralMesh>& geometryMesh) { m_geomUnstructuredGrid = geometryMesh; }
void findNearestParticleToVertex(const VecDataArray<double, 3>& points, const std::vector<std::vector<size_t>>& indices);
void setBoundaryConditions(std::shared_ptr<SPHBoundaryConditions> sphBoundaryConditions) { m_sphBoundaryConditions = sphBoundaryConditions; }
std::shared_ptr<SPHBoundaryConditions> getBoundaryConditions() { return m_sphBoundaryConditions; }
- void setHemorrhageModel(std::shared_ptr<SPHHemorrhage> sPHHemorrhage) { m_SPHHemorrhage = sPHHemorrhage; }
- std::shared_ptr<SPHHemorrhage> getHemorrhageModel() { return m_SPHHemorrhage; }
-
void setRestDensity(const Real restDensity) { m_modelParameters->m_restDensity = restDensity; }
std::shared_ptr<TaskNode> getFindParticleNeighborsNode() const { return m_findParticleNeighborsNode; }
@@ -293,19 +283,9 @@ private:
std::shared_ptr<VecDataArray<double, 3>> m_initialVelocities = nullptr;
std::shared_ptr<DataArray<double>> m_initialDensities = nullptr;
- double m_totalTime = 0;
- int m_timeStepCount = 0;
- double m_writeToOutputModulo = 0;
- double m_vtkPreviousTime = 0;
- double m_vtkTimeModulo = 0;
- double m_csvPreviousTime = 0;
- double m_csvTimeModulo = 0;
- Vec3d m_prevAvgVelThroughHemorrhage = Vec3d(0., 0., 0.);
+ int m_timeStepCount = 0;
- std::shared_ptr<TetrahedralMesh> m_geomUnstructuredGrid = nullptr;
std::shared_ptr<SPHBoundaryConditions> m_sphBoundaryConditions = nullptr;
- // \todo: Should be refactored out of the base SPHModel
- std::shared_ptr<SPHHemorrhage> m_SPHHemorrhage = nullptr;
std::vector<size_t> m_minIndices;
};
diff --git a/Source/Pulse/CMakeLists.txt b/Source/Pulse/CMakeLists.txt
deleted file mode 100644
index d180f45dafea057baeb310c0f56fb22f856c4cee..0000000000000000000000000000000000000000
--- a/Source/Pulse/CMakeLists.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-#-----------------------------------------------------------------------------
-# Create target
-#-----------------------------------------------------------------------------
-if(iMSTK_USE_Pulse)
- include(imstkAddLibrary)
- imstk_add_library( Pulse
- DEPENDS
- Scene
- Pulse::CommonPulseModels)
-endif()
\ No newline at end of file
diff --git a/Source/Pulse/imstkHemorrhageAction.cpp b/Source/Pulse/imstkHemorrhageAction.cpp
deleted file mode 100644
index a95059e69748df0d0ecf9fe937d339c3ea676a69..0000000000000000000000000000000000000000
--- a/Source/Pulse/imstkHemorrhageAction.cpp
+++ /dev/null
@@ -1,96 +0,0 @@
-/*=========================================================================
-
-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.
-
-=========================================================================*/
-
-#include "imstkHemorrhageAction.h"
-
-#include "PulsePhysiologyEngine.h"
-#include "CommonDataModel.h"
-#include "engine/SEEngineTracker.h"
-#include "engine/SEDataRequest.h"
-#include "engine/SEDataRequestManager.h"
-#include "engine/SEAction.h"
-#include "utils/DataTrack.h"
-#include "patient/actions/SEHemorrhage.h"
-#include "properties/SEScalarVolumePerTime.h"
-#include "compartment/SECompartmentManager.h"
-
-#include "properties/SEScalarTime.h"
-#include "engine/SEEngineTracker.h"
-#include "compartment/SECompartmentManager.h"
-#include "patient/actions/SESubstanceCompoundInfusion.h"
-#include "system/physiology/SEBloodChemistrySystem.h"
-#include "system/physiology/SECardiovascularSystem.h"
-#include "system/physiology/SEEnergySystem.h"
-#include "system/physiology/SERespiratorySystem.h"
-#include "substance/SESubstanceManager.h"
-#include "substance/SESubstanceCompound.h"
-#include "properties/SEScalar0To1.h"
-#include "properties/SEScalarFrequency.h"
-#include "properties/SEScalarMass.h"
-#include "properties/SEScalarMassPerVolume.h"
-#include "properties/SEScalarPressure.h"
-#include "properties/SEScalarTemperature.h"
-#include "properties/SEScalarTime.h"
-#include "properties/SEScalarVolume.h"
-#include "properties/SEScalarVolumePerTime.h"
-#include "properties/SEScalarVolumePerTimeArea.h"
-#include "compartment/fluid/SELiquidCompartmentGraph.h"
-
-namespace imstk
-{
-HemorrhageAction::HemorrhageAction(const Type t, const std::string& name)
-{
- m_hemorrhage = std::make_shared<SEHemorrhage>();
- this->setType(t);
- this->SetCompartment("pulse::" + name);
-}
-
-void
-HemorrhageAction::setRate(double val /*in milliLiters/sec*/)
-{
- m_hemorrhage->GetRate().SetValue(val, VolumePerTimeUnit::mL_Per_s);
-}
-
-void
-HemorrhageAction::setType(const Type t)
-{
- (t == Type::External) ? m_hemorrhage->SetType(eHemorrhage_Type::External) :
- m_hemorrhage->SetType(eHemorrhage_Type::External);
-}
-
-void
-HemorrhageAction::SetCompartment(const std::string& name)
-{
- m_hemorrhage->SetCompartment(name);
-}
-
-double
-HemorrhageAction::getRate() const
-{
- return m_hemorrhage->GetRate().GetValue(VolumePerTimeUnit::mL_Per_s);
-}
-
-std::shared_ptr<SEPatientAction>
-HemorrhageAction::getAction()
-{
- return std::dynamic_pointer_cast<SEPatientAction>(m_hemorrhage);
-}
-}
\ No newline at end of file
diff --git a/Source/Pulse/imstkHemorrhageAction.h b/Source/Pulse/imstkHemorrhageAction.h
deleted file mode 100644
index 67aac34aab683d107e3ee5304d828931e45d2352..0000000000000000000000000000000000000000
--- a/Source/Pulse/imstkHemorrhageAction.h
+++ /dev/null
@@ -1,68 +0,0 @@
-/*=========================================================================
-
-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.
-
-=========================================================================*/
-
-#pragma once
-
-#include "imstkPhysiologyModel.h"
-
-class SEHemorrhage;
-
-namespace imstk
-{
-class HemorrhageAction : public PhysiologyAction
-{
-public:
- enum class Type { External = 0, Internal };
-
- HemorrhageAction(const Type t, const std::string& name);
-
-public:
- ///
- /// \brief Set the rate of hemorrhage
- ///
- void setRate(double val /*in milliLiters/sec*/);
-
- ///
- /// \brief Set the rate of hemorrhage
- ///
- void setType(const Type t);
-
- ///
- /// \brief Set the vascular compartment for hemorrhage
- /// The string is expected to be pulse::VascularCompartment::<name_of_compartment>
- /// (Refer: PulsePhysiologyEngine.h)
- ///
- void SetCompartment(const std::string& name);
-
- ///
- /// \brief Get the rate of hemorrhage in milliLiters/sec
- ///
- double getRate() const;
-
- ///
- /// \brief
- ///
- std::shared_ptr<SEPatientAction> getAction();
-
-protected:
- std::shared_ptr<SEHemorrhage> m_hemorrhage;
-};
-}
\ No newline at end of file
diff --git a/Source/Pulse/imstkPhysiologyModel.cpp b/Source/Pulse/imstkPhysiologyModel.cpp
deleted file mode 100644
index 4215155d5ac89572ff9b61fdeed163251928d821..0000000000000000000000000000000000000000
--- a/Source/Pulse/imstkPhysiologyModel.cpp
+++ /dev/null
@@ -1,123 +0,0 @@
-/*=========================================================================
-
-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.
-
-=========================================================================*/
-
-#include "imstkPhysiologyModel.h"
-#include "imstkLogger.h"
-#include "imstkTaskGraph.h"
-
-// Pulse
-#include <PulsePhysiologyEngine.h>
-#include <engine/SEEngineTracker.h>
-#include <engine/SEDataRequestManager.h>
-#include <patient/actions/SEHemorrhage.h>
-#include <compartment/SECompartmentManager.h>
-
-namespace imstk
-{
-PhysiologyModel::PhysiologyModel() : AbstractDynamicalModel(DynamicalModelType::Physiology)
-{
- m_solveNode = m_taskGraph->addFunction("PhysiologyModel_Solve", std::bind(&PhysiologyModel::solve, this));
-}
-
-bool
-PhysiologyModel::initialize()
-{
- // Create the engine and load the patient
- m_pulseObj = CreatePulseEngine();
- m_pulseObj->GetLogger()->LogToConsole(m_config->m_enableLogging);
-
- std::string patientFile;
- switch (m_config->m_basePatient)
- {
- case PatientPhysiology::StandardMale:
- patientFile = iMSTK_DATA_ROOT "/PhysiologyState/StandardMale@0s.pbb";
- break;
- case PatientPhysiology::StandardFemale:
- patientFile = iMSTK_DATA_ROOT "/PhysiologyState/StandardFemale.json";
- break;
- default:
- LOG(WARNING) << "Could not find the patient. Initializing to StandardMale";
- patientFile = iMSTK_DATA_ROOT "/PhysiologyStates/StandardMale.json";
- }
-
- CHECK(m_pulseObj->SerializeFromFile(patientFile)) << "Could not load Pulse state file.";
-
- // Submit data requests
- for (auto dataPair : m_dataPairs)
- {
- m_pulseObj->GetEngineTracker()->GetDataRequestManager().CreatePhysiologyDataRequest(dataPair.first, dataPair.second);
- }
-
- return true;
-}
-
-void
-PhysiologyModel::addDataRequest(const std::string& property, SEDecimalFormat* dfault /*= nullptr*/)
-{
- m_dataPairs.push_back(PhysiologyDataRequestPair(property, dfault));
-}
-
-const SECompartment*
-PhysiologyModel::getCompartment(const PhysiologyCompartmentType type, const std::string& compartmentName) const
-{
- switch (type)
- {
- case PhysiologyCompartmentType::Gas:
- return (SECompartment*)m_pulseObj->GetCompartments().GetGasCompartment(compartmentName);
- break;
- case PhysiologyCompartmentType::Liquid:
- return (SECompartment*)m_pulseObj->GetCompartments().GetLiquidCompartment(compartmentName);
- break;
- case PhysiologyCompartmentType::Thermal:
- return (SECompartment*)m_pulseObj->GetCompartments().GetThermalCompartment(compartmentName);
- break;
- case PhysiologyCompartmentType::Tissue:
- return (SECompartment*)m_pulseObj->GetCompartments().GetTissueCompartment(compartmentName);
- break;
- default:
- LOG(WARNING) << "Could not find the compartment type";
- return nullptr;
- }
-}
-
-void
-PhysiologyModel::solve()
-{
- // Process all actions that are currently stored
- for (auto i : m_actions)
- {
- m_pulseObj->ProcessAction(*i.second->getAction().get());
- }
-
- // Advance physiology model in time
- m_pulseObj->AdvanceModelTime(m_config->m_timeStep, TimeUnit::s);
-
- m_currentTime += m_config->m_timeStep;
-}
-
-void
-PhysiologyModel::initGraphEdges(std::shared_ptr<TaskNode> source, std::shared_ptr<TaskNode> sink)
-{
- // Setup graph connectivity
- m_taskGraph->addEdge(source, m_solveNode);
- m_taskGraph->addEdge(m_solveNode, sink);
-}
-}// imstk
diff --git a/Source/Pulse/imstkPhysiologyModel.h b/Source/Pulse/imstkPhysiologyModel.h
deleted file mode 100644
index 47156a177ff19d451907d7311e6c007fe5136cb2..0000000000000000000000000000000000000000
--- a/Source/Pulse/imstkPhysiologyModel.h
+++ /dev/null
@@ -1,186 +0,0 @@
-/*=========================================================================
-
- 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.
-
-=========================================================================*/
-
-#pragma once
-
-#include <unordered_map>
-
-#include "imstkAbstractDynamicalModel.h"/*
-#include "properties/SEScalarVolumePerTime.h"
-#include "compartment/fluid/SELiquidCompartment.h"*/
-
-class PhysiologyEngine;
-class SELiquidCompartment;
-class SEDecimalFormat;
-class SEPatientAction;
-class VolumePerTimeUnit;
-class SECompartment;
-
-namespace imstk
-{
-using PhysiologyDataRequestPair = std::pair<std::string, SEDecimalFormat*>;
-
-enum class PatientPhysiology
-{
- StandardMale=0,
- StandardFemale
-};
-
-enum class PhysiologyCompartmentType
-{
- Gas = 0,
- Liquid,
- Thermal,
- Tissue
-};
-
-class PhysiologyAction
-{
-public:
- virtual std::shared_ptr<SEPatientAction> getAction() = 0;
-};
-
-///
-/// \struct PhysiologyModelConfig
-/// \brief Contains physiology model settings
-///
-struct PhysiologyModelConfig
-{
- PatientPhysiology m_basePatient = PatientPhysiology::StandardMale;
-
- double m_timeStep = 0.02; ///< Pulse time step
- bool m_enableLogging = false; ///< Enable Pulse engine logging
-};
-
-///
-/// \class PhysiologyModel
-/// \brief Human physiology dynamical model
-///
-class PhysiologyModel : public AbstractDynamicalModel
-{
-public:
- ///
- /// \brief Constructor
- ///
- PhysiologyModel();
-
- ///
- /// \brief Destructor
- ///
- virtual ~PhysiologyModel() override = default;
-
- ///
- /// \brief Set simulation parameters
- ///
- void configure(const std::shared_ptr<PhysiologyModelConfig>& params) { m_config = params; }
-
- ///
- /// \brief Initialize the dynamical model
- ///
- virtual bool initialize() override;
-
- ///
- /// \brief Get the solver task node
- ///
- std::shared_ptr<TaskNode> getSolveNode() const { return m_solveNode; }
-
- ///
- /// \brief Update states
- ///
- virtual void updateBodyStates(const Vectord&, const StateUpdateType) override {}
-
- ///
- /// \brief Set the default time step size,
- /// valid only if using a fixed time step for integration
- ///
- void setDefaultTimeStep(const Real) {}
-
- ///
- /// \brief Reset the physiology model to the initial state
- ///
- virtual void resetToInitialState() override {};
-
- ///
- /// \brief Add a data request that to output vitals to CSV files
- ///
- void addDataRequest(const std::string& property, SEDecimalFormat* dfault = nullptr);
-
- ///
- /// \brief Returns the time step size
- ///
- virtual double getTimeStep() const override { return m_config->m_timeStep; }
-
- ///
- /// \brief Set the time step of the pulse solver
- ///
- virtual void setTimeStep(const double t) override { m_config->m_timeStep = t; }
-
- ///
- /// \brief Add a new action
- ///
- void addAction(std::string name, std::shared_ptr<PhysiologyAction> action) { m_actions[name] = action; };
-
- std::shared_ptr<PhysiologyAction> getAction(std::string name) const { return (m_actions.count(name) == 0) ? nullptr : m_actions.at(name); }
-
- ///
- /// \brief Clear all actions
- ///
- void clearActions() { m_actions.clear(); }
-
- ///
- /// \brief Set the name of the file to write out the data requests
- ///
- void setDataWriteOutFileName(const std::string& filename) { m_dataWriteOutFile = filename; }
-
- ///
- /// \brief Get the physiology compartment model of the body
- ///
- const SECompartment* getCompartment(const PhysiologyCompartmentType type, const std::string& compartmentName) const;
-
-protected:
- ///
- /// \brief Setup physiology compute graph connectivity
- ///
- virtual void initGraphEdges(std::shared_ptr<TaskNode> source, std::shared_ptr<TaskNode> sink) override;
-
- ///
- /// \brief Advance one time step of the pulse engine solver
- ///
- void solve();
-
- std::shared_ptr<TaskNode> m_solveNode = nullptr;
-
- std::unordered_map<std::string, std::shared_ptr<PhysiologyAction>> m_actions; ///< container for all the actions
- std::vector<PhysiologyDataRequestPair> m_dataPairs; ///< container for data requests
-
-private:
- // main pulse object
- std::unique_ptr<PhysiologyEngine> m_pulseObj = nullptr;
-
- double m_currentTime = 0.; ///< Current total time (incremented every solve)
-
- std::string m_dataWriteOutFile = "pulseVitals.csv";
-
- // Physiology Model parameters (must be set before simulation)
- // empty for now but can be set if needed
- std::shared_ptr<PhysiologyModelConfig> m_config;
-};
-} // end namespace imstk
diff --git a/Source/Pulse/imstkPhysiologyObject.cpp b/Source/Pulse/imstkPhysiologyObject.cpp
deleted file mode 100644
index b792a785ae53254a0fadc155cc0cc2449ded1cd1..0000000000000000000000000000000000000000
--- a/Source/Pulse/imstkPhysiologyObject.cpp
+++ /dev/null
@@ -1,55 +0,0 @@
-/*=========================================================================
-
- 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.
-
-=========================================================================*/
-
-#include "imstkPhysiologyObject.h"
-#include "imstkLogger.h"
-#include "imstkPhysiologyModel.h"
-
-namespace imstk
-{
-PhysiologyObject::PhysiologyObject(const std::string& name) : DynamicObject(name)
-{
- this->m_type = Type::Physiology;
-}
-
-std::shared_ptr<PhysiologyModel>
-PhysiologyObject::getPhysiologyModel()
-{
- m_PhysiologyModel = std::dynamic_pointer_cast<PhysiologyModel>(m_dynamicalModel);
- return m_PhysiologyModel;
-};
-
-bool
-PhysiologyObject::initialize()
-{
- m_PhysiologyModel = std::dynamic_pointer_cast<PhysiologyModel>(m_dynamicalModel);
- if (m_PhysiologyModel == nullptr)
- {
- LOG(FATAL) << "Dynamics pointer cast failure in SPHObject::initialize()";
- return false;
- }
-
- DynamicObject::initialize();
- m_PhysiologyModel->initialize();
-
- return true;
-}
-} // end namespace imstk
diff --git a/Source/Pulse/imstkPhysiologyObject.h b/Source/Pulse/imstkPhysiologyObject.h
deleted file mode 100644
index 5fa31e1feb9cf94dfe52648310357ad7ccf0522c..0000000000000000000000000000000000000000
--- a/Source/Pulse/imstkPhysiologyObject.h
+++ /dev/null
@@ -1,53 +0,0 @@
-/*=========================================================================
-
- 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.
-
-=========================================================================*/
-
-#pragma once
-
-#include "imstkDynamicObject.h"
-
-namespace imstk
-{
-class PhysiologyModel;
-
-///
-/// \class PhysiologyObject
-///
-/// \brief Base class for Physiology objects
-///
-class PhysiologyObject : public DynamicObject
-{
-public:
- explicit PhysiologyObject(const std::string& name);
-
- virtual ~PhysiologyObject() override = default;
-
-public:
- ///
- /// \brief Initialize the Physiology scene object
- ///
- bool initialize() override;
-
- std::shared_ptr<PhysiologyModel> getPhysiologyModel();
-
-protected:
- std::shared_ptr<PhysiologyModel> m_PhysiologyModel = nullptr;
-};
-} // end namespace imstk
diff --git a/Source/Pulse/imstkSPHPhysiologyInteraction.cpp b/Source/Pulse/imstkSPHPhysiologyInteraction.cpp
deleted file mode 100644
index c008c2473f404afd76f665104edefaf07d2612cb..0000000000000000000000000000000000000000
--- a/Source/Pulse/imstkSPHPhysiologyInteraction.cpp
+++ /dev/null
@@ -1,107 +0,0 @@
-/*=========================================================================
-
-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.
-
-=========================================================================*/
-
-#include "imstkSPHPhysiologyInteraction.h"
-#include "imstkHemorrhageAction.h"
-#include "imstkPhysiologyObject.h"
-#include "imstkSPHModel.h"
-#include "imstkSPHObject.h"
-#include "imstkTaskGraph.h"
-
-// Pulse
-#include <PulsePhysiologyEngine.h>
-#include <compartment/fluid/SELiquidCompartmentGraph.h>
-
-namespace imstk
-{
-SPHPhysiologyObjectInteractionPair::SPHPhysiologyObjectInteractionPair(
- std::shared_ptr<SPHObject> obj1,
- std::shared_ptr<PhysiologyObject> obj2) :
- ObjectInteractionPair(obj1, obj2)
-{
- m_sphModel = obj1->getDynamicalSPHModel();
- m_physiologyModel = obj2->getPhysiologyModel();
-
- // Define where the boundary condition happens
- m_bcNode = std::make_shared<TaskNode>([&]() { computeInteraction(); },
- obj1->getName() + "_vs_" + obj2->getName() + "_boundaryCondition", true);
-
- // Define where solver interaction happens
- m_solveNodeInputs.first.push_back(m_sphModel->getTaskGraph()->getSource());
- m_solveNodeInputs.second.push_back(m_physiologyModel->getTaskGraph()->getSource());
-
- m_solveNodeOutputs.first.push_back(m_sphModel->getFindParticleNeighborsNode());
- m_solveNodeOutputs.second.push_back(m_physiologyModel->getSolveNode());
-}
-
-void
-SPHPhysiologyObjectInteractionPair::computeInteraction()
-{
- std::shared_ptr<SPHHemorrhage> hemorrhageModel = m_sphModel->getHemorrhageModel();
- const SELiquidCompartment* compartment = (SELiquidCompartment*)m_physiologyModel->getCompartment(m_compartmentType, m_compartmentName);
-
- // check if the hemorrhage is being used in SPH
- if (hemorrhageModel != nullptr && m_hemorrhageAction != nullptr && compartment != nullptr)
- {
- // compute the hemorrhage flow rate
- const double hemorrhageRate = m_sphModel->getHemorrhageModel()->getHemorrhageRate();
-
- // set the hemorrhage flow rate in Pulse
- m_hemorrhageAction->setRate(hemorrhageRate);
-
- // compute the femoral flow rate from Pulse
- const double flowRate = compartment->GetInFlow(VolumePerTimeUnit::mL_Per_s);
-
- // set the femoral flow rate as an SPH inlet boundary condition
- m_sphModel->getBoundaryConditions()->setInletVelocity(flowRate);
-
- // set how much time to run Pulse for
- m_physiologyModel->setTimeStep(m_sphModel->getTimeStep());
- }
-}
-
-void
-SPHPhysiologyObjectInteractionPair::apply()
-{
- // Add the SPH physiology interaction node to the task graph
- m_objects.first->getTaskGraph()->addNode(m_bcNode);
- m_objects.second->getTaskGraph()->addNode(m_bcNode);
-
- // Add the edges to the task graph
- for (size_t i = 0; i < m_solveNodeInputs.first.size(); i++)
- {
- m_objects.first->getTaskGraph()->addEdge(m_solveNodeInputs.first[i], m_bcNode);
- }
- for (size_t i = 0; i < m_solveNodeInputs.second.size(); i++)
- {
- m_objects.second->getTaskGraph()->addEdge(m_solveNodeInputs.second[i], m_bcNode);
- }
-
- for (size_t i = 0; i < m_solveNodeOutputs.first.size(); i++)
- {
- m_objects.first->getTaskGraph()->addEdge(m_bcNode, m_solveNodeOutputs.first[i]);
- }
- for (size_t i = 0; i < m_solveNodeOutputs.second.size(); i++)
- {
- m_objects.second->getTaskGraph()->addEdge(m_bcNode, m_solveNodeOutputs.second[i]);
- }
-}
-}
\ No newline at end of file
diff --git a/Source/Pulse/imstkSPHPhysiologyInteraction.h b/Source/Pulse/imstkSPHPhysiologyInteraction.h
deleted file mode 100644
index 7faa274b56d415577166163296fc702ece8b8208..0000000000000000000000000000000000000000
--- a/Source/Pulse/imstkSPHPhysiologyInteraction.h
+++ /dev/null
@@ -1,80 +0,0 @@
-/*=========================================================================
-
-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.
-
-=========================================================================*/
-
-#pragma once
-
-#include "imstkCollisionPair.h"
-#include "imstkPhysiologyModel.h"
-
-namespace imstk
-{
-class SPHObject;
-class PhysiologyObject;
-class SPHModel;
-class HemorrhageAction;
-
-///
-/// \class SPHPhysiologyObjectInteractionPair
-///
-/// \brief This class defines an interaction between SPH and physiology (Pulse)
-///
-class SPHPhysiologyObjectInteractionPair : public ObjectInteractionPair
-{
-public:
- SPHPhysiologyObjectInteractionPair(std::shared_ptr<SPHObject> obj1, std::shared_ptr<PhysiologyObject> obj2);
-
- virtual ~SPHPhysiologyObjectInteractionPair() override = default;
-
-public:
- void apply() override;
-
- ///
- /// \brief Computes hemorrhage interaction between SPH and physiology (Pulse)
- ///
- void computeInteraction();
-
- ///
- /// \brief Set the Pulse hemorrhage action that should be connected to the SPH hemorrhage model
- ///
- void setHemorrhageAction(std::shared_ptr<HemorrhageAction> hemorrhageAction) { m_hemorrhageAction = hemorrhageAction; }
-
- ///
- /// \brief Set the pulse compartment of the body where the hemorrhage is happening
- ///
- void setCompartment(const PhysiologyCompartmentType type, const std::string& compartmentName)
- {
- m_compartmentType = type;
- m_compartmentName = compartmentName;
- }
-
-private:
- Inputs m_solveNodeInputs;
- Outputs m_solveNodeOutputs;
- std::shared_ptr<SPHModel> m_sphModel = nullptr;
- std::shared_ptr<PhysiologyModel> m_physiologyModel = nullptr;
- std::shared_ptr<TaskNode> m_bcNode = nullptr;
-
- std::shared_ptr<HemorrhageAction> m_hemorrhageAction;
-
- PhysiologyCompartmentType m_compartmentType;
- std::string m_compartmentName;
-};
-}
\ No newline at end of file
diff --git a/Source/Scene/imstkRigidObjectCollisionPair.cpp b/Source/Scene/imstkRigidObjectCollisionPair.cpp
index c7f9241f9b2bfd8bf23e9a6e2322c099f783d1c5..0bb493f5066f459428f4b4c51eddc16483402289 100644
--- a/Source/Scene/imstkRigidObjectCollisionPair.cpp
+++ b/Source/Scene/imstkRigidObjectCollisionPair.cpp
@@ -90,8 +90,8 @@ RigidObjectCollisionPair::apply()
// 1.) Copy the vertices at the start of the frame
obj1->getTaskGraph()->insertBefore(obj1->getRigidBodyModel2()->getComputeTentativeVelocitiesNode(),
std::make_shared<TaskNode>([ = ]()
- {
- copyVertsToPrevious();
+ {
+ copyVertsToPrevious();
}, "CopyVertsToPrevious"));
// If you were to update to tentative, you'd do it here, then compute displacements
@@ -99,8 +99,8 @@ RigidObjectCollisionPair::apply()
// 2.) Compute the displacements after updating geometry
obj1->getTaskGraph()->insertAfter(obj1->getUpdateGeometryNode(),
std::make_shared<TaskNode>([ = ]()
- {
- measureDisplacementFromPrevious();
+ {
+ measureDisplacementFromPrevious();
}, "ComputeDisplacements"));
}
}
@@ -143,8 +143,8 @@ RigidObjectCollisionPair::measureDisplacementFromPrevious()
ParallelUtils::parallelFor(displacements->size(),
[&](const int i)
- {
- displacementsArr[i] = vertices[i] - prevVertices[i];
+ {
+ displacementsArr[i] = vertices[i] - prevVertices[i];
});
}
}
diff --git a/Source/Scene/imstkRigidObjectLevelSetCollisionPair.cpp b/Source/Scene/imstkRigidObjectLevelSetCollisionPair.cpp
index 7f18d2768948e019af4b5fd687ae20de34270670..3fb2e7d63ee793144c66c4c761399089a4a2a979 100644
--- a/Source/Scene/imstkRigidObjectLevelSetCollisionPair.cpp
+++ b/Source/Scene/imstkRigidObjectLevelSetCollisionPair.cpp
@@ -91,8 +91,8 @@ RigidObjectLevelSetCollisionPair::apply()
// 1.) Copy the vertices at the start of the frame
obj1->getTaskGraph()->insertBefore(obj1->getRigidBodyModel2()->getComputeTentativeVelocitiesNode(),
std::make_shared<TaskNode>([ = ]()
- {
- copyVertsToPrevious();
+ {
+ copyVertsToPrevious();
}, "CopyVertsToPrevious"));
// If you were to update to tentative, you'd do it here, then compute displacements
@@ -143,8 +143,8 @@ RigidObjectLevelSetCollisionPair::measureDisplacementFromPrevious()
ParallelUtils::parallelFor(displacements->size(),
[&](const int i)
- {
- displacementsArr[i] = vertices[i] - prevVertices[i];
+ {
+ displacementsArr[i] = vertices[i] - prevVertices[i];
});
}
}