Merge pull request #390 from favreau/master

Created USD (Universal Scene Description) file exporter (Work in progress)

Author: Cyrille Favreau

.gitmodules

@@ -13,3 +13,9 @@
 [submodule "platform/deps/MorphIO"]
 path = platform/deps/MorphIO
 url = https://github.com/BlueBrain/MorphIO.git
+[submodule "platform/deps/USD"]
+path = platform/deps/USD
+url = https://github.com/PixarAnimationStudios/USD.git
+[submodule "platform/deps/OpenSubdiv"]
+path = platform/deps/OpenSubdiv
+url = https://github.com/PixarAnimationStudios/OpenSubdiv.git

CMakeLists.txt

@@ -46,6 +46,8 @@ find_package(CGAL)
 find_package(LASlib OPTIONAL_COMPONENTS)
 find_package(MorphIO OPTIONAL_COMPONENTS)
 find_package(HighFive OPTIONAL_COMPONENTS)
+find_package(pxr)
+
 
 set(BIOEXPLORER_SOURCE_DIRS ${PROJECT_SOURCE_DIR} ${CMAKE_BINARY_DIR}/generated)
 
@@ -57,6 +59,10 @@ if(MorphIO_FOUND)
  message(STATUS "[Core] MorphIO module enabled")
 endif()
 
+if(pxr_FOUND)
+ message(STATUS "[Core] Pixar Universal Scene Description module enabled")
+endif()
+
 # Find the Intel C++ compiler
 find_program(CMAKE_CXX_COMPILER NAMES icpc)
 if(CMAKE_CXX_COMPILER)

README.md

@@ -197,6 +197,7 @@ References:
 * [Age and sex do not affect the volume, cell numbers, or cell size of the suprachiasmatic nucleus of the rat: An unbiased stereological](https://doi.org/10.1002/cne.903610404)
 * [Community-based Reconstruction and Simulation of a Full-scale Model of Region CA1 of Rat Hippocampus](https://www.biorxiv.org/content/10.1101/2023.05.17.541167v1)
 * [Modeling and Simulation of Neocortical Micro- and Mesocircuitry. Part II: Physiology and Experimentation](https://www.biorxiv.org/content/10.1101/2023.05.17.541168v2)
+* [Community-based reconstruction and simulation of a full-scale model of the rat hippocampus CA1 region](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002861)
 
 ### Astrocytes
 

bioexplorer/backend/CMakeLists.txt

@@ -62,6 +62,7 @@ set(${NAME}_SOURCES
  science/io/db/DBConnector.cpp
  science/io/cache/MemoryCache.cpp
  science/io/filesystem/MorphologyLoader.cpp
+ science/io/filesystem/USDExporter.cpp
  science/molecularsystems/EnzymeReaction.cpp
  science/molecularsystems/Molecule.cpp
  science/molecularsystems/Membrane.cpp
@@ -98,6 +99,7 @@ set(${NAME}_PUBLIC_HEADERS
  science/io/CacheLoader.h
  science/io/cache/MemoryCache.h
  science/io/filesystem/MorphologyLoader.h
+ science/io/filesystem/USDExporter.h
  science/io/db/DBConnector.h
  science/common/Assembly.h
  science/common/Node.h
@@ -169,6 +171,10 @@ if(MorphIO_FOUND)
  include_directories(${HDF5_INCLUDE_DIRS})
 endif()
 
+if(pxr_FOUND)
+ list(APPEND ${NAME}_PRIVATE_MODULE_LIBRARIES ${PXR_LIBRARIES})
+endif()
+
 # ==============================================================================
 # OSPRay module
 # ==============================================================================

bioexplorer/backend/plugins/Sonata/plugin/neuroscience/common/MorphologyLoader.cpp

@@ -750,21 +750,6 @@ void MorphologyLoader::_importMorphologyFromURI(const Gid& gid, const PropertyMa
  float srcRadius = _getCorrectedRadius(properties, srcDiameter);
  float dstRadius = _getCorrectedRadius(properties, dstDiameter);
 
-#if 0
- const float maxRadiusChange = 0.1f;
- if (sampleLength > 0.0001f && s != nbSamples - 1 &&
- dampenBranchThicknessChangerate)
- {
- const float radiusChange =
- std::min(std::abs(dstRadius - srcRadius),
- sampleLength * maxRadiusChange);
- if (srcRadius < dstRadius)
- srcRadius = dstRadius - radiusChange;
- else
- srcRadius = dstRadius + radiusChange;
- }
-#endif
-
  // Add Geometry
  if (s > 0)
  {
@@ -1161,8 +1146,7 @@ ModelDescriptorPtr MorphologyLoader::importFromStorage(const std::string& path,
  // the UI
  PropertyMap props = _defaults;
  props.merge(properties);
- // TODO: This needs to be done to work around wrong types coming from
- // the UI
+ // TODO: This needs to be done to work around wrong types coming from the UI
 
  auto model = _scene.createModel();
  auto modelContainer = importMorphology(0, props, path, 0, SynapsesInfo());

bioexplorer/backend/science/BioExplorerPlugin.cpp

@@ -35,6 +35,10 @@
 #include <science/morphologies/SpikeSimulationHandler.h>
 #include <science/vasculature/VasculatureLoader.h>
 
+#ifdef USE_PIXAR
+#include <science/io/filesystem/USDExporter.h>
+#endif // USE_PIXAR
+
 #include <platform/core/common/ActionInterface.h>
 #include <platform/core/common/Properties.h>
 #include <platform/core/common/scene/ClipPlane.h>
@@ -348,6 +352,13 @@ void BioExplorerPlugin::init()
  actionInterface->registerRequest<FileAccessDetails, Response>(endPoint, [&](const FileAccessDetails &payload)
  { return _exportToXYZ(payload); });
 
+#ifdef USE_PIXAR
+ endPoint = PLUGIN_API_PREFIX + "export-to-universal-scene-description-file";
+ PLUGIN_REGISTER_ENDPOINT(endPoint);
+ actionInterface->registerRequest<FileAccessDetails, Response>(endPoint, [&](const FileAccessDetails &payload)
+ { return _exportToUSDFile(payload); });
+#endif // USE_PIXAR
+
 #ifdef USE_LASLIB
  endPoint = PLUGIN_API_PREFIX + "export-to-las";
  PLUGIN_REGISTER_ENDPOINT(endPoint);
@@ -418,8 +429,7 @@ void BioExplorerPlugin::init()
  endPoint = PLUGIN_API_PREFIX + "get-model-transformation";
  PLUGIN_REGISTER_ENDPOINT(endPoint);
  actionInterface->registerRequest<ModelIdDetails, ModelTransformationDetails>(
- endPoint,
- [&](const ModelIdDetails &payload) -> ModelTransformationDetails
+ endPoint, [&](const ModelIdDetails &payload) -> ModelTransformationDetails
  { return _getModelTransformation(payload); });
 
  endPoint = PLUGIN_API_PREFIX + "get-model-bounds";
@@ -491,8 +501,7 @@ void BioExplorerPlugin::init()
 
  endPoint = PLUGIN_API_PREFIX + "get-vasculature-info";
  PLUGIN_REGISTER_ENDPOINT(endPoint);
- actionInterface->registerRequest<NameDetails, Response>(endPoint,
- [&](const NameDetails &payload) -> Response
+ actionInterface->registerRequest<NameDetails, Response>(endPoint, [&](const NameDetails &payload) -> Response
  { return _getVasculatureInfo(payload); });
 
  endPoint = PLUGIN_API_PREFIX + "set-vasculature-report";
@@ -1133,6 +1142,21 @@ Response BioExplorerPlugin::_exportToLas(const LASFileAccessDetails &payload)
 }
 #endif
 
+#ifdef USE_PIXAR
+Response BioExplorerPlugin::_exportToUSDFile(const FileAccessDetails &payload)
+{
+ Response response;
+ try
+ {
+ auto &scene = _api->getScene();
+ filesystem::USDExporter exporter(scene);
+ exporter.exportToFile(payload.filename);
+ }
+ CATCH_STD_EXCEPTION()
+ return response;
+}
+#endif // USE_PIXAR
+
 Response BioExplorerPlugin::_addGrid(const AddGridDetails &payload)
 {
  Response response;

bioexplorer/backend/science/BioExplorerPlugin.h

@@ -64,7 +64,12 @@ class BioExplorerPlugin : public core::ExtensionPlugin
  details::Response _exportToFile(const details::FileAccessDetails &payload);
  details::Response _importFromFile(const details::FileAccessDetails &payload);
  details::Response _exportToXYZ(const details::FileAccessDetails &payload);
+#ifdef USE_LASLIB
  details::Response _exportToLas(const details::LASFileAccessDetails &payload);
+#endif // USE_LASLIB
+#ifdef USE_PIXAR
+ details::Response _exportToUSDFile(const details::FileAccessDetails &payload);
+#endif // USE_PIXAR
 
  // DB
  details::Response _exportBrickToDatabase(const details::DatabaseAccessDetails &payload);

bioexplorer/backend/science/common/SDFGeometries.cpp

@@ -60,9 +60,8 @@ Vector4fs SDFGeometries::_getProcessedSectionPoints(const MorphologyRepresentati
  {
  case MorphologyRepresentation::bezier:
  {
- const uint64_t nbBezierPoints = std::max(static_cast<size_t>(3), points.size() / 10);
- const float step = 1.f / static_cast<float>(nbBezierPoints);
- for (float i = 0; i <= 1.f; i += step)
+ const float step = 1.f / (static_cast<float>(points.size()) / 2.0);
+ for (float i = 0; i < 1.f + step; i += step)
  localPoints.push_back(getBezierPoint(points, i));
  break;
  }
@@ -80,6 +79,7 @@ Vector4fs SDFGeometries::_getProcessedSectionPoints(const MorphologyRepresentati
  default:
  {
  localPoints = points;
+ break;
  }
  }
  return localPoints;

bioexplorer/backend/science/common/ThreadSafeContainer.cpp

@@ -31,7 +31,7 @@ namespace common
 {
 using namespace core;
 
-const float equalityEpsilon = 1e-6f;
+const float equalityEpsilon = 1e-3f;
 
 ThreadSafeContainer::ThreadSafeContainer(Model& model, const double alignToGrid, const Vector3d& position,
  const Quaterniond& rotation, const Vector3d& scale)
@@ -94,6 +94,7 @@ uint64_t ThreadSafeContainer::addCone(const Vector3f& sourcePosition, const floa
  getAlignmentToGrid(_alignToGrid, Vector3f(_position + _rotation * Vector3d(sourcePosition)) * scale);
  const Vector3f scaledDstPosition =
  getAlignmentToGrid(_alignToGrid, Vector3f(_position + _rotation * Vector3d(targetPosition)) * scale);
+
  if (useSdf)
  {
  const Vector3f scaledDisplacement{displacement.x * scale.x, displacement.y / scale.x, displacement.z};
@@ -109,13 +110,12 @@ uint64_t ThreadSafeContainer::addCone(const Vector3f& sourcePosition, const floa
  }
  if (fabs(sourceRadius - targetRadius) < equalityEpsilon)
  {
- const auto scaledSrcRadius = sourceRadius * scale.x;
- const auto scaledDstRadius = targetRadius * scale.x;
- _bounds.merge(scaledSrcPosition + scaledSrcRadius);
- _bounds.merge(scaledSrcPosition - scaledSrcRadius);
- _bounds.merge(scaledDstPosition + scaledDstRadius);
- _bounds.merge(scaledDstPosition - scaledDstRadius);
- return _addCylinder(materialId, {scaledSrcPosition, scaledDstPosition, sourceRadius * scale.x, userDataOffset});
+ const auto scaledRadius = sourceRadius * scale.x;
+ _bounds.merge(scaledSrcPosition + scaledRadius);
+ _bounds.merge(scaledSrcPosition - scaledRadius);
+ _bounds.merge(scaledDstPosition + scaledRadius);
+ _bounds.merge(scaledDstPosition - scaledRadius);
+ return _addCylinder(materialId, {scaledSrcPosition, scaledDstPosition, scaledRadius, userDataOffset});
  }
 
  const auto scaledSrcRadius = sourceRadius * scale.x;
@@ -124,8 +124,8 @@ uint64_t ThreadSafeContainer::addCone(const Vector3f& sourcePosition, const floa
  _bounds.merge(scaledSrcPosition - scaledSrcRadius);
  _bounds.merge(scaledDstPosition + scaledDstRadius);
  _bounds.merge(scaledDstPosition - scaledDstRadius);
- return _addCone(materialId, {scaledSrcPosition, scaledDstPosition, sourceRadius * scale.x, targetRadius * scale.x,
-   userDataOffset});
+ return _addCone(materialId,
+ {scaledSrcPosition, scaledDstPosition, scaledSrcRadius, scaledDstRadius, userDataOffset});
 }
 
 void ThreadSafeContainer::addConeOfSpheres(const Vector3f& sourcePosition, const float sourceRadius,

bioexplorer/backend/science/io/filesystem/MorphologyLoader.cpp

@@ -83,7 +83,7 @@ SectionMap MorphologyLoader::getNeuronSections(const std::string& filename,
  loadSection(section, sections, sectionTypes);
  return sections;
 #else
- PLUGIN_THROW("BioExplorer was not compiler with MorphIO");
+ PLUGIN_THROW("BioExplorer was not compiled with MorphIO");
 #endif
 }
 } // namespace filesystem