BRAYNS-661 Vector field. (#1282)

Adrien4193 · web-flow · commit b5ee397e16e0 · 2024-09-10T09:03:06.000+02:00
diff --git a/plugins/AtlasExplorer/api/AtlasFactory.cpp b/plugins/AtlasExplorer/api/AtlasFactory.cpp
@@ -24,6 +24,7 @@
 #include "atlases/LayerDistanceAtlas.h"
 #include "atlases/OrientationAtlas.h"
 #include "atlases/ScalarAtlas.h"
+#include "atlases/VectorAtlas.h"
 
 namespace
 {
@@ -60,6 +61,7 @@ AtlasFactory AtlasFactory::createDefault()
     builder.registerType<LayerDistanceAtlas>();
     builder.registerType<OrientationAtlas>();
     builder.registerType<ScalarAtlas>();
+    builder.registerType<VectorAtlas>();
     return AtlasFactory(std::move(builder.factories));
 }
 
diff --git a/plugins/AtlasExplorer/api/UseCaseManager.cpp b/plugins/AtlasExplorer/api/UseCaseManager.cpp
@@ -27,6 +27,7 @@
 #include <api/usecases/LayerDistance.h>
 #include <api/usecases/OrientationField.h>
 #include <api/usecases/OutlineShell.h>
+#include <api/usecases/VectorField.h>
 
 UseCaseManager UseCaseManager::createDefault()
 {
@@ -36,6 +37,7 @@ UseCaseManager UseCaseManager::createDefault()
     useCases.push_back(std::make_unique<HighlightColumn>());
     useCases.push_back(std::make_unique<LayerDistance>());
     useCases.push_back(std::make_unique<OrientationField>());
+    useCases.push_back(std::make_unique<VectorField>());
     useCases.push_back(std::make_unique<OutlineShell>());
     useCases.push_back(std::make_unique<FlatmapAreas>());
     return UseCaseManager(std::move(useCases));
diff --git a/plugins/AtlasExplorer/api/VoxelType.h b/plugins/AtlasExplorer/api/VoxelType.h
@@ -25,5 +25,6 @@ enum class VoxelType
     Scalar,
     Orientation,
     Flatmap,
-    LayerDistance
+    LayerDistance,
+    Vector,
 };
diff --git a/plugins/AtlasExplorer/api/atlases/VectorAtlas.cpp b/plugins/AtlasExplorer/api/atlases/VectorAtlas.cpp
@@ -0,0 +1,101 @@
+/* Copyright (c) 2015-2024, EPFL/Blue Brain Project
+ * All rights reserved. Do not distribute without permission.
+ * Responsible Author: Nadir Roman Guerrero <nadir.romanguerrero@epfl.ch>
+ *
+ * This file is part of Brayns <https://github.com/BlueBrain/Brayns>
+ *
+ * This library is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License version 3.0 as published
+ * by the Free Software Foundation.
+ *
+ * This library is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this library; if not, write to the Free Software Foundation, Inc.,
+ * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+
+#include "VectorAtlas.h"
+
+#include <cassert>
+
+namespace
+{
+float finiteOrZero(float value)
+{
+    if (std::isfinite(value))
+    {
+        return value;
+    }
+
+    return 0.0F;
+}
+
+brayns::Vector3f sanitizeVector(brayns::Vector3f vector)
+{
+    for (auto i = std::size_t(0); i < std::size_t(3); ++i)
+    {
+        vector[i] = finiteOrZero(vector[i]);
+    }
+
+    auto norm = brayns::math::length(vector);
+
+    if (norm == 0.0F)
+    {
+        return vector;
+    }
+
+    return vector / norm;
+}
+
+std::vector<brayns::Vector3f> extractVectors(const IDataMangler &data)
+{
+    auto floats = data.asFloats();
+    auto itemCount = floats.size() / 3;
+
+    auto result = std::vector<brayns::Vector3f>(itemCount);
+
+#pragma omp parallel for
+    for (size_t i = 0; i < itemCount; ++i)
+    {
+        auto index = i * 3;
+
+        auto x = floats[index];
+        auto y = floats[index + 1];
+        auto z = floats[index + 2];
+
+        result[i] = sanitizeVector({x, y, z});
+    }
+
+    return result;
+}
+}
+
+VectorAtlas::VectorAtlas(
+    const brayns::Vector3ui &size,
+    const brayns::Vector3f &spacing,
+    const IDataMangler &dataMangler):
+    Atlas(size, spacing),
+    _voxels(extractVectors(dataMangler))
+{
+}
+
+bool VectorAtlas::isValidVoxel(size_t index) const noexcept
+{
+    assert(_isValidIndex(index));
+    return brayns::math::dot(_voxels[index], _voxels[index]) > 0.f;
+}
+
+VoxelType VectorAtlas::getVoxelType() const noexcept
+{
+    return type;
+}
+
+const brayns::Vector3f &VectorAtlas::operator[](size_t index) const noexcept
+{
+    assert(_isValidIndex(index));
+    return _voxels[index];
+}
diff --git a/plugins/AtlasExplorer/api/atlases/VectorAtlas.h b/plugins/AtlasExplorer/api/atlases/VectorAtlas.h
@@ -0,0 +1,40 @@
+/* Copyright (c) 2015-2024, EPFL/Blue Brain Project
+ * All rights reserved. Do not distribute without permission.
+ * Responsible Author: Nadir Roman Guerrero <nadir.romanguerrero@epfl.ch>
+ *
+ * This file is part of Brayns <https://github.com/BlueBrain/Brayns>
+ *
+ * This library is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License version 3.0 as published
+ * by the Free Software Foundation.
+ *
+ * This library is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this library; if not, write to the Free Software Foundation, Inc.,
+ * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+
+#pragma once
+
+#include <api/Atlas.h>
+#include <api/DataMangler.h>
+
+class VectorAtlas final : public Atlas
+{
+public:
+    static inline const VoxelType type = VoxelType::Vector;
+
+public:
+    VectorAtlas(const brayns::Vector3ui &size, const brayns::Vector3f &spacing, const IDataMangler &dataMangler);
+
+    bool isValidVoxel(size_t linealIndex) const noexcept override;
+    VoxelType getVoxelType() const noexcept override;
+    const brayns::Vector3f &operator[](size_t index) const noexcept;
+
+private:
+    std::vector<brayns::Vector3f> _voxels;
+};
diff --git a/plugins/AtlasExplorer/api/usecases/VectorField.cpp b/plugins/AtlasExplorer/api/usecases/VectorField.cpp
@@ -0,0 +1,150 @@
+/* Copyright (c) 2015-2024, EPFL/Blue Brain Project
+ * All rights reserved. Do not distribute without permission.
+ * Responsible Author: Adrien Fleury <adrien.fleury@epfl.ch>
+ *
+ * This file is part of Brayns <https://github.com/BlueBrain/Brayns>
+ *
+ * This library is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License version 3.0 as published
+ * by the Free Software Foundation.
+ *
+ * This library is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this library; if not, write to the Free Software Foundation, Inc.,
+ * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+
+#include "VectorField.h"
+
+#include <brayns/engine/components/Geometries.h>
+#include <brayns/engine/components/GeometryViews.h>
+#include <brayns/engine/geometry/types/Capsule.h>
+#include <brayns/engine/systems/GenericBoundsSystem.h>
+#include <brayns/engine/systems/GeometryDataSystem.h>
+#include <ospray/ospray_cpp/ext/rkcommon.h>
+
+#include <api/ModelType.h>
+#include <api/atlases/VectorAtlas.h>
+
+#include <cassert>
+
+namespace
+{
+float getAxisColor(float value)
+{
+    return (value + 1.0F) / 2.0F;
+}
+
+brayns::Vector4f getVectorColor(const brayns::Vector3f &vector)
+{
+    return {
+        getAxisColor(vector.x),
+        getAxisColor(vector.y),
+        getAxisColor(vector.z),
+        1.0F,
+    };
+}
+
+std::vector<std::size_t> getNonEmptyVoxelIndices(const VectorAtlas &atlas)
+{
+    auto indices = std::vector<std::size_t>();
+
+    auto itemCount = atlas.getVoxelCount();
+
+    for (auto i = std::size_t(0); i < itemCount; ++i)
+    {
+        if (atlas[i] != brayns::Vector3f())
+        {
+            indices.push_back(i);
+        }
+    }
+
+    return indices;
+}
+
+struct ColoredCapsules
+{
+    std::vector<brayns::Capsule> capsules;
+    std::vector<brayns::Vector4f> colors;
+};
+
+ColoredCapsules createVectorCapsules(const VectorAtlas &atlas)
+{
+    auto indices = getNonEmptyVoxelIndices(atlas);
+    auto indexCount = indices.size();
+
+    auto result = ColoredCapsules();
+    result.capsules.resize(indexCount);
+    result.colors.resize(indexCount);
+
+#pragma omp parallel for
+    for (auto i = std::size_t(0); i < indexCount; ++i)
+    {
+        auto index = indices[i];
+        const auto &direction = atlas[index];
+
+        assert(direction != brayns::Vector3f());
+
+        auto bounds = atlas.getVoxelBounds(index);
+        auto origin = bounds.center();
+
+        const auto &spacing = atlas.getSpacing();
+        auto length = brayns::math::reduce_min(spacing) * 0.5F;
+
+        auto radius = 0.05F * length;
+
+        auto vector = direction * length;
+        auto tip = origin + vector;
+
+        result.capsules[i] = brayns::CapsuleFactory::cone(origin, radius, tip, 0.0F);
+        result.colors[i] = getVectorColor(direction);
+    }
+
+    return result;
+}
+
+void buildVectorModel(brayns::Model &model, ColoredCapsules capsules)
+{
+    auto &components = model.getComponents();
+
+    auto &geometries = components.add<brayns::Geometries>();
+    auto &geometry = geometries.elements.emplace_back(std::move(capsules.capsules));
+
+    auto &views = components.add<brayns::GeometryViews>();
+    auto &view = views.elements.emplace_back(geometry);
+    view.setColorPerPrimitive(ospray::cpp::CopiedData(capsules.colors));
+
+    auto &systems = model.getSystems();
+    systems.setBoundsSystem<brayns::GenericBoundsSystem<brayns::Geometries>>();
+    systems.setDataSystem<brayns::GeometryDataSystem>();
+}
+}
+
+std::string VectorField::getName() const
+{
+    return "Vector field";
+}
+
+bool VectorField::isValidAtlas(const Atlas &atlas) const
+{
+    return atlas.getVoxelType() == VoxelType::Vector;
+}
+
+std::shared_ptr<brayns::Model> VectorField::run(const Atlas &atlas, const brayns::JsonValue &payload) const
+{
+    (void)payload;
+
+    assert(dynamic_cast<const VectorAtlas *>(&atlas));
+    const auto &vectorAtlas = static_cast<const VectorAtlas &>(atlas);
+
+    auto capsules = createVectorCapsules(vectorAtlas);
+
+    auto model = std::make_shared<brayns::Model>(ModelType::atlas);
+    buildVectorModel(*model, std::move(capsules));
+
+    return model;
+}
diff --git a/plugins/AtlasExplorer/api/usecases/VectorField.h b/plugins/AtlasExplorer/api/usecases/VectorField.h
@@ -0,0 +1,31 @@
+/* Copyright (c) 2015-2024, EPFL/Blue Brain Project
+ * All rights reserved. Do not distribute without permission.
+ * Responsible Author: Adrien Fleury <adrien.fleury@epfl.ch>
+ *
+ * This file is part of Brayns <https://github.com/BlueBrain/Brayns>
+ *
+ * This library is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License version 3.0 as published
+ * by the Free Software Foundation.
+ *
+ * This library is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this library; if not, write to the Free Software Foundation, Inc.,
+ * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+
+#pragma once
+
+#include <api/IUseCase.h>
+
+class VectorField : public IUseCase
+{
+public:
+    std::string getName() const override;
+    bool isValidAtlas(const Atlas &atlas) const override;
+    std::shared_ptr<brayns::Model> run(const Atlas &atlas, const brayns::JsonValue &payload) const override;
+};
diff --git a/plugins/AtlasExplorer/io/NRRDLoadeParameters.h b/plugins/AtlasExplorer/io/NRRDLoadeParameters.h
@@ -40,7 +40,9 @@ struct EnumReflector<VoxelType>
             {"scalar", VoxelType::Scalar},
             {"orientation", VoxelType::Orientation},
             {"flatmap", VoxelType::Flatmap},
-            {"layer_distance", VoxelType::LayerDistance}};
+            {"layer_distance", VoxelType::LayerDistance},
+            {"vector", VoxelType::Vector},
+        };
     }
 };
 
diff --git a/python/brayns/__init__.py b/python/brayns/__init__.py
@@ -167,6 +167,7 @@
     AtlasOrientationField,
     AtlasShellOutline,
     AtlasUsecase,
+    AtlasVectorField,
     BbpCells,
     BbpLoader,
     BbpReport,
@@ -251,6 +252,7 @@
     "AtlasOrientationField",
     "AtlasShellOutline",
     "AtlasUsecase",
+    "AtlasVectorField",
     "Axis",
     "BbpCells",
     "BbpLoader",
diff --git a/python/brayns/plugins/__init__.py b/python/brayns/plugins/__init__.py
diff --git a/python/brayns/plugins/atlas.py b/python/brayns/plugins/atlas.py
diff --git a/python/brayns/plugins/nrrd.py b/python/brayns/plugins/nrrd.py

Original file line number	Diff line number	Diff line change
`@@ -24,6 +24,7 @@`
`24`	`24`	`#include "atlases/LayerDistanceAtlas.h"`
`25`	`25`	`#include "atlases/OrientationAtlas.h"`
`26`	`26`	`#include "atlases/ScalarAtlas.h"`
	`27`	`+#include "atlases/VectorAtlas.h"`
`27`	`28`
`28`	`29`	`namespace`
`29`	`30`	`{`
`@@ -60,6 +61,7 @@ AtlasFactory AtlasFactory::createDefault()`
`60`	`61`	`builder.registerType<LayerDistanceAtlas>();`
`61`	`62`	`builder.registerType<OrientationAtlas>();`
`62`	`63`	`builder.registerType<ScalarAtlas>();`
	`64`	`+ builder.registerType<VectorAtlas>();`
`63`	`65`	`return AtlasFactory(std::move(builder.factories));`
`64`	`66`	`}`
`65`	`67`