Mercurial > hg > orthanc-stone
changeset 1170:1644de437a7b broker
fixes related to swapped normal in sagittal geometry
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Wed, 20 Nov 2019 13:09:15 +0100 |
parents | ad4e21df4e40 |
children | ba08f2b0a779 |
files | Framework/Toolbox/DicomStructureSet.cpp Framework/Toolbox/DicomStructureSet.h Framework/Toolbox/LinearAlgebra.cpp Framework/Volumes/VolumeImageGeometry.cpp UnitTestsSources/UnitTestsMain.cpp |
diffstat | 5 files changed, 128 insertions(+), 53 deletions(-) [+] |
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--- a/Framework/Toolbox/DicomStructureSet.cpp Wed Nov 20 10:55:44 2019 +0100 +++ b/Framework/Toolbox/DicomStructureSet.cpp Wed Nov 20 13:09:15 2019 +0100 @@ -373,8 +373,10 @@ else if (GeometryToolbox::IsParallelOrOpposite (isOpposite, slice.GetNormal(), geometry_.GetAxisX())) { - // plane is constant X + // plane is constant X => Sagittal view (remember that in the + // sagittal projection, the normal must be swapped) + /* Please read the comments in the section above, by taking into account the fact that, in this case, the plane has a constant X, not Y (in @@ -427,10 +429,6 @@ slice.ProjectPoint2(x1, y1, p1); slice.ProjectPoint2(x2, y2, p2); - // TODO WHY THIS??? - y1 = -y1; - y2 = -y2; - return true; } }
--- a/Framework/Toolbox/DicomStructureSet.h Wed Nov 20 10:55:44 2019 +0100 +++ b/Framework/Toolbox/DicomStructureSet.h Wed Nov 20 13:09:15 2019 +0100 @@ -26,7 +26,7 @@ #include "Extent2D.h" #include "../Scene2D/Color.h" -#define USE_BOOST_UNION_FOR_POLYGONS 1 +//#define USE_BOOST_UNION_FOR_POLYGONS 1 #include <Plugins/Samples/Common/FullOrthancDataset.h>
--- a/Framework/Toolbox/LinearAlgebra.cpp Wed Nov 20 10:55:44 2019 +0100 +++ b/Framework/Toolbox/LinearAlgebra.cpp Wed Nov 20 13:09:15 2019 +0100 @@ -22,6 +22,7 @@ #include "LinearAlgebra.h" #include "../StoneException.h" +#include "GenericToolbox.h" #include <Core/Logging.h> #include <Core/OrthancException.h> @@ -123,6 +124,12 @@ return false; } +#elif 1 + if (!GenericToolbox::StringToDouble(target[i], items[i].c_str())) + { + return false; + } + #else /** * Fallback implementation using Boost (slower, but somewhat
--- a/Framework/Volumes/VolumeImageGeometry.cpp Wed Nov 20 10:55:44 2019 +0100 +++ b/Framework/Volumes/VolumeImageGeometry.cpp Wed Nov 20 13:09:15 2019 +0100 @@ -296,16 +296,18 @@ { return false; } - - unsigned int d = static_cast<unsigned int>(std::floor(z)); - if (d >= projectionDepth) - { - return false; - } else { - slice = d; - return true; + unsigned int d = static_cast<unsigned int>(std::floor(z)); + if (d >= projectionDepth) + { + return false; + } + else + { + slice = d; + return true; + } } } @@ -321,7 +323,18 @@ Vector dim = GetVoxelDimensions(projection); CoordinateSystem3D plane = GetProjectionGeometry(projection); - plane.SetOrigin(plane.GetOrigin() + static_cast<double>(z) * plane.GetNormal() * dim[2]); + Vector normal = plane.GetNormal(); + if (projection == VolumeProjection_Sagittal) + { + /** + * WARNING: In sagittal geometry, the normal points to REDUCING + * X-axis in the 3D world. This is necessary to keep the + * right-hand coordinate system. Hence the negation. + **/ + normal = -normal; + } + + plane.SetOrigin(plane.GetOrigin() + static_cast<double>(z) * dim[2] * normal); return plane; }
--- a/UnitTestsSources/UnitTestsMain.cpp Wed Nov 20 10:55:44 2019 +0100 +++ b/UnitTestsSources/UnitTestsMain.cpp Wed Nov 20 13:09:15 2019 +0100 @@ -570,17 +570,22 @@ static bool IsEqualVector(OrthancStone::Vector a, OrthancStone::Vector b) { - if (a.size() == 3 && - b.size() == 3) + if (a.size() != b.size()) { - OrthancStone::LinearAlgebra::NormalizeVector(a); - OrthancStone::LinearAlgebra::NormalizeVector(b); - return OrthancStone::LinearAlgebra::IsCloseToZero(boost::numeric::ublas::norm_2(a - b)); + return false; } else { - return false; - } + for (size_t i = 0; i < a.size(); i++) + { + if (!OrthancStone::LinearAlgebra::IsNear(a[i], b[i], 0.0001)) + { + return false; + } + } + + return true; + } } @@ -642,11 +647,13 @@ TEST(VolumeImageGeometry, Basic) { - OrthancStone::VolumeImageGeometry g; + using namespace OrthancStone; + + VolumeImageGeometry g; g.SetSizeInVoxels(10, 20, 30); g.SetVoxelDimensions(1, 2, 3); - OrthancStone::Vector p = g.GetCoordinates(0, 0, 0); + Vector p = g.GetCoordinates(0, 0, 0); ASSERT_EQ(3u, p.size()); ASSERT_DOUBLE_EQ(-1.0 / 2.0, p[0]); ASSERT_DOUBLE_EQ(-2.0 / 2.0, p[1]); @@ -657,66 +664,116 @@ ASSERT_DOUBLE_EQ(-2.0 / 2.0 + 20.0 * 2.0, p[1]); ASSERT_DOUBLE_EQ(-3.0 / 2.0 + 30.0 * 3.0, p[2]); - OrthancStone::VolumeProjection proj; + VolumeProjection proj; ASSERT_TRUE(g.DetectProjection(proj, g.GetAxialGeometry().GetNormal())); - ASSERT_EQ(OrthancStone::VolumeProjection_Axial, proj); + ASSERT_EQ(VolumeProjection_Axial, proj); ASSERT_TRUE(g.DetectProjection(proj, g.GetCoronalGeometry().GetNormal())); - ASSERT_EQ(OrthancStone::VolumeProjection_Coronal, proj); + ASSERT_EQ(VolumeProjection_Coronal, proj); ASSERT_TRUE(g.DetectProjection(proj, g.GetSagittalGeometry().GetNormal())); - ASSERT_EQ(OrthancStone::VolumeProjection_Sagittal, proj); + ASSERT_EQ(VolumeProjection_Sagittal, proj); - ASSERT_EQ(10u, g.GetProjectionWidth(OrthancStone::VolumeProjection_Axial)); - ASSERT_EQ(20u, g.GetProjectionHeight(OrthancStone::VolumeProjection_Axial)); - ASSERT_EQ(30u, g.GetProjectionDepth(OrthancStone::VolumeProjection_Axial)); - ASSERT_EQ(10u, g.GetProjectionWidth(OrthancStone::VolumeProjection_Coronal)); - ASSERT_EQ(30u, g.GetProjectionHeight(OrthancStone::VolumeProjection_Coronal)); - ASSERT_EQ(20u, g.GetProjectionDepth(OrthancStone::VolumeProjection_Coronal)); - ASSERT_EQ(20u, g.GetProjectionWidth(OrthancStone::VolumeProjection_Sagittal)); - ASSERT_EQ(30u, g.GetProjectionHeight(OrthancStone::VolumeProjection_Sagittal)); - ASSERT_EQ(10u, g.GetProjectionDepth(OrthancStone::VolumeProjection_Sagittal)); + ASSERT_EQ(10u, g.GetProjectionWidth(VolumeProjection_Axial)); + ASSERT_EQ(20u, g.GetProjectionHeight(VolumeProjection_Axial)); + ASSERT_EQ(30u, g.GetProjectionDepth(VolumeProjection_Axial)); + ASSERT_EQ(10u, g.GetProjectionWidth(VolumeProjection_Coronal)); + ASSERT_EQ(30u, g.GetProjectionHeight(VolumeProjection_Coronal)); + ASSERT_EQ(20u, g.GetProjectionDepth(VolumeProjection_Coronal)); + ASSERT_EQ(20u, g.GetProjectionWidth(VolumeProjection_Sagittal)); + ASSERT_EQ(30u, g.GetProjectionHeight(VolumeProjection_Sagittal)); + ASSERT_EQ(10u, g.GetProjectionDepth(VolumeProjection_Sagittal)); - p = g.GetVoxelDimensions(OrthancStone::VolumeProjection_Axial); + p = g.GetVoxelDimensions(VolumeProjection_Axial); ASSERT_EQ(3u, p.size()); ASSERT_DOUBLE_EQ(1, p[0]); ASSERT_DOUBLE_EQ(2, p[1]); ASSERT_DOUBLE_EQ(3, p[2]); - p = g.GetVoxelDimensions(OrthancStone::VolumeProjection_Coronal); + p = g.GetVoxelDimensions(VolumeProjection_Coronal); ASSERT_EQ(3u, p.size()); ASSERT_DOUBLE_EQ(1, p[0]); ASSERT_DOUBLE_EQ(3, p[1]); ASSERT_DOUBLE_EQ(2, p[2]); - p = g.GetVoxelDimensions(OrthancStone::VolumeProjection_Sagittal); + p = g.GetVoxelDimensions(VolumeProjection_Sagittal); ASSERT_EQ(3u, p.size()); ASSERT_DOUBLE_EQ(2, p[0]); ASSERT_DOUBLE_EQ(3, p[1]); ASSERT_DOUBLE_EQ(1, p[2]); - ASSERT_EQ(0, (int) OrthancStone::VolumeProjection_Axial); - ASSERT_EQ(1, (int) OrthancStone::VolumeProjection_Coronal); - ASSERT_EQ(2, (int) OrthancStone::VolumeProjection_Sagittal); + // Loop over all the voxels of the volume + for (unsigned int z = 0; z < g.GetDepth(); z++) + { + const float zz = (0.5f + static_cast<float>(z)) / static_cast<float>(g.GetDepth()); // Z-center of the voxel + + for (unsigned int y = 0; y < g.GetHeight(); y++) + { + const float yy = (0.5f + static_cast<float>(y)) / static_cast<float>(g.GetHeight()); // Y-center of the voxel + + for (unsigned int x = 0; x < g.GetWidth(); x++) + { + const float xx = (0.5f + static_cast<float>(x)) / static_cast<float>(g.GetWidth()); // X-center of the voxel + + const float sx = 1.0f; + const float sy = 2.0f; + const float sz = 3.0f; + + Vector p = g.GetCoordinates(xx, yy, zz); + + Vector q = (g.GetAxialGeometry().MapSliceToWorldCoordinates( + static_cast<double>(x) * sx, + static_cast<double>(y) * sy) + + z * sz * g.GetAxialGeometry().GetNormal()); + ASSERT_TRUE(IsEqualVector(p, q)); + + q = (g.GetCoronalGeometry().MapSliceToWorldCoordinates( + static_cast<double>(x) * sx, + static_cast<double>(g.GetDepth() - 1 - z) * sz) + + y * sy * g.GetCoronalGeometry().GetNormal()); + ASSERT_TRUE(IsEqualVector(p, q)); + + /** + * WARNING: In sagittal geometry, the normal points to + * REDUCING X-axis in the 3D world. This is necessary to keep + * the right-hand coordinate system. Hence the "-". + **/ + q = (g.GetSagittalGeometry().MapSliceToWorldCoordinates( + static_cast<double>(y) * sy, + static_cast<double>(g.GetDepth() - 1 - z) * sz) + + x * sx * (-g.GetSagittalGeometry().GetNormal())); + ASSERT_TRUE(IsEqualVector(p, q)); + } + } + } + + ASSERT_EQ(0, (int) VolumeProjection_Axial); + ASSERT_EQ(1, (int) VolumeProjection_Coronal); + ASSERT_EQ(2, (int) VolumeProjection_Sagittal); for (int p = 0; p < 3; p++) { - printf("=========== %d\n", p); - - OrthancStone::VolumeProjection projection = (OrthancStone::VolumeProjection) p; - const OrthancStone::CoordinateSystem3D& s = g.GetProjectionGeometry(projection); + VolumeProjection projection = (VolumeProjection) p; + const CoordinateSystem3D& s = g.GetProjectionGeometry(projection); ASSERT_THROW(g.GetProjectionSlice(projection, g.GetProjectionDepth(projection)), Orthanc::OrthancException); for (unsigned int i = 0; i < g.GetProjectionDepth(projection); i++) { - printf("------------- %d\n", i); - - OrthancStone::CoordinateSystem3D plane = g.GetProjectionSlice(projection, i); + CoordinateSystem3D plane = g.GetProjectionSlice(projection, i); - ASSERT_TRUE(IsEqualVector(plane.GetOrigin(), s.GetOrigin() + static_cast<double>(i) * - s.GetNormal() * g.GetVoxelDimensions(projection)[2])); + if (projection == VolumeProjection_Sagittal) + { + ASSERT_TRUE(IsEqualVector(plane.GetOrigin(), s.GetOrigin() + static_cast<double>(i) * + (-s.GetNormal()) * g.GetVoxelDimensions(projection)[2])); + } + else + { + ASSERT_TRUE(IsEqualVector(plane.GetOrigin(), s.GetOrigin() + static_cast<double>(i) * + s.GetNormal() * g.GetVoxelDimensions(projection)[2])); + } + ASSERT_TRUE(IsEqualVector(plane.GetAxisX(), s.GetAxisX())); ASSERT_TRUE(IsEqualVector(plane.GetAxisY(), s.GetAxisY())); unsigned int slice; - OrthancStone::VolumeProjection q; + VolumeProjection q; ASSERT_TRUE(g.DetectSlice(q, slice, plane)); ASSERT_EQ(projection, q); ASSERT_EQ(i, slice);