Mercurial > hg > orthanc-stone
view Framework/Toolbox/ShearWarpProjectiveTransform.cpp @ 270:2d64f4d39610 am-2
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author | am@osimis.io |
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date | Thu, 23 Aug 2018 14:45:04 +0200 |
parents | 5412adf19980 |
children | f5d5814a41a0 |
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/** * Stone of Orthanc * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics * Department, University Hospital of Liege, Belgium * Copyright (C) 2017-2018 Osimis S.A., Belgium * * This program is free software: you can redistribute it and/or * modify it under the terms of the GNU Affero General Public License * as published by the Free Software Foundation, either version 3 of * the License, or (at your option) any later version. * * This program 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 * Affero General Public License for more details. * * You should have received a copy of the GNU Affero General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. **/ #include "ShearWarpProjectiveTransform.h" #include "ImageGeometry.h" #include "Extent2D.h" #include "FiniteProjectiveCamera.h" #include "GeometryToolbox.h" #include <Core/Images/PixelTraits.h> #include <Core/Images/ImageProcessing.h> #include <Core/OrthancException.h> #include <Core/Logging.h> #include <boost/numeric/ublas/matrix_proxy.hpp> #include <boost/math/special_functions/round.hpp> #include <cassert> namespace OrthancStone { static bool IsValidShear(const Matrix& M_shear) { return (LinearAlgebra::IsCloseToZero(M_shear(0, 1)) && LinearAlgebra::IsCloseToZero(M_shear(1, 0)) && LinearAlgebra::IsCloseToZero(M_shear(2, 0)) && LinearAlgebra::IsCloseToZero(M_shear(2, 1)) && LinearAlgebra::IsNear(1.0, M_shear(2, 2)) && LinearAlgebra::IsCloseToZero(M_shear(2, 3)) && LinearAlgebra::IsCloseToZero(M_shear(3, 0)) && LinearAlgebra::IsCloseToZero(M_shear(3, 1)) && LinearAlgebra::IsNear(1.0, M_shear(3, 3))); } static void ComputeShearParameters(double& scaling, double& offsetX, double& offsetY, const Matrix& shear, double z) { // Check out: ../../Resources/Computations/ComputeShearParameters.py if (!LinearAlgebra::IsShearMatrix(shear)) { LOG(ERROR) << "Not a valid shear matrix"; throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } scaling = 1.0 / (shear(3,2) * z + 1.0); offsetX = shear(0,2) * z * scaling; offsetY = shear(1,2) * z * scaling; } ShearWarpProjectiveTransform:: ShearWarpProjectiveTransform(const Matrix& M_view, //const Matrix& P, // Permutation applied to the volume unsigned int volumeWidth, unsigned int volumeHeight, unsigned int volumeDepth, double pixelSpacingX, double pixelSpacingY, unsigned int imageWidth, unsigned int imageHeight) { eye_o.resize(4); { // Find back the camera center given the "M_view" matrix const double m11 = M_view(0, 0); const double m12 = M_view(0, 1); const double m13 = M_view(0, 2); const double m14 = M_view(0, 3); const double m21 = M_view(1, 0); const double m22 = M_view(1, 1); const double m23 = M_view(1, 2); const double m24 = M_view(1, 3); const double m41 = M_view(3, 0); const double m42 = M_view(3, 1); const double m43 = M_view(3, 2); const double m44 = M_view(3, 3); // Equations (A.8) to (A.11) on page 203. Also check out // "Finding the camera center" in "Multiple View Geometry in // Computer Vision - 2nd edition", page 163. const double vx[9] = { m12, m13, m14, m22, m23, m24, m42, m43, m44 }; const double vy[9] = { m11, m13, m14, m21, m23, m24, m41, m43, m44 }; const double vz[9] = { m11, m12, m14, m21, m22, m24, m41, m42, m44 }; const double vw[9] = { m11, m12, m13, m21, m22, m23, m41, m42, m43 }; Matrix m; LinearAlgebra::FillMatrix(m, 3, 3, vx); eye_o[0] = -LinearAlgebra::ComputeDeterminant(m); LinearAlgebra::FillMatrix(m, 3, 3, vy); eye_o[1] = LinearAlgebra::ComputeDeterminant(m); LinearAlgebra::FillMatrix(m, 3, 3, vz); eye_o[2] = -LinearAlgebra::ComputeDeterminant(m); LinearAlgebra::FillMatrix(m, 3, 3, vw); eye_o[3] = LinearAlgebra::ComputeDeterminant(m); if (LinearAlgebra::IsCloseToZero(eye_o[3])) { LOG(ERROR) << "The shear-warp projective transform is not applicable to affine cameras"; throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } } #if 0 // Assume "T_shift = I" (the eye does not lie on plane k = 0) const Matrix T_shift = LinearAlgebra::IdentityMatrix(4); // Equation (A.13) on page 204, given that the inverse of a // permutation matrix is its transpose (TODO CHECK). If no T_shift // or permutation P is applied, M'_view == M_view const Matrix MM_view = LinearAlgebra::Product( M_view, LinearAlgebra::Transpose(P), LinearAlgebra::InvertScalingTranslationMatrix(T_shift)); #else // This is a shortcut, as we take "T_shift = I" and "P = I" const Matrix MM_view = M_view; #endif // Equation (A.14) on page 207 Matrix MM_shear = LinearAlgebra::IdentityMatrix(4); MM_shear(0, 2) = -eye_o[0] / eye_o[2]; MM_shear(1, 2) = -eye_o[1] / eye_o[2]; MM_shear(3, 2) = -eye_o[3] / eye_o[2]; // Compute the extent of the intermediate image Extent2D extent; double maxScaling = 1; { // Compute the shearing factors of the two extreme planes of the // volume (z=0 and z=volumeDepth) double scaling, offsetX, offsetY; ComputeShearParameters(scaling, offsetX, offsetY, MM_shear, 0); if (scaling > 0) { extent.AddPoint(offsetX, offsetY); extent.AddPoint(offsetX + static_cast<double>(volumeWidth) * scaling, offsetY + static_cast<double>(volumeHeight) * scaling); if (scaling > maxScaling) { maxScaling = scaling; } } ComputeShearParameters(scaling, offsetX, offsetY, MM_shear, volumeDepth); if (scaling > 0) { extent.AddPoint(offsetX, offsetY); extent.AddPoint(offsetX + static_cast<double>(volumeWidth) * scaling, offsetY + static_cast<double>(volumeHeight) * scaling); if (scaling > maxScaling) { maxScaling = scaling; } } } if (LinearAlgebra::IsCloseToZero(extent.GetWidth()) || LinearAlgebra::IsCloseToZero(extent.GetHeight())) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } intermediateWidth_ = std::ceil(extent.GetWidth() / maxScaling); intermediateHeight_ = std::ceil(extent.GetHeight() / maxScaling); // This is the product "T * S" in Equation (A.16) on page 209 Matrix TS = LinearAlgebra::Product( GeometryToolbox::CreateTranslationMatrix(static_cast<double>(intermediateWidth_) / 2.0, static_cast<double>(intermediateHeight_) / 2.0, 0), GeometryToolbox::CreateScalingMatrix(1.0 / maxScaling, 1.0 / maxScaling, 1), GeometryToolbox::CreateTranslationMatrix(-extent.GetCenterX(), -extent.GetCenterY(), 0)); // This is Equation (A.16) on page 209. WARNING: There is an // error in Lacroute's thesis: "inv(MM_shear)" is used instead // of "MM_shear". M_shear = LinearAlgebra::Product(TS, MM_shear); if (!IsValidShear(M_shear)) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } // This is Equation (A.17) on page 209 Matrix tmp; LinearAlgebra::InvertMatrix(tmp, M_shear); M_warp = LinearAlgebra::Product(MM_view, tmp); // Intrinsic parameters of the camera k_ = LinearAlgebra::ZeroMatrix(3, 4); k_(0, 0) = 1.0 / pixelSpacingX; k_(0, 3) = static_cast<double>(imageWidth) / 2.0; k_(1, 1) = 1.0 / pixelSpacingY; k_(1, 3) = static_cast<double>(imageHeight) / 2.0; k_(2, 3) = 1.0; } FiniteProjectiveCamera *ShearWarpProjectiveTransform::CreateCamera() const { Matrix p = LinearAlgebra::Product(k_, M_warp, M_shear); return new FiniteProjectiveCamera(p); } void ShearWarpProjectiveTransform::ComputeShearOnSlice(double& a11, double& b1, double& a22, double& b2, double& shearedZ, const double sourceZ) { // Check out: ../../Resources/Computations/ComputeShearOnSlice.py assert(IsValidShear(M_shear)); const double s11 = M_shear(0, 0); const double s13 = M_shear(0, 2); const double s14 = M_shear(0, 3); const double s22 = M_shear(1, 1); const double s23 = M_shear(1, 2); const double s24 = M_shear(1, 3); const double s43 = M_shear(3, 2); double scaling = 1.0 / (s43 * sourceZ + 1.0); shearedZ = sourceZ * scaling; a11 = s11 * scaling; a22 = s22 * scaling; b1 = (s13 * sourceZ + s14) * scaling; b2 = (s23 * sourceZ + s24) * scaling; } Matrix ShearWarpProjectiveTransform::CalibrateView(const Vector& camera, const Vector& principalPoint, double angle) { if (camera.size() != 3 || principalPoint.size() != 3) { throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); } const double sid = boost::numeric::ublas::norm_2(camera - principalPoint); Matrix a; GeometryToolbox::AlignVectorsWithRotation(a, camera - principalPoint, LinearAlgebra::CreateVector(0, 0, -1)); Matrix r = LinearAlgebra::Product(GeometryToolbox::CreateRotationMatrixAlongZ(angle), a); a = LinearAlgebra::ZeroMatrix(4, 4); boost::numeric::ublas::subrange(a, 0, 3, 0, 3) = r; const Vector v = LinearAlgebra::Product(r, -camera); a(0, 3) = v[0]; a(1, 3) = v[1]; a(2, 3) = v[2]; a(3, 3) = 1; Matrix perspective = LinearAlgebra::ZeroMatrix(4, 4); // https://stackoverflow.com/questions/5267866/calculation-of-a-perspective-transformation-matrix perspective(0, 0) = sid; perspective(1, 1) = sid; perspective(2, 2) = sid; perspective(3, 2) = 1; Matrix M_view = LinearAlgebra::Product(perspective, a); assert(M_view.size1() == 4 && M_view.size2() == 4); { // Sanity checks Vector p1 = LinearAlgebra::CreateVector(camera[0], camera[1], camera[2], 1.0); Vector p2 = LinearAlgebra::CreateVector(principalPoint[0], principalPoint[1], principalPoint[2], 1.0); Vector v1 = LinearAlgebra::Product(M_view, p1); Vector v2 = LinearAlgebra::Product(M_view, p2); if (!LinearAlgebra::IsCloseToZero(v1[3]) || // Must be mapped to singularity (w=0) LinearAlgebra::IsCloseToZero(v2[3])) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } // The principal point must be mapped to (0,0,z,1) v2 /= v2[3]; if (!LinearAlgebra::IsCloseToZero(v2[0]) || !LinearAlgebra::IsCloseToZero(v2[1])) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } } return M_view; } template <Orthanc::PixelFormat SourceFormat, Orthanc::PixelFormat TargetFormat, bool MIP> static void ApplyAxialInternal(Orthanc::ImageAccessor& target, float& maxValue, const Matrix& M_view, const ImageBuffer3D& source, double pixelSpacing, unsigned int countSlices, ImageInterpolation shearInterpolation, ImageInterpolation warpInterpolation) { typedef Orthanc::PixelTraits<SourceFormat> SourceTraits; typedef Orthanc::PixelTraits<TargetFormat> TargetTraits; /** * Step 1: Precompute some information. **/ if (target.GetFormat() != TargetFormat || source.GetFormat() != SourceFormat || !std::numeric_limits<float>::is_iec559 || sizeof(float) != 4) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } if (countSlices > source.GetDepth()) { countSlices = source.GetDepth(); } if (countSlices == 0) { maxValue = 0; Orthanc::ImageProcessing::Set(target, 0); return; } LOG(INFO) << "Number of rendered slices: " << countSlices; /** * Step 2: Extract the shear-warp transform corresponding to * M_view. **/ // Compute the "world" matrix that maps the source volume to the // (0,0,0)->(1,1,1) unit cube Vector origin = source.GetCoordinates(0, 0, 0); Vector ps = source.GetVoxelDimensions(VolumeProjection_Axial); Matrix world = LinearAlgebra::Product( GeometryToolbox::CreateScalingMatrix(1.0 / ps[0], 1.0 / ps[1], 1.0 / ps[2]), GeometryToolbox::CreateTranslationMatrix(-origin[0], -origin[1], -origin[2])); Matrix worldInv; LinearAlgebra::InvertMatrix(worldInv, world); ShearWarpProjectiveTransform shearWarp(LinearAlgebra::Product(M_view, worldInv), /*LinearAlgebra::IdentityMatrix(4),*/ source.GetWidth(), source.GetHeight(), source.GetDepth(), pixelSpacing, pixelSpacing, target.GetWidth(), target.GetHeight()); const unsigned int intermediateWidth = shearWarp.GetIntermediateWidth(); const unsigned int intermediateHeight = shearWarp.GetIntermediateHeight(); /** * Step 3: Apply the "shear" part of the transform to form the * intermediate image. The sheared images are accumulated into the * Float32 image "accumulator". The number of samples available * for each pixel is stored in the "counter" image. **/ std::auto_ptr<Orthanc::ImageAccessor> accumulator, counter, intermediate; accumulator.reset(new Orthanc::Image(Orthanc::PixelFormat_Float32, intermediateWidth, intermediateHeight, false)); counter.reset(new Orthanc::Image(Orthanc::PixelFormat_Grayscale16, intermediateWidth, intermediateHeight, false)); intermediate.reset(new Orthanc::Image(SourceFormat, intermediateWidth, intermediateHeight, false)); Orthanc::ImageProcessing::Set(*accumulator, 0); Orthanc::ImageProcessing::Set(*counter, 0); // Loop around the slices of the volume for (unsigned int i = 0; i <= countSlices; i++) { // (3.a) Compute the shear for this specific slice unsigned int z = static_cast<unsigned int>( boost::math::iround(static_cast<double>(i) / static_cast<double>(countSlices) * static_cast<double>(source.GetDepth() - 1))); double a11, b1, a22, b2, vz; shearWarp.ComputeShearOnSlice(a11, b1, a22, b2, vz, static_cast<double>(z) + 0.5); { // (3.b) Detect the "useful" portion of the intermediate image // for this slice (i.e. the bounding box where the source // slice is mapped to by the shear), so as to update "counter" Matrix a = LinearAlgebra::ZeroMatrix(3, 3); a(0,0) = a11; a(0,2) = b1; a(1,1) = a22; a(1,2) = b2; a(2,2) = 1; unsigned int x1, y1, x2, y2; if (GetProjectiveTransformExtent(x1, y1, x2, y2, a, source.GetWidth(), source.GetHeight(), intermediateWidth, intermediateHeight)) { for (unsigned int y = y1; y <= y2; y++) { uint16_t* p = reinterpret_cast<uint16_t*>(counter->GetRow(y)) + x1; for (unsigned int x = x1; x <= x2; x++, p++) { if (MIP) { // TODO - In the case of MIP, "counter" could be // reduced to "PixelFormat_Grayscale8" to reduce // memory usage *p = 1; } else { *p += 1; } } } } } { // (3.c) Shear the source slice into a temporary image ImageBuffer3D::SliceReader reader(source, VolumeProjection_Axial, z); ApplyAffineTransform(*intermediate, reader.GetAccessor(), a11, 0, b1, 0, a22, b2, shearInterpolation); } for (unsigned int y = 0; y < intermediateHeight; y++) { // (3.d) Accumulate the pixels of the sheared image into "accumulator" const typename SourceTraits::PixelType* p = reinterpret_cast<const typename SourceTraits::PixelType*>(intermediate->GetConstRow(y)); float* q = reinterpret_cast<float*>(accumulator->GetRow(y)); for (unsigned int x = 0; x < intermediateWidth; x++) { float pixel = SourceTraits::PixelToFloat(*p); if (MIP) { // Get maximum for MIP if (*q < pixel) { *q = pixel; } } else { *q += pixel; } p++; q++; } } } /** * Step 4: The intermediate image (that will be transformed by the * "warp") is now available as an accumulator image together with * a counter image. "Flatten" these two images into one. **/ intermediate.reset(new Orthanc::Image (TargetFormat, intermediateWidth, intermediateHeight, false)); maxValue = 0; for (unsigned int y = 0; y < intermediateHeight; y++) { const float *qacc = reinterpret_cast<const float*>(accumulator->GetConstRow(y)); const uint16_t *qcount = reinterpret_cast<const uint16_t*>(counter->GetConstRow(y)); typename TargetTraits::PixelType *p = reinterpret_cast<typename TargetTraits::PixelType*>(intermediate->GetRow(y)); for (unsigned int x = 0; x < intermediateWidth; x++) { if (*qcount == 0) { TargetTraits::SetZero(*p); } else { *p = *qacc / static_cast<float>(*qcount); if (*p > maxValue) { maxValue = *p; } } p++; qacc++; qcount++; } } // We don't need the accumulator images anymore accumulator.reset(NULL); counter.reset(NULL); /** * Step 6: Apply the "warp" part of the transform to map the * intermediate image to the final image. **/ Matrix warp; { // (5.a) Compute the "warp" matrix by removing the 3rd row and // 3rd column from the GetWarp() matrix // Check out: ../../Resources/Computations/ComputeWarp.py Matrix fullWarp = LinearAlgebra::Product (shearWarp.GetIntrinsicParameters(), shearWarp.GetWarp()); const double v[] = { fullWarp(0,0), fullWarp(0,1), fullWarp(0,3), fullWarp(1,0), fullWarp(1,1), fullWarp(1,3), fullWarp(2,0), fullWarp(2,1), fullWarp(2,3) }; LinearAlgebra::FillMatrix(warp, 3, 3, v); } // (5.b) Apply the projective transform to the image ApplyProjectiveTransform(target, *intermediate, warp, warpInterpolation); } template <Orthanc::PixelFormat SourceFormat, Orthanc::PixelFormat TargetFormat> static void ApplyAxialInternal2(Orthanc::ImageAccessor& target, float& maxValue, const Matrix& M_view, const ImageBuffer3D& source, bool mip, double pixelSpacing, unsigned int countSlices, ImageInterpolation shearInterpolation, ImageInterpolation warpInterpolation) { if (mip) { ApplyAxialInternal<SourceFormat, TargetFormat, true> (target, maxValue, M_view, source, pixelSpacing, countSlices, shearInterpolation, warpInterpolation); } else { ApplyAxialInternal<SourceFormat, TargetFormat, false> (target, maxValue, M_view, source, pixelSpacing, countSlices, shearInterpolation, warpInterpolation); } } Orthanc::ImageAccessor* ShearWarpProjectiveTransform::ApplyAxial(float& maxValue, const Matrix& M_view, const ImageBuffer3D& source, Orthanc::PixelFormat targetFormat, unsigned int targetWidth, unsigned int targetHeight, bool mip, double pixelSpacing, unsigned int countSlices, ImageInterpolation shearInterpolation, ImageInterpolation warpInterpolation) { std::auto_ptr<Orthanc::ImageAccessor> target (new Orthanc::Image(targetFormat, targetWidth, targetHeight, false)); if (source.GetFormat() == Orthanc::PixelFormat_Grayscale16 && targetFormat == Orthanc::PixelFormat_Grayscale16) { ApplyAxialInternal2<Orthanc::PixelFormat_Grayscale16, Orthanc::PixelFormat_Grayscale16> (*target, maxValue, M_view, source, mip, pixelSpacing, countSlices, shearInterpolation, warpInterpolation); } else if (source.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16 && targetFormat == Orthanc::PixelFormat_SignedGrayscale16) { ApplyAxialInternal2<Orthanc::PixelFormat_SignedGrayscale16, Orthanc::PixelFormat_SignedGrayscale16> (*target, maxValue, M_view, source, mip, pixelSpacing, countSlices, shearInterpolation, warpInterpolation); } else { throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); } return target.release(); } }