# HG changeset patch # User Sebastien Jodogne # Date 1518595111 -3600 # Node ID a053ca7fa5c672f586b8fd3d59f6f0a3f9fc0a6d # Parent 2309e8d86efe7300dc4e010f73b2c8d874713083 LinearAlgebra toolbox diff -r 2309e8d86efe -r a053ca7fa5c6 Framework/Layers/CircleMeasureTracker.cpp --- a/Framework/Layers/CircleMeasureTracker.cpp Fri Feb 09 16:00:29 2018 +0100 +++ b/Framework/Layers/CircleMeasureTracker.cpp Wed Feb 14 08:58:31 2018 +0100 @@ -59,7 +59,7 @@ double y = (y1_ + y2_) / 2.0; Vector tmp; - GeometryToolbox::AssignVector(tmp, x2_ - x1_, y2_ - y1_); + LinearAlgebra::AssignVector(tmp, x2_ - x1_, y2_ - y1_); double r = boost::numeric::ublas::norm_2(tmp) / 2.0; context.SetSourceColor(color_[0], color_[1], color_[2]); diff -r 2309e8d86efe -r a053ca7fa5c6 Framework/Toolbox/CoordinateSystem3D.cpp --- a/Framework/Toolbox/CoordinateSystem3D.cpp Fri Feb 09 16:00:29 2018 +0100 +++ b/Framework/Toolbox/CoordinateSystem3D.cpp Wed Feb 14 08:58:31 2018 +0100 @@ -21,6 +21,7 @@ #include "CoordinateSystem3D.h" +#include "LinearAlgebra.h" #include "GeometryToolbox.h" #include @@ -36,8 +37,8 @@ // product of each direction cosine vector with itself shall be // unity." // http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.7.6.2.html - if (!GeometryToolbox::IsNear(boost::numeric::ublas::norm_2(axisX_), 1.0) || - !GeometryToolbox::IsNear(boost::numeric::ublas::norm_2(axisY_), 1.0)) + if (!LinearAlgebra::IsNear(boost::numeric::ublas::norm_2(axisX_), 1.0) || + !LinearAlgebra::IsNear(boost::numeric::ublas::norm_2(axisY_), 1.0)) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); } @@ -47,25 +48,25 @@ // column direction cosine vectors shall be orthogonal, i.e., // their dot product shall be zero." // http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.7.6.2.html - if (!GeometryToolbox::IsCloseToZero(boost::numeric::ublas::inner_prod(axisX_, axisY_))) + if (!LinearAlgebra::IsCloseToZero(boost::numeric::ublas::inner_prod(axisX_, axisY_))) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); } - GeometryToolbox::CrossProduct(normal_, axisX_, axisY_); + LinearAlgebra::CrossProduct(normal_, axisX_, axisY_); d_ = -(normal_[0] * origin_[0] + normal_[1] * origin_[1] + normal_[2] * origin_[2]); // Just a sanity check, it should be useless by construction - assert(GeometryToolbox::IsNear(boost::numeric::ublas::norm_2(normal_), 1.0)); + assert(LinearAlgebra::IsNear(boost::numeric::ublas::norm_2(normal_), 1.0)); } void CoordinateSystem3D::SetupCanonical() { - GeometryToolbox::AssignVector(origin_, 0, 0, 0); - GeometryToolbox::AssignVector(axisX_, 1, 0, 0); - GeometryToolbox::AssignVector(axisY_, 0, 1, 0); + LinearAlgebra::AssignVector(origin_, 0, 0, 0); + LinearAlgebra::AssignVector(axisX_, 1, 0, 0); + LinearAlgebra::AssignVector(axisY_, 0, 1, 0); CheckAndComputeNormal(); } @@ -88,8 +89,8 @@ std::string tmpOrientation = Orthanc::Toolbox::StripSpaces(imageOrientationPatient); Vector orientation; - if (!GeometryToolbox::ParseVector(origin_, tmpPosition) || - !GeometryToolbox::ParseVector(orientation, tmpOrientation) || + if (!LinearAlgebra::ParseVector(origin_, tmpPosition) || + !LinearAlgebra::ParseVector(orientation, tmpOrientation) || origin_.size() != 3 || orientation.size() != 6) { diff -r 2309e8d86efe -r a053ca7fa5c6 Framework/Toolbox/DicomFrameConverter.cpp --- a/Framework/Toolbox/DicomFrameConverter.cpp Fri Feb 09 16:00:29 2018 +0100 +++ b/Framework/Toolbox/DicomFrameConverter.cpp Wed Feb 14 08:58:31 2018 +0100 @@ -21,7 +21,7 @@ #include "DicomFrameConverter.h" -#include "GeometryToolbox.h" +#include "LinearAlgebra.h" #include #include @@ -48,8 +48,8 @@ SetDefaultParameters(); Vector c, w; - if (GeometryToolbox::ParseVector(c, dicom, Orthanc::DICOM_TAG_WINDOW_CENTER) && - GeometryToolbox::ParseVector(w, dicom, Orthanc::DICOM_TAG_WINDOW_WIDTH) && + if (LinearAlgebra::ParseVector(c, dicom, Orthanc::DICOM_TAG_WINDOW_CENTER) && + LinearAlgebra::ParseVector(w, dicom, Orthanc::DICOM_TAG_WINDOW_WIDTH) && c.size() > 0 && w.size() > 0) { diff -r 2309e8d86efe -r a053ca7fa5c6 Framework/Toolbox/DicomStructureSet.cpp --- a/Framework/Toolbox/DicomStructureSet.cpp Fri Feb 09 16:00:29 2018 +0100 +++ b/Framework/Toolbox/DicomStructureSet.cpp Wed Feb 14 08:58:31 2018 +0100 @@ -124,7 +124,7 @@ { std::string value; return (dataset.GetStringValue(value, tag) && - GeometryToolbox::ParseVector(target, value)); + LinearAlgebra::ParseVector(target, value)); } @@ -132,9 +132,9 @@ { if (hasSlice_) { - if (!GeometryToolbox::IsNear(GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal()), - projectionAlongNormal_, - sliceThickness_ / 2.0 /* in mm */)) + if (!LinearAlgebra::IsNear(GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal()), + projectionAlongNormal_, + sliceThickness_ / 2.0 /* in mm */)) { LOG(ERROR) << "This RT-STRUCT contains a point that is off the slice of its instance"; throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); @@ -203,8 +203,8 @@ double d = GeometryToolbox::ProjectAlongNormal(slice.GetOrigin(), geometry_.GetNormal()); - return (GeometryToolbox::IsNear(d, projectionAlongNormal_, - sliceThickness_ / 2.0)); + return (LinearAlgebra::IsNear(d, projectionAlongNormal_, + sliceThickness_ / 2.0)); } @@ -468,7 +468,7 @@ DICOM_TAG_CONTOUR_DATA)); Vector points; - if (!GeometryToolbox::ParseVector(points, slicesData) || + if (!LinearAlgebra::ParseVector(points, slicesData) || points.size() != 3 * countPoints) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); @@ -497,7 +497,7 @@ const Structure& structure = GetStructure(index); Vector center; - GeometryToolbox::AssignVector(center, 0, 0, 0); + LinearAlgebra::AssignVector(center, 0, 0, 0); if (structure.polygons_.empty()) { return center; @@ -614,7 +614,7 @@ std::string s; Vector v; if (dataset.CopyToString(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) && - GeometryToolbox::ParseVector(v, s) && + LinearAlgebra::ParseVector(v, s) && v.size() > 0) { thickness = v[0]; @@ -657,7 +657,7 @@ if (referencedSlices_.empty()) { Vector v; - GeometryToolbox::AssignVector(v, 0, 0, 1); + LinearAlgebra::AssignVector(v, 0, 0, 1); return v; } else diff -r 2309e8d86efe -r a053ca7fa5c6 Framework/Toolbox/GeometryToolbox.cpp --- a/Framework/Toolbox/GeometryToolbox.cpp Fri Feb 09 16:00:29 2018 +0100 +++ b/Framework/Toolbox/GeometryToolbox.cpp Wed Feb 14 08:58:31 2018 +0100 @@ -23,142 +23,20 @@ #include #include -#include -#include -#include +#include namespace OrthancStone { namespace GeometryToolbox { - void Print(const Vector& v) - { - for (size_t i = 0; i < v.size(); i++) - { - printf("%g\n", v[i]); - //printf("%8.2f\n", v[i]); - } - printf("\n"); - } - - - void Print(const Matrix& m) - { - for (size_t i = 0; i < m.size1(); i++) - { - for (size_t j = 0; j < m.size2(); j++) - { - printf("%g ", m(i,j)); - //printf("%8.2f ", m(i,j)); - } - printf("\n"); - } - printf("\n"); - } - - - bool ParseVector(Vector& target, - const std::string& value) - { - std::vector items; - Orthanc::Toolbox::TokenizeString(items, value, '\\'); - - target.resize(items.size()); - - for (size_t i = 0; i < items.size(); i++) - { - try - { - target[i] = boost::lexical_cast(Orthanc::Toolbox::StripSpaces(items[i])); - } - catch (boost::bad_lexical_cast&) - { - target.clear(); - return false; - } - } - - return true; - } - - - bool ParseVector(Vector& target, - const Orthanc::DicomMap& dataset, - const Orthanc::DicomTag& tag) - { - std::string value; - return (dataset.CopyToString(value, tag, false) && - ParseVector(target, value)); - } - - - void AssignVector(Vector& v, - double v1, - double v2) - { - v.resize(2); - v[0] = v1; - v[1] = v2; - } - - - void AssignVector(Vector& v, - double v1, - double v2, - double v3) - { - v.resize(3); - v[0] = v1; - v[1] = v2; - v[2] = v3; - } - - - bool IsNear(double x, - double y) - { - // As most input is read as single-precision numbers, we take the - // epsilon machine for float32 into consideration to compare numbers - return IsNear(x, y, 10.0 * std::numeric_limits::epsilon()); - } - - - void NormalizeVector(Vector& u) - { - double norm = boost::numeric::ublas::norm_2(u); - if (!IsCloseToZero(norm)) - { - u = u / norm; - } - } - - - void CrossProduct(Vector& result, - const Vector& u, - const Vector& v) - { - if (u.size() != 3 || - v.size() != 3) - { - throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); - } - - result.resize(3); - - result[0] = u[1] * v[2] - u[2] * v[1]; - result[1] = u[2] * v[0] - u[0] * v[2]; - result[2] = u[0] * v[1] - u[1] * v[0]; - } - - void ProjectPointOntoPlane(Vector& result, const Vector& point, const Vector& planeNormal, const Vector& planeOrigin) { double norm = boost::numeric::ublas::norm_2(planeNormal); - if (IsCloseToZero(norm)) + if (LinearAlgebra::IsCloseToZero(norm)) { // Division by zero throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); @@ -187,8 +65,8 @@ double normU = boost::numeric::ublas::norm_2(u); double normV = boost::numeric::ublas::norm_2(v); - if (IsCloseToZero(normU) || - IsCloseToZero(normV)) + if (LinearAlgebra::IsCloseToZero(normU) || + LinearAlgebra::IsCloseToZero(normV)) { return false; } @@ -198,12 +76,12 @@ // The angle must be zero, so the cosine must be almost equal to // cos(0) == 1 (or cos(180) == -1 if allowOppositeDirection == true) - if (IsCloseToZero(cosAngle - 1.0)) + if (LinearAlgebra::IsCloseToZero(cosAngle - 1.0)) { isOpposite = false; return true; } - else if (IsCloseToZero(fabs(cosAngle) - 1.0)) + else if (LinearAlgebra::IsCloseToZero(fabs(cosAngle) - 1.0)) { isOpposite = true; return true; @@ -237,10 +115,10 @@ // The direction of the line of intersection is orthogonal to the // normal of both planes - CrossProduct(direction, normal1, normal2); + LinearAlgebra::CrossProduct(direction, normal1, normal2); double norm = boost::numeric::ublas::norm_2(direction); - if (IsCloseToZero(norm)) + if (LinearAlgebra::IsCloseToZero(norm)) { // The two planes are parallel or coincident return false; @@ -250,7 +128,7 @@ double d2 = -boost::numeric::ublas::inner_prod(normal2, origin2); Vector tmp = d2 * normal1 - d1 * normal2; - CrossProduct(p, tmp, direction); + LinearAlgebra::CrossProduct(p, tmp, direction); p /= norm; return true; @@ -312,19 +190,19 @@ // Create the coordinates of the rectangle Vector x[4]; - AssignVector(x[0], xmin, ymin, 1.0); - AssignVector(x[1], xmax, ymin, 1.0); - AssignVector(x[2], xmax, ymax, 1.0); - AssignVector(x[3], xmin, ymax, 1.0); + LinearAlgebra::AssignVector(x[0], xmin, ymin, 1.0); + LinearAlgebra::AssignVector(x[1], xmax, ymin, 1.0); + LinearAlgebra::AssignVector(x[2], xmax, ymax, 1.0); + LinearAlgebra::AssignVector(x[3], xmin, ymax, 1.0); // Move to homogoneous coordinates in 2D Vector p; { Vector a, b; - AssignVector(a, ax, ay, 1.0); - AssignVector(b, bx, by, 1.0); - CrossProduct(p, a, b); + LinearAlgebra::AssignVector(a, ax, ay, 1.0); + LinearAlgebra::AssignVector(b, bx, by, 1.0); + LinearAlgebra::CrossProduct(p, a, b); } uint8_t c = 0; @@ -349,10 +227,10 @@ else { Vector a, b, e; - CrossProduct(e, x[i], x[(i + 1) % 4]); - CrossProduct(a, p, e); - CrossProduct(e, x[j], x[(j + 1) % 4]); - CrossProduct(b, p, e); + LinearAlgebra::CrossProduct(e, x[i], x[(i + 1) % 4]); + LinearAlgebra::CrossProduct(a, p, e); + LinearAlgebra::CrossProduct(e, x[j], x[(j + 1) % 4]); + LinearAlgebra::CrossProduct(b, p, e); // Go back to non-homogeneous coordinates x1 = a[0] / a[2]; @@ -371,7 +249,7 @@ { Vector v; - if (ParseVector(v, dicom, Orthanc::DICOM_TAG_PIXEL_SPACING)) + if (LinearAlgebra::ParseVector(v, dicom, Orthanc::DICOM_TAG_PIXEL_SPACING)) { if (v.size() != 2 || v[0] <= 0 || @@ -513,51 +391,5 @@ return true; } } - - - void FillMatrix(Matrix& target, - size_t rows, - size_t columns, - const double values[]) - { - target.resize(rows, columns); - - size_t index = 0; - - for (size_t y = 0; y < rows; y++) - { - for (size_t x = 0; x < columns; x++, index++) - { - target(y, x) = values[index]; - } - } - } - - - void FillVector(Vector& target, - size_t size, - const double values[]) - { - target.resize(size); - - for (size_t i = 0; i < size; i++) - { - target[i] = values[i]; - } - } - - - void Convert(Matrix& target, - const Vector& source) - { - const size_t n = source.size(); - - target.resize(n, 1); - - for (size_t i = 0; i < n; i++) - { - target(i, 0) = source[i]; - } - } } } diff -r 2309e8d86efe -r a053ca7fa5c6 Framework/Toolbox/GeometryToolbox.h --- a/Framework/Toolbox/GeometryToolbox.h Fri Feb 09 16:00:29 2018 +0100 +++ b/Framework/Toolbox/GeometryToolbox.h Wed Feb 14 08:58:31 2018 +0100 @@ -21,67 +21,12 @@ #pragma once -// Patch for ublas in Boost 1.64.0 -// https://github.com/dealii/dealii/issues/4302 -#include -#if BOOST_VERSION >= 106300 // or 64, need to check -# include -#endif - -#include - -#include -#include -#include +#include "LinearAlgebra.h" namespace OrthancStone { - typedef boost::numeric::ublas::matrix Matrix; - typedef boost::numeric::ublas::vector Vector; - namespace GeometryToolbox { - void Print(const Vector& v); - - void Print(const Matrix& m); - - bool ParseVector(Vector& target, - const std::string& s); - - bool ParseVector(Vector& target, - const Orthanc::DicomMap& dataset, - const Orthanc::DicomTag& tag); - - void AssignVector(Vector& v, - double v1, - double v2); - - void AssignVector(Vector& v, - double v1, - double v2, - double v3); - - inline bool IsNear(double x, - double y, - double threshold) - { - return fabs(x - y) < threshold; - } - - bool IsNear(double x, - double y); - - inline bool IsCloseToZero(double x) - { - return IsNear(x, 0.0); - } - - void NormalizeVector(Vector& u); - - void CrossProduct(Vector& result, - const Vector& u, - const Vector& v); - void ProjectPointOntoPlane(Vector& result, const Vector& point, const Vector& planeNormal, @@ -142,18 +87,6 @@ const Vector& origin, const Vector& direction); - void FillMatrix(Matrix& target, - size_t rows, - size_t columns, - const double values[]); - - void FillVector(Vector& target, - size_t size, - const double values[]); - - void Convert(Matrix& target, - const Vector& source); - inline float ComputeBilinearInterpolationInternal(float x, float y, float f00, // source(x, y) diff -r 2309e8d86efe -r a053ca7fa5c6 Framework/Toolbox/LinearAlgebra.cpp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Framework/Toolbox/LinearAlgebra.cpp Wed Feb 14 08:58:31 2018 +0100 @@ -0,0 +1,200 @@ +/** + * 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 . + **/ + + +#include "LinearAlgebra.h" + +#include +#include +#include + +#include +#include + +namespace OrthancStone +{ + namespace LinearAlgebra + { + void Print(const Vector& v) + { + for (size_t i = 0; i < v.size(); i++) + { + printf("%g\n", v[i]); + //printf("%8.2f\n", v[i]); + } + printf("\n"); + } + + + void Print(const Matrix& m) + { + for (size_t i = 0; i < m.size1(); i++) + { + for (size_t j = 0; j < m.size2(); j++) + { + printf("%g ", m(i,j)); + //printf("%8.2f ", m(i,j)); + } + printf("\n"); + } + printf("\n"); + } + + + bool ParseVector(Vector& target, + const std::string& value) + { + std::vector items; + Orthanc::Toolbox::TokenizeString(items, value, '\\'); + + target.resize(items.size()); + + for (size_t i = 0; i < items.size(); i++) + { + try + { + target[i] = boost::lexical_cast(Orthanc::Toolbox::StripSpaces(items[i])); + } + catch (boost::bad_lexical_cast&) + { + target.clear(); + return false; + } + } + + return true; + } + + + bool ParseVector(Vector& target, + const Orthanc::DicomMap& dataset, + const Orthanc::DicomTag& tag) + { + std::string value; + return (dataset.CopyToString(value, tag, false) && + ParseVector(target, value)); + } + + + void AssignVector(Vector& v, + double v1, + double v2) + { + v.resize(2); + v[0] = v1; + v[1] = v2; + } + + + void AssignVector(Vector& v, + double v1, + double v2, + double v3) + { + v.resize(3); + v[0] = v1; + v[1] = v2; + v[2] = v3; + } + + + bool IsNear(double x, + double y) + { + // As most input is read as single-precision numbers, we take the + // epsilon machine for float32 into consideration to compare numbers + return IsNear(x, y, 10.0 * std::numeric_limits::epsilon()); + } + + + void NormalizeVector(Vector& u) + { + double norm = boost::numeric::ublas::norm_2(u); + if (!IsCloseToZero(norm)) + { + u = u / norm; + } + } + + + void CrossProduct(Vector& result, + const Vector& u, + const Vector& v) + { + if (u.size() != 3 || + v.size() != 3) + { + throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); + } + + result.resize(3); + + result[0] = u[1] * v[2] - u[2] * v[1]; + result[1] = u[2] * v[0] - u[0] * v[2]; + result[2] = u[0] * v[1] - u[1] * v[0]; + } + + + void FillMatrix(Matrix& target, + size_t rows, + size_t columns, + const double values[]) + { + target.resize(rows, columns); + + size_t index = 0; + + for (size_t y = 0; y < rows; y++) + { + for (size_t x = 0; x < columns; x++, index++) + { + target(y, x) = values[index]; + } + } + } + + + void FillVector(Vector& target, + size_t size, + const double values[]) + { + target.resize(size); + + for (size_t i = 0; i < size; i++) + { + target[i] = values[i]; + } + } + + + void Convert(Matrix& target, + const Vector& source) + { + const size_t n = source.size(); + + target.resize(n, 1); + + for (size_t i = 0; i < n; i++) + { + target(i, 0) = source[i]; + } + } + } +} diff -r 2309e8d86efe -r a053ca7fa5c6 Framework/Toolbox/LinearAlgebra.h --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Framework/Toolbox/LinearAlgebra.h Wed Feb 14 08:58:31 2018 +0100 @@ -0,0 +1,96 @@ +/** + * 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 . + **/ + + +#pragma once + +// Patch for ublas in Boost 1.64.0 +// https://github.com/dealii/dealii/issues/4302 +#include +#if BOOST_VERSION >= 106300 // or 64, need to check +# include +#endif + +#include + +#include +#include + +namespace OrthancStone +{ + typedef boost::numeric::ublas::matrix Matrix; + typedef boost::numeric::ublas::vector Vector; + + namespace LinearAlgebra + { + void Print(const Vector& v); + + void Print(const Matrix& m); + + bool ParseVector(Vector& target, + const std::string& s); + + bool ParseVector(Vector& target, + const Orthanc::DicomMap& dataset, + const Orthanc::DicomTag& tag); + + void AssignVector(Vector& v, + double v1, + double v2); + + void AssignVector(Vector& v, + double v1, + double v2, + double v3); + + inline bool IsNear(double x, + double y, + double threshold) + { + return fabs(x - y) < threshold; + } + + bool IsNear(double x, + double y); + + inline bool IsCloseToZero(double x) + { + return IsNear(x, 0.0); + } + + void NormalizeVector(Vector& u); + + void CrossProduct(Vector& result, + const Vector& u, + const Vector& v); + + void FillMatrix(Matrix& target, + size_t rows, + size_t columns, + const double values[]); + + void FillVector(Vector& target, + size_t size, + const double values[]); + + void Convert(Matrix& target, + const Vector& source); + }; +} diff -r 2309e8d86efe -r a053ca7fa5c6 Framework/Toolbox/OrientedBoundingBox.cpp --- a/Framework/Toolbox/OrientedBoundingBox.cpp Fri Feb 09 16:00:29 2018 +0100 +++ b/Framework/Toolbox/OrientedBoundingBox.cpp Wed Feb 14 08:58:31 2018 +0100 @@ -237,7 +237,7 @@ double y = boost::numeric::ublas::inner_prod(q, v_) / (2.0 * hv_) + 0.5; double z = boost::numeric::ublas::inner_prod(q, w_) / (2.0 * hw_) + 0.5; - GeometryToolbox::AssignVector(target, x, y, z); + LinearAlgebra::AssignVector(target, x, y, z); } diff -r 2309e8d86efe -r a053ca7fa5c6 Framework/Toolbox/ParallelSlices.cpp --- a/Framework/Toolbox/ParallelSlices.cpp Fri Feb 09 16:00:29 2018 +0100 +++ b/Framework/Toolbox/ParallelSlices.cpp Wed Feb 14 08:58:31 2018 +0100 @@ -28,7 +28,7 @@ { ParallelSlices::ParallelSlices() { - GeometryToolbox::AssignVector(normal_, 0, 0, 1); + LinearAlgebra::AssignVector(normal_, 0, 0, 1); } diff -r 2309e8d86efe -r a053ca7fa5c6 Framework/Toolbox/Slice.cpp --- a/Framework/Toolbox/Slice.cpp Fri Feb 09 16:00:29 2018 +0100 +++ b/Framework/Toolbox/Slice.cpp Wed Feb 14 08:58:31 2018 +0100 @@ -87,7 +87,7 @@ return false; } - if (!GeometryToolbox::IsCloseToZero(offset0)) + if (!LinearAlgebra::IsCloseToZero(offset0)) { LOG(ERROR) << "Invalid syntax"; return false; @@ -304,9 +304,9 @@ return (GeometryToolbox::IsParallelOrOpposite(opposite, GetGeometry().GetNormal(), plane.GetNormal()) && - GeometryToolbox::IsNear(GetGeometry().ProjectAlongNormal(GetGeometry().GetOrigin()), - GetGeometry().ProjectAlongNormal(plane.GetOrigin()), - thickness_ / 2.0)); + LinearAlgebra::IsNear(GetGeometry().ProjectAlongNormal(GetGeometry().GetOrigin()), + GetGeometry().ProjectAlongNormal(plane.GetOrigin()), + thickness_ / 2.0)); } diff -r 2309e8d86efe -r a053ca7fa5c6 Framework/Volumes/ImageBuffer3D.cpp --- a/Framework/Volumes/ImageBuffer3D.cpp Fri Feb 09 16:00:29 2018 +0100 +++ b/Framework/Volumes/ImageBuffer3D.cpp Wed Feb 14 08:58:31 2018 +0100 @@ -122,7 +122,7 @@ computeRange_(computeRange), hasRange_(false) { - GeometryToolbox::AssignVector(voxelDimensions_, 1, 1, 1); + LinearAlgebra::AssignVector(voxelDimensions_, 1, 1, 1); LOG(INFO) << "Created an image of " << (GetEstimatedMemorySize() / (1024ll * 1024ll)) << "MB"; @@ -153,7 +153,7 @@ } { - GeometryToolbox::AssignVector(voxelDimensions_, x, y, z); + LinearAlgebra::AssignVector(voxelDimensions_, x, y, z); } } @@ -168,11 +168,11 @@ break; case VolumeProjection_Coronal: - GeometryToolbox::AssignVector(result, voxelDimensions_[0], voxelDimensions_[2], voxelDimensions_[1]); + LinearAlgebra::AssignVector(result, voxelDimensions_[0], voxelDimensions_[2], voxelDimensions_[1]); break; case VolumeProjection_Sagittal: - GeometryToolbox::AssignVector(result, voxelDimensions_[1], voxelDimensions_[2], voxelDimensions_[0]); + LinearAlgebra::AssignVector(result, voxelDimensions_[1], voxelDimensions_[2], voxelDimensions_[0]); break; default: diff -r 2309e8d86efe -r a053ca7fa5c6 Framework/Volumes/VolumeReslicer.cpp --- a/Framework/Volumes/VolumeReslicer.cpp Fri Feb 09 16:00:29 2018 +0100 +++ b/Framework/Volumes/VolumeReslicer.cpp Wed Feb 14 08:58:31 2018 +0100 @@ -849,7 +849,7 @@ slow.GetNearestCoordinates(qx, qy, qz); Vector d; - GeometryToolbox::AssignVector(d, px - qx, py - qy, pz - qz); + LinearAlgebra::AssignVector(d, px - qx, py - qy, pz - qz); double norm = boost::numeric::ublas::norm_2(d); if (norm > 0.0001) { diff -r 2309e8d86efe -r a053ca7fa5c6 Framework/dev.h --- a/Framework/dev.h Fri Feb 09 16:00:29 2018 +0100 +++ b/Framework/dev.h Wed Feb 14 08:58:31 2018 +0100 @@ -86,8 +86,8 @@ return false; } - if (!GeometryToolbox::IsNear(a.GetPixelSpacingX(), b.GetPixelSpacingX()) || - !GeometryToolbox::IsNear(a.GetPixelSpacingY(), b.GetPixelSpacingY())) + if (!LinearAlgebra::IsNear(a.GetPixelSpacingX(), b.GetPixelSpacingX()) || + !LinearAlgebra::IsNear(a.GetPixelSpacingY(), b.GetPixelSpacingY())) { LOG(ERROR) << "The pixel spacing of the slices change across the volume image"; return false; @@ -138,8 +138,8 @@ for (size_t i = 1; i < loader.GetSliceCount(); i++) { - if (!GeometryToolbox::IsNear(spacingZ, GetDistance(loader.GetSlice(i - 1), loader.GetSlice(i)), - 0.001 /* this is expressed in mm */)) + if (!LinearAlgebra::IsNear(spacingZ, GetDistance(loader.GetSlice(i - 1), loader.GetSlice(i)), + 0.001 /* this is expressed in mm */)) { LOG(ERROR) << "The distance between successive slices is not constant in a volume image"; SlicedVolumeBase::NotifyGeometryError(); diff -r 2309e8d86efe -r a053ca7fa5c6 Resources/CMake/OrthancStoneConfiguration.cmake --- a/Resources/CMake/OrthancStoneConfiguration.cmake Fri Feb 09 16:00:29 2018 +0100 +++ b/Resources/CMake/OrthancStoneConfiguration.cmake Wed Feb 14 08:58:31 2018 +0100 @@ -181,6 +181,7 @@ ${ORTHANC_STONE_DIR}/Framework/Toolbox/DownloadStack.cpp ${ORTHANC_STONE_DIR}/Framework/Toolbox/Extent2D.cpp ${ORTHANC_STONE_DIR}/Framework/Toolbox/GeometryToolbox.cpp + ${ORTHANC_STONE_DIR}/Framework/Toolbox/LinearAlgebra.cpp ${ORTHANC_STONE_DIR}/Framework/Toolbox/MessagingToolbox.cpp ${ORTHANC_STONE_DIR}/Framework/Toolbox/OrientedBoundingBox.cpp ${ORTHANC_STONE_DIR}/Framework/Toolbox/OrthancSlicesLoader.cpp @@ -195,9 +196,9 @@ ${ORTHANC_STONE_DIR}/Framework/Viewport/WidgetViewport.cpp ${ORTHANC_STONE_DIR}/Framework/Volumes/ImageBuffer3D.cpp ${ORTHANC_STONE_DIR}/Framework/Volumes/SlicedVolumeBase.cpp + ${ORTHANC_STONE_DIR}/Framework/Volumes/StructureSetLoader.cpp ${ORTHANC_STONE_DIR}/Framework/Volumes/VolumeLoaderBase.cpp ${ORTHANC_STONE_DIR}/Framework/Volumes/VolumeReslicer.cpp - ${ORTHANC_STONE_DIR}/Framework/Volumes/StructureSetLoader.cpp ${ORTHANC_STONE_DIR}/Framework/Widgets/CairoWidget.cpp ${ORTHANC_STONE_DIR}/Framework/Widgets/EmptyWidget.cpp ${ORTHANC_STONE_DIR}/Framework/Widgets/LayerWidget.cpp