Mercurial > hg > orthanc-stone
view Framework/Toolbox/DicomStructureSet.cpp @ 466:5055031f4a06 bgo-commands-codegen
- Added browserify to build. This allows using require calls for modules that
work with tsc compiler.
- removed older stuff related to Protocol Buffers and Flatbuffers
- changed triple-slash references to import statements
- module prefixes are now added at call sites
- added cmake module for filename handling
- switched to Ninja for sample build
- Added virtual dtor in ICommand
author | bgo-osimis |
---|---|
date | Mon, 11 Feb 2019 16:00:04 +0100 |
parents | b70e9be013e4 |
children | 11fa6f00e33c |
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/** * Stone of Orthanc * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics * Department, University Hospital of Liege, Belgium * Copyright (C) 2017-2019 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 "DicomStructureSet.h" #include "../Toolbox/GeometryToolbox.h" #include "../Toolbox/MessagingToolbox.h" #include <Core/Logging.h> #include <Core/OrthancException.h> #include <Plugins/Samples/Common/FullOrthancDataset.h> #include <Plugins/Samples/Common/DicomDatasetReader.h> #include <limits> #include <stdio.h> #include <boost/lexical_cast.hpp> #include <boost/geometry.hpp> #include <boost/geometry/geometries/point_xy.hpp> #include <boost/geometry/geometries/polygon.hpp> #include <boost/geometry/multi/geometries/multi_polygon.hpp> typedef boost::geometry::model::d2::point_xy<double> BoostPoint; typedef boost::geometry::model::polygon<BoostPoint> BoostPolygon; typedef boost::geometry::model::multi_polygon<BoostPolygon> BoostMultiPolygon; static void Union(BoostMultiPolygon& output, std::vector<BoostPolygon>& input) { for (size_t i = 0; i < input.size(); i++) { boost::geometry::correct(input[i]); } if (input.size() == 0) { output.clear(); } else if (input.size() == 1) { output.resize(1); output[0] = input[0]; } else { boost::geometry::union_(input[0], input[1], output); for (size_t i = 0; i < input.size(); i++) { BoostMultiPolygon tmp; boost::geometry::union_(output, input[i], tmp); output = tmp; } } } static BoostPolygon CreateRectangle(float x1, float y1, float x2, float y2) { BoostPolygon r; boost::geometry::append(r, BoostPoint(x1, y1)); boost::geometry::append(r, BoostPoint(x1, y2)); boost::geometry::append(r, BoostPoint(x2, y2)); boost::geometry::append(r, BoostPoint(x2, y1)); return r; } namespace OrthancStone { static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042); static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016); static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040); static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_DATA(0x3006, 0x0050); static const OrthancPlugins::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046); static const OrthancPlugins::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155); static const OrthancPlugins::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039); static const OrthancPlugins::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a); static const OrthancPlugins::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026); static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4); static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080); static const OrthancPlugins::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020); static uint8_t ConvertColor(double v) { if (v < 0) { return 0; } else if (v >= 255) { return 255; } else { return static_cast<uint8_t>(v); } } static bool ParseVector(Vector& target, const OrthancPlugins::IDicomDataset& dataset, const OrthancPlugins::DicomPath& tag) { std::string value; return (dataset.GetStringValue(value, tag) && LinearAlgebra::ParseVector(target, value)); } void DicomStructureSet::Polygon::CheckPoint(const Vector& v) { if (hasSlice_) { 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); } } } void DicomStructureSet::Polygon::AddPoint(const Vector& v) { CheckPoint(v); points_.push_back(v); } bool DicomStructureSet::Polygon::UpdateReferencedSlice(const ReferencedSlices& slices) { if (hasSlice_) { return true; } else { ReferencedSlices::const_iterator it = slices.find(sopInstanceUid_); if (it == slices.end()) { return false; } else { const CoordinateSystem3D& geometry = it->second.geometry_; hasSlice_ = true; geometry_ = geometry; projectionAlongNormal_ = GeometryToolbox::ProjectAlongNormal(geometry.GetOrigin(), geometry.GetNormal()); sliceThickness_ = it->second.thickness_; extent_.Reset(); for (Points::const_iterator it = points_.begin(); it != points_.end(); ++it) { CheckPoint(*it); double x, y; geometry.ProjectPoint(x, y, *it); extent_.AddPoint(x, y); } return true; } } } bool DicomStructureSet::Polygon::IsOnSlice(const CoordinateSystem3D& slice) const { bool isOpposite; if (points_.empty() || !hasSlice_ || !GeometryToolbox::IsParallelOrOpposite(isOpposite, slice.GetNormal(), geometry_.GetNormal())) { return false; } double d = GeometryToolbox::ProjectAlongNormal(slice.GetOrigin(), geometry_.GetNormal()); return (LinearAlgebra::IsNear(d, projectionAlongNormal_, sliceThickness_ / 2.0)); } bool DicomStructureSet::Polygon::Project(double& x1, double& y1, double& x2, double& y2, const CoordinateSystem3D& slice) const { // TODO Optimize this method using a sweep-line algorithm for polygons if (!hasSlice_ || points_.size() <= 1) { return false; } double x, y; geometry_.ProjectPoint(x, y, slice.GetOrigin()); bool isOpposite; if (GeometryToolbox::IsParallelOrOpposite (isOpposite, slice.GetNormal(), geometry_.GetAxisY())) { if (y < extent_.GetY1() || y > extent_.GetY2()) { // The polygon does not intersect the input slice return false; } bool isFirst = true; double xmin = std::numeric_limits<double>::infinity(); double xmax = -std::numeric_limits<double>::infinity(); double prevX, prevY; geometry_.ProjectPoint(prevX, prevY, points_[points_.size() - 1]); for (size_t i = 0; i < points_.size(); i++) { // Reference: ../../Resources/Computations/IntersectSegmentAndHorizontalLine.py double curX, curY; geometry_.ProjectPoint(curX, curY, points_[i]); if ((prevY < y && curY > y) || (prevY > y && curY < y)) { double p = (curX * prevY - curY * prevX + y * (prevX - curX)) / (prevY - curY); xmin = std::min(xmin, p); xmax = std::max(xmax, p); isFirst = false; } prevX = curX; prevY = curY; } if (isFirst) { return false; } else { Vector p1 = (geometry_.MapSliceToWorldCoordinates(xmin, y) + sliceThickness_ / 2.0 * geometry_.GetNormal()); Vector p2 = (geometry_.MapSliceToWorldCoordinates(xmax, y) - sliceThickness_ / 2.0 * geometry_.GetNormal()); slice.ProjectPoint(x1, y1, p1); slice.ProjectPoint(x2, y2, p2); return true; } } else if (GeometryToolbox::IsParallelOrOpposite (isOpposite, slice.GetNormal(), geometry_.GetAxisX())) { if (x < extent_.GetX1() || x > extent_.GetX2()) { return false; } bool isFirst = true; double ymin = std::numeric_limits<double>::infinity(); double ymax = -std::numeric_limits<double>::infinity(); double prevX, prevY; geometry_.ProjectPoint(prevX, prevY, points_[points_.size() - 1]); for (size_t i = 0; i < points_.size(); i++) { // Reference: ../../Resources/Computations/IntersectSegmentAndVerticalLine.py double curX, curY; geometry_.ProjectPoint(curX, curY, points_[i]); if ((prevX < x && curX > x) || (prevX > x && curX < x)) { double p = (curX * prevY - curY * prevX + x * (curY - prevY)) / (curX - prevX); ymin = std::min(ymin, p); ymax = std::max(ymax, p); isFirst = false; } prevX = curX; prevY = curY; } if (isFirst) { return false; } else { Vector p1 = (geometry_.MapSliceToWorldCoordinates(x, ymin) + sliceThickness_ / 2.0 * geometry_.GetNormal()); Vector p2 = (geometry_.MapSliceToWorldCoordinates(x, ymax) - sliceThickness_ / 2.0 * geometry_.GetNormal()); slice.ProjectPoint(x1, y1, p1); slice.ProjectPoint(x2, y2, p2); // TODO WHY THIS??? y1 = -y1; y2 = -y2; return true; } } else { // Should not happen return false; } } const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const { if (index >= structures_.size()) { throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); } return structures_[index]; } DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) { if (index >= structures_.size()) { throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); } return structures_[index]; } DicomStructureSet::DicomStructureSet(const OrthancPlugins::FullOrthancDataset& tags) { using namespace OrthancPlugins; DicomDatasetReader reader(tags); size_t count, tmp; if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) || !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) || tmp != count || !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) || tmp != count) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); } structures_.resize(count); for (size_t i = 0; i < count; i++) { structures_[i].interpretation_ = reader.GetStringValue (DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, DICOM_TAG_RT_ROI_INTERPRETED_TYPE), "No interpretation"); structures_[i].name_ = reader.GetStringValue (DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, DICOM_TAG_ROI_NAME), "No interpretation"); Vector color; if (ParseVector(color, tags, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, DICOM_TAG_ROI_DISPLAY_COLOR)) && color.size() == 3) { structures_[i].red_ = ConvertColor(color[0]); structures_[i].green_ = ConvertColor(color[1]); structures_[i].blue_ = ConvertColor(color[2]); } else { structures_[i].red_ = 255; structures_[i].green_ = 0; structures_[i].blue_ = 0; } size_t countSlices; if (!tags.GetSequenceSize(countSlices, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, DICOM_TAG_CONTOUR_SEQUENCE))) { countSlices = 0; } LOG(WARNING) << "New RT structure: \"" << structures_[i].name_ << "\" with interpretation \"" << structures_[i].interpretation_ << "\" containing " << countSlices << " slices (color: " << static_cast<int>(structures_[i].red_) << "," << static_cast<int>(structures_[i].green_) << "," << static_cast<int>(structures_[i].blue_) << ")"; for (size_t j = 0; j < countSlices; j++) { unsigned int countPoints; if (!reader.GetUnsignedIntegerValue (countPoints, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, DICOM_TAG_CONTOUR_SEQUENCE, j, DICOM_TAG_NUMBER_OF_CONTOUR_POINTS))) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); } //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; std::string type = reader.GetMandatoryStringValue (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, DICOM_TAG_CONTOUR_SEQUENCE, j, DICOM_TAG_CONTOUR_GEOMETRIC_TYPE)); if (type != "CLOSED_PLANAR") { LOG(WARNING) << "Ignoring contour with geometry type: " << type; continue; } size_t size; if (!tags.GetSequenceSize(size, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, DICOM_TAG_CONTOUR_SEQUENCE, j, DICOM_TAG_CONTOUR_IMAGE_SEQUENCE)) || size != 1) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); } std::string sopInstanceUid = reader.GetMandatoryStringValue (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, DICOM_TAG_CONTOUR_SEQUENCE, j, DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, DICOM_TAG_REFERENCED_SOP_INSTANCE_UID)); std::string slicesData = reader.GetMandatoryStringValue (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, DICOM_TAG_CONTOUR_SEQUENCE, j, DICOM_TAG_CONTOUR_DATA)); Vector points; if (!LinearAlgebra::ParseVector(points, slicesData) || points.size() != 3 * countPoints) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); } Polygon polygon(sopInstanceUid); polygon.Reserve(countPoints); for (size_t k = 0; k < countPoints; k++) { Vector v(3); v[0] = points[3 * k]; v[1] = points[3 * k + 1]; v[2] = points[3 * k + 2]; polygon.AddPoint(v); } structures_[i].polygons_.push_back(polygon); } } } Vector DicomStructureSet::GetStructureCenter(size_t index) const { const Structure& structure = GetStructure(index); Vector center; LinearAlgebra::AssignVector(center, 0, 0, 0); if (structure.polygons_.empty()) { return center; } double n = static_cast<double>(structure.polygons_.size()); for (Polygons::const_iterator polygon = structure.polygons_.begin(); polygon != structure.polygons_.end(); ++polygon) { if (!polygon->GetPoints().empty()) { center += polygon->GetPoints().front() / n; } } return center; } const std::string& DicomStructureSet::GetStructureName(size_t index) const { return GetStructure(index).name_; } const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const { return GetStructure(index).interpretation_; } void DicomStructureSet::GetStructureColor(uint8_t& red, uint8_t& green, uint8_t& blue, size_t index) const { const Structure& s = GetStructure(index); red = s.red_; green = s.green_; blue = s.blue_; } void DicomStructureSet::GetReferencedInstances(std::set<std::string>& instances) { for (Structures::const_iterator structure = structures_.begin(); structure != structures_.end(); ++structure) { for (Polygons::const_iterator polygon = structure->polygons_.begin(); polygon != structure->polygons_.end(); ++polygon) { instances.insert(polygon->GetSopInstanceUid()); } } } void DicomStructureSet::AddReferencedSlice(const std::string& sopInstanceUid, const std::string& seriesInstanceUid, const CoordinateSystem3D& geometry, double thickness) { if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()) { // This geometry is already known throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); } else { if (thickness < 0) { throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); } if (!referencedSlices_.empty()) { const ReferencedSlice& reference = referencedSlices_.begin()->second; if (reference.seriesInstanceUid_ != seriesInstanceUid) { LOG(ERROR) << "This RT-STRUCT refers to several different series"; throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); } if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal())) { LOG(ERROR) << "The slices in this RT-STRUCT are not parallel"; throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); } } referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness); for (Structures::iterator structure = structures_.begin(); structure != structures_.end(); ++structure) { for (Polygons::iterator polygon = structure->polygons_.begin(); polygon != structure->polygons_.end(); ++polygon) { polygon->UpdateReferencedSlice(referencedSlices_); } } } } void DicomStructureSet::AddReferencedSlice(const Orthanc::DicomMap& dataset) { CoordinateSystem3D slice(dataset); double thickness = 1; // 1 mm by default std::string s; Vector v; if (dataset.CopyToString(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) && LinearAlgebra::ParseVector(v, s) && v.size() > 0) { thickness = v[0]; } std::string instance, series; if (dataset.CopyToString(instance, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false) && dataset.CopyToString(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false)) { AddReferencedSlice(instance, series, slice, thickness); } else { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); } } void DicomStructureSet::CheckReferencedSlices() { for (Structures::iterator structure = structures_.begin(); structure != structures_.end(); ++structure) { for (Polygons::iterator polygon = structure->polygons_.begin(); polygon != structure->polygons_.end(); ++polygon) { if (!polygon->UpdateReferencedSlice(referencedSlices_)) { LOG(ERROR) << "Missing information about referenced instance: " << polygon->GetSopInstanceUid(); throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); } } } } Vector DicomStructureSet::GetNormal() const { if (referencedSlices_.empty()) { Vector v; LinearAlgebra::AssignVector(v, 0, 0, 1); return v; } else { return referencedSlices_.begin()->second.geometry_.GetNormal(); } } DicomStructureSet* DicomStructureSet::SynchronousLoad(OrthancPlugins::IOrthancConnection& orthanc, const std::string& instanceId) { const std::string uri = "/instances/" + instanceId + "/tags?ignore-length=3006-0050"; OrthancPlugins::FullOrthancDataset dataset(orthanc, uri); std::auto_ptr<DicomStructureSet> result(new DicomStructureSet(dataset)); std::set<std::string> instances; result->GetReferencedInstances(instances); for (std::set<std::string>::const_iterator it = instances.begin(); it != instances.end(); ++it) { Json::Value lookup; MessagingToolbox::RestApiPost(lookup, orthanc, "/tools/lookup", *it); if (lookup.type() != Json::arrayValue || lookup.size() != 1 || !lookup[0].isMember("Type") || !lookup[0].isMember("Path") || lookup[0]["Type"].type() != Json::stringValue || lookup[0]["ID"].type() != Json::stringValue || lookup[0]["Type"].asString() != "Instance") { throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); } OrthancPlugins::FullOrthancDataset slice (orthanc, "/instances/" + lookup[0]["ID"].asString() + "/tags"); Orthanc::DicomMap m; MessagingToolbox::ConvertDataset(m, slice); result->AddReferencedSlice(m); } result->CheckReferencedSlices(); return result.release(); } bool DicomStructureSet::ProjectStructure(std::vector< std::vector<PolygonPoint> >& polygons, Structure& structure, const CoordinateSystem3D& slice) { polygons.clear(); Vector normal = GetNormal(); bool isOpposite; if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetNormal())) { // This is an axial projection for (Polygons::iterator polygon = structure.polygons_.begin(); polygon != structure.polygons_.end(); ++polygon) { if (polygon->IsOnSlice(slice)) { polygons.push_back(std::vector<PolygonPoint>()); for (Points::const_iterator p = polygon->GetPoints().begin(); p != polygon->GetPoints().end(); ++p) { double x, y; slice.ProjectPoint(x, y, *p); polygons.back().push_back(std::make_pair(x, y)); } } } return true; } else if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisX()) || GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisY())) { #if 1 // Sagittal or coronal projection std::vector<BoostPolygon> projected; for (Polygons::iterator polygon = structure.polygons_.begin(); polygon != structure.polygons_.end(); ++polygon) { double x1, y1, x2, y2; if (polygon->Project(x1, y1, x2, y2, slice)) { projected.push_back(CreateRectangle(x1, y1, x2, y2)); } } BoostMultiPolygon merged; Union(merged, projected); polygons.resize(merged.size()); for (size_t i = 0; i < merged.size(); i++) { const std::vector<BoostPoint>& outer = merged[i].outer(); polygons[i].resize(outer.size()); for (size_t j = 0; j < outer.size(); j++) { polygons[i][j] = std::make_pair(outer[j].x(), outer[j].y()); } } #else for (Polygons::iterator polygon = structure.polygons_.begin(); polygon != structure.polygons_.end(); ++polygon) { double x1, y1, x2, y2; if (polygon->Project(x1, y1, x2, y2, slice)) { std::vector<PolygonPoint> p(4); p[0] = std::make_pair(x1, y1); p[1] = std::make_pair(x2, y1); p[2] = std::make_pair(x2, y2); p[3] = std::make_pair(x1, y2); polygons.push_back(p); } } #endif return true; } else { return false; } } }