orthanc-stl: Sources/Plugin.cpp comparison

comparison Sources/Plugin.cpp @ 1:0f03a8a0bd6f

encoding of RT-STRUCT as STL

author	Sebastien Jodogne <s.jodogne@gmail.com>
date	Mon, 17 Jul 2023 18:54:31 +0200
parents	4e889a8e8be2
children	2bdb9acb7dcf

comparison

equal deleted inserted replaced

-:4e889a8e8be2
+:0f03a8a0bd6f
 **/
 #include "../Resources/Orthanc/Plugins/OrthancPluginCppWrapper.h"
+#include <ChunkedBuffer.h>
+#include <DicomParsing/ParsedDicomFile.h>
+#include <Images/ImageProcessing.h>
 #include <Logging.h>
+#include <OrthancFramework.h>
+#include <SerializationToolbox.h>
 #include <SystemToolbox.h>
 #include <EmbeddedResources.h>
+#include <vtkImageData.h>
+#include <vtkImageResize.h>
+#include <vtkMarchingCubes.h>
+#include <vtkNew.h>
+#include <vtkPolyData.h>
+#include <vtkTriangle.h>
+#include <vtkSmoothPolyDataFilter.h>
+#include <vtkPolyDataNormals.h>
+#include <vtkImageConstantPad.h>
 #include <boost/thread/shared_mutex.hpp>
 // Forward declaration
 void ReadStaticAsset(std::string& target,
 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), Orthanc::EnumerationToString(Orthanc::MimeType_JavaScript));
 }
 else
 {
 cache_.Answer(output, file);
+}
+}
+#include <dcmtk/dcmdata/dcdeftag.h>
+#include <dcmtk/dcmdata/dcfilefo.h>
+#include <dcmtk/dcmdata/dcitem.h>
+#include <dcmtk/dcmdata/dcsequen.h>
+class Extent2D : public boost::noncopyable
+{
+private:
+bool    isEmpty_;
+double  x1_;
+double  y1_;
+double  x2_;
+double  y2_;
+void CheckNotEmpty() const
+{
+if (isEmpty_)
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+}
+}
+public:
+Extent2D() :
+isEmpty_(true),
+x1_(0),
+y1_(0),
+x2_(0),
+y2_(0)
+{
+}
+bool IsEmpty() const
+{
+return isEmpty_;
+}
+double GetMinX() const
+{
+CheckNotEmpty();
+return x1_;
+}
+double GetMaxX() const
+{
+CheckNotEmpty();
+return x2_;
+}
+double GetMinY() const
+{
+CheckNotEmpty();
+return y1_;
+}
+double GetMaxY() const
+{
+CheckNotEmpty();
+return y2_;
+}
+double GetWidth() const
+{
+CheckNotEmpty();
+return x2_ - x1_;
+}
+double GetHeight() const
+{
+CheckNotEmpty();
+return y2_ - y1_;
+}
+void Add(double x,
+double y)
+{
+if (isEmpty_)
+{
+x1_ = x2_ = x;
+y1_ = y2_ = y;
+isEmpty_ = false;
+}
+else
+{
+x1_ = std::min(x1_, x);
+x2_ = std::max(x2_, x);
+y1_ = std::min(y1_, y);
+y2_ = std::max(y2_, y);
+}
+}
+};
+static void GetStringValue(std::string& value,
+DcmItem& item,
+const DcmTagKey& key)
+{
+const char* s = NULL;
+if (!item.findAndGetString(key, s).good() ||
+s == NULL)
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+}
+else
+{
+value.assign(s);
+}
+}
+static void ListStructuresNames(std::set<std::string>& target,
+Orthanc::ParsedDicomFile& source)
+{
+target.clear();
+DcmSequenceOfItems* sequence = NULL;
+if (!source.GetDcmtkObject().getDataset()->findAndGetSequence(DCM_StructureSetROISequence, sequence).good() ||
+sequence == NULL)
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+}
+for (unsigned long i = 0; i < sequence->card(); i++)
+{
+DcmItem* item = sequence->getItem(i);
+if (item == NULL)
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+}
+else
+{
+std::string value;
+GetStringValue(value, *item, DCM_ROIName);
+target.insert(value);
+}
+}
+}
+static bool IsNear(double a,
+double b)
+{
+return std::abs(a - b) < 10.0 * std::numeric_limits<double>::epsilon();
+}
+class Vector3D
+{
+private:
+double x_;
+double y_;
+double z_;
+public:
+Vector3D() :
+x_(0),
+y_(0),
+z_(0)
+{
+}
+Vector3D(double x,
+double y,
+double z) :
+x_(x),
+y_(y),
+z_(z)
+{
+}
+Vector3D(const Vector3D& from,
+const Vector3D& to) :
+x_(to.x_ - from.x_),
+y_(to.y_ - from.y_),
+z_(to.z_ - from.z_)
+{
+}
+double GetX() const
+{
+return x_;
+}
+double GetY() const
+{
+return y_;
+}
+double GetZ() const
+{
+return z_;
+}
+double ComputeNorm() const
+{
+return sqrt(x_ * x_ + y_ * y_ + z_ * z_);
+}
+void Normalize()
+{
+double norm = ComputeNorm();
+if (!IsNear(norm, 0))
+{
+x_ /= norm;
+y_ /= norm;
+z_ /= norm;
+}
+}
+static Vector3D CrossProduct(const Vector3D& u,
+const Vector3D& v)
+{
+return Vector3D(u.GetY() * v.GetZ() - u.GetZ() * v.GetY(),
+u.GetZ() * v.GetX() - u.GetX() * v.GetZ(),
+u.GetX() * v.GetY() - u.GetY() * v.GetX());
+}
+static double DotProduct(const Vector3D& a,
+const Vector3D& b)
+{
+return a.GetX() * b.GetX() + a.GetY() * b.GetY() + a.GetZ() * b.GetZ();
+}
+};
+static bool MyParseDouble(double& value,
+const std::string& s)
+{
+#if 1
+char* end = NULL;
+value = strtod(s.c_str(), &end);
+return (end == s.c_str() + s.size());
+#else
+return Orthanc::SerializationToolbox::ParseDouble(value, s);
+#endif
+}
+class StructurePolygon : public boost::noncopyable
+{
+private:
+std::string            roiName_;
+std::string            referencedSopInstanceUid_;
+uint8_t                red_;
+uint8_t                green_;
+uint8_t                blue_;
+std::vector<Vector3D>  points_;
+public:
+StructurePolygon(Orthanc::ParsedDicomFile& dicom,
+unsigned long roiIndex,
+unsigned long contourIndex)
+{
+DcmDataset& dataset = *dicom.GetDcmtkObject().getDataset();
+DcmItem* structure = NULL;
+DcmItem* roi = NULL;
+DcmItem* contour = NULL;
+DcmSequenceOfItems* referenced = NULL;
+if (!dataset.findAndGetSequenceItem(DCM_StructureSetROISequence, structure, roiIndex).good() ||
+structure == NULL ||
+!dataset.findAndGetSequenceItem(DCM_ROIContourSequence, roi, roiIndex).good() ||
+roi == NULL ||
+!roi->findAndGetSequenceItem(DCM_ContourSequence, contour, contourIndex).good() ||
+contour == NULL ||
+!contour->findAndGetSequence(DCM_ContourImageSequence, referenced).good() ||
+referenced == NULL ||
+referenced->card() != 1)
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+}
+GetStringValue(roiName_, *structure, DCM_ROIName);
+GetStringValue(referencedSopInstanceUid_, *referenced->getItem(0), DCM_ReferencedSOPInstanceUID);
+std::string s;
+GetStringValue(s, *contour, DCM_ContourGeometricType);
+if (s != "CLOSED_PLANAR")
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+}
+{
+std::string color;
+GetStringValue(color, *roi, DCM_ROIDisplayColor);
+std::vector<std::string> tokens;
+Orthanc::Toolbox::TokenizeString(tokens, color, '\\');
+uint32_t r, g, b;
+if (tokens.size() != 3 ||
+!Orthanc::SerializationToolbox::ParseFirstUnsignedInteger32(r, tokens[0]) ||
+!Orthanc::SerializationToolbox::ParseFirstUnsignedInteger32(g, tokens[1]) ||
+!Orthanc::SerializationToolbox::ParseFirstUnsignedInteger32(b, tokens[2]) ||
+r > 255 ||
+g > 255 ||
+b > 255)
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+}
+red_ = r;
+green_ = g;
+blue_ = b;
+}
+{
+GetStringValue(s, *contour, DCM_ContourData);
+std::vector<std::string> tokens;
+Orthanc::Toolbox::TokenizeString(tokens, s, '\\');
+GetStringValue(s, *contour, DCM_NumberOfContourPoints);
+uint32_t countPoints;
+if (!Orthanc::SerializationToolbox::ParseUnsignedInteger32(countPoints, s) ||
+tokens.size() != 3 * countPoints)
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+}
+points_.reserve(countPoints);
+for (size_t i = 0; i < tokens.size(); i += 3)
+{
+double x, y, z;
+if (!MyParseDouble(x, tokens[i]) ||
+!MyParseDouble(y, tokens[i + 1]) ||
+!MyParseDouble(z, tokens[i + 2]))
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+}
+points_.push_back(Vector3D(x, y, z));
+}
+assert(points_.size() == countPoints);
+}
+}
+const std::string& GetRoiName() const
+{
+return roiName_;
+}
+const std::string& GetReferencedSopInstanceUid() const
+{
+return referencedSopInstanceUid_;
+}
+size_t GetPointsCount() const
+{
+return points_.size();
+}
+const Vector3D& GetPoint(size_t i) const
+{
+if (i >= points_.size())
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+}
+else
+{
+return points_[i];
+}
+}
+bool IsCoplanar(Vector3D& normal) const
+{
+if (points_.size() < 3)
+{
+return false;
+}
+bool hasNormal = false;
+for (size_t i = 0; i < points_.size(); i++)
+{
+normal = Vector3D::CrossProduct(Vector3D(points_[1], points_[0]),
+Vector3D(points_[2], points_[0]));
+if (!IsNear(normal.ComputeNorm(), 0))
+{
+normal.Normalize();
+hasNormal = true;
+}
+}
+if (!hasNormal)
+{
+return false;
+}
+double a = Vector3D::DotProduct(points_[0], normal);
+for (size_t i = 1; i < points_.size(); i++)
+{
+double b = Vector3D::DotProduct(points_[i], normal);
+if (!IsNear(a, b))
+{
+return false;
+}
+}
+return true;
+}
+void Add(Extent2D& extent,
+const Vector3D& axisX,
+const Vector3D& axisY) const
+{
+assert(IsNear(1, axisX.ComputeNorm()));
+assert(IsNear(1, axisY.ComputeNorm()));
+for (size_t i = 0; i < points_.size(); i++)
+{
+extent.Add(Vector3D::DotProduct(axisX, points_[i]),
+Vector3D::DotProduct(axisY, points_[i]));
+}
+}
+};
+struct IsNearPredicate
+{
+bool operator() (const double& a,
+const double& b)
+{
+return IsNear(a, b);
+}
+};
+static void RemoveDuplicateValues(std::vector<double>& v)
+{
+IsNearPredicate predicate;
+std::vector<double>::iterator last = std::unique(v.begin(), v.end(), predicate);
+v.erase(last, v.end());
+}
+class StructureSet : public boost::noncopyable
+{
+private:
+std::vector<StructurePolygon*>  polygons_;
+bool                            hasGeometry_;
+Vector3D                        slicesNormal_;
+double                          slicesSpacing_;
+double                          minProjectionAlongNormal_;
+double                          maxProjectionAlongNormal_;
+std::string                     patientId_;
+std::string                     studyInstanceUid_;
+std::string                     seriesInstanceUid_;
+std::string                     sopInstanceUid_;
+void ComputeGeometry()
+{
+std::list<double> positionsList;
+hasGeometry_ = false;
+for (size_t i = 0; i < polygons_.size(); i++)
+{
+assert(polygons_[i] != NULL);
+Vector3D n;
+if (polygons_[i]->IsCoplanar(n))
+{
+const Vector3D& point = polygons_[i]->GetPoint(0);
+double z = Vector3D::DotProduct(point, n);
+if (!hasGeometry_)
+{
+hasGeometry_ = true;
+slicesNormal_ = n;
+minProjectionAlongNormal_ = z;
+maxProjectionAlongNormal_ = z;
+}
+else if (!IsNear(std::abs(Vector3D::DotProduct(n, slicesNormal_)), 1))
+{
+hasGeometry_ = false;
+// RT-STRUCT with non-parallel slices
+throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
+}
+else
+{
+minProjectionAlongNormal_ = std::min(minProjectionAlongNormal_, z);
+maxProjectionAlongNormal_ = std::max(maxProjectionAlongNormal_, z);
+}
+positionsList.push_back(Vector3D::DotProduct(n, point));
+}
+}
+if (hasGeometry_)
+{
+std::vector<double> positions(positionsList.begin(), positionsList.end());
+assert(!positions.empty());
+std::sort(positions.begin(), positions.end());
+RemoveDuplicateValues(positions);
+assert(!positions.empty());
+if (positions.size() == 1)
+{
+hasGeometry_ = false;
+return;
+}
+std::vector<double> offsets;
+offsets.resize(positions.size() - 1);
+for (size_t i = 0; i < offsets.size(); i++)
+{
+offsets[i] = positions[i + 1] - positions[i];
+assert(offsets[i] > 0);
+}
+std::sort(offsets.begin(), offsets.end());
+RemoveDuplicateValues(offsets);
+slicesSpacing_ = offsets[0];
+for (size_t i = 1; i < offsets.size(); i++)
+{
+double d = offsets[i] / slicesSpacing_;
+if (!IsNear(d, round(d)))
+{
+// Irregular spacing between the slices
+hasGeometry_ = false;
+break;
+}
+}
+}
+}
+void CheckHasGeometry() const
+{
+if (!hasGeometry_)
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+}
+}
+public:
+explicit StructureSet(Orthanc::ParsedDicomFile& dicom) :
+hasGeometry_(false),
+slicesSpacing_(0),
+minProjectionAlongNormal_(0),
+maxProjectionAlongNormal_(0)
+{
+DcmDataset& dataset = *dicom.GetDcmtkObject().getDataset();
+GetStringValue(patientId_, dataset, DCM_PatientID);
+GetStringValue(studyInstanceUid_, dataset, DCM_StudyInstanceUID);
+GetStringValue(seriesInstanceUid_, dataset, DCM_SeriesInstanceUID);
+GetStringValue(sopInstanceUid_, dataset, DCM_SOPInstanceUID);
+DcmSequenceOfItems* rois = NULL;
+if (!dataset.findAndGetSequence(DCM_ROIContourSequence, rois).good() ||
+rois == NULL)
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+}
+std::vector<DcmSequenceOfItems*> contours(rois->card());
+size_t countPolygons = 0;
+for (unsigned long i = 0; i < rois->card(); i++)
+{
+DcmSequenceOfItems* contour = NULL;
+if (!rois->getItem(i)->findAndGetSequence(DCM_ContourSequence, contour).good() ||
+contour == NULL)
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+}
+else
+{
+contours[i] = contour;
+countPolygons += contour->card();
+}
+}
+polygons_.resize(countPolygons);
+size_t pos = 0;
+for (unsigned long i = 0; i < contours.size(); i++)
+{
+for (unsigned long j = 0; j < contours[i]->card(); j++, pos++)
+{
+polygons_[pos] = new StructurePolygon(dicom, i, j);
+}
+}
+assert(pos == countPolygons);
+ComputeGeometry();
+}
+~StructureSet()
+{
+for (size_t i = 0; i < polygons_.size(); i++)
+{
+assert(polygons_[i] != NULL);
+delete polygons_[i];
+}
+}
+const std::string& GetPatient() const
+{
+return patientId_;
+}
+const std::string& GetStudyInstanceUid() const
+{
+return studyInstanceUid_;
+}
+const std::string& GetSeriesInstanceUid() const
+{
+return seriesInstanceUid_;
+}
+const std::string& GetSopInstanceUid() const
+{
+return sopInstanceUid_;
+}
+std::string HashStudy() const
+{
+std::string s;
+Orthanc::Toolbox::ComputeSHA1(s, patientId_ + "|" + studyInstanceUid_);
+return s;
+}
+size_t GetPolygonsCount() const
+{
+return polygons_.size();
+}
+const StructurePolygon& GetPolygon(size_t i) const
+{
+if (i >= polygons_.size())
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+}
+else
+{
+assert(polygons_[i] != NULL);
+return *polygons_[i];
+}
+}
+bool HasGeometry() const
+{
+return hasGeometry_;
+}
+const Vector3D& GetSlicesNormal() const
+{
+CheckHasGeometry();
+return slicesNormal_;
+}
+double GetSlicesSpacing() const
+{
+CheckHasGeometry();
+return slicesSpacing_;
+}
+double GetMinProjectionAlongNormal() const
+{
+CheckHasGeometry();
+return minProjectionAlongNormal_;
+}
+double GetMaxProjectionAlongNormal() const
+{
+CheckHasGeometry();
+return maxProjectionAlongNormal_;
+}
+double ProjectAlongNormal(const StructurePolygon& polygon) const
+{
+CheckHasGeometry();
+return Vector3D::DotProduct(slicesNormal_, polygon.GetPoint(0));
+}
+size_t GetSlicesCount() const
+{
+CheckHasGeometry();
+double c = (maxProjectionAlongNormal_ - minProjectionAlongNormal_) / slicesSpacing_;
+assert(c >= 0);
+if (!IsNear(c, round(c)))
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
+}
+else
+{
+return static_cast<size_t>(round(c)) + 1;
+}
+}
+bool LookupSliceIndex(size_t& slice,
+const StructurePolygon& polygon) const
+{
+CheckHasGeometry();
+double z = ProjectAlongNormal(polygon);
+if (z < minProjectionAlongNormal_ ||
+z > maxProjectionAlongNormal_)
+{
+return false;
+}
+else
+{
+double c = (z - minProjectionAlongNormal_) / slicesSpacing_;
+if (IsNear(c, round(c)))
+{
+slice = static_cast<size_t>(round(c));
+return true;
+}
+else
+{
+return false;
+}
+}
+}
+bool LookupReferencedSopInstanceUid(std::string& sopInstanceUid) const
+{
+if (HasGeometry())
+{
+for (size_t i = 0; i < polygons_.size(); i++)
+{
+assert(polygons_[i] != NULL);
+Vector3D n;
+if (polygons_[i]->IsCoplanar(n) &&
+Vector3D::DotProduct(n, slicesNormal_))
+{
+sopInstanceUid = polygons_[i]->GetReferencedSopInstanceUid();
+return true;
+}
+}
+}
+return false;
+}
+};
+class XorFiller : public Orthanc::ImageProcessing::IPolygonFiller
+{
+private:
+Orthanc::ImageAccessor& target_;
+public:
+XorFiller(Orthanc::ImageAccessor& target) :
+target_(target)
+{
+}
+virtual void Fill(int y,
+int x1,
+int x2) ORTHANC_OVERRIDE
+{
+assert(x1 <= x2);
+if (y >= 0 &&
+y < static_cast<int>(target_.GetHeight()))
+{
+x1 = std::max(x1, 0);
+x2 = std::min(x2, static_cast<int>(target_.GetWidth()) - 1);
+uint8_t* p = reinterpret_cast<uint8_t*>(target_.GetRow(y)) + x1;
+for (int i = x1; i <= x2; i++, p++)
+{
+*p = (*p ^ 0xff);
+}
+}
+}
+};
+static void EncodeSTL(std::string& target /* out */,
+vtkPolyData& mesh /* in */)
+{
+// TODO - Conversion to little endian on big endian
+Orthanc::ChunkedBuffer buffer;
+uint8_t header[80];
+memset(header, 0, sizeof(header));
+buffer.AddChunk(header, sizeof(header));
+uint32_t n = mesh.GetNumberOfCells();
+buffer.AddChunk(&n, sizeof(n));
+for (vtkIdType i = 0; i < mesh.GetNumberOfCells(); i++)
+{
+vtkCell* cell = mesh.GetCell(i);
+vtkTriangle* triangle = dynamic_cast<vtkTriangle*>(cell);
+double p0[3];
+double p1[3];
+double p2[3];
+triangle->GetPoints()->GetPoint(0, p0);
+triangle->GetPoints()->GetPoint(1, p1);
+triangle->GetPoints()->GetPoint(2, p2);
+double normal[3];
+vtkTriangle::ComputeNormal(p0, p1, p2, normal);
+float d[4 * 3] = {
+static_cast<float>(normal[0]), static_cast<float>(normal[1]), static_cast<float>(normal[2]),
+static_cast<float>(p0[0]), static_cast<float>(p0[1]), static_cast<float>(p0[2]),
+static_cast<float>(p1[0]), static_cast<float>(p1[1]), static_cast<float>(p1[2]),
+static_cast<float>(p2[0]), static_cast<float>(p2[1]), static_cast<float>(p2[2]) };
+buffer.AddChunk(d, sizeof(d));
+uint16_t a = 0;
+buffer.AddChunk(&a, sizeof(a));
+}
+buffer.Flatten(target);
+}
+bool EncodeStructureSetMesh(std::string& stl,
+const StructureSet& structureSet,
+const std::set<std::string>& roiNames,
+unsigned int resolution,
+bool smooth)
+{
+if (!structureSet.HasGeometry())
+{
+return false;
+}
+if (resolution < 1)
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+}
+if (!IsNear(1, structureSet.GetSlicesNormal().ComputeNorm()))
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
+}
+// TODO - Axes could be retrieved from the referenced CT volume
+Vector3D axisX(1, 0, 0);
+Vector3D axisY = Vector3D::CrossProduct(structureSet.GetSlicesNormal(), axisX);
+if (!IsNear(1, axisX.ComputeNorm()) ||
+!IsNear(1, axisY.ComputeNorm()))
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
+}
+Extent2D extent;
+for (size_t i = 0; i < structureSet.GetPolygonsCount(); i++)
+{
+structureSet.GetPolygon(i).Add(extent, axisX, axisY);
+}
+const int depth = structureSet.GetSlicesCount();
+vtkNew<vtkImageData> volume;
+volume->SetDimensions(resolution, resolution, depth);
+volume->AllocateScalars(VTK_UNSIGNED_CHAR, 1);
+assert(sizeof(unsigned char) == 1);
+memset(volume->GetScalarPointer(), 0, resolution * resolution * depth);
+for (size_t i = 0; i < structureSet.GetPolygonsCount(); i++)
+{
+const StructurePolygon& polygon = structureSet.GetPolygon(i);
+if (roiNames.find(polygon.GetRoiName()) == roiNames.end())
+{
+// This polygon doesn't correspond to a ROI of interest
+continue;
+}
+size_t j;
+if (!structureSet.LookupSliceIndex(j, polygon))
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
+}
+std::vector<Orthanc::ImageProcessing::ImagePoint> points;
+points.reserve(polygon.GetPointsCount());
+for (size_t j = 0; j < polygon.GetPointsCount(); j++)
+{
+const Vector3D& point = polygon.GetPoint(j);
+double x = (Vector3D::DotProduct(point, axisX) - extent.GetMinX()) / extent.GetWidth() * static_cast<double>(resolution);
+double y = (Vector3D::DotProduct(point, axisY) - extent.GetMinY()) / extent.GetHeight() * static_cast<double>(resolution);
+points.push_back(Orthanc::ImageProcessing::ImagePoint(static_cast<int32_t>(std::floor(x)),
+static_cast<int32_t>(std::floor(y))));
+}
+Orthanc::ImageAccessor slice;
+slice.AssignWritable(Orthanc::PixelFormat_Grayscale8, resolution, resolution, resolution /* pitch */,
+reinterpret_cast<uint8_t*>(volume->GetScalarPointer()) + j * resolution * resolution);
+XorFiller filler(slice);
+Orthanc::ImageProcessing::FillPolygon(filler, points);
+}
+vtkNew<vtkImageResize> resize;
+resize->SetOutputDimensions(resolution, resolution, resolution);
+resize->SetInputData(volume.Get());
+resize->Update();
+resize->GetOutput()->SetSpacing(
+extent.GetWidth() / static_cast<double>(resolution),
+extent.GetHeight() / static_cast<double>(resolution),
+(structureSet.GetMaxProjectionAlongNormal() - structureSet.GetMinProjectionAlongNormal()) / static_cast<double>(resolution));
+// TODO
+// resize->GetOutput()->SetOrigin()
+vtkNew<vtkImageConstantPad> padding;
+padding->SetConstant(0);
+padding->SetOutputNumberOfScalarComponents(1);
+padding->SetOutputWholeExtent(-1, resolution, -1, resolution, -1, resolution);
+padding->SetInputData(resize->GetOutput());
+padding->Update();
+vtkNew<vtkMarchingCubes> surface;
+surface->SetInputData(padding->GetOutput());
+surface->ComputeNormalsOn();
+surface->SetValue(0, 128 /*isoValue*/);
+surface->Update();
+if (smooth)
+{
+vtkNew<vtkSmoothPolyDataFilter> smoothFilter;
+// Apply volume smoothing
+// https://examples.vtk.org/site/Cxx/PolyData/SmoothPolyDataFilter/
+smoothFilter->SetInputConnection(surface->GetOutputPort());
+smoothFilter->SetNumberOfIterations(15);
+smoothFilter->SetRelaxationFactor(0.1);
+smoothFilter->FeatureEdgeSmoothingOff();
+smoothFilter->BoundarySmoothingOn();
+smoothFilter->Update();
+vtkNew<vtkPolyDataNormals> normalGenerator;
+normalGenerator->SetInputConnection(smoothFilter->GetOutputPort());
+normalGenerator->ComputePointNormalsOn();
+normalGenerator->ComputeCellNormalsOn();
+normalGenerator->Update();
+EncodeSTL(stl, *normalGenerator->GetOutput());
+}
+else
+{
+EncodeSTL(stl, *surface->GetOutput());
+}
+return true;
+}
+void ListStructures(OrthancPluginRestOutput* output,
+const char* url,
+const OrthancPluginHttpRequest* request)
+{
+const std::string instanceId(request->groups[0]);
+if (request->method != OrthancPluginHttpMethod_Get)
+{
+OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "GET");
+return;
+}
+std::string dicom;
+if (!OrthancPlugins::RestApiGetString(dicom, "/instances/" + instanceId + "/file", false))
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource);
+}
+else
+{
+Orthanc::ParsedDicomFile parsed(dicom);
+std::set<std::string> names;
+ListStructuresNames(names, parsed);
+Json::Value answer = Json::arrayValue;
+for (std::set<std::string>::const_iterator it = names.begin(); it != names.end(); ++it)
+{
+answer.append(*it);
+}
+std::string s = answer.toStyledString();
+OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), Orthanc::MIME_JSON);
+}
+}
+void Encode(OrthancPluginRestOutput* output,
+const char* url,
+const OrthancPluginHttpRequest* request)
+{
+static const char* const KEY_INSTANCE = "Instance";
+static const char* const KEY_RESOLUTION = "Resolution";
+static const char* const KEY_ROI_NAMES = "RoiNames";
+static const char* const KEY_SMOOTH = "Smooth";
+static const char* const KEY_TAGS = "Tags";
+if (request->method != OrthancPluginHttpMethod_Post)
+{
+OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "POST");
+return;
+}
+Json::Value body;
+if (!Orthanc::Toolbox::ReadJson(body, request->body, request->bodySize))
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest);
+}
+const std::string instanceId = Orthanc::SerializationToolbox::ReadString(body, KEY_INSTANCE);
+const bool smooth = (body.isMember(KEY_SMOOTH) ?
+Orthanc::SerializationToolbox::ReadBoolean(body, KEY_SMOOTH) :
+true /* smooth by default */);
+const unsigned int resolution = (body.isMember(KEY_RESOLUTION) ?
+Orthanc::SerializationToolbox::ReadUnsignedInteger(body, KEY_RESOLUTION) :
+256 /* default value */);
+std::set<std::string> roiNames;
+Orthanc::SerializationToolbox::ReadSetOfStrings(roiNames, body, KEY_ROI_NAMES);
+std::string dicom;
+if (!OrthancPlugins::RestApiGetString(dicom, "/instances/" + instanceId + "/file", false))
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource);
+}
+else
+{
+Orthanc::ParsedDicomFile parsed(dicom);
+StructureSet structureSet(parsed);
+std::string stl;
+if (!EncodeStructureSetMesh(stl, structureSet, roiNames, resolution, smooth))
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, "Cannot encode STL");
+}
+else
+{
+std::string content;
+Orthanc::Toolbox::EncodeDataUriScheme(content, "model/stl", stl);
+Json::Value create;
+create["Content"] = content;
+create["Parent"] = structureSet.HashStudy();
+if (body.isMember(KEY_TAGS))
+{
+create[KEY_TAGS] = body[KEY_TAGS];
+}
+else
+{
+std::string description;
+for (std::set<std::string>::const_iterator it = roiNames.begin(); it != roiNames.end(); ++it)
+{
+if (!description.empty())
+{
+description += ", ";
+}
+description += *it;
+}
+create[KEY_TAGS] = Json::objectValue;
+create[KEY_TAGS]["SeriesDescription"] = description;
+}
+Json::Value answer;
+if (OrthancPlugins::RestApiPost(answer, "/tools/create-dicom", create.toStyledString(), false))
+{
+std::string s = answer.toStyledString();
+OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), Orthanc::MIME_JSON);
+}
+else
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "Cannot create DICOM from STL");
+}
+}
 }
 }
 extern "C"
 Orthanc::Logging::InitializePluginContext(context);
 #else
 Orthanc::Logging::Initialize(context);
 #endif
+Orthanc::InitializeFramework("", false);
 hasCreateDicomStl_ = OrthancPlugins::CheckMinimalOrthancVersion(1, 12, 1);
 if (!hasCreateDicomStl_)
 {
 LOG(WARNING) << "Your version of Orthanc (" << std::string(context->orthancVersion)
 << ") is insufficient to create DICOM STL, it should be above 1.12.1";
 }
 OrthancPluginSetDescription(context, "STL plugin for Orthanc.");
-OrthancPlugins::RegisterRestCallback<ServeFile>("/stl/(.*)", true);
+OrthancPlugins::RegisterRestCallback<ServeFile>("/stl/app/(.*)", true);
 // Extend the default Orthanc Explorer with custom JavaScript for STL
 std::string explorer;
 Orthanc::EmbeddedResources::GetFileResource(explorer, Orthanc::EmbeddedResources::ORTHANC_EXPLORER);
 OrthancPluginExtendOrthancExplorer(OrthancPlugins::GetGlobalContext(), explorer.c_str());
+OrthancPlugins::RegisterRestCallback<ListStructures>("/stl/rt-struct/([0-9a-f-]+)", true);
+if (hasCreateDicomStl_)
+{
+OrthancPlugins::RegisterRestCallback<Encode>("/stl/encode", true);
+}
 return 0;
 }
 ORTHANC_PLUGINS_API void OrthancPluginFinalize()
 {
+Orthanc::FinalizeFramework();
 }
 ORTHANC_PLUGINS_API const char* OrthancPluginGetName()
 {

Mercurial > hg > orthanc-stl

comparison Sources/Plugin.cpp @ 1:0f03a8a0bd6f