--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Sources/StructureSet.cpp	Thu Apr 04 20:37:08 2024 +0200
@@ -0,0 +1,170 @@
+/**
+ * SPDX-FileCopyrightText: 2023-2024 Sebastien Jodogne, UCLouvain, Belgium
+ * SPDX-License-Identifier: GPL-3.0-or-later
+ */
+
+/**
+ * STL plugin for Orthanc
+ * Copyright (C) 2023-2024 Sebastien Jodogne, UCLouvain, Belgium
+ *
+ * This program is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU 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
+ * General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ **/
+
+
+#include "StructureSet.h"
+
+#include "STLToolbox.h"
+
+#include <OrthancException.h>
+
+#include <dcmtk/dcmdata/dcdeftag.h>
+#include <dcmtk/dcmdata/dcfilefo.h>
+
+
+StructureSet::StructureSet(Orthanc::ParsedDicomFile& dicom) :
+  hasFrameOfReferenceUid_(false)
+{
+  DcmDataset& dataset = *dicom.GetDcmtkObject().getDataset();
+  patientId_ = STLToolbox::GetStringValue(dataset, DCM_PatientID);
+  studyInstanceUid_ = STLToolbox::GetStringValue(dataset, DCM_StudyInstanceUID);
+  seriesInstanceUid_ = STLToolbox::GetStringValue(dataset, DCM_SeriesInstanceUID);
+  sopInstanceUid_ = STLToolbox::GetStringValue(dataset, DCM_SOPInstanceUID);
+
+  DcmSequenceOfItems* frame = NULL;
+  if (!dataset.findAndGetSequence(DCM_ReferencedFrameOfReferenceSequence, frame).good() ||
+      frame == NULL)
+  {
+    throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+  }
+
+  if (frame->card() == 1)
+  {
+    const char* v = NULL;
+    if (frame->getItem(0)->findAndGetString(DCM_FrameOfReferenceUID, v).good() &&
+        v != NULL)
+    {
+      hasFrameOfReferenceUid_ = true;
+      frameOfReferenceUid_.assign(v);
+    }
+  }
+
+  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);
+}
+
+
+StructureSet::~StructureSet()
+{
+  for (size_t i = 0; i < polygons_.size(); i++)
+  {
+    assert(polygons_[i] != NULL);
+    delete polygons_[i];
+  }
+}
+
+
+std::string StructureSet::HashStudy() const
+{
+  Orthanc::DicomInstanceHasher hasher(patientId_, studyInstanceUid_, seriesInstanceUid_, sopInstanceUid_);
+  return hasher.HashStudy();
+}
+
+
+const StructurePolygon& StructureSet::GetPolygon(size_t i) const
+{
+  if (i >= polygons_.size())
+  {
+    throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+  }
+  else
+  {
+    assert(polygons_[i] != NULL);
+    return *polygons_[i];
+  }
+}
+
+
+const std::string& StructureSet::GetFrameOfReferenceUid() const
+{
+  if (hasFrameOfReferenceUid_)
+  {
+    return frameOfReferenceUid_;
+  }
+  else
+  {
+    throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+  }
+}
+
+
+void StructureSet::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
+    {
+      target.insert(STLToolbox::GetStringValue(*item, DCM_ROIName));
+    }
+  }
+}