Some initial work on contour propagation, also this corresponds to re…

…lease 1.2.2

Applications/CbctRecon/StructureSet.cxx

@@ -1,5 +1,87 @@
 #include "StructureSet.h"
+#include <itkImage.h>
+#include <itkVector.h>
 
-StructureSet::StructureSet() {}
+StructureSet::StructureSet() {
+  m_plan_ss = new Rtss();
+  m_rigid_ss = new Rtss();
+  m_deform_ss = new Rtss();
+}
 
-StructureSet::~StructureSet() {}
+StructureSet::~StructureSet() {
+  delete m_plan_ss;
+  delete m_rigid_ss;
+  delete m_deform_ss;
+}
+
+void StructureSet::set_planCT_ss(Rtss::Pointer &struct_set) {
+  m_plan_ss = struct_set.get();
+}
+void StructureSet::set_rigidCT_ss(Rtss::Pointer &struct_set) {
+  m_rigid_ss = struct_set.get();
+}
+void StructureSet::set_deformCT_ss(Rtss::Pointer &struct_set) {
+  m_deform_ss = struct_set.get();
+}
+
+// This function is very C, because Rtss is used.
+void clone_rtss(const Rtss *orig_ss, Rtss *new_ss) {
+  auto n_structs = orig_ss->num_structures;
+  for (auto i = 0; i < n_structs; i++) {
+    new_ss->add_structure( // reallocs slist
+        orig_ss->slist[i]->name, orig_ss->slist[i]->color,
+        orig_ss->slist[i]->id, orig_ss->slist[i]->bit);
+    auto n_contours = orig_ss->slist[i]->num_contours;
+
+    for (auto j = 0; j < n_contours; j++) {
+      auto n_verts = orig_ss->slist[i]->pslist[j]->num_vertices;
+      new_ss->slist[i]->add_polyline(n_verts); // mallocs x, y, z
+
+      new_ss->slist[i]->pslist[j]->slice_no =
+          orig_ss->slist[i]->pslist[j]->slice_no;
+      new_ss->slist[i]->pslist[j]->ct_slice_uid =
+          orig_ss->slist[i]->pslist[j]->ct_slice_uid;
+
+      for (auto k = 0; k < n_verts; k++) {
+        new_ss->slist[i]->pslist[j]->x[k] = orig_ss->slist[i]->pslist[j]->x[k];
+        new_ss->slist[i]->pslist[j]->y[k] = orig_ss->slist[i]->pslist[j]->y[k];
+        new_ss->slist[i]->pslist[j]->z[k] = orig_ss->slist[i]->pslist[j]->z[k];
+      }
+    }
+  }
+}
+
+void StructureSet::transform_by_vector(const ctType struct_set,
+                                       const FloatVector vec, Rtss *out_ss) {
+  if (out_ss->num_structures != 0) {
+    out_ss->clear();
+  }
+
+  switch (struct_set) {
+  case PLAN_CT:
+    clone_rtss(m_plan_ss, out_ss);
+    break;
+  case RIGID_CT:
+    clone_rtss(m_rigid_ss, out_ss);
+    break;
+  case DEFORM_CT:
+    clone_rtss(m_deform_ss, out_ss);
+    break;
+  }
+
+  auto n_structs = m_plan_ss->num_structures;
+#pragma omp parallel for
+  for (auto i = 0; i < n_structs; i++) {
+    Rtss_roi *cur_s = m_plan_ss->slist[i];
+    auto n_contours = cur_s->num_contours;
+    for (auto j = 0; j < n_contours; j++) {
+      Rtss_contour *cur_c = cur_s->pslist[j];
+      auto n_points = cur_c->num_vertices;
+      for (auto k = 0; k < n_points; k++) {
+        cur_c->x[k] += vec.x;
+        cur_c->y[k] += vec.y;
+        cur_c->z[k] += vec.z;
+      }
+    }
+  }
+}

Applications/CbctRecon/StructureSet.h

@@ -1,12 +1,37 @@
 #ifndef STRUCTURESET_H
 #define STRUCTURESET_H
+#include "cbctrecon.h"
 
-class StructureSet
-{
-public:
-	StructureSet();
-	~StructureSet();
+#include <rtss.h>
+#include <rtss_contour.h>
+#include <rtss_roi.h>
+
+struct FloatVector {
+  float x;
+  float y;
+  float z;
+};
+
+enum ctType {
+  PLAN_CT = 0,
+  RIGID_CT = 1,
+  DEFORM_CT = 2,
 };
 
+class StructureSet {
+public:
+  StructureSet();
+  ~StructureSet();
+
+  void set_planCT_ss(Rtss::Pointer &struct_set);
+  void set_rigidCT_ss(Rtss::Pointer &struct_set);
+  void set_deformCT_ss(Rtss::Pointer &struct_set);
+  void transform_by_vector(ctType struct_set, FloatVector vec, Rtss *out_ss);
+
+private:
+  Rtss *m_plan_ss;
+  Rtss *m_rigid_ss;
+  Rtss *m_deform_ss;
+};
 
 #endif

Applications/CbctRecon/cbctrecon.cpp

@@ -3406,6 +3406,7 @@ QString getBowtiePath(QWidget *parent, const QDir &calDir) {
       calDir.absolutePath(), "Projection (*.xim)", nullptr, nullptr);
 }
 
+
 std::tuple<bool, bool> CbctRecon::probeUser(const QString &guessDir) {
 
   QString dirPath = QFileDialog::getExistingDirectory(
@@ -3414,8 +3415,15 @@ std::tuple<bool, bool> CbctRecon::probeUser(const QString &guessDir) {
 
   bool dcm_success = false;
   if (!(dirPath.length() <= 1)) {
+    Dcmtk_rt_study drs(dirPath.toLocal8Bit().constData());
+    drs.parse_directory();
     Plm_image plmImg;
-    if (plmImg.load_native(dirPath.toLocal8Bit().constData())) {
+    plmImg.set(drs.get_image());
+
+    if(plmImg.have_image()){
+    //if (plmImg.load_native(dirPath.toLocal8Bit().constData())) {
+
+      m_structures->set_planCT_ss(drs.get_rtss());
 
       ShortImageType::Pointer spShortImg = plmImg.itk_short();
 

Applications/CbctRecon/cbctrecon.h

@@ -98,6 +98,7 @@
 #endif
 
 // Plastimatch
+#include <dcmtk_rt_study.h>
 #include <mha_io.h>
 #include <nki_io.h>
 #include <proj_volume.h>
@@ -209,6 +210,7 @@ class QStandardItemModel;
 class DlgRegistration;
 // class DlgHistogram;
 class DlgExternalCommand;
+class StructureSet;
 class QTimer;
 class QXmlStreamReader;