Merge branch 'feature/plugin/atrialfibres' into development

Author: Jose Alonso Solis-Lemus

CemrgApp/Modules/CemrgAppModule/include/CemrgCommonUtils.h

@@ -81,8 +81,8 @@ class MITKCEMRGAPPMODULE_EXPORT CemrgCommonUtils {
     static bool ConvertToCarto(std::string vtkPath, std::vector<double>, double, double, int, bool);
     static void CalculatePolyDataNormals(vtkSmartPointer<vtkPolyData>& pd, bool celldata=true);
     static void FillHoles(mitk::Surface::Pointer surf, QString dir="", QString vtkname="");
-    static mitk::Image::Pointer ImageFromSurfaceMesh(mitk::Surface::Pointer surf, double origin[3], double spacing[3]);
-    static void SaveImageFromSurfaceMesh(QString surfPath, double origin[3], double spacing[3], QString outputPath="");
+    static mitk::Image::Pointer ImageFromSurfaceMesh(mitk::Surface::Pointer surf, double origin[3], double spacing[3], int pad_num=0);
+    static void SaveImageFromSurfaceMesh(QString surfPath, double origin[3], double spacing[3], QString outputPath="", int pad_num=0);
     static double GetSphereParametersFromLandmarks(mitk::PointSet::Pointer landmarks, double * centre);
 
     //Tracking Utils

CemrgApp/Modules/CemrgAppModule/src/CemrgCommonUtils.cpp

@@ -342,6 +342,10 @@ mitk::Image::Pointer CemrgCommonUtils::PadImageWithConstant(mitk::Image::Pointer
 
     ImageType::Pointer outputImg = ImageType::New();
     ImageType::IndexType start;
+
+    double origin[3];
+    image->GetGeometry()->GetOrigin().ToArray(origin);
+
     start[0] = 0; start[1] = 0; start[2] = 0;
 
     ImageType::SizeType size;
@@ -377,6 +381,7 @@ mitk::Image::Pointer CemrgCommonUtils::PadImageWithConstant(mitk::Image::Pointer
     paste->SetDestinationIndex(indexForOutput);
 
     image = mitk::ImportItkImage(paste->GetOutput())->Clone();
+    image->GetGeometry()->SetOrigin(origin);
 
     return image;
 }
@@ -1155,11 +1160,18 @@ QJsonObject CemrgCommonUtils::CreateJSONObject(QStringList keys_list, QStringLis
     return jsonObj;
 }
 
-mitk::Image::Pointer CemrgCommonUtils::ImageFromSurfaceMesh(mitk::Surface::Pointer surf, double origin[3], double spacing[3]){
+mitk::Image::Pointer CemrgCommonUtils::ImageFromSurfaceMesh(mitk::Surface::Pointer surf, double origin[3], double spacing[3], int pad_num){
     vtkSmartPointer<vtkPolyData> pd = surf->GetVtkPolyData();
     double bounds[6];
     pd->GetBounds(bounds);
 
+    // prepare for padding (pad_num=0 by default, so it does not affect)
+    for (int ix = 0; ix < 3; ix++) {
+        double pad_offset = pad_num*spacing[ix];
+        bounds[2*ix] -= pad_offset;
+        bounds[2*ix + 1] += pad_offset;
+    }
+
     int dimensions[3];
     for (int ix = 0; ix < 3; ix++) {
         dimensions[ix] = static_cast<int>(std::ceil((bounds[ix * 2 + 1] - bounds[ix * 2]) / spacing[ix]));
@@ -1168,7 +1180,6 @@ mitk::Image::Pointer CemrgCommonUtils::ImageFromSurfaceMesh(mitk::Surface::Point
     for (int jx = 0; jx < 3; jx++) {
         origin[jx] = bounds[2*jx] + spacing[jx]/2;
     }
-    std::cout << "o = (" << origin[0] << ", " << origin[1] << ", " << origin[2] << ")"<< '\n';
 
     //Prepare empty image
     vtkSmartPointer<vtkImageData> whiteImage = vtkSmartPointer<vtkImageData>::New();
@@ -1211,7 +1222,7 @@ mitk::Image::Pointer CemrgCommonUtils::ImageFromSurfaceMesh(mitk::Surface::Point
 
 }
 
-void CemrgCommonUtils::SaveImageFromSurfaceMesh(QString surfPath, double origin[3], double spacing[3], QString outputPath){
+void CemrgCommonUtils::SaveImageFromSurfaceMesh(QString surfPath, double origin[3], double spacing[3], QString outputPath, int pad_num){
     QString out;
 
     if(outputPath.isEmpty()){
@@ -1221,7 +1232,7 @@ void CemrgCommonUtils::SaveImageFromSurfaceMesh(QString surfPath, double origin[
         out = outputPath;
     }
     mitk::Surface::Pointer surf = mitk::IOUtil::Load<mitk::Surface>(surfPath.toStdString());
-    mitk::Image::Pointer im = CemrgCommonUtils::ImageFromSurfaceMesh(surf, origin, spacing);
+    mitk::Image::Pointer im = CemrgCommonUtils::ImageFromSurfaceMesh(surf, origin, spacing, pad_num);
 
     mitk::IOUtil::Save(im, out.toStdString());
 }

CemrgApp/Plugins/kcl.cemrgapp.atrialfibres/src/internal/AtrialFibresClipperView.cpp

@@ -1261,9 +1261,17 @@ void AtrialFibresClipperView::KeyCallBackFunc(vtkObject*, long unsigned int, voi
 
         }//_if
     }//_if_main
+    //
+    if (key == "h" || key == "H"){
+        self->Help();
+    }
 
 }
 
+void AtrialFibresClipperView::Help(){
+    std::string str = GetHelp();
+    QMessageBox::information(NULL, "Help", str.c_str());
+}
 // helper functions
 void AtrialFibresClipperView::InitialisePickerObjects(){
     pickedSeedIds = vtkSmartPointer<vtkIdList>::New();
@@ -1319,6 +1327,7 @@ std::string AtrialFibresClipperView::GetShortcuts(){
     } else{
         res += "R: reset centrelines\nSpace: add seed point\nDelete: remove seed point";
     }
+    res += "\nH: Show help";
     return res;
 }
 
@@ -1457,3 +1466,25 @@ void AtrialFibresClipperView::PrintCorridorIds(){
         std::cout << "[PriontCorridorIds] No points in corridor" << '\n';
     }
 }
+
+
+std::string AtrialFibresClipperView::GetHelp(){
+    std::string msg = "";
+    if (automaticPipeline) {
+        msg += "FIX LABELS: \n\n  * Press X to select (blue) seed points for fixing labels\n";
+        msg += "  * Click the Fix Meshing button at the top.";
+        msg += "\n  * Select the structure (LA body, LSPV, LIPV, etc...)";
+        msg += "\n\nIDENITFY PVs";
+        msg += "\n  * Press SPACE to select (red) seed points";
+        msg += "\n  * Click the Store Landmarks and Labels, then the Click the Display PV Clippers button";
+        msg += "\n  * Edit the sphere clippers' size, then click Save Clippers";
+    } else{
+        msg += "\n\nIDENTIFY START OF PVs";
+        msg += "\n  * Press SPACE to select (red) seed points in all PVs and Appendage";
+        msg += "\n  * Click the Find Centrelines button";
+        msg += "\n  * Click the Display Disk Clippers button - edit disks";
+        msg += "\n  * Click the Mark PV Start on Image button";
+    }
+
+    return msg;
+}

CemrgApp/Plugins/kcl.cemrgapp.atrialfibres/src/internal/AtrialFibresClipperView.h

@@ -70,6 +70,7 @@ class AtrialFibresClipperView : public QmitkAbstractView {
 
     // helper functions
     std::string GetShortcuts();
+    std::string GetHelp();
     bool IsPointSelectionControlsAvailable();
     bool IsClipperManualControlsAvailable();
     void UserSelectPvLabel();
@@ -105,6 +106,7 @@ protected slots:
     void PvClipperSelector(int);
 
     void ClipPVs();
+    void Help();
 
 
 protected:

CemrgApp/Plugins/kcl.cemrgapp.atrialfibres/src/internal/AtrialFibresClipperViewControls.ui

@@ -33,7 +33,7 @@
      <item row="1" column="2">
       <widget class="QPushButton" name="button_man2_clippers">
        <property name="text">
-        <string>Display Clippers</string>
+        <string>Display Disk Clippers</string>
        </property>
       </widget>
      </item>

CemrgApp/Plugins/kcl.cemrgapp.atrialfibres/src/internal/AtrialFibresView.cpp

@@ -375,8 +375,10 @@ void AtrialFibresView::AnalysisChoice(){
             // Create fake segmentation image for labelling
             double origin[3] = {0, 0, 0};
             double spacing[3] = {1, 1, 1};
-            CemrgCommonUtils::SaveImageFromSurfaceMesh(Path(tagName+".vtk"), origin, spacing);
-            CemrgCommonUtils::SavePadImageWithConstant(Path(tagName+".nii"));
+            int pad_scale = 1; // pad_scale*spacing added to bounds in function below
+            QString output_path = ""; // makes input to be overwritten
+            CemrgCommonUtils::SaveImageFromSurfaceMesh(Path(tagName+".vtk"), origin, spacing, output_path, pad_scale);
+            // CemrgCommonUtils::SavePadImageWithConstant(Path(tagName+".nii"));
 
             mitk::Image::Pointer im = CemrgCommonUtils::ReturnBinarised(mitk::IOUtil::Load<mitk::Image>(StdStringPath(tagName+".nii")));
             // CemrgCommonUtils::Binarise(im);
@@ -1579,8 +1581,6 @@ void AtrialFibresView::ScarProjection(){
 
 void AtrialFibresView::Reset() {
 
-
-
     try {
 
         ctkPluginContext* context = mitk::kcl_cemrgapp_atrialfibres_Activator::getContext();
@@ -1639,7 +1639,14 @@ void AtrialFibresView::Reset() {
 
     //Clear project directory
     directory.clear();
-    this->GetSite()->GetPage()->ResetPerspective();
+    cnnPath.clear();
+    fileName.clear();
+    tagName.clear();
+    refinedSuffix.clear();
+
+        this->GetSite()
+            ->GetPage()
+            ->ResetPerspective();
 }