FIXED coding covention simple spacing (using astyle)

This is the result of running a basic
astyle --style=java -R *.cpp *.h
Signed-off-by: Emmanuel Promayon <Emmanuel.Promayon@imag.fr>

imaging/actions/itkfilters/Derivative.cpp

@@ -211,7 +211,7 @@ vtkSmartPointer<vtkImageData> Derivative::itkProcess(vtkSmartPointer<vtkImageDat
     resultImage->GetExtent(extent);
     result->SetExtent(extent);
     result->DeepCopy(resultImage);
- 
+
     // Set CamiTK progress bar back to zero (the processing filter is over)
     observer->Reset();
 

modeling/components/mmlcomponent/MMLComponent.cpp

@@ -174,7 +174,7 @@ void MMLComponent::connectPml() {
     pmlComponent = new PMLComponent( mmlGUI->getMonitoringManager()->takePml(),  mmlGUI->getMonitoringManager()->getPmlFileName().c_str());
     addChild(pmlComponent);
     refreshInterfaceNode();
-    
+
     // This is forced refresh (bad, breaking rules)
     // TODO: refresh should be called in the MMLDisplay connectPml() method instead)
     pmlComponent->refresh();

modeling/components/pmlcomponent/PMLComponent.h

@@ -171,7 +171,7 @@ public:
     /// Warning: this methods contains a forced/active refresh (breaking CamiTK programming guidelines)
     /// DO NOT CALL this method from a component, this method SHOULD ONLY be called from an action
     /// Raison d'être : this method force the vtk pipeline updates (needed when, for example, the points moved)
-    ///                 and then refresh the 3D viewer. The later is against CamiTK programming guidelines. 
+    ///                 and then refresh the 3D viewer. The later is against CamiTK programming guidelines.
     ///                 It is written here (in the component) because it is a helper method for actions
     ///                 that would need to refresh the mesh.
     void refreshDisplay();

modeling/components/pmlcomponent/PMLComponentExtension.cpp

@@ -43,186 +43,186 @@ using namespace camitk;
 
 // --------------- getName -------------------
 QString PMLComponentExtension::getName() const {
-  return "PML Component";
+    return "PML Component";
 }
 
 // --------------- getDescription -------------------
 QString PMLComponentExtension::getDescription() const {
-  return "<b>New PML COMPONENT!</b>";// Manage Physical Model <em>.pml</em> files in <b>CamiTK</b>.<br/>CamiTK was initially mainly developed to support this format. Lots of things are possible with a physical model!";
+    return "<b>New PML COMPONENT!</b>";// Manage Physical Model <em>.pml</em> files in <b>CamiTK</b>.<br/>CamiTK was initially mainly developed to support this format. Lots of things are possible with a physical model!";
 }
 
 // --------------- getFileExtensions -------------------
 QStringList PMLComponentExtension::getFileExtensions() const {
-  QStringList ext;
-  ext << "pml";
-  return ext;
+    QStringList ext;
+    ext << "pml";
+    return ext;
 }
 
 // --------------- open -------------------
 camitk::Component * PMLComponentExtension::open(const QString & fileName) throw(AbortException) {
 
-  Application::showStatusBarMessage("Loading " + fileName + "...");
+    Application::showStatusBarMessage("Loading " + fileName + "...");
 
-  // instanciate the component
-  PMLComponent * pmlComponent = new PMLComponent(fileName);
+    // instanciate the component
+    PMLComponent * pmlComponent = new PMLComponent(fileName);
 
-  // reset the progress bar
-  Application::resetProgressBar();
+    // reset the progress bar
+    Application::resetProgressBar();
 
-  return pmlComponent;
+    return pmlComponent;
 }
 
 // --------------- save -------------------
 bool PMLComponentExtension::save(camitk::Component * component) const {
-  PMLComponent * comp = dynamic_cast<PMLComponent *>(component);
-
-  if (comp) {
-    // easy!
-    // Just generate an ostream from the filename and then xmlPrint pop
-    std::ofstream outputFile(comp->getFileName().toStdString().c_str());
-    comp->getPhysicalModel()->xmlPrint(outputFile);
-    outputFile.close();
-    comp->setModified(false);
-    return true;
-  } else {
-    // save from generic MeshComponent
-    MeshComponent * meshComp = dynamic_cast<MeshComponent *>(component);
-
-    if (meshComp && meshComp->getPointSet()->GetNumberOfPoints() > 0) {
-      //-- create a new physical model
-      PhysicalModel * newPM = new PhysicalModel();
-
-      // extract the atoms from the Geometry
-      vtkSmartPointer<vtkPoints> thePoints = vtkSmartPointer<vtkPoints>::New();
-      thePoints->DeepCopy(meshComp->getPointSet()->GetPoints());
-
-      //-- create the structural components for the atoms
-      StructuralComponent * theAtoms = new StructuralComponent(newPM, "All Atoms");
-      double pos[3];
-
-      // create the atom structures
-      for (int i = 0; i < thePoints->GetNumberOfPoints(); i++) {
-	thePoints->GetPoint(i, pos);
-	theAtoms->addStructure(new Atom(newPM, pos), false);
-      }
-
-      // set the atom sc
-      newPM->setAtoms(theAtoms);
-
-      //-- create the unique structural components containing all the vtkCell, this is an exclusive component
-      unsigned int nrOfCells = meshComp->getPointSet()->GetNumberOfCells();
-      StructuralComponent * sc = new StructuralComponent(newPM, "All Cells");
-
-      // fill in this new structural component with all vtk cells
-      for (vtkIdType i = 0; i < (vtkIdType) nrOfCells; i++) {
-	// create a cell for each cell
-	vtkCell * theCell = meshComp->getPointSet()->GetCell(i);
-
-	// translate cell type
-	StructureProperties::GeometricType cellType;
-
-	switch (theCell->GetCellType()) {
-	case VTK_TETRA:
-	  cellType = StructureProperties::TETRAHEDRON;
-	  break;
-
-	case VTK_HEXAHEDRON:
-	  cellType = StructureProperties::HEXAHEDRON;
-	  break;
-
-	case VTK_WEDGE:
-	  cellType = StructureProperties::WEDGE;
-	  break;
-
-	case VTK_PYRAMID:
-	  cellType = StructureProperties::PYRAMID;
-	  break;
-
-	case VTK_LINE:
-	  cellType = StructureProperties::LINE;
-	  break;
-
-	case VTK_POLY_LINE:
-	  cellType = StructureProperties::POLY_LINE;
-	  break;
-
-	case VTK_POLY_VERTEX:
-	  cellType = StructureProperties::POLY_VERTEX;
-	  break;
-
-	case VTK_TRIANGLE:
-	  cellType = StructureProperties::TRIANGLE;
-	  break;
-
-	case VTK_QUAD:
-	  cellType = StructureProperties::QUAD;
-	  break;
-
-	default:
-	  cellType = StructureProperties::INVALID;
-	  break;
-	}
-
-	// create the corresponding PML cell
-	Cell * c = new Cell(newPM, cellType);
-
-	// fill-in the cell structures (atoms)
-	for (int i = 0; i < theCell->GetNumberOfPoints(); i++) {
-	  // get the corresponding atom
-	  Atom * a = newPM->getAtom(theCell->GetPointId(i)); // dynamic_cast<Atom *>(theAtoms->getStructure(theCell->GetPointId(i)));
-	  // set the corresponding atom as a structure composing the cell
-	  c->addStructure(a, false);
-	}
-
-	// insert the cell in the structure
-	sc->addStructure(c, false);
-      }
-
-      // create the exclusive multi-component
-      MultiComponent * exclusiveComponents = new MultiComponent(newPM);
-
-      // insert all the cells (i.e. the sc component)
-      exclusiveComponents->addSubComponent(sc);
-      exclusiveComponents->setName("Exclusive Components");
-
-      // insert this exclusive component into the pm
-      newPM->setExclusiveComponents(exclusiveComponents);
-      
-      // create the informative components from the selection
-      MultiComponent * informativeComponents =
-	new MultiComponent(newPM, "Informative Components");
-      newPM->setInformativeComponents(informativeComponents);
-
-      StructuralComponent* scinf;
-      vtkSmartPointer<vtkAbstractArray> idArray;
-      std::string selName;
-      
-      for (int i=0; i<meshComp->getNumberOfSelections(); i++) {
-	// TODO : test if it is a cell selection
-	selName = meshComp->getSelectionAt(i)->GetSelectionList()->GetName();
-	scinf = new StructuralComponent(newPM, selName);
-	idArray = meshComp->getSelectionAt(i)->GetSelectionList();
-
-	for (int j=0; j<idArray->GetNumberOfTuples(); j++) {
-	  Cell* c = sc->getCell(idArray->GetVariantValue(j).ToInt());
-	  // TODO : this don't work with the Explore PML Component
-	  // since it use cellRef that are not managed
-	  scinf->addStructure(c, false);
-	}
-
-	// add the selection component to the informative components.
-	newPM->getInformativeComponents()->addSubComponent(scinf);
-      }
-
-      // save it!
-      std::ofstream outputFile(meshComp->getFileName().toStdString().c_str());
-      newPM->xmlPrint(outputFile);
-      meshComp->setModified(false);
-      outputFile.close();
-      return true;
+    PMLComponent * comp = dynamic_cast<PMLComponent *>(component);
+
+    if (comp) {
+        // easy!
+        // Just generate an ostream from the filename and then xmlPrint pop
+        std::ofstream outputFile(comp->getFileName().toStdString().c_str());
+        comp->getPhysicalModel()->xmlPrint(outputFile);
+        outputFile.close();
+        comp->setModified(false);
+        return true;
+    } else {
+        // save from generic MeshComponent
+        MeshComponent * meshComp = dynamic_cast<MeshComponent *>(component);
+
+        if (meshComp && meshComp->getPointSet()->GetNumberOfPoints() > 0) {
+            //-- create a new physical model
+            PhysicalModel * newPM = new PhysicalModel();
+
+            // extract the atoms from the Geometry
+            vtkSmartPointer<vtkPoints> thePoints = vtkSmartPointer<vtkPoints>::New();
+            thePoints->DeepCopy(meshComp->getPointSet()->GetPoints());
+
+            //-- create the structural components for the atoms
+            StructuralComponent * theAtoms = new StructuralComponent(newPM, "All Atoms");
+            double pos[3];
+
+            // create the atom structures
+            for (int i = 0; i < thePoints->GetNumberOfPoints(); i++) {
+                thePoints->GetPoint(i, pos);
+                theAtoms->addStructure(new Atom(newPM, pos), false);
+            }
+
+            // set the atom sc
+            newPM->setAtoms(theAtoms);
+
+            //-- create the unique structural components containing all the vtkCell, this is an exclusive component
+            unsigned int nrOfCells = meshComp->getPointSet()->GetNumberOfCells();
+            StructuralComponent * sc = new StructuralComponent(newPM, "All Cells");
+
+            // fill in this new structural component with all vtk cells
+            for (vtkIdType i = 0; i < (vtkIdType) nrOfCells; i++) {
+                // create a cell for each cell
+                vtkCell * theCell = meshComp->getPointSet()->GetCell(i);
+
+                // translate cell type
+                StructureProperties::GeometricType cellType;
+
+                switch (theCell->GetCellType()) {
+                case VTK_TETRA:
+                    cellType = StructureProperties::TETRAHEDRON;
+                    break;
+
+                case VTK_HEXAHEDRON:
+                    cellType = StructureProperties::HEXAHEDRON;
+                    break;
+
+                case VTK_WEDGE:
+                    cellType = StructureProperties::WEDGE;
+                    break;
+
+                case VTK_PYRAMID:
+                    cellType = StructureProperties::PYRAMID;
+                    break;
+
+                case VTK_LINE:
+                    cellType = StructureProperties::LINE;
+                    break;
+
+                case VTK_POLY_LINE:
+                    cellType = StructureProperties::POLY_LINE;
+                    break;
+
+                case VTK_POLY_VERTEX:
+                    cellType = StructureProperties::POLY_VERTEX;
+                    break;
+
+                case VTK_TRIANGLE:
+                    cellType = StructureProperties::TRIANGLE;
+                    break;
+
+                case VTK_QUAD:
+                    cellType = StructureProperties::QUAD;
+                    break;
+
+                default:
+                    cellType = StructureProperties::INVALID;
+                    break;
+                }
+
+                // create the corresponding PML cell
+                Cell * c = new Cell(newPM, cellType);
+
+                // fill-in the cell structures (atoms)
+                for (int i = 0; i < theCell->GetNumberOfPoints(); i++) {
+                    // get the corresponding atom
+                    Atom * a = newPM->getAtom(theCell->GetPointId(i)); // dynamic_cast<Atom *>(theAtoms->getStructure(theCell->GetPointId(i)));
+                    // set the corresponding atom as a structure composing the cell
+                    c->addStructure(a, false);
+                }
+
+                // insert the cell in the structure
+                sc->addStructure(c, false);
+            }
+
+            // create the exclusive multi-component
+            MultiComponent * exclusiveComponents = new MultiComponent(newPM);
+
+            // insert all the cells (i.e. the sc component)
+            exclusiveComponents->addSubComponent(sc);
+            exclusiveComponents->setName("Exclusive Components");
+
+            // insert this exclusive component into the pm
+            newPM->setExclusiveComponents(exclusiveComponents);
+
+            // create the informative components from the selection
+            MultiComponent * informativeComponents =
+                new MultiComponent(newPM, "Informative Components");
+            newPM->setInformativeComponents(informativeComponents);
+
+            StructuralComponent* scinf;
+            vtkSmartPointer<vtkAbstractArray> idArray;
+            std::string selName;
+
+            for (int i=0; i<meshComp->getNumberOfSelections(); i++) {
+                // TODO : test if it is a cell selection
+                selName = meshComp->getSelectionAt(i)->GetSelectionList()->GetName();
+                scinf = new StructuralComponent(newPM, selName);
+                idArray = meshComp->getSelectionAt(i)->GetSelectionList();
+
+                for (int j=0; j<idArray->GetNumberOfTuples(); j++) {
+                    Cell* c = sc->getCell(idArray->GetVariantValue(j).ToInt());
+                    // TODO : this don't work with the Explore PML Component
+                    // since it use cellRef that are not managed
+                    scinf->addStructure(c, false);
+                }
+
+                // add the selection component to the informative components.
+                newPM->getInformativeComponents()->addSubComponent(scinf);
+            }
+
+            // save it!
+            std::ofstream outputFile(meshComp->getFileName().toStdString().c_str());
+            newPM->xmlPrint(outputFile);
+            meshComp->setModified(false);
+            outputFile.close();
+            return true;
+        }
     }
-  }
 
-  return false;
+    return false;
 
 }

modeling/libraries/mml/monitoring/AtomIterator.cpp

@@ -32,7 +32,7 @@ AtomIterator::AtomIterator(PhysicalModel* pml, std::string targetList) {
         for(unsigned int i=0; i<tlist.getNumberOfTargets(); i++) {
             atoms.push_back(pml->getAtom(tlist.getIndexedTarget(i)));
         }
-    } else {        
+    } else {
         for(unsigned int i=0; i<tlist.getNumberOfTargets(); i++) {
             StructuralComponent *sc = dynamic_cast<StructuralComponent *>(pml->getComponentByName(tlist.getNamedTarget(i)));
             if (sc) {

modeling/libraries/mml/monitoring/MonitorVolume.cpp

@@ -58,8 +58,8 @@ std::string MonitorVolume::getTypeName() {
 }
 
 // -------------------- write --------------------
-void MonitorVolume::write(){
-        // write data
+void MonitorVolume::write() {
+    // write data
     std::string s = "";
     for (unsigned int i = 0; i < values.size(); i++) {
         std::ostringstream ss;

modeling/libraries/mml/monitoring/MonitorVolume.h

@@ -51,7 +51,7 @@ public:
 
     /// return a string relative to monitor type
     std::string getTypeName();
-    
+
     virtual void write();
 };
 

modeling/libraries/mml/monitoring/Position.cpp

@@ -33,15 +33,14 @@
 
 // -------------------- constructor --------------------
 Position::Position(mml::Position* c,MonitoringManager* monitoringManager, MultipleCriterion* parent): Criterion(c,monitoringManager,parent) {
-    
+
     if (c->target().present()) {
         target=c->target().get();
-    }
-    else {
+    } else {
         // if target is not provided, use all atoms
         target = monitoringManager->getPml()->getAtoms()->getName();
     }
-    
+
     switch (c->unit()) {
     case mml::PositionUnit::nm:
         factor = 1000000;

modeling/libraries/mml/monitoring/Position.h

@@ -53,7 +53,7 @@ public:
 private:
     /// calculate stopping criteria data and store it into values vector
     void calculate();
-    
+
     /// the monitor targets describe as an LML TargetList string (e.g. "1-4,5"), @see TargetList
     std::string target;
 };

modeling/libraries/mml/monitoring/TimePeriodThreshold.cpp

@@ -40,7 +40,7 @@ bool  TimePeriodThreshold::individualTest(double tested) {
     if (tested <= value) {
         increment--;
     } else {
-        increment = iterations;    
+        increment = iterations;
     }
     return (increment == 0);
 }

modeling/libraries/mml/monitoring/TimePeriodThreshold.h

@@ -57,13 +57,13 @@ public:
 private:
     /// value of the threshold
     double value;
-    
+
     /// number of iterations defining the time period
     int iterations;
-    
+
     /// Needed to keep an eye on consecutive win
     int increment;
-    
+
     /// the xsdcxx object representing TimePeriodThreshold, used for serialization
     mml::TimePeriodThreshold* mappedObject;
 

modeling/libraries/pml/PhysicalModel.cpp

@@ -552,12 +552,12 @@ Component * PhysicalModel::getComponentByName ( const std::string n ) {
     if ( !foundC && informativeComponents ) {
         foundC = informativeComponents->getComponentByName ( n );
     }
-    
+
     //-- at last, just in case, look if this is not the name of the atoms SC
     if ( !foundC && getAtoms()->getName() == n) {
         foundC = getAtoms();
     }
-    
+
     return foundC;
 }
 

sdk/actions/application/OpenAction.cpp

@@ -40,7 +40,7 @@ OpenAction::OpenAction (ActionExtension * extension) : Action (extension) {
     setEmbedded (false);
     setDescription (tr("Open data (component) from a file"));
     setComponent ("");
-       
+
     // Setting classification family and tags
     setFamily ("Application");
     addTag (tr("Open"));

sdk/actions/frame/editframes/EditFrame.cpp

@@ -223,7 +223,7 @@ Action::ApplyStatus EditFrame::apply() {
 //--------------- save ------------
 void EditFrame::save() {
 
-	QString filename = QFileDialog::getSaveFileName(NULL, tr("Save Frame File"), "/home/myFrame.frame", tr("Frames (*.frame)"));
+    QString filename = QFileDialog::getSaveFileName(NULL, tr("Save Frame File"), "/home/myFrame.frame", tr("Frames (*.frame)"));
     QFile file(filename);
     if (file.open(QIODevice::WriteOnly)) {
         QTextStream stream(&file);
@@ -278,7 +278,7 @@ void EditFrame::save() {
 void EditFrame::load() {
 
     // choose the file to open
-	QString fileName = QFileDialog::getOpenFileName(NULL, tr("Open Frame File"), "/home", tr("Frames (*.frame)"));
+    QString fileName = QFileDialog::getOpenFileName(NULL, tr("Open Frame File"), "/home", tr("Frames (*.frame)"));
     QFile file(fileName);
     if(file.open(QIODevice::ReadOnly)) {
         QDomDocument doc("frame");

sdk/actions/image/multipicking/MultiPickingWidget.cpp

@@ -130,7 +130,7 @@ void MultiPickingWidget::updateTable() {
             header = headerString.split(",");
             ui.pointsTableWidget->setHorizontalHeaderLabels (header);
             createItems (pPM->getPixelIndexList(), pPM->getPixelValueList());
-        } else if (ui.coordinatesRadioButton->isChecked()){
+        } else if (ui.coordinatesRadioButton->isChecked()) {
             // case of image coordinates
             headerString = QString(HEADER_TABLE_IMG);
             header = headerString.split(",");
@@ -316,35 +316,35 @@ void MultiPickingWidget::manuallyModified(int i, int j) {
         int iPick = ui.pointsTableWidget->item(i, X_TABLE_INDEX)->text().toInt();
         int jPick = ui.pointsTableWidget->item(i, Y_TABLE_INDEX)->text().toInt();
         int kPick = ui.pointsTableWidget->item(i, Z_TABLE_INDEX)->text().toInt();
-        
+
         // Exceptionnally, we do not make this calculation by image picking and use image voxel size
         // to mimick a picking from the axial slice.
         double x = iPick * voxSize.x();
         double y = jPick * voxSize.y();
         double z = kPick * voxSize.z();
-        
+
         // check that this point is within image dimensions
-        
+
         if (((x < 0) || (x > imageDims[0]*voxSize.x())) ||
-            ((y < 0) || (y > imageDims[1]*voxSize.y())) ||
-            ((z < 0) || (z > imageDims[2]*voxSize.z()))) {
+                ((y < 0) || (y > imageDims[1]*voxSize.y())) ||
+                ((z < 0) || (z > imageDims[2]*voxSize.z()))) {
             QString msg = "The point (" + QString::number(x) + ", " + QString::number(y) + ", " + QString::number(z) + "), does not belong to the image " + img->getName() + ". Sorry...";
             QMessageBox::warning(this, "Impossible Operation", msg);
-            
+
             updateTable();
             return;
         }
-        
+
         // If right pixel, pick the image at this point
         // Cheat ! Say that your are its axial slice...
         img->getAxialSlices()->setSlice(z);
         img->pixelPicked(x, y, z, img->getAxialSlices());
         Application::refresh();
         pPM->modifyPixel(i);
-        
+
         updateTable();
-        
-    } else{ // Image Coordinates
+
+    } else { // Image Coordinates
         int * imageDims = img->getImageData()->GetDimensions();
         QVector3D voxSize = img->getVoxelSize();
         // Change the pixel index at this row
@@ -354,26 +354,26 @@ void MultiPickingWidget::manuallyModified(int i, int j) {
         double x = ui.pointsTableWidget->item(i, X_TABLE_INDEX)->text().toDouble();
         double y = ui.pointsTableWidget->item(i, Y_TABLE_INDEX)->text().toDouble();
         double z = ui.pointsTableWidget->item(i, Z_TABLE_INDEX)->text().toDouble();
-        
+
         // check that this point is within image dimensions
-        
+
         if (((x < 0) || (x > imageDims[0]*voxSize.x())) ||
-            ((y < 0) || (y > imageDims[1]*voxSize.y())) ||
-            ((z < 0) || (z > imageDims[2]*voxSize.z()))) {
+                ((y < 0) || (y > imageDims[1]*voxSize.y())) ||
+                ((z < 0) || (z > imageDims[2]*voxSize.z()))) {
             QString msg = "The point (" + QString::number(x) + ", " + QString::number(y) + ", " + QString::number(z) + "), does not belong to the image " + img->getName() + ". Sorry...";
             QMessageBox::warning(this, "Impossible Operation", msg);
-            
+
             updateTable();
             return;
         }