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/*****************************************************************************
* $CAMITK_LICENCE_BEGIN$
*
* CamiTK - Computer Assisted Medical Intervention ToolKit
* (c) 2001-2016 Univ. Grenoble Alpes, CNRS, TIMC-IMAG UMR 5525 (GMCAO)
*
* Visit http://camitk.imag.fr for more information
*
* This file is part of CamiTK.
*
* CamiTK is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License version 3
* only, as published by the Free Software Foundation.
*
* CamiTK 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 Lesser General Public License version 3 for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* version 3 along with CamiTK. If not, see <http://www.gnu.org/licenses/>.
*
* $CAMITK_LICENCE_END$
****************************************************************************/
// CamiTK stuff
#include <Action.h>
#include <InteractiveViewer.h>
#include <Log.h>
#include <Geometry.h>
#include <Property.h>
#include <Application.h>
#include <AbortException.h>
#include "PMLComponent.h"
// Qt stuff
#include <QFileInfo>
#include <QString>
#include <QMessageBox>
#include <QPixmap>
// PML library includes
#include <PhysicalModel.h>
#include <MultiComponent.h>
#include <Atom.h>
#include <StructuralComponent.h>
#include <CellProperties.h>
// VTK stuff
#include<vtkUnstructuredGrid.h>
#include <vtkCellArray.h>
#include <vtkCell.h>
#include <vtkHexahedron.h>
#include <vtkTetra.h>
#include <vtkWedge.h>
#include <vtkPyramid.h>
#include <vtkPolyLine.h>
#include <vtkLine.h>
#include <vtkTriangle.h>
#include <vtkQuad.h>
#include <vtkVertex.h>
#include <vtkPolyVertex.h>
#include <vtkProp.h>
#include <vtkDataSetMapper.h>
#include <vtkProperty.h>
#include <vtkPolyDataMapper.h>
#include <vtkSphereSource.h>
#include <vtkGlyph3D.h>
#include <vtkViewport.h>
#include <vtkSelection.h>
#include <vtkDoubleArray.h>
#include <vtkDataSetAttributes.h>
using namespace camitk;
//-------------------- Constructor -------------------
PMLComponent::PMLComponent ( const QString & file ) throw ( AbortException ) : MeshComponent ( file ) {
// Open the .pml file using library-pml
try {
Application::showStatusBarMessage ( "Loading " + QFileInfo ( file ).fileName() + "..." );
physicalModel = new PhysicalModel ( file.toStdString().c_str() );
} catch
( PMLAbortException & e ) {
throw AbortException ( "The PML XML document cannot be opened: " + std::string ( e.what() ) );
}
init();
}
PMLComponent::PMLComponent ( PhysicalModel * p, const QString & originalFile ) : MeshComponent ( originalFile ) {
physicalModel = p;
init();
}
//-------------------- Destructor -------------------
PMLComponent::~PMLComponent() {
atomPointIdMap.clear();
delete physicalModel;
physicalModel = NULL;
}
//-------------------- init -------------------
void PMLComponent::init() {
// Create the mesh corresponding to the model
Application::showStatusBarMessage ( "Creating PML 3D representation..." );
create3DStructure();
Application::showStatusBarMessage("Creating Atom VTK pipeline...");
createAtomSelectionVTKPipeline();
Application::showStatusBarMessage ( "PML Initialization done...", 1000 );
neverSelected = true;
Application::resetProgressBar();
}
//-------------------- setSelected -------------------
void PMLComponent::setSelected ( const bool selected, const bool recursive ) {
camitk::Component::setSelected ( selected, false );
// set the default action to be the PML explorer
if ( neverSelected && selected ) {
Action * defaultAction = Application::getAction ( "Explore PML Content" );
if ( defaultAction ) {
defaultAction->getQAction()->trigger();
}
neverSelected = false;
}
}
//-------------------- initDynamicProperties -------------------
void PMLComponent::initDynamicProperties() {
setName ( QString ( physicalModel->getName().c_str() ) );
// First add all generic mesh component properties
MeshComponent::initDynamicProperties();
// Then add all R/O specific properties
Property * nbOfAtomProp = new Property ( "Number of Atoms", QVariant ( ( int ) physicalModel->getNumberOfAtoms() ) , "The number of atoms in the PML file", "" );
nbOfAtomProp->setReadOnly ( true );
addProperty ( nbOfAtomProp );
Property * nbOfCellProp = new Property ( "Number of Cells", QVariant ( ( int ) physicalModel->getNumberOfCells() ) , "The number of cells in the PML file", "" );
nbOfCellProp->setReadOnly ( true );
addProperty ( nbOfCellProp );
Property * nbOfECProp = new Property ( "Number of Exclusive Components", QVariant ( ( int ) physicalModel->getNumberOfExclusiveComponents() ) , "The number of exclusive components in the PML file", "" );
nbOfECProp->setReadOnly ( true );
addProperty ( nbOfECProp );
Property * nbOfICProp = new Property ( "Number of Informative Components", QVariant ( ( int ) physicalModel->getNumberOfInformativeComponents() ) , "The number of exclusive components in the PML file", "" );
nbOfICProp->setReadOnly ( true );
addProperty ( nbOfICProp );
// finally add all the specific editable properties
for ( unsigned int i = 0; i < physicalModel->getProperties()->numberOfFields(); i++ ) {
addProperty ( new Property ( physicalModel->getProperties()->getField ( i ).c_str(), QVariant ( physicalModel->getProperties()->getString ( physicalModel->getProperties()->getField ( i ) ).c_str() ), "Custom property read from XML", "" ) );
}
}
//-------------------- updateProperty -------------------
void PMLComponent::updateProperty ( QString name, QVariant value ) {
// modify existing properties
Properties * pmProp = physicalModel->getProperties();
if ( pmProp->isAField ( name.toStdString() ) ) {
// set the corresponding property (field)
pmProp->set ( name.toStdString(), value.toString().toStdString() );
} else {
// this was not a property, check inherited class
MeshComponent::updateProperty ( name, value );
}
}
//-------------------- create3DStructure -------------------
void PMLComponent::create3DStructure() {
// The unstructured grid that will contain our 3D structure
if ( mainGrid ) {
mainGrid->Delete(); // free memory
atomPointIdMap.clear();
scCellIdArrayMap.clear();
scCellSelectionMap.clear();
}
mainGrid = vtkUnstructuredGrid::New();
mainGrid->Allocate ( physicalModel->getNumberOfCells(), physicalModel->getNumberOfCells() );
// Direct memory sharing of the position array (FAST!!!)
// see discussion http://public.kitware.com/pipermail/vtkusers/2010-January/056521.html
vtkSmartPointer<vtkDoubleArray> underlyingArray = vtkSmartPointer<vtkDoubleArray>::New();
underlyingArray->SetNumberOfComponents ( 3 ); // 3 dimensions
underlyingArray->SetArray ( physicalModel->getPositionPointer(), 3 * physicalModel->getNumberOfAtoms(), 1 );
// The points corresponding to the atoms
thePoints = vtkSmartPointer<vtkPoints>::New();
// we need double precision to share memory pointer
thePoints->SetData ( underlyingArray );
// to get the pointer from the vtkPoints, use:
// double * pts = (double *)thePoints->GetVoidPointer(0)
// build the correspondance map
for ( unsigned int atomOrderId = 0; atomOrderId < physicalModel->getAtoms()->getNumberOfStructures(); atomOrderId++ ) {
Atom * a = dynamic_cast<Atom *> ( physicalModel->getAtoms()->getStructure ( atomOrderId ) );
// register the atom, vtkPointId pair
atomPointIdMap.insert ( std::AtomPointIdPair ( a, atomOrderId ) );
}
mainGrid->SetPoints ( thePoints );
Application::setProgressBarValue ( ( int ) ( ( 1.0 / ( float ) ( physicalModel->getNumberOfAtoms() + physicalModel->getNumberOfCells() ) ) * 100.0 ) );
// Parse the exclusive components
MultiComponent * ecs = physicalModel->getExclusiveComponents();
parseMultiComponent ( ecs );
// Parse the informative components
MultiComponent * ics = physicalModel->getInformativeComponents();
if ( ics ) {
parseMultiComponent ( ics );
}
// set the component geometry to this one (initRepresentation also calls initDynamicProperties()...)
initRepresentation ( mainGrid );
// Tell this component is visible in the 3D viewer, otherwise we won't see it!
setVisibility ( InteractiveViewer::get3DViewer(), true );
}
//-------------------- parseMultiComponent -------------------
void PMLComponent::parseMultiComponent ( MultiComponent * parsedMC ) {
for ( unsigned int nbComp = 0; nbComp < parsedMC->getNumberOfSubComponents(); nbComp++ ) {
if ( StructuralComponent * sc = dynamic_cast<StructuralComponent *> ( parsedMC->getSubComponent ( nbComp ) ) ) {
// check if this structural component is made of cells or simply a list of atoms references.
if ( sc->getNumberOfCells() > 0 ) {
// create the 3D VTK structure for each cell and store it in the map
for ( unsigned int indexCell = 0; indexCell < sc->getNumberOfCells(); indexCell++ ) {
Cell * cellPML = sc->getCell ( indexCell );
vtkSmartPointer<vtkCell> cellVTK = cellToVTK ( cellPML );
int cellIndex = mainGrid->InsertNextCell ( cellVTK->GetCellType(), cellVTK->GetPointIds() );
cellPML->setIndex ( cellIndex );
}
} else {
vtkSmartPointer<vtkPolyVertex> scVTK = atomSCToVTK ( sc );
mainGrid->InsertNextCell ( scVTK->GetCellType(), scVTK->GetPointIds() );
}
} else if ( MultiComponent * mc = dynamic_cast<MultiComponent *> ( parsedMC->getSubComponent ( nbComp ) ) ) {
parseMultiComponent ( mc ); // recursive call to parse multicomponent children
} else {
CAMITK_ERROR ( "PMLComponent", "create3DStructure", "Component is neither a SC nor a MC: " + nbComp );
}
}
}
//-------------------- cellToVTK -------------------
vtkSmartPointer<vtkCell> PMLComponent::cellToVTK ( Cell * cell ) {
// The vtk cell we will construct, note that vtkCell is an abstract type (interface).
vtkSmartPointer<vtkCell> cell3D;
// Get the cell type
switch ( cell->getType() ) {
case StructureProperties::TETRAHEDRON:
cell3D = vtkTetra::New();
break;
case StructureProperties::HEXAHEDRON:
cell3D = vtkHexahedron::New();
break;
case StructureProperties::WEDGE:
cell3D = vtkWedge::New();
break;
case StructureProperties::PYRAMID:
cell3D = vtkPyramid::New();
break;
case StructureProperties::POLY_LINE:
cell3D = vtkPolyLine::New();
break;
case StructureProperties::LINE:
cell3D = vtkLine::New();
break;
case StructureProperties::POLY_VERTEX:
cell3D = vtkPolyVertex::New();
break;
case StructureProperties::TRIANGLE:
cell3D = vtkTriangle::New();
break;
case StructureProperties::QUAD:
cell3D = vtkQuad::New();
break;
default:
cell3D = vtkVertex::New();
break;
}
// insert the atoms of the cell by references
cell3D->GetPointIds()->SetNumberOfIds ( cell->getNumberOfStructures() );
for ( unsigned int i = 0; i < cell->getNumberOfStructures(); i++ ) {
Atom * a = ( Atom * ) cell->getStructure ( i );
cell3D->GetPointIds()->SetId ( i, getPointId ( a ) );
}
// Update progressbar status
static unsigned int cellCreated = 0;
cellCreated++;
Application::setProgressBarValue ( ( int ) ( ( ( float ) ( physicalModel->getNumberOfAtoms() + cellCreated ) / ( float ) ( physicalModel->getNumberOfAtoms() + physicalModel->getNumberOfCells() ) ) * 100.0 ) );
return cell3D;
}
//-------------------- atomSCToVTK -------------------
vtkSmartPointer<vtkPolyVertex> PMLComponent::atomSCToVTK ( StructuralComponent * sc ) {
// A structural component with no Cell information only contains a list of atoms references
// => It is a polygon
vtkSmartPointer<vtkPolyVertex> cellPolygon = vtkPolyVertex::New();
// insert the atoms of the cell by references
cellPolygon->GetPointIds()->SetNumberOfIds ( sc->getNumberOfStructures() );
for ( unsigned int i = 0; i < sc->getNumberOfStructures(); i++ ) {
Atom * a = ( Atom * ) sc->getStructure ( i );
cellPolygon->GetPointIds()->SetId ( i, getPointId ( a ) );
}
return cellPolygon;
}
//-------------------- refreshDisplay -------------------
void PMLComponent::refreshDisplay() {
// Force the modification flag of the point set (just in case position were modified somewhere else,
// for instance in a MML monitor) in order to obtain a real refresh
getPointSet()->Modified();
InteractiveViewer::get3DViewer()->refresh();
// shade the current selected component in order to see the selected item (SC, MC, Atoms or Cells)
myGeometry->setEnhancedModes ( InterfaceGeometry::Shaded );
}
//-------------------- createAtomSelectionVTKPipeline -------------------
void PMLComponent::createAtomSelectionVTKPipeline() {
// Create everything to manage atom selection
selectedAtomSelection = vtkSmartPointer<vtkSelection>::New();
vtkSmartPointer<vtkSelectionNode> selectedAtomSelectionNode = vtkSmartPointer<vtkSelectionNode>::New();
selectedAtomSelectionNode->SetFieldType ( vtkSelectionNode::POINT );
selectedAtomSelectionNode->SetContentType ( vtkSelectionNode::INDICES );
selectedAtomIdArray = vtkIdTypeArray::New();
// The selection extractor, attached to the selection and the 3D structure (unstructured grid)
vtkSmartPointer<vtkExtractSelection> selectedAtomExtractor = vtkSmartPointer<vtkExtractSelection>::New();
selectedAtomExtractor->SetInputConnection ( 0, getDataPort() );
selectedAtomExtractor->SetInputData ( 1, selectedAtomSelection );
// create the atom Glyph Actor
vtkSmartPointer<vtkSphereSource> glyphSphere = vtkSmartPointer<vtkSphereSource>::New();
glyphSphere->SetRadius ( getBoundingRadius() / 50.0 );
vtkSmartPointer<vtkGlyph3D> atomSphere = vtkSmartPointer<vtkGlyph3D>::New();
atomSphere->SetInputConnection ( selectedAtomExtractor->GetOutputPort() );
atomSphere->SetSourceConnection ( glyphSphere->GetOutputPort() );
vtkSmartPointer<vtkDataSetMapper> selectionMapper = vtkSmartPointer<vtkDataSetMapper>::New();
selectionMapper->SetInputConnection ( atomSphere->GetOutputPort() );
vtkSmartPointer<vtkActor> atomGlyphActor = vtkSmartPointer<vtkActor>::New();
atomGlyphActor->SetPickable ( false );
atomGlyphActor->GetProperty()->SetRepresentationToSurface();
atomGlyphActor->GetProperty()->SetColor ( 1, 0, 0 );
atomGlyphActor->GetProperty()->SetOpacity ( 0.8 );
atomGlyphActor->SetMapper ( selectionMapper );
atomGlyphActor->SetVisibility ( true );
// insert the glyph in the visualization pipeline, as an extraprop
removeProp("Selected Atoms");
addProp ( "Selected Atoms", atomGlyphActor );
}
//-------------------- createCellSelectionVTKPipeline -------------------
void PMLComponent::createCellSelectionVTKPipeline ( const StructuralComponent * sc ) {
// create the vtk pipeline if needed
if ( !scCellSelectionMap.contains ( sc->getName().c_str() ) ) {
// Create the vtkSelection
vtkSmartPointer<vtkSelection> selection = vtkSelection::New();
// The selection extractor, bound to the selection and the 3D structure (unstructured grid)
vtkSmartPointer<vtkExtractSelection> selectionExtractor = vtkSmartPointer<vtkExtractSelection>::New();
selectionExtractor->SetInputConnection ( 0, getDataPort() );
selectionExtractor->SetInputData ( 1, selection );
// The selection actor, with its color properties adapted to the input structural component
vtkSmartPointer<vtkActor> selectionActor = vtkSmartPointer<vtkActor>::New();
selectionActor->SetPickable ( false );
double color_R, color_G, color_B, color_A = 0.5;
sc->getColor ( &color_R, &color_G, &color_B, &color_A );
selectionActor->GetProperty()->SetColor ( color_R, color_G, color_B );
selectionActor->GetProperty()->SetPointSize ( 5 );
selectionActor->GetProperty()->SetOpacity ( 0.5 );
// The selection mapper to be used
vtkSmartPointer<vtkDataSetMapper> selectionMapper = vtkSmartPointer<vtkDataSetMapper>::New();
selectionActor->SetMapper ( selectionMapper );
selectionMapper->SetInputConnection ( selectionExtractor->GetOutputPort() );
// Register the actor for this structural component selection within the component
removeProp("Selected cells for " + QString ( sc->getName().c_str() ));
addProp ( "Selected cells for " + QString ( sc->getName().c_str() ), selectionActor );
// Store the references for selection in the corresponding QMap
vtkSmartPointer<vtkSelectionNode> selectionNodes = vtkSelectionNode::New();
selectionNodes->SetFieldType ( vtkSelectionNode::CELL );
selectionNodes->SetContentType ( vtkSelectionNode::INDICES );
vtkSmartPointer<vtkIdTypeArray> selectionIdTypesArray = vtkIdTypeArray::New();
scCellSelectionMap.insert ( QString ( sc->getName().c_str() ), selection );
scCellIdArrayMap.insert ( QString ( sc->getName().c_str() ), selectionIdTypesArray );
}
}
//-------------------- selectAtom -------------------
void PMLComponent::selectAtom ( const Atom * atom ) {
// insert the id for the selection.
selectedAtomIdArray->InsertNextValue ( getPointId ( atom ) );
}
//-------------------- selectCell -------------------
void PMLComponent::selectCell ( Cell * cell , bool showAtomGlyph ) {
const StructuralComponent * parent = cell->getParentSC();
// create the pipeline if needed
createCellSelectionVTKPipeline ( parent );
// Find the corresponding vtk selection node according to the parent
vtkSmartPointer<vtkIdTypeArray> array = scCellIdArrayMap.value ( parent->getName().c_str() );
if ( !array ) {
CAMITK_ERROR ( "PMLComponent", "selectCell", "array is null" );
}
array->InsertNextValue ( cell->getIndex() ); // the Cell's index = vtkCell's id in the 3D structure.
// select also the atom
if ( showAtomGlyph ) {
for ( unsigned int i=0; i<cell->getNumberOfStructures(); i++ ) {
Atom *a = dynamic_cast<Atom*> ( cell->getStructure ( i ) );
selectAtom ( a );
}
}
}
//-------------------- selectSC -------------------
void PMLComponent::selectSC ( StructuralComponent * sc , bool showAtomGlyph ) {
// Hightlight all the content of the given structural component
switch ( sc->composedBy() ) {
case StructuralComponent::ATOMS:
for ( unsigned int i = 0; i < sc->getNumberOfStructures(); i++ ) {
if ( Atom * a = dynamic_cast<Atom *> ( sc->getStructure ( i ) ) ) {
selectAtom ( a );
}
}
break;
case StructuralComponent::CELLS:
for ( unsigned int i = 0; i < sc->getNumberOfStructures(); i++ ) {
if ( Cell * c = dynamic_cast<Cell *> ( sc->getStructure ( i ) ) ) {
selectCell ( c, showAtomGlyph );
}
}
break;
default:
break;
}
}
//-------------------- selectMC -------------------
void PMLComponent::selectMC ( MultiComponent * selectedMC , bool showAtomGlyph ) {
// Select all the multicomponent subcomponents in the 3D structure
for ( unsigned int subCompIndex = 0; subCompIndex < selectedMC->getNumberOfSubComponents(); subCompIndex++ ) {
if ( MultiComponent * mc = dynamic_cast<MultiComponent *> ( selectedMC->getSubComponent ( subCompIndex ) ) ) {
selectMC ( mc, showAtomGlyph );
} else if ( StructuralComponent * sc = dynamic_cast<StructuralComponent *> ( selectedMC->getSubComponent ( subCompIndex ) ) ) {
selectSC ( sc, showAtomGlyph );
}
}
}
//-------------------- updateSelection -------------------
void PMLComponent::updateSelection() {
// refresh atom selection actors
selectedAtomSelection->RemoveAllNodes();
vtkSmartPointer<vtkSelectionNode> selectedAtomSelectionNode = vtkSmartPointer<vtkSelectionNode>::New();
selectedAtomSelectionNode->SetFieldType ( vtkSelectionNode::POINT );
selectedAtomSelectionNode->SetContentType ( vtkSelectionNode::INDICES );
selectedAtomSelectionNode->SetSelectionList ( selectedAtomIdArray );
selectedAtomSelection->AddNode ( selectedAtomSelectionNode );
MeshComponent::addSelection ( "Selected Atoms", vtkSelectionNode::POINT, vtkSelectionNode::INDICES, selectedAtomIdArray, MeshSelectionModel::REPLACE );
// refresh all cells selection actors + merge all in one big selection
vtkSmartPointer<vtkIdTypeArray> allSelectedCells = vtkSmartPointer<vtkIdTypeArray>::New();
for ( QMap<QString, vtkSmartPointer<vtkSelection> >::const_iterator it = scCellSelectionMap.constBegin();
it != scCellSelectionMap.constEnd(); it++ ) {
QString scName = it.key();
vtkSmartPointer<vtkSelection> cellsSelection = it.value();
vtkSmartPointer<vtkIdTypeArray> array = scCellIdArrayMap.value ( scName );
cellsSelection->RemoveAllNodes();
vtkSmartPointer<vtkSelectionNode> cellSelectionNode = vtkSelectionNode::New();
cellSelectionNode->SetFieldType ( vtkSelectionNode::CELL );
cellSelectionNode->SetContentType ( vtkSelectionNode::INDICES );
cellSelectionNode->SetSelectionList ( array );
cellsSelection->AddNode ( cellSelectionNode );
// merge the selection indices
for ( vtkIdType id = 0; id < array->GetNumberOfTuples(); id++ ) {
allSelectedCells->InsertNextTuple ( id, array );
}
}
MeshComponent::addSelection ( "Selected Cells", vtkSelectionNode::CELL, vtkSelectionNode::INDICES, allSelectedCells, MeshSelectionModel::REPLACE );
}
//-------------------- unselectItem -------------------
void PMLComponent::unselectItems() {
// reset selectedAtomIdArray
selectedAtomIdArray = vtkIdTypeArray::New();
// Reinsert a new vtkIdTypeArray for each SC in the Cells maps to clean selections
for ( QMap<QString, vtkSmartPointer<vtkIdTypeArray> >::const_iterator it = scCellIdArrayMap.constBegin();
it != scCellIdArrayMap.constEnd(); it++ ) {
scCellIdArrayMap.insert ( it.key(), vtkIdTypeArray::New() );
}
}
//------------------------ addSelection ---------------------
int PMLComponent::addSelection ( const QString & name, int fieldType, int contentType, vtkSmartPointer< vtkAbstractArray > array, MeshSelectionModel::InsertionPolicy policy ) {
if ( fieldType == vtkSelectionNode::POINT ) {
// point picked -> atom selection
vtkSmartPointer<vtkIdTypeArray> idTypeArray = vtkIdTypeArray::SafeDownCast ( array );
if ( idTypeArray ) {
selectedAtomIdArray = idTypeArray;
updateSelection();
return getSelectionIndex("Selected Atoms");
}
return -1;
} else {
// something else happened
return MeshComponent::addSelection ( name, fieldType, contentType, array, policy );
}
}
//------------------------ getPixmap ---------------------
#include "physicalmodel_20x20.xpm"
QPixmap * PMLComponent::myPixmap = NULL;
QPixmap PMLComponent::getIcon() {
if ( !myPixmap ) {
myPixmap = new QPixmap ( physicalmodel_20x20 );
}
return ( *myPixmap );
}
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