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/*LICENSE_START*/
/*
* Copyright 1995-2002 Washington University School of Medicine
*
* http://brainmap.wustl.edu
*
* This file is part of CARET.
*
* CARET 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 2 of the License, or
* (at your option) any later version.
*
* CARET 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 CARET; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*
*/
/*LICENSE_END*/
#include "BrainModelSurface.h"
#include "BrainModelSurfacePointLocator.h"
#include "BrainModelSurfaceSulcalDepth.h"
#include "BrainSet.h"
#include "DebugControl.h"
#include "MathUtilities.h"
#include "SurfaceShapeFile.h"
#include "TopologyFile.h"
#include "TopologyHelper.h"
/**
* Constructor.
*/
BrainModelSurfaceSulcalDepth::BrainModelSurfaceSulcalDepth(
BrainSet* bs,
BrainModelSurface* surfaceIn,
const QString& hullVtkFileNameIn,
SurfaceShapeFile* shapeFileIn,
const int hullSmoothingIterationsIn,
const int depthSmoothingIterationsIn,
const int depthColumnIn,
const int smoothedDepthColumnIn,
const QString& depthNameIn,
const QString& smoothedDepthNameIn,
CoordinateFile* outputHullCoordFileIn)
: BrainModelAlgorithm(bs)
{
surface = surfaceIn;
shapeFile = shapeFileIn;
depthColumn = depthColumnIn;
smoothedDepthColumn = smoothedDepthColumnIn;
hullSmoothingIterations = hullSmoothingIterationsIn;
depthSmoothingIterations = depthSmoothingIterationsIn;
hullVtkFileName = hullVtkFileNameIn;
depthName = depthNameIn;
smoothedDepthName = smoothedDepthNameIn;
outputHullCoordFile = outputHullCoordFileIn;
}
/**
* Destructor.
*/
BrainModelSurfaceSulcalDepth::~BrainModelSurfaceSulcalDepth()
{
}
/**
* execute the algorithm
*/
void
BrainModelSurfaceSulcalDepth::execute() throw (BrainModelAlgorithmException)
{
//
// Create surface shape columns if needed
//
if (depthColumn == DEPTH_COLUMN_CREATE_NEW) {
if (shapeFile->getNumberOfColumns() == 0) {
shapeFile->setNumberOfNodesAndColumns(surface->getNumberOfNodes(), 1);
}
else {
shapeFile->addColumns(1);
}
depthColumn = shapeFile->getNumberOfColumns() - 1;
}
if (smoothedDepthColumn == DEPTH_COLUMN_CREATE_NEW) {
if (shapeFile->getNumberOfColumns() == 0) {
shapeFile->setNumberOfNodesAndColumns(surface->getNumberOfNodes(), 1);
}
else {
shapeFile->addColumns(1);
}
smoothedDepthColumn = shapeFile->getNumberOfColumns() - 1;
}
//
// Set column names
//
if (depthColumn >= 0) {
shapeFile->setColumnName(depthColumn, depthName);
shapeFile->setColumnColorMappingMinMax(depthColumn, -30.0, 10.0);
}
if (smoothedDepthColumn >= 0) {
shapeFile->setColumnName(smoothedDepthColumn, smoothedDepthName);
shapeFile->setColumnColorMappingMinMax(smoothedDepthColumn, -30.0, 10.0);
}
//
// Convert the hull to a brain model surface
//
BrainSet hullBrainSet;
try {
hullBrainSet.importVtkSurfaceFile(hullVtkFileName, true, true, false,
BrainModelSurface::SURFACE_TYPE_FIDUCIAL,
TopologyFile::TOPOLOGY_TYPE_CLOSED);
}
catch (FileException& e) {
throw BrainModelAlgorithmException(e.whatQString());
}
//
// Hull should be first brain model
//
BrainModelSurface* hullSurface = hullBrainSet.getBrainModelSurface(0);
if (hullSurface == NULL) {
throw BrainModelAlgorithmException("Hull surface is missing.");
}
//
// Save hull prior to smoothing
//
const BrainModelSurface* unsmoothedHullSurface = new BrainModelSurface(*hullSurface);
const CoordinateFile* unsmoothedHullCoords = unsmoothedHullSurface->getCoordinateFile();
if (hullSmoothingIterations > 0) {
//
// Smooth the hull
//
hullSurface->arealSmoothing(1.0, hullSmoothingIterations, 0);
}
//
// Make sure hull's normals point outward
//
hullSurface->orientNormalsOut();
//
// Create a point locator for the hull surface
//
BrainModelSurfacePointLocator hullLocator(hullSurface,
true);
//
// Get surface and hull coordinates
//
const CoordinateFile* surfaceCoords = surface->getCoordinateFile();
const int numSurfaceNodes = surfaceCoords->getNumberOfCoordinates();
const CoordinateFile* hullCoords = hullSurface->getCoordinateFile();
//
// TopologyHelper for surface
//
const TopologyFile* surfaceTopologyFile = surface->getTopologyFile();
const TopologyHelper* surfaceTopologyHelper =
surfaceTopologyFile->getTopologyHelper(false, true, false);
//
// initialize hull coord file
//
if ((numSurfaceNodes > 0) &&
(outputHullCoordFile != NULL)) {
outputHullCoordFile->setNumberOfCoordinates(numSurfaceNodes);
}
//
// Determine depth values for surface nodes
//
for (int i = 0; i < numSurfaceNodes; i++) {
//
// initially set the depth to zero
//
if (depthColumn >= 0) {
shapeFile->setValue(i, depthColumn, 0.0);
}
if (smoothedDepthColumn >= 0) {
shapeFile->setValue(i, smoothedDepthColumn, 0.0);
}
//
// Make sure surface node has neighbors
//
if (surfaceTopologyHelper->getNodeHasNeighbors(i) == false) {
continue;
}
//
// coordinate of surface node
//
const float* surfaceXYZ = surfaceCoords->getCoordinate(i);
//
// Find node in hull that is nearest this surface node
//
const int nearestNode = hullLocator.getNearestPoint(surfaceXYZ);
//
// If nearest node found in hull
//
if (nearestNode >= 0) {
//
// Get the coordinate of the hull nearest node
//
const float* hullXYZ = hullCoords->getCoordinate(nearestNode);
//
// Get normal of hull node
//
const float* hullNormal = hullSurface->getNormal(nearestNode);
//
// Compute signed distance from surface not to point on plane from hull normal
//
const float distanceFromPlane =
MathUtilities::signedDistanceToPlane(hullNormal,
hullXYZ,
surfaceXYZ);
//
// Distance between surface and hull point
//
float distance = MathUtilities::distance3D(hullXYZ, surfaceXYZ);
//
// Set the sign for inside or outside the hull
//
if (distanceFromPlane < 0.0) {
distance = -distance;
}
if (DebugControl::getDebugOn()) {
if (i == DebugControl::getDebugNodeNumber()) {
const float* sn = surface->getNormal(i);
std::cout << "surface node: " << i << std::endl;
std::cout << " hull node: " << nearestNode << std::endl;
std::cout << " surface node: " << surfaceXYZ[0] << ", " << surfaceXYZ[1] << ", "
<< surfaceXYZ[2] << std::endl;
std::cout << " dot: " << MathUtilities::dotProduct(sn, hullNormal) << std::endl;
std::cout << " surface normal: " << sn[0] << ", " << sn[1] << ", "
<< sn[2] << std::endl;
std::cout << " hull node: " << hullXYZ[0] << ", " << hullXYZ[1] << ", "
<< hullXYZ[2] << std::endl;
std::cout << " hull normal: " << hullNormal[0] << ", " << hullNormal[1] << ", "
<< hullNormal[2] << std::endl;
std::cout << " distance: " << distance << std::endl;
std::cout << " distance/plane: " << distanceFromPlane << std::endl;
}
}
//
// Insert into the surface shape file
//
if (depthColumn >= 0) {
shapeFile->setValue(i, depthColumn, distance);
}
if (smoothedDepthColumn >= 0) {
shapeFile->setValue(i, smoothedDepthColumn, distance);
}
//
// output hull coord file
//
if (outputHullCoordFile != NULL) {
outputHullCoordFile->setCoordinate(i,
unsmoothedHullCoords->getCoordinate(nearestNode));
}
}
else {
//
// output hull coord file
//
if (outputHullCoordFile != NULL) {
outputHullCoordFile->setCoordinate(i, 0.0, 0.0, 0.0);
}
}
}
//
// if creating smoothed depth, smooth it
//
if ((smoothedDepthColumn >= 0) && (depthSmoothingIterations > 0)) {
shapeFile->smoothAverageNeighbors(smoothedDepthColumn,
smoothedDepthColumn,
shapeFile->getColumnName(smoothedDepthColumn),
1.0,
depthSmoothingIterations,
surface->getTopologyFile());
}
//
// Free memory
//
delete unsmoothedHullSurface;
}
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