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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 <cmath>
#include <limits>
#include <QProgressDialog>
#include "BrainModelSurface.h"
#include "BrainModelSurfaceFociUncertaintyToRgbPaint.h"
#include "BrainSet.h"
#include "FociProjectionFile.h"
#include "FociColorFile.h"
#include "MathUtilities.h"
#include "PreferencesFile.h"
#include "RgbPaintFile.h"
#include "vtkMath.h"
/**
* Constructor.
*/
BrainModelSurfaceFociUncertaintyToRgbPaint::BrainModelSurfaceFociUncertaintyToRgbPaint(
BrainSet* bsIn,
const BrainModelSurface* leftSurfaceIn,
const BrainModelSurface* rightSurfaceIn,
RgbPaintFile* rgbPaintFileIn,
const int leftRgbPaintFileColumnIn,
const QString& leftRgbPaintFileColumnNameIn,
const int rightRgbPaintFileColumnIn,
const QString& rightRgbPaintFileColumnNameIn,
const FociProjectionFile* fociProjectionFileIn,
const FociColorFile* fociColorFileIn,
const float lowerLimitIn,
const float middleLimitIn,
const float upperLimitIn)
: BrainModelAlgorithm(bsIn),
leftSurface(leftSurfaceIn),
rightSurface(rightSurfaceIn),
rgbPaintFile(rgbPaintFileIn),
leftRgbPaintFileColumn(leftRgbPaintFileColumnIn),
leftRgbPaintFileColumnName(leftRgbPaintFileColumnNameIn),
rightRgbPaintFileColumn(rightRgbPaintFileColumnIn),
rightRgbPaintFileColumnName(rightRgbPaintFileColumnNameIn),
fociProjectionFile(fociProjectionFileIn),
fociColorFile(fociColorFileIn),
lowerLimit(lowerLimitIn),
middleLimit(middleLimitIn),
upperLimit(upperLimitIn)
{
}
/**
* Destructor.
*/
BrainModelSurfaceFociUncertaintyToRgbPaint::~BrainModelSurfaceFociUncertaintyToRgbPaint()
{
}
/**
* execute the algorithm.
*/
void
BrainModelSurfaceFociUncertaintyToRgbPaint::execute() throw (BrainModelAlgorithmException)
{
if ((leftSurface == NULL) &&
(rightSurface == NULL)) {
throw BrainModelAlgorithmException("Both surfaces are invalid.");
}
if (rgbPaintFile == NULL) {
throw BrainModelAlgorithmException("The RGB Paint File is invalid.");
}
if (fociProjectionFile == NULL) {
throw BrainModelAlgorithmException("The Foci Projection File is invalid.");
}
if (fociColorFile == NULL) {
throw BrainModelAlgorithmException("The Foci Color File is invalid.");
}
if (fociProjectionFile->getNumberOfCellProjections() <= 0) {
throw BrainModelAlgorithmException("The Foci Projection File contains no foci.");
}
if (fociProjectionFile->getNumberOfCellClasses() <= 0) {
throw BrainModelAlgorithmException("There are no foci classes.");
}
int numNodes = 0;
if (leftSurface != NULL) {
numNodes += leftSurface->getNumberOfNodes();
}
if (rightSurface != NULL) {
numNodes += rightSurface->getNumberOfNodes();
}
createProgressDialog("Determining Foci Uncertainty",
numNodes,
"fociUncertainty");
int progressSteps = 0;
try {
if (leftSurface != NULL) {
generateLimits(leftSurface,
leftRgbPaintFileColumn,
leftRgbPaintFileColumnName,
progressSteps);
}
if (rightSurface != NULL) {
generateLimits(rightSurface,
rightRgbPaintFileColumn,
rightRgbPaintFileColumnName,
progressSteps);
}
}
catch (BrainModelAlgorithmException& e) {
removeProgressDialog();
throw e;
}
removeProgressDialog();
}
/**
* Convert foci uncertainty to rgb paint (returns true if successful).
*/
void
BrainModelSurfaceFociUncertaintyToRgbPaint::generateLimits(const BrainModelSurface* bms,
const int rgbPaintColumnIn,
const QString& rgbPaintColumnNewName,
int& progressSteps)
throw (BrainModelAlgorithmException)
{
//
const float upperLimitSquared = upperLimit*upperLimit;
//
// Get number of foci classes
//
const int numClasses = fociProjectionFile->getNumberOfCellClasses();
const int numFoci = fociProjectionFile->getNumberOfCellProjections();
const TopologyFile* tf = bms->getTopologyFile();
const CoordinateFile* cf = bms->getCoordinateFile();
const int numCoords = cf->getNumberOfCoordinates();
if (numCoords <= 0) {
throw BrainModelAlgorithmException("The surface has no coordinates.");
}
if (tf == NULL) {
throw BrainModelAlgorithmException("The surface has no topology.");
}
if (tf->getNumberOfTiles() <= 0) {
throw BrainModelAlgorithmException("The surface's topology contains no triangles.");
}
//
// Storage for number of nodes in each class
//
std::vector<int> nodeCount(numClasses, 0);
//
// Initialize color to foreground color
//
unsigned char foregroundColor[3];
PreferencesFile* pref = brainSet->getPreferencesFile();
pref->getSurfaceForegroundColor(foregroundColor[0], foregroundColor[1], foregroundColor[2]);
//
// Add a column to the rgb paint file
//
int rgbPaintColumn = rgbPaintColumnIn;
if (rgbPaintFile->getNumberOfNodes() == 0) {
rgbPaintFile->setNumberOfNodesAndColumns(bms->getNumberOfNodes(), 1);
rgbPaintColumn = 0;
}
else if ((rgbPaintColumn < 0) ||
(rgbPaintColumn >= rgbPaintFile->getNumberOfColumns())) {
rgbPaintColumn = rgbPaintFile->getNumberOfColumns();
rgbPaintFile->addColumns(1);
}
rgbPaintFile->setColumnName(rgbPaintColumn, rgbPaintColumnNewName);
rgbPaintFile->setScaleRed(rgbPaintColumn, 0, 255.0);
rgbPaintFile->setScaleGreen(rgbPaintColumn, 0, 255.0);
rgbPaintFile->setScaleBlue(rgbPaintColumn, 0, 255.0);
rgbPaintFile->setColumnComment(rgbPaintColumn,
"Created from foci uncertainty");
const bool fiducialSurfaceFlag = bms->getIsFiducialSurface();
const bool flatSurfaceFlag = bms->getIsFlatSurface();
const Structure::STRUCTURE_TYPE surfaceStructureType =
bms->getStructure().getType();
//
// Loop through fiducial coordinates
//
for (int i = 0; i < numCoords; i++) {
//
// Update progress
//
if (progressDialog != NULL) {
const float pctComplete = (static_cast<float>(progressSteps)
/ progressDialog->maximum()) * 100.0;
const QString pctString(QString::number(pctComplete, 'f', 1)
+ "% complete.");
updateProgressDialog(pctString, progressSteps);
}
else {
updateProgressDialog("Determining Uncertainty", progressSteps);
}
progressSteps++;
//
// Keep track of nodes in the various classes nearest to this node.
//
std::vector<int> focusNearestNode(numClasses, -1);
std::vector<float> focusDistanceToNode(numClasses,
std::numeric_limits<float>::max());
//
// Get the position of the node
//
const float* nodePos = cf->getCoordinate(i);
//
// Loop through foci
//
for (int k = 0; k < numFoci; k++) {
//
// Get the foci's and see if it is displayed
//
const CellProjection* focus = fociProjectionFile->getCellProjection(k);
if (focus->getDisplayFlag()) {
//
// Get the foci's class and see if it matches the current foci class
//
const int classNumber = focus->getClassIndex();
if (classNumber >= 0) {
//
// Get the foci's position and adjust for hemisphere
//
bool useFocus = false;
float fociPos[3];
if (focus->getProjectedPosition(cf,
tf,
fiducialSurfaceFlag,
flatSurfaceFlag,
false,
fociPos)) {
if (focus->getCellStructure() == surfaceStructureType) {
useFocus = true;
}
}
if (useFocus) {
//
// See how close this focus is to coordinate
//
const float distSQ = MathUtilities::distanceSquared3D(fociPos,
nodePos);
if ((distSQ < upperLimitSquared) &&
(distSQ < focusDistanceToNode[classNumber])) {
focusNearestNode[classNumber] = k;
focusDistanceToNode[classNumber] = distSQ;
}
}
}
}
}
for (int m = 0; m < numClasses; m++) {
focusDistanceToNode[m] = std::sqrt(focusDistanceToNode[m]);
}
//
// Node coloring
//
float nodeColor[3] = { -1.0, -1.0, -1.0 };
std::vector<int> nearbyFoci;
std::vector<float> nearbyFociDistances;
//
// Loop through foci classes
//
for (int j = 0; j < numClasses; j++) {
if (focusNearestNode[j] >= 0) {
if ((focusDistanceToNode[j] >= lowerLimit) &&
(focusDistanceToNode[j] <= upperLimit)) {
nearbyFoci.push_back(focusNearestNode[j]);
nearbyFociDistances.push_back(focusDistanceToNode[j]);
}
}
}
const int nearbyFociCount = static_cast<int>(nearbyFoci.size());
if (nearbyFociCount > 2) {
//
// Paint node gray
//
nodeColor[0] = 50.0;
nodeColor[1] = 50.0;
nodeColor[2] = 50.0;
}
else if (nearbyFociCount == 2) {
//
// Get color of foci nearest the node
//
int colorIndex = fociProjectionFile->getCellProjection(nearbyFoci[0])->getColorIndex();
unsigned char r, g, b;
if (colorIndex >= 0) {
fociColorFile->getColorByIndex(colorIndex, r, g, b);
}
else {
//
// Use foreground color
//
r = foregroundColor[0];
g = foregroundColor[1];
b = foregroundColor[2];
}
const float r1 = r;
const float g1 = g;
const float b1 = b;
//
// Get color of foci second nearest the node
//
colorIndex = fociProjectionFile->getCellProjection(nearbyFoci[1])->getColorIndex();
if (colorIndex >= 0) {
fociColorFile->getColorByIndex(colorIndex, r, g, b);
}
else {
//
// Use foreground color
//
r = foregroundColor[0];
g = foregroundColor[1];
b = foregroundColor[2];
}
const float r2 = r;
const float g2 = g;
const float b2 = b;
const float m = std::max(r1+r2, std::max(g1+g2, b1+b2));
nodeColor[0] = 255.0 * (r1 + r2) / m;
nodeColor[1] = 255.0 * (g1 + g2) / m;
nodeColor[2] = 255.0 * (b1 + b2) / m;
}
else if (nearbyFociCount == 1) {
//
// Use the foci's color
//
const int colorIndex = fociProjectionFile->getCellProjection(nearbyFoci[0])->getColorIndex();
if (colorIndex >= 0) {
unsigned char r, g, b;
fociColorFile->getColorByIndex(colorIndex, r, g, b);
nodeColor[0] = r;
nodeColor[1] = g;
nodeColor[2] = b;
}
else {
//
// Use foreground color
//
nodeColor[0] = foregroundColor[0];
nodeColor[1] = foregroundColor[1];
nodeColor[2] = foregroundColor[2];
}
//
// If within middle limit, whiten the node to produce a halo effect
//
if (nearbyFociDistances[0] < middleLimit) {
nodeColor[0] = 127.5 + 0.5 * nodeColor[0];
nodeColor[1] = 127.5 + 0.5 * nodeColor[1];
nodeColor[2] = 127.5 + 0.5 * nodeColor[2];
}
}
//
// Add to rgb paint file
//
const float max255 = 255.0;
nodeColor[0] = std::min(nodeColor[0], max255);
nodeColor[1] = std::min(nodeColor[1], max255);
nodeColor[2] = std::min(nodeColor[2], max255);
rgbPaintFile->setRgb(i, rgbPaintColumn, nodeColor[0], nodeColor[1], nodeColor[2]);
}
}
/**
* Convert foci uncertainty to rgb paint (returns true if successful).
*/
void
BrainModelSurfaceFociUncertaintyToRgbPaint::generateLimitsOLD(const BrainModelSurface* bms,
const int rgbPaintColumnIn,
const QString& rgbPaintColumnNewName)
throw (BrainModelAlgorithmException)
{
//
const float upperLimitSquared = upperLimit*upperLimit;
//
// Get number of foci classes
//
const int numClasses = fociProjectionFile->getNumberOfCellClasses();
const int numFoci = fociProjectionFile->getNumberOfCellProjections();
const TopologyFile* tf = bms->getTopologyFile();
const CoordinateFile* cf = bms->getCoordinateFile();
const int numCoords = cf->getNumberOfCoordinates();
if (numCoords <= 0) {
throw BrainModelAlgorithmException("There surface has no coordinates.");
}
if (tf == NULL) {
throw BrainModelAlgorithmException("There surface has no topology.");
}
if (tf->getNumberOfTiles() <= 0) {
throw BrainModelAlgorithmException("There surface's topology contains no triangles.");
}
//
// Storage for number of nodes in each class
//
std::vector<int> nodeCount(numClasses, 0);
//
// Initialize color to foreground color
//
unsigned char foregroundColor[3];
PreferencesFile* pref = brainSet->getPreferencesFile();
pref->getSurfaceForegroundColor(foregroundColor[0], foregroundColor[1], foregroundColor[2]);
//
// Add a column to the rgb paint file
//
int rgbPaintColumn = rgbPaintColumnIn;
if (rgbPaintFile->getNumberOfNodes() == 0) {
rgbPaintFile->setNumberOfNodesAndColumns(bms->getNumberOfNodes(), 1);
rgbPaintColumn = 0;
}
else if ((rgbPaintColumn < 0) ||
(rgbPaintColumn >= rgbPaintFile->getNumberOfColumns())) {
rgbPaintColumn = rgbPaintFile->getNumberOfColumns();
rgbPaintFile->addColumns(1);
}
rgbPaintFile->setColumnName(rgbPaintColumn, rgbPaintColumnNewName);
rgbPaintFile->setScaleRed(rgbPaintColumn, 0, 255.0);
rgbPaintFile->setScaleGreen(rgbPaintColumn, 0, 255.0);
rgbPaintFile->setScaleBlue(rgbPaintColumn, 0, 255.0);
rgbPaintFile->setColumnComment(rgbPaintColumn,
"Created from foci uncertainty");
const bool fiducialSurfaceFlag = bms->getIsFiducialSurface();
const bool flatSurfaceFlag = bms->getIsFlatSurface();
const Structure::STRUCTURE_TYPE surfaceStructureType =
bms->getStructure().getType();
//
// Loop through fiducial coordinates
//
for (int i = 0; i < numCoords; i++) {
//
// Keep track of nodes in the various classes nearest to this node.
//
std::vector<int> focusNearestNode(numClasses, -1);
std::vector<float> focusDistanceToNode(numClasses, 0.0);
//
// Get the position of the node
//
const float* nodePos = cf->getCoordinate(i);
//
// Loop through foci classes
//
for (int fociClass = 0; fociClass < numClasses; fociClass++) {
int closestFocus = -1;
float closestFocusDistance = std::numeric_limits<float>::max();
//
// Loop through foci
//
for (int k = 0; k < numFoci; k++) {
//
// Get the foci's and see if it is displayed
//
const CellProjection* focus = fociProjectionFile->getCellProjection(k);
if (focus->getDisplayFlag()) {
//
// Get the foci's class and see if it matches the current foci class
//
const int classNumber = focus->getClassIndex();
if (classNumber == fociClass) {
//
// Get the foci's position and adjust for hemisphere
//
bool useFocus = false;
float fociPos[3];
if (focus->getProjectedPosition(cf,
tf,
fiducialSurfaceFlag,
flatSurfaceFlag,
false,
fociPos)) {
if (focus->getCellStructure() == surfaceStructureType) {
useFocus = true;
}
}
if (useFocus) {
//
// See how close this focus is to coordinate
//
const float distSquared = vtkMath::Distance2BetweenPoints(fociPos, nodePos);
if ((distSquared < upperLimitSquared) && (distSquared < closestFocusDistance)) {
closestFocus = k;
closestFocusDistance = distSquared;
}
}
}
}
}
if (closestFocus >= 0) {
focusNearestNode[fociClass] = closestFocus;
focusDistanceToNode[fociClass] = std::sqrt(closestFocusDistance);
}
}
//
// Node coloring
//
float nodeColor[3] = { 0.0, 0.0, 0.0 };
std::vector<int> nearbyFoci;
std::vector<float> nearbyFociDistances;
//
// Loop through foci classes
//
for (int j = 0; j < numClasses; j++) {
if (focusNearestNode[j] >= 0) {
if ((focusDistanceToNode[j] >= lowerLimit) &&
(focusDistanceToNode[j] <= upperLimit)) {
nearbyFoci.push_back(focusNearestNode[j]);
nearbyFociDistances.push_back(focusDistanceToNode[j]);
}
}
}
const int nearbyFociCount = static_cast<int>(nearbyFoci.size());
if (nearbyFociCount > 2) {
//
// Paint node gray
//
nodeColor[0] = 50.0;
nodeColor[1] = 50.0;
nodeColor[2] = 50.0;
}
else if (nearbyFociCount == 2) {
//
// Get color of foci nearest the node
//
int colorIndex = fociProjectionFile->getCellProjection(nearbyFoci[0])->getColorIndex();
unsigned char r, g, b;
if (colorIndex >= 0) {
fociColorFile->getColorByIndex(colorIndex, r, g, b);
}
else {
//
// Use foreground color
//
r = foregroundColor[0];
g = foregroundColor[1];
b = foregroundColor[2];
}
const float r1 = r;
const float g1 = g;
const float b1 = b;
//
// Get color of foci second nearest the node
//
colorIndex = fociProjectionFile->getCellProjection(nearbyFoci[1])->getColorIndex();
if (colorIndex >= 0) {
fociColorFile->getColorByIndex(colorIndex, r, g, b);
}
else {
//
// Use foreground color
//
r = foregroundColor[0];
g = foregroundColor[1];
b = foregroundColor[2];
}
const float r2 = r;
const float g2 = g;
const float b2 = b;
const float m = std::max(r1+r2, std::max(g1+g2, b1+b2));
nodeColor[0] = 255.0 * (r1 + r2) / m;
nodeColor[1] = 255.0 * (g1 + g2) / m;
nodeColor[2] = 255.0 * (b1 + b2) / m;
}
else if (nearbyFociCount == 1) {
//
// Use the foci's color
//
const int colorIndex = fociProjectionFile->getCellProjection(nearbyFoci[0])->getColorIndex();
if (colorIndex >= 0) {
unsigned char r, g, b;
fociColorFile->getColorByIndex(colorIndex, r, g, b);
nodeColor[0] = r;
nodeColor[1] = g;
nodeColor[2] = b;
}
else {
//
// Use foreground color
//
nodeColor[0] = foregroundColor[0];
nodeColor[1] = foregroundColor[1];
nodeColor[2] = foregroundColor[2];
}
//
// If within middle limit, whiten the node to produce a halo effect
//
if (nearbyFociDistances[0] < middleLimit) {
nodeColor[0] = 127.5 + 0.5 * nodeColor[0];
nodeColor[1] = 127.5 + 0.5 * nodeColor[1];
nodeColor[2] = 127.5 + 0.5 * nodeColor[2];
}
}
//
// Add to rgb paint file
//
const float max255 = 255.0;
nodeColor[0] = std::min(nodeColor[0], max255);
nodeColor[1] = std::min(nodeColor[1], max255);
nodeColor[2] = std::min(nodeColor[2], max255);
rgbPaintFile->setRgb(i, rgbPaintColumn, nodeColor[0], nodeColor[1], nodeColor[2]);
}
}
|
