/**
* Generates an artificial topographyGrid of size numRows x numCols if no
* topographic data is available. Results are dumped into topographyGrid.
* @param topographyGrid A pointer to a zero-initialized Grid of size
* numRows x numCols.
* @param numRows The desired number of non-border rows in the resulting matrix.
* @param numCols The desired number of non-border cols in the resulting matrix.
*/
void simulatetopographyGrid(Grid* topographyGrid, int numRows, int numCols) {
Eigen::VectorXd refx = refx.LinSpaced(numCols, -2*M_PI, 2*M_PI);
Eigen::VectorXd refy = refx.LinSpaced(numRows, -2*M_PI, 2*M_PI);
Eigen::MatrixXd X = refx.replicate(1, numRows);
X.transposeInPlace();
Eigen::MatrixXd Y = refy.replicate(1, numCols);
// Eigen can only deal with two matrices at a time,
// so split the computation:
// topographyGrid = sin(X) * sin(Y) * abs(X) * abs(Y) -pi
Eigen::MatrixXd absXY = X.cwiseAbs().cwiseProduct(Y.cwiseAbs());
Eigen::MatrixXd sins = X.array().sin().cwiseProduct(Y.array().sin());
Eigen::MatrixXd temp;
temp.resize(numRows, numCols);
temp = absXY.cwiseProduct(sins);
// All this work to create a matrix of pi...
Eigen::MatrixXd pi;
pi.resize(numRows, numCols);
pi.setConstant(M_PI);
temp = temp - pi;
// And the final result.
topographyGrid->data.block(border, border, numRows, numCols) =
temp.block(0, 0, numRows, numCols);
// Ignore positive values.
topographyGrid->data =
topographyGrid->data.unaryExpr(std::ptr_fun(validateDepth));
topographyGrid->clearNA();
}
void Model::construct_contrast_matrix(Eigen::MatrixXd &C) {
if (n_alternatives > 1) {
C.setConstant(-1.0 / (n_alternatives - 1.0));
} else {
C.setZero();
}
for (unsigned int i = 0; i < n_alternatives; i++) {
C(i, i) = 1.0;
}
}
void colorEdgeMeshFaces(const Eigen::VectorXd &values,
const double &minimum,
const double &maximum,
Eigen::MatrixXd &C)
{
C.setConstant(Fbs.rows(),3,1);
Eigen::MatrixXd colors;
igl::jet(values, minimum, maximum, colors);
for (int ei = 0; ei<E.rows(); ++ei)
{
const Eigen::RowVector3d &this_color = colors.row(ei);
int f0 = E2F(ei,0);
int f1 = E2F(ei,1);
if(f0 != -1)
{
int i0 = -1;
for (int k = 0; k<3; k++)
if (F2E(f0,k)== ei)
{
i0 = k;
break;
}
C.row(3*f0+i0) = this_color;
}
if(f1 != -1)
{
int i1 = -1;
for (int k = 0; k<3; k++)
if (F2E(f1,k)== ei)
{
i1 = k;
break;
}
C.row(3*f1+i1) = this_color;
}
}
}
void display()
{
using namespace Eigen;
using namespace igl;
using namespace std;
if(!trackball_on && tot_num_samples < 10000)
{
if(S.size() == 0)
{
S.resize(V.rows());
S.setZero();
}
VectorXd Si;
const int num_samples = 20;
ambient_occlusion(ei,V,N,num_samples,Si);
S *= (double)tot_num_samples;
S += Si*(double)num_samples;
tot_num_samples += num_samples;
S /= (double)tot_num_samples;
}
// Convert to 1-intensity
C.conservativeResize(S.rows(),3);
if(ao_on)
{
C<<S,S,S;
C.array() = (1.0-ao_factor*C.array());
}else
{
C.setConstant(1.0);
}
if(ao_normalize)
{
C.col(0) *= ((double)C.rows())/C.col(0).sum();
C.col(1) *= ((double)C.rows())/C.col(1).sum();
C.col(2) *= ((double)C.rows())/C.col(2).sum();
}
C.col(0) *= color(0);
C.col(1) *= color(1);
C.col(2) *= color(2);
glClearColor(back[0],back[1],back[2],0);
glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
// All smooth points
glEnable( GL_POINT_SMOOTH );
glDisable(GL_LIGHTING);
if(lights_on)
{
lights();
}
push_scene();
glEnable(GL_DEPTH_TEST);
glDepthFunc(GL_LEQUAL);
glEnable(GL_NORMALIZE);
glEnable(GL_COLOR_MATERIAL);
glColorMaterial(GL_FRONT_AND_BACK,GL_AMBIENT_AND_DIFFUSE);
push_object();
// Draw the model
// Set material properties
glEnable(GL_COLOR_MATERIAL);
draw_mesh(V,F,N,C);
pop_object();
// Draw a nice floor
glPushMatrix();
const double floor_offset =
-2./bbd*(V.col(1).maxCoeff()-mid(1));
glTranslated(0,floor_offset,0);
const float GREY[4] = {0.5,0.5,0.6,1.0};
const float DARK_GREY[4] = {0.2,0.2,0.3,1.0};
draw_floor(GREY,DARK_GREY);
glPopMatrix();
pop_scene();
report_gl_error();
TwDraw();
glutSwapBuffers();
glutPostRedisplay();
}
int main() {
bool test = false, simulateBathy = false;
if (test) {
runTests();
return 0;
}
acousticParams.insert({ "debug", "0" });
acousticParams.insert({ "cellSize", "5" });
acousticParams.insert({ "fishmodel", "0" });
acousticParams.insert({ "suppressionRangeFactor", "1"}),
acousticParams.insert({ "suppressionMethod", "suppression.quick"}),
acousticParams.insert({ "userSensors", "100,100,0,0,100,0,0,200" });
acousticParams.insert({ "numOptimalSensors", "10" });
acousticParams.insert({ "numProjectedSensors", "2" });
acousticParams.insert({ "bias", "2" });
acousticParams.insert({ "ousdx", ".1" });
acousticParams.insert({ "ousdy", ".1" });
acousticParams.insert({ "oucor", "0" });
acousticParams.insert({ "mux", ".5" });
acousticParams.insert({ "muy", ".5" });
acousticParams.insert({ "fishmodel", "1" });
acousticParams.insert({ "minDepth", "15" });
acousticParams.insert({ "maxDepth", "30" });
acousticParams.insert({ "meanRelativePosition", "1" });
acousticParams.insert({ "relativePositionSD", "1" });
// acousticParams.insert({"inputFile", "himbsyn.bathy.v19.grd"});
acousticParams.insert({"inputFile", "himbsyn.bathytopo.1km.v19.grd"});
// acousticParams.insert({ "inputFile", "pal_5m.asc" });
acousticParams.insert({ "inputFileType", "netcdf" });
acousticParams.insert({ "seriesName", "z" });
acousticParams.insert({ "timestamp", "-1" });
acousticParams.insert({ "logScaleGraphColoring", "1" });
acousticParams.insert({ "contourDepths", "0,-20,-40,-80" });
double suppressionRangeFactor =
std::stod(acousticParams["suppressionRangeFactor"]),
ousdx = std::stod(acousticParams["ousdx"]),
ousdy = std::stod(acousticParams["ousdy"]),
oucor = std::stod(acousticParams["oucor"]),
mux = std::stod(acousticParams["mux"]),
muy = std::stod(acousticParams["muy"]),
fishmodel = std::stod(acousticParams["fishmodel"]),
networkSparsity = 0, absRecoveryRate = 0, uniqueRecoveryRate = 0,
goodnessGridComputationTime = 0, totalComputationTime = 0;
int startRow = 450,
startCol = 340, // 450,340,201,201 (1km)netcdf
rowDist = 1001, // 100 0 800 1500 (5m)netcdf
colDist = 1001, // 300 200 501 501 (palmyra) asc
height = 1000,
width = 1000,
bias = 2,
sensorDetectionRange = 4,
sensorDetectionDiameter = 2 * sensorDetectionRange + 1,
sensorPeakDetectionProbability = 1,
SDofSensorDetectionRange = 1,
i = 0,
row = 0,
col = 0,
cellSize = std::stoi(acousticParams["cellSize"]),
numOptimalSensors =
std::stoi(acousticParams["numOptimalSensors"]),
numProjectedSensors =
std::stoi(acousticParams["numProjectedSensors"]),
numSensorsToPlace = numOptimalSensors + numProjectedSensors,
suppressionDiameter = (2 * ceil(sensorDetectionRange * suppressionRangeFactor)) + 1;
// Set the global border size
border = sensorDetectionRange;
omp_set_num_threads(numThreads);
Eigen::setNbThreads(numThreads);
clock_t begin, end, vizBegin, vizEnd;
// TODO(Greg) Data validation
// Parse User Sensor Placements
std::cout << "\nReading userSensor List...\n";
std::vector<std::string> userSensors;
parseCDString(&userSensors, acousticParams["userSensors"], ',');
Eigen::MatrixXd userSensorList;
userSensorList.resize(userSensors.size()/2, 4);
for (i = 0; i < userSensorList.rows(); i ++) {
row = std::stoi(userSensors[2 * i]);
col = std::stoi(userSensors[2 * i + 1]);
if (row < 0 || col < 0 || row >= rowDist || col >= colDist) {
printError("A user-defined sensor is out of bounds.", 1,
acousticParams["timestamp"]);
}
// Translate user points to our internal grid
userSensorList(i, 0) = row;
userSensorList(i, 1) = col;
}
begin = clock();
// Compute contour depth meta data (used for graphical output)
std::vector<std::string> contourLevels;
parseCDString(&contourLevels, acousticParams["contourDepths"], ',');
// Note the number of contours we need to graph
acousticParams.insert({ "numContourDepths",
std::to_string(contourLevels.size()) });
// TODO(Greg) Sort is broken, throws segfaults. Possibly b/c file doesn't
// exist (tried with pal5m.asc). fix plx.
// sort(&contourLevels, &contourLevels + numContourDepths);
// File path variables
std::string outputDataFilePath = "data/", outputDataFileType = ".dat",
bathymetryTitle = "Topography", habitatTitle = "Habitat",
goodnessTitle = "Goodness",
coverageTitle = "Acoustic Coverage",
bathymetryFilePath = outputDataFilePath + bathymetryTitle +
outputDataFileType,
habitatFilePath = outputDataFilePath + habitatTitle +
outputDataFileType,
goodnessFilePath = outputDataFilePath + goodnessTitle +
outputDataFileType,
coverageFilePath = outputDataFilePath + coverageTitle +
outputDataFileType;
Grid bGrid(rowDist + 2 * border, colDist + 2 * border, "Behavior");
Grid gGrid(rowDist + 2 * border, colDist + 2 * border, "Goodness");
Grid tGrid(rowDist + 2 * border, colDist + 2 * border, "Topography");
Grid cGrid(rowDist + 2 * border, colDist + 2 * border, "Coverage");
Eigen::MatrixXd suppressionReference;
Eigen::MatrixXd distanceGradient;
Eigen::MatrixXd detectionGradient;
distanceGradient.resize(sensorDetectionDiameter, sensorDetectionDiameter);
distanceGradient.setConstant(0);
detectionGradient.resize(sensorDetectionDiameter, sensorDetectionDiameter);
detectionGradient.setConstant(0);
// Create a gradient of distances to avoid redundant computation
makeDistGradient(&distanceGradient, sensorDetectionRange);
// Create a gradient of probability of detection (due to sensorRange) to
// avoid redundant computation
makeDetectionGradient(&detectionGradient, & distanceGradient,
sensorPeakDetectionProbability, SDofSensorDetectionRange);
// Fetch or simulate topography
std::cout << "Getting topography...";
if (simulateBathy) {
// Simulate topography
simulatetopographyGrid(&tGrid, rowDist, colDist);
} else {
// Fetch actual topography
getBathy(&tGrid, acousticParams["inputFile"],
acousticParams["inputFileType"], size_t(startRow),
size_t(startCol), size_t(rowDist), size_t(colDist),
acousticParams["seriesName"], acousticParams["timestamp"]);
}
std::cout << bGrid.data;
// Fill in Behavior Grid
std::cout << "\nGetting Behavior...";
populateBehaviorGrid(&tGrid, &bGrid, bias, cellSize, ousdx, ousdy, oucor, mux,
muy, fishmodel);
// Initalize the Coverage Grid
cGrid.data.block(border, border, rowDist, colDist).setConstant(1);
// Mr. Gaeta, START THE CLOCK!
vizBegin = clock();
std::cout << "\nGetting Goodness...\nBias: " << bias << "\n";
// Calculate good sensor locations
calculateGoodnessGrid(&tGrid, &bGrid, &gGrid, &suppressionReference,
&detectionGradient, &distanceGradient, bias,
sensorDetectionRange, border, border,
rowDist, colDist);
vizEnd = clock();
goodnessGridComputationTime =
static_cast<double>(end - begin) / CLOCKS_PER_SEC;
std::cout << "Copying goodness grid...\n";
Grid UGGrid(&gGrid, "Unsuppressed Goodness");
// Find optimal placements
std::cout << "\nPlacing Sensors...\n";
Eigen::MatrixXd bestSensors;
bestSensors.resize(numSensorsToPlace, 4);
//============================
gGrid.name = "x1";
Graph x1Graph = Graph(&gGrid);
x1Graph.writeMat();
// Grab the top n sensor r,c locations and recovery rates.
selectTopSensorLocations(&tGrid, &bGrid, &gGrid, &UGGrid,
&bestSensors, &userSensorList, &suppressionReference,
&detectionGradient, &distanceGradient,
numSensorsToPlace,
sensorDetectionRange, bias, suppressionRangeFactor,
suppressionDiameter, sensorPeakDetectionProbability,
SDofSensorDetectionRange, acousticParams["timestamp"]);
gGrid.name = "x2";
Graph x2Graph = Graph(&gGrid);
x2Graph.writeMat();
std::cout << bestSensors << "\n";
std::cout << "Computing Statistics...\n";
getStats(&UGGrid, &gGrid, &bestSensors, sensorDetectionRange, &networkSparsity,
&absRecoveryRate, &uniqueRecoveryRate, &cGrid);
gGrid.name = "x3";
Graph x3Graph = Graph(&gGrid);
x3Graph.writeMat();
gGrid.name = "Goodness";
// Generate graphs
std::cout<< "\nWriting Graphs...";
Graph gGraph = Graph(&UGGrid);
Graph tGraph = Graph(&tGrid);
Graph bGraph = Graph(&bGrid);
Graph cGraph = Graph(&cGrid);
try {
// Print the matrix & data files for Topography Grid
tGraph.writeMat();
tGraph.writeDat();
// Print the contour file used by all graphs.
// (Do this just once as it takes a loooong time).
tGraph.printContourFile(&contourLevels);
// Graph the Topography Grid with contour lines.
bool plotSensors = true;
tGraph.printContourGraph(width, height, &contourLevels, plotSensors,
&userSensorList, &bestSensors,
numProjectedSensors, false);
// Print the matrix & data files for Bathymetry Grid
bGraph.writeMat();
bGraph.writeDat();
// Graph Behavior Grid with contour lines.
bGraph.printContourGraph(width, height, &contourLevels, plotSensors,
&userSensorList, &bestSensors,
numProjectedSensors, false);
// Print the matrix & data files for Goodness Grid
gGraph.writeMat();
gGraph.writeDat();
// Graph Goodness Grid with contour lines.
gGraph.printContourGraph(width, height, &contourLevels, plotSensors,
&userSensorList, &bestSensors,
numProjectedSensors, false);
// Print the matrix & data files for Goodness Grid
cGraph.writeMat();
cGraph.writeDat();
// Graph Goodness Grid with contour lines.
cGraph.printContourGraph(width, height, &contourLevels, plotSensors,
&userSensorList, &bestSensors,
numProjectedSensors, false);
} catch (int e) {
std::cout << "Error:" << e << "\n";
return 0;
}
end = clock();
goodnessGridComputationTime =
static_cast<double>(vizEnd - vizBegin) / CLOCKS_PER_SEC;
std::cout << "\nVisibility calculation took " <<
goodnessGridComputationTime << " s";
totalComputationTime = static_cast<double>(end - begin) / CLOCKS_PER_SEC;
std::cout << "\nEntire Run took " << totalComputationTime << " s";
return 0;
}