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examples.cpp
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examples.cpp
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#include <iostream>
#include "puma.h"
using namespace std;
//_____________________________________________________________________________
// main function for Examples
int main (int argc, char **argv)
//-----------------------------------------------------------------------------
{
// To run input one command line argument from the list of codes below
// e.g. you can enter individual examples by entering "prim1" or the whole category as "prim"
if (argc <= 1){
cout << endl << "Enter one of the following codes to run examples:" << endl;
cout << "Name of Examples Code and # of examples to input in command line argument" << endl;
cout << "all examples all" << endl;
cout << "primitives prim1-5" << endl;
cout << "export export1-5" << endl;
cout << "import import1-2" << endl;
cout << "volumefraction volfrac" << endl;
cout << "isosurface isosurf" << endl;
cout << "surfacearea surfarea" << endl;
cout << "medianfilter3d filter1-3" << endl;
cout << "generaterandomfibers genfibers1-6" << endl;
cout << "generaterandomspheres genspheres1-2" << endl;
cout << "generatetpms gentpms" << endl;
cout << "porespace pore1-2" << endl;
cout << "meaninterceptlength mil" << endl;
cout << "orientation orient1-6" << endl;
cout << "conductivity cond1-11" << endl;
cout << "tortuosity tort1-4" << endl;
} else {
//// primitives ////
// primitives: Matrix
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"prim1")) || (!strcmp(argv[1],"prim"))){
cout << endl << "Creating a matrix with user input size and printing a slice of it:"<< endl;
puma::Matrix<double> mat(10,10,10, 3.5); // sets all the elements to 3.5
// N.B. note that if a value is not specified, matrix just allocates the memory, does not set the matrix to zeros
mat.set(0,-1, 4,4, 4,4, 1); // creating a central solid fiber
// N.B. -1 specifies until the end of domain mat.X()-1
mat.printRange(0,-1, 0,-1, 4,5);
}
// primitives: Workspace
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"prim2")) || (!strcmp(argv[1],"prim"))){
cout << endl << "Creating a grayscale workspace:"<< endl;
puma::Workspace grayWS(10,10,10,1e-6, false); // automatically initializes it to zeros
// false prevents it from writing the log, unnecessary for these tutorials
grayWS.matrix.set(0,-1, 4,4, 4,4, 255); // creating a central solid fiber
grayWS.matrix.printRange(0,-1, 0,-1, 4,5);
cout << endl << "Segmenting it into a segmented workspace:"<< endl;
puma::Cutoff cutoff(0,89); // calling puma::Cutoff is equivalent to calling pair<int,int>
grayWS.setMaterialID(cutoff,0); // mask the segmented ws with the grayscale one, thresholding by assigning 0 to the range 0-89
grayWS.setMaterialID(puma::Cutoff(90,255),1); // assigning 1 to the range 90-255, with the direct cutoff pair
grayWS.matrix.printRange(0,-1, 0,-1, 4,5);
}
// primitives: Vec3
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"prim3")) || (!strcmp(argv[1],"prim"))){
cout << endl << "Creating a vector with three components:"<< endl;
puma::Vec3<double> vector(60,5,1);
vector.x = 1; // reassign one of the components
cout << "Computing magnitude of original vector: " << vector.magnitude() << endl; // compute the magnitude
cout << "Computing magnitude of normalized vector: " << (vector.norm()).magnitude() << endl; // compute the magnitude
puma::Vec3<double> vector2(50,0,0);
vector.dot(vector2); // dot product
vector.cross(vector2); // cross product
}
// primitives: Vec4
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"prim4")) || (!strcmp(argv[1],"prim"))){
cout << endl << "Creating a vector with three components and a time value" << endl;
puma::Vec4<float> vec1(1.2, -3.4, 5.6);
puma::Vec4<float> vec2(1.2, -3.4, 5.6, 1);
}
// primitives: MatVec3
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"prim5"))){
cout << endl << "Creating a direction matrix for a single fiber running along x:" << endl;
puma::MatVec3<double> directions(10,10,10); // initializes it to Vec3(0,0,0)
directions.set(0,-1, 4,4, 4,4, puma::Vec3<double>(1,0,0));
directions.printRange(0,-1, 0,-1, 4,5);
}
//// export3dtiff ////
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"export1")) || (!strcmp(argv[1],"export"))){
cout << endl << "Exporting a puma matrix to a tiff file:"<< endl;
puma::Matrix<int> mat(10,10,10, 0);
mat.set(0,-1, 4,4, 4,4, 150); // -1 specifies until the end of domain
puma::export_3DTiff(&mat, "cpp/examples/exampledata/matrix_example_notnorm", false); // not normalized
puma::export_3DTiff(&mat, "cpp/examples/exampledata/matrix_example_norm", true); // normalized --> 150 becomes 255 since highest value
cout<< endl << "Exporting a workspace to a tiff file:"<< endl;
puma::Workspace grayWS(10,10,10,1e-6, false);
grayWS.matrix.set(0,-1, 4,4, 4,4, 255);
puma::export_3DTiff(&grayWS, "cpp/examples/exampledata/workspace_example_notnorm", false);
}
//// exportbin ////
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"export2")) || (!strcmp(argv[1],"export"))){
cout << endl << "Exporting a puma matrix to a binary file:"<< endl;
puma::Matrix<int> mat(10,10,10, 0);
mat.set(0,-1, 4,4, 4,4, 150); // -1 specifies until the end of domain
puma::export_bin(&mat, "cpp/examples/exampledata/mat_example"); // to specify numThreads, add one more int to the inputs at the end
cout<< endl << "Exporting a workspace to a binary file:"<< endl;
puma::Workspace grayWS(10,10,10,1e-6, false);
grayWS.matrix.set(0,-1, 4,4, 4,4, 255);
puma::export_bin(&grayWS, "cpp/examples/exampledata/workspace_example");
}
//// exportvtk ////
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"export3")) || (!strcmp(argv[1],"export"))){
cout << endl << "Exporting a puma matrix to a vtk file:"<< endl;
puma::Matrix<int> mat(10,10,10, 0);
mat.set(0,-1, 4,4, 4,4, 150); // -1 specifies until the end of domain
puma::export_vtk(&mat, "cpp/examples/exampledata/mat_example"); // to specify numThreads, add one more int to the inputs at the end
puma::export_vtk(&mat, "cpp/examples/exampledata/mat_example_ASCII", 'a'); // export vtk it in ASCII instead of BINARY
puma::export_vtk(&mat, "cpp/examples/exampledata/mat_example_ASCII_unstructured", 'a', true); // export vtk to an unstructured grid (for import in code Aster)
cout<< endl << "Exporting a workspace to a vtk file:"<< endl;
puma::Workspace grayWS(10,10,10,1e-6, false);
grayWS.matrix.set(0,-1, 4,4, 4,4, 255);
puma::export_vtk(&grayWS, "cpp/examples/exampledata/workspace_example");
}
//// exportstl ////
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"export4")) || (!strcmp(argv[1],"export"))){
cout << endl << "Running the Marching Cubes as the previous example and exporting the triangles created to an stl file:"<< endl;
puma::Workspace grayWS(1e-6, false);
puma::import_3DTiff(&grayWS,"cpp/test/tiff/grayWS/200_FiberForm.tif",0);
// 1. Exporting the STL Directly
puma::export_STL(&grayWS, puma::Cutoff(90,255), false,"cpp/examples/exampledata/triangles1");
// 2. Computing the Triangles separately via the marching cubes algorithm, then exporting the STL
vector< puma::Triangle<float> > tris;
puma::isosurface_MarchingCubes(&tris, &grayWS, puma::Cutoff(90,255), true,1,false,0);
cout << endl << "Number of triangles generated: " << tris.size()<< endl;
puma::export_STL(&tris,false,"cpp/examples/exampledata/triangles2");
// 3. Segmenting the Workspace, then computing the Triangles separately via the marching cubes algorithm, then exporting the STL
grayWS.setMaterialID(puma::Cutoff(0,89),0);
grayWS.setMaterialID(puma::Cutoff(90,255),1);
puma::isosurface_MarchingCubes(&tris, &grayWS, puma::Cutoff(1,1), true,1,false,0);
cout << endl << "Number of triangles generated: " << tris.size()<< endl;
puma::export_STL(&tris,false,"cpp/examples/exampledata/triangles3");
}
//// exporttextfile ////
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"export5")) || (!strcmp(argv[1],"export"))){
cout << endl << "Exporting a puma matrix to a text file:"<< endl;
puma::Matrix<int> mat(10,10,10, 0);
mat.set(0,-1, 4,4, 4,4, 150); // -1 specifies until the end of domain
puma::export_Textfile(&mat, "cpp/examples/exampledata/mat_example"); // to specify numThreads, add one more int to the inputs at the end
cout<< endl << "Exporting a workspace to a text file:"<< endl;
puma::Workspace grayWS(10,10,10,1e-6, false);
grayWS.matrix.set(0,-1, 4,4, 4,4, 255);
puma::export_Textfile(&grayWS, "cpp/examples/exampledata/workspace_example");
}
//// import3dtiff ////
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"import1")) || (!strcmp(argv[1],"import"))){
cout << endl << "Importing a grayscale workspace of FiberForm and printing a subset of it:" << endl;
puma::Workspace grayWS(1e-6, false); // no need to specify the size since the import function takes care of it
puma::import_3DTiff(&grayWS, "cpp/test/tiff/grayWS/200_FiberForm.tif",0); // note that .tif is required
grayWS.matrix.printRange(150,(int)grayWS.X()-1, 150, (int)grayWS.Y()-1, 100,101);
cout << "Importing the same segmented workspace and printing the same subset of it:" << endl;
puma::Workspace segWS(1e-6, false); // no need to specify the size since the import function takes care of it
puma::import_3DTiff(&segWS, "cpp/test/tiff/segWS/200_FiberForm.tif",0);
segWS.matrix.printRange(150,(int)segWS.X()-1, 150, (int)segWS.Y()-1, 100,101);
}
//// importbin ////
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"import2")) || (!strcmp(argv[1],"import"))){
cout << endl << "Importing a puma matrix to a binary file:"<< endl;
// *** Note: Run first ExportBin_Example to generate the data imported in this example ***
puma::Matrix<int> mat(10,10,10, 0);
mat.set(0,-1, 4,4, 4,4, 150); // -1 specifies until the end of domain
puma::import_bin(&mat, "cpp/examples/exampledata/mat_example.puma"); // note that .puma is required
// to specify the number of processors used to read file (i.e. numThreads), add one more int to the inputs at the end
mat.printRange(0,-1, 0,-1, 4,5);
cout<< endl << "Importing a workspace to a binary file:"<< endl;
puma::Workspace grayWS(10,10,10,1e-6, false);
grayWS.matrix.set(0,-1, 4,4, 4,4, 255);
puma::import_bin(&grayWS, "cpp/examples/exampledata/workspace_example.puma");
grayWS.matrix.printRange(0,-1, 0,-1, 4,5);
}
//// volumefraction ////
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"volfrac"))){
cout << endl << "Computing Porosity and Volume Fraction of a segmented Fiberform sample:"<< endl;
puma::Workspace workspace(1.3, false);
puma::import_3DTiff(&workspace, "cpp/test/tiff/segWS/200_FiberForm.tif",0);
cout << endl << "Porosity: " << puma::compute_VolumeFraction(&workspace,0,0) << endl;
cout << "Fiber Volume Fraction: " << puma::compute_VolumeFraction(&workspace,1,0) << endl;
}
//// isosurface ////
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"isosurf"))){
cout << endl << "Running the Marching Cubes on a grayscale FiberForm sample, with closed edges and factor of 2:"<< endl;
puma::Workspace grayWS(1e-6, false);
puma::import_3DTiff(&grayWS,"cpp/test/tiff/grayWS/200_FiberForm.tif",0);
// 1. Computing the Triangles via the Marching Cubes Algorithm. Faster, but there can be small holes in the mesh. Good for visualizations, bad for simulations
vector< puma::Triangle<float> > tris;
puma::isosurface_MarchingCubes(&tris, &grayWS,puma::Cutoff(90,255), true,1,false,0);
cout << endl << "Number of triangles generated - Maching Cubes Regular: " << tris.size()<< endl;
// 2. Computing the Triangles via the Lewiner Marching Cubes Algorithm. Slower, more triangles, but gaurantees topologically correct surface
puma::isosurface_LewinerMarchingCubes(&tris, &grayWS,puma::Cutoff(90,255), true,1,false,0);
cout << endl << "Number of triangles generated - Maching Cubes Lewiner: " << tris.size()<< endl;
// 3. Segmenting the Workspace, then computing the Triangles separately via the marching cubes algorithm, then exporting the STL
grayWS.setMaterialID(puma::Cutoff(0,89),0);
grayWS.setMaterialID(puma::Cutoff(90,255),1);
puma::isosurface_MarchingCubes(&tris,&grayWS,puma::Cutoff(90,255),true,1,false,0);
cout << endl << "Number of triangles generated - Segmented: " << tris.size()<< endl;
}
//// surfacearea ////
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"surfarea"))){
cout << endl << "Computing the surface area of a sample of FiberForm:"<< endl;
puma::Workspace grayWS(1e-6, false);
puma::import_3DTiff(&grayWS,"cpp/test/tiff/grayWS/200_FiberForm.tif",0);
pair<double, double> sa = compute_SurfaceAreaMarchingCubes(&grayWS, puma::Cutoff(128, 255), true, 0);
cout << endl << "Raw Surface Area: " << sa.first << " m^2" << endl;
cout << "Specific Surface Area: " << sa.first << " 1/m" << endl;
}
//// medianfilter3d ////
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"filter1")) || (!strcmp(argv[1],"filter"))){
cout << endl << "Applying a Median filter to a FiberForm sample and printing a slice of it:"<< endl;
puma::Workspace grayWS(1e-6, false);
puma::import_3DTiff(&grayWS, "cpp/test/tiff/grayWS/100_FiberForm.tif",0);
cout << "Before Median filter:"<< endl;
grayWS.matrix.printRange(50,-1, 50, -1, 50,51);
//in this case, the return should be true since all values are valid
puma::filter_Median3D(&grayWS,3);
cout << endl << "After Median filter:"<< endl;
grayWS.matrix.printRange(50,-1, 50, -1, 50,51);
}
//// meanfilter3d ////
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"filter2")) || (!strcmp(argv[1],"filter"))){
cout << endl << "Applying a Mean filter to a FiberForm sample and printing a slice of it:"<< endl;
puma::Workspace grayWS(1e-6, false);
puma::import_3DTiff(&grayWS, "cpp/test/tiff/grayWS/100_FiberForm.tif",0);
cout << "Before Mean filter:"<< endl;
grayWS.matrix.printRange(50,-1, 50, -1, 50,51);
//in this case, the return should be true since all values are valid
puma::filter_Mean3D(&grayWS,3);
cout << endl << "After Mean filter:"<< endl;
grayWS.matrix.printRange(50,-1, 50, -1, 50,51);
}
//// bilateralfilter ////
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"filter3")) || (!strcmp(argv[1],"filter"))){
cout << endl << "Applying a Bilateral filter to a FiberForm sample and printing a slice of it:"<< endl;
puma::Workspace grayWS(1e-6, false);
puma::import_3DTiff(&grayWS, "cpp/test/tiff/grayWS/100_FiberForm.tif",0);
cout << "Before Bilateral filter:"<< endl;
grayWS.matrix.printRange(50,-1, 50, -1, 50,51);
//in this case, the return should be true since all values are valid
puma::filter_Bilateral(&grayWS,4,4,50);
cout << endl << "After Bilateral filter:"<< endl;
grayWS.matrix.printRange(50,-1, 50, -1, 50,51);
}
//// generaterandomfibers ////
// generaterandomfibers: straightCircle
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"genfibers1")) || (!strcmp(argv[1],"genfibers"))){
cout << endl << "Creating a 200^3 domain with non-intersecting random fibers having a circular cross section, slight preference for angle in XY:"<< endl;
// Creates an empty workspace
puma::Workspace grayWS(1e-6, false);
// Preparing inputs for fibers generation
RandomFibersInput input;
input.straightCircle(200,200,200,5,0,200,0,90,90,15,false,0.9,100);
input.print = true; // printing option can be turned off like this, ON as a default
// Generating fibers
puma::generateRandomFibers(&grayWS, input);
// Export to 3D tiff
puma::export_3DTiff(&grayWS,"cpp/examples/exampledata/RandomFibers_straightCircle_example.tiff",false);
}
// generaterandomfibers: curvedCircle
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"genfibers2")) || (!strcmp(argv[1],"genfibers"))){
puma::Workspace grayWS(1e-6, false);
RandomFibersInput input;
input.curvedCircle(100,100,100,5,0,50,0,90,90,15,false,0.95,100,150,0,1e-3);
puma::generateRandomFibers(&grayWS, input);
puma::Workspace grayWS2(1e-6, false);
RandomFibersInput input2;
input2.curvedCircle(100,100,100,5,0,50,0,90,90,15,true,0.9,100,150,0,1e-3);
puma::generateRandomFibers(&grayWS2, input2);
}
// generaterandomfibers: straightFlower
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"genfibers3")) || (!strcmp(argv[1],"genfibers"))){
puma::Workspace grayWS(1e-6, false);
RandomFibersInput input;
input.straightFlower(200,200,200,5,0,200,0,90,90,15,false,0.90,100,4,1,5,2,0);
puma::generateRandomFibers(&grayWS, input);
puma::Workspace grayWS2(1e-6, false);
RandomFibersInput input2;
input2.straightFlower(200,200,200,5,0,200,0,90,90,15,true,0.90,100,4,1,5,2,0);
puma::generateRandomFibers(&grayWS2, input2);
}
// generaterandomfibers: straightFlower_Hollow
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"genfibers4")) || (!strcmp(argv[1],"genfibers"))){
puma::Workspace grayWS(1e-6, false);
RandomFibersInput input;
input.straightFlower_Hollow(200,200,200,5,0,200,0,90,90,15,false,0.90,100,4,1,5,2,0,1,2.5,0);
puma::generateRandomFibers(&grayWS, input);
puma::Workspace grayWS2(1e-6, false);
RandomFibersInput input2;
input2.straightFlower_Hollow(200,200,200,5,0,200,0,90,90,15,true,0.90,100,4,1,5,2,0,1,2.5,0);
puma::generateRandomFibers(&grayWS2, input2);
}
// generaterandomfibers: curvedFlower
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"genfibers5")) || (!strcmp(argv[1],"genfibers"))){
puma::Workspace grayWS(1e-6, false);
RandomFibersInput input;
input.curvedFlower(100,100,100,5,0,100,0,90,90,15,false,0.95,100,120,0,1e-2,4,1,5,2,0);
puma::generateRandomFibers(&grayWS, input);
puma::Workspace grayWS2(1e-6, false);
RandomFibersInput input2;
input2.curvedFlower(100,100,100,5,0,100,0,90,90,15,true,0.95,100,120,0,1e-2,4,1,5,2,0);
puma::generateRandomFibers(&grayWS2, input2);
}
// generaterandomfibers: curvedFlower_Hollow
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"genfibers6")) || (!strcmp(argv[1],"genfibers"))){
puma::Workspace grayWS(1e-6, false);
RandomFibersInput input;
input.curvedFlower_Hollow(100,100,100,5,0,100,0,90,90,15,false,0.95,100,120,0,1e-2,4,1,5,2,0,1,2.5,0);
puma::generateRandomFibers(&grayWS, input);
puma::Workspace grayWS2(1e-6, false);
RandomFibersInput input2;
input2.curvedFlower_Hollow(100,100,100,5,0,100,0,90,90,15,true,0.95,100,120,0,1e-2,4,1,5,2,0,1,2.5,0);
puma::generateRandomFibers(&grayWS2, input2);
}
//// generaterandomspheres ////
// generaterandomspheres: non-intersecting large spheres
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"genspheres1")) || (!strcmp(argv[1],"genspheres"))){
cout << endl << "Creating a 200^3 domain with non-intersecting spheres:"<< endl;
puma::Timer t;
// Creates an empty workspace
puma::Workspace sphereWS(1e-6, false);
// Preparing inputs for spheres generation
RandomSpheresInput input(200,200,200,80.0,3.0,false,0.99,100);
// Generating spheres
puma::generateRandomSpheres(&sphereWS, input);
// Printing the elapsed time
cout << "Time: " << t.elapsed() << endl;
// Export to 3D tiff
puma::export_3DTiff(&sphereWS,"cpp/examples/exampledata/Generate_RandomSpheres_nonintersecting",false);
// Creating triangulated isosurface
vector<puma::Triangle<float> > Triangles;
puma::isosurface_MarchingCubes(&Triangles,&sphereWS,puma::Cutoff(128,255),true,1,false,40);
// Exporting to stl file
Export_STL test(&Triangles,false,"cpp/examples/exampledata/Generate_RandomSpheres_nonintersecting");
}
// generaterandomspheres: intersecting large spheres
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"genspheres2")) || (!strcmp(argv[1],"genspheres"))){
cout << endl << "Creating a 200^3 domain with intersecting spheres:"<< endl;
puma::Workspace sphereWS(1e-6, false);
RandomSpheresInput input(200,200,200,10.0,3.0,true,0.99,100);
puma::generateRandomSpheres(&sphereWS, input);
puma::export_3DTiff(&sphereWS,"cpp/examples/exampledata/Generate_RandomSpheres_intersecting.tif",false);
vector<puma::Triangle<float> > Triangles;
puma::isosurface_MarchingCubes(&Triangles,&sphereWS,puma::Cutoff(128,255),true,1,false);
Export_STL test(&Triangles,false,"cpp/examples/exampledata/Generate_RandomSpheres_intersecting.stl");
}
//// generatetpms ////
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"gentpms"))){
double diameter = 20; // in mm
double height = 38.1; // in mm
double p = 4.72;
double q = 0.5045;
bool circle = true;
bool exportSTL = false;
bool binaryTiff = true;
bool continuousTiff = true;
int equationNumber = 0; // equation 0, 1 or 2
std::string outputFolder = "cpp/test/out/stl/";
std::string outputLabel = "equation1";
int scale = 10; // keep between 5-20
int voxelsX = diameter * scale;
int voxelsY = diameter * scale;
int voxelsZ = height * scale;
double radius = diameter * scale / 2.0;
double p_scaled = p / scale;
puma::Workspace ws(1e-6,false);
// triply periodic minimal surface (TPMS)
TPMSInput input(voxelsX,voxelsY,voxelsZ,p_scaled,p_scaled,q,q, equationNumber);
bool success = puma::generateTPMS(&ws, input);
/// Comment out this section to keep rectangular
if(circle){
for(int i=0;i<ws.X();i++){
for(int j=0;j<ws.Y();j++){
for(int k=0;k<ws.Z();k++){
if(std::sqrt((i-ws.X()/2.0)*(i-ws.X()/2.0) + (j-ws.Y()/2.0)*(j-ws.Y()/2.0)) > radius ){
ws.matrix(i,j,k) = 0;
}
}
}
}
}
if (success) {
if(exportSTL){
puma::export_STL(&ws, puma::Cutoff(128, 255), false, outputFolder + outputLabel +"_tpms_test.stl");
}
if(continuousTiff) {
puma::export_3DTiff(&ws, outputFolder + outputLabel + "_tpms_test.tif", false);
}
if(binaryTiff) {
ws.setMaterialID(puma::Cutoff(0,127),0);
ws.setMaterialID(puma::Cutoff(128,255),255);
puma::export_3DTiff(&ws, outputFolder + outputLabel + "_tpms_test_binary.tif", false);
}
}
}
//// porespace ////
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"pore1")) || (!strcmp(argv[1],"pore"))){
puma::Workspace grayWS;
RandomFibersInput input;
input.straightFlower_Hollow(200,200,1, 30, 0, 1, 0, 0, 0, 90, true, 0.6, 2, 1, 0, 0, 0, 0, 1, 20, 0);
generateRandomFibers(&grayWS,input);
puma::Matrix<long> poreMatrix;
puma::identifyPoreSpace(&grayWS,&poreMatrix,puma::Cutoff(0,127));
double average = poreMatrix.average();
cout << "Average porespace: " << average << endl;
}
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"pore2")) || (!strcmp(argv[1],"pore"))) {
puma::Workspace grayWS;
RandomFibersInput input;
input.straightFlower_Hollow(200, 200, 1, 30, 0, 1, 0, 0, 0, 90, true, 0.6, 2, 1, 0, 0, 0, 0, 1, 20, 0);
generateRandomFibers(&grayWS, input);
puma::fillClosedPores(&grayWS, puma::Cutoff(0, 127), 255);
grayWS.setMaterialID(puma::Cutoff(0, 127), 0);
grayWS.setMaterialID(puma::Cutoff(128, 256), 1);
double average = grayWS.matrix.average();
cout << "Average porespace: " << average << endl;
}
//// meaninterceptlength ////
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"mil"))){
cout << endl << "Finding the mean intercept length of a FiberForm 200^3 sample:"<< endl;
// Creating empty workspace
puma::Workspace segWS(1e-6, false);
// Importing FiberForm 200^3 tiff, selecting only subsection of it
puma::import_3DTiff(&segWS,"cpp/test/tiff/segWS/200_FiberForm.tif");
// Computing the Mean Intercept Length
puma::Vec3<double> mil = puma::compute_MeanInterceptLength(&segWS,puma::Cutoff(0,0));
cout << "Mean Intercept Length: " << mil.x << ' ' << mil.y << ' ' << mil.z << endl;
}
//// orientation ////
// orientation: Ray Casting on Generated Random Fibers
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"orient1")) || (!strcmp(argv[1],"orient"))){
cout << endl << "Creating a random fiber domain and computing the Orientation via the ray casting method:"<< endl;
// Generating random fiber sample (see generateRandomFibers example for step-by-step description)
int scale = 50;
puma::Workspace grayWS(1e-5, false);
puma::MatVec3<double> tangents;
RandomFibersInput input;
input.straightCircle(scale,scale,scale,2,0,scale,0,90,90,90,false,0.9,1);
input.print = false; puma::generateRandomFibers(&grayWS,&tangents,input);
// Segmenting sample
puma::Workspace segWS(grayWS.shape(), false);
segWS.setMaterialID(&grayWS, puma::Cutoff(0,127),0);
segWS.setMaterialID(&grayWS, puma::Cutoff(128,255),1);
// Initializing orientation matrix
puma::MatVec3<double> dirs;
// Computing orientation using Cay Casting (RC)
puma::compute_orientationRC(&segWS, puma::Cutoff(1, 1), 15,5, &dirs, false);
// Initializing orientation error matrix
puma::Matrix<double> error;
// Computing orientation error between the estimated orientation (dirs) and the true orientation (tangents)
pair <double, double> MeanSD = puma::compute_orientationComparison(&segWS, &dirs, &tangents, &error, puma::Cutoff(1,1));
cout << "Mean: " << MeanSD.first << endl;
cout << "Standard Deviation: " << MeanSD.second << endl;
}
// orientation: Artificial Flux on Generated Random Fibers
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"orient3")) || (!strcmp(argv[1],"orient"))){
cout << endl << "Creating a random fiber domain and computing the Orientation via the artificial flux method:"<< endl;
// Generating random fiber sample (see generateRandomFibers example for step-by-step description)
int scale = 50;
puma::Workspace grayWS(1e-5, false);
puma::MatVec3<double> tangents;
RandomFibersInput input;
input.straightCircle(scale,scale,scale,2,0,scale,0,90,90,90,false,0.9,1);
input.print = false; puma::generateRandomFibers(&grayWS,&tangents,input);
puma::Workspace segWS(grayWS.shape(), false);
segWS.setMaterialID(&grayWS,puma::Cutoff(0,127),0);
segWS.setMaterialID(&grayWS,puma::Cutoff(128,255),1);
puma::MatVec3<double> dirs;
// Computing orientation using Artificial Flux (AF)
puma::compute_orientationAF(&segWS, &dirs, puma::Cutoff(1, 1), 1e-5, 10000,false);
puma::Matrix<double> error;
pair <double, double> MeanSD = puma::compute_orientationComparison(&segWS, &dirs, &tangents, &error, puma::Cutoff(1,1));
cout << "Mean: " << MeanSD.first << endl;
cout << "Standard Deviation: " << MeanSD.second << endl;
}
// orientation: Structure Tensor on Generated Random Fibers
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"orient5")) || (!strcmp(argv[1],"orient"))){
cout << endl << "Creating a random fiber domain and computing the Orientation via the structure tensor method:"<< endl;
// Generating random fiber sample (see generateRandomFibers example for step-by-step description)
int scale = 50;
puma::Workspace grayWS(1e-5, false);
puma::MatVec3<double> tangents;
RandomFibersInput input;
input.straightCircle(scale,scale,scale,2,0,scale,0,90,90,90,false,0.9,1);
input.print = false; puma::generateRandomFibers(&grayWS,&tangents,input);
puma::Workspace segWS(grayWS.shape(), false);
segWS.setMaterialID(&grayWS, puma::Cutoff(0,127),0);
segWS.setMaterialID(&grayWS, puma::Cutoff(128,255),1);
puma::MatVec3<double> dirs;
// Computing orientation using Structure Tensor (ST)
puma::compute_orientationST(&segWS, 0.7, 1.1, puma::Cutoff(1, 1), &dirs,false);
puma::Matrix<double> error;
pair <double, double> MeanSD = puma::compute_orientationComparison(&segWS, &dirs, &tangents, &error, puma::Cutoff(1,1));
cout << "Mean: " << MeanSD.first << endl;
cout << "Standard Deviation: " << MeanSD.second << endl;
}
//// conductivity ////
// fvthermalconductivity: Multiple materials in series
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"cond1")) || (!strcmp(argv[1],"cond"))){
cout << endl << "Computing the thermal conductivity using finite volume considering a locally isotropic sample having several materials in series:"<< endl;
// Initializing Workspace
puma::Workspace segWS(100,57,62,0,1e-6, false);
// Setting the workspace values of the materials in series
segWS.matrix.set(10,19,0,56,0,61,1);
segWS.matrix.set(20,29,0,56,0,61,2);
segWS.matrix.set(30,39,0,56,0,61,3);
segWS.matrix.set(40,49,0,56,0,61,4);
segWS.matrix.set(50,59,0,56,0,61,5);
segWS.matrix.set(60,69,0,56,0,61,6);
segWS.matrix.set(70,79,0,56,0,61,7);
segWS.matrix.set(80,89,0,56,0,61,8);
segWS.matrix.set(90,99,0,56,0,61,9);
// Initializing Temperature field
puma::Matrix<double> T;
// Initializing material conductivity
map<int, double> matCond;
matCond[0] = 1;
matCond[1] = 2;
matCond[2] = 3;
matCond[3] = 4;
matCond[4] = 5;
matCond[5] = 6;
matCond[6] = 7;
matCond[7] = 8;
matCond[8] = 9;
matCond[9] = 10;
// Running simulation
puma::Vec3<double> k = puma::compute_FVThermalConductivity(&segWS, &T, matCond,"periodic","bicgstab",'z',1e-3,10000,true);
cout << endl << "Conductivity: " << endl;
cout << "kxx " << k.x << " kxy " << k.y << " kxz " << k.z << endl;
}
// fvthermalconductivity: FiberForm 100^3
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"cond2")) || (!strcmp(argv[1],"cond"))){
cout << endl << "Computing the thermal conductivity using finite volume considering a locally isotropic FiberForm 100^3 sample:"<< endl;
// Initializing Workspace
puma::Workspace ws(1e-6, false);
// Importing 3D tiff
puma::import_3DTiff(&ws,"cpp/test/tiff/grayWS/100_FiberForm.tif");
// Segmenting workspace by thresholding
ws.setMaterialID(&ws,puma::Cutoff(0,89),0);
ws.setMaterialID(&ws,puma::Cutoff(90,255),1);
// Initializing Temperature field and material conductivity
puma::Matrix<double> T;
map<int, double> matCond;
matCond[0] = 0.0257; // air conductivity
matCond[1] = 12; // approximation to fiber conductivity
// Running simulation in three directions
puma::Vec3<double> kx = puma::compute_FVThermalConductivity(&ws, &T, matCond,"symmetric","cg",'x',1e-3,10000,true);
puma::Vec3<double> ky = puma::compute_FVThermalConductivity(&ws, &T, matCond,"symmetric","cg",'y',1e-3,10000,true);
puma::Vec3<double> kz = puma::compute_FVThermalConductivity(&ws, &T, matCond,"symmetric","cg",'z',1e-3,10000,true);
cout << endl << "Conductivity: " << endl;
cout << "kxx " << kx.x << " kxy " << kx.y << " kxz " << kx.z << endl;
cout << "kyx " << ky.x << " kyy " << ky.y << " kyz " << ky.z << endl;
cout << "kzx " << kz.x << " kzy " << kz.y << " kzz " << kz.z << endl;
}
// ejthermalconductivity: Multiple materials in series
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"cond3")) || (!strcmp(argv[1],"cond"))){
cout << endl << "Computing the thermal conductivity using explicit jump considering a locally isotropic sample having several materials in series:"<< endl;
// Initializing Workspace
puma::Workspace segWS(100,57,62,0,1e-6, false);
// Setting the workspace values of the materials in series
segWS.matrix.set(10,19,0,56,0,61,1);
segWS.matrix.set(20,29,0,56,0,61,2);
segWS.matrix.set(30,39,0,56,0,61,3);
segWS.matrix.set(40,49,0,56,0,61,4);
segWS.matrix.set(50,59,0,56,0,61,5);
segWS.matrix.set(60,69,0,56,0,61,6);
segWS.matrix.set(70,79,0,56,0,61,7);
segWS.matrix.set(80,89,0,56,0,61,8);
segWS.matrix.set(90,99,0,56,0,61,9);
// Initializing Temperature field
puma::Matrix<double> T;
// Initializing material conductivity
map<int, double> matCond;
matCond[0] = 1;
matCond[1] = 2;
matCond[2] = 3;
matCond[3] = 4;
matCond[4] = 5;
matCond[5] = 6;
matCond[6] = 7;
matCond[7] = 8;
matCond[8] = 9;
matCond[9] = 10;
// Running simulation
puma::Vec3<double> k = compute_EJThermalConductivity(&segWS, &T, matCond,'x',1e-3,10000,true);
cout << endl << "Conductivity: " << endl;
cout << "kxx " << k.x << " kxy " << k.y << " kxz " << k.z << endl;
}
// ejthermalconductivity: FiberForm 100^3
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"cond4")) || (!strcmp(argv[1],"cond"))){
cout << endl << "Computing the thermal conductivity using explicit jump considering a locally isotropic FiberForm 100^3 sample:"<< endl;
// Initializing Workspace
puma::Workspace ws(1e-6, false);
// Importing 3D tiff
puma::import_3DTiff(&ws,"cpp/test/tiff/grayWS/100_FiberForm.tif");
// Segmenting workspace by thresholding
ws.setMaterialID(&ws,puma::Cutoff(0,89),0);
ws.setMaterialID(&ws,puma::Cutoff(90,255),1);
// Initializing Temperature field and material conductivity
puma::Matrix<double> T;
map<int, double> matCond;
matCond[0] = 0.0257; // air conductivity
matCond[1] = 12; // approximation to fiber conductivity
// Running simulation in three directions
puma::Vec3<double> kx = compute_EJThermalConductivity(&ws, &T, matCond,'x',1e-3,10000,true);
puma::Vec3<double> ky = compute_EJThermalConductivity(&ws, &T, matCond,'x',1e-3,10000,true);
puma::Vec3<double> kz = compute_EJThermalConductivity(&ws, &T, matCond,'x',1e-3,10000,true);
cout << endl << "Conductivity: " << endl;
cout << "kxx " << kx.x << " kxy " << kx.y << " kxz " << kx.z << endl;
cout << "kyx " << ky.x << " kyy " << ky.y << " kyz " << ky.z << endl;
cout << "kzx " << kz.x << " kzy " << kz.y << " kzz " << kz.z << endl;
}
// fvanisotropicthermalconductivity: Multiple materials in series
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"cond5")) || (!strcmp(argv[1],"cond"))){
cout << endl << "Computing the thermal conductivity using finite volume considering a locally anisotropic sample having several materials in series:"<< endl;
// Initializing Workspace
puma::Workspace segWS(100,57,62,0,1e-6, false);
// Setting the workspace values of the materials in series
segWS.matrix.set(10,19,0,56,0,61,1);
segWS.matrix.set(20,29,0,56,0,61,2);
segWS.matrix.set(30,39,0,56,0,61,3);
segWS.matrix.set(40,49,0,56,0,61,4);
segWS.matrix.set(50,59,0,56,0,61,5);
segWS.matrix.set(60,69,0,56,0,61,6);
segWS.matrix.set(70,79,0,56,0,61,7);
segWS.matrix.set(80,89,0,56,0,61,8);
segWS.matrix.set(90,99,0,56,0,61,9);
// Initializing Temperature and Flux field
puma::Matrix<double> T;
puma::MatVec3<double> q;
// Initializing material conductivity
map<int, vector<double>> matCond;
matCond[0] = {1,1,1,0,0,0};
matCond[1] = {2,2,2,0,0,0};
matCond[2] = {3,3,3,0,0,0};
matCond[3] = {4,4,4,0,0,0};
matCond[4] = {5,5,5,0,0,0};
matCond[5] = {6,6,6,0,0,0};
matCond[6] = {7,7,7,0,0,0};
matCond[7] = {8,8,8,0,0,0};
matCond[8] = {9,9,9,0,0,0};
matCond[9] = {10,10,10,0,0,0};
// Running simulation
puma::Vec3<double> k = puma::compute_FVanisotropicThermalConductivity(&segWS, &T, &q, matCond, "mpfa", "symmetric","bicgstab",'x',1e-2,10000,true);
cout << endl << "Conductivity: " << endl;
cout << "kxx " << k.x << " kxy " << k.y << " kxz " << k.z << endl;
}
// fvanisotropicthermalconductivity: FiberForm 100^3
if((!strcmp(argv[1],"all")) || (!strcmp(argv[1],"cond6")) || (!strcmp(argv[1],"cond"))){
cout << endl << "Computing the thermal conductivity using finite volume considering a locally anisotropic FiberForm 100^3 sample:"<< endl;
// Initializing Workspace
puma::Workspace ws(1e-6, false);
// Importing 3D tiff
puma::import_3DTiff(&ws,"cpp/test/tiff/grayWS/100_FiberForm.tif");
// Computing orientations using Structure Tensor (ST) method
puma::MatVec3< double> tangents;
puma::compute_orientationST(&ws, 0.7, 0.7, puma::Cutoff(89,255), &tangents);
// Initializing Temperature, flux field and material conductivity
puma::Matrix<double> T;
puma::MatVec3<double> q;
map<int, vector<double>> matCond;
matCond[89] = {0.0257}; // air conductivity
matCond[255] = {15, 8}; // approximation to fiber conductivity, here considered isotropic as an example