int plotGridImg(signed int * grids, unsigned int t, int X, int Y, signed burnPropAge) {
// gnuplot has a "with image" option...
int myX, myY;
Gnuplot g1=Gnuplot();
//
g1.cmd("set xrange[0 : %d]", X+1);
g1.cmd("set yrange[0 : %d]", Y+1);
g1.cmd("plot '-' with image");
//
int imax = (X+2)*(Y+2);
int treeAge;
int i = 0;
while (i < imax) {
//printf("starting i: %d\n", i);
//if (int(i/20)==float(i)/20) yodapause();
myY = i/(X+2);
myX = i-myY*(X+2);
//myVal = *(grids + i);
treeAge=getGridStatus(*(grids+i), t);
if (treeAge==0) treeAge=0;
if (treeAge>=burnPropAge) treeAge=8;
if (treeAge>0 and treeAge < burnPropAge) treeAge=4;
if (treeAge<0 and treeAge>-burnPropAge) treeAge=12;
if (treeAge<= -burnPropAge) treeAge=16;
if (i<(int(xmax)+2)) treeAge=int(i/16); // this to get some pallet normalization...
g1.cmd("%d,\t%d,\t%d", myX, myY, treeAge);
i++;
};
g1.cmd("e");
yodapause();
return 0;
};
int plotGrid(signed int * grids, int X, int Y) {
printf("we'll plot the grid here...");
// yodapause();
//std::string strArray("");
//std::string strNewRow("");
int myX, myY, myVal;
Gnuplot g1=Gnuplot();
//
// note: grids[x][y] (maybe we should just make our own 1d array) is like: grids->[x=0][{y}],[x=1][{y}],etc.
// so we have to transpose this. get the 1st of every row, the second of every row, etc.
//g1.cmd("plot '-' using 1:2 with points 8 ");
// g1.cmd("set multiplot");
g1.cmd("set xrange[0 : %d]", X+1);
g1.cmd("set yrange[0 : %d]", Y+1);
g1.cmd("plot '-' with points 4, '-' with points 7");
//g1.cmd("3 4");
//g1.cmd("e");
//g1.cmd("plot '-' with points 4");
int imax = (X+2)*(Y+2);
int i = 0;
while (i < imax) {
//printf("starting i: %d\n", i);
//if (int(i/20)==float(i)/20) yodapause();
myY = i/(X+2);
myX = i-myY*(X+2);
myVal = *(grids + i);
// printf("thisX, thisY, thisVal: (%d, %d, %d)\n", thisX, thisY, thisVal);
// yodacode::yodapause();
if (myVal >= 1) {
//printf("(%i) thisX, thisY, thisVal: (%d, %d, %d)\n", i, myX, myY, myVal);
//if (int(i/20)==float(i)/20) yodapause();
g1.cmd("%d %d", myX, myY);
//g1.cmd("%s %s", yodacode::intToStr(thisX).c_str(), yodacode::intToStr(thisY).c_str());
};
i++;
};
g1.cmd("e");
// yodapause();
//
//printf("now plot fires?\n");
i = 0;
//g1.cmd("plot '-' using 1:2 with linespoints 0 ");
while (i < imax) {
myY = i/(X+2);
myX = i-myY*(X+2);
myVal = *(grids + i);
if (myVal==-1) {
g1.cmd("%d %d", myX, myY);
};
i++;
};
g1.cmd("e");
yodacode::yodapause();
return 0;
};
int plotGridSimple(signed int * grids, unsigned int t, int X, int Y) {
//printf("we'll plot the grid here...");
// yodapause();
//std::string strArray("");
//std::string strNewRow("");
int myX, myY, treeAge;
Gnuplot g1=Gnuplot();
//
g1.cmd("set xrange[0 : %d]", X+1);
g1.cmd("set yrange[0 : %d]", Y+1);
//g1.cmd("plot '-' title 'young' with points 3, '-' title 'older' with points, '-' title 'young-burn' with points 7, '-' title 'old-burn' with points 9");
g1.cmd("plot '-' title 'trees' with points 3, '-' title 'burn' with points 9");
//g1.cmd("3 4");
//g1.cmd("e");
//g1.cmd("plot '-' with points 4");
int imax = (X+2)*(Y+2);
int i = 0;
while (i < imax) {
myY = i/(X+2);
myX = i-myY*(X+2);
treeAge=0;
//treeAge = getGridStatus(*(grids+i), t);
g1.cmd("0,\t0");
treeAge = *(grids+i);
if (treeAge > 0) {
//if (treeAge > burnAge and treeAge < burnPropAge) {
g1.cmd("%d,\t%d", myX, myY);
};
i++;
};
g1.cmd("e");
//
i = 0;
while (i < imax) {
myY = i/(X+2);
myX = i-myY*(X+2);
treeAge=0;
g1.cmd("0,\t0");
treeAge = *(grids+i);
if (treeAge < 0) {
//if (treeAge > burnAge and treeAge < burnPropAge) {
g1.cmd("%d,\t%d", myX, myY);
};
i++;
};
g1.cmd("e");
//
yodapause();
return 0;
};
int plotGrid(signed int * grids, unsigned int t, int X, int Y, signed burnPropAge) {
//printf("we'll plot the grid here...");
// yodapause();
//std::string strArray("");
//std::string strNewRow("");
int myX, myY, treeAge;
Gnuplot g1=Gnuplot();
//
// note: grids[x][y] (maybe we should just make our own 1d array) is like: grids->[x=0][{y}],[x=1][{y}],etc.
// so we have to transpose this. get the 1st of every row, the second of every row, etc.
//g1.cmd("plot '-' using 1:2 with points 8 ");
// g1.cmd("set multiplot");
g1.cmd("set xrange[0 : %d]", X+1);
g1.cmd("set yrange[0 : %d]", Y+1);
//g1.cmd("plot '-' title 'young' with points 3, '-' title 'older' with points, '-' title 'young-burn' with points 7, '-' title 'old-burn' with points 9");
g1.cmd("plot '-' title 'young' with points 3, '-' title 'older' with points, '-' title 'young-burn' with points 7, '-' title 'old-burn' with points 9, '-' title 'rocks' with points");
//g1.cmd("3 4");
//g1.cmd("e");
//g1.cmd("plot '-' with points 4");
int imax = (X+2)*(Y+2);
int i = 0;
while (i < imax) {
myY = i/(X+2);
myX = i-myY*(X+2);
treeAge=0;
//treeAge = getGridStatus(*(grids+i), t);
g1.cmd("0,\t0");
treeAge = *(grids+i);
if (treeAge > 0 and treeAge < burnPropAge) {
//if (treeAge > burnAge and treeAge < burnPropAge) {
g1.cmd("%d,\t%d", myX, myY);
};
i++;
};
g1.cmd("e");
//
i = 0;
while (i < imax) {
myY = i/(X+2);
myX = i-myY*(X+2);
treeAge=0;
//treeAge = getGridStatus(*(grids+i), t);
g1.cmd("0,\t0");
treeAge = *(grids+i);
if (treeAge >= burnPropAge and treeAge<rockAge) {
g1.cmd("%d,\t%d", myX, myY);
};
i++;
};
g1.cmd("e");
//
//// Burning Fires:
i = 0;
while (i < imax) {
myY = i/(X+2);
myX = i-myY*(X+2);
treeAge=0;
g1.cmd("0,\t0");
//treeAge = getGridStatus(*(grids+i), t);
treeAge = *(grids+i);
if (treeAge<=-1 and treeAge>-burnPropAge) {
g1.cmd("%d,\t%d", myX, myY);
};
i++;
};
g1.cmd("e");
i = 0;
//
while (i < imax) {
myY = i/(X+2);
myX = i-myY*(X+2);
treeAge=0;
g1.cmd("0,\t0");
//treeAge = getGridStatus(*(grids+i), t);
treeAge = *(grids+i);
if (treeAge <= -burnPropAge) {
g1.cmd("%d,\t%d", myX, myY);
};
i++;
};
g1.cmd("e");
//
// Rocks:
i = 0;
while (i < imax) {
myY = i/(X+2);
myX = i-myY*(X+2);
treeAge=0;
g1.cmd("0,\t0");
//treeAge = getGridStatus(*(grids+i), t);
treeAge = *(grids+i);
if (treeAge >= rockAge) {
g1.cmd("%d,\t%d", myX, myY);
};
i++;
};
g1.cmd("e");
//
yodapause();
return 0;
};
int TestMHD(int argc, char *argv[]) {
real cfl = 0.2;
real tmax = 0.1;
bool writemsh = false;
real vmax = 6.0;
bool usegpu = false;
real dt = 0.0;
for (;;) {
int cc = getopt(argc, argv, "c:t:w:D:P:g:s:");
if (cc == -1) break;
switch (cc) {
case 0:
break;
case 'c':
cfl = atof(optarg);
break;
case 'g':
usegpu = atoi(optarg);
break;
case 't':
tmax = atof(optarg);
break;
case 'w':
writemsh = true;
break;
case 'D':
ndevice_cl= atoi(optarg);
break;
case 'P':
nplatform_cl = atoi(optarg);
break;
default:
printf("Error: invalid option.\n");
printf("Usage:\n");
printf("./testmanyv -c <cfl> -d <deg> -n <nraf> -t <tmax> -C\n -P <cl platform number> -D <cl device number> FIXME");
exit(1);
}
}
bool test = true;
field f;
init_empty_field(&f);
f.varindex = GenericVarindex;
f.model.m = 9;
f.model.cfl = cfl;
strcpy(f.model.name,"MHD");
f.model.NumFlux=MHDNumFluxP2;
f.model.BoundaryFlux=MHDBoundaryFlux;
f.model.InitData=MHDInitData;
f.model.ImposedData=MHDImposedData;
char buf[1000];
sprintf(buf, "-D _M=%d", f.model.m);
strcat(cl_buildoptions, buf);
sprintf(numflux_cl_name, "%s", "MHDNumFluxP2");
sprintf(buf," -D NUMFLUX=");
strcat(buf, numflux_cl_name);
strcat(cl_buildoptions, buf);
sprintf(buf, " -D BOUNDARYFLUX=%s", "MHDBoundaryFlux");
strcat(cl_buildoptions, buf);
// Set the global parameters for the Vlasov equation
f.interp.interp_param[0] = f.model.m; // _M
f.interp.interp_param[1] = 1; // x direction degree
f.interp.interp_param[2] = 1; // y direction degree
f.interp.interp_param[3] = 0; // z direction degree
f.interp.interp_param[4] = 10; // x direction refinement
f.interp.interp_param[5] = 10; // y direction refinement
f.interp.interp_param[6] = 1; // z direction refinement
//set_vlasov_params(&(f.model));
// Read the gmsh file
//ReadMacroMesh(&(f.macromesh), "test/testcartesiangrid2d2.msh");
ReadMacroMesh(&(f.macromesh), "test/testOTgrid.msh");
//ReadMacroMesh(&(f.macromesh), "test/testcube.msh");
// Try to detect a 2d mesh
Detect2DMacroMesh(&(f.macromesh));
bool is2d=f.macromesh.is2d;
assert(is2d);
f.macromesh.period[0]=6.2831853;
f.macromesh.period[1]=6.2831853;
// Mesh preparation
BuildConnectivity(&(f.macromesh));
// Prepare the initial fields
Initfield(&f);
// Prudence...
CheckMacroMesh(&(f.macromesh), f.interp.interp_param + 1);
Plotfield(0, (1==0), &f, "Rho", "dginit.msh");
f.vmax=vmax;
real executiontime;
if(usegpu) {
printf("Using OpenCL:\n");
//executiontime = seconds();
//assert(1==2);
RK2(&f, tmax, dt);
//executiontime = seconds() - executiontime;
} else {
printf("Using C:\n");
//executiontime = seconds();
RK2(&f, tmax, dt);
//executiontime = seconds() - executiontime;
}
Plotfield(0,false,&f, "Rho", "dgvisu.msh");
Gnuplot(&f,0,0.0,"data1D.dat");
printf("tmax: %f, cfl: %f\n", tmax, f.model.cfl);
printf("deltax:\n");
printf("%f\n", f.hmin);
printf("deltat:\n");
printf("%f\n", dt);
printf("DOF:\n");
printf("%d\n", f.wsize);
printf("executiontime (s):\n");
printf("%f\n", executiontime);
printf("time per RK2 (s):\n");
printf("%f\n", executiontime / (real)f.itermax);
return test;
}
static int main(int argc, char *argv[]) {
const string DEFAULT_TITLE = "Sequence Coverage Plot";
const string DEFAULT_X_LABEL = "X";
const string DEFAULT_Y_LABEL = "Y";
const int32_t DEFAULT_X_MAX = 1000;
const int32_t DEFAULT_Y_MAX = 1000;
const uint32_t DEFAULT_FASTA_INDEX = 0;
path sect_file;
string output_type;
path output;
string title;
string x_label;
string y_label;
uint16_t width;
uint16_t height;
uint32_t x_max;
uint32_t y_max;
bool y_logscale;
uint32_t fasta_index;
string fasta_header;
bool verbose;
bool help;
// Declare the supported options.
po::options_description generic_options(PlotProfile::helpMessage(), 100);
generic_options.add_options()
("output_type,p", po::value<string>(&output_type)->default_value("png"),
"The plot file type to create: png, ps, pdf. Warning... if pdf is selected please ensure your gnuplot installation can export pdf files.")
("output,o", po::value<path>(&output),
"The path to the output file")
("title,t", po::value<string>(&title)->default_value(DEFAULT_TITLE),
"Title for plot")
("x_label,a", po::value<string>(&x_label)->default_value(DEFAULT_X_LABEL),
"Label for the x-axis (value taken from matrix metadata if present)")
("y_label,b", po::value<string>(&y_label)->default_value(DEFAULT_Y_LABEL),
"Label for the y-axis (value taken from matrix metadata if present)")
("x_max,x", po::value<uint32_t>(&x_max)->default_value(DEFAULT_X_MAX),
"Maximum value for the x-axis (value taken from matrix metadata if present)")
("y_max,y", po::value<uint32_t>(&y_max)->default_value(DEFAULT_Y_MAX),
"Maximum value for the y-axis (value taken from matrix metadata if present)")
("width,w", po::value<uint16_t>(&width)->default_value(1024),
"Width of canvas")
("height,h", po::value<uint16_t>(&height)->default_value(1024),
"Height of canvas")
("index,n", po::value<uint32_t>(&fasta_index)->default_value(DEFAULT_FASTA_INDEX),
"Index of fasta entry to plot. First entry is 1.")
("header,d", po::value<string>(&fasta_header),
"Fasta header of fasta entry to plot. NOTE: \'--header\' has priority over index")
("y_logscale,m", po::bool_switch(&y_logscale)->default_value(false),
"Y-axis is logscale. This overrides the y_min and y_max limits.")
("verbose,v", po::bool_switch(&verbose)->default_value(false),
"Print extra information.")
("help", po::bool_switch(&help)->default_value(false), "Produce help message.")
;
// Hidden options, will be allowed both on command line and
// in config file, but will not be shown to the user.
po::options_description hidden_options("Hidden options");
hidden_options.add_options()
("sect_file,s", po::value<path>(§_file), "Path to the sect profile file to plot.")
;
// Positional option for the input bam file
po::positional_options_description p;
p.add("sect_file", 1);
// Combine non-positional options
po::options_description cmdline_options;
cmdline_options.add(generic_options).add(hidden_options);
// Parse command line
po::variables_map vm;
po::store(po::command_line_parser(argc, argv).options(cmdline_options).positional(p).run(), vm);
po::notify(vm);
// Output help information the exit if requested
if (help || argc <= 1) {
cout << generic_options << endl;
return 1;
}
// Check input file exists
if (!bfs::exists(sect_file) && !bfs::symbolic_link_exists(sect_file)) {
cerr << endl << "Could not find matrix file at: " << sect_file << "; please check the path and try again." << endl << endl;
return 1;
}
string header;
string coverages;
if (!fasta_header.empty()) {
header.assign(fasta_header);
getEntryFromFasta(sect_file, header, coverages);
}
else if (fasta_index > 0) {
getEntryFromFasta(sect_file, fasta_index, header, coverages);
}
if (coverages.length() == 0) {
cerr << "Could not find requested fasta header in sect coverages fasta file" << endl;
}
else {
if (verbose)
cerr << "Found requested sequence : " << header << endl << coverages << endl << endl;
// Split coverages
vector<uint32_t> cvs = kat::splitUInt32(coverages, ' ');
uint32_t maxCvgVal = y_max != DEFAULT_Y_MAX ? y_max : (*(std::max_element(cvs.begin(), cvs.end())) + 1);
string t = autoTitle(title, header);
if (verbose)
cerr << "Acquired K-mer counts" << endl;
// Initialise gnuplot
Gnuplot profile_plot = Gnuplot("lines");
profile_plot.configurePlot(output_type, output.string(), width, height);
profile_plot.set_title(t);
profile_plot.set_xlabel(x_label);
profile_plot.set_ylabel(y_label);
profile_plot.set_xrange(0, cvs.size());
profile_plot.set_yrange(0, maxCvgVal);
profile_plot.cmd("set style data linespoints");
std::ostringstream data_str;
for(uint32_t i = 0; i < cvs.size(); i++)
{
uint32_t index = i+1;
double val = y_logscale ? (double)std::log(cvs[i]) : (double)cvs[i];
data_str << index << " " << val << "\n";
}
std::ostringstream plot_str;
plot_str << "plot '-'\n" << data_str.str() << "e\n";
profile_plot.cmd(plot_str.str());
if (verbose)
cerr << "Plotted data: " << plot_str.str() << endl;
}
return 0;
}
