//**********************************************************************************************************************
vector<string> HeatMapCommand::setParameters(){
try {
CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(plist);
CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(prabund);
CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(psabund);
CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(pshared);
CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(prelabund);
CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
CommandParameter pscale("scale", "Multiple", "log10-log2-linear", "log10", "", "", "","",false,false); parameters.push_back(pscale);
CommandParameter psorted("sorted", "Multiple", "none-shared-topotu-topgroup", "shared", "", "", "","",false,false); parameters.push_back(psorted);
CommandParameter pnumotu("numotu", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pnumotu);
CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "","",false,false); parameters.push_back(pfontsize);
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "HeatMapCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
vector<string> GetRAbundCommand::setParameters(){
try {
CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
CommandParameter psorted("sorted", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(psorted);
CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "GetRAbundCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
vector<string> HClusterCommand::setParameters(){
try {
CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","list-rabund-sabund",false,false,true); parameters.push_back(pphylip);
CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName","",false,false,true); parameters.push_back(pname);
CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName","list-rabund-sabund",false,false,true); parameters.push_back(pcolumn);
CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false,true); parameters.push_back(pcutoff);
CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "","",false,false); parameters.push_back(pmethod);
CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
CommandParameter psorted("sorted", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psorted);
CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshowabund);
CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptiming);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "HClusterCommand", "setParameters");
exit(1);
}
}
void ProgVolumePCA::run()
{
show();
produce_side_info();
const MultidimArray<int> &imask=mask.imask;
size_t Nvoxels=imask.sum();
MultidimArray<float> v;
v.initZeros(Nvoxels);
// Add all volumes to the analyzer
FileName fnVol;
FOR_ALL_OBJECTS_IN_METADATA(mdVols)
{
mdVols.getValue(MDL_IMAGE,fnVol,__iter.objId);
V.read(fnVol);
// Construct vector
const MultidimArray<double> &mV=V();
size_t idx=0;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mV)
{
if (DIRECT_MULTIDIM_ELEM(imask,n))
DIRECT_MULTIDIM_ELEM(v,idx++)=DIRECT_MULTIDIM_ELEM(mV,n);
}
analyzer.addVector(v);
}
// Construct PCA basis
analyzer.subtractAvg();
analyzer.learnPCABasis(NPCA,100);
// Project onto the PCA basis
Matrix2D<double> proj;
analyzer.projectOnPCABasis(proj);
std::vector<double> dimredProj;
dimredProj.resize(NPCA);
int i=0;
FOR_ALL_OBJECTS_IN_METADATA(mdVols)
{
memcpy(&dimredProj[0],&MAT_ELEM(proj,i,0),NPCA*sizeof(double));
mdVols.setValue(MDL_DIMRED,dimredProj,__iter.objId);
i++;
}
if (fnVolsOut!="")
mdVols.write(fnVolsOut);
else
mdVols.write(fnVols);
// Save the basis
const MultidimArray<double> &mV=V();
for (int i=NPCA-1; i>=0; --i)
{
V().initZeros();
size_t idx=0;
const MultidimArray<double> &mPCA=analyzer.PCAbasis[i];
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mV)
{
if (DIRECT_MULTIDIM_ELEM(imask,n))
DIRECT_MULTIDIM_ELEM(mV,n)=DIRECT_MULTIDIM_ELEM(mPCA,idx++);
}
if (fnBasis!="")
V.write(fnBasis,i+1,true,WRITE_OVERWRITE);
}
// Generate the PCA volumes
if (listOfPercentiles.size()>0 && fnOutStack!="" && fnAvgVol!="")
{
Image<double> Vavg;
if (fnAvgVol!="")
Vavg.read(fnAvgVol);
else
Vavg().initZeros(V());
Matrix1D<double> p;
proj.toVector(p);
Matrix1D<double> psorted=p.sort();
Image<double> Vpca;
Vpca()=Vavg();
createEmptyFile(fnOutStack,(int)XSIZE(Vavg()),(int)YSIZE(Vavg()),(int)ZSIZE(Vavg()),listOfPercentiles.size());
std::cout << "listOfPercentiles.size()=" << listOfPercentiles.size() << std::endl;
for (size_t i=0; i<listOfPercentiles.size(); i++)
{
int idx=(int)round(textToFloat(listOfPercentiles[i].c_str())/100.0*VEC_XSIZE(p));
std::cout << "Percentile " << listOfPercentiles[i] << " -> idx=" << idx << " p(idx)=" << psorted(idx) << std::endl;
Vpca()+=psorted(idx)*V();
Vpca.write(fnOutStack,i+1,true,WRITE_REPLACE);
}
}
}
