String AudioProcessor::getParameterName (int index, int maximumStringLength)
{
if (AudioProcessorParameter* p = managedParameters[index])
return p->getName (maximumStringLength);
return getParameterName (index).substring (0, maximumStringLength);
}
void OscController::parameterChanged(ofAbstractParameter & parameter){
string paramName = getParameterName(parameter);
string address = getAddressByParamName(paramName);
if(address == ""){
return;
}
ofxOscMessage msg;
msg.setAddress(address);
// NOTE: all parameters are sent as float args
if(parameter.type()==typeid(ofParameter<int>).name()){
//msg.addFloatArg(parameter.cast<int>());
ofParameter<int> & p = parameter.cast<int>();
msg.addFloatArg( ofMap(p.get(), p.getMin(), p.getMax(), 0.0, 1.0) );
}else if(parameter.type()==typeid(ofParameter<float>).name()){
//msg.addFloatArg(parameter.cast<float>());
ofParameter<float> & p = parameter.cast<float>();
msg.addFloatArg( ofMap(p.get(), p.getMin(), p.getMax(), 0.0, 1.0) );
}else if(parameter.type()==typeid(ofParameter<bool>).name()){
msg.addFloatArg(parameter.cast<bool>());
}
// send message
// for (int i = 0; i < oscOut.size(); i++) {
// oscOut[i]->sendMessage(msg);
// }
//senderTouchOSC.sendMessage(msg);
senderVezer.sendMessage(msg);
}
//==============================================================================
void SuperSpreadAudioProcessor::getStateInformation (MemoryBlock& destData)
{
XmlElement xml("STATE");
for (int i=0; i<getNumParameters(); ++i)
xml.setAttribute(getParameterName(i), getParameter(i));
copyXmlToBinary(xml, destData);
}
//==============================================================================
void LuftikusAudioProcessor::getStateInformation (MemoryBlock& destData)
{
XmlElement xml("LUFTIKUSDATA");
for (int i=0; i<getNumParameters(); ++i)
xml.setAttribute(getParameterName(i).replace(" ", "_", false).replace(".", "-", false), getParameter(i));
xml.setAttribute("tooltips", showTooltips ? 1 : 0);
copyXmlToBinary(xml, destData);
}
void SuperSpreadAudioProcessor::setStateInformation (const void* data, int sizeInBytes)
{
ScopedPointer<XmlElement> xml(getXmlFromBinary(data, sizeInBytes));
if (xml != nullptr)
{
for (int i=0; i<getNumParameters(); ++i)
setParameterNotifyingHost(i, static_cast<float> (xml->getDoubleAttribute(getParameterName(i), getParameter(i))));
}
}
void LuftikusAudioProcessor::setStateInformation (const void* data, int sizeInBytes)
{
ScopedPointer<XmlElement> xml(getXmlFromBinary(data, sizeInBytes));
if (xml != nullptr)
{
for (int i=0; i<getNumParameters(); ++i)
setParameterNotifyingHost(i, (float) xml->getDoubleAttribute(getParameterName(i).replace(" ", "_", false).replace(".", "-", false)));
showTooltips = xml->getBoolAttribute("tooltips", true);
}
}
//==============================================================================
void PitchedDelayAudioProcessor::getStateInformation (MemoryBlock& destData)
{
XmlElement xml("PitchedDelay");
for (int i=0; i<getNumParameters(); ++i)
xml.setAttribute(getParameterName(i), getParameter(i));
xml.setAttribute("currenttab", jmax(0, currentTab));
xml.setAttribute("showtooltips", showTooltips ? 1 : 0);
xml.setAttribute("extended", "1");
copyXmlToBinary(xml, destData);
}
std::set< const CCopasiObject * > CReactionInterface::getDeletedParameters() const
{
std::set< const CCopasiObject * > ToBeDeleted;
// We need to compare the current visible local parameter with the one stored
// in the reaction.
const CReaction * pReaction
= dynamic_cast< CReaction *>(CCopasiRootContainer::getKeyFactory()->get(mReactionReferenceKey));
if (pReaction == NULL)
return ToBeDeleted;
if (pReaction->getFunction() == NULL)
return ToBeDeleted;
const CFunctionParameters & OriginalParameters
= pReaction->getFunction()->getVariables();
size_t j, jmax = size();
size_t i, imax = OriginalParameters.size();
const CFunctionParameter * pParameter;
for (i = 0; i < imax; ++i)
{
pParameter = OriginalParameters[i];
if (pParameter->getUsage() == CFunctionParameter::PARAMETER &&
pReaction->isLocalParameter(i))
{
const std::string & Name = pParameter->getObjectName();
//find parameter with same name in current parameters
for (j = 0; j < jmax; ++j)
if (Name == getParameterName(j)) break;
if (j < jmax && mIsLocal[j])
continue;
// The old parameter is either not found or is no longer local, i.e., it needs to
// be added to values to be deleted.
ToBeDeleted.insert(pReaction->getParameters().getParameter(Name));
}
}
return ToBeDeleted;
}
//-------------------------------------------------------------------------------------------------------
VstIntPtr AudioEffect::dispatcher (VstInt32 opcode, VstInt32 index, VstIntPtr value, void* ptr, float opt)
{
VstIntPtr v = 0;
switch (opcode)
{
case effOpen: open (); break;
case effClose: close (); break;
case effSetProgram: if (value < numPrograms) setProgram ((VstInt32)value); break;
case effGetProgram: v = getProgram (); break;
case effSetProgramName: setProgramName ((char*)ptr); break;
case effGetProgramName: getProgramName ((char*)ptr); break;
case effGetParamLabel: getParameterLabel (index, (char*)ptr); break;
case effGetParamDisplay: getParameterDisplay (index, (char*)ptr); break;
case effGetParamName: getParameterName (index, (char*)ptr); break;
case effSetSampleRate: setSampleRate (opt); break;
case effSetBlockSize: setBlockSize ((VstInt32)value); break;
case effMainsChanged: if (!value) suspend (); else resume (); break;
#if !VST_FORCE_DEPRECATED
case effGetVu: v = (VstIntPtr)(getVu () * 32767.); break;
#endif
//---Editor------------
case effEditGetRect: if (editor) v = editor->getRect ((ERect**)ptr) ? 1 : 0; break;
case effEditOpen: if (editor) v = editor->open (ptr) ? 1 : 0; break;
case effEditClose: if (editor) editor->close (); break;
case effEditIdle: if (editor) editor->idle (); break;
#if (TARGET_API_MAC_CARBON && !VST_FORCE_DEPRECATED)
case effEditDraw: if (editor) editor->draw ((ERect*)ptr); break;
case effEditMouse: if (editor) v = editor->mouse (index, value); break;
case effEditKey: if (editor) v = editor->key (value); break;
case effEditTop: if (editor) editor->top (); break;
case effEditSleep: if (editor) editor->sleep (); break;
#endif
case DECLARE_VST_DEPRECATED (effIdentify): v = CCONST ('N', 'v', 'E', 'f'); break;
//---Persistence-------
case effGetChunk: v = getChunk ((void**)ptr, index ? true : false); break;
case effSetChunk: v = setChunk (ptr, (VstInt32)value, index ? true : false); break;
}
return v;
}
//-----------------------------------------------------------------------------
long AudioEffect::dispatcher(long opCode, long index, long value, void *ptr, float opt)
{
long v = 0;
switch(opCode)
{
case effOpen: open(); break;
case effClose: close(); break;
case effSetProgram: if(value < numPrograms) setProgram(value); break;
case effGetProgram: v = getProgram(); break;
case effSetProgramName: setProgramName((char *)ptr); break;
case effGetProgramName: getProgramName((char *)ptr); break;
case effGetParamLabel: getParameterLabel(index, (char *)ptr); break;
case effGetParamDisplay: getParameterDisplay(index, (char *)ptr); break;
case effGetParamName: getParameterName(index, (char *)ptr); break;
case effSetSampleRate: setSampleRate(opt); break;
case effSetBlockSize: setBlockSize(value); break;
case effMainsChanged: if(!value) suspend(); else resume(); break;
case effGetVu: v = (long)(getVu() * 32767.); break;
// editor
case effEditGetRect: if(editor) v = editor->getRect((ERect **)ptr); break;
case effEditOpen: if(editor) v = editor->open(ptr); break;
case effEditClose: if(editor) editor->close(); break;
case effEditIdle: if(editor) editor->idle(); break;
#if MAC
case effEditDraw: if(editor) editor->draw((ERect *)ptr); break;
case effEditMouse: if(editor) v = editor->mouse(index, value); break;
case effEditKey: if(editor) v = editor->key(value); break;
case effEditTop: if(editor) editor->top(); break;
case effEditSleep: if(editor) editor->sleep(); break;
#endif
// new
case effIdentify: v = 'NvEf'; break;
case effGetChunk: v = getChunk((void**)ptr, index ? true : false); break;
case effSetChunk: v = setChunk(ptr, value, index ? true : false); break;
}
return v;
}
void OscController::enableParameterSync(){
if(bParamenterSyncEnabled){
return;
}
bParamenterSyncEnabled = true;
// we need this because a group can only have one parent
// because the parent of this parameter might not be
// the panel group, we need to find the current parent.
// with multiple parents we could just have added the listener to the panel.
// iterate through the stored controls
for(map<string,ofxBaseGui*>::iterator it=controls.begin(); it!=controls.end(); ++it){
string controlName = it->first;
ofxBaseGui* control = it->second;
string oscAddress = getAddressByControlName(controlName);
ofAbstractParameter& parameter = control->getParameter();
// if this control is mapped to an address, create a link between
// the parameter name and the osc address
if(oscAddress != ""){
string paramName = getParameterName(parameter);
paramNameToAddress[paramName] = oscAddress;
}
// what is the last parent of this param?
ofParameterGroup* lastParent = parameter.getParent();
while(lastParent->getParent()){
lastParent = lastParent->getParent();
}
lastParents[ lastParent->getName() ] = lastParent; // use a map to store the lastParent of the parameter
}
// add listerner
for(map<string,ofParameterGroup*>::iterator it=lastParents.begin(); it!=lastParents.end(); ++it){
ofParameterGroup* lastParent = it->second;
cout << lastParent->getName() << endl;
ofAddListener(lastParent->parameterChangedE, this, &OscController::parameterChanged);
}
}
void CReactionInterface::printDebug() const
{
std::cout << "Reaction interface " << std::endl;
std::cout << " Function: " << getFunctionName() << std::endl;
std::cout << " ChemEq: " << getChemEqString() << std::endl;
size_t i, imax = size();
for (i = 0; i < imax; ++i)
{
std::cout << " --- " << i << ": " << getParameterName(i)
<< ", vector: " << isVector(i) << " local: " << isLocalValue(i)
<< ", value: " << mValues[i] << std::endl;
size_t j, jmax = mNameMap[i].size();
for (j = 0; j < jmax; ++j)
std::cout << " " << mNameMap[i][j] << std::endl;
}
std::cout << std::endl;
}
void CParameterObject::parametersChanged()
{
std::list<paramPair>::iterator it = parameterObjects->begin();
for (;it != parameterObjects->end(); it ++)
{
string prefix = (*it).second;
for (int i = 0; i < getNumParameters(); i++)
{
string paramName = getParameterName(i);
double value = getParameter(paramName);
if (prefix == paramName.substr(0, prefix.length()))
{
paramName = paramName.substr(prefix.length());
if ((*it).first->getParameterIndex(paramName) >= 0 && fabs((*it).first->getParameter(paramName) - value) > 0.00001)
{
(*it).first->setParameter(paramName, value);
}
}
}
}
onParametersChanged();
}
String AudioProcessor::getParameterName (int parameterIndex, int maximumStringLength)
{
return getParameterName (parameterIndex).substring (0, maximumStringLength);
}
plugMainUnion plugMain(DWORD functionCode, DWORD inputValue, DWORD instanceID)
#endif
{
plugMainUnion retval;
// declare pPlugObj - pointer to this instance
CFreeFrameGLPlugin* pPlugObj;
// typecast DWORD into pointer to a CFreeFrameGLPlugin
pPlugObj = (CFreeFrameGLPlugin*) instanceID;
switch (functionCode) {
case FF_GETINFO:
retval.PISvalue = (PluginInfoStruct*)getInfo();
break;
case FF_INITIALISE:
retval.ivalue = initialise();
break;
case FF_DEINITIALISE:
retval.ivalue = deInitialise();
break;
case FF_GETNUMPARAMETERS:
retval.ivalue = getNumParameters();
break;
case FF_GETPARAMETERNAME:
retval.svalue = getParameterName(inputValue);
break;
case FF_GETPARAMETERDEFAULT:
retval.ivalue = getParameterDefault(inputValue);
break;
case FF_GETPLUGINCAPS:
retval.ivalue = getPluginCaps(inputValue);
break;
case FF_GETEXTENDEDINFO:
retval.ivalue = (DWORD) getExtendedInfo();
break;
case FF_GETPARAMETERTYPE:
retval.ivalue = getParameterType(inputValue);
break;
case FF_GETPARAMETERDISPLAY:
if (pPlugObj != NULL)
retval.svalue = pPlugObj->GetParameterDisplay(inputValue);
else
retval.svalue = (char*)FF_FAIL;
break;
case FF_SETPARAMETER:
if (pPlugObj != NULL)
retval.ivalue = pPlugObj->SetParameter((const SetParameterStruct*) inputValue);
else
retval.ivalue = FF_FAIL;
break;
case FF_GETPARAMETER:
if (pPlugObj != NULL)
retval.ivalue = pPlugObj->GetParameter(inputValue);
else
retval.ivalue = FF_FAIL;
break;
case FF_INSTANTIATEGL:
retval.ivalue = (DWORD)instantiateGL((const FFGLViewportStruct *)inputValue);
break;
case FF_DEINSTANTIATEGL:
if (pPlugObj != NULL)
retval.ivalue = deInstantiateGL(pPlugObj);
else
retval.ivalue = FF_FAIL;
break;
case FF_GETIPUTSTATUS:
if (pPlugObj != NULL)
retval.ivalue = pPlugObj->GetInputStatus(inputValue);
else
retval.ivalue = FF_FAIL;
break;
case FF_PROCESSOPENGL:
if (pPlugObj != NULL)
{
ProcessOpenGLStruct *pogls = (ProcessOpenGLStruct *)inputValue;
if (pogls!=NULL)
retval.ivalue = pPlugObj->ProcessOpenGL(pogls);
else
retval.ivalue = FF_FAIL;
}
else
retval.ivalue = FF_FAIL;
break;
case FF_SETTIME:
if (pPlugObj != NULL)
{
double *inputTime = (double *)inputValue;
if (inputTime!=NULL)
retval.ivalue = pPlugObj->SetTime(*inputTime);
else
retval.ivalue = FF_FAIL;
}
else
retval.ivalue = FF_FAIL;
break;
//these old FF functions must always fail for FFGL plugins
case FF_INSTANTIATE:
case FF_DEINSTANTIATE:
case FF_PROCESSFRAME:
case FF_PROCESSFRAMECOPY:
default:
retval.ivalue = FF_FAIL;
break;
}
return retval;
}
void QFFCSMaxEntEvaluationItem::doFit(QFRawDataRecord* record, int index, int model, int defaultMinDatarange, int defaultMaxDatarange, int runAvgWidth, int residualHistogramBins) {
bool doEmit=record->isEmitResultsChangedEnabled();
bool thisDoEmitResults=get_doEmitResultsChanged();
bool thisDoEmitProps=get_doEmitResultsChanged();
set_doEmitResultsChanged(false);
set_doEmitPropertiesChanged(false);
record->disableEmitResultsChanged();
//qDebug() << "START DEBUGGING 0: We enter the do fit Method with MODEL = " << model;
/* IMPLEMENT THIS
Ergebnisse koennen einfach mit einer der setFitResult... Methoden gespeichert werden:
// PARAMETERNAME WERT
setFitResultValueBool(record, index, model, "evaluation_completed", true);
// PARAMETERNAME WERT FEHLER und EINHEIT (z.B. "ms") dazu
setFitResultValue(record, index, model, "my_parameter", value, error, unit);
*/
// HERE IS A DUMMY IMPLEMENTATION THAT OUTPUTS A SIMPLE GAUSSIAN
QFRDRFCSDataInterface* data=qobject_cast<QFRDRFCSDataInterface*>(record);
if (data) {
getProject()->getServices()->log_text(tr("running MaxEnt fit with model '%1' on raw data record '%2', run %3 ... \n").arg(getModelName(model)).arg(record->getName()).arg(index));
// which datapoints should we actually use?
int rangeMinDatarange=0;
int rangeMaxDatarange=data->getCorrelationN();
if (defaultMinDatarange>=0) rangeMinDatarange=defaultMinDatarange;
if (defaultMaxDatarange>=0) rangeMaxDatarange=defaultMaxDatarange;
getProject()->getServices()->log_text(tr(" - fit data range: %1...%2 (%3 datapoints)\n").arg(defaultMinDatarange).arg(defaultMaxDatarange).arg(defaultMaxDatarange-defaultMinDatarange));
uint32_t N=data->getCorrelationN();
double* taus=data->getCorrelationT();
double* distTaus=NULL;//(double*)qfCalloc(Ndist,sizeof(double));
double* distDs=NULL;//(double*)qfCalloc(Ndist,sizeof(double));
double* dist=NULL;//(double*)qfCalloc(Ndist,sizeof(double));
double* modelEval=(double*)qfMalloc(N*sizeof(double));
bool weightsOK=false;
double* corrdata=data->getCorrelationMean();
if (index>=0) corrdata=data->getCorrelationRun(index);
double* weights=allocWeights(&weightsOK, record, index);
if (!weightsOK) getProject()->getServices()->log_warning(tr(" - weights have invalid values => setting all weights to 1\n"));
//////////Load Algorithm Parameters ////////////////////////////////////////////////
double alpha=getFitValue(record,index,model,"maxent_alpha");
int NumIter=getFitValue(record,index,model,"maxent_numiter");
uint32_t Ndist=getFitValue(record,index,model,"maxent_Ndist");
////////////////////////////////////////////////////////////////////////////////////
bool fitSuccess=false;
//qDebug() << "DEBUG #1: alpha = " << alpha << " NumIter = " << NumIter << "Ndist =" << Ndist ;
//////////Load Model Parameters//////////////////////////////////////////////////////
//int parameter_count=getParameterCount(model);
QVector<double> param_vector(getParameterCount(model));
switch(model)
{
// FCS 3D diffusion with triplet
case 0: param_vector[0]=getFitValue(record,index,model,"trip_tau")*1e-6;
param_vector[1]=getFitValue(record,index,model,"trip_theta");
param_vector[2]=getFitValue(record,index,model,"focus_struct_fac");
param_vector[3]=getFitValue(record,index,model,"offset");
break;
// FCS 3D diffusion with 2 blinking components
case 1:
param_vector[0]=getFitValue(record,index,model,"trip_tau")*1e-6;
param_vector[1]=getFitValue(record,index,model,"trip_theta");
param_vector[2]=getFitValue(record,index,model,"focus_struct_fac");
param_vector[3]=getFitValue(record,index,model,"dark_tau")*1e-6;
param_vector[4]=getFitValue(record,index,model,"dark_theta");
param_vector[5]=getFitValue(record,index,model,"offset");
break;
// FCS 2D diffusion with 2 blinking components
case 2:
param_vector[0]=getFitValue(record,index,model,"trip_tau")*1e-6;
param_vector[1]=getFitValue(record,index,model,"trip_theta");
param_vector[2]=getFitValue(record,index,model,"dark_tau")*1e-6;
param_vector[3]=getFitValue(record,index,model,"dark_theta");
param_vector[4]=getFitValue(record,index,model,"offset");
break;
case 3: param_vector[0]=getFitValue(record,index,model,"A");
break;
case 4: param_vector[0]=getFitValue(record,index,model,"tau_1")*1e-6;
param_vector[1]=getFitValue(record,index,model,"tau_2")*1e-6;
param_vector[2]=getFitValue(record,index,model,"focus_struct_fac");
param_vector[3]=getFitValue(record,index,model,"fraction");
param_vector[4]=getFitValue(record,index,model,"particle_number");
param_vector[5]=getFitValue(record,index,model,"offset");
break;
case 5: //param_vector[0]=getFitValue(record,index,model,"maxent_wxy")*1e-3;
param_vector[0]=getFitValue(record,index,model,"focus_height")*1e-3;
param_vector[1]=getFitValue(record,index,model,"pixel_size")*1e-3;
param_vector[2]=getFitValue(record,index,model,"offset");
break;
case 6: param_vector[0]=getFitValue(record,index,model,"pixel_size")*1e-3;
param_vector[1]=getFitValue(record,index,model,"offset");
break;
}
double *param_list=param_vector.data();
//////////////////////////////////////////////////////////////////////////////////////////////////
/*
double kappa=getFitValue(record,index,model,"focus_struct_fac");
double tripTau=getFitValue(record,index,model,"trip_tau")*1e-6;
double tripTheta=getFitValue(record,index,model,"trip_theta");
*/
QVector<double> init_tau=getFitValueNumberArray(record, index, model, "maxent_tau");
QVector<double> init_dist=getFitValueNumberArray(record, index, model, "maxent_distribution");
//qDebug()<<init_tau;
bool old_distribution=false; // default value
if (init_tau.size()>0 && init_dist.size()>0)
{
Ndist=qMin(init_tau.size(), init_dist.size());
distTaus=(double*)qfCalloc(Ndist,sizeof(double));
dist=(double*)qfCalloc(Ndist,sizeof(double));
for (uint32_t i=0; i<Ndist; i++)
{
distTaus[i]=init_tau[i];
dist[i]=init_dist[i];
}
old_distribution=true;
//qDebug()<< "OLDDIST TRUE";
}
else
{
distTaus=NULL;
dist=NULL;
old_distribution=false;
//qDebug()<< "OLDDIST FALSE";
if (int64_t(Ndist)>(rangeMaxDatarange-rangeMinDatarange))
{
Ndist=(rangeMaxDatarange-rangeMinDatarange);
}
}
QElapsedTimer time;
time.start();
/////////////////////////////////////////////////////////
/// MaxEnt Implementation ///////////////////////////////
/////////////////////////////////////////////////////////
double tau_min=getFitValue(record,index,model,"maxent_taumin");
double tau_max=getFitValue(record,index,model,"maxent_taumax");
MaxEntB040::TauMode tau_mode= (MaxEntB040::TauMode)getFitValue(record,index,model,"maxent_taumode");
MaxEntB040 mem;
mem.setData(taus,corrdata,weights,N,rangeMinDatarange,rangeMaxDatarange,Ndist,dist,distTaus, model,getParameterCount(model),param_list, getFitValue(record,index,model,"maxent_wxy")*1e-3, tau_mode, tau_min, tau_max);
mem.run(alpha,NumIter,param_list,model,getParameterCount(model));
fitSuccess=true;
if (old_distribution==false)
{
distTaus=(double*)qfCalloc(Ndist,sizeof(double));
dist=(double*)qfCalloc(Ndist,sizeof(double));
}
mem.writeDistTaus(distTaus);
mem.writeDistribution(dist);
/////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////
// reset all NAN to 0
for (unsigned int i=0; i<Ndist; i++) {
double d=dist[i];
if (!QFFloatIsOK(dist[i])) dist[i]=0;
//qDebug()<<distTaus[i]<<" ,\t"<<d<<" ,\t"<<dist[i];
}
//////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////
/*
// REPLACE THIS WITH THE ACTUAL MAXENT FIT!!!
double T0=1e-4;
double sigma=2e-5;
double dSum=0;
for (int i=rangeMinDatarange; i<rangeMaxDatarange; i++) {
const double t=taus[i];
dist[i]=exp(-0.5*sqr(t-T0)/sqr(sigma));
dSum=dSum+dist[i];
}
for (int i=rangeMinDatarange; i<rangeMaxDatarange; i++) {
dist[i]=dist[i]/dSum;
}
fitSuccess=true;
// FIT CODE COMPLETE
*/
// duration measurement
double duration=double(time.elapsed())/1000.0;
getProject()->getServices()->log_text(tr(" - fit completed after %1 msecs with result %2\n").arg(duration).arg(fitSuccess?tr("success"):tr("no convergence")));
distDs=(double*)qfCalloc(Ndist, sizeof(double));
if (model!=3) {
const double wxy=getWXY();
for (uint32_t i=0; i<Ndist; i++) {
distDs[i]=wxy*wxy/1000000.0/(4.0*distTaus[i]);
}
} else if (model==3) {
const double q2=qfSqr(getDLSQ());
//qDebug()<<"q2="<<q2;
for (uint32_t i=0; i<Ndist; i++) {
distDs[i]=1.0/(q2*distTaus[i]);
}
}
// now store the results:
QString param,paramtau,paramD,parammem;
setFitResultValueNumberArray(record, index, model, paramtau=param="maxent_tau", distTaus, Ndist, QString("seconds"));
setFitResultGroup(record, index, model, param, tr("fit results"));
setFitResultLabel(record, index, model, param, tr("MaxEnt distribution: lag times"), QString("MaxEnt distribution: lag times <i>τ</i>"));
setFitResultSortPriority(record, index, model, param, true);
setFitResultValueNumberArray(record, index, model, paramD=param="maxent_D", distDs, Ndist, QString("seconds"));
setFitResultGroup(record, index, model, param, tr("fit results"));
setFitResultLabel(record, index, model, param, tr("MaxEnt distribution: diffusion coefficients"), QString("MaxEnt distribution: diffusion coefficients <i>D</i>"));
setFitResultSortPriority(record, index, model, param, true);
setFitResultValueNumberArray(record, index, model, parammem=param="maxent_distribution", dist, Ndist);
setFitResultGroup(record, index, model, param, tr("fit results"));
setFitResultLabel(record, index, model, param, tr("MaxEnt distribution"), QString("MaxEnt distribution: <i>p(τ)</i>"));
setFitResultSortPriority(record, index, model, param, true);
setFitResultValueInt(record, index, model, param="maxent_taumode", tau_mode);
setFitResultGroup(record, index, model, param, tr("fit results"));
setFitResultLabel(record, index, model, param, tr("MaxEnt distribution: tau mode"), tr("MaxEnt distribution: tau mode"));
setFitResultSortPriority(record, index, model, param, true);
QFRawDataRecord::evaluationCompoundResult comp;
comp.type=QFRawDataRecord::qfrdrctGraph1D;
comp.metadata["logX"]=true;
comp.metadata["logY"]=false;
comp.metadata["labelX"]=tr("correlation time \\tau_D [s]");
comp.metadata["labelY"]=tr("MaxEnt distribution");
comp.label=tr("MaxEnt(tauD)");
comp.referencedResults<<paramtau<<parammem;
record->resultsCompoundSet(getEvaluationResultID(index, model), "maxent_tau_curve", comp);
comp.metadata["labelX"]=tr("diffusion coefficient D [{\\mu}m^2/s]");
comp.label=tr("MaxEnt(D)");
comp.referencedResults.clear();
comp.referencedResults<<paramD<<parammem;
record->resultsCompoundSet(getEvaluationResultID(index, model), "maxent_d_curve", comp);
if (tau_mode>2) {
double wxy=getFitValue(record,index,model,"maxent_wxy")*1e-3;
setFitResultValue(record, index, model, param="maxent_taumax", wxy*wxy/(4.0*distTaus[0]), QString("seconds"));
setFitResultGroup(record, index, model, param, tr("fit results"));
setFitResultLabel(record, index, model, param, tr("MaxEnt distribution: minimum distribution times"), QString("MaxEnt distribution: minimum distribution times <i>τ<sub>min</sub></i>"));
setFitResultSortPriority(record, index, model, param, true);
setFitResultValue(record, index, model, param="maxent_taumin", wxy*wxy/(4.0*distTaus[Ndist-1]), QString("seconds"));
setFitResultGroup(record, index, model, param, tr("fit results"));
setFitResultLabel(record, index, model, param, tr("MaxEnt distribution: maximum distribution times"), QString("MaxEnt distribution: maximum distribution times <i>τ<sub>max</sub></i>"));
setFitResultSortPriority(record, index, model, param, true);
} else {
setFitResultValue(record, index, model, param="maxent_taumin", distTaus[0], QString("seconds"));
setFitResultGroup(record, index, model, param, tr("fit results"));
setFitResultLabel(record, index, model, param, tr("MaxEnt distribution: minimum distribution times"), QString("MaxEnt distribution: minimum distribution times <i>τ<sub>min</sub></i>"));
setFitResultSortPriority(record, index, model, param, true);
setFitResultValue(record, index, model, param="maxent_taumax", distTaus[Ndist-1], QString("seconds"));
setFitResultGroup(record, index, model, param, tr("fit results"));
setFitResultLabel(record, index, model, param, tr("MaxEnt distribution: maximum distribution times"), QString("MaxEnt distribution: maximum distribution times <i>τ<sub>max</sub></i>"));
setFitResultSortPriority(record, index, model, param, true);
}
// save all the default values for all fit parameters as results.
for (int i=0; i<getParameterCount(model); i++) {
param=getParameterID(model, i);
double value=getFitValue(record, index, model, param);
//qDebug()<<"model param "<<i<<": "<<param<<" = "<<value;
setFitResultValue(record, index, model, param, value, getParameterUnit(model, i, false));
setFitResultGroup(record, index, model, param, tr("fit results"));
setFitResultLabel(record, index, model, param, getParameterName(model, i, false), getParameterName(model, i, true));
setFitResultSortPriority(record, index, model, param, true);
//qDebug()<<"model param "<<i<<": "<<param<<" = "<< getFitValue(record, index, model, param)<<getParameterUnit(model, i, false);
}
// you can overwrite certain of these parameters using code like this:
/*setFitResultValue(record, index, model, param="focus_struct_fac", getFitValue(record, index, model, param));
setFitResultGroup(record, index, model, param, tr("fit results"));
setFitResultLabel(record, index, model, param, tr("focus structure factor"), QString("focus structure factor <i>γ</i>"));
setFitResultSortPriority(record, index, model, param, true);*/
// store number of iterations ... you may also store more fit algorithm properties like this
setFitResultValue(record, index, model, param="maxent_alpha", alpha);
setFitResultGroup(record, index, model, param, tr("fit properties"));
setFitResultLabel(record, index, model, param, tr("MaxEnt scaling parameter alpha"), tr("scaling parameter α"));
setFitResultValueInt(record, index, model, param="maxent_iterations", ceil(getFitValue(record, index, model, param)+NumIter));
setFitResultGroup(record, index, model, param, tr("fit properties"));
setFitResultLabel(record, index, model, param, tr("number of MaxEnt iterations"), tr("number of MaxEnt iterations"));
setFitResultValueInt(record, index, model, param="maxent_numiter", NumIter);
setFitResultGroup(record, index, model, param, tr("fit properties"));
setFitResultLabel(record, index, model, param, tr("number of MaxEnt iterations in last run of algorithm"), tr("last MaxEnt iterations"));
setFitResultValueString(record, index, model, param="used_model", getModelName(model));
setFitResultGroup(record, index, model, param, tr("fit properties"));
setFitResultLabel(record, index, model, param, tr("used model name"), tr("used model name"));
setFitResultValueInt(record, index, model, param="maxent_Ndist",Ndist);
setFitResultGroup(record, index, model, param, tr("fit properties"));
setFitResultLabel(record, index, model, param, tr("MaxEnt number of distribution points"), tr("MaxEnt number of distribution points"));
setFitResultValueInt(record, index, model, param="used_model_id", model);
setFitResultGroup(record, index, model, param, tr("fit properties"));
setFitResultLabel(record, index, model, param, tr("used model id"), tr("used model id"));
setFitResultValueInt(record, index, model, param="used_run", index);
setFitResultGroup(record, index, model, param, tr("fit properties"));
setFitResultLabel(record, index, model, param, tr("used run"), tr("used run"));
setFitResultValue(record, index, model, param="runtime", duration, tr("seconds"));
setFitResultGroup(record, index, model, param, tr("fit properties"));
setFitResultLabel(record, index, model, param, tr("fit runtime"), tr("fit runtime"));
setFitResultValueString(record, index, model, param="fitalg_message", tr("MaxEnt finished successfully after %1 iterations with alpha=%2").arg(NumIter).arg(alpha));
setFitResultGroup(record, index, model, param, tr("fit properties"));
setFitResultLabel(record, index, model, param, tr("MaxEnt message"), tr("MaxEnt message"));
setFitResultValueString(record, index, model, param="fitalg_messageHTML", tr("<b>MaxEnt finished successfully</b><br>after %1 iterations with α=%2").arg(NumIter).arg(alpha));
setFitResultGroup(record, index, model, param, tr("fit properties"));
setFitResultLabel(record, index, model, param, tr("MaxEnt message"), tr("MaxEnt message"));
// CALCULATE FIT STATISTICS
// now we evaluate the model for the given distribution
/////////////////////////
/////////////////////////
// I changed the 7th argument in the evaluateModel call from &(taus[rangeMindatarange]) to &(distTaus[rangeMinDatarange])
// this is what the 7th and 8th argument used to be like: &(distTaus[rangeMinDatarange]), &(dist[rangeMinDatarange])
// this was the last argument: rangeMaxDatarange-rangeMinDatarange, now changed to Ndist
////////////////////////
evaluateModel(record, index, model, taus, modelEval, N, distTaus,dist,Ndist);
// then we can call calcFitStatistics()
QFFitStatistics fit_stat=calcFitStatistics(record, index, model, taus, corrdata, N,Ndist, rangeMinDatarange, rangeMaxDatarange, runAvgWidth, residualHistogramBins);
// finally we have to free the memory allocated in the calcFitStatistics() result.
fit_stat.free();
qfFree(dist);
qfFree(weights);
qfFree(modelEval);
qfFree(distTaus);
qfFree(distDs);
}
if (doEmit) record->enableEmitResultsChanged(true);
set_doEmitResultsChanged(thisDoEmitResults);
set_doEmitPropertiesChanged(thisDoEmitProps);
}
plugMainUnion plugMain( DWORD functionCode, LPVOID pParam, LPVOID instanceID )
#endif
{
plugMainUnion retval;
// declare pPlugObj - pointer to this instance
WhorldPlug *pPlugObj;
// typecast LPVOID into pointer to a WhorldPlug
pPlugObj = (WhorldPlug*) instanceID;
switch(functionCode) {
case FF_GETINFO:
retval.PISvalue = getInfo();
break;
case FF_INITIALISE:
retval.ivalue = initialise();
break;
case FF_DEINITIALISE:
retval.ivalue = deInitialise(); // todo: pass on instance IDs etc
break;
case FF_GETNUMPARAMETERS:
retval.ivalue = getNumParameters();
break;
case FF_GETPARAMETERNAME:
retval.svalue = getParameterName( (DWORD) pParam );
break;
case FF_GETPARAMETERDEFAULT:
retval.fvalue = getParameterDefault( (DWORD) pParam );
break;
case FF_GETPARAMETERDISPLAY:
retval.svalue = pPlugObj->getParameterDisplay( (DWORD) pParam );
break;
// parameters are passed in here as a packed struct of two DWORDS:
// index and value
case FF_SETPARAMETER:
retval.ivalue= pPlugObj->setParameter( (SetParameterStruct*) pParam );
break;
case FF_PROCESSFRAME:
retval.ivalue = pPlugObj->processFrame(pParam);
break;
case FF_GETPARAMETER:
retval.fvalue = pPlugObj->getParameter((DWORD) pParam);
break;
case FF_GETPLUGINCAPS:
retval.ivalue = getPluginCaps( (DWORD) pParam);
break;
// Russell - FF 1.0 upgrade in progress ...
case FF_INSTANTIATE:
retval.ivalue = (DWORD) instantiate( (VideoInfoStruct*) pParam);
break;
case FF_DEINSTANTIATE:
retval.ivalue = deInstantiate(pPlugObj);
break;
case FF_GETEXTENDEDINFO:
retval.ivalue = (DWORD) getExtendedInfo();
break;
case FF_PROCESSFRAMECOPY:
retval.ivalue = pPlugObj->processFrameCopy((ProcessFrameCopyStruct*)pParam);
break;
case FF_GETPARAMETERTYPE:
// not implemented yet
retval.ivalue = FF_FAIL;
break;
// ....................................
default:
retval.ivalue = FF_FAIL;
break;
}
return retval;
}
int getOptModelParameterName(emb_optimizer optim, int name_idx, char par_name[], size_t maxlen, size_t *reqlen)
{
return getParameterName(myModel, name_idx, par_name, maxlen, reqlen);
}
void CReactionInterface::copyMapping()
{
if (!mpParameters) //nothing to copy
{
initMapping();
return;
}
// save the old information
CFunctionParameters *oldParameters = mpParameters;
std::vector<std::vector<std::string> > oldMap = mNameMap;
std::vector<C_FLOAT64> oldValues = mValues;
std::vector<bool> oldIsLocal = mIsLocal;
//create new mapping
initMapping();
//try to preserve as much information from the old mapping as possible
size_t j, jmax = oldParameters->size();
size_t i, imax = size();
for (i = 0; i < imax; ++i)
{
//find parameter with same name in old parameters
for (j = 0; j < jmax; ++j)
if ((*oldParameters)[j]->getObjectName() == getParameterName(i)) break;
if (j == jmax) continue;
//see if usage matches
if (getUsage(i) != (*oldParameters)[j]->getUsage()) continue;
//see if vector property matches
if (isVector(i) != ((*oldParameters)[j]->getType() == CFunctionParameter::VFLOAT64))
continue;
mIsLocal[i] = oldIsLocal[j];
mValues[i] = oldValues[j];
switch (getUsage(i))
{
case CFunctionParameter::SUBSTRATE:
case CFunctionParameter::PRODUCT:
//TODO: check with chemeq
mNameMap[i] = oldMap[j];
break;
case CFunctionParameter::MODIFIER:
//TODO: check existence?
mNameMap[i] = oldMap[j];
//TODO: add to chemeq
break;
case CFunctionParameter::PARAMETER:
case CFunctionParameter::VOLUME:
case CFunctionParameter::TIME:
//TODO: check existence?
mNameMap[i] = oldMap[j];
break;
default:
break;
}
}
pdelete(oldParameters);
}
double CParameters::getParameterFromIndex(unsigned int index)
{
return getParameter(getParameterName(index));
}
bool CReactionInterface::writeBackToReaction(CReaction * rea)
{
bool success = true;
//CReaction *rea;
if (rea == NULL)
rea = dynamic_cast< CReaction *>(CCopasiRootContainer::getKeyFactory()->get(mReactionReferenceKey));
if (rea == NULL) return false;
// Now we can safely write to the equation as we are sure that only unique metabolites
// may have the empty string as compartments
mChemEqI.writeToChemEq(rea->getChemEq());
if (!isValid()) return false; // do nothing
if (mpFunction == NULL) return false;
if (mpFunction->getObjectName() == "undefined") return false;
if (mpParameters == NULL) return false;
if (!(*mpParameters == mpFunction->getVariables())) return false; // do nothing
// TODO. check if function has changed since it was set in the R.I.
rea->setFunction(mpFunction->getObjectName());
size_t j, jmax;
size_t i, imax = size();
std::pair< std::string, std::string > Names;
for (i = 0; i < imax; ++i)
{
switch (getUsage(i))
{
case CFunctionParameter::PARAMETER:
if (mIsLocal[i])
rea->setParameterValue(getParameterName(i), mValues[i]);
else
{
rea->setParameterValue(getParameterName(i), mValues[i], false);
rea->setParameterMapping(i, mpModel->getModelValues()[mNameMap[i][0]]->getKey());
}
break;
case CFunctionParameter::VOLUME:
rea->setParameterMapping(i, mpModel->getCompartments()[mNameMap[i][0]]->getKey());
break;
case CFunctionParameter::TIME:
rea->setParameterMapping(i, mpModel->getKey()); //time is the value of the model
break;
case CFunctionParameter::SUBSTRATE:
case CFunctionParameter::PRODUCT:
case CFunctionParameter::MODIFIER:
if (isVector(i))
{
rea->clearParameterMapping(i);
jmax = mNameMap[i].size();
for (j = 0; j < jmax; ++j)
{
Names = CMetabNameInterface::splitDisplayName(mNameMap[i][j]);
rea->addParameterMapping(i, CMetabNameInterface::getMetaboliteKey(mpModel, Names.first, Names.second));
}
}
else
{
Names = CMetabNameInterface::splitDisplayName(mNameMap[i][0]);
rea->setParameterMapping(i, CMetabNameInterface::getMetaboliteKey(mpModel, Names.first, Names.second));
}
break;
default:
break;
}
}
rea->compile();
mpModel->setCompileFlag(); //TODO: check if really necessary
return success;
}
bool CReactionInterface::loadMappingAndValues(const CReaction & rea)
{
bool success = true;
std::vector< std::vector<std::string> >::const_iterator it;
std::vector< std::vector<std::string> >::const_iterator iEnd;
std::vector<std::string>::const_iterator jt;
std::vector<std::string>::const_iterator jEnd;
size_t i;
std::string metabName;
const CModelEntity* pObj;
std::vector<std::string> SubList;
SubList.resize(1);
SubList[0] = "unknown";
mNameMap.resize(size());
for (i = 0; i != size(); ++i)
{
mNameMap[i] = SubList;
}
mValues.resize(size(), 0.1);
mIsLocal.resize(size(), false);
it = rea.getParameterMappings().begin();
iEnd = rea.getParameterMappings().end();
for (i = 0; it != iEnd; ++it, ++i)
{
if (isVector(i))
{
assert((getUsage(i) == CFunctionParameter::SUBSTRATE)
|| (getUsage(i) == CFunctionParameter::PRODUCT)
|| (getUsage(i) == CFunctionParameter::MODIFIER));
SubList.clear();
for (jt = it->begin(), jEnd = it->end(); jt != jEnd; ++jt)
{
metabName = CMetabNameInterface::getDisplayName(mpModel, *jt, true);
assert(metabName != "");
SubList.push_back(metabName);
}
}
else
{
assert(it->size() == 1);
SubList.resize(1); SubList[0] = "unknown";
switch (getUsage(i))
{
case CFunctionParameter::SUBSTRATE:
case CFunctionParameter::PRODUCT:
case CFunctionParameter::MODIFIER:
metabName = CMetabNameInterface::getDisplayName(mpModel, *(it->begin()), true);
// assert(metabName != "");
SubList[0] = metabName;
//TODO: check if the metabolite is in the chemical equation with the correct rule
break;
case CFunctionParameter::VOLUME:
pObj = dynamic_cast<const CCompartment*>(CCopasiRootContainer::getKeyFactory()->get(*(it->begin())));
assert(pObj);
SubList[0] = pObj->getObjectName();
break;
case CFunctionParameter::TIME:
pObj = dynamic_cast<const CModel*>(CCopasiRootContainer::getKeyFactory()->get(*(it->begin())));
assert(pObj);
SubList[0] = pObj->getObjectName();
break;
case CFunctionParameter::PARAMETER:
{
const CCopasiParameter * pParameter = rea.getParameters().getParameter(getParameterName(i));
if (pParameter != NULL)
{
mValues[i] = * pParameter->getValue().pDOUBLE;
}
else
{
mValues[i] = std::numeric_limits< C_FLOAT64 >::quiet_NaN();
}
mIsLocal[i] = rea.isLocalParameter(i);
if (!mIsLocal[i])
{
pObj = dynamic_cast<const CModelValue*>(CCopasiRootContainer::getKeyFactory()->get(*(it->begin())));
if (pObj)
{
SubList[0] = pObj->getObjectName();
mValues[i] = pObj->getInitialValue();
}
}
}
break;
default:
break;
}
}
mNameMap[i] = SubList;
}
return success;
}
void
RemotePluginServer::dispatchControlEvents()
{
RemotePluginOpcode opcode = RemotePluginNoOpcode;
static float *parameterBuffer = 0;
tryRead(m_controlRequestFd, &opcode, sizeof(RemotePluginOpcode));
switch (opcode) {
case RemotePluginGetVersion:
writeFloat(m_controlResponseFd, getVersion());
break;
case RemotePluginGetName:
writeString(m_controlResponseFd, getName());
break;
case RemotePluginGetMaker:
writeString(m_controlResponseFd, getMaker());
break;
case RemotePluginTerminate:
terminate();
break;
case RemotePluginGetInputCount:
m_numInputs = getInputCount();
writeInt(m_controlResponseFd, m_numInputs);
break;
case RemotePluginGetOutputCount:
m_numOutputs = getOutputCount();
writeInt(m_controlResponseFd, m_numOutputs);
break;
case RemotePluginGetParameterCount:
writeInt(m_controlResponseFd, getParameterCount());
break;
case RemotePluginGetParameterName:
writeString(m_controlResponseFd, getParameterName(readInt(m_controlRequestFd)));
break;
case RemotePluginGetParameter:
writeFloat(m_controlResponseFd, getParameter(readInt(m_controlRequestFd)));
break;
case RemotePluginGetParameterDefault:
writeFloat(m_controlResponseFd, getParameterDefault(readInt(m_controlRequestFd)));
break;
case RemotePluginGetParameters:
{
if (!parameterBuffer) {
parameterBuffer = new float[getParameterCount()];
}
int p0 = readInt(m_controlRequestFd);
int pn = readInt(m_controlRequestFd);
getParameters(p0, pn, parameterBuffer);
tryWrite(m_controlResponseFd, parameterBuffer, (pn - p0 + 1) * sizeof(float));
break;
}
case RemotePluginHasMIDIInput:
{
bool m = hasMIDIInput();
tryWrite(m_controlResponseFd, &m, sizeof(bool));
break;
}
case RemotePluginGetProgramCount:
writeInt(m_controlResponseFd, getProgramCount());
break;
case RemotePluginGetProgramName:
writeString(m_controlResponseFd, getProgramName(readInt(m_controlRequestFd)));
break;
case RemotePluginIsReady:
{
if (!m_shm) sizeShm();
bool b(isReady());
std::cerr << "isReady: returning " << b << std::endl;
tryWrite(m_controlResponseFd, &b, sizeof(bool));
}
case RemotePluginSetDebugLevel:
{
RemotePluginDebugLevel newLevel = m_debugLevel;
tryRead(m_controlRequestFd, &newLevel, sizeof(RemotePluginDebugLevel));
setDebugLevel(newLevel);
m_debugLevel = newLevel;
break;
}
case RemotePluginWarn:
{
bool b = warn(readString(m_controlRequestFd));
tryWrite(m_controlResponseFd, &b, sizeof(bool));
break;
}
case RemotePluginShowGUI:
{
showGUI(readString(m_controlRequestFd));
break;
}
case RemotePluginHideGUI:
{
hideGUI();
break;
}
//Deryabin Andrew: vst chunks support
case RemotePluginGetVSTChunk:
{
std::vector<char> chunk = getVSTChunk();
writeRaw(m_controlResponseFd, chunk);
break;
}
case RemotePluginSetVSTChunk:
{
std::vector<char> chunk = readRaw(m_controlRequestFd);
setVSTChunk(chunk);
break;
}
//Deryabin Andrew: vst chunks support: end code
case RemotePluginNoOpcode:
break;
case RemotePluginReset:
reset();
break;
default:
std::cerr << "WARNING: RemotePluginServer::dispatchControlEvents: unexpected opcode "
<< opcode << std::endl;
}
}
const String DemoJuceFilter::getParameterXMLName (int index)
{
String name = getParameterName(index);
name = name.replace(T(" "), T("_"));
return name;
}
