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GnuPlotterTrajectoryObserver.cpp

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// GnuPlotterTrajectoryObserver.cpp: implementation of the GnuPlotterTrajectoryObserver class.
//

#include "GnuPlotterTrajectoryObserver.h"

// Construction/Destruction

GnuPlotterTrajectoryObserver::GnuPlotterTrajectoryObserver(int chemX, int chemY, int chemZ)
{
        this->chemX = chemX;
        this->chemY = chemY;
        this->chemZ = chemZ;
}

GnuPlotterTrajectoryObserver::~GnuPlotterTrajectoryObserver()
{

}

void GnuPlotterTrajectoryObserver::AddChemicalToList(int chemNumber)
{
        otherChem.push_back(chemNumber);
}

void GnuPlotterTrajectoryObserver::Update(Subject *theChangedSubject)
{
        int i;
        // static cast may be dangerous
        SingleNetworkMinimizable *nM = (SingleNetworkMinimizable *)theChangedSubject;

        // reopen the temp file
        freopen(buffername,"w",buffer);

        int maxTime = nM->GetCellObserver()->GetNumberOfTimeSteps();
        
        char chemXName[100],chemYName[100],chemZName[100];
        char titlestring[100],commandstring[1000];
        char xLabelString[100],yLabelString[100],zLabelString[100];

        // 2D plot
        if(chemZ == -1)
        {
                // try to normalize
                double basalX = nM->GetCellObserver()->GetAverageConcentration()[chemX][0];
                double basalY = nM->GetCellObserver()->GetAverageConcentration()[chemY][0];
                sprintf(chemXName,nM->GetExperiment()->GetReactionNetwork()->GetChemical(chemX)->GetName().c_str());
                sprintf(chemYName,nM->GetExperiment()->GetReactionNetwork()->GetChemical(chemY)->GetName().c_str());
                double rescale;
                if(basalX > 0.0)
                {
                        rescale = basalX;
                        sprintf(xLabelString,"set xlabel \"[%s]/[%s]_0\"\n",chemXName,chemXName);
                        sprintf(yLabelString,"set ylabel \"[%s]/[%s]_0\"\n",chemYName,chemXName);
                }
                else if(basalY > 0.0)
                {
                        rescale = basalY;
                        sprintf(xLabelString,"set xlabel \"[%s]/[%s]_0\"\n",chemXName,chemYName);
                        sprintf(yLabelString,"set ylabel \"[%s]/[%s]_0\"\n",chemYName,chemYName);
                }
                else
                {       
                        rescale = 1.0;
                        sprintf(xLabelString,"set xlabel \"[%s]\"\n",chemXName);
                        sprintf(yLabelString,"set ylabel \"[%s]\"\n",chemYName);

                }
        
                // loop over the time points and draw the trajectory
                // vectors are set to be 1/4 the length between adjacent 
                // points
        
                double firstX,firstY,secondX,secondY,deltaX,deltaY;

                // uses vectors
                for(i = 0; i < maxTime - 2; i++)
                {
                        // get the appropriate points
                        firstX = (nM->GetCellObserver()->GetAverageConcentration()[chemX][i])/rescale;
                        firstY = (nM->GetCellObserver()->GetAverageConcentration()[chemY][i])/rescale;

                        secondX = (nM->GetCellObserver()->GetAverageConcentration()[chemX][i+1])/rescale;
                        secondY = (nM->GetCellObserver()->GetAverageConcentration()[chemY][i+1])/rescale;

                        deltaX = .25*(secondX - firstX);
                        deltaY = .25*(secondY - firstY);

                        // write to the buffer
                        fprintf(buffer,"%e\t%e\t%e\t%e\n",firstX,firstY,deltaX,deltaY);
                }
                // print the last line, using the previous vector length for
                // the last vector length
                fprintf(buffer,"%e\t%e\t%e\t%e\n",secondX,secondY,deltaX,deltaY);
                // pad with double newlines
                fprintf(buffer,"\n\n");

        }
        else // 3D plot
        {
                // try to normalize
                double basalX = nM->GetCellObserver()->GetAverageConcentration()[chemX][0];
                double basalY = nM->GetCellObserver()->GetAverageConcentration()[chemY][0];
                double basalZ = nM->GetCellObserver()->GetAverageConcentration()[chemZ][0];
                sprintf(chemXName,nM->GetExperiment()->GetReactionNetwork()->GetChemical(chemX)->GetName().c_str());
                sprintf(chemYName,nM->GetExperiment()->GetReactionNetwork()->GetChemical(chemY)->GetName().c_str());
                sprintf(chemZName,nM->GetExperiment()->GetReactionNetwork()->GetChemical(chemZ)->GetName().c_str());
                double rescale;
                if(basalX > 0.0)
                {
                        rescale = basalX;
                        sprintf(xLabelString,"set xlabel \"[%s]/[%s]_0\"\n",chemXName,chemXName);
                        sprintf(yLabelString,"set ylabel \"[%s]/[%s]_0\"\n",chemYName,chemXName);
                        sprintf(zLabelString,"set zlabel \"[%s]/[%s]_0\"\n",chemZName,chemXName);

                }
                else if(basalY > 0.0)
                {
                        rescale = basalY;
                        sprintf(xLabelString,"set xlabel \"[%s]/[%s]_0\"\n",chemXName,chemYName);
                        sprintf(yLabelString,"set ylabel \"[%s]/[%s]_0\"\n",chemYName,chemYName);
                        sprintf(zLabelString,"set zlabel \"[%s]/[%s]_0\"\n",chemZName,chemYName);
                }
                else if(basalZ > 0.0)
                {       
                        rescale = basalZ;
                        sprintf(xLabelString,"set xlabel \"[%s]/[%s]_0\"\n",chemXName,chemZName);
                        sprintf(yLabelString,"set ylabel \"[%s]/[%s]_0\"\n",chemYName,chemZName);
                        sprintf(zLabelString,"set zlabel \"[%s]/[%s]_0\"\n",chemZName,chemZName);

                }
                else
                {
                        rescale = 1.0;
                        sprintf(xLabelString,"set xlabel \"[%s]\"\n",chemXName);
                        sprintf(yLabelString,"set ylabel \"[%s]\"\n",chemYName);
                        sprintf(zLabelString,"set zlabel \"[%s]\"\n",chemZName);
                }
        
                // no vector support for splot in current GNUplot version
                for(i = 0; i < maxTime - 2; i++)
                {
                        // get the appropriate points
                        double x = (nM->GetCellObserver()->GetAverageConcentration()[chemX][i])/rescale;
                        double y = (nM->GetCellObserver()->GetAverageConcentration()[chemY][i])/rescale;
                        double z = (nM->GetCellObserver()->GetAverageConcentration()[chemZ][i])/rescale; 
                        // write to the buffer
                        fprintf(buffer,"%e\t%e\t%e\n",x,y,z);
                }
                // pad with double newlines
                fprintf(buffer,"\n\n");
        }
        // now dump the time series data for the chemicals to the temp file
        for(i = 0; i < otherChem.size(); i++)
        {
                for(int t = 0; t < (maxTime-1); t++)
                {
                        double time = double (t);
                        double sim = nM->GetCellObserver()->GetAverageConcentration()[otherChem[i]][t];
                        fprintf(buffer,"%e\t\t%e\n",time,sim);
                }
                // pad each series with two newlines
                fprintf(buffer,"\n\n");
        }
        
        // set up for multiplot
        // first index is for the trajectory plot (one data series) and successive
        // indices are for the additional time series
        // FIRST PLOT
        SendPlotCommand("set multiplot\n");
        SendPlotCommand("set origin 0.0,0.0\n");
        SendPlotCommand("set size 0.5,1.0\n");
        sprintf(titlestring,"set title \"Chemical Trajectory\"\n");
        SendPlotCommand(titlestring);
        SendPlotCommand("set grid\n");
        SendPlotCommand("set nokey\n");
        
        if(chemZ == -1)
        {
                // now plot all the style stuff
                sprintf(commandstring,"plot \"%s\" index 0 w vector\n",buffername);
                fflush(buffer);
                SendPlotCommand(xLabelString);
                SendPlotCommand(yLabelString);
        }
        else
        {
                // now all the style stuff
                sprintf(commandstring,"splot \"%s\" index 0 w linespoints\n",buffername);
                fflush(buffer);
                SendPlotCommand("set ticslevel 0\n");
                SendPlotCommand("set border 4095\n");
                SendPlotCommand(xLabelString);
                SendPlotCommand(yLabelString);
                SendPlotCommand(zLabelString);
        }
        
        // change single backslashes to forward slashes to keep windows happy
#ifdef _WIN32
        int iterator = 0;
        while(commandstring[iterator] != '\0')
        {
                if(commandstring[iterator] == '\\') {commandstring[iterator] = '/';}
                iterator++;
        }
#endif
        
        SendPlotCommand(commandstring);
        
        // SECOND PLOT
        SendPlotCommand("set origin 0.5,0.0\n");
        SendPlotCommand("set size 0.5,1.0\n");
        sprintf(titlestring,"set title \"Time Series Monitor\"\n");
        SendPlotCommand(titlestring);
        SendPlotCommand("set xlabel \"time (min)\"\n");
        SendPlotCommand("set ylabel \"[Chemical] (molecules)\"\n");
        SendPlotCommand("set key\n");
        // plot the first chemical manually
        char namestring[200];
        sprintf(namestring,nM->GetExperiment()->GetReactionNetwork()->GetChemical(otherChem[0])->GetName().c_str());
        sprintf(commandstring,"plot \"%s\" index 1 t \"%s\" w lines",buffername,namestring);
        // the rest - experiment first
        for(i = 1; i < otherChem.size(); i++)
        {
                char tempbuffer[500];
                sprintf(namestring,nM->GetExperiment()->GetReactionNetwork()->GetChemical(otherChem[i])->GetName().c_str());
                sprintf(tempbuffer,",\"%s\" index %i t \"%s\" w lines",buffername,i+1,namestring);
                strcat(commandstring,tempbuffer);
        }
        strcat(commandstring,"\n");
        fflush(buffer);
        
        // change single backslashes to forward slashes to keep windows happy
#ifdef _WIN32
        iterator = 0;
        while(commandstring[iterator] != '\0')
        {
                if(commandstring[iterator] == '\\') {commandstring[iterator] = '/';}
                iterator++;
        }
#endif
        
        SendPlotCommand(commandstring);
}

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