#include <TROOT.h>
#include "TFile.h"
#include "TTree.h"
#include "TCanvas.h"
#include "TImage.h"
#include "TMath.h"
#include "TH1F.h"
#include "TH2F.h"
#include "TObject.h"
#include "TPad.h"
#include "TStyle.h"
#include "TSystem.h"
#include "TGeoManager.h"
#include "TGeoMatrix.h"
#include "TVector3.h"
#include "TColor.h"
#include "TGeoCompositeShape.h"
#include "TGeoBBox.h"
#include "TGLViewer.h"
#include "TVirtualGL.h"
#include "TGLPerspectiveCamera.h"
#include "TGraph.h"
#include <sstream>
#include <iostream>
#include <string>
#include <vector>
#include <fstream>
#include <time.h>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include "TGLAnnotation.h"

using namespace std;

void neuro_graphical() {

char OutputFile[200]="C:\Users\nvashkev\My_Projects\CAA_Model_Project\neuro\data\root_files"; //all it does is save the histogram
char imfolder[200]="C:\Users\nvashkev\My_Projects\CAA_Model_Project\neuro\data\run_images"; //must end in "/"
  
  //////////////////////////////////// ROOT PREP /////////////////////////////////////////////////
  gROOT->SetStyle("Plain"); 
  gStyle->SetOptStat(kFALSE);
  TFile * DATAFILE = (TFile *) gROOT->FindObject(OutputFile); 
  if(DATAFILE) DATAFILE->Close();
  DATAFILE = new TFile(OutputFile,"RECREATE");
  TH1F * structure_sizes=new TH1F("structure_sizes","Histogram of Bleed Sizes;Number of Pixels (natural log);Counts",24,0,12);
  TCanvas * c2 = new TCanvas ("c2","c2");
  structure_sizes->Draw();

  ////////////////////////////////// OPENGL PREP ////////////////////////////////////////////////
  // Setup environment and box objects
  cout << "\nSetting up OpenGL"<<endl;
  TCanvas * c1 = new TCanvas("glc","This Cycle",700,500);
  gSystem->Load("libGeom");
  TGeoManager * geom = new TGeoManager("boxtest", "Test of building boxes for neurons!");
  TGeoMaterial *matEmptySpace = new TGeoMaterial("EmptySpace", 0, 0, 0);
  TGeoMaterial *matBox        = new TGeoMaterial("Box"       , 0, 0, 0);
  TGeoMaterial *transBox      = new TGeoMaterial("Box"       , 0, 0, 0);
  transBox->SetTransparency(100);
  TGeoMedium *EmptySpace = new TGeoMedium("Empty", 1, matEmptySpace);
  TGeoMedium *medBox     = new TGeoMedium("medBox", 1, matBox);
  TGeoMedium *transMedBox= new TGeoMedium("transMedBox",1, transBox);
  TGeoVolume *top = geom->MakeBox("WORLD", EmptySpace, brainsize, brainsize, brainsize); 
  geom->SetTopVolume(top);
  TGeoVolume * redBox = geom->MakeBox("redBox",medBox,0.5,0.5,0.5);
  redBox->SetLineColor(kRed);
  TGeoVolume * blueBox = geom->MakeBox("blueBox",medBox,0.5,0.5,0.5);
  blueBox->SetLineColor(kBlue);
  TGeoBBox *bigBox    = new TGeoBBox("bigBox",viewsize,viewsize,viewsize);
  TGeoVolume * comp = new TGeoVolume("COMP",bigBox);
  comp->SetMedium(transMedBox);
  top->AddNode(comp,0);
  geom->SetVisLevel(0);
  top->Draw("ogl");
  int num_boxes=0;

  // Setup colors for the boxes
  gStyle->SetPalette(1);
  TGeoVolume * coloredBox[ncolors];
  char boxName[200];
  TVector3 col1(260,260,260);  //change if you want to alter box colors
  TVector3 col2(0,0,200);
  double temp_xyz[3];
  string opti;
  int nimg=0;
  for (int i=0;i<ncolors;i++) {
    TVector3 col(col1-col2);
    sprintf(boxName,"boxcolor_%i",i);
    coloredBox[i]=geom->MakeBox(boxName,medBox,0.5,0.5,0.5);
    col.SetMag(col.Mag()/double(ncolors)*double(i+1));
    col.GetXYZ(temp_xyz);
    for (int j=0;j<3;j++) temp_xyz[j]+=col2[j];
    sprintf(boxName,"boxcolor_%i",i);
    coloredBox[i]=geom->MakeBox(boxName,medBox,0.5,0.5,0.5);
    coloredBox[i]->SetLineColor(TColor::GetColor(int(temp_xyz[0]),int(temp_xyz[1]),int(temp_xyz[2])));
  }

  // Final setup, including annotation
  TGLViewer * view = (TGLViewer*)gPad->GetViewer3D();;
  char annName[200];
  sprintf(annName,"Bleed #%i, Size %i",1,1);
  TGLAnnotation * ann = new TGLAnnotation(view,annName,0.05,0.95);
  ann->SetTextSize(0.05);
  view->SetViewport(0,0,600,600); //may need to change if view problems

  cout<<"End Test"<<endl;
}