neurontracing_mip_plugin.cpp

/* neurontracing_mip_plugin.cpp
 * This is a test plugin, you can use it as a demo.
 * 2014-06-17 : by Zhi Zhou
 */
 
#include "v3d_message.h"
#include <vector>
#include "neurontracing_mip_plugin.h"
#include "my_surf_objs.h"
#include "smooth_curve.h"
#include "stackutil.h"
#include "volimg_proc.h"

//#include "../../../hackathon/zhi/APP2_large_scale/readRawfile_func.h"

#include "fastmarching_linker.h"

using namespace std;
Q_EXPORT_PLUGIN2(neurontracing_mip, neurontracing_mip);

struct Point;
struct Point
{
    double x,y,z,r;
    V3DLONG type;
    Point* p;
    V3DLONG childNum;
};

struct APP2_LS_PARA
{
    int is_gsdt;
    int is_break_accept;
    int  bkg_thresh;
    double length_thresh;
    int  cnn_type;
    int  channel;
    double SR_ratio;
    int  b_256cube;
    int b_RadiusFrom2D;
    int root_1st[3];
    int mip_plane; //0 for XY, 1 for XZ, 2 for YZ
    QString in_markerfile;
    int b_resample;
    int link_dist;
    QString out_file;

    Image4DSimple * image;

    QString inimg_file;
    QString mip_image_file;
};

typedef vector<Point*> Segment;
typedef vector<Point*> Tree;

void autotrace_largeScale_mip(V3DPluginCallback2 &callback, QWidget *parent,APP2_LS_PARA &p,bool bmenu);
void autotrace_largeScale_raw(V3DPluginCallback2 &callback, QWidget *parent,APP2_LS_PARA &p,bool bmenu);

QString getAppPath();

 
QStringList neurontracing_mip::menulist() const
{
	return QStringList() 
        <<tr("trace_mip")
		<<tr("about");
}

QStringList neurontracing_mip::funclist() const
{
	return QStringList()
        <<tr("trace_mip")
		<<tr("help");
}

bool saveSWC_file_TreMap(string swc_file, vector<MyMarker*> & outmarkers)
{
    if(swc_file.find_last_of(".dot") == swc_file.size() - 1) return saveDot_file(swc_file, outmarkers);

    cout<<"marker num = "<<outmarkers.size()<<", save swc file to "<<swc_file<<endl;
    map<MyMarker*, int> ind;
    ofstream ofs(swc_file.c_str());

    if(ofs.fail())
    {
        cout<<"open swc file error"<<endl;
        return false;
    }
    ofs<<"#name "<<"TreMap_Tracing"<<endl;
    ofs<<"#comment "<<endl;

    ofs<<"##n,type,x,y,z,radius,parent"<<endl;
    for(int i = 0; i < outmarkers.size(); i++) ind[outmarkers[i]] = i+1;

    for(int i = 0; i < outmarkers.size(); i++)
    {
        MyMarker * marker = outmarkers[i];
        int parent_id;
        if(marker->parent == 0) parent_id = -1;
        else parent_id = ind[marker->parent];
        if(parent_id == 0)  parent_id = -1;
        ofs<<i+1<<" "<<marker->type<<" "<<marker->x<<" "<<marker->y<<" "<<marker->z<<" "<<marker->radius<<" "<<parent_id<<endl;
    }
    ofs.close();
    return true;
}

void neurontracing_mip::domenu(const QString &menu_name, V3DPluginCallback2 &callback, QWidget *parent)
{
    if (menu_name == tr("trace_mip"))
	{
        APP2_LS_PARA P;
        bool bmenu = true;
        mipTracingeDialog dialog(callback, parent);
        if (!dialog.image)
            return;
      //  if(dialog.listLandmarks.count() ==0)
      //      return;

      //  LocationSimple tmpLocation(0,0,0);
      //  tmpLocation = dialog.listLandmarks.at(0);
      //  tmpLocation.getCoord(P.root_1st[0],P.root_1st[1],P.root_1st[2]);

        if (dialog.exec()!=QDialog::Accepted)
            return;
        P.inimg_file = dialog.image->getFileName();

        P.is_gsdt = dialog.is_gsdt;
        P.is_break_accept = dialog.is_break_accept;
        P.bkg_thresh = dialog.bkg_thresh;
        P.length_thresh = dialog.length_thresh;
        P.cnn_type = dialog.cnn_type;
        P.channel = dialog.channel;
        P.SR_ratio = dialog.SR_ratio;
        P.b_256cube = dialog.b_256cube;
        P.b_RadiusFrom2D = dialog.b_RadiusFrom2D;
        P.mip_plane = dialog.mip_plane;

        autotrace_largeScale_mip(callback,parent,P,bmenu);
    }
	else
	{
		v3d_msg(tr("This is a test plugin, you can use it as a demo.. "
			"Developed by Zhi Zhou, 2014-06-17"));
	}
}

bool neurontracing_mip::dofunc(const QString & func_name, const V3DPluginArgList & input, V3DPluginArgList & output, V3DPluginCallback2 & callback,  QWidget * parent)
{
    if (func_name == tr("trace_mip"))
	{
        APP2_LS_PARA P;
        bool bmenu = false;

        vector<char*> * pinfiles = (input.size() >= 1) ? (vector<char*> *) input[0].p : 0;
        vector<char*> * pparas = (input.size() >= 2) ? (vector<char*> *) input[1].p : 0;
        vector<char*>* outfiles = (output.size() >= 1) ? (vector<char*>*) output[0].p: 0;
        vector<char*> infiles = (pinfiles != 0) ? * pinfiles : vector<char*>();
        vector<char*> paras = (pparas != 0) ? * pparas : vector<char*>();

        P.inimg_file = infiles[0];
        P.out_file = outfiles != 0 ? outfiles->at(0): "";
        int k=0;
         //try to use as much as the default value in the PARA_APP2 constructor as possible
        P.in_markerfile = (paras.size() >= k+1) ? paras[k]: "NULL"; k++;
        P.mip_plane = (paras.size() >= k+1) ? atoi(paras[k]) : 0;  k++;
        P.channel = (paras.size() >= k+1) ? atoi(paras[k]) : 1;  k++;
        P.bkg_thresh = paras.size() >= k+1 ? atoi(paras[k]) : 10; k++;
        P.b_256cube = (paras.size() >= k+1) ? atoi(paras[k]) : 0; k++;
        P.is_gsdt = (paras.size() >= k+1) ? atoi(paras[k]) : 0; k++;
        P.is_break_accept = (paras.size() >= k+1) ? atoi(paras[k]) : 0; k++;
        P.length_thresh = (paras.size() >= k+1) ? atof(paras[k]) : 5; k++;
        P.b_resample = (paras.size() >= k+1) ? atoi(paras[k]) : 1; k++;
        P.link_dist = (paras.size() >= k+1) ? atoi(paras[k]) : 20; k++;

        P.cnn_type = 2;
        P.SR_ratio = 3.0/9.0;
        P.b_RadiusFrom2D = 1;
        autotrace_largeScale_mip(callback,parent,P,bmenu);

	}
//    else if (func_name == tr("trace_raw"))
//    {

//        APP2_LS_PARA P;
//        bool bmenu = false;

//        vector<char*> * pinfiles = (input.size() >= 1) ? (vector<char*> *) input[0].p : 0;
//        vector<char*> * pparas = (input.size() >= 2) ? (vector<char*> *) input[1].p : 0;
//        vector<char*> infiles = (pinfiles != 0) ? * pinfiles : vector<char*>();
//        vector<char*> paras = (pparas != 0) ? * pparas : vector<char*>();

//        P.inimg_file = infiles[0];
//        int k=0;
//         //try to use as much as the default value in the PARA_APP2 constructor as possible
//        P.mip_image_file = paras[0]; k++;
//        P.channel = (paras.size() >= k+1) ? atoi(paras[k]) : 1;  k++;
//        P.bkg_thresh = (paras.size() >= k+1) ? atoi(paras[k]) : 10; k++;
//        P.b_256cube = (paras.size() >= k+1) ? atoi(paras[k]) : 0; k++;
//        P.is_gsdt = (paras.size() >= k+1) ? atoi(paras[k]) : 0; k++;
//        P.is_break_accept = (paras.size() >= k+1) ? atoi(paras[k]) : 0; k++;
//        P.length_thresh = (paras.size() >= k+1) ? atof(paras[k]) : 5; k++;

//        P.cnn_type = 2;
//        P.SR_ratio = 3.0/9.0;
//        P.b_RadiusFrom2D = 1;

//        autotrace_largeScale_raw(callback,parent,P,bmenu);

//    }
	else if (func_name == tr("help"))
	{

        printf("\n**** Usage of TReMAP tracing ****\n");
        printf("vaa3d -x plugin_name -f trace_mip -i <inimg_file> -p <in_markerfile> <mip_plane> <channel> <bkg_thresh> <b_256cube> <is_gsdt> <is_gap> <length_thresh> <b_resample> <link_dist>\n");
        printf("inimg_file       Should be 8/16/32bit image\n");
        printf("in_markerfile    If no input marker file, please set this para to NULL and it will detect soma automatically. \n"
                       "         When the file is set, then the first marker is used as root/soma.\n");
        printf("mip_plane        Maximum projection plane, 0 for XY plane, 1 for XZ plane, 2 for YZ plane, Default 0\n");
        printf("channel          Data channel for tracing. Start from 1 (default 1).\n");
        printf("bkg_thresh       Default 10 (if specified as 0 then auto-thresolding)\n");

        printf("b_256cube        If trace in a auto-downsampled volume (1 for yes, and 0 for no. Default 0.)\n");
        printf("is_gsdt          If use gray-scale distance transform (1 for yes and 0 for no. Default 0.)\n");
        printf("is_gap           If allow gap (1 for yes and 0 for no. Default 0.)\n");
        printf("length_thresh    Default 5\n");
        printf("b_resample       Whether to do resample(1 for yes and 0 for no). Default 1\n");
        printf("link_dist        In the final sorting of swc, max dist gap between the broken nodes to be linked. Default 20.\n");

        printf("outswc_file      Will be named automatically based on the input image file name, so you don't have to specify it.\n\n");


	}
	else return false;

	return true;
}

void autotrace_largeScale_mip(V3DPluginCallback2 &callback, QWidget *parent,APP2_LS_PARA &Para,bool bmenu)
{
    unsigned char* data1d = 0;
    V3DLONG N,M,P,C;
    QString image_name = Para.inimg_file;

    if(bmenu)
    {
        v3dhandle curwin = callback.currentImageWindow();
        Image4DSimple* p4DImage = callback.getImage(curwin);
        data1d = p4DImage->getRawData();

        N = p4DImage->getXDim();
        M = p4DImage->getYDim();
        P = p4DImage->getZDim();
        C = p4DImage->getCDim();
    }
    else
    {
        V3DLONG im_sz[4];
        int datatype = 0;
        if (!simple_loadimage_wrapper(callback,image_name.toStdString().c_str(), data1d, im_sz, datatype))
        {
            fprintf (stderr, "Error happens in reading the subject file [%s]. Exit. \n",image_name.toStdString().c_str());
            return;
        }
        N = im_sz[0];
        M = im_sz[1];
        P = im_sz[2];
        C = im_sz[3];

    }

    double imgAve, imgStd;
    if (Para.bkg_thresh == 0)
    if (Para.channel > 0 && Para.channel <= C)
    {
        mean_and_std(data1d + N*M*P*(C-1), N*M*P, imgAve, imgStd);
        Para.bkg_thresh = imgAve+0.5*imgStd ; //(imgAve < imgStd)? imgAve : (imgAve+imgStd)*.5;
        printf("auto thr = %d\n", Para.bkg_thresh);
    }
    else
    {
        fprintf(stderr, "Channel out of range. Exit. \n");
        return;
    }

    int th = Para.bkg_thresh;
    QString tmpfolder = QFileInfo(image_name).path()+("/") + QFileInfo(image_name).completeBaseName()+("_tmp");
    system(qPrintable(QString("mkdir %1").arg(tmpfolder.toStdString().c_str())));
    if(tmpfolder.isEmpty())
    {

        printf("Can not create a tmp folder!\n");
        return;
    }

    //V3DLONG tmpx,tmpy,tmpz;
    //tmpx = Para.root_1st[0];
    //tmpy = Para.root_1st[1];
    //tmpz = Para.root_1st[2];

    V3DLONG mip_sz[3];
    mip_sz[0] = N;
    mip_sz[1] = M;
    mip_sz[2] = P;
    switch (Para.mip_plane)
    {
        case 0: mip_sz[2] = 1; break;
        case 1: mip_sz[1] = 1; break;
        case 2: mip_sz[0] = 1; break;
        default:
            return;
    }
    V3DLONG pagesz_mip = mip_sz[0]*mip_sz[1]*mip_sz[2];
    unsigned char *image_mip=0;
    try {image_mip = new unsigned char [pagesz_mip];}
    catch(...)  {v3d_msg("cannot allocate memory for image_mip.", bmenu); return;}

    switch (Para.mip_plane)
    {
        case 0:
                for(V3DLONG iy = 0; iy < M; iy++)
                {
                    V3DLONG offsetj = iy*N;
                    for(V3DLONG ix = 0; ix < N; ix++)
                    {
                        int max_mip = 0;
                        for(V3DLONG iz = 0; iz < P; iz++)
                        {
                            V3DLONG offsetk = iz*M*N;
                            if(data1d[offsetk + offsetj + ix] >= max_mip)
                            {
                                image_mip[iy*N + ix] = data1d[offsetk + offsetj + ix];
                                max_mip = data1d[offsetk + offsetj + ix];
                            }
                        }
                    }
                }
                break;
        case 1:
                for(V3DLONG iz = 0; iz < P; iz++)
                {
                    V3DLONG offsetk = iz*M*N;
                    for(V3DLONG ix = 0; ix < N; ix++)
                    {
                        int max_mip = 0;
                        for(V3DLONG iy = 0; iy < M; iy++)
                        {
                            V3DLONG offsetj = iy*N;
                            if(data1d[offsetk + offsetj + ix] >= max_mip)
                            {
                                image_mip[iz*N + ix] = data1d[offsetk + offsetj + ix];
                                max_mip = data1d[offsetk + offsetj + ix];
                            }
                        }
                    }
                }
                break;
        case 2:
                for(V3DLONG iz = 0; iz < P; iz++)
                {
                    V3DLONG offsetk = iz*M*N;
                    for(V3DLONG iy = 0; iy < M; iy++)
                    {
                        V3DLONG offsetj = iy*N;
                        int max_mip = 0;
                        for(V3DLONG ix = 0; ix < N; ix++)
                        {
                            if(data1d[offsetk + offsetj + ix] >= max_mip)
                            {
                                image_mip[iz*M + iy] = data1d[offsetk + offsetj + ix];
                                max_mip = data1d[offsetk + offsetj + ix];
                            }
                        }
                    }
                }
                break;
        default:
            return;
    }

    unsigned char *image_binary=0;
    try {image_binary = new unsigned char [pagesz_mip];}
    catch(...)  {v3d_msg("cannot allocate memory for image_binary.", bmenu); return;}
    for(V3DLONG i = 0; i < pagesz_mip; i++)
    {
        if(image_mip[i] > th)
            image_binary[i] = 255;
        else
            image_binary[i] = 0;
    }

    unsigned char *image_binary_median=0;
    try {image_binary_median = new unsigned char [pagesz_mip];}
    catch(...)  {v3d_msg("cannot allocate memory for image_binary_median.", bmenu); return;}

    int *arr,tmp;
    int ii,jj;
    int size = 3*3;
    arr = new int[size];

    for(V3DLONG iz = 0; iz < mip_sz[2]; iz++)
    {
        V3DLONG offsetk = iz*mip_sz[1]*mip_sz[0];
        for(V3DLONG iy = 0; iy < mip_sz[1]; iy++)
        {
            V3DLONG offsetj = iy*mip_sz[0];
            for(V3DLONG ix = 0; ix < mip_sz[0]; ix++)
            {

                V3DLONG xb = ix-1; if(xb<0) xb = 0;
                V3DLONG xe = ix+1; if(xe>=mip_sz[0]-1) xe = mip_sz[0]-1;
                V3DLONG yb = iy-1; if(yb<0) yb = 0;
                V3DLONG ye = iy+1; if(ye>=mip_sz[1]-1) ye = mip_sz[1]-1;
                V3DLONG zb = iz-1; if(zb<0) zb = 0;
                V3DLONG ze = iz+1; if(ze>=mip_sz[2]-1) ze = mip_sz[2]-1;
                ii = 0;

                for(V3DLONG k=zb; k<=ze; k++)
                {
                    V3DLONG offsetkl = k*mip_sz[1]*mip_sz[0];
                    for(V3DLONG j=yb; j<=ye; j++)
                    {
                        V3DLONG offsetjl = j*mip_sz[0];
                        for(V3DLONG i=xb; i<=xe; i++)
                        {
                            int dataval = image_binary[offsetkl + offsetjl + i];
                            arr[ii] = dataval;
                            if (ii>0)
                            {
                                jj = ii;
                                while(jj > 0 && arr[jj-1]>arr[jj])
                                {
                                    tmp = arr[jj];
                                    arr[jj] = arr[jj-1];
                                    arr[jj-1] = tmp;
                                    jj--;
                                }
                            }
                            ii++;
                        }
                    }
                }

                V3DLONG index_pim = offsetk + offsetj + ix;
                image_binary_median[index_pim] = arr[int(0.5*ii)+1];
            }
        }
    }


    if(image_binary) {delete []image_binary; image_binary = 0;}
    V3DLONG in_sz[4];
    in_sz[0] = N;
    in_sz[1] = M;
    in_sz[2] = P;
    in_sz[3] = 1;
    switch (Para.mip_plane)
    {
        case 0: in_sz[2] = 1; break;
        case 1: in_sz[1] = 1; break;
        case 2: in_sz[0] = 1; break;
        default:
            return;
    }
    QString input_image_name = tmpfolder + "/binary_median.raw";
    simple_saveimage_wrapper(callback, input_image_name.toStdString().c_str(),  (unsigned char *)image_binary_median, in_sz, V3D_UINT8);

    if(image_binary_median) {delete []image_binary_median; image_binary_median = 0;}

    QString output_image_name = tmpfolder +"/region.raw";

    #if  defined(Q_OS_LINUX)
        QString cmd_region = QString("%1/vaa3d -x regiongrow -f rg -i %2 -o %3 -p 1 0 1 400").arg(getAppPath().toStdString().c_str()).arg(input_image_name.toStdString().c_str()).arg(output_image_name.toStdString().c_str());
        system(qPrintable(cmd_region));
    #elif defined(Q_OS_MAC)
        QString cmd_region = QString("%1/vaa3d64.app/Contents/MacOS/vaa3d64 -x regiongrow -f rg -i %2 -o %3 -p 1 0 1 400").arg(getAppPath().toStdString().c_str()).arg(input_image_name.toStdString().c_str()).arg(output_image_name.toStdString().c_str());
        system(qPrintable(cmd_region));
    #else
        v3d_msg("The OS is not Linux or Mac. Do nothing.", bmenu);
        return;
    #endif

   unsigned char * image_region = 0;
   int datatype;
   V3DLONG in_zz[4];
   if(!simple_loadimage_wrapper(callback, output_image_name.toStdString().c_str(), image_region, in_zz, datatype))
   {
       v3d_msg("Fail to load image", bmenu);
       return;
   }

   int groupNum = 0;
   for(V3DLONG i = 0; i < pagesz_mip; i++)
   {
       if(image_region[i] > groupNum)
           groupNum = image_region[i];
   }

   int *groupArray = new int[groupNum];
   int *groupIndex = new int[groupNum];

   for(int i = 0; i < groupNum; i++)
   {
       groupArray[i] = 0;
       groupIndex[i] = i+1;
   }

   for(V3DLONG i = 0; i < pagesz_mip; i++)
   {
       if(image_region[i] > 0)
           groupArray[image_region[i] - 1] += 1;
   }

   int tmp_index;
   for(V3DLONG i = 0; i < groupNum; i++)
   {
       if (i > 0)
       {
           V3DLONG j = i;
           while(j > 0 && groupArray[j-1]<groupArray[j])
           {
               tmp = groupArray[j];
               groupArray[j] = groupArray[j-1];
               groupArray[j-1] = tmp;

               tmp_index = groupIndex[j];
               groupIndex[j] = groupIndex[j-1];
               groupIndex[j-1] = tmp_index;

               j--;
           }
       }
   }


   int groupmax = 30;
   if(groupNum <= groupmax) groupmax = groupNum;
   vector<MyMarker*> outswc_final;

   for(int dd = 0; dd < groupmax; dd++)
   {
       unsigned char *image_region_one = new unsigned char [pagesz_mip];
       V3DLONG group_type = groupIndex[dd];


       for(V3DLONG i = 0; i < pagesz_mip*datatype; i++)
       {

           if(image_region[i] == group_type)
               image_region_one[int(i/datatype)] = image_mip[int(i/datatype)];
           else
               image_region_one[int(i/datatype)] = 0;
       }

       /* switch (Para.mip_plane)
        {
            case 0: group_type = image_region[tmpy*N + tmpx]; break;
            case 1: group_type = image_region[tmpz*N + tmpx]; break;
            case 2: group_type = image_region[tmpz*M + tmpy];break;
            default:
                return;
        }


       tmpx /= groupArray[0];
       tmpy /= groupArray[0];
       tmpz = 0;

       v3d_msg(QString("x is %1 and y is %2").arg(tmpx).arg(tmpy));
       return;

       ImageMarker S;
       QList <ImageMarker> marklist;
       S.x = tmpx;
       S.y = tmpy;
       S.z = tmpz;
       switch (Para.mip_plane)
       {
           case 0: S.z = 0; break;
           case 1: S.y = 0; break;
           case 2: S.x = 0; break;
           default:
               return;
       }

       marklist.append(S);
       QString markerpath = tmpfolder +("/root.marker");
       writeMarker_file(markerpath.toStdString().c_str(),marklist);*/
       QString APP2_image_name = tmpfolder + "/group_one.raw";
       simple_saveimage_wrapper(callback, APP2_image_name.toStdString().c_str(),  (unsigned char *)image_region_one, in_sz, V3D_UINT8);
       if(image_region_one) {delete []image_region_one; image_region_one = 0;}
       QString APP2_swc =  APP2_image_name + QString("_group_%1.swc").arg(group_type);

        int thr = Para.bkg_thresh - 5;
        if (thr < 0) thr = 0;
        printf("app2_bkg_thr = %d\n", thr);
        #if  defined(Q_OS_LINUX)
            QString cmd_APP2 = QString("%1/vaa3d -x Vaa3D_Neuron2 -f app2 -i %2 -o %3 -p NULL %4 %5 %6 %7 %8 %9 %10 %11").arg(getAppPath().toStdString().c_str()).arg(APP2_image_name.toStdString().c_str()).arg(APP2_swc.toStdString().c_str())
                    .arg(Para.channel-1).arg(thr).arg(Para.b_256cube).arg(Para.b_RadiusFrom2D).arg(Para.is_gsdt).arg(Para.is_break_accept).arg(Para.length_thresh).arg(Para.b_resample);
            system(qPrintable(cmd_APP2));
            if (Para.b_resample)
            {
                QString cmd_resample = QString("%1/vaa3d -x resample_swc -f resample_swc -i %2 -o %3 -p 2").arg(getAppPath().toStdString().c_str()).arg(APP2_swc.toStdString().c_str()).arg(APP2_swc.toStdString().c_str());
                system(qPrintable(cmd_resample));
            }
        #elif defined(Q_OS_MAC)
            QString cmd_APP2 = QString("%1/vaa3d64.app/Contents/MacOS/vaa3d64 -x Vaa3D_Neuron2 -f app2 -i %2 -o %3 -p NULL %4 %5 %6 %7 %8 %9 %10 %11").arg(getAppPath().toStdString().c_str()).arg(APP2_image_name.toStdString().c_str()).arg(APP2_swc.toStdString().c_str())
                    .arg(Para.channel-1).arg(thr).arg(Para.b_256cube).arg(Para.b_RadiusFrom2D).arg(Para.is_gsdt).arg(Para.is_break_accept).arg(Para.length_thresh).arg(Para.b_resample);
            system(qPrintable(cmd_APP2));
            if (Para.b_resample)
            {
                system(qPrintable(cmd_resample));
                QString cmd_resample = QString("%1//vaa3d64.app/Contents/MacOS/vaa3d64 -x resample_swc -f resample_swc -i %2 -o %3 -p 2").arg(getAppPath().toStdString().c_str()).arg(APP2_swc.toStdString().c_str()).arg(APP2_swc.toStdString().c_str());
            }
        #else
                 v3d_msg("The OS is not Linux or Mac. Do nothing.", bmenu);
                 return;
        #endif

       /*QString APP2_swc;
       switch (Para.mip_plane)
       {
           case 0: APP2_swc = APP2_image_name + QString("_x%1_y%2_z%3_app2.swc").arg(S.x-1).arg(S.y-1).arg(S.z); break;
           case 1: APP2_swc = APP2_image_name + QString("_x%1_y%2_z%3_app2.swc").arg(S.x-1).arg(S.y).arg(S.z-1); break;
           case 2: APP2_swc = APP2_image_name + QString("_x%1_y%2_z%3_app2.swc").arg(S.x).arg(S.y-1).arg(S.z-1); break;
           default:
               return;
       }*/

       NeuronTree nt = readSWC_file(APP2_swc);

       V3DLONG siz = nt.listNeuron.size();
       Tree tree;
       for (V3DLONG i=0;i<siz;i++)
       {
           NeuronSWC s = nt.listNeuron[i];
           Point* pt = new Point;
           pt->x = s.x;
           pt->y = s.y;
           pt->z = s.z;
           pt->r = s.r;
           pt ->type = s.type;
           pt->p = NULL;
           pt->childNum = 0;
           tree.push_back(pt);
       }
       for (V3DLONG i=0;i<siz;i++)
       {
           if (nt.listNeuron[i].pn<0) continue;
           V3DLONG pid = nt.hashNeuron.value(nt.listNeuron[i].pn);
           tree[i]->p = tree[pid];
           tree[pid]->childNum++;
       }
    //	printf("tree constructed.\n");
       vector<Segment*> seg_list;
       for (V3DLONG i=0;i<siz;i++)
       {
           if (tree[i]->childNum!=1)//tip or branch point
           {
               Segment* seg = new Segment;
               Point* cur = tree[i];
               do
               {
                   seg->push_back(cur);
                   cur = cur->p;
               }
               while(cur && cur->childNum==1);
               seg_list.push_back(seg);
           }
       }
       vector<MyMarker*> outswc;

       for (V3DLONG i=0;i<seg_list.size();i++)
       {
           vector<MyMarker> nearpos_vec, farpos_vec; // for near/far locs testing
           nearpos_vec.clear();
           farpos_vec.clear();
           if(seg_list[i]->size() > 2)
           {
               for (V3DLONG j=0;j<seg_list[i]->size();j++)
               {
                   Point* node = seg_list[i]->at(j);
                   XYZ loc0_t, loc1_t;
                   loc0_t = XYZ(node->x, node->y,  node->z);
                   switch (Para.mip_plane)
                   {
                       case 0:  loc1_t = XYZ(node->x, node->y,  P-1); break;
                       case 1:  loc1_t = XYZ(node->x, M-1,  node->z); break;
                       case 2:  loc1_t = XYZ(N-1, node->y,  node->z); break;
                       default:
                           return;
                   }

                   XYZ loc0 = loc0_t;
                   XYZ loc1 = loc1_t;

                   nearpos_vec.push_back(MyMarker(loc0.x, loc0.y, loc0.z));
                   farpos_vec.push_back(MyMarker(loc1.x, loc1.y, loc1.z));
               }

               fastmarching_drawing_dynamic(nearpos_vec, farpos_vec, (unsigned char*)data1d, outswc, N,M,P, 1, 5);
             //  smooth_curve(outswc,5);


               for(V3DLONG d = 0; d <outswc.size(); d++)
               {
                   outswc[d]->radius = 2;
                   outswc[d]->type = dd + 2;
                   outswc_final.push_back(outswc[d]);

               }
               outswc.clear();

           }
           else if(seg_list[i]->size() == 2)
           {
               Point* node1 = seg_list[i]->at(0);
               Point* node2 = seg_list[i]->at(1);

               for (V3DLONG j=0;j<3;j++)
               {
                   XYZ loc0_t, loc1_t;
                   if(j ==0)
                   {
                       loc0_t = XYZ(node1->x, node1->y,  node1->z);
                       switch (Para.mip_plane)
                       {
                           case 0:  loc1_t = XYZ(node1->x, node1->y,  P-1); break;
                           case 1:  loc1_t = XYZ(node1->x, M-1,  node1->z); break;
                           case 2:  loc1_t = XYZ(N-1, node1->y,  node1->z); break;
                           default:
                               return;
                       }
                   }
                   else if(j ==1)
                   {
                       loc0_t = XYZ(0.5*(node1->x + node2->x), 0.5*(node1->y + node2->y),  0.5*(node1->z + node2->z));
                       switch (Para.mip_plane)
                       {
                           case 0:  loc1_t = XYZ(0.5*(node1->x + node2->x),  0.5*(node1->y + node2->y),  P-1); break;
                           case 1:  loc1_t = XYZ(0.5*(node1->x + node2->x), M-1,   0.5*(node1->z + node2->z)); break;
                           case 2:  loc1_t = XYZ(N-1,  0.5*(node1->y + node2->y),   0.5*(node1->z + node2->z)); break;
                           default:
                               return;
                       }
                   }
                   else
                   {
                       loc0_t = XYZ(node2->x, node2->y,  node2->z);
                       switch (Para.mip_plane)
                       {
                           case 0:  loc1_t = XYZ(node2->x, node2->y,  P-1); break;
                           case 1:  loc1_t = XYZ(node2->x, M-1,  node2->z); break;
                           case 2:  loc1_t = XYZ(N-1, node2->y,  node2->z); break;
                           default:
                               return;
                       }               }

                   XYZ loc0 = loc0_t;
                   XYZ loc1 = loc1_t;

                   nearpos_vec.push_back(MyMarker(loc0.x, loc0.y, loc0.z));
                   farpos_vec.push_back(MyMarker(loc1.x, loc1.y, loc1.z));
                }

               fastmarching_drawing_dynamic(nearpos_vec, farpos_vec, (unsigned char*)data1d, outswc, N,M,P, 1, 5);
             //  smooth_curve(outswc,5);


               for(V3DLONG d = 0; d <outswc.size(); d++)
               {
                   outswc[d]->radius = 2;
                   outswc[d]->type = dd + 2;
                   outswc_final.push_back(outswc[d]);

               }
               outswc.clear();
           }
       }
       // clear
       for (int i = 0; i < seg_list.size(); ++i)
       {
           if (seg_list[i])
           {
               delete seg_list[i];
               seg_list[i] = NULL;
           }
       }
       for (int i = 0; i < tree.size(); ++i)
       {
           if (tree[i])
           {
               delete tree[i];
               tree[i] = NULL;
           }
       }
//       QString group_swc = tmpfolder + QString("/raw_%1.swc").arg(dd);
//       saveSWC_file(group_swc.toStdString(), outswc_final);
//       outswc_final.clear();
    }

   if(image_mip) {delete []image_mip; image_mip = 0;}
   if(image_region) {delete []image_region; image_region = 0;}
   if(groupArray) {delete []groupArray; groupArray = 0;}
   if(groupIndex) {delete []groupIndex; groupIndex = 0;}

   QString swc_2D,final_swc;
   if (Para.out_file != "")
       final_swc = Para.out_file;
   else
       switch (Para.mip_plane)
       {
           case 0: swc_2D = image_name + "_XY_2D_mip.swc"; final_swc = image_name + "_XY_3D_TreMap.swc"; break;
           case 1: swc_2D = image_name + "_XZ_2D_mip.swc"; final_swc = image_name + "_XZ_3D_TreMap.swc"; break;
           case 2: swc_2D = image_name + "_YZ_2D_mip.swc"; final_swc = image_name + "_YZ_3D_TreMap.swc"; break;
           default:
               return;
       }

   saveSWC_file(final_swc.toStdString(), outswc_final);
   outswc_final.clear();


   // system(qPrintable(QString("mv %1 %2").arg(APP2_swc.toStdString().c_str()).arg(swc_2D.toStdString().c_str())));
   system(qPrintable(QString("rm -r %1").arg(tmpfolder.toStdString().c_str())));

   V3DPluginArgItem arg;
   V3DPluginArgList input_resample;
   V3DPluginArgList input_sort;
   V3DPluginArgList output;
    std:: string fileName_Qstring(final_swc.toStdString());char* fileName_string =  new char[fileName_Qstring.length() + 1]; strcpy(fileName_string, fileName_Qstring.c_str());

   if (Para.b_resample)
   {
       arg.type = "random";std::vector<char*> arg_input_resample;
       arg_input_resample.push_back(fileName_string);
       arg.p = (void *) & arg_input_resample; input_resample<< arg;
       arg.type = "random";std::vector<char*> arg_resample_para; arg_resample_para.push_back("10");arg.p = (void *) & arg_resample_para; input_resample << arg;
       arg.type = "random";std::vector<char*> arg_output;arg_output.push_back(fileName_string); arg.p = (void *) & arg_output; output<< arg;

       QString full_plugin_name_resample = "resample_swc";
       QString func_name_resample = "resample_swc";
       callback.callPluginFunc(full_plugin_name_resample,func_name_resample,input_resample,output);
   }
   int minn = -1;
   if(Para.in_markerfile != "NULL")
   {

       vector<MyMarker> file_inmarkers = readMarker_file(string(qPrintable(Para.in_markerfile)));
       vector<LocationSimple> landmarks;
       LocationSimple t;
       for(int i = 0; i < file_inmarkers.size(); i++)
       {
           t.x = file_inmarkers[i].x;
           t.y = file_inmarkers[i].y;
           t.z = file_inmarkers[i].z;
           if(t.x<0 || t.x>=N || t.y<0 || t.y>=M || t.z<0 || t.z>=P)
           {
               if(i==0)
               {
                   v3d_msg("The first marker is invalid.", bmenu);
                   return;
               }
               else continue;
           }
           landmarks.push_back(t);
       }
       if (landmarks.size() > 0)
       {
           t = landmarks[0];
           NeuronTree nt = readSWC_file(final_swc);
           float mindist = 0;
           for (int i = 0; i < nt.listNeuron.size(); ++i)
           {
                float xx = t.x - nt.listNeuron[i].x;
                float yy = t.y - nt.listNeuron[i].y;
                float zz = t.z - nt.listNeuron[i].z;
                float dist = xx * xx + yy * yy + zz * zz;
                if (dist < mindist || minn == -1)
                {
                    mindist = dist;
                    minn = nt.listNeuron[i].n;
                }
           }
       }
   }

   arg.type = "random";std::vector<char*> arg_input_sort;
   arg_input_sort.push_back(fileName_string);
   arg.p = (void *) & arg_input_sort; input_sort<< arg;
   arg.type = "random";std::vector<char*> arg_sort_para;
   QString link_dist = QString::number(Para.link_dist);
   char* link_dist_str = new char[link_dist.length() + 1];
   strcpy(link_dist_str, link_dist.toStdString().c_str());
   arg_sort_para.push_back(link_dist_str);
   QString minn_qs = QString::number(minn);
   char* minn_str = new char[minn_qs.length() + 1];
   if (minn != -1)
   {
       strcpy(minn_str, minn_qs.toStdString().c_str());
       arg_sort_para.push_back(minn_str);
   }
   arg.p = (void *) & arg_sort_para; input_sort << arg;
   arg.type = "random";std::vector<char*> arg_output;arg_output.push_back(fileName_string); arg.p = (void *) & arg_output; output<< arg;
   QString full_plugin_name_sort = "sort_neuron_swc";
   QString func_name_sort = "sort_swc";
   callback.callPluginFunc(full_plugin_name_sort,func_name_sort, input_sort,output);

   vector<MyMarker*> temp_out_swc = readSWC_file(final_swc.toStdString());
   saveSWC_file_TreMap(final_swc.toStdString(), temp_out_swc);
   temp_out_swc.clear();
   if (link_dist_str)
   {
       delete [] link_dist_str;
       link_dist_str = NULL;
   }
   if (minn_str)
   {
       delete [] minn_str;
       minn_str = NULL;
   }
   if(!bmenu)
   {
       if(data1d) {delete []data1d; data1d = 0;}
   }

   if (fileName_string)
   {
       delete [] fileName_string;
       fileName_string = NULL;
   }
   v3d_msg(QString("Now you can drag and drop the generated swc fle [%1] into Vaa3D.").arg(final_swc.toStdString().c_str()),bmenu);

   return;
}

//void autotrace_largeScale_raw(V3DPluginCallback2 &callback, QWidget *parent,APP2_LS_PARA &Para,bool bmenu)
//{
//    QString image_name = Para.inimg_file;
//    QString image_mip_name = Para.mip_image_file;

//    unsigned char *image_mip=0;
//    V3DLONG *im_sz = 0;
//    int datatype = 0;
//    if (loadImage(const_cast<char *>(image_mip_name.toStdString().c_str()), image_mip, im_sz, datatype)!=true)
//    {
//        fprintf (stderr, "Error happens in reading the subject file [%s]. Exit. \n",image_name.toStdString().c_str());
//        return;
//    }

//    QString tmpfolder = QFileInfo(image_name).path()+("/") + QFileInfo(image_name).completeBaseName()+("_tmp");
//    system(qPrintable(QString("mkdir %1").arg(tmpfolder.toStdString().c_str())));
//    if(tmpfolder.isEmpty())
//    {

//        printf("Can not create a tmp folder!\n");
//        return;
//    }

//    QString output_image_name = tmpfolder +"/region.raw";

//    #if  defined(Q_OS_LINUX)
//    QString cmd_region = QString("%1/vaa3d -x regiongrow -f rg -i %2 -o %3 -p 1 2 1 200 %4").arg(getAppPath().toStdString().c_str()).arg(image_mip_name.toStdString().c_str()).arg(output_image_name.toStdString().c_str()).arg(Para.bkg_thresh);
//        system(qPrintable(cmd_region));
//    #elif defined(Q_OS_MAC)
//        QString cmd_region = QString("%1/vaa3d64.app/Contents/MacOS/vaa3d64 -x regiongrow -f rg -i %2 -o %3 -p 1 2 1 200 %4").arg(getAppPath().toStdString().c_str()).arg(image_mip_name.toStdString().c_str()).arg(output_image_name.toStdString().c_str()).arg(Para.bkg_thresh);
//        system(qPrintable(cmd_region));
//    #else
//        v3d_msg("The OS is not Linux or Mac. Do nothing.");
//        return;
//    #endif

//    unsigned char * image_region = 0;
//    V3DLONG in_zz[4];
//    if(!simple_loadimage_wrapper(callback, output_image_name.toStdString().c_str(), image_region, in_zz, datatype))
//    {
//       v3d_msg("Fail to load image");
//       return;
//    }

//    V3DLONG pagesz_mip = in_zz[0]*in_zz[1]*in_zz[2];
//    int groupNum = 0;
//    for(V3DLONG i = 0; i < pagesz_mip; i++)
//    {
//        if(image_region[i] > groupNum)
//            groupNum = image_region[i];
//    }

//    int *groupArray = new int[groupNum];
//    int *groupIndex = new int[groupNum];

//    for(int i = 0; i < groupNum; i++)
//    {
//        groupArray[i] = 0;
//        groupIndex[i] = i+1;
//    }

//    for(V3DLONG i = 0; i < pagesz_mip; i++)
//    {
//        if(image_region[i] > 0)
//            groupArray[image_region[i] - 1] += 1;
//    }

//    int tmp_index,tmp;
//    for(V3DLONG i = 0; i < groupNum; i++)
//    {
//        if (i > 0)
//        {
//            V3DLONG j = i;
//            while(j > 0 && groupArray[j-1]<groupArray[j])
//            {
//                tmp = groupArray[j];
//                groupArray[j] = groupArray[j-1];
//                groupArray[j-1] = tmp;

//                tmp_index = groupIndex[j];
//                groupIndex[j] = groupIndex[j-1];
//                groupIndex[j-1] = tmp_index;

//                j--;
//            }
//        }
//    }


//    int groupmax = 5;
//    if(groupNum <= groupmax) groupmax = groupNum;
//    vector<MyMarker*> outswc_final;
//    for(int dd = 0; dd < groupmax; dd++)
//    {
//        unsigned char *image_region_one = new unsigned char [pagesz_mip];
//        V3DLONG group_type = groupIndex[dd];


//        for(V3DLONG i = 0; i < pagesz_mip*datatype; i++)
//        {

//            if(image_region[i] == group_type)
//                image_region_one[int(i/datatype)] = image_mip[int(i/datatype)];
//            else
//                image_region_one[int(i/datatype)] = 0;
//        }

//        QString APP2_image_name = tmpfolder + "/group_one.raw";
//        simple_saveimage_wrapper(callback, APP2_image_name.toStdString().c_str(),  (unsigned char *)image_region_one, im_sz, V3D_UINT8);
//        if(image_region_one) {delete []image_region_one; image_region_one = 0;}

//        QString APP2_swc =  APP2_image_name + QString("_group_%1.swc").arg(group_type);


//#if  defined(Q_OS_LINUX)
//        QString cmd_APP2 = QString("%1/vaa3d -x Vaa3D_Neuron2 -f app2 -i %2 -o %3 -p NULL %4 %5 %6 %7 %8 %9 %10").arg(getAppPath().toStdString().c_str()).arg(APP2_image_name.toStdString().c_str()).arg(APP2_swc.toStdString().c_str())
//                .arg(Para.channel-1).arg(Para.bkg_thresh - 5).arg(Para.b_256cube).arg(Para.b_RadiusFrom2D).arg(Para.is_gsdt).arg(Para.is_break_accept).arg(Para.length_thresh);
//        system(qPrintable(cmd_APP2));
//        QString cmd_resample = QString("%1/vaa3d -x resample_swc -f resample_swc -i %2 -o %3 -p 2").arg(getAppPath().toStdString().c_str()).arg(APP2_swc.toStdString().c_str()).arg(APP2_swc.toStdString().c_str());
//        system(qPrintable(cmd_resample));
//#elif defined(Q_OS_MAC)
//        QString cmd_APP2 = QString("%1/vaa3d64.app/Contents/MacOS/vaa3d64 -x Vaa3D_Neuron2 -f app2 -i %2 -o %3 -p NULL %4 %5 %6 %7 %8 %9 %10").arg(getAppPath().toStdString().c_str()).arg(APP2_image_name.toStdString().c_str()).arg(APP2_swc.toStdString().c_str())
//                .arg(Para.channel-1).arg(Para.bkg_thresh - 5).arg(Para.b_256cube).arg(Para.b_RadiusFrom2D).arg(Para.is_gsdt).arg(Para.is_break_accept).arg(Para.length_thresh);
//        system(qPrintable(cmd_APP2));
//        QString cmd_resample = QString("%1//vaa3d64.app/Contents/MacOS/vaa3d64 -x resample_swc -f resample_swc -i %2 -o %3 -p 2").arg(getAppPath().toStdString().c_str()).arg(APP2_swc.toStdString().c_str()).arg(APP2_swc.toStdString().c_str());
//        system(qPrintable(cmd_resample));
//#else
//        v3d_msg("The OS is not Linux or Mac. Do nothing.");
//        return;
//#endif
//        NeuronTree nt = readSWC_file(APP2_swc);

//        V3DLONG siz = nt.listNeuron.size();
//        Tree tree;
//        for (V3DLONG i=0;i<siz;i++)
//        {
//            NeuronSWC s = nt.listNeuron[i];
//            Point* pt = new Point;
//            pt->x = s.x;
//            pt->y = s.y;
//            pt->z = s.z;
//            pt->r = s.r;
//            pt ->type = s.type;
//            pt->p = NULL;
//            pt->childNum = 0;
//            tree.push_back(pt);
//        }
//        for (V3DLONG i=0;i<siz;i++)
//        {
//            if (nt.listNeuron[i].pn<0) continue;
//            V3DLONG pid = nt.hashNeuron.value(nt.listNeuron[i].pn);
//            tree[i]->p = tree[pid];
//            tree[pid]->childNum++;
//        }
//     //	printf("tree constructed.\n");
//        vector<Segment*> seg_list;
//        for (V3DLONG i=0;i<siz;i++)
//        {
//            if (tree[i]->childNum!=1)//tip or branch point
//            {
//                Segment* seg = new Segment;
//                Point* cur = tree[i];
//                do
//                {
//                    seg->push_back(cur);
//                    cur = cur->p;
//                }
//                while(cur && cur->childNum==1);
//                seg_list.push_back(seg);
//            }
//        }

//        vector<MyMarker*> outswc;

//        unsigned char * data1d = 0;
//        V3DLONG *im3D_zz = 0;
//        V3DLONG *im3D_sz = 0;

//        int datatype;
//        if (!loadRawRegion(const_cast<char *>(image_name.toStdString().c_str()), data1d, im3D_zz, im3D_sz,datatype,0,0,0,1,1,1))
//        {
//            return;
//        }

//        if(data1d) {delete []data1d; data1d = 0;}
//        V3DLONG N = im3D_zz[0];
//        V3DLONG M = im3D_zz[1];
//        V3DLONG P = im3D_zz[2];


//        for (V3DLONG i=0;i<seg_list.size();i++)
//        {
//            V3DLONG xb = N-1;
//            V3DLONG xe = 0;
//            V3DLONG yb = M-1;
//            V3DLONG ye = 0;

//            for (V3DLONG j=0;j<seg_list[i]->size();j++)
//            {
//                Point* node = seg_list[i]->at(j);
//                if(node->x < xb) xb = node->x;
//                if(node->x > xe) xe = node->x;
//                if(node->y < yb) yb = node->y;
//                if(node->y > ye) ye = node->y;
//            }

//            vector<MyMarker> nearpos_vec, farpos_vec; // for near/far locs testing
//            nearpos_vec.clear();
//            farpos_vec.clear();
//            if(seg_list[i]->size() > 2)
//            {
//                for (V3DLONG j=0;j<seg_list[i]->size();j++)
//                {
//                    Point* node = seg_list[i]->at(j);
//                    XYZ loc0_t, loc1_t;
//                    loc0_t = XYZ(node->x, node->y,  node->z);
//                    loc1_t = XYZ(node->x, node->y,  P-1);
//                    XYZ loc0 = loc0_t;
//                    XYZ loc1 = loc1_t;

//                    nearpos_vec.push_back(MyMarker(loc0.x - xb, loc0.y - yb, loc0.z));
//                    farpos_vec.push_back(MyMarker(loc1.x - xb, loc1.y - yb, loc1.z));
//                }

//                if (!loadRawRegion(const_cast<char *>(image_name.toStdString().c_str()), data1d, im3D_zz, im3D_sz,datatype,xb,yb,0,xe+1,ye+1,P))
//                {
//                    printf("can not load the region");
//                    if(data1d) {delete []data1d; data1d = 0;}
//                    return;
//                }

//                fastmarching_drawing_dynamic(nearpos_vec, farpos_vec, (unsigned char*)data1d, outswc, xe-xb+1,ye-yb+1,P, 1, 5);
//             //   smooth_curve(outswc,5);

//                for(V3DLONG d = 0; d <outswc.size(); d++)
//                {
//                    outswc[d]->radius = 2;
//                    outswc[d]->type = dd + 2;
//                    outswc[d]->x = outswc[d]->x + xb;
//                    outswc[d]->y = outswc[d]->y + yb;
//                    outswc_final.push_back(outswc[d]);
//                }
//                if(data1d) {delete []data1d; data1d = 0;}
//                outswc.clear();
//            }
//            else if(seg_list[i]->size() == 2)
//            {
//                Point* node1 = seg_list[i]->at(0);
//                Point* node2 = seg_list[i]->at(1);

//                for (V3DLONG j=0;j<3;j++)
//                {
//                    XYZ loc0_t, loc1_t;
//                    if(j ==0)
//                    {
//                        loc0_t = XYZ(node1->x, node1->y,  node1->z);
//                        loc1_t = XYZ(node1->x, node1->y,  P-1);
//                    }
//                    else if(j ==1)
//                    {
//                        loc0_t = XYZ(0.5*(node1->x + node2->x), 0.5*(node1->y + node2->y),  0.5*(node1->z + node2->z));
//                        loc1_t = XYZ(0.5*(node1->x + node2->x),  0.5*(node1->y + node2->y),  P-1);

//                    }
//                    else
//                    {
//                        loc0_t = XYZ(node2->x, node2->y,  node2->z);
//                        loc1_t = XYZ(node2->x, node2->y,  P-1);
//                    }

//                    XYZ loc0 = loc0_t;
//                    XYZ loc1 = loc1_t;

//                    nearpos_vec.push_back(MyMarker(loc0.x - xb, loc0.y - yb, loc0.z));
//                    farpos_vec.push_back(MyMarker(loc1.x - xb, loc1.y - yb, loc1.z));
//                 }

//                if (!loadRawRegion(const_cast<char *>(image_name.toStdString().c_str()), data1d, im3D_zz, im3D_sz,datatype,xb,yb,0,xe+1,ye+1,P))
//                {
//                    printf("can not load the region");
//                    if(data1d) {delete []data1d; data1d = 0;}
//                    return;
//                }

//                fastmarching_drawing_dynamic(nearpos_vec, farpos_vec, (unsigned char*)data1d, outswc, xe-xb+1,ye-yb+1,P, 1, 5);
//               // smooth_curve(outswc,5);


//                for(V3DLONG d = 0; d <outswc.size(); d++)
//                {
//                    outswc[d]->radius = 2;
//                    outswc[d]->type = dd + 2;
//                    outswc[d]->x = outswc[d]->x + xb;
//                    outswc[d]->y = outswc[d]->y + yb;
//                    outswc_final.push_back(outswc[d]);
//                }
//                if(data1d) {delete []data1d; data1d = 0;}
//                outswc.clear();

//            }
////            QString APP2_image_name = tmpfolder +  QString("/raw_%1.raw").arg(i);
////            simple_saveimage_wrapper(callback, APP2_image_name.toStdString().c_str(),  (unsigned char *)data1d, im3D_sz, V3D_UINT8);
////            QString final_swc = tmpfolder + QString("/raw_%1.swc").arg(i);
////            saveSWC_file(final_swc.toStdString(), outswc_final);
////            outswc_final.clear();

//        }
//  //      return;

//    }

//    QString final_swc = image_name + "_raw_3D_TreMap.swc";
//   // system(qPrintable(QString("rm -r %1").arg(tmpfolder.toStdString().c_str())));

//    saveSWC_file(final_swc.toStdString(), outswc_final);

//    V3DPluginArgItem arg;
//    V3DPluginArgList input_resample;
//    V3DPluginArgList input_sort;
//    V3DPluginArgList output;

//    arg.type = "random";std::vector<char*> arg_input_resample;
//    std:: string fileName_Qstring(final_swc.toStdString());char* fileName_string =  new char[fileName_Qstring.length() + 1]; strcpy(fileName_string, fileName_Qstring.c_str());
//    arg_input_resample.push_back(fileName_string);
//    arg.p = (void *) & arg_input_resample; input_resample<< arg;
//    arg.type = "random";std::vector<char*> arg_resample_para; arg_resample_para.push_back("10");arg.p = (void *) & arg_resample_para; input_resample << arg;
//    arg.type = "random";std::vector<char*> arg_output;arg_output.push_back(fileName_string); arg.p = (void *) & arg_output; output<< arg;

//    QString full_plugin_name_resample = "resample_swc";
//    QString func_name_resample = "resample_swc";
//    callback.callPluginFunc(full_plugin_name_resample,func_name_resample,input_resample,output);

//    arg.type = "random";std::vector<char*> arg_input_sort;
//    arg_input_sort.push_back(fileName_string);
//    arg.p = (void *) & arg_input_sort; input_sort<< arg;
//    arg.type = "random";std::vector<char*> arg_sort_para; arg_sort_para.push_back("20");arg.p = (void *) & arg_sort_para; input_sort << arg;
//    QString full_plugin_name_sort = "sort_neuron_swc";
//    QString func_name_sort = "sort_swc";
//    callback.callPluginFunc(full_plugin_name_sort,func_name_sort, input_sort,output);

//    vector<MyMarker*> temp_out_swc = readSWC_file(final_swc.toStdString());
//    saveSWC_file_TreMap(final_swc.toStdString(), temp_out_swc);

//    v3d_msg(QString("Now you can drag and drop the generated swc fle [%1] into Vaa3D.").arg(final_swc.toStdString().c_str()),bmenu);

//    return;
//}

QString getAppPath()
{
    QString v3dAppPath("~/Work/v3d_external/v3d");
    QDir testPluginsDir = QDir(qApp->applicationDirPath());

#if defined(Q_OS_WIN)
    if (testPluginsDir.dirName().toLower() == "debug" || testPluginsDir.dirName().toLower() == "release")
        testPluginsDir.cdUp();
#elif defined(Q_OS_MAC)
    if (testPluginsDir.dirName() == "MacOS") {
        QDir testUpperPluginsDir = testPluginsDir;
        testUpperPluginsDir.cdUp();
        testUpperPluginsDir.cdUp();
        testUpperPluginsDir.cdUp(); // like foo/plugins next to foo/v3d.app
        if (testUpperPluginsDir.cd("plugins")) testPluginsDir = testUpperPluginsDir;
        testPluginsDir.cdUp();
    }
#endif

    v3dAppPath = testPluginsDir.absolutePath();
    return v3dAppPath;
}