void GVFplugin::domenu(const QString &menu_name, V3DPluginCallback2 &callback, QWidget *parent)
{
if (menu_name == tr("Gradient vector flow based Segmentation"))
{
// the GVF function wants a pointer to a Vol3DSimple, which I haven't seen before.
// this code below generates it (take from plugin_FL_cellseg)
// check what's up with the current window: is there a valid image pointer?
v3dhandle curwin = callback.currentImageWindow();
if (!curwin)
{
v3d_msg("Please open an image.");
return;
}
Image4DSimple* subject = callback.getImage(curwin);
QString m_InputFileName = callback.getImageName(curwin);
if (!subject)
{
QMessageBox::information(0, "", QObject::tr("No image is open."));
return;
}
if (subject->getDatatype()!=V3D_UINT8)
{
QMessageBox::information(0, "", QObject::tr("This demo program only supports 8-bit data. Your current image data type is not supported."));
return;
}
V3DLONG sz0 = subject->getXDim();
V3DLONG sz1 = subject->getYDim();
V3DLONG sz2 = subject->getZDim();
V3DLONG sz3 = subject->getCDim();
Image4DProxy<Image4DSimple> pSub(subject);
V3DLONG channelsz = sz0*sz1*sz2;
float *pLabel = 0;
unsigned char *pData = 0;
gvfsegPara segpara; // set these fields one at a time:
segpara.diffusionIteration= 5;
segpara.fusionThreshold = 10;
segpara.minRegion = 10;
segpara.sigma = 3; // doesn't seem to be used in the actual function?
//input parameters
bool ok1;
int c=1;
if (sz3>1) //only need to ask if more than one channel
{
c = QInputDialog::getInteger(parent, "Channel",
"Choose channel for segmentation:",
1, 1, sz3, 1, &ok1);
c = c-1; //channels are indexed to 0 in Image4DSimple->getRawDataAtChannel
if (!ok1)
return;
}
// read in parameters
segpara.diffusionIteration = QInputDialog::getInteger(parent, "Diffusion Iterations",
"Choose Number of Diffusion Iterations:",
5, 1, 10, 1, &ok1);
if (!ok1)
return;
segpara.fusionThreshold = QInputDialog::getInteger(parent, "Fusion Threshold",
"Choose Fusion Threshold :",
2, 1, 10, 1, &ok1);
if (!ok1)
return;
segpara.minRegion= QInputDialog::getInteger(parent, "Minimum Region",
"Choose Minimum Region Size (voxels):",
10, 1, 1000, 1, &ok1);
if (!ok1)
return;
// allocate memory for the images
Vol3DSimple <unsigned char> * tmp_inimg = 0;
Vol3DSimple <USHORTINT16> * tmp_outimg = 0;
try
{
tmp_inimg = new Vol3DSimple <unsigned char> (sz0, sz1, sz2);
tmp_outimg = new Vol3DSimple <USHORTINT16> (sz0, sz1, sz2);
}
catch (...)
{
v3d_msg("Unable to allocate memory for processing.");
if (tmp_inimg) {delete tmp_inimg; tmp_inimg=0;}
if (tmp_outimg) {delete tmp_outimg; tmp_outimg=0;}
return;
}
//copy image data into our new memory
memcpy((void *)tmp_inimg->getData1dHandle(), (void *)subject->getRawDataAtChannel(c), sz0*sz1*sz2);
//now do computation
//bool b_res = gvfCellSeg(img3d, outimg3d, segpara);
bool b_res = gvfCellSeg(tmp_inimg, tmp_outimg, segpara);
// clear out temporary space
if (tmp_inimg) {delete tmp_inimg; tmp_inimg=0;}
if (!b_res)
{
v3d_msg("image segmentation using gvfCellSeg() failed \n");
}
else
{ // now display the results
// parameters for the new image data
V3DLONG new_sz0 = tmp_outimg->sz0();
V3DLONG new_sz1 = tmp_outimg->sz1();
V3DLONG new_sz2 = tmp_outimg->sz2();
V3DLONG new_sz3 = 1;
V3DLONG tunits = new_sz0*new_sz1*new_sz2*new_sz3;
//
USHORTINT16 * outvol1d = new USHORTINT16 [tunits];
// USHORTINT16 * tmpImg_d1d = (USHORTINT16 *)(tmp_outimg->getData1dHandle());
memcpy((void *)outvol1d, (void *)tmp_outimg->getData1dHandle(), tunits*sizeof(USHORTINT16));
if (tmp_outimg) {delete tmp_outimg; tmp_outimg=0;} //free the space immediately for better use of memory
Image4DSimple p4DImage;
p4DImage.setData((unsigned char*)outvol1d, sz0, sz1, sz2, 1, V3D_UINT16);
v3dhandle newwin = callback.newImageWindow();
callback.setImage(newwin, &p4DImage);
callback.setImageName(newwin, QString("Segmented Image"));
callback.updateImageWindow(newwin);
}
return;
}
else
{
v3d_msg(tr("A plugin for cell segmentation using Gradient Vector Flow. "
"Developed based on the source code developed by Tianming Liu, Fuhui Long, and Hanchuan Peng (2010-2014)"));
}
}
//void startVesselTracing ( V3DPluginCallback2 &v3d, QWidget *parent )
void startVesselTracing(V3DPluginCallback2 &v3d,int xflag,int yflag,int zflag,int xbegin, int xend,int xdis,int ybegin,int yend,int ydis,int zbegin,int zend,int zdis,QString swcfile,int slipsize,int pruning_flag,int c)
{
v3dhandle curwin = v3d.currentImageWindow();
if (!curwin)
{
v3d_msg("You don't have any image open in the main window.");
return;
}
//ensure the 3d viewer window is open; if not, then open it
// v3d.open3DWindow(curwin);
// get land mark list
LandmarkList seedList = v3d.getLandmark(curwin);
Image4DSimple* oldimg = v3d.getImage(curwin);
unsigned char* data1d = oldimg->getRawDataAtChannel(c-1);
ImagePixelType pixeltype = oldimg->getDatatype();
V3DLONG pagesz = oldimg->getTotalUnitNumberPerChannel();
unsigned char *output_image=0;
switch (pixeltype)
{
case V3D_UINT8:
try {output_image = new unsigned char [pagesz];}
catch(...) {v3d_msg("cannot allocate memory for output_image."); return;}
for(V3DLONG i = 0; i<pagesz; i++)
output_image[i] = data1d[i];
break;
default: v3d_msg("Invalid data type. Do nothing."); return;
}
V3DLONG in_sz[4];
in_sz[0] = oldimg->getXDim(); in_sz[1] = oldimg->getYDim(); in_sz[2] = oldimg->getZDim();in_sz[3] = 1;
// simple_saveimage_wrapper(v3d, "temp.v3draw", (unsigned char *)output_image, in_sz, pixeltype);
MOSTImage img;
// set data
img.setData( (unsigned char*)output_image, oldimg->getXDim(),oldimg->getYDim(),oldimg->getZDim(),oldimg->getCDim(),oldimg->getDatatype());
if ( seedList.isEmpty() )
{
QTime qtime_seed;
qtime_seed.start();
//img.auto_detect_seedz(seedList,img.getZDim()/2);
if(xflag)
{
for(int i =xbegin;i<=xend;i+=xdis)
img.auto_detect_seedx(seedList,i,InitThreshold,seed_size_all);
// img.auto_detect_seedx(seedList,xend);
}
if(yflag)
{
for(int i =ybegin;i<=yend;i+=ydis)
img.auto_detect_seedy(seedList,i,InitThreshold,seed_size_all);
// img.auto_detect_seedy(seedList,yend);
}
if(zflag)
{
for(int i =zbegin;i<=zend;i+=zdis)
img.auto_detect_seedz(seedList,i,InitThreshold,seed_size_all);
//img.auto_detect_seedz(seedList,zend);
}
qDebug(" cost time seed = %g sec", qtime_seed.elapsed()*0.001);
}
// clear visited, only excute once
static long init_flag = 0;
/* if ( init_flag <= 0 )
{
visited.fill( false, oldimg->getTotalUnitNumber());
init_flag ++;
}*/
for(init_flag = 0;init_flag<oldimg->getTotalUnitNumber();init_flag++)
{
visited.push_back(false);
}
// converte the formate
NeuronTree vt;
QTime qtime;
qtime.start();
vt = img.trace_seed_list(seedList, visited,InitThreshold,res_x_all,res_y_all,res_z_all,swcfile,slipsize,pruning_flag);
qDebug(" cost time totol= %g sec", qtime.elapsed()*0.001);
v3d_msg(QString("Now you can drag and drop the generated swc fle [%1] into Vaa3D.").arg(swcfile),1);
// NeuronTree vt_old = v3d.getSWC(curwin);
// visualization
// v3d.setLandmark(curwin, seedList);
// v3d.setSWC(curwin,vt);
// v3d.pushObjectIn3DWindow(curwin);
// v3d.updateImageWindow(curwin);
//img.~MOSTImage();
}
void bwlabelimg(V3DPluginCallback2 &callback, QWidget *parent, int method_code)
{
v3dhandle curwin = callback.currentImageWindow();
if (!curwin)
{
v3d_msg("You don't have any image open in the main window.");
return;
}
if (method_code!=3 && method_code!=2)
{
v3d_msg("Invalid BWLabel method code. You should never see this message. Report this bug to the developer");
return;
}
LabelImgObjectParaDialog dialog(callback, parent);
if (!dialog.image)
return;
if (dialog.exec()!=QDialog::Accepted)
return;
V3DLONG ch = dialog.ch;
V3DLONG th_idx = dialog.th_idx;
double tt = dialog.thresh;
V3DLONG volsz_thres = (dialog.b_filtersmallobjs) ? dialog.volsz : 0; //the threshold to filter out small objects
int start_t = clock(); // record time
Image4DSimple* subject = callback.getImage(curwin);
QString m_InputFileName = callback.getImageName(curwin);
if (!subject)
{
QMessageBox::information(0, title, QObject::tr("No image is open."));
return;
}
if (subject->getDatatype()!=V3D_UINT8)
{
QMessageBox::information(0, title, QObject::tr("This demo program only supports 8-bit data. Your current image data type is not supported."));
return;
}
if (th_idx==0 || th_idx==1)
{
double mm, vv;
mean_and_std(subject->getRawDataAtChannel(ch), subject->getTotalUnitNumberPerChannel(), mm, vv);
tt = (th_idx == 0) ? mm : mm+vv;
v3d_msg(QString("in fast image object labeling: ch=%1 mean=%2 std=%2").arg(ch).arg(mm).arg(vv), 0);
}
Image4DProxy<Image4DSimple> pSub(subject);
V3DLONG sz0 = subject->getXDim();
V3DLONG sz1 = subject->getYDim();
V3DLONG sz2 = subject->getZDim();
V3DLONG sz3 = subject->getCDim();
//----------------------------------------------------------------------------------------------------------------------------------
V3DLONG channelsz = sz0*sz1*sz2;
unsigned short int *pLabel = 0;
unsigned char *pData = 0;
try
{
pLabel = new unsigned short int [channelsz];
pData = new unsigned char [channelsz];
}
catch (...)
{
v3d_msg("Fail to allocate memory in Fast Object Labeling Plugin.");
if (pLabel) {delete []pLabel; pLabel=0;}
if (pData) {delete []pData; pData=0;}
return;
}
unsigned char * pSubtmp = pSub.begin();
for(V3DLONG i = 0; i < channelsz; i++)
{
pData[i] = (pSubtmp[i]<=tt) ? 0 : 1;
}
// dist transform
V3DLONG sz_data[4]; sz_data[0]=sz0; sz_data[1]=sz1; sz_data[2]=sz2; sz_data[3]=1;
V3DLONG nobjs=0;
if (method_code==3)
{
V3DLONG nh_code=26; //6,18,or 26
nobjs = findConnectedComponent(pData, sz_data, 3, nh_code, pLabel);
}
else if (method_code==2)
{
V3DLONG nh_code=8; //4 or 8
nobjs = findConnectedComponent(pData, sz_data, 2, nh_code, pLabel);
}
else
{
v3d_msg("Invalid BWLabelN method code. You should never see this message. Report this bug to the developer");
return;
}
if (pData) {delete []pData; pData=0;}
if (volsz_thres>0) //filter out small objects
{
try {
float * hh = new float [nobjs];
float * mapval = new float [nobjs];
V3DLONG j;
for (j=0;j<nobjs;j++) {hh[j]=0; mapval[j]=j;} //of course, 0 also map to 0!
for (j=0;j<channelsz;j++)
{
//pLabel[j]--; //it seems Fuhui's data is 1-based, so subtract 1. Is this correct?
hh[pLabel[j]]++;
}
V3DLONG k=0;
for (j=1;j<nobjs;j++) //start from 1 as it is the background!
{
if (hh[j]<volsz_thres)
{
mapval[j]=0; //if less than a thres, then map to 0, which is background
}
else
{
printf("Obj [%ld] = [%ld]\n", V3DLONG(j), V3DLONG(hh[j]));
k++;
mapval[j] = k; //otherwise map to a continous label-value
}
}
for (j=0;j<channelsz;j++)
pLabel[j] = mapval[pLabel[j]];
if (hh) {delete []hh; hh=0;}
if (mapval) {delete []mapval; mapval=0;}
}
catch (...) {
v3d_msg("Unable to allocate memory to filter small objects. Thus skip it.");
}
}
//----------------------------------------------------------------------------------------------------------------------------------
int end_t = clock();
printf("time eclapse %d s for labeling objects!\n", (end_t-start_t)/1000000);
Image4DSimple p4DImage;
p4DImage.setData((unsigned char*)pLabel, sz0, sz1, sz2, 1, V3D_UINT16);
v3dhandle newwin = callback.newImageWindow();
callback.setImage(newwin, &p4DImage);
callback.setImageName(newwin, QString("Object-Labeled Image"));
callback.updateImageWindow(newwin);
}
bool autotrace(const V3DPluginArgList & input, V3DPluginArgList & output,V3DPluginCallback2 &callback)
{
cout<<"Welcome to MOST tracing"<<endl;
unsigned int c=1;
int InitThreshold = 20;
seed_size_all = 20;
int slipsize=20;
if (input.size()>=2)
{
vector<char*> paras = (*(vector<char*> *)(input.at(1).p));
cout<<paras.size()<<endl;
if(paras.size() >= 1) c = atoi(paras.at(0));
if(paras.size() >= 2) InitThreshold = atoi(paras.at(1));
if(paras.size() >= 3) seed_size_all = atoi(paras.at(2));
if(paras.size() >= 4) slipsize = atoi(paras.at(3));
}
char * inimg_file = ((vector<char*> *)(input.at(0).p))->at(0);
cout<<"ch = "<<c<<endl;
cout<<"threshold = "<<InitThreshold<<endl;
cout<<"inimg_file = "<<inimg_file<<endl;
cout<<"seedsize = "<<seed_size_all<<endl;
cout<<"slipsize = "<<slipsize<<endl;
Image4DSimple *subject = callback.loadImage(inimg_file);
if(!subject || !subject->valid())
{
v3d_msg("Fail to load the input image.",0);
if (subject) {delete subject; subject=0;}
return false;
}
if( c < 1 || c > subject->getCDim())
{
v3d_msg("Invalid channel input.",0);
if (subject) {delete subject; subject=0;}
return false;
}
V3DLONG N = subject->getXDim();
V3DLONG M = subject->getYDim();
V3DLONG P = subject->getZDim();
V3DLONG pagesz = N*M*P;
int datatype = subject->getDatatype();
unsigned char *data1d = subject->getRawDataAtChannel(c-1);
unsigned char *output_image=0;
switch (datatype)
{
case V3D_UINT8:
try {output_image = new unsigned char [pagesz];}
catch(...) {v3d_msg("cannot allocate memory for output_image.",0); return false;}
for(V3DLONG i = 0; i<pagesz; i++)
output_image[i] = data1d[i];
break;
default: v3d_msg("Invalid data type. Do nothing.",0); return false;
}
MOSTImage img;
img.setData( (unsigned char*)output_image, subject->getXDim(),subject->getYDim(),subject->getZDim(),subject->getCDim(),subject->getDatatype());
QString swcfile = QString(inimg_file) + "_MOST.swc";
LandmarkList seedList;
QTime qtime_seed;
qtime_seed.start();
if(1)
{
for(int i =1;i<=N;i+=20)
img.auto_detect_seedx(seedList,i,InitThreshold,seed_size_all);
}
if(1)
{
for(int i =1;i<=M;i+=20)
img.auto_detect_seedy(seedList,i,InitThreshold,seed_size_all);
}
if(1)
{
for(int i =1;i<=P;i+=20)
img.auto_detect_seedz(seedList,i,InitThreshold,seed_size_all);
}
qDebug(" cost time seed = %g sec", qtime_seed.elapsed()*0.001);
static long init_flag = 0;
for(init_flag = 0;init_flag<subject->getTotalUnitNumberPerChannel();init_flag++)
{
visited.push_back(false);
}
// converte the formate
NeuronTree vt;
QTime qtime;
qtime.start();
vt = img.trace_seed_list(seedList, visited,InitThreshold,1.0,1.0,1.0,swcfile,slipsize,0);
qDebug(" cost time totol= %g sec", qtime.elapsed()*0.001);
v3d_msg(QString("\nNow you can drag and drop the generated swc fle [%1] into Vaa3D.").arg(swcfile),0);
if (subject) {delete subject; subject=0;}
return true;
}
void FL_cellseg(V3DPluginCallback2 &callback, QWidget *parent)
{
v3dhandle curwin = callback.currentImageWindow();
if (!curwin)
{
v3d_msg("You don't have any image open in the main window.");
return;
}
Image4DSimple* subject = callback.getImage(curwin);
QString m_InputFileName = callback.getImageName(curwin);
if (!subject)
{
QMessageBox::information(0, title, QObject::tr("No image is open."));
return;
}
if (subject->getDatatype()!=V3D_UINT8)
{
QMessageBox::information(0, title, QObject::tr("This demo program only supports 8-bit data. Your current image data type is not supported."));
return;
}
V3DLONG sz0 = subject->getXDim();
V3DLONG sz1 = subject->getYDim();
V3DLONG sz2 = subject->getZDim();
V3DLONG sz3 = subject->getCDim();
Image4DProxy<Image4DSimple> pSub(subject);
//----------------------------------------------------------------------------------------------------------------------------------
V3DLONG channelsz = sz0*sz1*sz2;
float *pLabel = 0;
unsigned char *pData = 0;
//get the segmentation parameters
segParameter segpara;
dialog_watershed_para *p_mydlg=0;
if (!p_mydlg) p_mydlg = new dialog_watershed_para(&segpara, subject);
int res = p_mydlg->exec();
if (res!=QDialog::Accepted)
return;
else
p_mydlg->fetchData(&segpara);
if (p_mydlg) {delete p_mydlg; p_mydlg=0;}
// now allocate memory and do computation
int start_t = clock();
Vol3DSimple <unsigned char> * tmp_inimg = 0;
Vol3DSimple <USHORTINT16> * tmp_outimg = 0;
try
{
tmp_inimg = new Vol3DSimple <unsigned char> (sz0, sz1, sz2);
tmp_outimg = new Vol3DSimple <USHORTINT16> (sz0, sz1, sz2);
}
catch (...)
{
v3d_msg("Unable to allocate memory for processing. Do nothing.");
if (tmp_inimg) {delete tmp_inimg; tmp_inimg=0;}
if (tmp_outimg) {delete tmp_outimg; tmp_outimg=0;}
return;
}
//do computation
memcpy((void *)tmp_inimg->getData1dHandle(), (void *)subject->getRawDataAtChannel(segpara.channelNo), sz0*sz1*sz2);
bool b_res = FL_cellseg(tmp_inimg, tmp_outimg, segpara);
if (tmp_inimg) {delete tmp_inimg; tmp_inimg=0;} //free the space immediately for better use of memory
if (!b_res)
{
v3d_msg("Fail to do the cell segmentation using FL_cellseg().\n");
}
else
{
V3DLONG new_sz0 = tmp_outimg->sz0();
V3DLONG new_sz1 = tmp_outimg->sz1();
V3DLONG new_sz2 = tmp_outimg->sz2();
V3DLONG new_sz3 = 1;
V3DLONG tunits = new_sz0*new_sz1*new_sz2*new_sz3;
USHORTINT16 * outvol1d = new USHORTINT16 [tunits];
USHORTINT16 * tmpImg_d1d = (USHORTINT16 *)(tmp_outimg->getData1dHandle());
memcpy((void *)outvol1d, (void *)tmp_outimg->getData1dHandle(), tunits*sizeof(USHORTINT16));
if (tmp_outimg) {delete tmp_outimg; tmp_outimg=0;} //free the space immediately for better use of memory
Image4DSimple p4DImage;
p4DImage.setData((unsigned char*)outvol1d, sz0, sz1, sz2, 1, V3D_UINT16);
v3dhandle newwin = callback.newImageWindow();
callback.setImage(newwin, &p4DImage);
callback.setImageName(newwin, QString("Segmented Image"));
callback.updateImageWindow(newwin);
}
//----------------------------------------------------------------------------------------------------------------------------------
int end_t = clock();
printf("time eclapse %d s for labeling objects!\n", (end_t-start_t)/1000000);
}
