void processImage(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* p4DImage = callback.getImage(curwin);
QString imgname = callback.getImageName(curwin);
if (!p4DImage)
{
v3d_msg("The image pointer is invalid. Ensure your data is valid and try again!");
return;
}
int tmpx,tmpy,tmpz,x1,y1,z1;
LandmarkList listLandmarks = callback.getLandmark(curwin);
LocationSimple tmpLocation(0,0,0);
int marknum = listLandmarks.count();
if(marknum ==0)
{
v3d_msg("No markers in the current image, please double check.");
return;
}
UndirectedGraph g(marknum);
for (int i=0;i<marknum;i++)
{
tmpLocation = listLandmarks.at(i);
tmpLocation.getCoord(tmpx,tmpy,tmpz);
x1 = tmpx;
y1 = tmpy;
z1 = tmpz;
for (int j=0;j<marknum;j++)
{
EdgeQuery edgeq = edge(i, j, *&g);
if (!edgeq.second && i!=j)
{
tmpLocation = listLandmarks.at(j);
tmpLocation.getCoord(tmpx,tmpy,tmpz);
double Vedge = sqrt(double(x1-tmpx)*double(x1-tmpx) + double(y1-tmpy)*double(y1-tmpy) + double(z1-tmpz)*double(z1-tmpz));
add_edge(i, j, LastVoted(i, Weight(Vedge)), *&g);
}
}
}
// property_map<UndirectedGraph, edge_weight_t>::type weightmap = get(edge_weight, *&g);
vector < graph_traits < UndirectedGraph >::vertex_descriptor > p(num_vertices(*&g));
prim_minimum_spanning_tree(*&g, &p[0]);
NeuronTree marker_MST;
QList <NeuronSWC> listNeuron;
QHash <int, int> hashNeuron;
listNeuron.clear();
hashNeuron.clear();
for (std::size_t i = 0; i != p.size(); ++i)
{
NeuronSWC S;
tmpLocation = listLandmarks.at(i);
tmpLocation.getCoord(tmpx,tmpy,tmpz);
int pn;
if(p[i] == i)
pn = -1;
else
pn = p[i] + 1;
S.n = i+1;
S.type = 7;
S.x = tmpx;
S.y = tmpy;
S.z = tmpz;
S.r = 1;
S.pn = pn;
listNeuron.append(S);
hashNeuron.insert(S.n, listNeuron.size()-1);
}
marker_MST.n = -1;
marker_MST.on = true;
marker_MST.listNeuron = listNeuron;
marker_MST.hashNeuron = hashNeuron;
/*
double** markEdge = new double*[marknum];
for(int i = 0; i < marknum; i++)
{
markEdge[i] = new double[marknum];
}
for (int i=0;i<marknum;i++)
{
tmpLocation = listLandmarks.at(i);
tmpLocation.getCoord(tmpx,tmpy,tmpz);
x1 = tmpx;
y1 = tmpy;
z1 = tmpz;
for (int j=0;j<marknum;j++)
{
tmpLocation = listLandmarks.at(j);
tmpLocation.getCoord(tmpx,tmpy,tmpz);
markEdge[i][j] = sqrt(double(x1-tmpx)*double(x1-tmpx) + double(y1-tmpy)*double(y1-tmpy) + double(z1-tmpz)*double(z1-tmpz));
}
}
//NeutronTree structure
NeuronTree marker_MST;
QList <NeuronSWC> listNeuron;
QHash <int, int> hashNeuron;
listNeuron.clear();
hashNeuron.clear();
//set node
NeuronSWC S;
tmpLocation = listLandmarks.at(0);
tmpLocation.getCoord(tmpx,tmpy,tmpz);
S.n = 1;
S.type = 7;
S.x = tmpx;
S.y = tmpy;
S.z = tmpz;
S.r = 1;
S.pn = -1;
listNeuron.append(S);
hashNeuron.insert(S.n, listNeuron.size()-1);
int* pi = new int[marknum];
for(int i = 0; i< marknum;i++)
pi[i] = 0;
pi[0] = 1;
int indexi,indexj;
for(int loop = 0; loop<marknum;loop++)
{
double min = INF;
for(int i = 0; i<marknum; i++)
{
if (pi[i] == 1)
{
for(int j = 0;j<marknum; j++)
{
if(pi[j] == 0 && min > markEdge[i][j])
{
min = markEdge[i][j];
indexi = i;
indexj = j;
}
}
}
}
if(indexi>=0)
{
tmpLocation = listLandmarks.at(indexj);
tmpLocation.getCoord(tmpx,tmpy,tmpz);
S.n = indexj+1;
S.type = 7;
S.x = tmpx;
S.y = tmpy;
S.z = tmpz;
S.r = 1;
S.pn = indexi+1;
listNeuron.append(S);
hashNeuron.insert(S.n, listNeuron.size()-1);
}else
{
break;
}
pi[indexj] = 1;
indexi = -1;
indexj = -1;
}
marker_MST.n = -1;
marker_MST.on = true;
marker_MST.listNeuron = listNeuron;
marker_MST.hashNeuron = hashNeuron;
*/
QString outfilename = imgname + "_boost_marker.swc";
if (outfilename.startsWith("http", Qt::CaseInsensitive))
{
QFileInfo ii(outfilename);
outfilename = QDir::home().absolutePath() + "/" + ii.fileName();
}
//v3d_msg(QString("The anticipated output file is [%1]").arg(outfilename));
writeSWC_file(outfilename,marker_MST);
v3d_msg(QString("You have totally [%1] markers for the file [%2] and the computed MST has been saved to the file [%3]").arg(marknum).arg(imgname).arg(outfilename));
return;
}
void reconstruction_func(V3DPluginCallback2 &callback, QWidget *parent, input_PARA &PARA, bool bmenu)
{
unsigned char* data1d = 0;
V3DLONG N,M,P,sc,c;
V3DLONG in_sz[4];
v3dhandle curwin;
if(bmenu)
{
curwin = callback.currentImageWindow();
v3dhandle curwin = callback.currentImageWindow();
if (!curwin)
{
QMessageBox::information(0, "", "You don't have any image open in the main window.");
return;
}
Image4DSimple* p4DImage = callback.getImage(curwin);
if (!p4DImage)
{
QMessageBox::information(0, "", "The image pointer is invalid. Ensure your data is valid and try again!");
return;
}
data1d = p4DImage->getRawData();
N = p4DImage->getXDim();
M = p4DImage->getYDim();
P = p4DImage->getZDim();
sc = p4DImage->getCDim();
in_sz[0] = N;
in_sz[1] = M;
in_sz[2] = P;
in_sz[3] = sc;
PARA.inimg_file = p4DImage->getFileName();
}
else
{
int datatype = 0;
if (!simple_loadimage_wrapper(callback,PARA.inimg_file.toStdString().c_str(), data1d, in_sz, datatype))
{
fprintf (stderr, "Error happens in reading the subject file [%s]. Exit. \n",PARA.inimg_file.toStdString().c_str());
return;
}
N = in_sz[0];
M = in_sz[1];
P = in_sz[2];
sc = in_sz[3];
}
//main neuron reconstruction code
//// THIS IS WHERE THE DEVELOPERS SHOULD ADD THEIR OWN NEURON TRACING CODE
// ofstream oImgInfofile;
string sImgPath = PARA.inimg_file.toStdString();
g_sAppDir = normalizePath(parentPath(sImgPath));
// g_sImageInfoPath = g_sAppDir + g_sImageInfoName;
// g_sInputRawFilePath = g_sAppDir + g_sInputRawFileName;
QString swc_name = PARA.inimg_file + "_nctuTW.swc";
g_sOutSwcFilePath = swc_name.toStdString();
//g_sOutSwcFilePath = g_sAppDir+ g_sOutSwcFileName;
size_t nDataSize = N * M * P * sc ;
width = N;
height = M;
zSize = P;
// oImgInfofile.open(g_sImageInfoPath.data(), ios::out|ios::binary);
// if(oImgInfofile.is_open()){
// oImgInfofile << N << " " << M << " " << P << endl;
// oImgInfofile.close();
// }
imgBuf_raw = new unsigned char [nDataSize];
memcpy(imgBuf_raw, data1d, nDataSize);
// ofstream oRawFile;
// oRawFile.open(g_sInputRawFilePath.data(), ios::out|ios::binary);
// if(oRawFile.is_open()){
// oRawFile.write((char *)data1d, nDataSize);
// oRawFile.close();
// }
/*
// For debug
if(nParaState == QDialog::Accepted){
std::string sPara = "Threshold = " + toString(g_rThreshold) + "; " +
"Soma = (" + toString(g_nSomaX) + ", " + toString(g_nSomaY) + ", " + toString(g_nSomaZ) + ")";
v3d_msg(QString(sPara.c_str()));
}
*/
QDlgPara* pqDlgPara;
g_nSomaX = -1;
g_nSomaY = -1;
g_nSomaZ = -1;
int nParaState = 1;
if(bmenu) //ui
{
LandmarkList Landmark;
Landmark = callback.getLandmark(curwin);
if(Landmark.size()>0)
{
g_nSomaX = Landmark.at(0).x-1;
g_nSomaY = Landmark.at(0).y-1;
g_nSomaZ = Landmark.at(0).z-1;
}
pqDlgPara = new QDlgPara(parent);
nParaState = pqDlgPara->exec();
}
else //command line
{
QList<ImageMarker> file_inmarkers;
if(!PARA.inmarker_file.isEmpty())
{
file_inmarkers = readMarker_file(PARA.inmarker_file);
g_nSomaX = file_inmarkers.at(0).x;
g_nSomaY = file_inmarkers.at(0).y;
g_nSomaZ = file_inmarkers.at(0).z;
}
else
{
g_nSomaX = -1;
g_nSomaY = -1;
g_nSomaZ = -1;
}
g_rThreshold = PARA.threshold;
}
if(nParaState)
{
NeuronTracingMain();
v3d_msg(QString("Now you can drag and drop the generated swc fle [%1] into Vaa3D.").arg(swc_name.toStdString().c_str()),bmenu);
}
if(bmenu) delete pqDlgPara;
bmenu=true;
//Output
// NeuronTree nt;
//QString swc_name = PARA.inimg_file + "_nctuTW.swc";
// nt.name = "nctuTW";
// writeSWC_file(swc_name.toStdString().c_str(),nt);
//QString swc_name(g_sOutSwcFilePath.data());
//Output
if(!bmenu)
{
if(data1d) {delete []data1d; data1d = 0;}
}
delete [] imgBuf_raw;
return;
}
//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();
}
bool do_AtlasGuidedStrAnno(V3DPluginCallback2 &callback,
QString &qs_filename_img, QString &qs_filename_marker_input, // input files
QString &qs_filename_atals_input, QString &qs_filename_celloi_input, QString &qs_filename_celloi_2_input,
CSParas ¶s_str, CParas ¶s_anno, bool &b_use_celloi_2, // paras
QString &qs_filename_atals_output, QString &qs_filename_seglabel_output ) // output files
{
//------------------------------------------------------------------------------------------------------------------------------------
printf("1. Import image. \n");
unsigned char *p_img_input=0;
V3DLONG sz_img_input[4];
int datatype_input=0;
if(!paras_str.b_imgfromV3D)
{
if(qs_filename_img.isEmpty())
{
v3d_msg(QString("invalid image path!"));
return false;
}
if(!simple_loadimage_wrapper(callback, (char *)qPrintable(qs_filename_img),p_img_input,sz_img_input,datatype_input))
{
v3d_msg(QString("open file [%1] failed!").arg(qs_filename_img));
return false;
}
printf("\t>>read image file [%s] complete.\n",qPrintable(qs_filename_img));
}
else
{
printf("\t>>import image from V3D. \n");
v3dhandleList h_wndlist=callback.getImageWindowList();
if(h_wndlist.size()<1)
{
v3d_msg(QString("Make sure there are at least 1 image in V3D!"));
return false;
}
Image4DSimple* image=callback.getImage(callback.currentImageWindow());
p_img_input=image->getRawData();
//sz_img_input=new V3DLONG[4]();
sz_img_input[0]=image->getXDim(); sz_img_input[1]=image->getYDim(); sz_img_input[2]=image->getZDim(); sz_img_input[3]=image->getCDim();
datatype_input=image->getDatatype();
}
printf("\t\timage size: [w=%ld, h=%ld, z=%ld, c=%ld]\n",sz_img_input[0],sz_img_input[1],sz_img_input[2],sz_img_input[3]);
printf("\t\tdatatype: %d\n",datatype_input);
//------------------------------------------------------------------------------------------------------------------------------------
printf("2. Convert image datatype to uint8. \n");
unsigned char * p_img_8u=0;
{
V3DLONG l_npixels=sz_img_input[0]*sz_img_input[1]*sz_img_input[2]*sz_img_input[3];
p_img_8u=new unsigned char[l_npixels];
if(!p_img_8u)
{
printf("ERROR: Fail to allocate memory. Do nothing. \n");
if(p_img_input && !paras_str.b_imgfromV3D) {delete []p_img_input; p_img_input=0;}
//if(sz_img_input) {delete []sz_img_input; sz_img_input=0;}
return false;
}
if(datatype_input==1)
{
printf("\t>>convert image data from uint8 to uint8. \n");
for(V3DLONG i=0;i<l_npixels;i++)
p_img_8u[i]=p_img_input[i];
}
else if(datatype_input==2)
{
printf("\t>>convert image data from uint16 to uint8. \n");
double min,max;
if(!rescale_to_0_255_and_copy((unsigned short int *)p_img_input,l_npixels,min,max,p_img_8u))
{
printf("ERROR: rescale_to_0_255_and_copy() return false.\n");
if(p_img_8u) {delete []p_img_8u; p_img_8u=0;}
if(p_img_input && !paras_str.b_imgfromV3D) {delete []p_img_input; p_img_input=0;}
//if(sz_img_input) {delete []sz_img_input; sz_img_input=0;}
return false;
}
}
else if(datatype_input==4)
{
printf("\t>>convert image data from float to uint8. \n");
double min,max;
if(!rescale_to_0_255_and_copy((float *)p_img_input,l_npixels,min,max,p_img_8u))
{
printf("ERROR: rescale_to_0_255_and_copy() return false.\n");
if(p_img_8u) {delete []p_img_8u; p_img_8u=0;}
if(p_img_input && !paras_str.b_imgfromV3D) {delete []p_img_input; p_img_input=0;}
//if(sz_img_input) {delete []sz_img_input; sz_img_input=0;}
return false;
}
}
else
{
v3d_msg(QString("Unknown datatype!\n"));
if(p_img_8u) {delete []p_img_8u; p_img_8u=0;}
if(p_img_input && !paras_str.b_imgfromV3D) {delete []p_img_input; p_img_input=0;}
//if(sz_img_input) {delete []sz_img_input; sz_img_input=0;}
return false;
}
}
//------------------------------------------------------------------------------------------------------------------------------------
printf("3. Import markers. \n");
//get initial head and tail marker position from V3D
vector< vector<double> > vec2d_markers;
if(!paras_str.b_markerfromV3D)
{
if(qs_filename_marker_input.isEmpty() || qs_filename_marker_input.toUpper()=="NULL")
{
v3d_msg(QString("Invalid marker path! Ignore it!"), 0);
vec2d_markers.clear();
/* //commented by PHC 2013-08-21
if(p_img_8u) {delete []p_img_8u; p_img_8u=0;}
if(p_img_input && !paras_str.b_imgfromV3D) {delete []p_img_input; p_img_input=0;}
if(sz_img_input) {delete []sz_img_input; sz_img_input=0;}
return false;
*/
}
else
{
QList<ImageMarker> ql_markers=readMarker_file(qs_filename_marker_input);
printf("\t>>read %d markers from file: %s.\n",ql_markers.size(),qPrintable(qs_filename_marker_input));
vector<double> vec_marker(3,0);
for(V3DLONG i=0;i<ql_markers.size();i++)
{
vec_marker[0]=ql_markers[i].x;
vec_marker[1]=ql_markers[i].y;
vec_marker[2]=ql_markers[i].z;
vec2d_markers.push_back(vec_marker);
}
}
}
else
{
printf("\t>>import markers from V3D. \n");
v3dhandleList h_wndlist=callback.getImageWindowList();
if(h_wndlist.size()<1)
{
v3d_msg(QString("Make sure there are at least 1 image in V3D!"));
if(p_img_8u) {delete []p_img_8u; p_img_8u=0;}
if(p_img_input && !paras_str.b_imgfromV3D) {delete []p_img_input; p_img_input=0;}
//if(sz_img_input) {delete []sz_img_input; sz_img_input=0;}
return false;
}
LandmarkList ml_makers=callback.getLandmark(callback.currentImageWindow());
vector<double> vec_marker(3,0);
for(V3DLONG i=0;i<ml_makers.size();i++)
{
vec_marker[0]=ml_makers[i].x;
vec_marker[1]=ml_makers[i].y;
vec_marker[2]=ml_makers[i].z;
vec2d_markers.push_back(vec_marker);
}
}
//------------------------------------------------------------------------------------------------------------------------------------
printf("4. Read atlas apo file. \n");
QList<CellAPO> ql_atlasapo;
ql_atlasapo=readAPO_file(qs_filename_atals_input);
printf("\t>>read %d points from [%s]\n",ql_atlasapo.size(),qPrintable(qs_filename_atals_input));
if(ql_atlasapo.size()<=0)
{
v3d_msg(QString("Given atlas file is empty or invalid!"));
if(p_img_8u) {delete []p_img_8u; p_img_8u=0;}
if(p_img_input && !paras_str.b_imgfromV3D) {delete []p_img_input; p_img_input=0;}
//if(sz_img_input) {delete []sz_img_input; sz_img_input=0;}
return false;
}
//------------------------------------------------------------------------------------------------------------------------------------
printf("5. Read interesting cell file. \n");
QList<QString> ql_celloi_name;
if(!readCelloi_file(qs_filename_celloi_input,ql_celloi_name))
{
printf("ERROR: readCelloi_file() return false! \n");
if(p_img_8u) {delete []p_img_8u; p_img_8u=0;}
if(p_img_input && !paras_str.b_imgfromV3D) {delete []p_img_input; p_img_input=0;}
//if(sz_img_input) {delete []sz_img_input; sz_img_input=0;}
return false;
}
printf("\t>>interesting cell:\n");
for(V3DLONG i=0;i<ql_celloi_name.size();i++)
printf("\t\t%s\n",qPrintable(ql_celloi_name[i]));
//------------------------------------------------------------------------------------------------------------------------------------
printf("6. Do Straightening. \n");
unsigned char *p_strimg=0;
V3DLONG *sz_strimg=0;
vector< vector< vector< vector<V3DLONG> > > > vec4d_mappingfield_str2ori;
if(vec2d_markers.size()<2)
{
printf("\t>>marker num < 2, skip straightening.\n");
}
else
{
printf("\t>>marker num >= 2, do straightening.\n");
V3DLONG l_width=paras_str.l_radius_cuttingplane*2+1;
QList<ImageMarker> ql_marker;
for(unsigned V3DLONG i=0;i<vec2d_markers.size();i++)
{
ImageMarker tmp;
tmp.x=vec2d_markers[i][0];
tmp.y=vec2d_markers[i][1];
tmp.z=vec2d_markers[i][2];
ql_marker.push_back(tmp);
}
if(!q_celegans_restacking_xy(
p_img_8u,sz_img_input,
ql_marker,l_width,
p_strimg,sz_strimg,
vec4d_mappingfield_str2ori))
{
printf("ERROR: q_celegans_restacking_xy() return false! \n");
if(p_img_8u) {delete []p_img_8u; p_img_8u=0;}
if(p_img_input && !paras_str.b_imgfromV3D) {delete []p_img_input; p_img_input=0;}
//if(sz_img_input) {delete []sz_img_input; sz_img_input=0;}
return false;
}
}
//------------------------------------------------------------------------------------------------------------------------------------
printf("7. Do Annotation. \n");
QList<CellAPO> ql_musclecell_output;
unsigned char *p_img8u_seglabel=0;
COutputInfo outputinfo;
{
unsigned char *p_img_anno=0;
V3DLONG *sz_img_anno=0;
if(vec2d_markers.size()<2) //on non-straightened image
{
p_img_anno=p_img_input;
sz_img_anno=sz_img_input;
}
else //on straightened image
{
p_img_anno=p_strimg;
sz_img_anno=sz_strimg;
}
if(paras_anno.l_mode==-1) //non-partial annotation
{
if(!q_atlas2image(paras_anno,callback,
p_img_anno,sz_img_anno,ql_atlasapo,ql_celloi_name,
ql_musclecell_output,p_img8u_seglabel,outputinfo))
{
printf("ERROR: q_atlas2image() return false!\n");
if(p_strimg) {delete []p_strimg; p_strimg=0;}
if(sz_strimg) {delete []sz_strimg; sz_strimg=0;}
if(p_img_8u) {delete []p_img_8u; p_img_8u=0;}
if(p_img_input && !paras_str.b_imgfromV3D) {delete []p_img_input; p_img_input=0;}
//if(sz_img_input) {delete []sz_img_input; sz_img_input=0;}
return false;
}
}
else if(paras_anno.l_mode==4) //align dapi
{
if(!q_align_dapicells(paras_anno,callback,
p_img_anno,sz_img_anno,ql_atlasapo,ql_celloi_name,
ql_musclecell_output,outputinfo))
{
printf("ERROR: q_atlas2image_partial() return false!\n");
if(p_strimg) {delete []p_strimg; p_strimg=0;}
if(sz_strimg) {delete []sz_strimg; sz_strimg=0;}
if(p_img_8u) {delete []p_img_8u; p_img_8u=0;}
if(p_img_input && !paras_str.b_imgfromV3D) {delete []p_img_input; p_img_input=0;}
//if(sz_img_input) {delete []sz_img_input; sz_img_input=0;}
return false;
}
}
else //partial annotation
{
if(!q_atlas2image_partial(paras_anno,callback,
p_img_anno,sz_img_anno,ql_atlasapo,ql_celloi_name,
ql_musclecell_output,outputinfo))
{
printf("ERROR: q_atlas2image_partial() return false!\n");
if(p_strimg) {delete []p_strimg; p_strimg=0;}
if(sz_strimg) {delete []sz_strimg; sz_strimg=0;}
if(p_img_8u) {delete []p_img_8u; p_img_8u=0;}
if(p_img_input && !paras_str.b_imgfromV3D) {delete []p_img_input; p_img_input=0;}
//if(sz_img_input) {delete []sz_img_input; sz_img_input=0;}
return false;
}
}
}
if(outputinfo.b_rotate90)
v3d_msg("The deformed atlas maybe wrongly 90 degree rotated!\nCheck result!\n");
//------------------------------------------------------------------------------------------------------------------------------------
//warping the secondary interesting cells if provided based on the TPS paras obtained from the first group result
QList<CellAPO> ql_cellio2_tps;
if( b_use_celloi_2 || !qs_filename_celloi_2_input.isEmpty()) // b_use_celloi_2 = DLG_stranno.checkBox_celloi_2->isChecked()
{
printf("8-9. Warping the secondary interesting cells. \n");
QList<QString> ql_celloi2_name;
if(!readCelloi_file(qs_filename_celloi_2_input,ql_celloi2_name))
{
printf("ERROR: readCelloi_file() return false! \n");
return false;
}
vector<point3D64F> vec_cellio1_ori,vec_cellio1_tps,vec_cellio2_ori;
QList<CellAPO> ql_cellio2_ori;
point3D64F tmp;
//extract first interesting cells
for(V3DLONG i=0;i<ql_atlasapo.size();i++)
{
QString qs_cellname=ql_atlasapo[i].name;
qs_cellname=qs_cellname.simplified();
qs_cellname=qs_cellname.toUpper();
ql_atlasapo[i].name=qs_cellname;
for(V3DLONG j=0;j<ql_celloi_name.size();j++)
{
if(ql_celloi_name[j].contains("*"))
{
QString qs_cellnamevalid=ql_celloi_name[j];
qs_cellnamevalid.remove("*");
if(qs_cellname.contains(qs_cellnamevalid,Qt::CaseInsensitive))
{
tmp.x=ql_atlasapo[i].x; tmp.y=ql_atlasapo[i].y; tmp.z=ql_atlasapo[i].z;
vec_cellio1_ori.push_back(tmp);
}
}
else if(qs_cellname.compare(ql_celloi_name[j],Qt::CaseInsensitive)==0)
{
tmp.x=ql_atlasapo[i].x; tmp.y=ql_atlasapo[i].y; tmp.z=ql_atlasapo[i].z;
vec_cellio1_ori.push_back(tmp);
}
}
}
for(V3DLONG i=0;i<ql_musclecell_output.size();i++)
{
tmp.x=ql_musclecell_output[i].x;
tmp.y=ql_musclecell_output[i].y;
tmp.z=ql_musclecell_output[i].z;
vec_cellio1_tps.push_back(tmp);
}
//extract secondary interesting cells
for(V3DLONG i=0;i<ql_atlasapo.size();i++)
{
QString qs_cellname=ql_atlasapo[i].name;
qs_cellname=qs_cellname.simplified();
qs_cellname=qs_cellname.toUpper();
ql_atlasapo[i].name=qs_cellname;
for(V3DLONG j=0;j<ql_celloi2_name.size();j++)
{
if(ql_celloi2_name[j].contains("*"))
{
QString qs_cellnamevalid=ql_celloi2_name[j];
qs_cellnamevalid.remove("*");
if(qs_cellname.contains(qs_cellnamevalid,Qt::CaseInsensitive))
{
ql_cellio2_ori.push_back(ql_atlasapo[i]);
tmp.x=ql_atlasapo[i].x; tmp.y=ql_atlasapo[i].y; tmp.z=ql_atlasapo[i].z;
vec_cellio2_ori.push_back(tmp);
}
}
else if(qs_cellname.compare(ql_celloi2_name[j],Qt::CaseInsensitive)==0)
{
ql_cellio2_ori.push_back(ql_atlasapo[i]);
tmp.x=ql_atlasapo[i].x; tmp.y=ql_atlasapo[i].y; tmp.z=ql_atlasapo[i].z;
vec_cellio2_ori.push_back(tmp);
}
}
}
ql_cellio2_tps=ql_cellio2_ori;
printf("\t>>[%d] cells in the secondary intereting cell group.\n",ql_cellio2_ori.size());
//compute TPS paras
Matrix x4x4_affine,xnx4_c,xnxn_K;
if(!q_TPS_cd(vec_cellio1_ori,vec_cellio1_tps,0,x4x4_affine,xnx4_c,xnxn_K))
{
printf("ERROR: q_TPS_cd() return false!\n");
return false;
}
//compute TPS kernal matrix
Matrix xmxn_K;
if(!q_TPS_k(vec_cellio2_ori,vec_cellio1_ori,xmxn_K))
{
printf("ERROR: q_TPS_k() return false!\n");
return false;
}
//warp the secondary cells
Matrix x_ori(ql_cellio2_ori.size(),4),x_tps(ql_cellio2_ori.size(),4);
for(V3DLONG i=0;i<ql_cellio2_ori.size();i++)
{
x_ori(i+1,1)=1.0;
x_ori(i+1,2)=ql_cellio2_ori[i].x;
x_ori(i+1,3)=ql_cellio2_ori[i].y;
x_ori(i+1,4)=ql_cellio2_ori[i].z;
}
x_tps=x_ori*x4x4_affine+xmxn_K*xnx4_c;
for(V3DLONG i=0;i<ql_cellio2_tps.size();i++)
{
ql_cellio2_tps[i].x=x_tps(i+1,2)/x_tps(1,1);
ql_cellio2_tps[i].y=x_tps(i+1,3)/x_tps(1,1);
ql_cellio2_tps[i].z=x_tps(i+1,4)/x_tps(1,1);
}
}
//------------------------------------------------------------------------------------------------------------------------------------
printf("10. Map the annotated cell back to non-straightened image. \n");
QList<CellAPO> ql_musclecell_output_ori(ql_musclecell_output);
//map back to non-straightened image
if(vec2d_markers.size()>=2)
{
for(V3DLONG i=0;i<ql_musclecell_output.size();i++)
{
V3DLONG x=ql_musclecell_output[i].x;
V3DLONG y=ql_musclecell_output[i].y;
V3DLONG z=ql_musclecell_output[i].z;
ql_musclecell_output_ori[i].x=vec4d_mappingfield_str2ori[y][x][z][0];
ql_musclecell_output_ori[i].y=vec4d_mappingfield_str2ori[y][x][z][1];
ql_musclecell_output_ori[i].z=vec4d_mappingfield_str2ori[y][x][z][2];
}
}
if(b_use_celloi_2 || !qs_filename_celloi_2_input.isEmpty()) // b_use_celloi_2=DLG_stranno.checkBox_celloi_2->isChecked()
ql_musclecell_output_ori.append(ql_cellio2_tps);
//save deformed point cloud to apo file
if(!qs_filename_atals_output.isEmpty())
writeAPO_file(qPrintable(qs_filename_atals_output),ql_musclecell_output_ori);
//show deformed atlas pts in V3D
// if(!(paras_anno.b_showatlas || paras_anno.b_showsegmentation))
{
v3dhandle curwin=callback.currentImageWindow();
// v3dhandle curwin=callback.getImageWindowList()[0];
callback.open3DWindow(curwin);
LandmarkList curlist;
for(int i=0;i<ql_musclecell_output_ori.size();i++)
{
LocationSimple s;
s.x=ql_musclecell_output_ori[i].x+1;//note: marker coord start from 1 instead of 0
s.y=ql_musclecell_output_ori[i].y+1;//note: marker coord start from 1 instead of 0
s.z=ql_musclecell_output_ori[i].z+1;//note: marker coord start from 1 instead of 0
s.name=ql_musclecell_output_ori[i].name.toStdString();
s.radius=10;
curlist << s;
}
callback.setLandmark(curwin,curlist);
callback.updateImageWindow(curwin);
callback.pushObjectIn3DWindow(curwin);
}
//------------------------------------------------------------------------------------------------------------------------------------
printf("11. Save segmentation label image to file. \n");
if(!qs_filename_seglabel_output.isEmpty() && p_img8u_seglabel)
{
V3DLONG sz_seglabelimg[4]={sz_img_input[0],sz_img_input[1],sz_img_input[2],1};
simple_saveimage_wrapper(callback, qPrintable(qs_filename_seglabel_output),p_img8u_seglabel,sz_seglabelimg,1);
}
//------------------------------------------------------------------------------------------------------------------------------------
//free memory
printf(">>Free memory\n");
if(p_img8u_seglabel) {delete []p_img8u_seglabel; p_img8u_seglabel=0;}
if(p_strimg) {delete []p_strimg; p_strimg=0;}
if(sz_strimg) {delete []sz_strimg; sz_strimg=0;}
if(p_img_8u) {delete []p_img_8u; p_img_8u=0;}
if(p_img_input && !paras_str.b_imgfromV3D) {delete []p_img_input; p_img_input=0;}
//if(sz_img_input) {delete []sz_img_input; sz_img_input=0;}
//------------------------------------------------------------------------------------------------------------------------------------
v3d_msg("Program exit successfully!\n", 0);
return true;
}
int v3dneuron_tracing(V3DPluginCallback2 &callback, QWidget *parent)
{
v3dhandleList win_list = callback.getImageWindowList();
if(win_list.size()<1)
{
QMessageBox::information(0, title, QObject::tr("No image is open."));
return -1;
}
v3dhandle curwin = callback.currentImageWindow();
LandmarkList landmarks = callback.getLandmark(curwin);
if(landmarks.empty())
{
v3d_msg("Please set a landmark!");
return 0;
}
QList <ImageMarker> imagemarks;
for(int i = 0; i < landmarks.size(); i++)
{
ImageMarker m;
LocationSimple l = landmarks.at(i);
m.x = l.x;
m.y = l.y;
m.z = l.z;
imagemarks.push_back(m);
}
system("rm -f /tmp/mymarks.marker");
system("rm -f /tmp/tmp_out*");
writeMarker_file("/tmp/mymarks.marker",imagemarks);
QString img_file = callback.getImageName(curwin);
bool ok;
QString nt_path = QInputDialog::getText(0, QObject::tr("Set path"), QObject::tr("v3dneuron_tracing path : "), QLineEdit::Normal, "~/Local/bin/v3dneuron_tracing", &ok);
//QString paras = QObject::tr("v3dneuron_tracing -s %1 -S /tmp/mymarks.marker -o /tmp/tmp_out").arg(img_file);
QString paras = QObject::tr("%1 -s \"%2\" -S /tmp/mymarks.marker -o /tmp/tmp_out").arg(nt_path).arg(img_file);
qDebug(paras.toStdString().c_str());
//QMessageBox::information(0,"",paras);
system(paras.toStdString().c_str());
NeuronTree nt = readSWC_file("/tmp/tmp_out_0.swc");
//nt.editable = false;
callback.setSWC(curwin, nt);
callback.updateImageWindow(curwin);
callback.open3DWindow(curwin);
//callback.getView3DControl(curwin)->setShowSurfObjects(2);
//TestDialog dialog(callback, parent);
//if (dialog.exec()!=QDialog::Accepted) return -1;
//dialog.update();
//int i = dialog.i;
//int c = dialog.channel;
//Image4DSimple *p4DImage = callback.getImage(win_list[i]);
//if(p4DImage->getCDim() <= c) {v3d_msg(QObject::tr("The channel isn't existed.")); return -1;}
//V3DLONG sz[3];
//sz[0] = p4DImage->getXDim();
//sz[1] = p4DImage->getYDim();
//sz[2] = p4DImage->getZDim();
//unsigned char * inimg1d = p4DImage->getRawDataAtChannel(c);
//v3dhandle newwin;
//if(QMessageBox::Yes == QMessageBox::question(0, "", QString("Do you want to use the existing windows?"), QMessageBox::Yes, QMessageBox::No))
//newwin = callback.currentImageWindow();
//else
//newwin = callback.newImageWindow();
//p4DImage->setData(inimg1d, sz[0], sz[1], sz[2], sz[3]);
//callback.setImage(newwin, p4DImage);
//callback.setImageName(newwin, QObject::tr("v3dneuron_tracing"));
//callback.updateImageWindow(newwin);
return 1;
}
