void setSeeds(V3DPluginCallback2 &v3d, QWidget *parent )
{
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);
}
void MovieFrom3Dviewer(V3DPluginCallback2 & v3d, QWidget * parent)
{
v3dhandle curwin = v3d.currentImageWindow();
if (!curwin)
{
v3d_msg("You don't have any image open in the main window.");
return;
}
v3d.open3DWindow(curwin);
if (controlPanel::m_pLookPanel)
{
controlPanel::m_pLookPanel->show();
return;
}
controlPanel* p = new controlPanel(v3d, parent);
if (p) p->show();
}
void SnapShoot3Dviewer(V3DPluginCallback2 & v3d, QWidget * parent)
{
v3dhandle curwin = v3d.currentImageWindow();
if (!curwin)
{
v3d_msg("You don't have any image opened in the main window.");
return;
}
v3d.open3DWindow(curwin);
QFileDialog d(parent);
d.setWindowTitle(QObject::tr("Choose output snapshot filename"));
d.setAcceptMode(QFileDialog::AcceptSave);
if (!d.exec()) return;
QString BMPfilename = (d.selectedFiles())[0];
if (BMPfilename.endsWith(".BMP", Qt::CaseInsensitive))
BMPfilename.resize(BMPfilename.length()-4); //by PHC
v3d.screenShot3DWindow(curwin, BMPfilename);
QMessageBox::information(0, title, QString("Snapshot was saved to: %1.BMP\n").arg(BMPfilename));
}
bool anisodiff_func(V3DPluginCallback2 &callback, QWidget *parent, input_PARA &PARA, bool bmenu)
{
unsigned char* p_img_input = 0;
V3DLONG sz_img_input[4];
if(bmenu)
{
v3dhandle curwin = callback.currentImageWindow();
if (!curwin)
{
QMessageBox::information(0, "", "You don't have any image open in the main window.");
return false;
}
Image4DSimple* p4DImage = callback.getImage(curwin);
if (!p4DImage)
{
QMessageBox::information(0, "", "The image pointer is invalid. Ensure your data is valid and try again!");
return false;
}
if(p4DImage->getDatatype()!=V3D_UINT8)
{
QMessageBox::information(0, "", "Please convert the image to be UINT8 and try again!");
return false;
}
if(p4DImage->getCDim()!=1)
{
QMessageBox::information(0, "", "The input image is not one channel image!");
return false;
}
p_img_input = p4DImage->getRawData();
sz_img_input[0] = p4DImage->getXDim();
sz_img_input[1] = p4DImage->getYDim();
sz_img_input[2] = p4DImage->getZDim();
sz_img_input[3] = 1;
}
else
{
int datatype = 0;
if (!simple_loadimage_wrapper(callback,PARA.inimg_file.toStdString().c_str(), p_img_input, sz_img_input, datatype))
{
fprintf (stderr, "Error happens in reading the subject file [%s]. Exit. \n",PARA.inimg_file.toStdString().c_str());
return false;
}
if(PARA.channel < 1 || PARA.channel > sz_img_input[3])
{
fprintf (stderr, "Invalid channel number. \n");
return false;
}
if(datatype !=1)
{
fprintf (stderr, "Please convert the image to be UINT8 and try again!\n");
return false;
}
}
//-----------------------------------------------------------------------------------------
printf("1. Find the bounding box and crop image. \n");
long l_boundbox_min[3],l_boundbox_max[3];//xyz
V3DLONG sz_img_crop[4];
long l_npixels_crop;
unsigned char *p_img8u_crop=0;
{
//find bounding box
unsigned char ***p_img8u_3d=0;
if(!new3dpointer(p_img8u_3d,sz_img_input[0],sz_img_input[1],sz_img_input[2],p_img_input))
{
printf("ERROR: Fail to allocate memory for the 4d pointer of image.\n");
if(p_img8u_3d) {delete3dpointer(p_img8u_3d,sz_img_input[0],sz_img_input[1],sz_img_input[2]);}
return false;
}
l_boundbox_min[0]=sz_img_input[0]; l_boundbox_min[1]=sz_img_input[1]; l_boundbox_min[2]=sz_img_input[2];
l_boundbox_max[0]=0; l_boundbox_max[1]=0; l_boundbox_max[2]=0;
for(long X=0;X<sz_img_input[0];X++)
for(long Y=0;Y<sz_img_input[1];Y++)
for(long Z=0;Z<sz_img_input[2];Z++)
if(p_img8u_3d[Z][Y][X]>0.1)
{
if(l_boundbox_min[0]>X) l_boundbox_min[0]=X; if(l_boundbox_max[0]<X) l_boundbox_max[0]=X;
if(l_boundbox_min[1]>Y) l_boundbox_min[1]=Y; if(l_boundbox_max[1]<Y) l_boundbox_max[1]=Y;
if(l_boundbox_min[2]>Z) l_boundbox_min[2]=Z; if(l_boundbox_max[2]<Z) l_boundbox_max[2]=Z;
}
printf(">>boundingbox: x[%ld~%ld],y[%ld~%ld],z[%ld~%ld]\n",l_boundbox_min[0],l_boundbox_max[0],
l_boundbox_min[1],l_boundbox_max[1],
l_boundbox_min[2],l_boundbox_max[2]);
//crop image
sz_img_crop[0]=l_boundbox_max[0]-l_boundbox_min[0]+1;
sz_img_crop[1]=l_boundbox_max[1]-l_boundbox_min[1]+1;
sz_img_crop[2]=l_boundbox_max[2]-l_boundbox_min[2]+1;
sz_img_crop[3]=1;
l_npixels_crop=sz_img_crop[0]*sz_img_crop[1]*sz_img_crop[2];
p_img8u_crop=new(std::nothrow) unsigned char[l_npixels_crop]();
if(!p_img8u_crop)
{
printf("ERROR: Fail to allocate memory for p_img32f_crop!\n");
if(p_img8u_3d) {delete3dpointer(p_img8u_3d,sz_img_input[0],sz_img_input[1],sz_img_input[2]);}
return false;
}
unsigned char *p_tmp=p_img8u_crop;
for(long Z=0;Z<sz_img_crop[2];Z++)
for(long Y=0;Y<sz_img_crop[1];Y++)
for(long X=0;X<sz_img_crop[0];X++)
{
*p_tmp = p_img8u_3d[Z+l_boundbox_min[2]][Y+l_boundbox_min[1]][X+l_boundbox_min[0]];
p_tmp++;
}
if(p_img8u_3d) {delete3dpointer(p_img8u_3d,sz_img_input[0],sz_img_input[1],sz_img_input[2]);}
}
//saveImage("d:/SVN/Vaa3D_source_code/v3d_external/released_plugins/v3d_plugins/anisodiffusion_littlequick/crop.raw",p_img8u_crop,sz_img_crop,1);
//-----------------------------------------------------------------------------------------
//convert image data type to float
printf("2. Convert image data to float and scale to [0~255]. \n");
float *p_img32f_crop=0;
{
p_img32f_crop=new(std::nothrow) float[l_npixels_crop]();
if(!p_img32f_crop)
{
printf("ERROR: Fail to allocate memory for p_img32f_crop!\n");
if(p_img8u_crop) {delete []p_img8u_crop; p_img8u_crop=0;}
if(p_img32f_crop) {delete []p_img32f_crop; p_img32f_crop=0;}
return false;
}
//find the maximal intensity value
float d_maxintensity_input=0.0;
for(long i=0;i<l_npixels_crop;i++)
if(p_img8u_crop[i]>d_maxintensity_input)
d_maxintensity_input=p_img8u_crop[i];
//convert and rescale
for(long i=0;i<l_npixels_crop;i++)
p_img32f_crop[i]=p_img8u_crop[i]/d_maxintensity_input*255.0;
printf(">>d_maxintensity=%.2f\n",d_maxintensity_input);
//free input image to save memory
//if(p_img_input) {delete []p_img_input; p_img_input=0;}
if(p_img8u_crop) {delete []p_img8u_crop; p_img8u_crop=0;}
}
//-----------------------------------------------------------------------------------------
//do anisotropic diffusion
printf("3. Do anisotropic diffusion... \n");
float *p_img32f_crop_output=0;
if(!q_AnisoDiff3D(p_img32f_crop,sz_img_crop,p_img32f_crop_output))
{
printf("ERROR: q_AnisoDiff3D() return false!\n");
if(p_img8u_crop) {delete []p_img8u_crop; p_img8u_crop=0;}
if(p_img32f_crop) {delete []p_img32f_crop; p_img32f_crop=0;}
if(p_img32f_crop_output) {delete []p_img32f_crop_output; p_img32f_crop_output=0;}
return false;
}
if(p_img32f_crop) {delete []p_img32f_crop; p_img32f_crop=0;}
//-----------------------------------------------------------------------------------------
printf("4. Reconstruct processed crop image back to original size. \n");
unsigned char *p_img8u_output=0;
long l_npixels=sz_img_input[0]*sz_img_input[1]*sz_img_input[2]*sz_img_input[3];
{
p_img8u_output=new(std::nothrow) unsigned char[l_npixels]();
if(!p_img8u_output)
{
printf("ERROR: Fail to allocate memory for p_img8u_output!\n");
if(p_img32f_crop_output) {delete []p_img32f_crop_output; p_img32f_crop_output=0;}
return false;
}
//copy original image data to output image
for(long i=0;i<l_npixels;i++)
p_img8u_output[i]=p_img_input[i];
unsigned char ***p_img8u_3d=0;
if(!new3dpointer(p_img8u_3d,sz_img_input[0],sz_img_input[1],sz_img_input[2],p_img8u_output))
{
printf("ERROR: Fail to allocate memory for the 4d pointer of image.\n");
if(p_img8u_output) {delete []p_img8u_output; p_img8u_output=0;}
if(p_img32f_crop_output) {delete []p_img32f_crop_output; p_img32f_crop_output=0;}
return false;
}
float *p_tmp=p_img32f_crop_output;
for(long Z=0;Z<sz_img_crop[2];Z++)
for(long Y=0;Y<sz_img_crop[1];Y++)
for(long X=0;X<sz_img_crop[0];X++)
{
p_img8u_3d[Z+l_boundbox_min[2]][Y+l_boundbox_min[1]][X+l_boundbox_min[0]]=(unsigned char)(*p_tmp);
p_tmp++;
}
if(p_img8u_3d) {delete3dpointer(p_img8u_3d,sz_img_input[0],sz_img_input[1],sz_img_input[2]);}
if(p_img32f_crop_output) {delete []p_img32f_crop_output; p_img32f_crop_output=0;}
}
//-----------------------------------------------------------------------------------------
//save or display
if(bmenu)
{
printf("5. Display the processed image in Vaa3D. \n");
//push result image back to v3d
v3dhandle newwin=callback.newImageWindow("output");
Image4DSimple img4D_output;
img4D_output.setData(p_img8u_output,sz_img_input[0],sz_img_input[1],sz_img_input[2],1,V3D_UINT8);
callback.setImage(newwin,&img4D_output);
callback.updateImageWindow(newwin);
callback.open3DWindow(newwin);
}
else
{
printf("5. Save the processed image to file. \n");
QString str_outimg_filename = PARA.inimg_file + "_anisodiff.raw";
saveImage(qPrintable(str_outimg_filename),p_img8u_output,sz_img_input,1);
if(p_img8u_output) {delete []p_img8u_output; p_img8u_output=0;}
}
printf(">>Program complete success!\n");
return true;
}
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;
}
