bool GVFplugin::dofunc(const QString & func_name, const V3DPluginArgList & input, V3DPluginArgList & output, V3DPluginCallback2 & callback, QWidget * parent)
{
if (func_name == tr("gvf_segmentation"))
{
int c=1;
gvfsegPara segpara; // default values
segpara.diffusionIteration = 5;
segpara.fusionThreshold = 3;
segpara.minRegion = 10;
vector<char*> infiles, inparas, outfiles;
if(input.size() >= 1) infiles = *((vector<char*> *)input.at(0).p);
if(input.size() >= 2)
{
inparas = *((vector<char*> *)input.at(1).p);
if(inparas.size() >= 1) c = atoi(inparas.at(0));
if(inparas.size() >= 2) segpara.diffusionIteration = atoi(inparas.at(1));
if(inparas.size() >= 3) segpara.fusionThreshold = atoi(inparas.at(2));
if(inparas.size() >= 4) segpara.minRegion = atoi(inparas.at(3));
if(output.size() >= 1) outfiles = *((vector<char*> *)output.at(0).p);
}
char * inimg_file = ((vector<char*> *)(input.at(0).p))->at(0);
char * outimg_file = ((vector<char*> *)(output.at(0).p))->at(0);
cout<<"channel choice "<<c<<endl;
cout<<"diffusion Iterations "<<segpara.diffusionIteration<<endl;
cout<<"fusion threshold "<<segpara.fusionThreshold<<endl;
cout<<"minimum region size "<<segpara.minRegion<<endl;
cout<<"inimg_file = "<<inimg_file<<endl;
cout<<"outimg_file = "<<outimg_file<<endl;
// check the input parameters for invalid choices:
if ((segpara.diffusionIteration<1)||(segpara.fusionThreshold<1)||(segpara.minRegion)<0)
{
cout<< "* * * * * * * * * * * * * "<<endl;
cout<< "*"<<endl;
cout<< "INVALID parameter selection, type "<<endl;
cout<<" vaa3d -x gvf_cellseg -f help "<<endl;
cout<<"for more information"<<endl;
cout<< "* * * * * * * * * * * * * "<<endl;
cout<<""<<endl;
return false;
}
V3DLONG in_sz[4];
int datatype;
unsigned char * data1d = 0;
if(!simple_loadimage_wrapper(callback, inimg_file, data1d, in_sz, datatype))
{
cerr<<"load image "<<inimg_file<<" error!"<<endl;
return false;
}
// allocate memory for the images
Vol3DSimple <unsigned char> * tmp_inimg = 0;
Vol3DSimple <USHORTINT16> * tmp_outimg = 0;
try
{
tmp_inimg = new Vol3DSimple <unsigned char> (in_sz[0], in_sz[1], in_sz[2]);
tmp_outimg = new Vol3DSimple <USHORTINT16> (in_sz[0], in_sz[1], in_sz[2]);
}
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 false;
}
//load image
//
Image4DSimple * temp4D = callback.loadImage(inimg_file);
in_sz[0]=temp4D->getXDim();
in_sz[1]=temp4D->getYDim();
in_sz[2]=temp4D->getZDim();
in_sz[3]=temp4D->getCDim();
if (in_sz[3]==1)
{
c=1;
cout<< "Image only has 1 channel, segmenting channel 1"<<endl;
}
if ((c>in_sz[3])||(c<1))
{
cout<< "* * * * * * * * * * * * * "<<endl;
cout<< "*"<<endl;
cout<< "INVALID CHANNEL SELECTION: User selected channel "<<c<< "; image has "<< in_sz[3] << " channels."<<endl;
cout<< " aborting segmentation !"<<endl;
cout<<"*"<<endl;
cout<< "* * * * * * * * * * * * * "<<endl;
cout<<""<<endl;
return false;
}
//transfer single channel of data from Image4DSimple to old Vol3DSimple class
memcpy((void *)tmp_inimg->getData1dHandle(), (void *)temp4D->getRawDataAtChannel(c-1), in_sz[0]*in_sz[1]*in_sz[2]);
//now do computation using external function call
bool b_res = gvfCellSeg(tmp_inimg, tmp_outimg, segpara);
// clear out temporary space
if (tmp_inimg) {delete tmp_inimg; tmp_inimg=0;}
// now write to file
in_sz[3]=1;//for single channel output from gvfCellSeg
simple_saveimage_wrapper(callback, outimg_file, (unsigned char *)tmp_outimg->getData1dHandle(), in_sz, 2); //the output of gvfCellSeg is in 16bit
// clear out temporary space
if (tmp_outimg) {delete tmp_outimg; tmp_outimg=0;}
if (temp4D) {delete temp4D; temp4D=0;}
cout<<"Finished GVF Segmentation"<<endl;
}
else if (func_name == tr("help"))
{
cout<<endl;
cout<<endl;
cout<<" GVF segmentation plugin usage : vaa3d -x gvf_cellseg -f gvf_segmentation -i <input filename> -o <output filename -p <c> <iter> <fusion> <size>"<<endl;
cout<<" parameters: (default values in parentheses) "<<endl;
cout<<"c = channel of input file to use for segmentation (1) "<<endl;
cout<<"iter = number of diffusion iterations (must be > 0) (5) "<<endl;
cout<<"fusion = fusion size threshold (must be > 0) (3) "<<endl;
cout<<"size = minimum region size in voxels (10)"<<endl;
}
else return false;
return true;
}
bool profile_swc_func(V3DPluginCallback2 &callback, const V3DPluginArgList & input, V3DPluginArgList & output)
{
vector<char*> infiles, inparas, outfiles;
if(input.size() >= 1) infiles = *((vector<char*> *)input.at(0).p);
if(input.size() >= 2) inparas = *((vector<char*> *)input.at(1).p);
if(output.size() >= 1) outfiles = *((vector<char*> *)output.at(0).p);
if(infiles.size() != 2 && infiles.size() != 3)
{
cerr<<"Invalid input"<<endl;
return false;
}
QString imageFileName = QString(infiles[0]);
QString swcFileName = QString(infiles[1]);
QString output_csv_file;
if(!outfiles.empty())
output_csv_file = QString(outfiles[0]);
else
output_csv_file = swcFileName + ".csv";
float dilate_ratio = (inparas.size() >= 1) ? atof(inparas[0]) : 3.0;
int flip = (inparas.size() >= 2) ? atoi(inparas[1]) : 1;
int invert = (inparas.size() >= 3) ? atoi(inparas[2]) : 1;
cout<<"inimg_file = "<< imageFileName.toStdString()<<endl;
cout<<"inswc_file = "<< swcFileName.toStdString()<<endl;
cout<<"output_file = "<< output_csv_file.toStdString()<<endl;
cout<<"dilate_ratio = "<< dilate_ratio<<endl;
cout<<"flip y = "<< flip <<endl;
cout<<"invert intensity = "<< invert <<endl;
NeuronTree neuronTree;
if (swcFileName.endsWith(".swc") || swcFileName.endsWith(".SWC"))
{
neuronTree = readSWC_file(swcFileName);
}
else
{
cout<<"The file type you specified is not supported."<<endl;
return false;
}
Image4DSimple *image = callback.loadImage((char * )imageFileName.toStdString().c_str());
QList<IMAGE_METRICS> result_metrics = intensity_profile(neuronTree, image, dilate_ratio,flip,invert, callback);
IMAGE_METRICS m_stats = result_metrics[0];
/*
ENSEMBLE_METRICS m_stats = stats_ensemble(result_metrics);
*/
cout << "Overall Contrast-to-Background Ratio:" << m_stats.cnr << "\n"
<< "Overall Dynamic Range:"<< m_stats.dy << "\n"
<< "Mean BG Intensity:" << m_stats.bg_mean << ", with std = " << m_stats.bg_std << "\n"
<< "Mean FG Intensity:" << m_stats.fg_mean << ", with std = " << m_stats.fg_std << "\n"
<< "Mean Tubularity:" << m_stats.tubularity_mean << ", with std = " << m_stats.tubularity_std << "\n"
<< endl;
if (result_metrics.isEmpty())
{
cout<<"Error in intensity_profile() !"<<endl;
return false;
}
else{
if (!writeMetrics2CSV(result_metrics, output_csv_file))
{
cout<< "error in writeMetrics2CSV()" <<endl;
}
}
cout << "Segment type-specific screening metrics are exported in: " << output_csv_file.toStdString() <<endl;
return true;
}
bool findedgeimg(V3DPluginCallback2 &callback, const V3DPluginArgList & input, V3DPluginArgList & output)
{
cout<<"Welcome to Label edge of a mask image"<<endl;
if (output.size() != 1) return false;
int method_code = 0;
if (input.size()>=2)
{
vector<char*> paras = (*(vector<char*> *)(input.at(1).p));
if(paras.size() >= 1) method_code = atoi(paras.at(0));
}
char * inimg_file = ((vector<char*> *)(input.at(0).p))->at(0);
char * outimg_file = ((vector<char*> *)(output.at(0).p))->at(0);
cout<<"method_code = "<<method_code<<endl;
cout<<"inimg_file = "<<inimg_file<<endl;
cout<<"outimg_file = "<<outimg_file<<endl;
Image4DSimple *image = callback.loadImage(inimg_file);
if (!image || !image->valid())
{
cerr<<"load image "<<inimg_file<<" error!"<<endl;
return false;
}
V3DLONG szx=image->getXDim(),
szy=image->getYDim(),
szz=image->getZDim(),
szc=image->getCDim();
V3DLONG N = image->getTotalUnitNumber();
//create the output buffer
unsigned char *outputData = 0;
try
{
outputData = new unsigned char [N];
for (V3DLONG tmpi=0; tmpi<N; ++tmpi) outputData[tmpi] = 0; //preset to be all 0
}
catch (...)
{
v3d_msg("Fail to allocate memory.");
if (outputData) {
delete []outputData;
outputData=0;
}
return false;
}
Image4DSimple outputImage;
outputImage.setData((unsigned char*)outputData, szx, szy, szz, szc, V3D_UINT8);
Image4DProxy<Image4DSimple> outputIProxy(&outputImage);
//now do computation
{
bool bset255 = (method_code==0) ? false : true;
Image4DProxy<Image4DSimple> p(image);
Image4DProxy_foreach(p, ix, iy, iz, ic)
{
double v = p.value_at(ix, iy, iz, ic);
V3DLONG cx, cy, cz;
bool bb=false;
for (cz = iz-1; cz<iz+2; ++cz)
{
for (cy = iy-1; cy<iy+2; ++cy)
{
for (cx = ix-1; cx<ix+2; ++cx)
{
if (!p.is_inner(cx, cy, cz, ic))
continue;
if (v!=p.value_at(cx, cy, cz, ic))
{
*outputIProxy.at(ix, iy, iz, ic) = (bset255) ? 255 : v;
bb = true;
break;
}
}
if (bb) break;
}
if (bb) break;
}
//note that all value had been preset as 0, thus no need to set as the background color in case not an edge point
}
}
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;
}
bool dark_pruning_func(const V3DPluginArgList & input, V3DPluginArgList & output, V3DPluginCallback2 &callback)
{
if(input.size() <2 )
{
cerr<<"You must specify input eswc file and the corresponding image file."<<endl;
return false;
}
//parsing input
vector<char *> * inlist = (vector<char*> *)(input.at(0).p);
if (inlist->size()<2)
{
cerr<<"You must specify input eswc file and the corresponding image file."<<endl;
return false;
}
//parsing output
vector<char *> * outlist = (vector<char*> *)(output.at(0).p);
if (outlist->size() > 1)
{
cerr << "You can only specify one output file"<<endl;
return false;
}
//parsing parameters
int visible_thre =0;
vector<char*> * paras = (vector<char*> *)(input.at(1).p);
if (paras->size() == 1)
{
visible_thre = atoi(paras->at(0));
cout<<"The visible threshold for dark pruning is: "<<visible_thre<<endl;
}
else
{
cerr<<"One ( and only one) parameter is required."<<endl;
return false;
}
QString input_swc_fn = QString(inlist->at(0));
NeuronTree input_nt = readSWC_file(input_swc_fn);
Image4DSimple * p4dImage = callback.loadImage( inlist->at(1) );
if (!p4dImage || !p4dImage->valid())
return false;
QString outfileName;
if (outlist->size()==0)
outfileName = input_swc_fn + "_dark_pruned.swc";
else
outfileName = QString(outlist->at(0));
QList<NeuronSWC> result_swc;
if (!dark_pruning (input_nt, result_swc,p4dImage,visible_thre))
{
cerr<<"Error in dark pruning."<<endl;
return false;
}
export_listNeuron_2swc(result_swc,qPrintable(outfileName));
printf("%s has been generated successfully\n",qPrintable(outfileName));
return true;
}
