bool open_fiji::dofunc(const QString & func_name, const V3DPluginArgList & input, V3DPluginArgList & output, V3DPluginCallback2 & callback, QWidget * parent)
{
if (func_name == tr("openfiji"))
{
vector<char*> infiles, outfiles;
if(input.size()==0) {
cout<<"for usage type: vaa3d -x open_fiji -f help"<<endl;
return false;
}
if(input.size() >= 1) infiles = *((vector<char*> *)input.at(0).p);
if(input.size() >= 2)
{
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);
call_open_using_imagej(false, QString(inimg_file ),QString(outimg_file), callback);
}
else if (func_name == tr("help"))
{
cout<<"Usage : vaa3d -x open_fiji -f openfiji -i <input_file_name> -o <output_file_name> "<<endl;
}
else return false;
return true;
}
bool mostVesselTracerPlugin::dofunc(const QString & func_name, const V3DPluginArgList & input, V3DPluginArgList & output, V3DPluginCallback2 & callback, QWidget * parent)
{
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 (func_name == tr("MOST_trace"))
{
return autotrace(input, output,callback);
}
else if (func_name == tr("help"))
{
cout<<"Usage : v3d -x dllname -f MOST_trace -i <inimg_file> -p <ch> <th> <seed> <slip>"<<endl;
cout<<endl;
cout<<"ch the input channel value, start from 1, default 1"<<endl;
cout<<"th the threshold value, default 20"<<endl;
cout<<"seed window size of the seed, default 20"<<endl;
cout<<"slip window size to slip from seed, default 20"<<endl;
cout<<"The output swc file will be named automatically based on the input image file nmae"<<endl;
cout<<endl;
cout<<endl;
}
else return false;
return true;
}
bool SigenPlugin::dofunc(
const QString &func_name,
const V3DPluginArgList &input,
V3DPluginArgList & /* output */,
V3DPluginCallback2 &callback,
QWidget *parent) {
using std::vector;
if (func_name == tr("trace")) {
input_PARA PARA;
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 *>();
if (infiles.empty()) {
fprintf(stderr, "Need input image. \n");
return false;
} else {
PARA.inimg_file = infiles[0];
}
int k = 0;
PARA.channel = ((int)paras.size() >= k + 1) ? atoi(paras[k]) : 1;
k++;
reconstruction_func(callback, parent, PARA, /* via_gui = */ false);
} else if (func_name == tr("help")) {
////HERE IS WHERE THE DEVELOPERS SHOULD UPDATE THE USAGE OF THE PLUGIN
printf("**** Usage of SIGEN tracing **** \n");
printf("vaa3d -x SIGEN -f trace -i <inimg_file> -p <channel> <other parameters>\n");
printf("inimg_file The input image\n");
printf("channel Data channel for tracing. Start from 1 (default 1).\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;
}
bool processImage(V3DPluginCallback2 &callback, const V3DPluginArgList & input, V3DPluginArgList & output, unsigned int rotateflag)
{
cout<<"Welcome to Rotate image"<<endl;
if (input.size() != 1 || output.size() != 1) return false;
char * inimg_file = ((vector<char*> *)(input.at(0).p))->at(0);
char * outimg_file = ((vector<char*> *)(output.at(0).p))->at(0);
cout<<"rotateflag = "<<rotateflag<<endl;
cout<<"inimg_file = "<<inimg_file<<endl;
cout<<"outimg_file = "<<outimg_file<<endl;
unsigned char * data1d = 0;
V3DLONG in_sz[4];
int datatype;
if(!simple_loadimage_wrapper(callback, inimg_file, data1d, in_sz, datatype))
{
cerr<<"load image "<<inimg_file<<" error!"<<endl;
return false;
}
unsigned char* outimg = 0;
V3DLONG szx=in_sz[0], szy=in_sz[1], szz=in_sz[2], szc=in_sz[3];
switch (datatype)
{
case 1: rotateimage(data1d, in_sz, V3D_UINT8, rotateflag, outimg); break;
case 2: rotateimage(data1d, in_sz, V3D_UINT16, rotateflag, outimg); break;
case 4: rotateimage(data1d, in_sz, V3D_FLOAT32, rotateflag, outimg); break;
default:
v3d_msg("Invalid datatype.");
if (data1d) {delete []data1d; data1d=0;}
return false;
}
// save image
switch(rotateflag)
{
case 1:
case 2:
in_sz[0]=szy; in_sz[1]=szx;
simple_saveimage_wrapper(callback, outimg_file, (unsigned char *)outimg, in_sz, datatype);
break;
case 3:
in_sz[0]=szx; in_sz[1]=szy;
simple_saveimage_wrapper(callback, outimg_file, (unsigned char *)outimg, in_sz, datatype);
break;
default:
break;
}
if (outimg) {delete []outimg; outimg =0;}
if (data1d) {delete []data1d; data1d=0;}
return true;
}
bool swc2eswc_io(const V3DPluginArgList & input, V3DPluginArgList & output)
{
cout<<"Welcome to swc2eswc_io"<<endl;
vector<char*>* inlist = (vector<char*>*)(input.at(0).p);
vector<char*>* outlist = NULL;
if(input.size() != 1)
{
printf("Please specify both input file name.\n");
return false;
}
QString fileOpenName = QString(inlist->at(0));
QString fileSaveName;
QString tmp = fileOpenName;
if (output.size()==0)
{
printf("No outputfile specified.\n");
tmp.chop(3);
fileSaveName = tmp + "eswc";
}
else if (output.size()==1)
{
outlist = (vector<char*>*)(output.at(0).p);
fileSaveName = QString(outlist->at(0));
}
else
{
printf("You have specified more than 1 output file.\n");
return false;
}
NeuronTree neuron;
vector<V3DLONG> segment_id, segment_layer;
if (fileOpenName.endsWith(".swc") || fileOpenName.endsWith(".SWC"))
{
neuron = readSWC_file(fileOpenName);
segment_id, segment_layer;
if (!swc2eswc(neuron,segment_id, segment_layer))
{
v3d_msg("Cannot convert swc to eswc.", 0);
return false;
}
}
else {
v3d_msg("The file type you specified is not supported. Please check.", 0);
return false;
}
if (!export_eswc(neuron,segment_id,segment_layer,qPrintable(fileOpenName),qPrintable(fileSaveName)))
{
v3d_msg("fail to write the output eswc file.", 0);
return false;
}
return true;
}
bool retype_swc::dofunc(const QString & func_name, const V3DPluginArgList & input, V3DPluginArgList & output, V3DPluginCallback2 & callback, QWidget * parent)
{
vector<char*> infiles, paras, outfiles;
if(input.size() >= 1) infiles = *((vector<char*> *)input.at(0).p);
if(input.size() >= 2) paras = *((vector<char*> *)input.at(1).p);
if(output.size() >= 1) outfiles = *((vector<char*> *)output.at(0).p);
if (func_name == tr("retype"))
{
cout<<"Welcome to swc retyping plugin"<<endl;
if(infiles.empty())
{
cerr<<"Need input swc file"<<endl;
return false;
}
QString inswc_file = infiles[0];
int k=0;
int type = (paras.size() >= k+1) ? atoi(paras[k]) : 3; k++;//0;
QString outswc_file;
if(!outfiles.empty())
outswc_file = outfiles[0];
else
outswc_file = inswc_file + "_retyped.swc";
cout<<"inswc_file = "<<inswc_file.toStdString().c_str()<<endl;
cout<<"node type = "<<type<<endl;
cout<<"outswc_file = "<<outswc_file.toStdString().c_str()<<endl;
NeuronTree nt;
nt = readSWC_file(inswc_file);
for(V3DLONG i = 0; i < nt.listNeuron.size(); i++)
{
if(nt.listNeuron[i].parent == -1)
nt.listNeuron[i].type = 1;
else
nt.listNeuron[i].type = type;
}
if (!export_list2file(nt.listNeuron,outswc_file,inswc_file))
{
v3d_msg("fail to write the output swc file.");
return false;
}
}
else if (func_name == tr("help"))
{
cout<<"Usage : v3d -x dllname -f retype -i <inswc_file> -o <outswc_file> -p <type>"<<endl;
cout<<endl;
}
else return false;
return true;
}
bool file_transform::dofunc(const QString & func_name, const V3DPluginArgList & input, V3DPluginArgList & output, V3DPluginCallback2 & callback, QWidget * parent)
{
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 (func_name == tr("affineImage"))
{
qDebug()<<"==== affine and combine images ====";
if(infiles.size()!=3 || outfiles.size()!=1){
qDebug()<<"ERROR: please set input and output!";
printHelp();
return false;
}
QString fname_img_tar=((vector<char*> *)(input.at(0).p))->at(0);
QString fname_img_sub=((vector<char*> *)(input.at(0).p))->at(1);
QString fname_amat=((vector<char*> *)(input.at(0).p))->at(2);
QString fname_output=((vector<char*> *)(output.at(0).p))->at(0);
//init parameters
bool b_channelSeperate = false;
bool b_negativeShift = true;
int interpMethod = 0;
if(input.size() >= 2){
vector<char*> paras = (*(vector<char*> *)(input.at(1).p));
if(paras.size()>0){
int tmp=atoi(paras.at(0));
if(tmp==1)
interpMethod = 1;
}
if(paras.size()>1){
int tmp=atoi(paras.at(1));
if(tmp==0)
b_negativeShift = false;
}
if(paras.size()>2){
int tmp=atoi(paras.at(2));
if(tmp==1)
b_channelSeperate = true;
}
}
doAffineImage(callback, fname_img_tar, fname_img_sub, fname_amat, fname_output, interpMethod, b_negativeShift, b_channelSeperate);
}
else if (func_name == tr("help"))
{
printHelp();
}
else return false;
return true;
}
bool RivuletPlugin::dofunc(const QString & func_name, const V3DPluginArgList & input, V3DPluginArgList & output, V3DPluginCallback2 & callback, QWidget * parent)
{
if (func_name == tr("tracing_func"))
{
bool bmenu = false;
input_PARA PARA;
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*>();
if(infiles.empty())
{
fprintf (stderr, "Need input image. \n");
return false;
}
else
PARA.inimg_file = infiles[0];
int k=0;
PARA.channel = (paras.size() >= k+1) ? atoi(paras[k]) : 1; k++;
PARA.threshold = (paras.size() >= k+1) ? atoi(paras[k]) : 10; k++;
PARA.stepsize = (paras.size() >= k+1) ? atoi(paras[k]) : 1; k++;
PARA.gap = (paras.size() >= k+1) ? atoi(paras[k]) : 15; k++;
PARA.dumpbranch = (paras.size() >= k+1) ? atoi(paras[k]) : 0; k++;
PARA.connectrate = (paras.size() >= k+1) ? atof(paras[k]) : 1.5; k++;
PARA.percentage = (paras.size() >= k+1) ? atof(paras[k]) : 0.98; k++;
if (PARA.percentage > 1.0)
PARA.percentage = 1.0;
PARA.sigma = (paras.size() >= k+1) ? atoi(paras[k]) : 1; k++;
PARA.alpha_one = (paras.size() >= k+1) ? atoi(paras[k]) : 1; k++;
PARA.alpha_two = (paras.size() >= k+1) ? atoi(paras[k]) : 1; k++;
reconstruction_func(callback,parent,PARA,bmenu);
}
else if (func_name == tr("help"))
{
printf("**** Usage of Rivulet tracing **** \n");
printf("vaa3d -x Rivulet -f tracing_func -i <inimg_file> -p <channel> <threshold> <stepsize> <gap> <dumpbranch> <connectrate> <percentage>\n");
printf("inimg_file\tThe input image\n");
printf("channel\tData channel for tracing. Start from 1 (default 1).\n");
printf("threshold\tThe background threshold for segmentation (default 10).\n");
printf("stepsize\tThe step size of gradient descent tracing (default 1).\n");
printf("gap\tThe gap allowed for steps on background voxels. Useful for noisy images (default 15)\n");
printf("dumpbranch\tWhether the unconnected branches will be dumpped. (default 0)\n");
printf("connectrate\tBranch terminis within connectrate*(radius+3) will be connected to the trunk. (default 1.5)\n");
printf("percentage\tThe converage expected on the binary image before stopping tracing. (default 0.98)\n");
printf("outswc_file\tWill 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;
}
bool neurontracing_rotation::dofunc(const QString & func_name, const V3DPluginArgList & input, V3DPluginArgList & output, V3DPluginCallback2 & callback, QWidget * parent)
{
if (func_name == tr("tracing_func"))
{
bool bmenu = false;
input_PARA PARA;
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*>();
if(infiles.empty())
{
fprintf (stderr, "Need input image. \n");
return false;
}
PARA.inimg_file = infiles[0];
PARA.image = 0;
int k=0;
// QString inmarker_file = paras.empty() ? "" : paras[k]; if(inmarker_file == "NULL") inmarker_file = ""; k++;
PARA.rotation_degree = (paras.size() >= k+1) ? atoi(paras[k]) : 36; k++;
PARA.channel = (paras.size() >= k+1) ? atoi(paras[k]) : 1; k++;
PARA.bkg_thresh = (paras.size() >= k+1) ? atoi(paras[k]) : 10; if(PARA.bkg_thresh == atoi("AUTO")) PARA.bkg_thresh = -1;k++;
PARA.b_256cube = (paras.size() >= k+1) ? atoi(paras[k]) : 0; k++;
PARA.b_RadiusFrom2D = (paras.size() >= k+1) ? atoi(paras[k]) : 1; k++;
PARA.is_gsdt = (paras.size() >= k+1) ? atoi(paras[k]) : 0; k++;
PARA.is_break_accept = (paras.size() >= k+1) ? atoi(paras[k]) : 0; k++;
PARA.length_thresh = (paras.size() >= k+1) ? atoi(paras[k]) : 5; k++;
reconstruction_func(callback,parent,PARA,bmenu);
}
else if (func_name == tr("help"))
{
////HERE IS WHERE THE DEVELOPERS SHOULD UPDATE THE USAGE OF THE PLUGIN
printf("**** Usage of neurontracing_rotation tracing **** \n");
printf("vaa3d -x neurontracing_rotation -f tracing_func -i <inimg_file> -p <channel> <other parameters>\n");
printf("inimg_file The input image\n");
printf("channel Data channel for tracing. Start from 1 (default 1).\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;
}
bool NeuroStalker::dofunc(const QString & func_name,
const V3DPluginArgList & input,
V3DPluginArgList & output,
V3DPluginCallback2 & callback,
QWidget * parent)
{
if (func_name == tr("tracing_func"))
{
bool bmenu = false;
input_PARA PARA;
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*>();
if(infiles.empty())
{
fprintf (stderr, "Need input image. \n");
return false;
}
else
PARA.inimg_file = infiles[0];
int k=0;
PARA.channel = (paras.size() >= k+1) ? atoi(paras[k]) : 1; k++;
PARA.preprocessing = (paras.size() >= k+1) ? atoi(paras[k]) : 1; k++;
PARA.unittest = (paras.size() >= k+1) ? atoi(paras[k]) : 1; k++;
PARA.step = (paras.size() >= k+1) ? atoi(paras[k]) : 1; k++;
PARA.stepsize = (paras.size() >= k+1) ? atoi(paras[k]) : 1; k++;
PARA.threshold = (paras.size() >= k+1) ? atoi(paras[k]) : 1; k++;
cout<<"Input step test: "<<PARA.step<<endl;
reconstruction_func(callback,parent,PARA,bmenu);
}
else if (func_name == tr("help"))
{
////HERE IS WHERE THE DEVELOPERS SHOULD UPDATE THE USAGE OF THE PLUGIN
printf("**** Usage of NeuroStalker tracing **** \n");
printf("vaa3d -x NeuroStalker -f tracing_func -i <inimg_file> -p <channel> <preprocessing> <run unit-tests>\n");
printf("inimg_file The input image\n");
printf("channel Data channel for tracing. Start from 1 (default 1).\n");
printf("preprocessing The preprocessing flag - 1: Crop Only; 2: Downsample; 3: Downsample and crop; \n");
printf("run unit-tests - 1: Run Tracing Only; 2: Run unit-tests only; 3: Run Both Unit Tests and Tracing; \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;
}
bool resample_swc(const V3DPluginArgList & input, V3DPluginArgList & output)
{
cout<<"Welcome to resample_swc"<<endl;
vector<char*>* inlist = (vector<char*>*)(input.at(0).p);
vector<char*>* outlist = NULL;
vector<char*>* paralist = NULL;
if(input.size() != 2)
{
printf("Please specify both input file and step length parameter.\n");
return false;
}
paralist = (vector<char*>*)(input.at(1).p);
if (paralist->size()!=1)
{
printf("Please specify only one parameter - the resampling step length.\n");
return false;
}
double step = atof(paralist->at(0));
QString fileOpenName = QString(inlist->at(0));
QString fileSaveName;
if (output.size()==0)
{
printf("No outputfile specified.\n");
fileSaveName = fileOpenName + "_resampled.swc";
}
else if (output.size()==1)
{
outlist = (vector<char*>*)(output.at(0).p);
fileSaveName = QString(outlist->at(0));
}
else
{
printf("You have specified more than 1 output file.\n");
return false;
}
NeuronTree nt;
if (fileOpenName.toUpper().endsWith(".SWC") || fileOpenName.toUpper().endsWith(".ESWC"))
nt = readSWC_file(fileOpenName);
NeuronTree result = resample(nt,step);
if (!export_list2file(result.listNeuron, fileSaveName, fileOpenName))
{
printf("fail to write the output swc file.\n");
return false;
}
return true;
}
bool border_tips::dofunc(const QString & func_name, const V3DPluginArgList & input, V3DPluginArgList & output, V3DPluginCallback2 & callback, QWidget * parent)
{
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 (func_name == tr("help"))
{
qDebug()<<"No do func available.";
}
else return false;
return true;
}
bool markertree::dofunc(const QString & func_name, const V3DPluginArgList & input, V3DPluginArgList & output, V3DPluginCallback2 & callback, QWidget * parent)
{
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 (func_name == tr("help"))
{
v3d_msg("To be implemented");
}
else return false;
return true;
}
bool BlastNeuronPlugin::dofunc(const QString & func_name, const V3DPluginArgList & input, V3DPluginArgList & output, V3DPluginCallback2 & callback, QWidget * parent)
{
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 (func_name == tr("global_retrieve"))
{
return(global_retrieve_main(input, output));
}
else if (func_name == tr("local_alignment"))
{
return(local_alignment_main(input, output));
}
else if (func_name == tr("batch_compute"))
{
return (batch_compute_main(input, output));
}
else if (func_name == tr("pre_processing"))
{
return (pre_processing_main(input, output));
}
else if (func_name == tr("inverse_projection"))
{
return (inverse_projection_main(input, output));
}
else
{
printf("\nBlastNeuron Plugin: rapid global retrieval and local alignent of 3D neuron morphologies. This plugin also includes pre-processing, inverse projection and batch feature computation. by Yinan Wan.\n\n");
printf("Functions:\n");
printf("\t pre_processing prune, resample and align neuron swcs.\n");
printf("\t global_retrieve given a query neuron, retrieve morphologically similar neurons from a neuron feature database.\n");
printf("\t local_alignment point to point alignment of two morphologically similar neurosn.\n");
printf("\t batch_compute generate neuron feature database (.nfb) file first to speed up neuron retrieve\n");
printf("\t invert_projection find an optimal affine transform between neuron structures regardless of topology.\n\n");
printf("Example: \n");
printf("\t vaa3d -x blastneuron -f pre_processing -p \"#i input.swc #o result.swc #l 3 #s 2 #r 1 \"\n");
printf("\t vaa3d -x blastneuron -f batch_compute -p \"#i mydatabase.ano #o features.nfb\"\n");
printf("\t vaa3d -x blastneuron -f global_retrieve -p \"#d features.nfb #q query.swc #n 10 #m 1,2,4 #o retrieve.ano\"\n");
printf("\t vaa3d -x blastneuron -f local_alignment -p \"#t target.swc #s subject.swc #o match.swc\"\n");
printf("\t vaa3d -x blastneuron -f inverse_projection -p \"#i target.swc #o target_invp.swc\"\n\n");
printf("Type vaa3d -x blastneuron -f <function_name> for instructions to run individual functions.\n");
printf("Alternatively, you can run a query search from the neuron feature database with a bash script: try \"sh blastneuron_plugin.sh\" for detailed instruction\n\n");
return true;
}
}
bool AnisoDiffPlugin_littlequick::dofunc(const QString & func_name, const V3DPluginArgList & input, V3DPluginArgList & output, V3DPluginCallback2 & callback, QWidget * parent)
{
if (func_name == tr("anisodiff_littlequick_menu"))
{
cout<<"============== Welcome to anisodiff function ================="<<endl;
bool bmenu = false;
input_PARA PARA;
vector<char*> * pinfiles = (input.size() >= 1) ? (vector<char*> *) input[0].p : 0;
vector<char*> infiles = (pinfiles != 0) ? * pinfiles : vector<char*>();
if(infiles.empty())
{
fprintf (stderr, "Need input image. \n");
return false;
}
else
PARA.inimg_file = infiles[0];
anisodiff_func(callback,parent,PARA,bmenu);
}
else
{
printHelp();
}
return true;
}
bool neuronScore::dofunc(const QString & func_name, const V3DPluginArgList & input, V3DPluginArgList & output, V3DPluginCallback2 & callback, QWidget * parent)
{
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 (func_name == tr("calculate_score"))
{
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*> * poutfiles = (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*>();
vector<char*> outfiles = (poutfiles != 0) ? * poutfiles : vector<char*>();
if(infiles.size()<2)
{
fprintf (stderr, "Need input image and swc. \n");
printHelp();
return false;
}
if(outfiles.empty())
{
fprintf (stderr, "Need output file name. \n");
printHelp();
return false;
}
int k=0;
int scoreType = (paras.size() >= k+1) ? atoi(paras[k]) : 1; k++;
float radiusFactor = (paras.size() >= k+1) ? atof(paras[k]) : 2; k++;
doCalculateScore(callback, infiles[0],infiles[1],outfiles[0],scoreType,radiusFactor,0);
}
else if (func_name == tr("help"))
{
printHelp();
}
else return false;
return true;
}
bool median_swc_func(const V3DPluginArgList & input, V3DPluginArgList & output)
{
if(input.size()==0) return false;
//parsing input
vector<char *> * inlist = (vector<char*> *)(input.at(0).p);
if (inlist->size() == 0)
{
cerr<<"You must specify input linker or swc files"<<endl;
return false;
}
V3DLONG neuronNum = 0;
vector<NeuronTree> nt_list;
QString qs_linker;
QStringList nameList;
for (int i=0;i<inlist->size();i++)
{
qs_linker = QString(inlist->at(i));
if (qs_linker.toUpper().endsWith(".ANO"))
{
cout<<"(0). reading a linker file."<<endl;
P_ObjectFileType linker_object;
if (!loadAnoFile(qs_linker,linker_object))
{
fprintf(stderr,"Error in reading the linker file.\n");
return 1;
}
nameList = linker_object.swc_file_list;
neuronNum += nameList.size();
for (V3DLONG i=0;i<neuronNum;i++)
{
NeuronTree tmp = readSWC_file(nameList.at(i));
nt_list.push_back(tmp);
}
}
else if (qs_linker.toUpper().endsWith(".SWC"))
{
cout<<"(0). reading an swc file"<<endl;
NeuronTree tmp = readSWC_file(qs_linker);
nt_list.push_back(tmp);
neuronNum++;
}
}
cout << "There are "<<nt_list.size() <<" input neurons."<<endl;
int idx = median_swc(nt_list);
if (idx <0){
cerr << "error in median_swc()" << endl;
return false;
}
cout<<"Median swc is " << idx << endl;
return true;
}
bool nctuTW::dofunc(const QString & func_name, const V3DPluginArgList & input, V3DPluginArgList & output, V3DPluginCallback2 & callback, QWidget * parent)
{
if (func_name == tr("tracing_func"))
{
bool bmenu = false;
input_PARA PARA;
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*>();
if(infiles.empty())
{
fprintf (stderr, "Need input image. \n");
return false;
}
else
PARA.inimg_file = infiles[0];
int k=0;
PARA.inmarker_file = paras.empty() ? "" : paras[k]; if(PARA.inmarker_file == "NULL") PARA.inmarker_file = ""; k++;
PARA.threshold = (paras.size() >= k+1) ? atof(paras[k]) : 0.9;
reconstruction_func(callback,parent,PARA,bmenu);
}
else if (func_name == tr("help"))
{
////HERE IS WHERE THE DEVELOPERS SHOULD UPDATE THE USAGE OF THE PLUGIN
printf("**** Usage of nctuTW tracing **** \n");
printf("vaa3d -x nctuTW -f tracing_func -i <inimg_file> -p <inmarker_file> <threshold>\n");
printf("inimg_file The input image\n");
printf("inmarker_file If no input marker file, please set this para to NULL and it will detect soma automatically.\n");
printf("threshold Default 0.9, otherwise the threshold (from 0 to 1) specified by a user will be used.\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;
}
bool v3dneuron_tracing(const V3DPluginArgList & input, V3DPluginArgList & output)
{
cout<<"Welcome to v3dneuron_tracing"<<endl;
if(input.size() != 2 || output.size() != 1) return false;
char * paras = 0;
if(((vector<char*> *)(input.at(1).p))->empty()){paras = new char[1]; paras[0]='\0';}
else paras = (*(vector<char*> *)(input.at(1).p)).at(0);
cout<<"paras : "<<paras<<endl;
for(int i = 0; i < strlen(paras); i++)
{
if(paras[i] == '#') paras[i] = '-';
}
cout<<"paras : "<<paras<<endl;
cout<<string("v3dneuron_tracing ").append(paras).c_str()<<endl;
system(string("v3dneuron_tracing ").append(paras).c_str());
return true;
}
bool SWCRadiusPlugin::dofunc(const QString & func_name, const V3DPluginArgList & input, V3DPluginArgList & output, V3DPluginCallback2 & callback, QWidget * parent)
{
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 (func_name == tr("neuron_radius"))
{
if(infiles.size() != 2 && infiles.size() != 3)
{
cerr<<"Invalid input"<<endl;
return false;
}
string inimg_file = infiles[0];
string inswc_file = infiles[1];
string outswc_file = (infiles.size() == 3) ? infiles[2] : "";
if(outswc_file == "") outswc_file = inswc_file + ".out.swc";
double bkg_thresh = (inparas.size() >= 1) ? atof(inparas[0]) : 40;
bool is_2d = (inparas.size() == 2) ? atoi(inparas[1]) : 0;
cout<<"inimg_file = "<<inimg_file<<endl;
cout<<"inswc_file = "<<inswc_file<<endl;
cout<<"outswc_file = "<<outswc_file<<endl;
cout<<"bkg_thresh = "<<bkg_thresh<<endl;
cout<<"is2d = "<< (int)is_2d <<endl;
unsigned char * inimg1d = 0;
V3DLONG * in_sz = 0;
int datatype;
if(!loadImage((char*)inimg_file.c_str(), inimg1d, in_sz, datatype)) return false;
vector<MyMarker*> inswc = readSWC_file(inswc_file);
if(inswc.empty()) return false;
for(int i = 0; i < inswc.size(); i++)
{
MyMarker * marker = inswc[i];
if(is_2d)
marker->radius = markerRadiusXY(inimg1d, in_sz, *marker, bkg_thresh);
else
marker->radius = markerRadius(inimg1d, in_sz, *marker, bkg_thresh);
//printf("2d=%5.3f \t 3d=%5.3f\n", markerRadiusXY(inimg1d, in_sz, *marker, bkg_thresh),
// markerRadius(inimg1d, in_sz, *marker, bkg_thresh));
}
saveSWC_file(outswc_file, inswc);
cout<<"The output swc is saved to "<<outswc_file<<endl;
for(int i = 0; i < inswc.size(); i++) delete inswc[i];
if(inimg1d){delete [] inimg1d; inimg1d = 0;}
if(in_sz){delete [] in_sz; in_sz = 0;}
}
else //if (func_name == tr("help"))
{
cout<<"v3d -x <plugin_dll> -f neuron_radius -i <inimg_file> <inswc_file> -p <threshold> [<is2d>]"
<<endl
<<"The output will be appended .out.swc automatically"
<<endl;
}
return true;
}
bool smartTrace_plugin::dofunc(const QString & func_name, const V3DPluginArgList & input, V3DPluginArgList & output, V3DPluginCallback2 & callback, QWidget * parent)
{
if (func_name == tr("tracing_func"))
{
bool bmenu = false;
input_PARA PARA;
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*>();
if(infiles.empty())
{
fprintf (stderr, "Need input image. \n");
return false;
}
else
PARA.inimg_file = infiles[0];
int k=0;
PARA.channel = (paras.size() >= k+1) ? atoi(paras[k]) : 1; k++;
reconstruction_func(callback,parent,PARA,bmenu);
}
else if(func_name == tr("selfCorrection"))
{
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*> * poutfiles = (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*>();
vector<char*> outfiles = (poutfiles != 0) ? * poutfiles : vector<char*>();
if(infiles.size()<2)
{
fprintf (stderr, "Need input image and swc file. \n");
return false;
}
if(outfiles.empty())
{
fprintf (stderr, "Need output file. \n");
return false;
}
if(paras.empty())
{
fprintf (stderr, "Need confidential score file. \n");
return false;
}
nt_selfcorrect_func tracefunc;
tracefunc.correct_tracing(infiles.at(0), infiles.at(1), paras.at(0), outfiles.at(0), &callback);
}
else if (func_name == tr("smartTrace"))
{
bool bmenu = false;
input_PARA PARA;
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*>();
if(infiles.empty())
{
fprintf (stderr, "Need input image. \n");
return false;
}
else
PARA.inimg_file = infiles[0];
int k=0;
PARA.channel = (paras.size() >= k+1) ? atoi(paras[k]) : 1; k++;
nt_selfcorrect_func tracefunc;
tracefunc.smart_tracing(PARA.inimg_file,PARA.inimg_file+"_smartTracing",&callback);
}
else if (func_name == tr("help"))
{
////HERE IS WHERE THE DEVELOPERS SHOULD UPDATE THE USAGE OF THE PLUGIN
printf("\n\n**** Usage of smartTrace tracing **** \n");
printf("vaa3d -x smartTrace -f selfCorrection -i <inimg_file> <inswc_file> -o <output> -p <score.txt> \n");
printf("inimg_file The input image\n");
printf("inswc_file The input tracing\n");
printf("score.txt Confidential score calculated by plugin: calculate_reliability_score.\n");
printf("\n\nvaa3d -x smartTrace -f smartTrace -i <inimg_file> -p <channel>\n");
printf("inimg_file The input image\n");
printf("channel Data channel for tracing. Start from 1 (default 1).\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;
}
bool ITilingPlugin::dofunc(const QString & func_name, const V3DPluginArgList & input, V3DPluginArgList & output, V3DPluginCallback2 & callback, QWidget * parent)
{
if (func_name == tr("help"))
{
printf("\nUsage: v3d -x imageTiling.dylib -f itiling -i <input_image_file> -o <output_images_prefix_string> \n");
return true;
}
else if (func_name == tr("itiling"))
{
// subpixel translation registration based on pixel-level translation estimation
if(input.size()<1) return false; // no inputs
vector<char*> * infilelist = (vector<char*> *)(input.at(0).p);
vector<char*> * paralist;
vector<char*> * outfilelist;
if(infilelist->empty())
{
//print Help info
printf("\nUsage: v3d -x imageTiling.dylib -f itiling -i <input_image_file> -o <output_images_prefix_string> \n");
return true;
}
char * infile = infilelist->at(0); // input_image_folder
char * paras = NULL; // parameters
char * outfile = NULL; // output_image_file
if(output.size()>0) { outfilelist = (vector<char*> *)(output.at(0).p); outfile = outfilelist->at(0);} // specify output
if(input.size()>1) { paralist = (vector<char*> *)(input.at(1).p); paras = paralist->at(0);} // parameters
// init
int channel1 = 0;
bool img_show = true; // save stitching file
bool success = false;
ImagePixelType imgdatatype;
V3DLONG cdim;
// parsing parameters
if(paras)
{
int argc = 0;
int len = strlen(paras);
int posb[200];
char * myparas = new char[len];
strcpy(myparas, paras);
for(int i = 0; i < len; i++)
{
if(i==0 && myparas[i] != ' ' && myparas[i] != '\t')
{
posb[argc++] = i;
}
else if((myparas[i-1] == ' ' || myparas[i-1] == '\t') && (myparas[i] != ' ' && myparas[i] != '\t'))
{
posb[argc++] = i;
}
}
char ** argv = new char* [argc];
for(int i = 0; i < argc; i++)
{
argv[i] = myparas + posb[i];
}
for(int i = 0; i < len; i++)
{
if(myparas[i]==' ' || myparas[i]=='\t')
myparas[i]='\0';
}
char* key;
for(int i=0; i<argc; i++)
{
if(i+1 != argc) // check that we haven't finished parsing yet
{
key = argv[i];
qDebug()<<">>key ..."<<key;
if (*key == '#')
{
while(*++key)
{
if (!strcmp(key, "c"))
{
channel1 = atoi( argv[i+1] ) - 1; // red 1 green 2 blue 3
i++;
}
else if (!strcmp(key, "s"))
{
img_show = atoi( argv[i+1] )?true:false;
i++;
}
else
{
cout<<"parsing ..."<<key<<i<<"Unknown command. Type 'v3d -x plugin_name -f function_name' for usage"<<endl;
return false;
}
}
}
else
{
cout<<"parsing ..."<<key<<i<<"Unknown command. Type 'v3d -x plugin_name -f function_name' for usage"<<endl;
return false;
}
}
}
// error check
if(channel1<0)
{
cout<<"illegal input parameters"<<endl;
return false;
}
//free space
if (argv) {delete []argv; argv=0;}
if (myparas) {delete []myparas; myparas=0;}
}
// get stitch configuration
//QDir myDir(infile);
// group stitch in subspace
int start_t = clock();
//
int datatype_tile = 0; // assume all tiles with the same datatype
V3DLONG *sz_relative = 0;
unsigned char* relative1d = 0;
if(QFile(QString(infile)).exists())
{
if (!loadImage(const_cast<char *>(infile), relative1d, sz_relative, datatype_tile))
{
if (!do_blockwise_read(const_cast<char *>(infile)), outfile)
{
fprintf(stderr, "Error happens in reading the subject file [%s]. Exit. \n",infile);
return false;
}
else
{
v3d_msg("Succeed!");
return true;
}
}
}
else
{
v3d_msg("The input file is not supported!",0);
return false;
}
//
switch (datatype_tile) {
case V3D_UINT8:
if (!imgtiling<unsigned char, V3DLONG>((unsigned char *)relative1d, sz_relative[0], sz_relative[1], sz_relative[2], sz_relative[3], QString(outfile), datatype_tile))
{
v3d_msg("Fail to call function imgtiling (8bit)! \n", 0);
return false;
}
break;
case V3D_UINT16:
if (!imgtiling<unsigned short, V3DLONG>((unsigned short *)relative1d, sz_relative[0], sz_relative[1], sz_relative[2], sz_relative[3], QString(outfile), datatype_tile))
{
v3d_msg("Fail to call function imgtiling (16bit)! \n", 0);
return false;
}
break;
case V3D_FLOAT32:
if (!imgtiling<float, V3DLONG>((float *)relative1d, sz_relative[0], sz_relative[1], sz_relative[2], sz_relative[3], QString(outfile), datatype_tile))
{
v3d_msg("Fail to call function imgtiling (32bit)! \n", 0);
return false;
}
break;
default:
v3d_msg("Currently this program only support UINT8, UINT16, and FLOAT32 datatype.\n",0);
return false;
}
cout<<"time elapse ... "<<clock()-start_t<<endl;
return true;
}
else
{
v3d_msg("\nWrong function specified.\n",0);
return false;
}
return true;
}
bool eswc2swc_io(const V3DPluginArgList & input, V3DPluginArgList & output)
{
cout<<"Welcome to eswc2swc_io"<<endl;
vector<char*>* inlist = (vector<char*>*)(input.at(0).p);
vector<char*>* outlist = NULL;
if(input.size() != 1)
{
printf("Please specify both input file name.\n");
return false;
}
QString fileOpenName = QString(inlist->at(0));
QString fileSaveName;
QString tmp = fileOpenName;
if (output.size()==0)
{
printf("No outputfile specified.\n");
tmp.chop(4);
fileSaveName = tmp + "swc";
}
else if (output.size()==1)
{
outlist = (vector<char*>*)(output.at(0).p);
fileSaveName = QString(outlist->at(0));
}
else
{
printf("You have specified more than 1 output file.\n");
return false;
}
NeuronTree neuron;
vector<V3DLONG> segment_id, segment_layer;
vector<double> feature;
if (fileOpenName.endsWith(".eswc") || fileOpenName.endsWith(".ESWC"))
{
neuron = read_eswc(segment_id, segment_layer, feature, fileOpenName);
if (!swc2eswc(neuron,segment_id, segment_layer))
{
v3d_msg("Cannot convert eswc to swc.\n");
return false;
}
}
else {
v3d_msg("The file type you specified is not supported. Please check.");
return false;
}
int ret = QMessageBox::Yes;
if (check_eswc(neuron, segment_id, segment_layer)==-1)
{
v3d_msg("WARNING: Something is wrong with the eswc file", 0);
v3d_msg("But we still put convert it to swc format", 0);
}
QString fileDefaultName = fileOpenName;
fileDefaultName.chop(4);
fileDefaultName += QString("swc");
//write new SWC to file
if (!export_swc(neuron,qPrintable(fileSaveName)))
{
v3d_msg("fail to write the output swc file.", 0);
return false;
}
return true;
}
bool batch_compute_main(const V3DPluginArgList & input, V3DPluginArgList & output)
{
printf("\nwelcome to batch_compute\n");
vector<char*>* inlist = (vector<char*>*)(input.at(0).p);
vector<char*>* outlist = NULL;
vector<char*>* paralist = NULL;
if(input.size() != 2)
{
printf("Please specify parameter set.\n");
printHelp_batch_compute();
return false;
}
paralist = (vector<char*>*)(input.at(1).p);
if (paralist->size()!=1)
{
printf("Please specify all paramters in one text string.\n");
printHelp_batch_compute();
return false;
}
char * paras = paralist->at(0);
int argc = 1;
enum {kArgMax = 64};
char *argv[kArgMax];
//parsing parameters
if (paras)
{
int len = strlen(paras);
for (int i=0;i<len;i++)
{
if (paras[i]=='#')
paras[i] = '-';
}
char* pch = strtok(paras, " ");
while (pch && argc<kArgMax)
{
argv[argc++] = pch;
pch = strtok(NULL, " ");
}
}
else
printHelp_batch_compute();
//read arguments
char *dfile_database = NULL;
char *dfile_result = NULL;
double step_size = 2;
int c;
static char optstring[] = "h:i:o:";
opterr = 0;
while ((c = getopt(argc, argv, optstring))!=-1)
{
switch (c)
{
case 'h':
printHelp_batch_compute();
return 0;
break;
case 'i':
if (strcmp(optarg,"(null)")==0 || optarg[0]=='-')
{
fprintf(stderr, "Found illegal or NULL parameter for the option -i.\n");
return 1;
}
dfile_database = optarg;
break;
case 'o':
if (strcmp(optarg,"(null)")==0 || optarg[0]=='-')
{
fprintf(stderr, "Found illegal or NULL parameter for the option -o.\n");
return 1;
}
dfile_result = optarg;
break;
case '?':
fprintf(stderr,"Unknown option '-%c' or incomplete argument lists.\n",optopt);
return 1;
break;
}
}
//read database file
QStringList nameList, filePathList;
V3DLONG neuronNum;
QString qs_database(dfile_database);
QList<double*> morph_list, gmi_list;
qs_database = qs_database.simplified();
if (qs_database.endsWith(".ano") || qs_database.endsWith(".ANO"))
{
printf("(0). reading a linker file.\n");
P_ObjectFileType linker_object;
if (!loadAnoFile(QString(dfile_database),linker_object))
{
fprintf(stderr,"Error in reading the linker file.\n");
return 1;
}
nameList = linker_object.swc_file_list;
neuronNum = nameList.size();
for (V3DLONG i=0;i<neuronNum;i++)
{
NeuronTree tmp = readSWC_file(nameList.at(i));
printf(qPrintable("calculating features for" + tmp.file +".\n"));
filePathList.append(tmp.file);
// it makes more sense to run pre_processing seperately, so that the pre_processed steps can be adjusted (tuning step size), saved and verified.
//NeuronTree tmp_preprocessed = pre_process(tmp, step_size);
double * feature_morph = new double[21];
double * feature_gmi = new double[14];
computeFeature(tmp, feature_morph);
computeGMI(tmp, feature_gmi);
morph_list.append(feature_morph);
gmi_list.append(feature_gmi);
}
}
else {
fprintf(stderr, "the reference file/list you specified is not supported.\n");
return 1;
}
QString outfile(dfile_result);
if (!dfile_result)
{
outfile = qs_database + "features.nfb";
}
//if sepcified format is csv file
if (outfile.right(4) == ".csv")
{
FILE * fp;
fp = fopen(qPrintable(outfile), "w");
QString header = "swc_file,num_nodes,soma_surface,num_stems,"
"num_bifurcations,num_branches,num_of_tips,"
"overall_x_span,overall_y_span,overall_z_span,"
"average_diameter,total_length,total_surface,"
"total_volume,max_euclidean_distance,max_path_distance,"
"max_branch_order,average_contraction,average_fragmentation,"
"parent_daughter_ratio,bifurcation_angle_local,"
"bifurcation_angle_remote,"
"moment1,moment2,moment3,moment4,moment5,moment6,"
"moment7,moment8,moment9,moment10,moment11,moment12,"
"moment13,ave_R\n";
fprintf(fp,qPrintable(header));
for (V3DLONG i=0;i<neuronNum;i++)
{
fprintf(fp, qPrintable(filePathList[i]));
for (int j=0;j<21;j++)
fprintf(fp,", %.8f", morph_list[i][j]);
for (int j=0;j<14;j++)
fprintf(fp,", %.8f", gmi_list[i][j]);
fprintf(fp,"\n");
}
fclose(fp);
}
else{
//output a neuron featurebase (.nfb) file
FILE * fp;
fp = fopen(qPrintable(outfile), "w");
for (V3DLONG i=0;i<neuronNum;i++)
{
fprintf(fp, qPrintable("SWCFILE=" + filePathList[i]));
fprintf(fp, "\n");
for (int j=0;j<21;j++)
fprintf(fp,"%.8f\t", morph_list[i][j]);
fprintf(fp,"\n");
for (int j=0;j<14;j++)
fprintf(fp,"%.8f\t", gmi_list[i][j]);
fprintf(fp,"\n");
}
fclose(fp);
}
for (V3DLONG i=0;i<neuronNum;i++)
{
if (morph_list[i]) {delete []morph_list[i]; morph_list[i]=NULL;}
if (gmi_list[i]) {delete []gmi_list[i]; gmi_list[i]=NULL;}
}
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 processImage(V3DPluginCallback2 &callback, const V3DPluginArgList & input, V3DPluginArgList & output)
{
if(input.size() < 1 || output.size() != 1)
return false;
V3DLONG c = -1;
if (input.size()>=2)
{
vector<char*> paras = *(vector<char*> *)(input.at(1).p);
if(paras.size() >= 1) c = atoi(paras.at(0));
}
if (c<0)
{
v3d_msg("You explicitly or implicitly specified a channel number < 0, which means split-all-channels. \n",0);
}
char * inimg_file = ((vector<char*> *)(input.at(0).p))->at(0);
char * outimg_file = ((vector<char*> *)(output.at(0).p))->at(0);
cout<<"channel = "<<c<<endl;
cout<<"inimg_file = "<<inimg_file<<endl;
cout<<"outimg_file = "<<outimg_file<<endl;
bool b_res=false;
unsigned char * data1d = 0;
V3DLONG in_sz[4];
void* outimg = 0;
V3DLONG cb, ce, k;
int datatype;
if(!simple_loadimage_wrapper(callback, inimg_file, data1d, in_sz, datatype))
{
cerr<<"load image "<<inimg_file<<" error!"<<endl;
return false;
}
if (c>=in_sz[3])
{
v3d_msg("The specified channel is not valid. Do nothing.", 0);
goto Label_exit;
}
if (c<0) {cb=0; ce=in_sz[3]-1;}
else {cb = ce = c;}
for (k=cb; k<=ce; k++)
{
printf("\n... processing [%d] channel now...\n", k);
switch(datatype)
{
case 1: b_res = extract_a_channel(data1d, in_sz, k, outimg); break;
case 2: b_res = extract_a_channel((unsigned short int *)data1d, in_sz, k, outimg); break;
case 4: b_res = extract_a_channel((float *)data1d, in_sz, k, outimg); break;
default:
b_res = false;
v3d_msg("Right now this plugin supports only UINT8/UINT16/FLOAT32 data. Do nothing."); goto Label_exit;
}
// save image
V3DLONG oldc = in_sz[3]; in_sz[3]=1;
if (cb==ce)
simple_saveimage_wrapper(callback, outimg_file, (unsigned char *)outimg, in_sz, datatype);
else
simple_saveimage_wrapper(callback,
qPrintable(QString("").setNum(k).prepend("_C").prepend(outimg_file).append(".v3draw")),
(unsigned char *)outimg, in_sz, datatype);
//
in_sz[3] = oldc; //this sentence is important
printf("b_res=[%s]\n", (b_res)?"true":"false");
}
Label_exit:
if (data1d) {delete []data1d; data1d=0;}
//should never delete outimg here, as it is just a wrapper. by PHC 20131105
return b_res;
}
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 compute(V3DPluginCallback2 &callback, const V3DPluginArgList & input, V3DPluginArgList & output)
{
cout<<"Welcome to histogram"<<endl;
if(output.size() != 1) return true;
vector<char*>* inlist = (vector<char*>*) (input.at(0).p);
if (inlist->size() != 1)
{
cerr<<"You must specify 1 input file!"<<endl;
return false;
}
char * infile = inlist->at(0);
cout<<"input file: "<<infile<<endl;
unsigned char * inimg1d = NULL;
V3DLONG sz[4];
int datatype;
if (!simple_loadimage_wrapper(callback, infile, inimg1d, sz, datatype))
{
cerr<<"faile to load image"<<endl;
return false;
}
//Read the output file
vector<char*>* outlist = (vector<char*>*) (output.at(0).p);
if (outlist->size()!=1)
{
cerr<<"You must specify 1 output file!"<<endl;
return false;
}
char* outfile = outlist->at(0);
cout<<"output file: "<<outfile<<endl;
if (datatype!=1)
{
v3d_msg("Now we only support 8 bit image.\n");
return -1;
}
//TODO add datatype judgment
double max_value = 256;
V3DLONG histscale = 256;
QVector<QVector<int> > hist_vec;
int nChannel = sz[3];
for (int c=0;c<nChannel;c++)
{
QVector<int> tmp;
getHistogram(inimg1d+ c*sz[0]*sz[1]*sz[2], sz[0]*sz[1]*sz[2], max_value, histscale, tmp);
hist_vec.append(tmp);
}
//output histogram to csv file
FILE *fp;
fp = fopen(outfile, "w");
for (int i=0;i<hist_vec.size();i++)
{
for (int j=0;j<hist_vec[i].size();j++)
fprintf(fp, "%d,", hist_vec[i][j]);
fprintf(fp,"\n");
}
fclose(fp);
if (inimg1d) {delete []inimg1d; inimg1d=NULL;}
return true;
}
bool IBioformatIOPlugin::dofunc(const QString & func_name, const V3DPluginArgList & input, V3DPluginArgList & output, V3DPluginCallback2 & callback, QWidget * parent)
{
if (func_name == tr("imgiobiof"))
{
cout<<"Welcome to imageIOBioformat loader"<<endl;
if(input.size() != 1 || output.size() != 1) return false;
char * inimg_file = ((vector<char*> *)(input.at(0).p))->at(0);
char * outimg_file = ((vector<char*> *)(output.at(0).p))->at(0);
cout<<"inimg_file = "<<inimg_file<<endl;
cout<<"outimg_file = "<<outimg_file<<endl;
QString m_FileName(inimg_file); // use inimge_file name
if(m_FileName.isEmpty())
{
printf("\nError: Your image does not exist!\n");
return false;
}
// temp
QString baseName = QFileInfo(m_FileName).baseName();
//QString tmpfile = QDir::tempPath().append("/").append(baseName).append(".tif");
QString tmpfile(outimg_file); //use outimg_file name
//
QFile tmpqfile(tmpfile);
if (tmpqfile.exists()) system(qPrintable(QString("rm -f \"%1\"").arg(tmpfile)));
//look for loci_tools.jar
QString lociDir = ("loci_tools.jar");
if (!QFile(lociDir).exists())
{
printf("loci_tools.jar is not in current directory, search v3d app path.\n");
lociDir = getAppPath().append("/loci_tools.jar");
printf(qPrintable(lociDir));
printf("\n");
if (!QFile(lociDir).exists())
{
v3d_msg("Cannot find loci_tools.jar, please download it and make sure it is put under the Vaa3D executable folder, parallel to the Vaa3D executable and the plugins folder.", 0);
return false;
}
}
QString cmd_loci = QString("java -cp %1 loci.formats.tools.ImageConverter \"%2\" \"%3\"").arg(lociDir.toStdString().c_str()).arg(m_FileName.toStdString().c_str()).arg(tmpfile.toStdString().c_str());
v3d_msg(cmd_loci, 0);
system(qPrintable(cmd_loci));
if (!tmpqfile.exists())
{
v3d_msg("The temprary file does not exist. The conversion of format using Bioformats has failed. Please use another way to convert and load using Vaa3D.\n");
return false;
}
return true;
}
else if(func_name == tr("help"))
{
cout<<"Usage : v3d -x imageIO_Bioformat -f imgiobiof -i <inimg_file> -o <outimg_file>"<<endl;
cout<<"e.g. v3d -x imageIO_Bioformat -f imgiobiof -i input.raw -o output.raw"<<endl;
cout<<endl;
return true;
}
}
bool MovieConverter::dofunc(const QString & func_name, const V3DPluginArgList & input, V3DPluginArgList & output, V3DPluginCallback2 & callback, QWidget * parent)
{
if (func_name == tr("convert_frames_to_movie"))
{
cout<<"Welcome to movie converter"<<endl;
char * inimg_file = ((vector<char*> *)(input.at(0).p))->at(0);
QString check_ffmpeg;
const char * ffmpeg_file;
#if defined(Q_OS_MAC)
ffmpeg_file = getAppPath().append("/mac_ffmpeg").toStdString().c_str();
#elif defined(Q_OS_LINUX)
ffmpeg_file = getAppPath().append("/linux_ffmpeg").toStdString().c_str();
#elif defined(Q_OS_WIN32)
ffmpeg_file = getAppPath().append("/linux_ffmpeg").toStdString().c_str();
#else
v3d_msg("The OS is not recognized (not Mac, Linux or Windows). Do nothing.");
return false;
#endif
char * inimg_format = "a[NUM].BMP";
char * output_fps = "14";
char * output_Type = "avi";
unsigned int c = 1;
if (input.size()>=2)
{
vector<char*> paras = (*(vector<char*> *)(input.at(1).p));
cout<<paras.size()<<endl;
if(paras.size() >= 1) check_ffmpeg = paras[0];
if(check_ffmpeg != "NULL") ffmpeg_file = paras[0] ;
if(paras.size() >= 2) inimg_format = paras[1];
if(paras.size() >= 3) output_fps = paras[2];
if(paras.size() >= 4) output_Type = paras.at(3);
if(paras.size() >= 5) c = atoi(paras.at(4));
}
cout<<"input_folder = "<<inimg_file<<endl;
cout<<"ffmpeg_file = "<<ffmpeg_file<<endl;
cout<<"input_format = "<<inimg_format<<endl;
cout<<"output_fps = "<<output_fps<<endl;
cout<<"output_type = "<<output_Type<<endl;
cout<<"compress = "<<c<<endl;
QString selectedFile(inimg_file);
QString selectffmpeg(ffmpeg_file);
QString filename(inimg_format);
QString fps(output_fps);
QString videoType(output_Type);
if (!QFile(selectffmpeg).exists())
{
printf("Can not find ffmpeg, please select again or download from http://www.ffmpeg.org");
return false;
}
int indexL = filename.indexOf("[");
QString filenameL = filename.left(indexL);
int indexR = filename.indexOf("]");
QString filenameR = filename.right(filename.size()-indexR-1);
QString compress;
if(videoType == "mp4")
{
compress = "-vcodec mpeg4 -acodec aac";
}
else if (videoType == "mpg")
{
compress = "-vcodec mpeg2video";
}
else if (c == 1 && videoType == "avi")
{
compress = "-vcodec mjpeg -qscale 0";
}
else if (c == 0 && videoType == "avi")
{
compress = "-vcodec rawvideo";
}
else
{
return false;
}
#if defined(Q_OS_WIN32)
QString cmd_ffmpeg = QString("\"\"%1\" -r %2 -i \"%3/%4%d%5\" -y %6 \"%7/movie.%8\"\"").arg(selectffmpeg.toStdString().c_str()).arg(fps.toStdString().c_str()).arg(selectedFile.toStdString().c_str()).arg(filenameL.toStdString().c_str()).arg(filenameR.toStdString().c_str()).arg(compress.toStdString().c_str()).arg(selectedFile.toStdString().c_str()).arg(videoType.toStdString().c_str());
#else
QString cmd_ffmpeg = QString("\"%1\" -r %2 -i \"%3/%4%d%5\" -y %6 \"%7/movie.%8\"").arg(selectffmpeg.toStdString().c_str()).arg(fps.toStdString().c_str()).arg(selectedFile.toStdString().c_str()).arg(filenameL.toStdString().c_str()).arg(filenameR.toStdString().c_str()).arg(compress.toStdString().c_str()).arg(selectedFile.toStdString().c_str()).arg(videoType.toStdString().c_str());
#endif
system(qPrintable(cmd_ffmpeg));
//-vcodec mjpeg -qscale 0
QString movieDir = selectedFile.append(QString("/movie.%1").arg(videoType));
if (!QFile(movieDir).exists())
{
printf("The format is not supported, or can not find ffmpeg, please select again or download from http://www.ffmpeg.org\n");
return false;
}
else
{
cout<<"The movie is saved in "<<movieDir.toStdString()<<endl;
return true;
}
}
else if (func_name == tr("help"))
{
printf("\n**** Usage of Movie Converter ****\n");
printf("vaa3d -x plugin_name -f convert_frames_to_movie -i <inimg_folder> -p <converter_path> <frame_format> <output_fps> <video_type> <is_compress>\n");
printf("inimg_folder the video frame folder path \n");
printf("converter_path the movie converter(ffmpeg) path. If do not know, please set this para to NULL and the default path will be the vaa3d main path.\n");
printf("frame_format the format of video frames,e.g. for a1.BMP, please set this para to be a[NUM].BMP\n");
printf("output_fps the fps for the output video. Default 14\n");
printf("video_type the output video type (avi, mpg, or mp4). Default avi.\n");
printf("is_compress if compress the video (1 for yes and 0 for no). Default 1.\n");
return true;
}
else return false;
}