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 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 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 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 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 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 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 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 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 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 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 resample_swc_toolbox(const V3DPluginArgList & input)
{
vaa3d_neurontoolbox_paras * paras = (vaa3d_neurontoolbox_paras *)(input.at(0).p);
NeuronTree nt = paras->nt;
QString fileOpenName = nt.file;
bool ok;
double step = QInputDialog::getDouble(0, "Please specify the resampling step length","Step length:",1,0,2147483647,0.1,&ok);
if (!ok)
return true;
NeuronTree result = resample(nt,step);
QString fileDefaultName = fileOpenName+QString("_resampled.swc");
//write new SWC to file
QString fileSaveName = QFileDialog::getSaveFileName(0, QObject::tr("Save File"),
fileDefaultName,
QObject::tr("Supported file (*.swc)"
";;Neuron structure (*.swc)"
));
if (!export_list2file(result.listNeuron,fileSaveName,fileOpenName))
{
v3d_msg("fail to write the output swc file.");
return false;
}
return true;
}
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 neuron_toolbox_func(V3DPluginCallback2 & callback, QWidget * parent, const V3DPluginArgList & input, V3DPluginArgList & output)
{
QString test_str1 = QString(((vaa3d_neurontoolbox_paras *)(input.at(0).p))->nt.file);
QString test_str = QFileInfo(test_str1).baseName() + "." + QFileInfo(test_str1).completeSuffix();
SelectPluginDlg * selectDlg = new SelectPluginDlg(parent, callback, input);
selectDlg->setWindowTitle(test_str + " - Select plugin to run...");
selectDlg->show();
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 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;
}
int eswc2swc_toolbox(const V3DPluginArgList & input)
{
vaa3d_neurontoolbox_paras * paras = (vaa3d_neurontoolbox_paras *)(input.at(0).p);
NeuronTree neuron = paras->nt;
QString fileOpenName = neuron.file;
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 -1;
}
}
else {
v3d_msg("The file type you specified is not in .eswc format. Please check.");
return -1;
}
int ret = QMessageBox::Yes;
if (check_eswc(neuron, segment_id, segment_layer)==-1)
{
QMessageBox msgBox;
msgBox.setText("Something is wrong with the eswc file.");
msgBox.setInformativeText("Do you still want to convert it to swc?");
msgBox.setStandardButtons(QMessageBox::Yes | QMessageBox::Cancel);
msgBox.setDefaultButton(QMessageBox::Cancel);
ret = msgBox.exec();
}
if (ret==QMessageBox::Cancel)
return -1;
QString fileDefaultName = fileOpenName;
fileDefaultName.chop(4);
fileDefaultName += QString("swc");
//write new SWC to file
QString fileSaveName = QFileDialog::getSaveFileName(0, QObject::tr("Save File"),
fileDefaultName,
QObject::tr("Supported file (*.swc)"
";;Neuron structure (*.eswc)"
));
if (!export_swc(neuron,qPrintable(fileSaveName)))
{
v3d_msg("fail to write the output swc file.");
return -1;
}
return 1;
}
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 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;
}
void nf_main(const V3DPluginArgList & input, V3DPluginArgList & output)
{
//cout<<"Welcome to nf_main"<<"\n";
vector<char*>* inlist = (vector<char*>*)(input.at(0).p);
//char * out = (*(vector<char*>*)(input.at(0).p)).at(0);
//QString outfileName = QString(out);
//QFile file(outfileName);
//file.open(QIODevice::WriteOnly|QIODevice::Text);
//QTextStream myfile(&file);
int neuronNum = (int)inlist->size();
for (int i=0;i<neuronNum;i++)
{
Neuron * n = new Neuron((char*)inlist->at(i));
cout<<"\n--------------Neuron #"<<(i+1)<<"----------------\n";
//myfile<<"Neuron #"<<(i+1)<<"\n";
//Node #
cout<<"Number of Nodes: "<<n->read<<"\n";
//myfile<<"Neuron #"<<n->read<<"\n";
computeStems(n);
computeBifs(n);
computeBranches(n);
computeTips(n);
computeWidth(n);
computeHeight(n);
computeDepth(n);
avgType(n);
avgDia(n);
computeLength(n);
computeSurface(n);
computeVol(n);
computeHausdorff(n);
//computeFractalDim(n);
}
// file.close();
}
int check_eswc_toolbox(const V3DPluginArgList & input)
{
vaa3d_neurontoolbox_paras * paras = (vaa3d_neurontoolbox_paras *)(input.at(0).p);
NeuronTree neuron = paras->nt;
QString fileOpenName = neuron.file;
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);
else {
v3d_msg("The file type you specified is not in eswc format. Please check.");
return -1;
}
int check_result = check_eswc(neuron, segment_id, segment_layer);
if (check_result==-1 || check_result==0)
{
QMessageBox msgBox;
if (check_result==-1)
msgBox.setText("Something is wrong with the eswc file.");
else
msgBox.setText("Your eswc is written in default values.");
msgBox.setInformativeText("Do you still want to overwrite it with a standard one?");
msgBox.setStandardButtons(QMessageBox::Yes | QMessageBox::Cancel);
msgBox.setDefaultButton(QMessageBox::Cancel);
if (msgBox.exec()==QMessageBox::Yes)
{
swc2eswc(neuron, segment_id, segment_layer);
export_eswc(neuron, segment_id, segment_layer, qPrintable(fileOpenName), qPrintable(fileOpenName));
v3d_msg(QString("%1 has been updated!").arg(fileOpenName));
}
else return -1;
}
else
v3d_msg("Your eswc file is in correct format!");
return 1;
}
int swc2eswc_toolbox(const V3DPluginArgList & input)
{
vaa3d_neurontoolbox_paras * paras = (vaa3d_neurontoolbox_paras *)(input.at(0).p);
NeuronTree neuron = paras->nt;
QString fileOpenName = neuron.file;
vector<V3DLONG> segment_id, segment_layer;
if (fileOpenName.endsWith(".swc") || fileOpenName.endsWith(".SWC"))
{
segment_id, segment_layer;
if (!swc2eswc(neuron,segment_id, segment_layer))
{
v3d_msg("Cannot convert swc to eswc.\n");
return -1;
}
}
else {
v3d_msg("The file type you specified is not in swc format. Please check.");
return -1;
}
QString fileDefaultName = fileOpenName;
fileDefaultName.chop(3);
fileDefaultName += QString("eswc");
//write new SWC to file
QString fileSaveName = QFileDialog::getSaveFileName(0, QObject::tr("Save File"),
fileDefaultName,
QObject::tr("Supported file (*.eswc)"
";;Extended Neuron structure (*.eswc)"
));
if (!export_eswc(neuron,segment_id,segment_layer,qPrintable(fileOpenName),qPrintable(fileSaveName)))
{
v3d_msg("fail to write the output eswc file.");
return -1;
}
return 1;
}
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 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 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;
}
}
