graphmod::Instances from_conll(vector<string> file_names, vector<string> _keep_verbs, int window, unsigned int limit=0, unsigned int per_verb_limit=0){
Instances instances;
set<string> keep_verbs;
for(string verb: _keep_verbs){
keep_verbs.insert(verb);
}
std::map<std::string, unsigned int> verb_counts;
ConllLoader sentences(file_names);
//boost::regex expr("\\n\\s*\\n", boost::regex::perl);
//boost::regex_iterator
//int total = 0;
while(not sentences.eof() and (limit == 0 or instances.size() < limit)){
auto cs = sentences.next();
for(ConllWord cw: cs){
if(cw.get_fine_tag()[0] == 'V' and (keep_verbs.count(cw.get_lemma()) > 0 or keep_verbs.size() == 0)){
map<string, vector<string> > instance;
int verb_index = cw.get_index();
instance["verb"] = {cw.get_lemma()};
if(per_verb_limit > 0 and verb_counts[cw.get_lemma()] > per_verb_limit){
continue;
}
verb_counts[cw.get_lemma()]++;
instance["verb_tag"] = {cw.get_fine_tag()};
instance["tag"].resize(0);
instance["gr"].resize(0);
instance["lemma"].resize(0);
if(window > 0){
for(ConllWord ow: cs.get_near(cw, window)){
string tag = ow.get_fine_tag();
instance["tag"].push_back(ow.get_fine_tag());
instance["lemma"].push_back(ow.get_lemma());
stringstream ss;
ss << ow.get_index() - verb_index;
instance["gr"].push_back(ss.str());
}
}
else{
//instance["relation"].resize(0);
for(ConllWord ow: cs.get_related(cw)){
stringstream ss;
string tag = ow.get_fine_tag(), gr = ow.get_relation();
if(function_tag(tag[0]) == true){
ss << gr << "(" << tag << "-" << ow.get_lemma() << "," << cw.get_fine_tag() << ")";
}
else{
ss << gr << "(" << tag << "," << cw.get_fine_tag() << ")";
}
instance["tag"].push_back(tag);
//instance["gr"].push_back(ss.str());
instance["gr"].push_back(gr);
instance["lemma"].push_back(ow.get_lemma());
}
}
instances.add(instance);
}
}
}
return instances;
//cout << total << endl;
}
void Series::Load3DImage(void* target,
Orthanc::PixelFormat format,
size_t lineStride,
size_t stackStride,
Orthanc::ThreadedCommandProcessor::IListener* listener)
{
using namespace Orthanc;
// Choose the extraction mode, depending on the format of the
// target image.
uint8_t bytesPerPixel;
ImageExtractionMode mode;
switch (format)
{
case PixelFormat_RGB24:
bytesPerPixel = 3;
mode = ImageExtractionMode_Preview;
break;
case PixelFormat_Grayscale8:
bytesPerPixel = 1;
mode = ImageExtractionMode_UInt8; // Preview ???
break;
case PixelFormat_Grayscale16:
bytesPerPixel = 2;
mode = ImageExtractionMode_UInt16;
break;
case PixelFormat_SignedGrayscale16:
bytesPerPixel = 2;
mode = ImageExtractionMode_UInt16;
format = PixelFormat_Grayscale16;
break;
default:
throw OrthancException(ErrorCode_NotImplemented);
}
// Check that the target image is properly sized
unsigned int sx = GetWidth();
unsigned int sy = GetHeight();
if (lineStride < sx * bytesPerPixel ||
stackStride < sx * sy * bytesPerPixel)
{
throw OrthancException(ErrorCode_BadRequest);
}
if (sx == 0 || sy == 0 || GetInstanceCount() == 0)
{
// Empty image, nothing to do
if (listener)
listener->SignalSuccess(0);
return;
}
/**
* Order the stacks according to their distance along the slice
* normal (using the "Image Position Patient" tag). This works
* even if the "SliceLocation" tag is absent.
**/
SliceLocator locator(GetInstance(0));
typedef std::map<float, Instance*> Instances;
Instances instances;
for (unsigned int i = 0; i < GetInstanceCount(); i++)
{
float dist = locator.ComputeSliceLocation(GetInstance(i));
instances[dist] = &GetInstance(i);
}
if (instances.size() != GetInstanceCount())
{
// Several instances have the same Z coordinate
throw OrthancException(ErrorCode_NotImplemented);
}
// Submit the download of each stack as a set of commands
ThreadedCommandProcessor processor(connection_.GetThreadCount());
if (listener != NULL)
{
processor.SetListener(*listener);
}
uint8_t* stackTarget = reinterpret_cast<uint8_t*>(target);
for (Instances::iterator it = instances.begin(); it != instances.end(); it++)
{
processor.Post(new ImageDownloadCommand(*it->second, format, mode, stackTarget, lineStride));
stackTarget += stackStride;
}
// Wait for all the stacks to be downloaded
if (!processor.Join())
{
throw OrthancException(ErrorCode_NetworkProtocol);
}
}
