bool Line::intersect(
float pickAngle, // The angle which makes the cone
const Vec3f& v0, // One endpoint of the line segment
const Vec3f& v1, // The other endpoint of the line segment
Vec3f& intersection) const // The intersection point
{
Vec3f ptOnLine;
Line inputLine(v0, v1);
float distance;
bool validIntersection = false;
if(getClosestPoints(inputLine, ptOnLine, intersection))
{
// check to make sure the intersection is within the line segment
if((intersection - v0).dot(v1 - v0) < 0)
{
intersection = v0;
}
else if((intersection - v1).dot(v0 - v1) < 0)
{
intersection = v1;
}
distance = (ptOnLine - intersection).getLength();
if (pickAngle < 0.0) return (distance < -pickAngle);
validIntersection = ((distance / (ptOnLine - getPosition()).getLength())
< pickAngle);
}
return validIntersection;
}
// -----------------------------------------------------------------------------
int Action_NMRrst::ReadNmrRestraints( std::string const& rstfilename )
{
BufferedLine infile;
if (infile.OpenFileRead( rstfilename )) return 1;
// Try to determine what kind of file.
const char* ptr = infile.Line();
// Try to skip past any blank lines and comments
while ( SkipChar( ptr ) )
ptr = infile.Line();
if (ptr == 0) {
mprinterr("Error: Unexpected end of restraint file.\n");
return 1;
}
std::string inputLine( ptr );
infile.CloseFile();
// Re-open file
if (infile.OpenFileRead( rstfilename )) return 1;
int err = 0;
if ( inputLine.compare(0, 7, "*HEADER")==0 ||
inputLine.compare(0, 6, "*TITLE")==0 ||
inputLine.compare(0, 6, "assign")==0 )
// XPLOR
err = ReadXplor( infile );
else
// Assume DIANA/Amber
err = ReadAmber( infile );
infile.CloseFile();
if (err != 0) {
mprinterr("Error: Could not parse restraint file.\n");
return 1;
}
return 0;
}
bool InputWidget::eventFilter(QObject *watched, QEvent *event)
{
if (event->type() != QEvent::KeyPress)
return false;
QKeyEvent *keyEvent = static_cast<QKeyEvent *>(event);
// keys from BufferView should be sent to (and focus) the input line
BufferView *view = qobject_cast<BufferView *>(watched);
if (view) {
if (keyEvent->text().length() == 1 && !(keyEvent->modifiers() & (Qt::ControlModifier ^ Qt::AltModifier))) { // normal key press
QChar c = keyEvent->text().at(0);
if (c.isLetterOrNumber() || c.isSpace() || c.isPunct() || c.isSymbol()) {
setFocus();
QCoreApplication::sendEvent(inputLine(), keyEvent);
return true;
}
}
return false;
}
else if (watched == ui.inputEdit) {
if (keyEvent->matches(QKeySequence::Find)) {
QAction *act = GraphicalUi::actionCollection()->action("ToggleSearchBar");
if (act) {
act->toggle();
return true;
}
}
return false;
}
return false;
}
void File::loadFileCIF( const string filename , const int ID) {
cerr<<"opening file into iofile\n";
ifstream file( filename.c_str() );
if ( !file ) {
cerr << "[ERROR] Input file (" << filename << ") could not be opened!\n";
exit( 1 );
} // end if
// cout<<"loadCIF\n";
const int MAX_BUFFER_SIZE = 10000;
char buffer[ MAX_BUFFER_SIZE ];
string whatIS;
Color color;
clsRepository->currentModel = 0;
undefineds.clear();
while ( true ) {
file.getline( buffer, MAX_BUFFER_SIZE, '\n' );
//if ( file.eof() ) {cout<< "EOF\n"; break; }
if ( !file ) {
cerr << "[WARNING] Premature end of file.\n";
return;
} // end if
istringstream inputLine( buffer );
//cout << inputLine.str() << "\n";
inputLine >> whatIS;
if ( !inputLine ) // linha vazia
continue;
if ( whatIS == "94" ) { parseLabelCIF( inputLine ); continue; } // SightLabel
if ( whatIS == "B" ) { parseRectangleCIF( inputLine , ID); continue; } // Box
if ( whatIS == "L" ) { parseLayerCIF( inputLine ); continue; } // Layer
if ( whatIS == "W" ) { continue; } // Wire
if ( whatIS == "C" ) { parseCallCIF( inputLine, ID ); continue; } // Call
if ( whatIS == "R" ) { continue; } // Roundflash
if ( whatIS == "P" ) { continue; } // Polygon
if ( whatIS == "DS" ) { state = MODEL; parseModelCIF( inputLine ); continue; } // Define Subrotine
if ( whatIS == "9" ) { parseModelName( inputLine ); continue;} // define model name
if ( whatIS == "DF;" ) { state = FREE; continue; } // Define Finished
if ( whatIS == "DD" ) { continue; } // Delete Subrotine
if ( whatIS == "E;" || whatIS == "END;" || whatIS == "E" || whatIS == "END" ) {
clsRepository->start();
return;
}// End of CIF File
if ( whatIS[0] == '(' ) continue;
cerr << "[INFO] Ignoring line: " << inputLine.str() << "\n";
} // end while
} // end function
int main(int argc, char* argv[])
{
const std::string testKey = "abcdfgteqsdfrtedfsretkdpbdltesas";
Crypto28147SimpleReplacement crp(testKey);
std::string encrypted;
std::string decrypted;
if (argc > 1)
{
if (0 == strcmp(argv[1], "-encr"))
{
std::cin >> std::noskipws;
std::istream_iterator<char> it(std::cin);
std::istream_iterator<char> end;
std::string inputLine(it, end);
crp.encrypt(inputLine, encrypted);
std::cout << encrypted << std::endl;
}
else if (0 == strcmp(argv[1], "-decr"))
Item getStreamExtraction (std::string prompt, Item itemForTypeResolution, std::string itemName )
{
do
{
std::istringstream inputLine( getLine(prompt) );
Item userInput;
inputLine >> userInput;
if ( inputLine.fail() )
{
std::cout << "Input format error: please give an " << itemName << "." << std::endl;
continue;
}
char junk;
inputLine >> junk;
if ( !inputLine.fail() )
{
std::cout << "Input format error: please give ONLY an " << itemName << "." << std::endl;
continue;
}
return userInput;
}
while ( true );
}
void InputHandle::start(){
sout << LogSystem::getLogString(LogSystem::Note, "System", "Welcome to RunCode Command Mode!");
loop:
sout << ">";
this->sout.flush();
QString line = sin.readLine();
QStringList inputLine(line.split(QRegExp("\\s"), QString::SkipEmptyParts));
if(inputLine.size() == 0){
//sout << LogSystem::getLogString(LogSystem::Error, "System", "No command found.");
goto loop;
}
QString cmd = inputLine.at(0);
if(cmd == "quit" || cmd == "exit"){
sout << LogSystem::getLogString(LogSystem::Info, "System", "Quitting...");
//emit this->requestToExit();
return;
}else if(cmd == "help"){
sout << LogSystem::getLogString(LogSystem::Info, "System", "Usage:");
sout << LogSystem::getLogString(LogSystem::Info, "System", "Can Use Command:");
sout << LogSystem::getLogString(LogSystem::Info, "System", "exit quit say");
goto loop;
}else if(cmd == "say"){
for(auto i = inputLine.begin() + 1; i != inputLine.end(); i++){
sout << *i << " ";
}
sout << "\n";
goto loop;
}else if(cmd == "output"){
//TODO: 之后完善, 组件全部移入MainController, 这个只做功能设置
}else{
sout << LogSystem::getLogString(LogSystem::Error, "System", QString("Unknown Command: %1").arg(cmd));
goto loop;
}
goto loop;
}
InputWidget::InputWidget(QWidget *parent)
: AbstractItemView(parent),
_networkId(0)
{
ui.setupUi(this);
connect(ui.ownNick, SIGNAL(activated(QString)), this, SLOT(changeNick(QString)));
layout()->setAlignment(ui.ownNick, Qt::AlignBottom);
layout()->setAlignment(ui.inputEdit, Qt::AlignBottom);
layout()->setAlignment(ui.showStyleButton, Qt::AlignBottom);
layout()->setAlignment(ui.styleFrame, Qt::AlignBottom);
ui.styleFrame->setVisible(false);
setFocusProxy(ui.inputEdit);
ui.ownNick->setFocusProxy(ui.inputEdit);
ui.ownNick->setSizeAdjustPolicy(QComboBox::AdjustToContents);
ui.ownNick->installEventFilter(new MouseWheelFilter(this));
ui.inputEdit->installEventFilter(this);
ui.inputEdit->setMinHeight(1);
ui.inputEdit->setMaxHeight(5);
ui.inputEdit->setMode(MultiLineEdit::MultiLine);
ui.inputEdit->setPasteProtectionEnabled(true);
ui.boldButton->setIcon(SmallIcon("format-text-bold"));
ui.italicButton->setIcon(SmallIcon("format-text-italic"));
ui.underlineButton->setIcon(SmallIcon("format-text-underline"));
ui.textcolorButton->setIcon(SmallIcon("format-text-color"));
ui.highlightcolorButton->setIcon(SmallIcon("format-fill-color"));
ui.encryptionIconLabel->hide();
_colorMenu = new QMenu();
_colorFillMenu = new QMenu();
QStringList names;
names << tr("White") << tr("Black") << tr("Dark blue") << tr("Dark green") << tr("Red") << tr("Dark red") << tr("Dark magenta") << tr("Orange")
<< tr("Yellow") << tr("Green") << tr("Dark cyan") << tr("Cyan") << tr("Blue") << tr("Magenta") << tr("Dark gray") << tr("Light gray");
QPixmap pix(16, 16);
for (int i = 0; i < inputLine()->mircColorMap().count(); i++) {
pix.fill(inputLine()->mircColorMap().values()[i]);
_colorMenu->addAction(pix, names[i])->setData(inputLine()->mircColorMap().keys()[i]);
_colorFillMenu->addAction(pix, names[i])->setData(inputLine()->mircColorMap().keys()[i]);
}
pix.fill(Qt::transparent);
_colorMenu->addAction(pix, tr("Clear Color"))->setData("");
_colorFillMenu->addAction(pix, tr("Clear Color"))->setData("");
ui.textcolorButton->setMenu(_colorMenu);
connect(_colorMenu, SIGNAL(triggered(QAction *)), this, SLOT(colorChosen(QAction *)));
ui.highlightcolorButton->setMenu(_colorFillMenu);
connect(_colorFillMenu, SIGNAL(triggered(QAction *)), this, SLOT(colorHighlightChosen(QAction *)));
new TabCompleter(ui.inputEdit);
UiStyleSettings fs("Fonts");
fs.notify("UseCustomInputWidgetFont", this, SLOT(setUseCustomFont(QVariant)));
fs.notify("InputWidget", this, SLOT(setCustomFont(QVariant)));
if (fs.value("UseCustomInputWidgetFont", false).toBool())
setCustomFont(fs.value("InputWidget", QFont()));
UiSettings s("InputWidget");
#ifdef HAVE_KDE
s.notify("EnableSpellCheck", this, SLOT(setEnableSpellCheck(QVariant)));
setEnableSpellCheck(s.value("EnableSpellCheck", false));
#endif
s.notify("EnableEmacsMode", this, SLOT(setEnableEmacsMode(QVariant)));
setEnableEmacsMode(s.value("EnableEmacsMode", false));
s.notify("ShowNickSelector", this, SLOT(setShowNickSelector(QVariant)));
setShowNickSelector(s.value("ShowNickSelector", true));
s.notify("ShowStyleButtons", this, SLOT(setShowStyleButtons(QVariant)));
setShowStyleButtons(s.value("ShowStyleButtons", true));
s.notify("EnablePerChatHistory", this, SLOT(setEnablePerChatHistory(QVariant)));
setEnablePerChatHistory(s.value("EnablePerChatHistory", false));
s.notify("MaxNumLines", this, SLOT(setMaxLines(QVariant)));
setMaxLines(s.value("MaxNumLines", 5));
s.notify("EnableScrollBars", this, SLOT(setScrollBarsEnabled(QVariant)));
setScrollBarsEnabled(s.value("EnableScrollBars", true));
s.notify("EnableLineWrap", this, SLOT(setLineWrapEnabled(QVariant)));
setLineWrapEnabled(s.value("EnableLineWrap", false));
s.notify("EnableMultiLine", this, SLOT(setMultiLineEnabled(QVariant)));
setMultiLineEnabled(s.value("EnableMultiLine", true));
ActionCollection *coll = QtUi::actionCollection();
Action *activateInputline = coll->add<Action>("FocusInputLine");
connect(activateInputline, SIGNAL(triggered()), SLOT(setFocus()));
activateInputline->setText(tr("Focus Input Line"));
activateInputline->setShortcut(QKeySequence(Qt::CTRL + Qt::Key_L));
connect(inputLine(), SIGNAL(textEntered(QString)), SLOT(onTextEntered(QString)), Qt::QueuedConnection); // make sure the line is already reset, bug #984
connect(inputLine(), SIGNAL(currentCharFormatChanged(QTextCharFormat)), this, SLOT(currentCharFormatChanged(QTextCharFormat)));
}
void InputWidget::currentChanged(const QModelIndex ¤t, const QModelIndex &previous)
{
BufferId currentBufferId = current.data(NetworkModel::BufferIdRole).value<BufferId>();
BufferId previousBufferId = previous.data(NetworkModel::BufferIdRole).value<BufferId>();
if (_perChatHistory) {
//backup
historyMap[previousBufferId].history = inputLine()->history();
historyMap[previousBufferId].tempHistory = inputLine()->tempHistory();
historyMap[previousBufferId].idx = inputLine()->idx();
historyMap[previousBufferId].inputLine = inputLine()->html();
//restore
inputLine()->setHistory(historyMap[currentBufferId].history);
inputLine()->setTempHistory(historyMap[currentBufferId].tempHistory);
inputLine()->setIdx(historyMap[currentBufferId].idx);
inputLine()->setHtml(historyMap[currentBufferId].inputLine);
inputLine()->moveCursor(QTextCursor::End, QTextCursor::MoveAnchor);
// FIXME this really should be in MultiLineEdit (and the const int on top removed)
QTextBlockFormat format = inputLine()->textCursor().blockFormat();
format.setLeftMargin(leftMargin); // we want a little space between the frame and the contents
inputLine()->textCursor().setBlockFormat(format);
}
NetworkId networkId = current.data(NetworkModel::NetworkIdRole).value<NetworkId>();
if (networkId == _networkId)
return;
setNetwork(networkId);
updateNickSelector();
updateEnabledState();
}
InputStream
openFTPStream(ParsedURL *pu, URLFile *uf)
{
Str tmp;
int status;
char *user = NULL;
char *pass = NULL;
Str uname = NULL;
Str pwd = NULL;
int add_auth_cookie_flag = FALSE;
char *realpathname = NULL;
if (!pu->host)
return NULL;
if (pu->user == NULL && pu->pass == NULL) {
if (find_auth_user_passwd(pu, NULL, &uname, &pwd, 0)) {
if (uname)
user = uname->ptr;
if (pwd)
pass = pwd->ptr;
}
}
if (user)
/* do nothing */ ;
else if (pu->user)
user = pu->user;
else
user = "******";
if (current_ftp.host) {
if (!strcmp(current_ftp.host, pu->host) &&
current_ftp.port == pu->port && !strcmp(current_ftp.user, user)) {
ftp_command(¤t_ftp, "NOOP", NULL, &status);
if (status != 200)
ftp_close(¤t_ftp);
else
goto ftp_read;
}
else
ftp_quit(¤t_ftp);
}
if (pass)
/* do nothing */ ;
else if (pu->pass)
pass = pu->pass;
else if (pu->user) {
pwd = NULL;
find_auth_user_passwd(pu, NULL, &uname, &pwd, 0);
if (pwd == NULL) {
if (fmInitialized) {
term_raw();
pwd = Strnew_charp(inputLine("Password: "******"Password: "******"Password: "******"anonymous");
#else
tmp = Strnew_charp("anonymous");
#endif /* __MINGW32_VERSION */
Strcat_char(tmp, '@');
pass = tmp->ptr;
}
if (!current_ftp.host) {
current_ftp.host = allocStr(pu->host, -1);
current_ftp.port = pu->port;
current_ftp.user = allocStr(user, -1);
current_ftp.pass = allocStr(pass, -1);
if (!ftp_login(¤t_ftp))
return NULL;
}
if (add_auth_cookie_flag)
add_auth_user_passwd(pu, NULL, uname, pwd, 0);
ftp_read:
ftp_command(¤t_ftp, "TYPE", "I", &status);
if (ftp_pasv(¤t_ftp) < 0) {
ftp_quit(¤t_ftp);
return NULL;
}
if (pu->file == NULL || *pu->file == '\0' ||
pu->file[strlen(pu->file) - 1] == '/')
goto ftp_dir;
realpathname = file_unquote(pu->file);
if (*realpathname == '/' && *(realpathname + 1) == '~')
realpathname++;
/* Get file */
uf->modtime = ftp_modtime(¤t_ftp, realpathname);
ftp_command(¤t_ftp, "RETR", realpathname, &status);
if (status == 125 || status == 150)
return newFileStream(current_ftp.data, (void (*)())closeFTPdata);
ftp_dir:
pu->scheme = SCM_FTPDIR;
return NULL;
}
int main(int argc, char* argv[]) {
if (argc < 2) {
std::cout << "Usage: SpeckleFitting xmlinputfile [outputdirectory]" << std::endl;
return -1;
}
//Read the input file and get marker details
XMLInputReader reader(argv[1]);
//Get the transformation matrix related to the various views
std::map<int, std::string> transforms = reader.getImagePlaneTransformations();
if (argc > 2) {
if (std::string(argv[2]) == ".") {
std::cout << "ISO Surfaces " << std::endl;
std::string viewnames[] = { "", "aplax", "tch", "fch", "saxapex", "saxmid", "saxbase" };
for (int i = 1; i < 7; i++) {
if (transforms.find(i) != transforms.end()) {
printISOSurfaceGFX(reader.getImagePlaneTransformation(static_cast<MarkerTypes>(i)), viewnames[i]);
}
}
std::cout << "Transformations " << std::endl;
for (int i = 1; i < 7; i++) {
if (transforms.find(i) != transforms.end()) {
std::cout << viewnames[i] << "\t" << transforms[i] << std::endl;
}
}
}
}
std::cout << "WORKLOAD:3" << std::endl;
std::cout << "STEP TRANFORMATION completed" << std::endl;
unsigned int numberOfFrames = reader.getNumberOfFrames();
//Create a LVMesh, let the cmgui context name be CMISS and create a LVmesh with numberOfFrames meshes
LVHeartMesh mesh("CMISS", reader);
mesh.fixWallLengths();
//Create a RV mesh that follows the user input and also ensure that the myocardial volume is conserved
mesh.fixToMarkers();
std::cout << "STEP FIT completed" << std::endl;
//Compute various strain measures
StrainMeasures measure(mesh, reader);
//Compute the measures for all long axis views, note the long axis information
//for all the views may not be provided, even though the resulting mesh is 3D
bool views[] = { true, true, true, false };
measure.setActiveViews(views);
//If a directory is specified, output the mesh and strain data to that directory
if (argc > 2) {
if (std::string(argv[2]) == ".") {
std::cout << "Heart\t" << mesh.getTransformation() << std::endl;
std::vector<std::string> strains = measure.getSixteenSegmentStrains();
std::vector<std::string> speckleStrains = measure.getSpeckleStrains(true);
//std::vector<std::string> fibreStrains = measure.getSixteenSegmentFibreStrains(0.0);
measure.Print("strain.csv", strains);
measure.Print("speckle.csv", speckleStrains);
mesh.outputMesh("test", argv[2]);
}
}
std::cout << "STEP MEASUREMENT completed" << std::endl;
//If DICOM filename is not provided create the files in the given output directory
if (reader.getDICOMFile() == "") {
//Output mesh, strains, transformation in an xml file
boost::filesystem::path dir(reader.getOutputDirectory());
//Create a file name with modelname in the specified directory
std::string filename = reader.getModelName() + ".xml";
boost::filesystem::path qfilename = dir / filename;
//Output the result in an xml formatted form
std::ofstream file(qfilename.string().c_str(), std::ios_base::binary);
std::string output(XMLSerialiser::buildXMLString(mesh, measure, reader.getDuration(), &transforms));
boost::replace_all(output, "</CMISSCAPIO>", "");
boost::trim(output);
file << output << std::endl;
file << "<SPECKLETRACKINGOUTPUT>" << std::endl;
tinyxml2::XMLDocument* XMLdoc = new tinyxml2::XMLDocument();
if (XMLdoc->LoadFile(argv[1]) == tinyxml2::XML_SUCCESS) {
tinyxml2::XMLPrinter printer;
XMLdoc->Print(&printer);
std::string inputLine(printer.CStr());
boost::replace_all(inputLine, "</SEGMENTATION>", "");
std::string tag("<SEGMENTATION>");
int index = inputLine.find(tag);
std::string inputT = inputLine.substr(index + tag.length());
boost::trim(inputT);
file << inputT << std::endl;
}
file << "</SPECKLETRACKINGOUTPUT>" << std::endl;
file << "</CMISSCAPIO>";
file.close();
} else { //If a dicom file is specified - store the data in the dicom file (in the overlay tag)
gdcm::Reader gdcmReader;
//Read the dicom file
std::string dicomFile(reader.getDICOMFile());
gdcmReader.SetFileName(dicomFile.c_str());
if (!gdcmReader.Read()) {
std::stringstream msg;
msg << "Unable to read file " << dicomFile;
throw new BundleToDICOMException(msg.str());
}
gdcm::File &file = gdcmReader.GetFile();
gdcm::DataSet &ds = file.GetDataSet();
std::string output(XMLSerialiser::buildXMLString(mesh, measure, reader.getDuration(), &transforms));
boost::replace_all(output, "</CMISSCAPIO>", "");
boost::trim(output);
std::ostringstream sfx;
sfx << output << std::endl;
sfx << "<SPECKLETRACKINGOUTPUT>" << std::endl;
tinyxml2::XMLDocument* XMLdoc = new tinyxml2::XMLDocument();
if (XMLdoc->LoadFile(argv[1]) == tinyxml2::XML_SUCCESS) {
tinyxml2::XMLPrinter printer;
XMLdoc->Print(&printer);
std::string inputLine(printer.CStr());
std::string tag("<SEGMENTATION");
int index = inputLine.find(tag);
std::string inputT = inputLine.substr(index);
boost::trim(inputT);
sfx << inputT << std::endl;
}
sfx << "</SPECKLETRACKINGOUTPUT>" << std::endl;
sfx << "</CMISSCAPIO>";
//Compress the string.. wado seems to have a trouble with ascii data
boost::iostreams::filtering_streambuf<boost::iostreams::input> in;
in.push(boost::iostreams::gzip_compressor());
std::istringstream uncompressed_string(sfx.str());
in.push(uncompressed_string);
std::ostringstream compressed_string;
boost::iostreams::copy(in, compressed_string);
std::string tagValue = compressed_string.str();
gdcm::Tag oytag(0x6000, 0x3000); //Overlay data tag
ds.Remove(oytag); //Remove the data associated with the tag else it doesnt get updated
gdcm::DataElement de;
de.SetTag(oytag);
de.SetVR(gdcm::VR::OB);
de.SetByteValue(tagValue.c_str(), tagValue.length());
ds.Insert(de);
//Write the file
gdcm::Writer writer;
writer.SetFile(file);
writer.SetFileName(dicomFile.c_str());
writer.Write();
}
std::cout << argv[0] << ":completed" << std::endl;
return 0;
}
