void medJobRunner::run()
{
emit m_job->running(true);
medAbstractJob::medJobExitStatus jobExitStatus = medAbstractJob::MED_JOB_EXIT_FAILURE;
try
{
jobExitStatus = m_job->run();
if(jobExitStatus == medAbstractJob::MED_JOB_EXIT_CANCELLED)
{
dtkDebug() << "job aborted (cancelled)"
<< m_job->caption() << m_job;
}
}
catch(std::exception &err)
{
QString errorMessage = QString::fromLatin1(err.what());
dtkWarn() << "Error occured while runing job"
<< m_job->caption() << m_job
<< "\n\t" <<errorMessage;
emit exceptionCaught(errorMessage);
}
catch(...)
{
dtkWarn() << "Error occured while runing job"
<< m_job->caption() << m_job;
}
emit m_job->finished(jobExitStatus);
emit m_job->running(false);
}
void dtkComposerNodeVectorRealExtractor::run(void)
{
if (!d->receiver_vector.isEmpty() && !d->receiver_index.isEmpty()) {
dtkVectorReal *vector = d->receiver_vector.data();
qlonglong index = *d->receiver_index.data();
if (!vector) {
dtkError() << "Input vector is not defined.";
return;
}
if (index >= vector->size()) {
dtkWarn() << "index > size of the input vector. Zero is returned.";
d->value = 0;
} else {
d->value = (*vector)[index];
}
} else {
dtkWarn() << "Inputs not specified. Zero is returned.";
d->value = 0;
}
}
void dtkComposerNodeArrayScalarOperatorDivide::run(void)
{
if (!d->receiver_array.isEmpty() && !d->receiver_index.isEmpty() && !d->receiver_value.isEmpty() ) {
dtkContainerVectorReal *array = d->receiver_array.data();
if (!array) {
dtkError() << "Input array is not defined.";
d->emitter_array.clearData();
return;
}
qlonglong index = *d->receiver_index.data<qlonglong>();
qreal value = *d->receiver_value.data<qreal>();
if (index >= array->count()) {
dtkWarn() << "index > size of the vector. Same array is returned.";
} else {
if (value == 0)
dtkWarn() << "Value is zero. Same array is returned." ;
else
(*array)[index] /= value;
}
d->emitter_array.setData(array);
} else {
dtkWarn() << "Inputs not specified. Nothing is done";
d->emitter_array.clearData();
}
}
void dtkComposerGraphView::update(void)
{
if (!d->graphviz_avail)
return;
QByteArray content = d->graph->toString().append("\n").toLocal8Bit() ;
// run dot
QStringList arglist;
arglist << "-Tsvg";
QString command = "dot";
QProcess cmd;
QStringList PATH = QProcessEnvironment::systemEnvironment().value("PATH").split(":") ;
QDir::setSearchPaths("bin",PATH);
if(QFile("bin:"+command).exists()) {
dtkTrace() << "run graphviz dot" ;
cmd.start(command, arglist, QProcess::Unbuffered | QProcess::ReadWrite);
cmd.write(content);
cmd.closeWriteChannel();
cmd.waitForBytesWritten();
qlonglong timeout = 3000;
QString stdout_data;
if (cmd.waitForFinished(timeout)) {
QByteArray svg = cmd.readAllStandardOutput();
this->load(svg);
} else {
dtkWarn() << "graphviz timeout !";
}
} else {
d->graphviz_avail = false;
dtkWarn() << "can't find 'dot' binary in PATH, graphviz probably not installed";
}
}
void dtkComposerNodeArrayScalarOperatorModifierAllDivide::run(void)
{
if (!d->receiver_array.isEmpty() && !d->receiver_value.isEmpty() ) {
dtkContainerVectorReal *array = d->receiver_array.data();
if (!array) {
dtkError() << "Input array is not defined.";
d->emitter_array.clearData();
return;
}
qreal value = *d->receiver_value.data<qreal>();
if (value == 0) {
dtkWarn() << "Value is zero. Same array is returned." ;
} else {
for(qlonglong i = 0 ; i < array->count(); ++i)
(*array)[i] /= value ;
}
d->emitter_array.setData(array);
} else {
dtkWarn() << "Inputs not specified. Nothing is done";
d->emitter_array.clearData();
}
}
bool undoRedoRegistrationPlugin::initialize(void)
{
if (!undoRedoRegistration::registered()) { dtkWarn() << "Unable to register undoRedoRegistration type"; }
if (!undoRedoRegistrationToolBox::registered()) { dtkWarn() << "Unable to register undoRedoRegistration toolbox"; }
return true;
}
QByteArray dtkDistributedServerDaemon::waitForData(int rank, QString jobid)
{
dtkDistributedSocket *socket = d->sockets.value(qMakePair(rank, jobid), NULL);
if(!socket) {
dtkWarn() << "No socket found for rank " << rank;
return QByteArray();
}
socket->blockSignals(true);
dtkDistributedMessage *data = NULL;
if (socket->waitForReadyRead(30000))
data = socket->parseRequest();
else
dtkWarn() << "Data not ready for rank " << rank;
socket->blockSignals(false);
if (data) {
return data->content();
} else {
dtkWarn() << "Message not allocated - return void QByteArray";
return QByteArray();
}
}
bool medVtkViewPlugin::initialize()
{
if (!medVtkView::registered()) { dtkWarn() << "Unable to register medVtkView type"; }
if (!medVtkViewNavigator::registered()) { dtkWarn() << "Unable to register medVtkViewNavigator type"; }
return true;
}
itkPhilipsRECDataImageReader::FloatImageType::PointType itkPhilipsRECDataImageReader::ExtractPARRECImageOrigin (
FloatImageType::DirectionType direction)
{
typedef FloatImageType::PointType PointType;
PointType nullorigin;
nullorigin[0] = nullorigin[1] = nullorigin[2] = 0.0;
if (!this->io->GetFileName())
{
dtkWarn() << "io doesn't have a filename, call readInformation first";
return nullorigin;
}
itk::MetaDataDictionary PARheader = this->io->GetMetaDataDictionary();
typedef itk::PhilipsRECImageIO::OffCentreMidSliceType OffCentreType;
OffCentreType offcenter;
bool valid = itk::ExposeMetaData<OffCentreType>(PARheader, "PAR_OffCentreMidSlice", offcenter);
if (!valid)
{
dtkWarn() << "cannot find off-center information in PAR header, no correction";
return nullorigin;
}
double dimensions[3];
dimensions[0] = this->io->GetDimensions (0);
dimensions[1] = this->io->GetDimensions (1);
dimensions[2] = this->io->GetDimensions (2);
FloatImageType::SpacingType midoffset;
midoffset[0] = this->io->GetSpacing (0) * (dimensions[0] - 1) / 2.0;
midoffset[1] = this->io->GetSpacing (1) * (dimensions[1] - 1) / 2.0;
midoffset[2] = this->io->GetSpacing (2) * (dimensions[2] - 1) / 2.0;
midoffset = direction * midoffset;
PointType offcenterpoint;
offcenterpoint[0] = offcenter[0];
offcenterpoint[1] = offcenter[1];
offcenterpoint[2] = offcenter[2];
FloatImageType::DirectionType AFRtoLPS;
AFRtoLPS.Fill (0);
AFRtoLPS[0][2] = 1;
AFRtoLPS[1][0] = 1;
AFRtoLPS[2][1] = 1;
offcenterpoint = AFRtoLPS * offcenterpoint;
offcenterpoint -= midoffset;
return offcenterpoint;
}
bool itkN4BiasCorrectionPlugin::initialize()
{
if(!itkN4BiasCorrection::registered())
{
dtkWarn() << "Unable to register itkN4BiasCorrection type";
}
if ( !itkN4BiasCorrectionToolBox::registered() )
{
dtkWarn() << "Unable to register itkN4BiasCorrection toolbox";
}
return true;
}
bool iterativeClosestPointPlugin::initialize()
{
if(!iterativeClosestPointProcess::registered())
{
dtkWarn() << "Unable to register iterativeClosestPoint type";
}
if(!iterativeClosestPointToolBox::registered())
{
dtkWarn() << "Unable to register iterativeClosestPoint toolbox";
}
return true;
}
bool manualRegistrationPlugin::initialize()
{
if(!manualRegistration::registered())
{
dtkWarn() << "Unable to register manualRegistration type";
}
if ( !manualRegistrationToolBox::registered() )
{
dtkWarn() << "Unable to register manualRegistration toolbox";
}
return true;
}
bool MyPluginPlugin::initialize(void)
{
MyPluginPlugin::dataFactSingleton = dtkAbstractDataFactory::instance();
//dataFactorySingleton();
MyPluginPlugin::processFactSingleton = dtkAbstractProcessFactory::instance();
//processFactorySingleton();
if(!MyPluginDefaultProcess::registered())
dtkWarn() << "Unable to register MyPluginProcess type";
if(!MyPluginDefaultProcessDialog::registered())
dtkWarn() << "Unable to register MyPluginProcessDialog type";
if(!MyPluginDefaultData::registered())
dtkWarn() << "Unable to register MyPluginData type";
if(!MyPluginDefaultDataDialog::registered())
dtkWarn() << "Unable to register MyPluginDataDialog type";
if(!MyPluginDefaultDataReader::registered())
dtkWarn() << "Unable to register MyPluginDataReader type";
if(!MyPluginDefaultDataWriter::registered())
dtkWarn() << "Unable to register MyPluginDataWriter type";
if(!MyPluginDefaultDataConverter::registered())
dtkWarn() << "Unable to register MyPluginDataConverter type";
if(!MyPluginDefaultDataCreatorProcessDialog::registered())
dtkWarn() << "Unable to register MyPluginDataCreatorProcessDialog type";
return true;
}
void dtkComposerNodeStringListSet::run(void)
{
if (!d->receiver_list.isEmpty() && !d->receiver_value.isEmpty()&& !d->receiver_index.isEmpty() ) {
d->list = *(d->receiver_list.data());
qlonglong index = d->receiver_index.data();
if (index >= 0 && index < d->list.size())
d->list.replace(index, d->receiver_value.data());
else
dtkWarn() << "bad index value in set string list" << index;
} else {
dtkWarn() << "Inputs not specified. Nothing is done";
d->emitter.clearData();
}
}
bool itkDataTensorImageWriterBase::write(const QString& path)
{
if (!this->data())
return false;
if (this->io.IsNull())
return false;
if (medAbstractData *medData = dynamic_cast<medAbstractData*>(this->data()) ) {
if(medData->identifier()=="itkDataTensorImageFloat3") {
float dummy = 0;
write(path, dummy);
}
else if(medData->identifier()=="itkDataTensorImageDouble3") {
double dummy = 0;
write(path, dummy);
}
else {
dtkWarn() << "Unrecognized pixel type";
return false;
}
}
return true;
}
void medRegistrationWorkspace::updateFromRegistrationSuccess(medAbstractData *output)
{
if(!d->registrationToolBox)
return;
//TODO disconnect because we dont want to change input of the undo redo process.
// find a better way to do it ? - RDE
d->movingContainer->disconnect(this);
d->movingContainer->removeView();
d->movingContainer->addData(output);
d->fuseContainer->removeView();
d->fuseContainer->addData(d->registrationToolBox->fixedData());
d->fuseContainer->addData(output);
// Relink the views...
medAbstractLayeredView* movingView = dynamic_cast<medAbstractLayeredView*>(d->movingContainer->view());
if(!movingView)
{
dtkWarn() << "Non layered view are not suported yet in registration workspace.";
return;
}
medAbstractLayeredView* fuseView = dynamic_cast<medAbstractLayeredView*>(d->fuseContainer->view());
if(!fuseView)
{
dtkWarn() << "Non layered view are not suported yet in registration workspace.";
return;
}
d->viewGroup->addImpactedView(movingView);
d->viewGroup->addImpactedView(fuseView);
d->viewGroup->removeParameter("DataList");
d->movingLayerGroup->addImpactedlayer(movingView, output);
d->movingLayerGroup->addImpactedlayer(fuseView, output);
connect(d->movingContainer,SIGNAL(viewContentChanged()),
this, SLOT(updateFromMovingContainer()));
connect(d->movingContainer,SIGNAL(viewRemoved()),
this, SLOT(updateFromMovingContainer()));
}
bool itkDataDiffusionGradientListPlugin::initialize()
{
if (!itkDataDiffusionGradientList::registered()) {
dtkWarn() << "Unable to register itkDataDiffusionGradientList type";
}
return true;
}
void medRegistrationWorkspace::updateFromFixedContainer()
{
if(!d->registrationToolBox)
return;
if(!d->fixedContainer->view())
{
medAbstractLayeredView* fuseView = dynamic_cast<medAbstractLayeredView*>(d->fuseContainer->view());
if(fuseView)
{
if(fuseView->layer(d->registrationToolBox->fixedData()) == 0)
{
d->fuseContainer->removeView();
d->fuseContainer->addData(d->registrationToolBox->movingData());
}
else
fuseView->removeLayer(1);
}
d->registrationToolBox->setFixedData(NULL);
return;
}
medAbstractLayeredView* fixedView = dynamic_cast<medAbstractLayeredView*>(d->fixedContainer->view());
if(!fixedView)
{
dtkWarn() << "Non layered view are not suported yet in registration workspace.";
return;
}
medAbstractData *fixedData = fixedView->layerData(fixedView->currentLayer());
medAbstractLayeredView* fuseView = dynamic_cast<medAbstractLayeredView*>(d->fuseContainer->view());
if(fuseView)
fuseView->removeData(fixedData);
d->fuseContainer->addData(fixedData);
fuseView = dynamic_cast<medAbstractLayeredView*>(d->fuseContainer->view());
if(fixedData)
{
d->viewGroup->addImpactedView(fixedView);
d->viewGroup->addImpactedView(fuseView);
d->viewGroup->removeParameter("DataList");
d->fixedLayerGroup->addImpactedlayer(fixedView, fixedData);
d->fixedLayerGroup->addImpactedlayer(fuseView, fixedData);
}
if (!d->registrationToolBox->setFixedData(fixedData))
{
// delete the view because something failed at some point
d->viewGroup->removeImpactedView(fixedView);
d->fixedLayerGroup->removeImpactedlayer(fixedView, fixedData);
d->fixedLayerGroup->removeImpactedlayer(fuseView, fixedData);
fixedView->deleteLater();
}
}
bool itkDataSHImageWriterPlugin::initialize()
{
if(!itkMetaDataSHImageWriter::registered())
{
dtkWarn() << "Unable to register itkMetaDataSHImageWriter type";
}
return true;
}
void dtkComposerNodeMetaContainerAt::run(void)
{
if(!d->receiver_container.isEmpty()) {
QVariant var_container = d->receiver_container.data();
dtkMetaContainerSequential m_c = var_container.value<dtkMetaContainerSequential>();
if(!d->receiver_index.isEmpty()) {
d->emitter_value.setData(m_c.at(d->receiver_index.data()));
} else {
dtkWarn() << "No input index for the at operation. First item of the container is returned.";
d->emitter_value.setData(m_c.at(0));
}
} else {
dtkWarn() << "No input container for at operation. Nothing is emitted.";
d->emitter_value.clearData();
}
}
inline void deref(int index, QString & s, const QRegExp & regex, const QHash<QString, QString> & vars, int lineCount) {
QString varName = regex.cap(1).isEmpty() ? regex.cap(2) : regex.cap(1);
if (vars.contains(varName)) {
s.replace(index, regex.matchedLength(), vars[varName]);
} else {
s.replace(index, regex.matchedLength(), "");
dtkWarn() << "Unknown variable name line " << lineCount << " :" << varName;
}
}
// set method, and also, if necessary, jobid and rank
void dtkDistributedMessage::setMethod(QString method)
{
QStringList tokens = QString(method).split(QRegExp("/"));
if (method.startsWith("GET /status")) {
d->method = STATUS;
} else if (method.startsWith("PUT /job HTTP")) {
d->method = NEWJOB;
} else if (method.startsWith("DELETE /job")) {
d->jobid = tokens[2].remove("HTTP").trimmed();
if (d->headers.contains("x-dtk-finished")) {
d->method = ENDJOB;
} else {
d->method = DELJOB;
}
} else if (method.startsWith("DELETE /")) {
d->method = STOP;
} else if (method.startsWith("POST /data")) {
d->method = DATA;
d->jobid = tokens[2];
if (tokens.size() > 2)
d->rank = tokens[3].remove("HTTP").toInt();
} else if (method.startsWith("PUT /rank")) {
d->method = SETRANK;
d->jobid = tokens[2];
d->rank = tokens[3].remove("HTTP").toInt();
} else if (method.startsWith("HTTP/1.1 200 OK")) {
if (d->headers.contains("x-dtk-status")) {
d->method = OKSTATUS;
} else {
dtkWarn() << "Unsupported method " << method;
}
} else if (method.startsWith("HTTP/1.1 201 OK")) {
d->method = OKJOB;
} else if (method.startsWith("HTTP/1.1 204 OK")) {
d->method = OKDEL;
} else if (method.startsWith("HTTP/1.1 400 OK")) {
d->method = ERRORJOB;
} else if (method.startsWith("HTTP/1.1 410 OK")) {
d->method = ERRORDEL;
} else {
dtkWarn() << "Unsupported method " << method;
}
}
bool exampleProcessImageFilterPlugin::initialize() {
// Register the process
if (!exampleProcessImageFilter::registered())
dtkWarn() << "Unable to register exampleProcessImageFilter type";
else
dtkWarn() << "ABLE to register exampleProcessImageFilter type";
// Register the toolbox of the process with the Custon diffusionToolBox
if (!medToolBoxFactory::instance()->registerToolBox
<exampleProcessImageFilterToolBox>("exampleProcessImageFilter", name(), description(), QStringList()<<"diffusion"))
qDebug() << "Unable to register exampleProcessImageFilter toolbox";
else
qDebug() << "ABLE to register exampleProcessImageFilter toolbox";
return true;
}
void dtkComposerNodeVectorRealExtractorSubVector::run(void)
{
if (!d->receiver_vector.isEmpty() && !d->receiver_from.isEmpty()) {
dtkVectorReal *vector = d->receiver_vector.data();
if (!vector) {
dtkError() << DTK_PRETTY_FUNCTION << "Input vector is not defined.";
d->emitter_subvector.clearData();
return;
}
qlonglong from = *d->receiver_from.data();
if (from >= vector->size()) {
dtkWarn() << DTK_PRETTY_FUNCTION << "Starting value from is greater than vector size:" << from << ">=" << vector->size();
d->emitter_subvector.clearData();
return;
}
qlonglong length = vector->size();
if (!d->receiver_length.isEmpty())
length = *d->receiver_length.data();
if (length < 0) {
dtkWarn() << DTK_PRETTY_FUNCTION << "Length value is negative:" << length << "<" << 0;
d->emitter_subvector.clearData();
return;
}
qlonglong to = qMin((from + length), static_cast<qlonglong>(vector->size()));
qlonglong size = to - from;
if (d->subvector->size() != size)
d->subvector->allocate(size);
for(qlonglong i = from, count = 0; i < to; ++i, ++count)
(*d->subvector)[count] = (*vector)[i];
} else {
dtkWarn() << DTK_PRETTY_FUNCTION << "Inputs not specified. Nothing is done";
d->emitter_subvector.clearData();
}
}
bool itkDataTensorImagePlugin::initialize()
{
if (!itkDataTensorImageDouble3::registered()) { dtkWarn() << "Unable to register itkDataTensorImageDouble3 type"; }
if (!itkDataTensorImageFloat3::registered()) { dtkWarn() << "Unable to register itkDataTensorImageFloat3 type"; }
if (!itkDataTensorImageVtkViewInteractor::registered()) { dtkWarn() << "Unable to register itkDataTensorImageVtkViewInteractor type"; }
if (!itkMetaDataTensorImageWriter::registered()) { dtkWarn() << "Unable to register itkMetaDataTensorImageWriter type"; }
if (!itkNiftiDataTensorImageWriter::registered()) { dtkWarn() << "Unable to register itkNiftiDataTensorImageWriter type"; }
if (!itkNrrdDataTensorImageWriter::registered()) { dtkWarn() << "Unable to register itkNrrdDataTensorImageWriter type"; }
if (!itkMetaDataTensorImageReader::registered()) { dtkWarn() << "Unable to register itkMetaDataTensorImageReader type"; }
if (!itkNiftiDataTensorImageReader::registered()) { dtkWarn() << "Unable to register itkNiftiDataTensorImageReader type"; }
if (!itkNrrdDataTensorImageReader::registered()) { dtkWarn() << "Unable to register itkNrrdDataTensorImageReader type"; }
return true;
}
bool medVtkFibersDataPlugin::initialize()
{
if (!medVtkFibersData::registered()) {
dtkWarn() << "Unable to register medVtkFibersData type";
}
if (!medVtkFibersDataWriter::registered()) {
dtkWarn() << "Unable to register medVtkFibersDataWriter type";
}
if (!medVtkFibersDataReader::registered()) {
dtkWarn() << "Unable to register medVtkFibersDataReader type";
}
if (!medVtkFibersDataInteractor::registered()) {
dtkWarn() << "Unable to register medVtkFibersDataInteractor";
}
return true;
}
bool reformatPlugin::initialize()
{
if(!medReformatWorkspace::registered())
{
dtkWarn() << "Unable to register medReformatWorkspace type";
}
if (!resliceToolBox::registered())
{
dtkWarn() << "Unable to register resliceToolBox type";
}
if (!medCropToolBox::registered())
{
dtkWarn() << "Unable to register medCropToolBox type";
}
if (!resampleProcess::registered())
{
dtkWarn() << "Unable to register resample process";
}
return true;
}
void dtkComposerNodeVectorIntegerOperatorUnaryScalarNorm::run(void)
{
if (d->receiver_vec.isEmpty()){
dtkWarn() << "Input not specified. Nothing is done";
d->value = -1.;
} else {
d->value = d->receiver_vec.data()->norm();
}
}
void dtkComposerNodeStringListExtract::run(void)
{
if (!d->receiver_list.isEmpty() && !d->receiver_index.isEmpty() ) {
QStringList *list = d->receiver_list.data();
d->value = list->at(d->receiver_index.data());
d->emitter.setData(d->value);
} else {
dtkWarn() << "Inputs not specified. Nothing is done";
d->emitter.clearData();
}
}
void dtkComposerNodeMetaContainerAppend::run(void)
{
if(!d->receiver_container.isEmpty()) {
QVariant var_container = d->receiver_container.data();
if(!d->receiver_value.isEmpty()) {
dtkMetaContainerSequential m_c = var_container.value<dtkMetaContainerSequential>();
m_c.append(d->receiver_value.data());
} else {
dtkWarn() << "No input value to append to the container. The container is not modified.";
}
d->emitter_container.setData(var_container);
} else {
dtkWarn() << "No input container for append operation. Nothing is emitted.";
d->emitter_container.clearData();
}
}