// Standard includes
#include <iostream>
+#include <fstream>
#include <sstream>
#include <iomanip>
#define COLUMN_IMAGE_NAME 7
#ifdef CLITK_PRIVATE_FEATURES
-#define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz *.usf)"
+#define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz *.usf *.svl)"
#else
#define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz)"
#endif
documentation = new vvDocumentation();
help_dialog = new vvHelpDialog();
dicomSeriesSelector = new vvDicomSeriesSelector();
+ PacsConnection = new vvPacsConnection();
inverseButton->setEnabled(0);
actionAdd_overlay_image_to_current_image->setEnabled(0);
connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
- connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
+ // connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
- connect(overlayPanel, SIGNAL(FusionSequenceSignalButtonPressed()), this, SLOT(SelectFusionSequenceTemporalSignal()));
+ connect(overlayPanel, SIGNAL(FusionSequenceCorrespondancesButtonPressed()), this, SLOT(SelectFusionSequenceCorrespondances()));
///////////////////////////////////////////////
brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
brush.setStyle(Qt::SolidPattern);
item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
- item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
+ // item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
for (int j = 1; j <= 4; j++)
item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
{
std::vector<std::string> files;
- std::cout << "dicomSeriesSelector " << std::endl;
+ //std::cout << "dicomSeriesSelector " << std::endl;
if (dicomSeriesSelector->exec() == QDialog::Accepted) {
files = *(dicomSeriesSelector->GetFilenames());
LoadImages(files, vvImageReader::DICOM);
}
+
+ void vvMainWindow::ConnectPacs()
+{
+ std::vector<std::string> files;
+
+ //std::cout << "dicomSeriesSelector " << std::endl;
+ if (PacsConnection->exec() == QDialog::Accepted) {
+ files = *(PacsConnection->GetFilenames());
+ LoadImages(files, vvImageReader::DICOM);
+ }
+
}
//------------------------------------------------------------------------------
double range[2];
mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
if ((range[0] == 0) && (range[1] == 1)) {
- presetComboBox->setCurrentIndex(5);// binary
+ presetComboBox->setCurrentIndex(WL_BINARY);// binary
} else {
// TODO
}
dim += pixelType + ")";
infoPanel->setFileName(image);
+ std::string creationImageTimeValue("No creation time");
+ itk::ExposeMetaData< std::string > (*imageSelected->GetFirstMetaDataDictionary(), "creationImageTime", creationImageTimeValue);
+ infoPanel->setImageCreationTime(QString(creationImageTimeValue.c_str()));
infoPanel->setDimension(dim);
infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
}
//if the slicer manager was involved in a fusion sequence visualization...
if ( mSlicerManagers[index]->IsInvolvedInFusionSequence() ) {
+ //in both cases, close the overlay: find it... and close it
+ //ideally, I should duplicate the code, and avoid calling CloseImage, since this pops up another interactive box
+ QTreeWidgetItem* overlayItem;
+ if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
+ for (unsigned i=0 ; i<item->childCount() ; i++) {
+ overlayItem = item->child(i);
+ this->CloseImage( overlayItem, 0 );
+ }
+ }
+ else {
+ QTreeWidgetItem* linkedItem = this->GetItemFromSlicerManager( mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()] );
+ for (unsigned i=0 ; i<linkedItem->childCount() ; i++) {
+ overlayItem = linkedItem->child(i);
+ this->CloseImage( overlayItem, 0 );
+ }
+ }
+
+ /* -- this is normally already done when closing the overlay.
//reset the transforms
overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
}
-
- //TODO: also remove the image overlaid with the main sequence, as it is becoming invalid...
+ */
}
linkPanel->removeImage(index);
//------------------------------------------------------------------------------
void vvMainWindow::WindowLevelEdited()
{
- presetComboBox->setCurrentIndex(6);
+ presetComboBox->setCurrentIndex(WL_USER);
UpdateWindowLevel();
}
//------------------------------------------------------------------------------
{
windowSpinBox->setValue(w);
levelSpinBox->setValue(l);
- presetComboBox->setCurrentIndex(6);
+ presetComboBox->setCurrentIndex(WL_USER);
colorMapComboBox->setCurrentIndex(0);
UpdateWindowLevel();
}
void vvMainWindow::UpdateWindowLevel()
{
if (DataTree->selectedItems().size()) {
- if (presetComboBox->currentIndex() == 7) //For ventilation
+ if (presetComboBox->currentIndex() == WL_VENTILATION) //For ventilation
colorMapComboBox->setCurrentIndex(5);
int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
{
int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
int window = mSlicerManagers[index]->GetColorWindow();
- presetComboBox->setCurrentIndex(6);
+ presetComboBox->setCurrentIndex(WL_USER);
windowSpinBox->setValue(-window);
UpdateWindowLevel();
}
continue;
mSlicerManagers[i]->SetColorWindow(window);
mSlicerManagers[i]->SetColorLevel(level);
- mSlicerManagers[i]->SetPreset(6);
+ mSlicerManagers[i]->SetPreset(WL_USER);
mSlicerManagers[i]->Render();
}
}
if (mSlicerManagers[i] == NULL)
continue;
mSlicerManagers[i]->SetColorWindow(window);
- mSlicerManagers[i]->SetPreset(6);
+ mSlicerManagers[i]->SetPreset(WL_USER);
mSlicerManagers[i]->Render();
}
}
if (mSlicerManagers[i] == NULL)
continue;
mSlicerManagers[i]->SetColorLevel(level);
- mSlicerManagers[i]->SetPreset(6);
+ mSlicerManagers[i]->SetPreset(WL_USER);
mSlicerManagers[i]->Render();
}
}
QString Extensions = EXTENSIONS;
Extensions += ";;All Files (*)";
- QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
- if (!file.isEmpty())
- AddFusionImage(index,file);
+ QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Fusion image"),mInputPathName,Extensions);
+ if (files.isEmpty())
+ return;
+
+ std::vector<std::string> vecFileNames;
+ for (int i = 0; i < files.size(); i++) {
+ vecFileNames.push_back(files[i].toStdString());
+ }
+ AddFusionImage(index,vecFileNames,vvImageReader::IMAGE);
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-void vvMainWindow::AddFusionImage(int index, QString file)
+void vvMainWindow::AddFusionImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
{
+ QString file(fileNames[0].c_str());
if (QFile::exists(file))
{
mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
- reader->SetFileName(file.toStdString().c_str());
+ reader->SetFileName(fileNames[0].c_str());
reader->ReadImageInformation();
std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
- if (reader) {
- QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
- vvProgressDialog progress("Opening fusion");
- qApp->processEvents();
+ int dimension = reader->GetNumberOfDimensions();
+ QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
+ vvProgressDialog progress("Opening fusion");
+ qApp->processEvents();
- std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
- if (mSlicerManagers[index]->SetFusion(file.toStdString(),
- reader->GetNumberOfDimensions(), component)) {
- //create an item in the tree with good settings
- QTreeWidgetItem *item = new QTreeWidgetItem();
- item->setData(0,Qt::UserRole,file.toStdString().c_str());
- item->setData(1,Qt::UserRole,tr("fusion"));
- QFileInfo fileinfo(filename.c_str()); //Do not show the path
+ std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
+ if (mSlicerManagers[index]->SetFusion(fileNames,dimension, component,type)) {
+ //create an item in the tree with good settings
+ QTreeWidgetItem *item = new QTreeWidgetItem();
+ item->setData(0,Qt::UserRole,file.toStdString().c_str());
+ item->setData(1,Qt::UserRole,tr("fusion"));
+ QFileInfo fileinfo(file); //Do not show the path
item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
qApp->processEvents();
- for (int j = 1; j <= 4; j++) {
- item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
- }
-
- //Create the buttons for reload and close
- qApp->processEvents();
- QTreePushButton* cButton = new QTreePushButton;
- cButton->setItem(item);
- cButton->setColumn(COLUMN_CLOSE_IMAGE);
- cButton->setToolTip(tr("close image"));
- cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
- connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
- this,SLOT(CloseImage(QTreeWidgetItem*, int)));
-
- QTreePushButton* rButton = new QTreePushButton;
- rButton->setItem(item);
- rButton->setColumn(COLUMN_RELOAD_IMAGE);
- rButton->setToolTip(tr("reload image"));
- rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
- connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
- this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
-
- DataTree->topLevelItem(index)->setExpanded(1);
- DataTree->topLevelItem(index)->addChild(item);
- DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
- DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
-
- //set the id of the image
- QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
- item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
- UpdateTree();
- qApp->processEvents();
- ImageInfoChanged();
- QApplication::restoreOverrideCursor();
- } else {
- QApplication::restoreOverrideCursor();
- QString error = "Cannot import the new image.\n";
- error += mSlicerManagers[index]->GetLastError().c_str();
- QMessageBox::information(this,tr("Problem reading image !"),error);
+ for (int j = 1; j <= 4; j++) {
+ item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
}
+
+ //Create the buttons for reload and close
+ qApp->processEvents();
+ QTreePushButton* cButton = new QTreePushButton;
+ cButton->setItem(item);
+ cButton->setColumn(COLUMN_CLOSE_IMAGE);
+ cButton->setToolTip(tr("close image"));
+ cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
+ connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
+ this,SLOT(CloseImage(QTreeWidgetItem*, int)));
+
+ QTreePushButton* rButton = new QTreePushButton;
+ rButton->setItem(item);
+ rButton->setColumn(COLUMN_RELOAD_IMAGE);
+ rButton->setToolTip(tr("reload image"));
+ rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
+ connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
+ this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
+
+ DataTree->topLevelItem(index)->setExpanded(1);
+ DataTree->topLevelItem(index)->addChild(item);
+ DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
+ DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
+
+ //set the id of the image
+ QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
+ item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
+ UpdateTree();
+ qApp->processEvents();
+ ImageInfoChanged();
+ QApplication::restoreOverrideCursor();
+
+ // Update the display to update, e.g., the sliders
+ for(int i=0; i<4; i++)
+ DisplaySliders(index, i);
} else {
+ QApplication::restoreOverrideCursor();
QString error = "Cannot import the new image.\n";
+ error += mSlicerManagers[index]->GetLastError().c_str();
QMessageBox::information(this,tr("Problem reading image !"),error);
}
+ WindowLevelChanged();
}
else
QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
//------------------------------------------------------------------------------
-void vvMainWindow::SelectFusionSequenceTemporalSignal() {
+void vvMainWindow::SelectFusionSequenceCorrespondances() {
//make sure the index is right?
//in the end, I should attach the temporal data to the right sequence!
}
//open a dialog box to find a file
- QString Extensions = EXTENSIONS;
- Extensions += ";;All Files (*)";
+ //QString Extensions = EXTENSIONS;
+ QString Extensions = ";;All Files (*)";
QString fileName = QFileDialog::getOpenFileName(this,tr("Load respiratory signal for fused sequence"),mInputPathName,Extensions);
if (fileName.isNull())
return;
//read it as a vector of values
- std::vector<double> signal;
- //...TODO, look for itk functions that can do that... vnl in the worst case.
- signal.push_back(1);signal.push_back(2);
-
- //TODO: instead: if the loaded signal is longer, just crop it...
- //this allows loading only the first few frames when testing.
- //->maybe raise a message that this behavior may be unsafe...
-
- //if compatible with the fused image sequence (number of images = number of entries), enable the temporalSync
- if ( signal.size() >= mSlicerManagers[index]->GetFusionSequenceNbFrames()) {
- //for convenience, associate this sequence to both the current slicer manager, and to the linked one
- mSlicerManagers[index]->SetFusionSequenceTemporalSignal(signal);
- mSlicerManagers[ mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager() ]->SetFusionSequenceTemporalSignal(signal);
- overlayPanel->enableFusionSequenceTemporalSync();
- QMessageBox::information(this,tr("Adding signal"),"would add the signal from file: "+ fileName);
+ vnl_vector<double> tmpVect;
+
+ std::ifstream file;
+ file.open(fileName.toStdString().c_str());
+ tmpVect.read_ascii(file);
+ file.close();
+
+ //if compatible with the fused image sequence (number of entries = nb of entries in main sequence + nb of entries in joint sequence), enable the temporalSync
+ bool signalOK = true;
+ unsigned nbFrameMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
+ unsigned nbFrameSecondary = mSlicerManagers[index]->GetFusionSequenceNbFrames();
+std::cout<<"nbFrameMain = "<<nbFrameMain<<", nbFrameSecondary= "<<nbFrameSecondary<<", signal size: "<<tmpVect.size()<<std::endl;
+ std::vector<unsigned> temporalCorrespondances;
+ if ( tmpVect.size() == nbFrameMain + nbFrameSecondary ) {
+ for (unsigned i=0 ; i<tmpVect.size() ; i++) {
+ if (i<nbFrameMain) { //first part of the file: i -> index in secondary seq.
+ if ( tmpVect(i)<nbFrameSecondary ) temporalCorrespondances.push_back(tmpVect(i));
+ else { signalOK=false; break; } //pointing outside the secondary sequence...
+ }
+ else { //first part of the file -> index in secondary seq.
+ if ( tmpVect(i)<nbFrameMain ) temporalCorrespondances.push_back(tmpVect(i));
+ else { signalOK=false; break; } //pointing outside the secondary sequence...
+ }
+ }
}
- else {//else, send a message to signal the failure...
- QString error = "The provided signal doesn't have the same duration as the sequence\n";
+ else {signalOK=false;}
+ if (!signalOK) {//else, send a message to signal the failure...
+ QString error = "The provided temporal correspondances is invalid - check tooltip.\n";
error += "Ignoring file: " + fileName;
- QMessageBox::information(this,tr("Problem adding signal!"),error);
+ QMessageBox::information(this,tr("Problem adding temporal correspondances!"),error);
return;
}
+ else {
+ //for convenience, associate this sequence to both the current slicer manager, and to the linked one
+ mSlicerManagers[index]->SetFusionSequenceCorrespondances(temporalCorrespondances);
+ mSlicerManagers[ mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager() ]->SetFusionSequenceCorrespondances(temporalCorrespondances);
+ overlayPanel->enableFusionSequenceTemporalSync();
+ }
}
//------------------------------------------------------------------------------
mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
+ std::sort (fileNames.begin(), fileNames.end());//make sure the files are sorted.
reader->SetFileName(fileNames[0].c_str());
reader->ReadImageInformation();
std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
//This loads the secondary sequence (US) as an independent sequence
LoadImages(fileNames, type);
- //reset the transforms to identiy
+ //reset the transforms to identity
+ //FIX -- and set the thickness of the US slices to a large value (necessary for visualization purposes...)
+ double sp_x, sp_y, sp_z;
+ mSlicerManagers[indexParent]->GetImage()->GetVTKImages()[0]->GetSpacing(sp_x, sp_y, sp_z);
+ sp_z = std::max(sp_x, std::max(sp_y, sp_z)) + 0.5; //
for (unsigned i=0 ; i<mSlicerManagers.back()->GetImage()->GetTransform().size() ; i++) {
+ sp_x = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[0];
+ sp_y = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[1];
+ mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->SetSpacing( sp_x, sp_y, sp_z);
mSlicerManagers.back()->GetImage()->GetTransform()[i]->Identity();
mSlicerManagers.back()->GetImage()->GetTransform()[i]->Update();
}
error += mSlicerManagers[index]->GetLastError().c_str();
QMessageBox::information(this,tr("Problem reading image !"),error);
}
- //WindowLevelChanged();
+ WindowLevelChanged();
ImageInfoChanged(); //this internally calls WindowLevelChanged...
}
else {
if (spatialSyncFlag) { //reslice the CT
if (temporalSyncFlag) { //do the temporal synchronisation
- //TODO: add the temporal synchronisation stuff
- //if the button is checked, get the phase of the requested US frame from the available signal
- //and select the corresponding one in the CT. (check the one just before, and the one just after, and select the closest)
-
- //TODO: do it also the other way around, when modifying the time index related to CT, select a close frame
- //this should not be done here directly, but the code should be inspired from the one here
- //->find a good US frame such that when calling this function with this US frame, it produces the expected result
-
-
- //TODO: select the right CT image to display
int mainSequenceFrameIndex=0;
//estimate the TSlice to set to the CT
-
+ unsigned nbFramesMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
+ mainSequenceFrameIndex = mSlicerManagers[index]->GetFusionSequenceCorrespondances()[ nbFramesMain + fusionSequenceFrameIndex];
//and set it!
mSlicerManagers[index]->SetTSlice(mainSequenceFrameIndex, false);
+ //warning, there is a loopback, and modification of the TSlice in main sequence forces an update of the TSlice in secondary, etc...
}
if (mSlicerManagers[i]->GetFusionSequenceTemporalSyncFlag()) {
//WARNING: for some obscure reason, there are problems when accessing mSlicerManagers[mSlicerManagers[i]->GetFusionSequenceIndexOfLinkedManager()]->GetFusionSequenceFrameIndex();
- //int estimatedValue=mSlicerManagers[mSlicerManagers[i]->GetFusionSequenceIndexOfLinkedManager()]->GetFusionSequenceFrameIndex();
int estimatedValue=0;
- //TODO: if temporal sync is active
//estimate a corresponding time index for the secondary (US) sequence, and update it accordingly.
- //estimatedValue = ...
- overlayPanel->updateFusionSequenceSliderValueFromWindow(estimatedValue, true);
+ estimatedValue = mSlicerManagers[i]->GetFusionSequenceCorrespondances()[ value ];
+ //TODO: at the moment, there is a loop in TSlice modifications
+ //modifying sequence 1 causes seq 2 to update, which in turns update seq1...
+ //I disable control on seq1 at the moment.
+ //overlayPanel->updateFusionSequenceSliderValueFromWindow(estimatedValue, true);
}
}
}
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff