// 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
contextMenu.addAction(actionAdd_fusion_image);
contextActions.push_back(actionAdd_fusion_image);
+#ifdef CLITK_EXPERIMENTAL
contextMenu.addAction(actionAdd_USSequence_toCT);
contextActions.push_back(actionAdd_USSequence_toCT);
+#endif
contextMenu.addSeparator();
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()));
///////////////////////////////////////////////
connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double, bool)),
this,SLOT(SetFusionProperty(int,int,int,double,double, bool)));
connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
+ connect(landmarksPanel,SIGNAL(SelectedPointChanged()),this,SLOT(GoToLandmark()));
connect(overlayPanel,SIGNAL(FusionSequencePropertyUpdated(int, bool, unsigned int, bool)),
this,SLOT(SetFusionSequenceProperty(int, bool,unsigned int, bool)));
{
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);
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
}
}
DataTree->topLevelItem(selected)->setSelected(1);
mCurrentSelectedImageId = id;
+
+ landmarksPanel->SetCurrentLandmarks(mSlicerManagers[selected]->GetLandmarks(),
+ mSlicerManagers[selected]->GetTSlice());
+ landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
+ landmarksPanel->SetCurrentImage(mSlicerManagers[selected]->GetFileName().c_str());
+
emit SelectedImageHasChanged(mSlicerManagers[selected]);
}
//------------------------------------------------------------------------------
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));
infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
- mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
+ mSlicerManagers[index]->GetTSlice());
landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
}
}
- infoPanel->setFileName(image);
- infoPanel->setDimension(dim);
- infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
- infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
- infoPanel->setOrigin(GetVectorDoubleAsString(origin));
- infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
- infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
-
- landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
- mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
- landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
- landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
-
- overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
- for (int i = 0; i < 4; i++) {
- if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
- mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
- break;
- }
- }
+// infoPanel->setFileName(image);
+// infoPanel->setDimension(dim);
+// infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
+// infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
+// infoPanel->setOrigin(GetVectorDoubleAsString(origin));
+// infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
+// infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
+//
+// landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
+// mSlicerManagers[index]->GetTSlice());
+// landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
+// landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
+//
+// overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
+// for (int i = 0; i < 4; i++) {
+// if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
+// mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
+// break;
+// }
+// }
WindowLevelChanged();
slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
}
if (overlay_type=="fusionSequence") {
//removing the overlay sequence in a fusion sequence visualization mode
- //TODO: remove the synchronization (transform matrices, etc...)
+ //reset the transforms
+ overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
- //=> unlink and untie the slicer managers
+ //unlink and untie the slicer managers
RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
+ for (unsigned i=0 ; i<4 ; i++) {
+ mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
+ mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
+ }
}
mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
for (int i = 0; i < index; i++) {
Manageriter++;
}
- linkPanel->removeImage(index);
- mSlicerManagers[index]->RemoveActors();
-
//if the slicer manager was involved in a fusion sequence visualization...
- if ( item->data(1,Qt::UserRole).toString().toStdString() == "fusionSequence" ) {
- //TODO
- //make sure both SlicerManager exit the FusionSequence visualization mode
- //disable the temporal and spatial sync? make sure we reset the spatial transforms to their initial states...
+ 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);
+
+ //unlink and untie the slicer managers
+ RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
+ for (unsigned i=0 ; i<4 ; i++) {
+ mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
+ mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
+ }
+ */
}
+ linkPanel->removeImage(index);
+ mSlicerManagers[index]->RemoveActors();
+
//remove the slicer manager
delete mSlicerManagers[index];
mSlicerManagers.erase(Manageriter);
//------------------------------------------------------------------------------
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();
}
}
QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
}
//------------------------------------------------------------------------------
-
+//------------------------------------------------------------------------------
+void vvMainWindow::AddLandmarks(int index, std::vector<std::string> files)
+{
+ if (!landmarksPanel->LoadFromFile(files))
+ QMessageBox::information(this,tr("Problem reading Landmarks !"),"File doesn't exist!");
+
+ landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
+ landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
+}
//------------------------------------------------------------------------------
void vvMainWindow::OpenField()
//------------------------------------------------------------------------------
-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);
}
}
}
}
//------------------------------------------------------------------------------
+//------------------------------------------------------------------------------
+void vvMainWindow::GoToLandmark()
+{
+ int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
+ for (int column = 1; column < 5; column++) {
+ if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
+ double* cursorPos = landmarksPanel->GetSelectedPoint();
+ mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
+ cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
+ mSlicerManagers[index]->UpdateViews(1,column-1);
+ mSlicerManagers[index]->UpdateLinked(column-1);
+ break;
+ }
+ }
+}
+//------------------------------------------------------------------------------
+
//------------------------------------------------------------------------------
void vvMainWindow::PlayPause()
{
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff