(1) fix relative path problem for MR_Volume during scene loading

(2) fix update of slice_spacing problem for loading MR volume from folder
(3) read image size from dicom header instead of using fixed 512x512 matrix size

src/geometry/SystemGeometryDefinitions.cxx

@@ -38,14 +38,6 @@ int SystemGeometryDefinitions::TABLE_POSITION_X = 0; // lat.
 int SystemGeometryDefinitions::TABLE_POSITION_Y = 0; // long.
 int SystemGeometryDefinitions::TABLE_POSITION_Z = 0; //vert. = höhe
 
-// target size is set to keep the original ratio
-int SystemGeometryDefinitions::TARGET_SIZE_X = 512;
-int SystemGeometryDefinitions::TARGET_SIZE_Y = 512;
-
-// X-ray image size on the image plane (this is needed for positioning the X-ray plane)
-int SystemGeometryDefinitions::IMAGE_SIZE_X = 512;
-int SystemGeometryDefinitions::IMAGE_SIZE_Y = 512;
-
 int SystemGeometryDefinitions::FIELD_DISTANCE = 25;
 double SystemGeometryDefinitions::DETECTOR_SIZE = 174.98;	//174.98 mm - Detector size at FD = 25 cm;
 //double SystemGeometryDefinitions::DETECTOR_SIZE = 132.902;	//132.902 mm - Detector size at FD = 19 cm;

src/geometry/SystemGeometryDefinitions.h

@@ -5,10 +5,6 @@
 struct SystemGeometryDefinitions {
 	static int CAMERA_SIZE_X; /// original width of the xray image (Live Signal format = monitor format)
 	static int CAMERA_SIZE_Y; /// original height of the xray image
-	static int TARGET_SIZE_X; /// width of the xray image (it will be scaled if necessary)
-	static int TARGET_SIZE_Y; /// height of the xray image (it will be scaled if necessary)
-	static int IMAGE_SIZE_X; /// displayed width of the xray image (used to position the image plane)
-	static int IMAGE_SIZE_Y; /// displayed height of the xray image (used to position the image plane)
 
 	static int LAPTOP_SIZE_X;
 	static int LAPTOP_SIZE_Y;

src/gui/MainWindow.cpp

@@ -543,7 +543,7 @@ void MainWindow::saveScene(const char* file)
 	/*settings.setValue("MR_INPUT_YES", theOverlayScene->getMRInputFileForMesh());*/
 	settings.setValue("MESH_ORIENTATION", MeshOrientation);
 	settings.setValue("MR_VOLUME", theOverlayScene->GetMRVisualizer()->getInputFile());
-	
+
 	OverlayScene::MR_ITK;
 
 	QString save = file;
@@ -739,14 +739,16 @@ void MainWindow::loadScene(const char* file)
 	QString MRVolumeFile = settings.value("MR_VOLUME").toString();
 	string MRVolumeFileString = qPrintable(MRVolumeFile);
 
+
 	QDir d = QFileInfo(MRVolumeFile).absoluteDir();
 	QString absoluteDir = d.absolutePath();
-	string MRVolumeDirString = qPrintable(absoluteDir);
-
+	string MRVolumeDirString = qPrintable(absoluteDir);	
 
 
 	if (MRVolumeFile.startsWith(".")) {
 		MRVolumeFileString = qPrintable(dir.absoluteFilePath(MRVolumeFile));
+		MRVolumeDirString = qPrintable(dir.absoluteFilePath(MRVolumeFile).section("/", 0, -2));
+
 	}
 
 	if (MRVolumeFile != QString("")) {
@@ -756,6 +758,7 @@ void MainWindow::loadScene(const char* file)
 		case 0:
 			theOverlayScene->SetCTVisualizer(MRVolumeFileString, MRVolumeDirString, orientation);
 			reloadFile = MRVolumeFileString;
+			reloadDir = MRVolumeDirString;
 			MeshOrientation = 0;
 			break;
 		case 1:
@@ -767,11 +770,13 @@ void MainWindow::loadScene(const char* file)
 		case 2:
 			theOverlayScene->SetCTVisualizer(MRVolumeFileString, MRVolumeDirString, orientation);
 			reloadFile = MRVolumeFileString;
+			reloadDir = MRVolumeDirString;
 			MeshOrientation = 2;
 			break;
 		case 3:
 			theOverlayScene->SetCTVisualizer(MRVolumeFileString, MRVolumeDirString, orientation);
 			reloadFile = MRVolumeFileString;
+			reloadDir = MRVolumeDirString;
 			MeshOrientation = 3;
 			break;
 		default:

src/pipeline/DICOMVisualizer.cxx

@@ -96,7 +96,16 @@ DICOMVisualizer::~DICOMVisualizer()
 
 const char* DICOMVisualizer::getInputFile() const
 {
-	return theDICOMReader->GetFileName();
+	const char* filename = theDICOMReader->GetFileName();
+
+	if (filename == NULL)
+	{
+		vtkStringArray *filenames = theDICOMReader->GetFileNames();
+		filename = filenames->GetValue(0).c_str();
+
+	}
+
+	return filename;
 }
 
 
@@ -210,6 +219,7 @@ void DICOMVisualizer::setCTInputFile(string theFilename, string theFoldername, i
 	s.SetComputeZSpacing(true);
 
 	s.SetZSpacingTolerance(1e-3);
+	//std::cout << "z-spacing" << s.GetZSpacing() << std::endl;
 
 	bool b = s.Sort(filenames);
 

src/pipeline/OverlayScene.cxx

@@ -2278,7 +2278,7 @@ void OverlayScene::transformFromWorldToImageCoordinates(unsigned int streamNumbe
 }
 
 void OverlayScene::setBiplaneGeometry(unsigned int streamNumber, int SID, int sourcePatDist, double primAngle, double secAngle,
-	int lateralPos, int longitudinalPos, int verticalPos, double mmPerPxl)
+	int lateralPos, int longitudinalPos, int verticalPos, double mmPerPxl, int imageSizeX, int imageSizeY)
 {
 	//printf("setting geometry with first SID: %.0f and second SID: %.0f\n", SID[0], SID[1]);
 	/* compute geometry */
@@ -2295,8 +2295,8 @@ void OverlayScene::setBiplaneGeometry(unsigned int streamNumber, int SID, int so
 	}
 
 	geometry->setImageDimension(
-		SystemGeometryDefinitions::IMAGE_SIZE_X,
-		SystemGeometryDefinitions::IMAGE_SIZE_Y
+		imageSizeX, 
+		imageSizeY
 		);
 	geometry->setIsFramegrabber(isFramegrabber);
 	geometry->setTablePosition((double)lateralPos, (double)longitudinalPos, (double)verticalPos);
@@ -2489,13 +2489,13 @@ void OverlayScene::setupGeometryFromFramegrabber(int index)
 }
 
 
-void OverlayScene::setMainGeometryByDICOM(int SID, int sourcePatDist, double primAngle, double secAngle, int lateralPos, int longitudinalPos, int verticalPos, double mmPerPixel)
+void OverlayScene::setMainGeometryByDICOM(int SID, int sourcePatDist, double primAngle, double secAngle, int lateralPos, int longitudinalPos, int verticalPos, double mmPerPixel, int imageSizeX, int imageSizeY)
 {
 
 	theBiplaneGeometry.mainSystem.setIsFramegrabber(isFramegrabber);
 	theBiplaneGeometry.mainSystem.setImageDimension(
-		SystemGeometryDefinitions::IMAGE_SIZE_X,
-		SystemGeometryDefinitions::IMAGE_SIZE_Y
+		imageSizeX,
+		imageSizeY
 		);
 
 	double angles[2] = { primAngle, secAngle};
@@ -3104,10 +3104,10 @@ void OverlayScene::showFrame(int index, int frame)
 
 void OverlayScene::setMainXRAYInputToFile(const char* file)
 {
-	int SID, sourcePatDist;
+	int SID, sourcePatDist, imageSizeX, imageSizeY;
 	double primAngle, secAngle, mmPerPixel;
 	int lateralPos, longitudinalPos, verticalPos;
-	bool ok[8];
+	bool ok[10];
 
 
 	readerMainXRAY = XRAYReader::New();
@@ -3121,8 +3121,8 @@ void OverlayScene::setMainXRAYInputToFile(const char* file)
 	theMotionCorrections->SetInputConnection(resliceMainXRAY->GetOutputPort(0));
 	actorMainXRAY->GetMapper()->SetInputConnection(theMotionCorrections->GetOutputPort());
 
-	this->getDicomGeometryValues(SID, sourcePatDist, primAngle, secAngle, lateralPos, longitudinalPos, verticalPos, mmPerPixel, ok);
-	setMainGeometryByDICOM(SID, sourcePatDist, primAngle, secAngle, lateralPos, longitudinalPos, verticalPos, mmPerPixel);
+	this->getDicomGeometryValues(SID, sourcePatDist, primAngle, secAngle, lateralPos, longitudinalPos, verticalPos, mmPerPixel, imageSizeX, imageSizeY, ok);
+	setMainGeometryByDICOM(SID, sourcePatDist, primAngle, secAngle, lateralPos, longitudinalPos, verticalPos, mmPerPixel, imageSizeX, imageSizeY);
 
 	//rendererMainXRAY->ResetCamera();
 	//renWinMainXRAY->Render();
@@ -3379,10 +3379,10 @@ void OverlayScene::setInputToFile(const char* file, int streamNumber)
 
 	theXRAYReaders[streamNumber]->Delete();
 
-	int SID, sourcePatDist;
+	int SID, sourcePatDist, imageSizeX, imageSizeY;
 	double primAngle, secAngle, mmPerPixel;
 	int lateralPos, longitudinalPos, verticalPos;
-	bool ok[8];
+	bool ok[10];
 
 	XRAYReader* readerXRAY = XRAYReader::New();
 	readerXRAY->setInputFile(file);
@@ -3396,7 +3396,7 @@ void OverlayScene::setInputToFile(const char* file, int streamNumber)
 	theXRAYActors3D[streamNumber]->GetMapper()->SetInputConnection(theXRAYReslicers[streamNumber]->GetOutputPort());
 	theXRAYReslicers[streamNumber]->SetResliceAxesOrigin(0.0, 0.0, 0.0); // to display the first frame, even if there is only one image in a stream
 
-	this->getDicomReferenceGeometryValues(streamNumber, SID, sourcePatDist, primAngle, secAngle, lateralPos, longitudinalPos, verticalPos, mmPerPixel, ok);
+	this->getDicomReferenceGeometryValues(streamNumber, SID, sourcePatDist, primAngle, secAngle, lateralPos, longitudinalPos, verticalPos, mmPerPixel, imageSizeX, imageSizeY, ok);
 	// berechnung fehlt!!!!!!!!!!!!!!!!!
 	if (!alreadyConstructedPipelineDICOM[streamNumber]) {
 
@@ -3412,15 +3412,15 @@ void OverlayScene::setInputToFile(const char* file, int streamNumber)
 
 		}
 	}
-	setBiplaneGeometry(streamNumber, SID, sourcePatDist, primAngle, secAngle, lateralPos, longitudinalPos, verticalPos, mmPerPixel); 
+	setBiplaneGeometry(streamNumber, SID, sourcePatDist, primAngle, secAngle, lateralPos, longitudinalPos, verticalPos, mmPerPixel, imageSizeX, imageSizeY);
 
 	renderer3D->ResetCamera();
 	renWin3D->Render();
 
 }
 
 void OverlayScene::getDicomReferenceGeometryValues(int streamNumber, int& SID, int& sourcePatDist, double& primAngle, double& secAngle, 
-	int& lateralPos, int& longitudinalPos, int& verticalPos, double& mmPerPixel, bool ok[8])
+	int& lateralPos, int& longitudinalPos, int& verticalPos, double& mmPerPixel, int& imageSizeX, int& imageSizeY, bool ok[10])
 {
 	SID = theXRAYReaders[streamNumber]->GetSID(&ok[0]);
 	sourcePatDist = theXRAYReaders[streamNumber]->GetSourcePatientDistance(&ok[1]);
@@ -3430,11 +3430,13 @@ void OverlayScene::getDicomReferenceGeometryValues(int streamNumber, int& SID, i
 	longitudinalPos = theXRAYReaders[streamNumber]->GetTableTopLongitudinalPosition(&ok[5]);
 	verticalPos = theXRAYReaders[streamNumber]->GetTableTopVerticalPosition(&ok[6]);
 	mmPerPixel = theXRAYReaders[streamNumber]->GetMillimeterPerPixelScaling(&ok[7]);
+	imageSizeX = theXRAYReaders[streamNumber]->GetImageSizeX(&ok[8]);
+	imageSizeY = theXRAYReaders[streamNumber]->GetImageSizeY(&ok[9]);
 }
 
 
 void OverlayScene::getDicomGeometryValues(int& SID, int& sourcePatDist, double& primAngle, double& secAngle,
-	int& lateralPos, int& longitudinalPos, int& verticalPos, double& mmPerPixel, bool ok[8])
+	int& lateralPos, int& longitudinalPos, int& verticalPos, double& mmPerPixel, int& imageSizeX, int&imageSizeY, bool ok[10])
 {
 	SID = readerMainXRAY->GetSID(&ok[0]);	
 	sourcePatDist = readerMainXRAY->GetSourcePatientDistance(&ok[1]);
@@ -3444,7 +3446,8 @@ void OverlayScene::getDicomGeometryValues(int& SID, int& sourcePatDist, double&
 	longitudinalPos = readerMainXRAY->GetTableTopLongitudinalPosition(&ok[5]);
 	verticalPos = readerMainXRAY->GetTableTopVerticalPosition(&ok[6]);
 	mmPerPixel = readerMainXRAY->GetMillimeterPerPixelScaling(&ok[7]);
-
+	imageSizeX = readerMainXRAY->GetImageSizeX(&ok[8]);
+	imageSizeY = readerMainXRAY->GetImageSizeY(&ok[9]);
 }
 
 

src/pipeline/OverlayScene.h

@@ -102,8 +102,8 @@ class OverlayScene {
 	void reloadPipelineFramegrabber();
 
 	void setBiplaneGeometry(unsigned int streamNumber, int SID, int sourcePatDist, double primAngle, double secAngle, 
-		int lateralPos, int longitudinalPos, int verticalPos, double mmPerPxl);
-	void setMainGeometryByDICOM(int SID, int sourcePatDist, double primAngle, double secAngle, int lateralPos, int longitudinalPos, int verticalPos, double mmPerPixel);
+		int lateralPos, int longitudinalPos, int verticalPos, double mmPerPxl, int imageSizeX, int imageSizeY);
+	void setMainGeometryByDICOM(int SID, int sourcePatDist, double primAngle, double secAngle, int lateralPos, int longitudinalPos, int verticalPos, double mmPerPixel, int imageSizeX, int imageSizeY);
 	void setFramegrabberGeometry(int index, int SID, double primAngle, double secAngle, int lateralPos, int longitudinalPos, int verticalPos, double FDoderMMPerPxl, bool play);
 	void setFramegrabberGeometryLive(int index);
 	void setFramegrabberGeometryBiplaneLive(int index);
@@ -207,9 +207,9 @@ class OverlayScene {
 	void setDICOMAnglesToWindowRef(int index, double primAngle, double secAngle);
 	void getDICOMAnglesToWindowRef(int index, double& primAngle, double& secAngle);
 	void getDicomReferenceGeometryValues(int streamNumber, int& SID, int& sourcePatDist, double& primAngle, double& secAngle, 
-		int& lateralPos, int& longitudinalPos, int& verticalPos, double& mmPerPixel, bool ok[8]);
+		int& lateralPos, int& longitudinalPos, int& verticalPos, double& mmPerPixel, int& imageSizeX, int& imageSizeY, bool ok[10]);
 	void getDicomGeometryValues(int& SID, int& sourcePatDist, double& primAngle, double& secAngle,
-		int& lateralPos, int& longitudinalPos, int& verticalPos, double& mmPerPixel, bool ok[8]);
+		int& lateralPos, int& longitudinalPos, int& verticalPos, double& mmPerPixel, int& imageSizeX, int& imageSizeY, bool ok[10]);
 	/// set/get input file (CT or MR) in order to calculate correct mesh position in OverlayScene->AddOverlayMesh(), because for CT file with wrong spacing the mesh position has to be recalculated
 	void setMRInputFileForMesh(int meshOrientation);
 	int getMRInputFileForMesh();

src/pipeline/XRAYReader.cxx

@@ -798,3 +798,77 @@ double XRAYReader::GetTableTopLateralPosition(bool* valid)
 	*valid = true;
 	return lateralPos;
 }
+
+
+int XRAYReader::GetImageSizeX(bool* valid)
+{
+	gdcm::Reader* dicomReader = new gdcm::Reader;
+	dicomReader->SetFileName(theFilename.c_str());
+
+	int imageSizeX = 0;
+
+	if (!dicomReader->CanRead())
+	{
+		std::cout << "DICOM header is not readable! " <<
+			"Can not retrieve image size (columns) from file!" << std::endl;
+		*valid = false; return -1;
+	}
+
+	bool success = dicomReader->Read();
+	if (!success)
+	{
+		std::cerr << "cannot read DICOM!" << std::endl;
+		*valid = false; return -1;
+	}
+
+	gdcm::File dicomFile = dicomReader->GetFile();
+	gdcm::StringFilter* dicomStringFilter = new gdcm::StringFilter;
+	dicomStringFilter->SetFile(dicomFile);
+
+	gdcm::Tag tag = gdcm::Tag(0x0028, 0x0011);
+	std::string strImageSizeX = dicomStringFilter->ToString(tag);
+	imageSizeX = atoi(strImageSizeX.c_str());
+
+	//delete(dicomStringFilter);	//TODO
+	delete(dicomReader);
+
+	*valid = true;
+	return imageSizeX;
+}
+
+
+int XRAYReader::GetImageSizeY(bool* valid)
+{
+	gdcm::Reader* dicomReader = new gdcm::Reader;
+	dicomReader->SetFileName(theFilename.c_str());
+
+	int imageSizeY = 0;
+
+	if (!dicomReader->CanRead())
+	{
+		std::cout << "DICOM header is not readable! " <<
+			"Can not retrieve image size (rows) from file!" << std::endl;
+		*valid = false; return -1;
+	}
+
+	bool success = dicomReader->Read();
+	if (!success)
+	{
+		std::cerr << "cannot read DICOM!" << std::endl;
+		*valid = false; return -1;
+	}
+
+	gdcm::File dicomFile = dicomReader->GetFile();
+	gdcm::StringFilter* dicomStringFilter = new gdcm::StringFilter;
+	dicomStringFilter->SetFile(dicomFile);
+
+	gdcm::Tag tag = gdcm::Tag(0x0028, 0x0010);
+	std::string strImageSizeY = dicomStringFilter->ToString(tag);
+	imageSizeY = atoi(strImageSizeY.c_str());
+
+	//delete(dicomStringFilter);	//TODO
+	delete(dicomReader);
+
+	*valid = true;
+	return imageSizeY;
+}

src/pipeline/XRAYReader.h

@@ -45,6 +45,8 @@ class XRAYReader : public vtkImageReader2
 	double GetTableTopVerticalPosition(bool* valid);
 	double GetTableTopLongitudinalPosition(bool* valid);
 	double GetTableTopLateralPosition(bool* valid);
+	int GetImageSizeX(bool* valid);
+	int GetImageSizeY(bool* valid);
 
 	void ReadGeometryFramegrabber(double& primAngleRead, double& secAngleRead, int& longRead, int& latRead, int& HoeheRead, int& SIDRead, double& mmPerPxlRead, int& FDRead, int& SODRead);
 	void ReadGeometryFramegrabberAngle(double& primAngleRead, double& secAngleRead);