Merge pull request #5 from smistad/upgrade-fast

FX-19: Upgraded fast to latest version and implemented manual seed point

install/cx/build/cxComponents.py

@@ -526,14 +526,12 @@ def help(self):
 #    def path(self):
 #        return self.controlData.getWorkingPath() + "/FAST"
     def sourcePath(self):
-        return self.controlData.getWorkingPath() + "/FAST/FAST/source"
+        return self.controlData.getWorkingPath() + "/FAST/FAST/"
     def repository(self):
-		#return 'git@github.com:smistad/FAST'
-		return 'git@github.com:jbake/FAST'
+		return 'git@github.com:smistad/FAST'
     def update(self):
         self._getBuilder().gitSetRemoteURL(self.repository())
-        self._getBuilder().gitCheckout('75627f9c63891584d9a8028568294f4c831a87df')
-#        self._getBuilder().gitCheckoutBranch('set_kernel_root_dir')
+        self._getBuilder().gitCheckout('c2522765d3bb369142ad53dd20dfb6d54c8e95ac')
 #        branch = 'set_kernel_root_dir'
 #        self._getBuilder()._changeDirToSource()
 #        runShell('git checkout %s' % branch, ignoreFailure=False)
@@ -544,9 +542,14 @@ def configure(self):
         add = builder.addCMakeOption
         append = builder.appendCMakeOption
         add('FAST_MODULE_OpenIGTLink:BOOL', False)
+        add('FAST_MODULE_Visualization:BOOL', False)
+        add('FAST_MODULE_Python:BOOL', False)
+        add('FAST_MODULE_NeuralNetwork:BOOL', False)
+        add('FAST_MODULE_VTK:BOOL', True)
+        add('FAST_DOWNLOAD_TEST_DATA:BOOL', False)
         add('FAST_BUILD_EXAMPLES:BOOL', False)
+        add('FAST_BUILD_TOOLS:BOOL', False)
         add('FAST_BUILD_TESTS:BOOL', False)
-        add('FAST_VTK_INTEROP:BOOL', True)
         add('VTK_DIR:PATH', self._createSibling(VTK).configPath())
         add('EIGEN3_INCLUDE_DIR:PATH', '%s' % self._createSibling(Eigen).sourcePath())
         if(platform.system() == 'Windows'):

source/plugins/org.custusx.filter.airways/CMakeLists.txt

@@ -1,21 +1,19 @@
 project(org_custusx_filter_airways)
 
-add_definitions(-DBOOST_SYSTEM_NO_DEPRECATED)
-
 include(cxInstallUtilities)
 
 macro(cx_initialize_FAST)
-    find_package( FAST REQUIRED)
-    include(${FAST_USE_FILE})
+    find_package(FAST REQUIRED)
+    include_directories("${FAST_DIR}/../FAST/source/")
+    link_directories("${FAST_DIR}/lib/")
+    add_definitions("-DFAST_SOURCE_DIR=\"${FAST_DIR}/../FAST/source/FAST/\"")
     message("===========================")
     message("Initializing FAST in Airways plugin")
-    message("-- ${FAST_LIBRARY_DIRS}")
+    message("-- ${FAST_DIR}/../FAST/source/")
     message("===========================")
-    cx_install_add_library_dirs(${FAST_LIBRARY_DIRS})
+    cx_install_add_library_dirs(${FAST_DIR}/lib/)
 endmacro()
 
-find_package(GLEW REQUIRED)
-find_package(OpenCL REQUIRED)
 cx_initialize_FAST()
 
 #### Enable C++11
@@ -75,11 +73,9 @@ set(PLUGIN_target_libraries
     ${PLUGIN_target_libraries}
 
     PRIVATE
-    OpenCLUtilityLibrary
     FAST
     Qt5::OpenGL
     ${OPENCL_LIBRARIES}
-    ${GLEW_LIBRARY}
     cxResource
     cxResourceFilter
     cxResourceVisualization

source/plugins/org.custusx.filter.airways/cxAirwaysFilterService.cpp

@@ -57,7 +57,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include "FAST/Algorithms/CenterlineExtraction/CenterlineExtraction.hpp"
 #include "FAST/Importers/ImageFileImporter.hpp"
 #include "FAST/Exporters/VTKImageExporter.hpp"
-#include "FAST/Exporters/VTKLineSetExporter.hpp"
+#include "FAST/Exporters/VTKMeshExporter.hpp"
 #include "FAST/Data/Segmentation.hpp"
 #include "FAST/SceneGraph.hpp"
 
@@ -93,13 +93,85 @@ QString AirwaysFilter::getHelp() const
 	        "</html>";
 }
 
+
+Vector3D AirwaysFilter::getSeedPointFromTool(SpaceProviderPtr spaceProvider, DataPtr data)
+{
+	// Retrieve position of tooltip and use it as seed point
+	Vector3D point = spaceProvider->getActiveToolTipPoint(
+			spaceProvider->getD(data));
+
+	// Have to multiply by the inverse of the spacing to get the voxel position
+	ImagePtr image = boost::dynamic_pointer_cast<Image>(data);
+	double spacingX, spacingY, spacingZ;
+	image->getBaseVtkImageData()->GetSpacing(spacingX, spacingY, spacingZ);
+	point(0) = point(0) * (1.0 / spacingX);
+	point(1) = point(1) * (1.0 / spacingY);
+	point(2) = point(2) * (1.0 / spacingZ);
+
+	std::cout << "the selected seed point is: " << point(0) << " " << point(1)
+			<< " " << point(2) << "\n";
+
+	return point;
+}
+
+int * getImageSize(DataPtr inputImage)
+{
+	ImagePtr image = boost::dynamic_pointer_cast<Image>(inputImage);
+	return image->getBaseVtkImageData()->GetDimensions();
+}
+
+bool AirwaysFilter::isSeedPointInsideImage(Vector3D seedPoint, DataPtr image)
+{
+	int * size = getImageSize(image);
+	std::cout << "size of image is: " << size[0] << " " << size[1] << " "
+			<< size[2] << "\n";
+	int x = (int) seedPoint(0);
+	int y = (int) seedPoint(1);
+	int z = (int) seedPoint(2);
+	bool result = x >= 0 && y >= 0 && z >= 0 && x < size[0] && y < size[1]
+			&& z < size[2];
+	return result;
+}
+
+bool AirwaysFilter::preProcess()
+{
+    DataPtr inputImage = mInputTypes[0].get()->getData();
+	if (!inputImage)
+	{
+		CX_LOG_ERROR() << "No input data selected";
+		return false;
+	}
+
+	if (inputImage->getType() != "image")
+	{
+		CX_LOG_ERROR() << "Input data has to be an image";
+		return false;
+	}
+
+	std::string filename = (patientService()->getActivePatientFolder()
+			+ "/" + inputImage->getFilename()).toStdString();
+
+    // only check seed point inside image if use seed point is checked
+	bool useManualSeedPoint = getManualSeedPointOption(mOptions)->getValue();
+	if(useManualSeedPoint)
+	{
+		seedPoint = getSeedPointFromTool(mServices->spaceProvider(), inputImage);
+		if(!isSeedPointInsideImage(seedPoint, inputImage)) {
+			CX_LOG_ERROR() << "Seed point is not inside image. Use cursor to set seed point inside trachea in the CT image.";
+			return false;
+		}
+	}
+	mInputImage = patientService()->getData<Image>(inputImage->getUid());
+
+	return true;
+}
+
 bool AirwaysFilter::execute()
 {
     CX_LOG_INFO() << "EXECUTING AIRWAYS FILTER";
-    ImagePtr input = this->getCopiedInputImage();
-	if (!input)
+	// Check if pre process went ok:
+    if(!mInputImage)
 		return false;
-	mInputImage = input;
 
     QString q_filename = "";
     QString activePatienFolder = patientService()->getActivePatientFolder();
@@ -111,10 +183,10 @@ bool AirwaysFilter::execute()
 
     std::string filename = q_filename.toStdString();
 	try {
-        QString kernelDir = cx::DataLocations::findConfigFolder("/FAST", FAST_SOURCE_DIR);
-        fast::DeviceManager::getInstance().setKernelRootPath(kernelDir.toStdString());
+		fast::Config::getTestDataPath(); // needed for initialization
         QString cacheDir = cx::DataLocations::getCachePath();
-        fast::DeviceManager::getInstance().setWritableCachePath(cacheDir.toStdString());
+        fast::Config::setKernelBinaryPath(cacheDir.toStdString());
+		fast::Config::setKernelSourcePath(std::string(FAST_SOURCE_DIR));
 
         // Import image data from disk
 		fast::ImageFileImporter::pointer importer = fast::ImageFileImporter::New();
@@ -126,7 +198,22 @@ bool AirwaysFilter::execute()
 
         // Do segmentation
         fast::AirwaySegmentation::pointer segmentation = fast::AirwaySegmentation::New();
+		bool useManualSeedPoint = getManualSeedPointOption(mOptions)->getValue();
+        if(useManualSeedPoint)
+		{
+			CX_LOG_INFO() << "Using seed point: " << seedPoint.transpose();
+			segmentation->setSeedPoint(seedPoint(0), seedPoint(1), seedPoint(2));
+		}
 	    segmentation->setInputConnection(importer->getOutputPort());
+        try {
+			segmentation->update();
+		} catch(fast::Exception &e) {
+
+			CX_LOG_ERROR() << "The airways filter failed.";
+			if(!useManualSeedPoint)
+                CX_LOG_ERROR() << "Try to set the seed point manually.";
+			return false;
+		}
 
 	    // Convert fast segmentation data to VTK data which CX can use
         vtkSmartPointer<fast::VTKImageExporter> vtkExporter = fast::VTKImageExporter::New();
@@ -147,7 +234,7 @@ bool AirwaysFilter::execute()
         centerline->setInputConnection(segmentation->getOutputPort());
 
         // Get centerline
-	    vtkSmartPointer<fast::VTKLineSetExporter> vtkCenterlineExporter = fast::VTKLineSetExporter::New();
+	    vtkSmartPointer<fast::VTKMeshExporter> vtkCenterlineExporter = fast::VTKMeshExporter::New();
 	    vtkCenterlineExporter->setInputConnection(centerline->getOutputPort());
 	    mCenterlineOutput = vtkCenterlineExporter->GetOutput();
 	    vtkCenterlineExporter->Update();
@@ -205,7 +292,6 @@ bool AirwaysFilter::postProcess()
 	// Set output
 	mOutputTypes[1]->setValue(contour->getUid());
 
-	// TODO get centerline somehow
 	QString uid = mInputImage->getUid() + "_centerline%1";
 	QString name = mInputImage->getName() + " centerline%1";
 	MeshPtr centerline = patientService()->createSpecificData<Mesh>(uid, name);
@@ -220,6 +306,7 @@ bool AirwaysFilter::postProcess()
 
 void AirwaysFilter::createOptions()
 {
+	mOptionsAdapters.push_back(this->getManualSeedPointOption(mOptions));
 }
 
 void AirwaysFilter::createInputTypes()
@@ -251,5 +338,19 @@ void AirwaysFilter::createOutputTypes()
 }
 
 
+BoolPropertyPtr AirwaysFilter::getManualSeedPointOption(QDomElement root)
+{
+	BoolPropertyPtr retval =
+			BoolProperty::initialize("Use manual seed point",
+					"",
+					"If the automatic seed point detection algorithm fails you can use cursor to set the seed point "
+                    "inside trachea of the patient. "
+                    "Then tick this checkbox to use the manual seed point in the airways filter.",
+					false, root);
+	return retval;
+
+}
+
+
 } /* namespace cx */
 

source/plugins/org.custusx.filter.airways/cxAirwaysFilterService.h

@@ -54,12 +54,9 @@ typedef vtkSmartPointer<class vtkPolyData> vtkPolyDataPtr;
 namespace cx {
 
 /**
- * Filter for segmenting and extract the centerline of a volume.
+ * Filter for airway segmentation and centerline extraction of a CT volume.
  *
- * This filter can run either on the gpu or cpu.
- *
- * Algorithm written by Erik Smistad. For more information, see paper:
- * "GPU-Based Airway Segmentation and Centerline Extraction for Image Guided Bronchoscopy."
+ * Algorithm written by Erik Smistad.
  *
  */
 class org_custusx_filter_airways_EXPORT AirwaysFilter : public FilterImpl
@@ -75,6 +72,7 @@ Q_INTERFACES(cx::Filter)
 	virtual QString getName() const;
 	virtual QString getHelp() const;
 
+    bool preProcess();
 	virtual bool execute();
 	virtual bool postProcess();
 
@@ -84,11 +82,14 @@ Q_INTERFACES(cx::Filter)
 	virtual void createOutputTypes();
 
 private:
-	//DoublePropertyPtr getNoiseLevelOption(QDomElement root);
+    static Vector3D getSeedPointFromTool(SpaceProviderPtr spaceProvider, DataPtr image);
+    static bool isSeedPointInsideImage(Vector3D, DataPtr);
+	BoolPropertyPtr getManualSeedPointOption(QDomElement root);
 	vtkImageDataPtr mSegmentationOutput;
 	vtkPolyDataPtr mCenterlineOutput;
 	Transform3D mTransformation;
 	ImagePtr mInputImage;
+    Vector3D seedPoint;
 
 };
 typedef boost::shared_ptr<class AirwaysFilter> AirwaysFilterPtr;