├── .classpath ├── .gitignore ├── .project ├── .settings └── org.eclipse.core.resources.prefs ├── README.md ├── conrad_paper.pdf ├── copying.txt ├── data ├── KEVS_models │ ├── 100kev.lin.classifier.model │ ├── 120kev.lin.classifier.model │ ├── 140kev.lin.classifier.model │ ├── 40kev.lin.classifier.model │ ├── 60kev.lin.classifier.model │ ├── 80kev.lin.classifier.model │ ├── iodine.lin.classifier.model │ └── iodine.reptree.classifier.model ├── MSL_Liver │ └── BestFeatures.ser ├── configfiles │ ├── forbild │ │ ├── HeadPhantom.pha │ │ ├── HipPhantom.pha │ │ ├── JawPhantom.pha │ │ ├── Ribs.pha │ │ ├── Shoulders.pha │ │ ├── ThoraxPhantom.pha │ │ └── Vertebra.pha │ ├── maps │ │ ├── compositionToAbsorptionEdge.xml │ │ ├── formulaToNameMap.xml │ │ └── nameToFormulaMap.xml │ ├── massAttenuationData │ │ ├── actinium.xml │ │ ├── aluminium.xml │ │ ├── antimony.xml │ │ ├── argon.xml │ │ ├── arsenic.xml │ │ ├── astatine.xml │ │ ├── barium.xml │ │ ├── beryllium.xml │ │ ├── bismuth.xml │ │ ├── boron.xml │ │ ├── bromine.xml │ │ ├── cadmium.xml │ │ ├── calcium.xml │ │ ├── carbon.xml │ │ ├── cerium.xml │ │ ├── cesium.xml │ │ ├── chlorine.xml │ │ ├── chromium.xml │ │ ├── cobalt.xml │ │ ├── copper.xml │ │ ├── dysprosium.xml │ │ ├── erbium.xml │ │ ├── europium.xml │ │ ├── fluorine.xml │ │ ├── francium.xml │ │ ├── gadolinium.xml │ │ ├── gallium.xml │ │ ├── germanium.xml │ │ ├── gold.xml │ │ ├── hafnium.xml │ │ ├── helium.xml │ │ ├── holmium.xml │ │ ├── hydrogen.xml │ │ ├── indium.xml │ │ ├── iodine.xml │ │ ├── iridium.xml │ │ ├── iron.xml │ │ ├── krypton.xml │ │ ├── lanthanum.xml │ │ ├── lead.xml │ │ ├── lithium.xml │ │ ├── lutetium.xml │ │ ├── magnesium.xml │ │ ├── manganese.xml │ │ ├── mercury.xml │ │ ├── molybdenum.xml │ │ ├── neodymium.xml │ │ ├── neon.xml │ │ ├── nickel.xml │ │ ├── niobium.xml │ │ ├── nitrogen.xml │ │ ├── osmium.xml │ │ ├── oxygen.xml │ │ ├── palladium.xml │ │ ├── phosphorus.xml │ │ ├── platinum.xml │ │ ├── polonium.xml │ │ ├── potassium.xml │ │ ├── praseodymium.xml │ │ ├── promethium.xml │ │ ├── protactinium.xml │ │ ├── radium.xml │ │ ├── radon.xml │ │ ├── rhenium.xml │ │ ├── rhodium.xml │ │ ├── rubidium.xml │ │ ├── ruthenium.xml │ │ ├── samarium.xml │ │ ├── scandium.xml │ │ ├── selenium.xml │ │ ├── silicon.xml │ │ ├── silver.xml │ │ ├── sodium.xml │ │ ├── strontium.xml │ │ ├── sulfur.xml │ │ ├── tantalum.xml │ │ ├── technetium.xml │ │ ├── tellurium.xml │ │ ├── terbium.xml │ │ ├── thallium.xml │ │ ├── thorium.xml │ │ ├── thulium.xml │ │ ├── tin.xml │ │ ├── titanium.xml │ │ ├── tungsten.xml │ │ ├── uranium.xml │ │ ├── vacuum.xml │ │ ├── vanadium.xml │ │ ├── xenon.xml │ │ ├── ytterbium.xml │ │ ├── yttrium.xml │ │ ├── zinc.xml │ │ └── zirconium.xml │ └── materials │ │ ├── AbsorptionEdgeEnergies.txt │ │ ├── compounds.txt │ │ ├── elements.txt │ │ └── mixtures.txt ├── matCon │ ├── CONRAD.m │ ├── Conrad.xml │ ├── Documentation │ │ ├── Matlab_Conrad_setup.txt │ │ └── startup.m │ ├── MatlabCONRADtutorial.m │ ├── OpenCLBackProjection.m │ ├── OpenCLForwardProjection.m │ ├── conradCleanUp.m │ ├── fourierTestConrad.m │ ├── grid3D2mat.m │ ├── loadImageJVolume.m │ ├── mat2Grid3D.m │ └── reconstructionHelper.m ├── materials │ ├── actinium.xml │ ├── adipose.xml │ ├── air.xml │ ├── aluminium.xml │ ├── antimony.xml │ ├── aorta.xml │ ├── argon.xml │ ├── arsenic.xml │ ├── astatine.xml │ ├── barium.xml │ ├── beryllium.xml │ ├── bgo.xml │ ├── bismuth.xml │ ├── blood.xml │ ├── body.xml │ ├── bone.xml │ ├── bonedense.xml │ ├── bonelight.xml │ ├── bonemarrow.xml │ ├── boron.xml │ ├── brain.xml │ ├── braindown.xml │ ├── brainup.xml │ ├── breast.xml │ ├── breastEDP.xml │ ├── bromine.xml │ ├── cadmium.xml │ ├── calcium.xml │ ├── carbon.xml │ ├── cartilage.xml │ ├── cerium.xml │ ├── cesium.xml │ ├── chlorine.xml │ ├── chromium.xml │ ├── claviculum.xml │ ├── cobalt.xml │ ├── copper.xml │ ├── coronaryartery.xml │ ├── cranium.xml │ ├── czt.xml │ ├── dysprosium.xml │ ├── erbium.xml │ ├── europium.xml │ ├── fat.xml │ ├── femur.xml │ ├── fluorine.xml │ ├── francium.xml │ ├── gadolinium.xml │ ├── gallium.xml │ ├── germanium.xml │ ├── glass.xml │ ├── gold.xml │ ├── gso.xml │ ├── hafnium.xml │ ├── heart.xml │ ├── heartlesion.xml │ ├── helium.xml │ ├── hematoma.xml │ ├── holmium.xml │ ├── humerus.xml │ ├── hydrogen.xml │ ├── indium.xml │ ├── intestine.xml │ ├── iodine.xml │ ├── iridium.xml │ ├── iron.xml │ ├── kidney.xml │ ├── kortikalis.xml │ ├── krypton.xml │ ├── lanthanum.xml │ ├── lead.xml │ ├── lithium.xml │ ├── liver.xml │ ├── liverEDP.xml │ ├── lso.xml │ ├── luap.xml │ ├── lung.xml │ ├── lungEDP.xml │ ├── lungmoby.xml │ ├── lutetium.xml │ ├── luyap-70.xml │ ├── luyap-80.xml │ ├── lymph.xml │ ├── lyso.xml │ ├── magnesium.xml │ ├── mandibula.xml │ ├── manganese.xml │ ├── mercury.xml │ ├── molybdenum.xml │ ├── muscle.xml │ ├── muscleEDP.xml │ ├── nai.xml │ ├── neodymium.xml │ ├── neon.xml │ ├── nickel.xml │ ├── niobium.xml │ ├── nitrogen.xml │ ├── omnipaque350.xml │ ├── osmium.xml │ ├── oxygen.xml │ ├── palladium.xml │ ├── pancreas.xml │ ├── phosphorus.xml │ ├── plastic.xml │ ├── platinum.xml │ ├── plexiglass.xml │ ├── pmma.xml │ ├── polonium.xml │ ├── polyethylene.xml │ ├── potassium.xml │ ├── praseodymium.xml │ ├── promethium.xml │ ├── protactinium.xml │ ├── ptfe.xml │ ├── pvc.xml │ ├── pwo.xml │ ├── quartz.xml │ ├── radium.xml │ ├── radon.xml │ ├── rhenium.xml │ ├── rhodium.xml │ ├── ribbone.xml │ ├── rips_10th.xml │ ├── rips_2nd.xml │ ├── rubidium.xml │ ├── ruthenium.xml │ ├── samarium.xml │ ├── scandium.xml │ ├── scinti-c9h10.xml │ ├── selenium.xml │ ├── silicon.xml │ ├── silver.xml │ ├── skapulum.xml │ ├── skull.xml │ ├── sodium.xml │ ├── spinebone.xml │ ├── spleen.xml │ ├── spongiosa.xml │ ├── ss304.xml │ ├── sternum.xml │ ├── strontium.xml │ ├── sulfur.xml │ ├── tantalum.xml │ ├── technetium.xml │ ├── teeth.xml │ ├── tellurium.xml │ ├── terbium.xml │ ├── testis.xml │ ├── thallium.xml │ ├── thorium.xml │ ├── thulium.xml │ ├── tin.xml │ ├── titanium.xml │ ├── titaniumEDP.xml │ ├── tungsten.xml │ ├── ultravist150.xml │ ├── ultravist240.xml │ ├── ultravist300.xml │ ├── ultravist370.xml │ ├── uranium.xml │ ├── urine.xml │ ├── vacuum.xml │ ├── vanadium.xml │ ├── water.xml │ ├── waterEDP.xml │ ├── xenon.xml │ ├── yap.xml │ ├── ytterbium.xml │ ├── yttrium.xml │ ├── zinc.xml │ └── zirconium.xml └── mipda │ ├── output │ ├── .gitignore │ └── info │ └── vessel.jpg ├── lib ├── BoneJ_.jar ├── ImageJ_SURF_2009-12-01_08.19.jar ├── Jama-1.0.2.jar ├── fastica-1.11-src.zip ├── fastica-1.11.jar ├── gluegen-java-src.zip ├── gluegen-rt-natives-linux-amd64.jar ├── gluegen-rt-natives-linux-i586.jar ├── gluegen-rt-natives-macosx-universal.jar ├── gluegen-rt-natives-solaris-amd64.jar ├── gluegen-rt-natives-solaris-i586.jar ├── gluegen-rt-natives-windows-amd64.jar ├── gluegen-rt-natives-windows-i586.jar ├── gluegen-rt.jar ├── hough-0.1.jar ├── ij.jar ├── ij149v-src.zip ├── jcublas-0.3.0a.jar ├── jcuda-0.3.0a.jar ├── jcudpp-0.3.0a.jar ├── jcufft-0.3.0a.jar ├── jmathplot-license.pdf ├── jmathplot.jar ├── joal-java-src.zip ├── joal-natives-linux-amd64.jar ├── joal-natives-linux-i586.jar ├── joal-natives-macosx-universal.jar ├── joal-natives-solaris-amd64.jar ├── joal-natives-solaris-i586.jar ├── joal-natives-windows-amd64.jar ├── joal-natives-windows-i586.jar ├── joal.jar ├── jocl-java-src.zip ├── jocl-natives-linux-amd64.jar ├── jocl-natives-linux-i586.jar ├── jocl-natives-macosx-universal.jar ├── jocl-natives-solaris-amd64.jar ├── jocl-natives-solaris-i586.jar ├── jocl-natives-windows-amd64.jar ├── jocl-natives-windows-i586.jar ├── jocl.jar ├── jogl-all-natives-linux-amd64.jar ├── jogl-all-natives-linux-i586.jar ├── jogl-all-natives-macosx-universal.jar ├── jogl-all-natives-solaris-amd64.jar ├── jogl-all-natives-solaris-i586.jar ├── jogl-all-natives-windows-amd64.jar ├── jogl-all-natives-windows-i586.jar ├── jogl-all.jar ├── jogl-java-src.zip ├── jpop.0.7.5.jar ├── jtransforms-2.3.jar ├── junit-4.8.2.jar ├── jzlib-1.0.7.jar ├── latexlet.jar ├── qdox-1.12.1.jar ├── sis-jhdf5-batteries_included.jar ├── trainablesegmentation.jar ├── trainablesegmentation.zip ├── weka-src.jar ├── weka.jar ├── wekaBRF_1.jar └── yacas.1.2.2.jar ├── plugins ├── 3D │ ├── Interactive_3D_Surface_Plot.jar │ ├── Stack 3D Surface Plot.ijm │ └── Volume_Viewer.jar ├── Analyze │ ├── Batch_Measure.txt │ ├── Cell_Counter.jar │ ├── Color_Histogram.jar │ ├── Grid_.class │ ├── Measure_And_Label.txt │ ├── Measure_And_Set_Label.txt │ └── Measure_RGB.txt ├── CONRAD │ ├── Apply_Filter.class │ ├── Apply_ROI_Method.class │ ├── CLE_Utils.class │ ├── Create_Numerical_Phantom$1.class │ ├── Create_Numerical_Phantom.class │ ├── Dennerlein_Writer.class │ ├── Explore_DICOM_Header.class │ ├── Export_Geometry.class │ ├── Generate_Absorption_Plot.class │ ├── Generate_Spectrum.class │ ├── Measure_All_Slices.class │ ├── OpenCL_Back_Projector.class │ ├── OpenCL_Forward_Projector.class │ ├── OpenCL_Forward_Projector_With_Motion.class │ ├── OpenCL_Volume_Renderer.class │ └── Raw_Data_Opener.class ├── Examples │ ├── IPDemoRunner.class │ ├── IP_Demo.class │ ├── Image_Inverter.class │ ├── Plasma2_.class │ ├── Red_And_Blue.class │ └── Table_Tricks.txt ├── FeatureJ_.jar ├── Filters │ └── Kalman_Stack_Filter.class ├── Graphics │ ├── Dynamic_Profiler.class │ └── Example_Plot.class ├── Input-Output │ ├── Animated_Gif.jar │ ├── Biorad_Reader.class │ ├── DM3_Reader.class │ ├── Deltavision_Opener.jar │ ├── HandleExtraFileTypes.class │ ├── IPLab_Reader.class │ ├── LSM_Reader.jar │ ├── QuickTime_Plugins.jar │ ├── Viva_Reader.class │ ├── ZVI_Reader$ZVIBlock.class │ ├── ZVI_Reader.class │ ├── loci_tools.jar │ ├── nifti_io.jar │ └── ome_tools.jar ├── JavaScriptEvaluator.class ├── JavaScriptEvaluator.source ├── MacAdapter.class ├── MacAdapter.source ├── Macros │ ├── About Plugin Macros │ ├── About_Plugin_Macros.txt │ ├── Batch_Convert.txt │ ├── BullsEye.ijm │ ├── Polygon.ijm │ ├── Pong.ijm │ ├── RGB_Histogram.txt │ └── Show_All_LUTs.txt ├── Nrrd │ ├── BioradWithNrrd_Writer.class │ ├── NrrdFileInfo.class │ ├── NrrdHeaderFromFile_Writer.class │ ├── Nrrd_Reader.class │ └── Nrrd_Writer.class ├── README.txt ├── Scripts │ ├── About Scripts │ ├── About_Scripts.js │ ├── AlwaysOnTop.js │ └── AutoThresholdingDemo.js ├── Split_Volume.class ├── Stacks │ ├── Measure_Stack.txt │ ├── Stack_Inserter.class │ ├── Stack_Reducer.class │ └── Stack_Reverser.class ├── Tools │ ├── Close_All_Without_Saving.txt │ ├── ImageJ_Updater_.class │ └── JavaScript.jar ├── TurboReg │ ├── TurboReg_.class │ ├── turboRegCredits$1.class │ ├── turboRegCredits.class │ ├── turboRegDialog$1.class │ ├── turboRegDialog$10.class │ ├── turboRegDialog$11.class │ ├── turboRegDialog$12.class │ ├── turboRegDialog$13.class │ ├── turboRegDialog$14.class │ ├── turboRegDialog$15.class │ ├── turboRegDialog$16.class │ ├── turboRegDialog$2.class │ ├── turboRegDialog$3.class │ ├── turboRegDialog$4.class │ ├── turboRegDialog$5.class │ ├── turboRegDialog$6.class │ ├── turboRegDialog$7.class │ ├── turboRegDialog$8.class │ ├── turboRegDialog$9.class │ ├── turboRegDialog.class │ ├── turboRegFinalAction.class │ ├── turboRegImage.class │ ├── turboRegMask.class │ ├── turboRegPointAction.class │ ├── turboRegPointHandler.class │ ├── turboRegPointToolbar.class │ ├── turboRegProgressBar.class │ └── turboRegTransform.class ├── VolumeJ │ ├── Backprojector_.class │ ├── Depth_Coded_Stack_.class │ ├── Diffusion_.class │ ├── FlowJ_.class │ ├── MI_.class │ ├── PCA_.class │ ├── Register_ROI.class │ ├── Register_ROI_MI.class │ ├── Register_ROI_MI_Edges.class │ ├── SurfaceJ_.class │ ├── VolumeJ_.class │ ├── Volume_Reconstructor_.class │ └── bij.jar ├── imagescience.jar ├── jars │ └── Compiler.jar ├── mcib3d-core2.7.jar └── mcib3d_plugins2.7.jar └── src ├── .gitignore ├── Anisotropic_Filtering.java ├── Apply_Filter.java ├── Apply_ROI_Method.java ├── Check_Trajectory_Consistency.java ├── Convert_to_16_bit.java ├── Copy_Convolution.java ├── Count_Edge_Points.java ├── Create_Numerical_Phantom.java ├── Dennerlein_Reader.java ├── Dennerlein_Writer.java ├── FlexibleFileOpener.java ├── Generate_Absorption_Plot.java ├── Generate_Beam_Hardening_Lookup_Table.java ├── Generate_Photon_Mass_Attenuation_Plot.java ├── Generate_Spectrum.java ├── HDF5_Reader_Vibez.java ├── HDF5_Simple_Reader.java ├── HDF5_Simple_Writer.java ├── HDF5_Writer_Vibez.java ├── HandleExtraFileTypes.java ├── Load_Recent.java ├── MKT_Reader.java ├── Measure_All_Slices.java ├── Measure_MTF_Droege.java ├── Measure_MTF_Wire.java ├── Measure_Slanted_Edge.java ├── Normalize_Image.java ├── Normalize_Image_CutOff.java ├── Normalize_Image_MinMax.java ├── Nrrd_Reader.java ├── Nrrd_Writer.java ├── Nurbs_Reader.java ├── OpenCL_Back_Projector.java ├── OpenCL_Forward_Projector.java ├── OpenCL_Forward_Projector_With_Motion.java ├── OpenCL_Volume_Renderer.java ├── Raw_Data_Opener.java ├── Raw_Data_Opener_Standalone.java ├── Replace_Intensity_Value_Tool.java ├── SaveAs_Viva.java ├── Visualize_Ramp_Filter.java ├── Viva_Reader.java ├── ZIP_Reader.java ├── ZIP_Reader_Standalone.java ├── de └── unifreiburg │ └── informatik │ └── lmb │ ├── HDF5ImageJ.java │ ├── StackToHDF5GroupsMapping.java │ └── TableColumnAdjuster.java └── edu └── stanford └── rsl ├── apps ├── Conrad.java ├── activeshapemodel │ ├── BuildCONRADCardiacModel.java │ ├── CreateARFF.java │ ├── LeaveOneOutTest.java │ ├── PcaHotfixScript.java │ ├── Specificity.java │ ├── Specificity4D.java │ └── package-info.java ├── gui │ ├── Citeable.java │ ├── ConfigurationFrame.java │ ├── ConfigurePipelineFrame.java │ ├── FileTextFieldTransferHandler.java │ ├── GUICompatibleObjectVisualizationPanel.java │ ├── GUIConfigurable.java │ ├── PhantomMaker.java │ ├── RawDataOpener.java │ ├── ReconstructionPipelineFrame.java │ ├── RegistryEditor.java │ ├── TimeLinePlot.java │ ├── TrajectoryEditor.java │ ├── UpdateableGUI.java │ ├── XCatMetricPhantomCreator.java │ ├── blobdetection │ │ ├── AutomaticMarkerDetectionWorker.java │ │ ├── ConnectedComponent3D.java │ │ ├── MarkerDetection.java │ │ └── MarkerDetectionWorker.java │ ├── opengl │ │ ├── BSplineVolumeRenderer.java │ │ ├── MeshViewer.java │ │ ├── OpenGLViewer.java │ │ ├── PointCloudViewer.java │ │ ├── SurfaceTest.java │ │ └── TrajectoryViewer.java │ ├── package-info.java │ ├── pointselector │ │ ├── PointSelector.java │ │ └── PointSelectorWorker.java │ └── roi │ │ ├── CompareGrayValues.java │ │ ├── ComputeIndependentComponents.java │ │ ├── CopyROI.java │ │ ├── DefineHounsfieldScaling.java │ │ ├── EvaluateROI.java │ │ ├── LearnHounsfieldScaling.java │ │ ├── LinewiseFill.java │ │ ├── Measure2DBeadMTFAngularRange.java │ │ ├── Measure2DBeadMTFMultiDirection.java │ │ ├── Measure3DBeadMTF.java │ │ ├── MeasureEdgeMTF.java │ │ ├── MeasureInlayMTF.java │ │ ├── MeasureMTFDroege.java │ │ ├── MeasureNoise.java │ │ ├── MeasurePatternMTF.java │ │ ├── MeasureSlantMTF.java │ │ ├── ZeroFill.java │ │ └── package-info.java └── package-info.java ├── conrad ├── angio │ ├── graphs │ │ ├── connectedness │ │ │ ├── Dijkstra2D.java │ │ │ ├── Dijkstra3D.java │ │ │ ├── DijkstraPointList.java │ │ │ ├── MinSpanTreeReprojection.java │ │ │ ├── MinimumSpanningTree.java │ │ │ ├── SkeletonEdge.java │ │ │ ├── components │ │ │ │ ├── Edge.java │ │ │ │ ├── Graph.java │ │ │ │ ├── Node.java │ │ │ │ ├── VesselBranch.java │ │ │ │ ├── VesselBranchPoint.java │ │ │ │ └── VesselTree.java │ │ │ └── util │ │ │ │ └── HierarchyOnMST.java │ │ ├── cuts │ │ │ ├── GraphCut.java │ │ │ └── util │ │ │ │ ├── Edge.java │ │ │ │ └── Node.java │ │ ├── skeleton │ │ │ ├── Skeleton.java │ │ │ ├── SkeletonUtil.java │ │ │ └── util │ │ │ │ ├── BranchPoint.java │ │ │ │ ├── Edge.java │ │ │ │ ├── Graph.java │ │ │ │ ├── Point.java │ │ │ │ ├── SkeletonBranch.java │ │ │ │ ├── SkeletonCorrespondence.java │ │ │ │ ├── SkeletonInfo.java │ │ │ │ ├── SkeletonResult.java │ │ │ │ ├── Skeletonize.java │ │ │ │ └── Vertex.java │ │ └── tools │ │ │ └── EdgeListUtil.java │ ├── motion │ │ ├── Gating.java │ │ ├── OneImagePerCycleGating.java │ │ ├── cardiac │ │ │ ├── CardiacMotionComp.java │ │ │ ├── GraMoCa.java │ │ │ └── GraMoOptimFunc.java │ │ └── respiratory │ │ │ ├── MaxErrorBP.cl │ │ │ ├── MaxErrorBackProjCL.java │ │ │ └── graphicalMoCo │ │ │ ├── BSplineParametrization.java │ │ │ ├── StandardParametrization.java │ │ │ └── tools │ │ │ └── Container.java │ ├── points │ │ ├── DistanceTransform2D.java │ │ ├── DistanceTransform3D.java │ │ ├── DistanceTransformUtil.java │ │ ├── distanceTransform2DCL.cl │ │ └── distanceTransform3DCL.cl │ ├── preprocessing │ │ ├── PreprocessingPipeline.java │ │ ├── VolumetricSegmentationPipeline.java │ │ ├── background │ │ │ ├── Inpainting.java │ │ │ ├── SpectralInterpolation.java │ │ │ └── TiledInpainting.java │ │ ├── noise │ │ │ ├── AnisotropicDiffusion.java │ │ │ └── NoiseFiltering.java │ │ └── segmentation │ │ │ ├── gradient │ │ │ ├── Koller2D.java │ │ │ ├── Medialness2D.java │ │ │ ├── Medialness2DGPU.java │ │ │ └── medialness2DCL.cl │ │ │ ├── hessian │ │ │ ├── Frangi2D.java │ │ │ ├── Sato2D.java │ │ │ └── tools │ │ │ │ ├── ComputeCurvatures.java │ │ │ │ ├── GaussianGenerationCallback.java │ │ │ │ ├── HessianEvalueProcessor.java │ │ │ │ ├── TubenessProcessor.java │ │ │ │ └── VesselnessProcessor.java │ │ │ └── morphological │ │ │ ├── ExtractConnectedComponents.java │ │ │ ├── HysteresisThresholding.java │ │ │ ├── Morphology.java │ │ │ ├── Morphology3D.java │ │ │ └── tools │ │ │ ├── StructuringElement.java │ │ │ └── StructuringElement3D.java │ ├── reconstruction │ │ ├── autofocus │ │ │ ├── HistoAutofocus.java │ │ │ ├── PointsAboveThresholdAutofocus.java │ │ │ └── PointsBelowThresholdAutofocus.java │ │ ├── proximal │ │ │ ├── CondatOptimization.java │ │ │ ├── LinearOperator.java │ │ │ ├── ProximableFunction.java │ │ │ ├── RunCondat.java │ │ │ ├── SmoothFunction.java │ │ │ ├── linearOperators │ │ │ │ ├── SpatialGradient.java │ │ │ │ └── TemporalGradient.java │ │ │ ├── proximableFunctions │ │ │ │ ├── CharacteristicFunctionRplus.java │ │ │ │ └── OneTwoNorm.java │ │ │ ├── smoothFunctions │ │ │ │ └── SquaredResidual.java │ │ │ └── util │ │ │ │ ├── BackProjCL.java │ │ │ │ ├── CondatTools.java │ │ │ │ ├── ConeBeamBackProjector.cl │ │ │ │ ├── ForwProjCL.java │ │ │ │ ├── MultiChannelGridOperators.java │ │ │ │ └── projectCL.cl │ │ └── symbolic │ │ │ ├── ExhaustiveGraphCutBasedReconstruction.java │ │ │ ├── GraphCutCostMapRecon.java │ │ │ └── blondel │ │ │ ├── BlondelReconstructionPipeline.java │ │ │ ├── EpipolarReconGeometry.java │ │ │ └── util │ │ │ ├── BlondelDynamicProgrammingDijkstra.java │ │ │ ├── DynamicCorrespondence.java │ │ │ ├── Edge.java │ │ │ ├── Fuse.java │ │ │ ├── Graph.java │ │ │ └── Node.java │ └── util │ │ ├── apodization │ │ ├── ApodizationWindow.java │ │ ├── BlackmanHarrisWindow.java │ │ ├── BlackmanWindow.java │ │ ├── HammingWindow.java │ │ ├── HannWindow.java │ │ └── WelchWindow.java │ │ ├── data │ │ ├── collection │ │ │ ├── DataSet.java │ │ │ ├── DataSets.java │ │ │ ├── PostproSettings.java │ │ │ ├── PreproSettings.java │ │ │ └── ReconSettings.java │ │ └── organization │ │ │ ├── Angiogram.java │ │ │ ├── AngiographicView.java │ │ │ ├── ComparablePoint2D.java │ │ │ └── KDTree2D.java │ │ ├── image │ │ ├── HistogramPercentile.java │ │ └── ImageOps.java │ │ └── io │ │ ├── EcgIO.java │ │ ├── EdgeListIO.java │ │ ├── EllipsoidIO.java │ │ ├── PlyIO.java │ │ ├── PointAndRadiusIO.java │ │ └── ProjMatIO.java ├── calibration │ ├── 1240x960_0.3x0.3_120x3.xml │ ├── 1240x960_0.3x0.3_300x0.3.xml │ ├── 620x480_0.6x0.6_120x3.xml │ ├── CalibrationBead.java │ ├── Factorization.java │ ├── GeometricCalibration.java │ ├── GeometricCalibrationGUI.java │ ├── PrincipalComponentAnalysis2D.java │ ├── crossratios │ │ ├── BeadDetection.java │ │ ├── CreateCalibration.java │ │ └── CreateProjectionData.java │ └── package-info.java ├── cuda │ ├── AdjustablePointer.java │ ├── CUDABackProjector.java │ ├── CUDACompensatedBackProjector.java │ ├── CUDAFFTVolumeHandle.java │ ├── CUDAForwardProjector.java │ ├── CUDAForwardProjectorWithMotion.java │ ├── CUDAUtil.java │ ├── CUDAVolume3D.java │ ├── CUDAVolumeOperator.java │ ├── CUDAVolumeTest.java │ ├── ImagePlusVolumeRenderer.java │ ├── JCudaDriverTextureSample.java │ ├── JCudaRuntimeSample.java │ ├── MouseControl.java │ ├── MouseControlable.java │ ├── package-info.java │ └── splines │ │ ├── CUDABSpline.java │ │ └── package-info.java ├── data │ ├── Grid.java │ ├── OpenCLMemoryDelegate.java │ ├── PointwiseIterator.java │ ├── generic │ │ ├── GenericGrid.java │ │ ├── GenericGridOperator.java │ │ ├── GenericGridOperatorInterface.java │ │ ├── GenericInterpolationOperators.java │ │ ├── GenericPointwiseOperators.java │ │ ├── complex │ │ │ ├── ComplexGrid.java │ │ │ ├── ComplexGrid1D.java │ │ │ ├── ComplexGrid2D.java │ │ │ ├── ComplexGrid3D.java │ │ │ ├── ComplexGridOperator.java │ │ │ ├── ComplexGridOperatorInterface.java │ │ │ ├── ComplexPointwiseOperators.java │ │ │ ├── Fourier.java │ │ │ ├── OpenCLComplexGridOperator.java │ │ │ ├── OpenCLComplexMemoryDelegate.java │ │ │ ├── OpenCLGridTest.java │ │ │ ├── OpenCLTestClass.java │ │ │ └── PointwiseOperators.cl │ │ ├── datatypes │ │ │ ├── Complex.java │ │ │ ├── Double.java │ │ │ ├── Float.java │ │ │ ├── Gridable.java │ │ │ ├── Integer.java │ │ │ └── OpenCLable.java │ │ ├── iterators │ │ │ ├── GenericFloatIterator.java │ │ │ └── GenericPointwiseIteratorND.java │ │ └── opencl │ │ │ ├── OpenCLGenericGridInterface.java │ │ │ └── OpenCLGenericGridOperators.java │ ├── numeric │ │ ├── BurtPyramid.java │ │ ├── Grid1D.java │ │ ├── Grid1DComplex.java │ │ ├── Grid2D.java │ │ ├── Grid2DComplex.java │ │ ├── Grid3D.java │ │ ├── Grid4D.java │ │ ├── InterpolationOperators.java │ │ ├── MultiChannelGrid2D.java │ │ ├── MultiChannelGrid3D.java │ │ ├── NumericGrid.java │ │ ├── NumericGridOperator.java │ │ ├── NumericPointwiseOperators.java │ │ ├── iterators │ │ │ ├── NumericFloatIterator.java │ │ │ └── NumericPointwiseIteratorND.java │ │ └── opencl │ │ │ ├── ExtendedOpenCLGridOperators.java │ │ │ ├── ExtendedPointwiseOperators.cl │ │ │ ├── OpenCLBenchmark.java │ │ │ ├── OpenCLGrid1D.java │ │ │ ├── OpenCLGrid2D.java │ │ │ ├── OpenCLGrid3D.java │ │ │ ├── OpenCLGridInterface.java │ │ │ ├── OpenCLGridOperators.java │ │ │ ├── OpenCLGridTest.java │ │ │ ├── OpenCLSynchProblemExample.java │ │ │ ├── PointwiseOperators.cl │ │ │ ├── delegates │ │ │ ├── OpenCLNumericMemoryDelegate3D.java │ │ │ ├── OpenCLNumericMemoryDelegate4D.java │ │ │ └── OpenCLNumericMemoryDelegateLinear.java │ │ │ └── package-info.java │ ├── package-info.java │ └── test │ │ ├── FFTTests.java │ │ └── package-info.java ├── dimreduction │ ├── DimensionalityReduction.java │ ├── LagrangianOptimization.java │ ├── LocallyLinearEmbedding.java │ ├── PCA.java │ ├── Test.java │ ├── objfunctions │ │ ├── DistanceSquareObjectiveFunction.java │ │ ├── InnerProductObjectiveFunction.java │ │ ├── LagrangianDistanceObjectiveFunction.java │ │ ├── LagrangianDistanceSquareObjectiveFunction.java │ │ ├── LagrangianInnerProductObjectiveFunction.java │ │ ├── SammonObjectiveFunction.java │ │ └── WeightedInnerProductObjectiveFunction.java │ └── utils │ │ ├── ConfidenceMeasure.java │ │ ├── ConvexityTest.java │ │ ├── Cube.java │ │ ├── Error.java │ │ ├── FileHandler.java │ │ ├── GUI.java │ │ ├── GUIAdditionalPlots.java │ │ ├── GUIOptFunc.java │ │ ├── GUIOptimizationMode.java │ │ ├── GUIshowCode.java │ │ ├── HelperClass.java │ │ ├── Improvement.java │ │ ├── MyException.java │ │ ├── OptimizationHelper.java │ │ ├── PlotHelper.java │ │ ├── PlotIterationsError.java │ │ ├── PlotKError.java │ │ ├── PlotParameterKError.java │ │ ├── PointCloud.java │ │ ├── PointCloudViewableOptimizableFunction.java │ │ └── ScatterPlot.java ├── filtering │ ├── AbsoluteValueTool.java │ ├── ApplyHounsfieldScaling.java │ ├── ApplyLambdaWeightingTool.java │ ├── AtractResidual2D.java │ ├── BilateralFilteringTool.java │ ├── CosineWeightingTool.java │ ├── DynamicDensityOptimizationScatterCorrectionTool.java │ ├── ExtremeValueTruncationFilter.java │ ├── FastRadialSymmetryTool.java │ ├── FiducialMarkerDetectionTool.java │ ├── Filtering2DTool.java │ ├── HideOnUIAnnotation.java │ ├── HilbertFilteringTool.java │ ├── HorizontalFlippingTool.java │ ├── HoughFilteringTool.java │ ├── ImageConstantMathFilter.java │ ├── ImageFilteringTool.java │ ├── ImageJParallelTool.java │ ├── ImageMathFilter.java │ ├── IndividualImageFilteringTool.java │ ├── KinectBasedDetectorSaturationCorrectionTool.java │ ├── LaplaceFilteringTool.java │ ├── LogPoissonNoiseFilteringTool.java │ ├── MeanFilteringTool.java │ ├── MeanMarkerBasedProjectionShiftingTool.java │ ├── MeanMarkerBasedProjectionShiftingToolForXCAT.java │ ├── MedianFilteringTool.java │ ├── NonLinearGainCorrectionTool.java │ ├── NumericalDerivativeComputationTool.java │ ├── NumericalLinewiseAntiderivativeFilteringTool.java │ ├── PatchwiseComponentComputationTool.java │ ├── PoissonNoiseFilteringTool.java │ ├── PrimaryModulationScatterCorrectionTool.java │ ├── RampFilteringTool.java │ ├── Rotate90DegreeLeftTool.java │ ├── SelectChannelTool.java │ ├── SimulateXRayDetector.java │ ├── ThinPlateSplinesBasedProjectionWarpingTool.java │ ├── ThinPlateSplinesBasedProjectionWarpingToolForXCAT.java │ ├── TruncationCorrectionTool.java │ ├── VolumeAttenuationFactorCorrectionTool.java │ ├── multiprojection │ │ ├── BackgroundSeparationTool.java │ │ ├── BilateralFilter3D.java │ │ ├── BlockWiseMultiProjectionFilter.java │ │ ├── BlockWiseStructureTensor.java │ │ ├── BlockwiseBilateralFilter3DCL.java │ │ ├── ConvertToMultiChannelImageTool.java │ │ ├── DiaphragmTrackingTool.java │ │ ├── DigitalSubtractionAngiographyTool.java │ │ ├── IdentityTransformFilter.java │ │ ├── IterativeReconstructionFilter.java │ │ ├── Lambda3DDerivativeFilter.java │ │ ├── MultiProjectionFilter.java │ │ ├── ProjectionSortingFilter.java │ │ ├── Triangulation.java │ │ ├── anisotropic │ │ │ ├── AnisotropicFilterFunction.java │ │ │ ├── AnisotropicStructureTensorNoiseFilter.java │ │ │ ├── CUDAAnisotropicStructureTensorNoiseFilter.java │ │ │ ├── CUDAFFTAnisotropicStructureTensorNoiseFilter.java │ │ │ └── package-info.java │ │ ├── blocks │ │ │ ├── AnisotropicStructureTensorBlock.java │ │ │ ├── BilateralFilter3DBlock.java │ │ │ ├── BilateralFilter3DCLBlock.java │ │ │ ├── IdentityTransformBlock.java │ │ │ ├── ImageProcessingBlock.java │ │ │ ├── IterativeReconstructionBlock.java │ │ │ └── package-info.java │ │ └── package-info.java │ ├── opencl │ │ ├── BilateralFiltering3DTool.java │ │ ├── Binarization2DTool.java │ │ ├── Kernel3x3Filtering2DTool.java │ │ ├── MeanFiltering2DTool.java │ │ ├── MeanFiltering2DinGrid3DTool.java │ │ ├── MeanFiltering3DTool.java │ │ ├── OpenCLFilteringTool2D.java │ │ ├── OpenCLFilteringTool3D.java │ │ ├── bilateralFilter3D.cl │ │ ├── binarization2D.cl │ │ ├── kernel3x3Filter2D.cl │ │ ├── meanFilter2D.cl │ │ ├── meanFilter2DinGrid3D.cl │ │ └── meanFilter6Surrounding3D.cl │ ├── package-info.java │ ├── rampfilters │ │ ├── ArbitraryRampFilter.java │ │ ├── CosineRampFilter.java │ │ ├── HammingRampFilter.java │ │ ├── HanningRampFilter.java │ │ ├── IRRFilter.java │ │ ├── RamLakRampFilter.java │ │ ├── RampFilter.java │ │ ├── SheppLoganRampFilter.java │ │ ├── SheppLoganRampFilterWithRollOff.java │ │ └── package-info.java │ └── redundancy │ │ ├── NooWeightingTool.java │ │ ├── ParkerWeightingTool.java │ │ ├── RiessWeightingTool.java │ │ ├── SilverWeightingTool.java │ │ ├── TrajectoryParkerWeightingTool.java │ │ ├── WesargWeightingTool.java │ │ └── package-info.java ├── fitting │ ├── ConstrainedRANSACFittedFunction.java │ ├── Function.java │ ├── GaussianFunction.java │ ├── IdentityFunction.java │ ├── LinearFunction.java │ ├── LogarithmicFunction.java │ ├── PolynomialFunction.java │ ├── Quadric.java │ ├── RANSACFittedFunction.java │ ├── Surface.java │ ├── package-info.java │ └── test │ │ ├── FunctionTest.java │ │ └── package-info.java ├── geometry │ ├── AbstractCurve.java │ ├── AbstractShape.java │ ├── AbstractSurface.java │ ├── Axis.java │ ├── ConvexHull.java │ ├── CoordinateSystem.java │ ├── General.java │ ├── Projection.java │ ├── Rotations.java │ ├── SeparableFootprints.java │ ├── bounds │ │ ├── AbstractBoundingCondition.java │ │ ├── BoundingBox.java │ │ ├── HalfSpaceBoundingCondition.java │ │ ├── QuadricBoundingCondition.java │ │ └── package-info.java │ ├── motion │ │ ├── AbstractAffineMotionField.java │ │ ├── AffineMotionField.java │ │ ├── AnalyticalAffineMotionField.java │ │ ├── AnalyticalAffineMotionFieldAxisAngle.java │ │ ├── AnalyticalAffineMotionFieldEuler.java │ │ ├── ArtificialMotionField.java │ │ ├── CombinedBreathingHeartMotionField.java │ │ ├── CompressionMotionField.java │ │ ├── ConstantMotionField.java │ │ ├── DualMotionField.java │ │ ├── MixedSurfaceBSplineMotionField.java │ │ ├── MotionField.cl │ │ ├── MotionField.java │ │ ├── MotionUtil.java │ │ ├── MovingCenterRotationMotionField.java │ │ ├── OpenCLParzenWindowMotionField.java │ │ ├── ParzenWindowMotionField.java │ │ ├── PlanarMotionField.java │ │ ├── PointBasedMotionField.java │ │ ├── RotationMotionField.java │ │ ├── SimpleMotionField.java │ │ ├── TimeVariantSurfaceBSplineListMotionField.java │ │ ├── TimeVariantSurfaceBSplineMotionField.java │ │ ├── VICONMarkerMotionField.java │ │ ├── WeightBearingBeadPositionBuilder.java │ │ ├── package-info.java │ │ └── timewarp │ │ │ ├── CombinedTimeWarper.java │ │ │ ├── ConstantTimeWarper.java │ │ │ ├── DualPhasePeriodicTimeWarper.java │ │ │ ├── HarmonicTimeWarper.java │ │ │ ├── IdentityTimeWarper.java │ │ │ ├── PeriodicTimeWarper.java │ │ │ ├── RestPhaseTimeWarper.java │ │ │ ├── ScaledIdentitiyTimeWarper.java │ │ │ ├── SigmoidTimeWarper.java │ │ │ ├── TimeWarper.java │ │ │ └── package-info.java │ ├── package-info.java │ ├── shapes │ │ ├── ArbitrarySurface.java │ │ ├── StandardCoordinateSystem.java │ │ ├── activeshapemodels │ │ │ ├── ActiveShapeModel.java │ │ │ ├── GPA.java │ │ │ ├── KPCA.java │ │ │ ├── LightPCA.java │ │ │ ├── PCA.java │ │ │ ├── VarianceMeasure.java │ │ │ ├── kernels │ │ │ │ ├── GaussianKernel.java │ │ │ │ ├── KernelFunction.java │ │ │ │ ├── PolynomialKernel.java │ │ │ │ ├── RadialKernel.java │ │ │ │ └── package-info.java │ │ │ └── package-info.java │ │ ├── compound │ │ │ ├── CompoundShape.java │ │ │ ├── LinearOctree.java │ │ │ ├── NestedOctree.java │ │ │ ├── TriangleMesh.java │ │ │ └── package-info.java │ │ ├── mesh │ │ │ ├── AlexaEmbedding.java │ │ │ ├── DataMatrix.java │ │ │ ├── Mesh.java │ │ │ ├── Mesh4D.java │ │ │ ├── MeshUtil.java │ │ │ └── package-info.java │ │ ├── package-info.java │ │ └── simple │ │ │ ├── Box.java │ │ │ ├── Cone.java │ │ │ ├── Cylinder.java │ │ │ ├── Edge.java │ │ │ ├── Ellipsoid.java │ │ │ ├── GeometryTests.java │ │ │ ├── LineComparator1D.java │ │ │ ├── Plane3D.java │ │ │ ├── Point2D.java │ │ │ ├── Point3D.java │ │ │ ├── PointND.java │ │ │ ├── ProjectPointToLineComparator.java │ │ │ ├── Pyramid.java │ │ │ ├── QuadricSurface.java │ │ │ ├── SimpleSurface.java │ │ │ ├── SortablePoint.java │ │ │ ├── Sphere.java │ │ │ ├── StraightLine.java │ │ │ ├── SwissRoll.java │ │ │ ├── Triangle.java │ │ │ ├── VectorPoint3D.java │ │ │ └── package-info.java │ ├── splines │ │ ├── BSpline.java │ │ ├── ClosedCubicBSpline.java │ │ ├── MotionDefectTimeVariantSurfaceBSpline.java │ │ ├── NearestNeighborTimeVariantSurfaceBSpline.java │ │ ├── ShiftTimeVariantSurfaceBSpline.java │ │ ├── SplineTests.java │ │ ├── SurfaceBSpline.java │ │ ├── SurfaceBSplineVolumePhantom.java │ │ ├── SurfaceUniformCubicBSpline.java │ │ ├── TimeVariantSurfaceBSpline.java │ │ ├── TorsionalMotionTimeVariantSurfaceBSpline.java │ │ ├── TorsionalMotionTimeVariantSurfaceBSpline2.java │ │ ├── UniformCubicBSpline.java │ │ ├── fitting │ │ │ ├── BSplineCurveInterpolation.java │ │ │ └── BSplineSurfaceInterpolation.java │ │ └── package-info.java │ ├── test │ │ ├── CurveTests.java │ │ ├── GeometryTests.java │ │ ├── ProjectionTest.java │ │ ├── SurfaceTests.java │ │ └── package-info.java │ ├── trajectories │ │ ├── CirclePlusLineTrajectory.java │ │ ├── CircularTrajectory.java │ │ ├── ConfigFileBasedTrajectory.java │ │ ├── DennerleinProjectionTableFileTrajectory.java │ │ ├── ExtrapolatedTrajectory.java │ │ ├── HelicalTrajectory.java │ │ ├── MultiSweepTrajectory.java │ │ ├── ProjectionTableFileTrajectory.java │ │ ├── SystemGeometryConfigFileTrajectory.java │ │ ├── Trajectory.java │ │ └── package-info.java │ └── transforms │ │ ├── AffineTransform.java │ │ ├── ComboTransform.java │ │ ├── Quaternion.java │ │ ├── ScaleRotate.java │ │ ├── Transform.java │ │ ├── Transformable.java │ │ ├── Translation.java │ │ ├── package-info.java │ │ └── test │ │ ├── TestAffineTransform.java │ │ ├── TestComboTransform.java │ │ ├── TestScaleRotate.java │ │ ├── TestTransform.java │ │ ├── TestTranslation.java │ │ └── package-info.java ├── io │ ├── AdditionalDicomTag.java │ ├── ConfigFile.java │ ├── ConfigFileParser.java │ ├── DennerleinProjectionSource.java │ ├── DicomProjectionSource.java │ ├── FileProjectionSource.java │ ├── FlexibleFileOpener.java │ ├── GridRawIOUtil.java │ ├── ImagePlusDataSink.java │ ├── ImagePlusProjectionDataSource.java │ ├── IndividualFilesProjectionDataSink.java │ ├── InteractiveConfigFileReader.java │ ├── KEVSDicomTag.java │ ├── KpcaIO.java │ ├── MKTProjectionSource.java │ ├── MotionFieldReader.java │ ├── NRRDProjectionSource.java │ ├── NrrdFileInfo.java │ ├── NrrdFileReader.java │ ├── NrrdFileWriter.java │ ├── ParseInfoFile.java │ ├── PcaIO.java │ ├── ProjectionRawIOUtil.java │ ├── RotTransIO.java │ ├── SEQProjectionSource.java │ ├── STLFileUtil.java │ ├── SafeSerializable.java │ ├── SelectionCancelledException.java │ ├── SerializableFloatProcessor.java │ ├── TestGridRawDataIO.java │ ├── TiffProjectionSource.java │ ├── VTKMeshIO.java │ ├── VTKMeshReader.java │ ├── VTKVectorField.java │ ├── ZipProjectionSource.java │ └── package-info.java ├── metric │ ├── ImageMetric.java │ ├── MeanSquareErrorMetric.java │ ├── NormalizedImageMetric.java │ ├── NormalizedImprovement.java │ ├── RootMeanSquareErrorMetric.java │ └── package-info.java ├── numerics │ ├── DecompositionQR.java │ ├── DecompositionRQ.java │ ├── DecompositionSVD.java │ ├── DoubleFunction.java │ ├── SimpleMatrix.java │ ├── SimpleOperators.java │ ├── SimpleVector.java │ ├── Solvers.java │ ├── mathexpressions │ │ ├── AbstractMathExpression.java │ │ ├── CompoundExpression.java │ │ ├── Evaluator.java │ │ ├── ExpressionParser.java │ │ ├── FloatExpression.java │ │ ├── FunctionExpression.java │ │ ├── IdentifierExpression.java │ │ ├── MathExpression.java │ │ ├── RealExpression.java │ │ └── package-info.java │ ├── package-info.java │ └── test │ │ ├── RQTest.java │ │ ├── SimpleMatrixTest.java │ │ ├── SimpleOperatorsTest.java │ │ ├── SimpleVectorTest.java │ │ ├── SolversTest.java │ │ ├── TestExpressions.java │ │ └── package-info.java ├── opencl │ ├── GLCLDemo │ │ ├── GLCLInteroperabilityDemo.java │ │ ├── JoglInterop.cl │ │ ├── UserSceneInteraction.java │ │ └── package-info.java │ ├── OpenCLAppendBufferRenderer.java │ ├── OpenCLBackProjector.java │ ├── OpenCLDetectorMotionBackProjector.java │ ├── OpenCLEdgeForwardProjector.cl │ ├── OpenCLEdgeForwardProjector.java │ ├── OpenCLEvaluatable.java │ ├── OpenCLForwardProjector.java │ ├── OpenCLForwardProjectorDynamicVolume.java │ ├── OpenCLForwardProjectorWithMotion.java │ ├── OpenCLJointBilateralFilteringTool.java │ ├── OpenCLMaterialPathLengthPhantomRenderer.java │ ├── OpenCLProjectionPhantomRenderer.java │ ├── OpenCLRenderer.java │ ├── OpenCLSurfacePhantomRenderer.java │ ├── OpenCLUtil.java │ ├── OpenCLYBufferRenderer.java │ ├── TestOpenCL.java │ ├── VectorAdd.cl │ ├── appendBuffer.cl │ ├── appendBufferConvex.cl │ ├── appendBufferNonConvexMessedUp.cl │ ├── backprojectCL.cl │ ├── bspline.cl │ ├── filter.cl │ ├── package-info.java │ ├── projectCL.cl │ ├── projection.cl │ ├── rendering │ │ ├── MouseControl.java │ │ ├── MouseControlable.java │ │ ├── OpenCLTextureRendering.java │ │ ├── OpenCLVolumeRenderer.java │ │ ├── package-info.java │ │ └── volumeRender.cl │ ├── shapes │ │ ├── OpenCLBox.java │ │ ├── OpenCLCompoundShape.java │ │ ├── OpenCLCone.java │ │ ├── OpenCLCylinder.java │ │ ├── OpenCLEllipsoid.java │ │ ├── OpenCLPyramid.java │ │ ├── OpenCLSphere.java │ │ ├── OpenCLTextureTimeVariantSurfaceBSpline.java │ │ ├── OpenCLTimeVariantSurfaceBSpline.java │ │ ├── OpenCLUniformBSpline.java │ │ ├── OpenCLUniformSurfaceBSpline.java │ │ ├── OpenCLUniformTextureBSpline.java │ │ ├── OpenCLUniformTextureSurfaceBSpline.java │ │ └── package-info.java │ ├── simpleObjects.cl │ ├── triangleAppendBuffer.cl │ └── yxdraw.cl ├── optimization │ ├── CombinedGradientOptimizableFunction.java │ ├── LMA.java │ ├── LSqMinNorm.java │ ├── OptimizableFunction.java │ └── package-info.java ├── package-info.java ├── parallel │ ├── NamedParallelizableRunnable.java │ ├── ParallelThread.java │ ├── ParallelThreadExecutor.java │ ├── ParallelizableRunnable.java │ ├── SimpleParallelThread.java │ └── package-info.java ├── phantom │ ├── AbstractCalibrationPhantom.java │ ├── AffineMotionPhantom.java │ ├── AnalyticPhantom.java │ ├── AnalyticPhantom4D.java │ ├── AsciiSTLMeshPhantom.java │ ├── BeadRemovalPhantom.java │ ├── BonePhantom.java │ ├── BoxPhantom.java │ ├── CatheterPhantom.java │ ├── CatphanCTP528.java │ ├── CirclesPhantom.java │ ├── ConePhantom.java │ ├── DefrisePhantom.java │ ├── EllipsoidPhantom.java │ ├── MTFBeadPhantom.java │ ├── MathematicalPhantom.java │ ├── MovingBallPhantom.java │ ├── NumericalSheppLogan3D.java │ ├── PyramidPhantom.java │ ├── RandomDistributionPhantom.java │ ├── RandomizedHelixPhantom.java │ ├── SevenBeadPhantom.java │ ├── SheppLogan3D.java │ ├── SheppLoganPhantom.java │ ├── SimpleShapeTestPhantom.java │ ├── SinoPhantom.java │ ├── SpherePhantom.java │ ├── TrigonometryPhantom.java │ ├── WaterCylinderPhantom.java │ ├── XNPhantom.java │ ├── asmheart │ │ ├── CONRADCardiacModel3D.java │ │ ├── CONRADCardiacModel4D.java │ │ ├── CONRADCardiacModelConfig.java │ │ ├── PredefinedModels.java │ │ └── package-info.java │ ├── electrondensity │ │ ├── CrisEDPhantomGUI.java │ │ ├── CrisEDPhantomM062.java │ │ ├── EDInnerDisk.java │ │ ├── EDOuterDisk.java │ │ ├── Insert.java │ │ ├── QuadricDisk.java │ │ └── package-info.java │ ├── forbild │ │ ├── ForbildParser.java │ │ ├── ForbildPhantom.java │ │ ├── ForbildShapeFactory.java │ │ ├── package-info.java │ │ └── shapes │ │ │ ├── ForbildBox.java │ │ │ ├── ForbildCone.java │ │ │ ├── ForbildCylinder.java │ │ │ ├── ForbildEllipsoid.java │ │ │ ├── ForbildSphere.java │ │ │ └── package-info.java │ ├── package-info.java │ ├── renderer │ │ ├── AnalyticPhantomProjector.java │ │ ├── CylinderPhantomRenderer.java │ │ ├── MetricPhantomRenderer.java │ │ ├── ParallelProjectionPhantomRenderer.java │ │ ├── PhantomRenderer.java │ │ ├── RampProjectionPhantomRenderer.java │ │ ├── SliceParallelVolumePhantomRenderer.java │ │ ├── StreamingPhantomRenderer.java │ │ └── package-info.java │ ├── workers │ │ ├── AnalyticPhantom3DVolumeRenderer.java │ │ ├── AnalyticPhantomProjectorWorker.java │ │ ├── DiracProjectionPhantom.java │ │ ├── MultiMaterialPhantom3DVolumeRenderer.java │ │ ├── SheppLoganPhantomWorker.java │ │ ├── SliceWorker.java │ │ ├── VolumeOfInterestPhantom.java │ │ └── package-info.java │ └── xcat │ │ ├── BreathingScene.java │ │ ├── CombinedBreathingHeartScene.java │ │ ├── CoronaryScene.java │ │ ├── DynamicSquatScene.java │ │ ├── HeartScene.java │ │ ├── SquatScene.java │ │ ├── TessellationThread.java │ │ ├── ViconAffineTransform.java │ │ ├── ViconMarkerBuilder.java │ │ ├── WholeBodyScene.java │ │ ├── XCatMaterialGenerator.java │ │ ├── XCatScene.java │ │ └── package-info.java ├── physics │ ├── Constants.java │ ├── EnergyDependentCoefficients.java │ ├── HalfValueLayerFunction.java │ ├── LambdaFunction.java │ ├── PhysicalObject.java │ ├── PhysicalPoint.java │ ├── PolychromaticXRaySpectrum.java │ ├── XRaySpectrum.java │ ├── absorption │ │ ├── AbsorptionModel.java │ │ ├── DensityAbsorptionModel.java │ │ ├── PathLengthHistogramCreatingAbsorptionModel.java │ │ ├── PolychromaticAbsorptionModel.java │ │ ├── SelectableEnergyMonochromaticAbsorptionModel.java │ │ ├── SelectableEnergyMonochromaticAbsorptionModelWithNoise.java │ │ └── package-info.java │ ├── detector │ │ ├── MaterialPathLengthDetector.java │ │ ├── PolychromaticDetectorWithNoise.java │ │ ├── SimpleMonochromaticDetector.java │ │ ├── SimplePolychromaticDetector.java │ │ ├── XRayDetector.java │ │ └── package-info.java │ ├── materials │ │ ├── Compound.java │ │ ├── Element.java │ │ ├── Material.java │ │ ├── Mixture.java │ │ ├── WeightedAtomicComposition.java │ │ ├── database │ │ │ ├── CompositionToAbsorptionEdgeMap.java │ │ │ ├── ElementalMassAttenuationData.java │ │ │ ├── FormulaToNameMap.java │ │ │ ├── MaterialsDB.java │ │ │ ├── NameToFormulaMap.java │ │ │ ├── OnlineMassAttenuationDB.java │ │ │ ├── package-info.java │ │ │ └── xmldatagenerators │ │ │ │ ├── RebuildDatabase.java │ │ │ │ ├── RebuildMaps.java │ │ │ │ ├── RebuildMaterialDatabase.java │ │ │ │ └── package-info.java │ │ ├── materialsTest │ │ │ ├── TestMassAttenuationData.java │ │ │ └── package-info.java │ │ ├── package-info.java │ │ └── utils │ │ │ ├── AttenuationRetrievalMode.java │ │ │ ├── AttenuationType.java │ │ │ ├── LocalMassAttenuationCalculator.java │ │ │ ├── MaterialUtils.java │ │ │ ├── WeightedAtomicComposition.java │ │ │ └── package-info.java │ ├── package-info.java │ └── photoncounting │ │ ├── LearnMaterialROI.java │ │ ├── PhotonCountingEnergyResolvingDetector.java │ │ └── PredictMaterial.java ├── pipeline │ ├── BufferedProjectionSink.java │ ├── DevNullSink.java │ ├── IndividualImagePipelineFilteringTool.java │ ├── ParallelImageFilterPipeliner.java │ ├── ParallelImageFilterSink.java │ ├── ParallelProjectionDataSinkFeeder.java │ ├── PipelineTests.java │ ├── ProjectionSink.java │ ├── ProjectionSource.java │ └── package-info.java ├── pyconrad │ ├── PyConrad.java │ └── PythonCallback.java ├── reconstruction │ ├── CPUSuperShortScanBackprojector.java │ ├── DistanceDrivenBasedReconstruction.java │ ├── FBPReconstructionFilter.java │ ├── IterativeReconstruction.java │ ├── LolaBunnyBackprojector.java │ ├── ModelBasedIterativeReconstruction.java │ ├── MotionCompensatedSubVolumeBackprojector.java │ ├── MotionCompensatedVOIBasedReconstructionFilter.java │ ├── RayDrivenBasedReconstruction.java │ ├── RayWeightCorrectingCPUSuperShortScanBackprojector.java │ ├── ReconstructionFilter.java │ ├── RigidBody3DTransformationVOIBasedReconstructionFilter.java │ ├── RigidBody3DTransformationVOIBasedReconstructionFilterForXCAT.java │ ├── SeparableFootprintsBasedReconstruction.java │ ├── SimpleIterativeReconstruction.java │ ├── SubVolumeBackprojector.java │ ├── SuperShortScanBackprojection.java │ ├── VOIBasedReconstructionFilter.java │ ├── iterative │ │ ├── DistanceDrivenBasedReconstruction.java │ │ ├── IterativeReconstruction.java │ │ ├── LeastSquaresCG.java │ │ ├── ModelBasedIterativeReconstruction.java │ │ ├── PenalizedLeastSquareART.java │ │ ├── RayDrivenBasedReconstruction.java │ │ ├── SeparableFootprints.java │ │ ├── SeparableFootprintsBasedReconstruction.java │ │ ├── huberPenalty.java │ │ └── package-info.java │ ├── package-info.java │ ├── test │ │ ├── IterativeReconstructionTestA.java │ │ ├── IterativeReconstructionTestB.java │ │ └── package-info.java │ └── voi │ │ ├── CylinderBasedVolumeOfInterest.java │ │ ├── PolygonBasedVolumeOfInterest.java │ │ ├── VolumeOfInterest.java │ │ └── package-info.java ├── rendering │ ├── AbstractRayTracer.java │ ├── AbstractScene.java │ ├── PrioritizableScene.java │ ├── Priority1DRayTracer.java │ ├── PriorityRayTracer.java │ ├── RayDetector.java │ ├── Simple1DRayTracer.java │ ├── SimpleRayTracer.java │ ├── SimpleScene.java │ ├── WatertightRayTracer.java │ └── package-info.java ├── segmentation │ ├── GLCMFeatureExtractor.java │ ├── GridFeatureExtractor.java │ ├── HistogramFeatureExtractor.java │ ├── ImageJFeatureExtractor.java │ ├── MetaFeatureExtractor.java │ ├── MultiChannelGridFeatureExtractor.java │ ├── PolynomialMultiChannelGridFeatureExtractor.java │ ├── SegmentationTest.java │ └── VesselnessFeatureExtractor.java ├── utils │ ├── BilinearInterpolatingDoubleArray.java │ ├── CONRAD.java │ ├── Configuration.java │ ├── ConfigurationUpdater.java │ ├── DicomConfigurationUpdater.java │ ├── DicomDecoder.java │ ├── DoubleArrayUtil.java │ ├── DoublePrecisionPointUtil.java │ ├── FFTUtil.java │ ├── FHTUtil.java │ ├── FileJoiner.java │ ├── FileUtil.java │ ├── FloatArrayUtil.java │ ├── GUIUtil.java │ ├── ImageGridBuffer.java │ ├── ImageUtil.java │ ├── LinearInterpolatingDoubleArray.java │ ├── RegKeys.java │ ├── StatisticsUtil.java │ ├── StringFileFilter.java │ ├── TessellationUtil.java │ ├── TestingTools.java │ ├── UserUtil.java │ ├── VisualizationUtil.java │ ├── XmlUtils.java │ ├── interpolation │ │ ├── Interpolator.java │ │ ├── LinearInterpolator.java │ │ ├── LogLinearInterpolator.java │ │ ├── LogLogInterpolator.java │ │ ├── NumberInterpolatingTreeMap.java │ │ └── package-info.java │ ├── package-info.java │ └── parsers │ │ ├── ParserFactory.java │ │ ├── SceneFileParser.java │ │ ├── SliceWorkerParser.java │ │ └── package-info.java └── volume3d │ ├── FFTVolumeHandle.java │ ├── JTransformsFFTVolumeHandle.java │ ├── MaxEigenValue.java │ ├── ParallelVolumeOperator.java │ ├── Volume3D.java │ ├── VolumeOperator.java │ ├── operations │ ├── AddSlabScalar.java │ ├── AddSlabs.java │ ├── CopySlabData.java │ ├── DivideSlabs.java │ ├── FFTShifter.java │ ├── InitializeGaussian.java │ ├── InitializeHighPass.java │ ├── InitializeLowPass.java │ ├── InitializeSquaredCosine.java │ ├── InitializeSquaredCosineR.java │ ├── MaxOfSlab.java │ ├── MeanOfSlab.java │ ├── MinOfSlab.java │ ├── MinOfSlabs.java │ ├── MultiplySlabScalar.java │ ├── MultiplySlabs.java │ ├── ParallelVolumeOperation.java │ ├── SquareRootSlab.java │ ├── UpperLimitSlab.java │ ├── VoxelOperation.java │ └── package-info.java │ └── package-info.java └── tutorial ├── DisplayReconstruction.java ├── DisplaySinogram.java ├── DisplayUniformCircle.java ├── FanBeamParallelBeamComparison.java ├── RamLakFilteringExample.java ├── RotationalAngiography └── ResidualMotionCompensation │ ├── ECG │ ├── Angiogram.java │ └── ECGGating.java │ ├── MotionCompensatedRecon.java │ ├── mip │ ├── OpenCLMaximumIntensityProjection.java │ └── mipCL.cl │ ├── morphology │ ├── Morphology.java │ └── StructuringElement.java │ ├── reconWithStreakReduction │ ├── ConeBeamBackprojectorStreakReduction.cl │ ├── ConeBeamBackprojectorStreakReduction.java │ ├── ConeBeamBackprojectorStreakReductionIterateOverY.cl │ ├── ConeBeamBackprojectorStreakReductionWithMotionCompensation.cl │ ├── ConeBeamBackprojectorStreakReductionWithMotionCompensation.java │ ├── OpenCLBackProjectorStreakReduction.java │ └── backprojectCLStreakReduction.cl │ └── registration │ ├── UnwarpJ_.java │ ├── bUnwarpJ_ │ ├── BSplineModel.java │ ├── ClearAll.java │ ├── Credits.java │ ├── CumulativeQueue.java │ ├── EvaluateSimilarityTile.java │ ├── FinalAction.java │ ├── GrayscaleResultTileMaker.java │ ├── IODialog.java │ ├── MainDialog.java │ ├── Mask.java │ ├── MathTools.java │ ├── MiscTools.java │ ├── Param.java │ ├── PointAction.java │ ├── PointHandler.java │ ├── PointToolbar.java │ ├── ProgressBar.java │ ├── Transformation.java │ ├── bUnwarpJ_.java │ └── package-info.java │ └── math │ └── BSpline.java ├── atract ├── AtractExample.java ├── AtractFilter1D.java ├── AtractFilter2D.java ├── AtractKernel1D.java ├── AtractKernel1D_test.java ├── AtractKernel2D.java ├── AtractWithBinaryWeight.java ├── BorderRemoval1D.java ├── BorderRemoval2D.java ├── DisplayAtract.java ├── Kollimator.java ├── LaplaceKernel1D.java ├── LaplaceKernel2D.java └── package-info.java ├── basics ├── MHDImageLoader.java ├── PointCloudMaker.java ├── ReadImageDataFromFile.java ├── ReadImageDataFromFileExample.java ├── RotationMatrixExamples.java ├── SammonMappingExample.java └── videoTutorials │ ├── addValuePI.cl │ ├── tutorialASM.java │ ├── videoTutorialsFilterTools.java │ ├── videoTutorialsImageJ.java │ ├── videoTutorialsOpenCL.java │ ├── videotutorialsGeometricShapes.java │ ├── videotutorialsGrids.java │ └── videotutorialsMathOperations.java ├── cone ├── ConeBeamBackProjector.cl ├── ConeBeamBackprojector.java ├── ConeBeamCosineFilter.java ├── ConeBeamProjector.cl ├── ConeBeamProjector.java ├── ConeBeamReconstructionExample.java └── package-info.java ├── dmip ├── DMIP_FanBeamBackProjector2D.java ├── DMIP_ParallelBeam.java ├── DefectPixelInterpolation.java ├── ImageUndistortion.java ├── Intro.java ├── Proton.png ├── RANSAC.java ├── Registration1.java ├── Registration2.java ├── Registration3.java ├── SVDandFT.java ├── Sinogram0.tif ├── Sinogram1.tif ├── Sinogram2.tif ├── T1.png ├── frame32.jpg ├── frame90.jpg ├── mask.bmp ├── mr12.dcm ├── testimg.bmp ├── undistorted.jpg └── yu_fill.jpg ├── ecc ├── EpipolarConsistency.java └── EpipolarConsistencyExample.java ├── fan ├── CosineFilter.java ├── FanBeamBackProjectorPixel.cl ├── FanBeamBackProjectorRay.cl ├── FanBeamBackprojector2D.java ├── FanBeamComparisonToCONRAD.java ├── FanBeamProjector.cl ├── FanBeamProjector2D.java ├── FanBeamReconstructionExample.java ├── RbRFanBeamReconstructionExample.java ├── dynamicCollimation │ ├── copyRedundantData.java │ └── package-info.java ├── package-info.java └── redundancy │ ├── BinaryWeights.java │ ├── BinaryWeights_Normal.java │ ├── BinaryWeights_erodeByOne.java │ ├── CompensationWeights.java │ ├── FanBeamWeightingComparison.java │ ├── ParkerWeights.java │ ├── SilverWeights.java │ └── package-info.java ├── filters ├── DerivativeKernel.java ├── EstimateRamLakFilter.java ├── GridKernel.java ├── HilbertKernel.java ├── RamLakKernel.java ├── RamLakKernelLinux.java ├── RayByRayFiltering.java └── SheppLoganKernel.java ├── fourierConsistency ├── coneBeam │ └── package-info.java └── wedgefilter │ ├── DoubleWedgeFilter.java │ ├── DoubleWedgeFilterFanEA.java │ ├── DoubleWedgeFilterFanES.java │ ├── DoubleWedgeFilterParallel.java │ └── ProjectionEstimationExample.java ├── interpolation ├── FanParameters.java └── Interpolation.java ├── iterative ├── Etv.java ├── GDTest.java ├── GridOp.java ├── IterativeReconstructionTest.java ├── Sart.java ├── SartCL.java ├── SartCL2D.java └── SartCPU.java ├── mammography ├── Mammogram.java └── inbreast │ ├── ReadMammograms.java │ └── XMLparser.java ├── modelObserver ├── Channels.java ├── CreateImages.java ├── ImageHelper.java ├── ModelDemo.java ├── Observer.java ├── ObserverPipeline.java ├── ROC.java └── TestModelGenerator.java ├── motion ├── ApplyDenseMotionFieldExample.java ├── CreateMotionProfile.java ├── MotionCompensatedReconExample.java ├── compensation │ ├── OpenCLCompensatedBackProjector.java │ ├── OpenCLCompensatedBackProjector1DCompressionField.java │ ├── OpenCLCompensatedBackProjectorTPS.java │ ├── OpenCLMotionCompensatedBackProjector.java │ ├── applyMotionDenseMotionField.cl │ ├── compensatedBackprojectCL.cl │ ├── compensatedBackprojectCL1DCompression.cl │ ├── compensatedBackprojectCLTPS.cl │ └── generalMotionCompensatedBackprojectCL.cl └── estimation │ ├── CylinderVolumeMask.java │ ├── EstimateBSplineSurface.java │ ├── EstimateCubic2DSpline.java │ ├── InitialOptimization.java │ ├── OpenCLSplineRenderer.java │ ├── OptimizeMotionField.java │ ├── ProjectionLoader.java │ ├── RadialBasisFunctionInterpolation.java │ ├── RunMotionEstimation.java │ ├── SmoothKernel1D.java │ ├── SobelKernel1D.java │ ├── ThinPlateSplineInterpolation.java │ └── package-info.java ├── noncircularfov ├── Boundaries.java ├── Correspondences.java ├── EllipseGrid2D.java ├── RectangleGrid2D.java ├── TrajectoryExample.java ├── TwoCirclesGrid.java └── TwoCirclesGridMod.java ├── oct └── CreateMotionArtifactScan.java ├── package-info.java ├── parallel ├── ParallelBackprojector2D.java ├── ParallelMedianReconExample.java ├── ParallelOnlineBackprojectionExample.java ├── ParallelOnlineReconstructionExample.java ├── ParallelProjectionExample.java ├── ParallelProjector.cl ├── ParallelProjector2D.java ├── ParallelReconExample.java └── package-info.java ├── phantoms ├── BrainPerfusionPhantom.java ├── BrainPerfusionPhantomConfig.java ├── CreateOpenCLProjectionPhantomExample.java ├── DotsGrid2D.java ├── Ellipsoid.java ├── FilePhantom.java ├── MTFphantom.java ├── MickeyMouseGrid2D.java ├── MockupFlow4D.java ├── Phantom.java ├── Phantom3D.java ├── PohlmannPhantom.java ├── SheppLogan.java ├── SimpleCubes3D.java ├── SimpleGridsForTruncationCorrection.java ├── Sphere3D.java ├── TestObject1.java ├── TestObject2.java ├── UniformCircleGrid2D.java └── package-info.java ├── physics ├── CreateCustomMaterial.java ├── DistributionTest.java ├── NHelperFkt.java ├── SingleMaterialMonteCarlo.java ├── SpectralAbsorption.java ├── XRayAnalytics.java ├── XRayComparator.java ├── XRayHitVertex.java ├── XRayTracer.java ├── XRayTracerSampling.java ├── XRayVPL.java ├── XRayVRay.java ├── XRayViewer.java ├── XRayWorker.java ├── package-info.java └── workingClass │ ├── AbstractWorker.java │ ├── RayWorker.java │ ├── TestControlUnit.java │ ├── VirtualPointWorker.java │ └── VirtualRayWorker.java ├── pyconrad ├── PyConradExample.java └── square.cpp ├── ringArtifactCorrection ├── PolarConverter.java ├── RingArtifactCorrectionExample.java └── RingArtifactCorrector.java ├── scalespace └── ScaleSpaceStudies.java ├── test ├── CharacterEncodingTest.java ├── MaxThreadsTest.java └── VolumeCenteringTest.java ├── truncation ├── ConstantValueZeroArtifactImage.java ├── NonZeroArtifactImage.java ├── PolynomialTruncationCorrectionExample.java ├── WaterCylinderFBPExample.java └── package-info.java ├── weightedtv ├── Perform2DWeightedTV.java ├── Perform3DWeightedTV.java ├── TVGradient.java ├── TVGradient3D.java ├── TVOpenCLGridOperators.java ├── TVPointwiseOperators.cl └── package-info.java └── weka ├── ClassificationExample.java ├── RegressionExample.java ├── StartWeka.java └── TreeExample.java /.classpath: -------------------------------------------------------------------------------- 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