catsim-test 0.0.5__cp313-cp313-manylinux_2_31_x86_64.whl

gecatsim/cfg/Phantom_Default.cfg

@@ -0,0 +1,7 @@
+# Phantom
+phantom.callback = "Phantom_Voxelized"      # name of function that reads and models phantom
+phantom.projectorCallback = "C_Projector_Voxelized" # name of function that performs projection through phantom
+phantom.projectorNumThreads = 4             # Number of CPU threads, only works for Linux
+phantom.filename = 'CatSim_logo_1024.json'   # phantom filename
+phantom.centerOffset = [0.0, 0.0, 0.0]      # offset of phantom center relative to origin (in mm)
+phantom.scale = 1.0                         # re-scale the size of phantom

gecatsim/cfg/Physics_Default.cfg

@@ -0,0 +1,38 @@
+# Geometric and energy sampling
+physics.energyCount = 20                    # number of energy bins
+physics.monochromatic = -1                  # -1 for polychromatic (see protocol.cfg);
+                                            #     for monoenergetic specify the energy in keV
+physics.colSampleCount = 2                  # number of samples of detector cells in lateral direction
+physics.rowSampleCount = 2                  # number of samples of detector cells in longitudinal direction
+physics.srcXSampleCount = 2                 # number of samples of focal spot in lateral direction
+physics.srcYSampleCount = 2                 # number of samples of focal spot cells in longitudinal direction
+physics.viewSampleCount = 2                 # number of samples of each view angle range in rotational direction
+
+# Flags to determine what has to be recalculated each view
+physics.recalcDet = 0                       # recalculate detector geometry
+physics.recalcSrc = 0                       # recalculate source geometry and relative intensity
+physics.recalcRayAngle = 0                  # recalculate source-to-detector-cell ray angles
+physics.recalcSpec = 0                      # recalculate spectrum
+physics.recalcFilt = 0                      # recalculate filters
+physics.recalcFlux = 0                      # recalculate flux
+physics.recalcPht = 0                       # recalculate phantom
+
+# Noise on/off settings
+physics.enableQuantumNoise = 1              # enable quantum noise
+physics.enableElectronicNoise = 1           # enable electronic noise
+
+# Internal physics models
+physics.rayAngleCallback = "Detector_RayAngles_2D" # name of function to calculate source-to-detector-cell ray angles
+physics.fluxCallback = "Detection_Flux"     # name of function to calculate flux
+physics.scatterCallback = ""                # name of function to calculate scatter
+physics.scatterKernelCallback = ""          # name of function to calculate scatter kernel ("" for default kernel)
+physics.scatterScaleFactor = 1              # scale factor, 1 appropriate for 64-mm detector and 20-cm water
+physics.prefilterCallback = "Detection_prefilter" # name of function to calculate detection pre-filter
+physics.crosstalkCallback = ""              # name of function to calculate X-ray crosstalk in the detector
+physics.lagCallback = ""                    # name of function to calculate detector lag
+physics.opticalCrosstalkCallback = ""       # name of function to calculate optical crosstalk in the detector
+physics.DASCallback = "Detection_DAS"       # name of function to calculate the detection process
+
+# I/O preferences
+physics.outputCallback = "WriteRawView"     # name of function to produce the simulation output
+physics.dump_period = 100 # dump data every 100 views

gecatsim/cfg/Protocol_Default.cfg

@@ -0,0 +1,33 @@
+protocol.scanTypes = [1, 1, 1, 1]           # flags for airscan, offset scan, phantom scan, prep
+
+# Table and gantry
+protocol.scanTrajectory = "Gantry_Helical"  # name of the function that defines the scanning trajectory and model
+protocol.viewsPerRotation = 1000            # total numbers of view per rotation
+protocol.viewCount = 1000                   # total number of views in scan
+protocol.startViewId = 0                    # index of the first view in the scan
+protocol.stopViewId = protocol.startViewId + protocol.viewCount - 1 # index of the last view in the scan
+protocol.airViewCount = 1                   # number of views averaged for air scan
+protocol.offsetViewCount = 1                # number of views averaged for offset scan
+protocol.rotationTime = 1.0                 # gantry rotation period (in seconds)
+protocol.rotationDirection = 1              # gantry rotation direction (1=CW, -1 CCW, seen from table foot-end)
+protocol.startAngle = 0                     # relative to vertical y-axis (n degrees)
+protocol.tableSpeed = 0                     # speed of table translation along positive z-axis (in mm/sec)
+protocol.startZ = 0                         # start z-position of table
+protocol.tiltAngle = 0                      # gantry tilt angle towards negative z-axis (in degrees)
+protocol.wobbleDistance = 0.0               # focalspot wobble distance
+protocol.focalspotOffset = [0, 0, 0]        # focalspot position offset
+
+# X-ray tube technique and filtration
+protocol.mA = 200                           # tube current (in mA)
+protocol.spectrumCallback = "Spectrum"      # name of function that reads and models the X-ray spectrum
+protocol.spectrumFilename = "tungsten_tar7.0_120_filt.dat" # name of the spectrum file
+protocol.spectrumScaling = 1                # scaling factor, works for both mono- and poly-chromatic spectra
+protocol.spectrumUnit_mm = 0                # Is the spectrum file in units of photons/sec/mm^2/<current>?
+protocol.spectrumUnit_mA = 1                # Is the spectrum file in units of photons/sec/<area>/mA?
+protocol.bowtie = "large.txt"               # name of the bowtie file (or [] for no bowtie)
+protocol.filterCallback = "Xray_Filter"     # name of function to compute additional filtration
+protocol.flatFilter = ['Al',3.0]            # additional filtration - materials and thicknesses (in mm)
+protocol.dutyRatio = 1.0                    # tube ON time fraction (for pulsed tubes)
+
+# Pre- and Post-log processes
+protocol.maxPrep = -1                       # set the upper limit of prep, non-positive will disable this feature

gecatsim/cfg/Recon_Default.cfg

@@ -0,0 +1,22 @@
+# Copyright 2024, GE Precision HealthCare. All rights reserved. See https://github.com/xcist/main/tree/master/license
+
+recon.fov = 500.0                       # diameter of the reconstruction field-of-view (in mm)
+recon.imageSize = 512                   # number of columns and rows to be reconstructed (square)
+recon.sliceCount = 1                    # number of slices to reconstruct
+recon.sliceThickness = 1.0              # reconstruction slice thickness AND inter-slice interval (in mm)
+recon.centerOffset = [0.0, 0.0, 0.0]    # reconstruction offset relative to center of rotation (in mm)
+recon.reconType = 'fdk_equiAngle'       # Name of the recon function to call
+recon.kernelType = 'standard'           # 'R-L' for the Ramachandran-Lakshminarayanan (R-L) filter, rectangular window function
+                                        # 'S-L' for the Shepp-Logan (S-L) filter, sinc window function
+                                        # 'soft', 'standard', 'bone' for kernels similar to those on clinical scanners
+recon.startAngle = 0                    # in degrees; 0 is with the X-ray source at the top
+recon.unit = 'HU'                       # '/mm', '/cm', or 'HU'
+recon.mu = 0.02                         # in /mm; typically around 0.02/mm
+recon.huOffset = -1000                  # unit is HU, -1000 HU by definition but sometimes something else is preferable
+recon.printReconParameters = False      # Flag to print the recon parameters
+recon.saveImageVolume = True            # Flag to save recon results as one big file
+recon.saveSingleImages = False          # Flag to save recon results as individual images
+recon.displayImagePictures = False      # Flag to display the recon results as .png images
+recon.saveImagePictureFiles = False     # Flag to save the recon results as .png images
+recon.displayImagePictureAxes = False   # Flag to display the axes on the .png images
+recon.displayImagePictureTitles = False # Flag to display the titles on the .png images

gecatsim/cfg/Scanner_Default.cfg

@@ -0,0 +1,31 @@
+# Scanner geometry
+scanner.detectorCallback = "Detector_ThirdgenCurved" # name of function that defines the detector shape and model
+scanner.sid = 540.0                         # source-to-iso distance (in mm)
+scanner.sdd = 950.0                         # source-to-detector distance (in mm)
+scanner.detectorColsPerMod = 1              # number of detector columns per module
+scanner.detectorRowsPerMod = 16             # number of detector rows per module
+scanner.detectorColOffset = 0.25            # detector column offset relative to centered position (in detector columns)
+scanner.detectorRowOffset = 0.0             # detector row offset relative to centered position (in detector rows)
+scanner.detectorColSize = 1.0               # detector column pitch or size (in mm)
+scanner.detectorRowSize = 1.0               # detector row pitch or size (in mm)
+scanner.detectorColCount = 900              # total number of detector columns
+scanner.detectorRowCount = scanner.detectorRowsPerMod     # total number of detector rows
+scanner.detectorPrefilter = ['graphite', 1.0]  # detector filter
+
+# X-ray tube
+scanner.focalspotCallback = "SetFocalspot"  # name of function that defines the focal spot shape and model
+scanner.focalspotShape = "Gaussian"         # Parameterize the model, defaults to None, needs to be initialized
+scanner.targetAngle = 7.0                   # target angle relative to scanner XY-plane (in degrees)
+scanner.focalspotWidthThreshold = 0.5       # For Gaussian focal spot, at <this number>*max intensity will be scanner.focalspotWidth
+scanner.focalspotLengthThreshold = 0.5
+scanner.focalspotWidth = 1.0                # Fo Uniform focal spot, it's the width; For Gaussian, it's the width at focalspotWidthThreshold*max intensity (in mm)
+scanner.focalspotLength = 1.0
+
+# Detector
+scanner.detectorMaterial = "Lumex"          # detector sensor material
+scanner.detectorDepth = 3.0                 # detector sensor depth (in mm)
+scanner.detectionCallback = "Detection_EI"  # name of function that defines the detection process (conversion from X-rays to detector signal)
+scanner.detectionGain = 17.0                # factor to convert energy to electrons (electrons / keV)
+scanner.detectorColFillFraction = 0.9       # active fraction of each detector cell in the column direction
+scanner.detectorRowFillFraction = 0.9       # active fraction of each detector cell in the row direction
+scanner.eNoise = 3500.0                     # standard deviation of Gaussian electronic noise (in electrons)

gecatsim/clib_build/BuildLinux64

@@ -0,0 +1,6 @@
+# Copyright 2024, GE Precision HealthCare. All rights reserved. See https://github.com/xcist/main/tree/master/license
+
+cd src
+make -j4 -f ../Makefile
+make -f ../Makefile clean
+cd ..

gecatsim/clib_build/BuildWin64.bat

@@ -0,0 +1,17 @@
+ECHO OFF
+REM Copyright 2024, GE Precision HealthCare. All rights reserved. See https://github.com/xcist/main/tree/master/license
+ECHO ON
+
+set PATH=C:\mingw64\bin;%PATH%
+CD src
+
+C:\mingw64\bin\mingw32-make -f ..\MakeWindows64
+move /Y libcatsim64.dll ..\..\lib
+@PAUSE
+
+C:\mingw64\bin\mingw32-make -f ..\MakeWindows64 clean
+
+CD ..
+
+@ECHO Windows build complete
+@PAUSE

gecatsim/clib_build/MakeMacOS

@@ -0,0 +1,48 @@
+# Copyright 2024, GE Precision HealthCare. All rights reserved. See https://github.com/xcist/main/tree/master/license
+
+include ../MakeVariables_1
+include ../MakeVariables_2
+include ../MakeVariables_3
+
+CFLAGS = -fPIC -O3
+CXXFLAGS = -Wall -fPIC -O3
+
+LDFLAGS = -fPIC -lpthread -lstdc++
+
+all: libcatsim_macos.so
+
+p_nlog_inline.o: p_nlog_inline.c
+	#gcc -O0 -g -Wall -static -msse -masm=intel -fPIC -c p_nlog_inline.c
+	# For a Mac OS machine with the M1/M2/M3 chip, remove the "-msse" flag in the line below.
+	/usr/local/opt/gcc/bin/gcc-14 -O0 -g -Wall -static -msse -fPIC -c p_nlog_inline.c
+
+64bitLibrary = libcatsim_macos.so
+
+$(64bitLibrary): $(OBJECTS)
+	@echo ............................................
+	@echo .
+	@echo . Building system-specific library ...
+	@echo .
+	@echo .
+	$(CXX) $(CXXFLAGS) -stdlib=libc++ -std=c11 -o $(64bitLibrary) -shared $(OBJECTS) $(LDFLAGS)
+	mv libcatsim_macos.so ../../lib
+	@echo .
+	@echo .
+	@echo . Done building system-specific library.
+	@echo .
+	@echo ............................................
+
+clean:
+	@echo ............................................
+	@echo .
+	@echo . Cleaning ...
+	@echo .
+	@echo .
+	rm -f *.o
+	@echo .
+	@echo .
+	@echo . Done cleaning.
+	@echo .
+	@echo ............................................
+
+# DO NOT DELETE

gecatsim/clib_build/MakeVariables_1

@@ -0,0 +1,19 @@
+# Copyright 2024, GE Precision HealthCare. All rights reserved. See https://github.com/xcist/main/tree/master/license
+
+CSOURCES = \
+gemsfilt.c \
+pd3dbpsemi.c \
+DD2Back.c \
+DD2Proj.c \
+DD2WBack.c \
+DD3WBack.c \
+pd2dbpcurved.c \
+pd2dbpflat.c \
+extractsino.c \
+viewshift.c \
+spline.c \
+xybowtie.c \
+DD2ParProj.c \
+analytic_projector.c \
+rndpoi.c \
+nCAT_main.c

gecatsim/clib_build/MakeVariables_2

@@ -0,0 +1,5 @@
+# Copyright 2024, GE Precision HealthCare. All rights reserved. See https://github.com/xcist/main/tree/master/license
+
+CSOURCES += \
+fm_gethostid.c \
+fm_getrandpid.c

gecatsim/clib_build/MakeVariables_3

@@ -0,0 +1,33 @@
+# Copyright 2024, GE Precision HealthCare. All rights reserved. See https://github.com/xcist/main/tree/master/license
+
+CPPSOURCES = \
+MatVec.cpp \
+BaseObject.cpp \
+ClipPlane.cpp \
+Transformation.cpp \
+Intersection.cpp \
+TreePhantom.cpp \
+Cube.cpp \
+Sphere.cpp \
+Cylinder.cpp \
+Interpolate.cpp \
+main.cpp \
+Photon.cpp \
+CrossSectionHandler.cpp \
+Volume.cpp \
+Detector.cpp \
+CrossSection.cpp \
+Phantom.cpp \
+DD3Proj.cpp \
+DD3Proj_roi_notrans_mm.cpp \
+voxelized_projector.cpp \
+getMemorySize.cpp \
+negative_log.cpp
+
+OBJECTS = $(patsubst %.cpp,%.o,$(CPPSOURCES))
+OBJECTS += $(patsubst %.c,%.o,$(CSOURCES))
+OBJECTS += phantom.tab.o phantom.lex.o
+
+# use path to user installed gcc instead of simple gcc on mac
+CC = gcc #/usr/local/opt/gcc/bin/gcc-14 
+CXX = g++ #/usr/local/opt/gcc/bin/g++-14

gecatsim/clib_build/MakeVariables_3.1

@@ -0,0 +1,32 @@
+# Copyright 2024, GE Precision HealthCare. All rights reserved. See https://github.com/xcist/main/tree/master/license
+
+CPPSOURCES = \
+MatVec.cpp \
+BaseObject.cpp \
+ClipPlane.cpp \
+Transformation.cpp \
+Intersection.cpp \
+Cube.cpp \
+Sphere.cpp \
+Cylinder.cpp \
+Interpolate.cpp \
+main.cpp \
+Photon.cpp \
+CrossSectionHandler.cpp \
+Volume.cpp \
+Detector.cpp \
+CrossSection.cpp \
+Phantom.cpp \
+DD3Proj.cpp \
+DD3Proj_roi_notrans_mm.cpp \
+voxelized_projector.cpp \
+getMemorySize.cpp \
+negative_log.cpp
+
+OBJECTS = $(patsubst %.cpp,%.o,$(CPPSOURCES))
+OBJECTS += $(patsubst %.c,%.o,$(CSOURCES))
+OBJECTS += phantom.tab.o phantom.lex.o
+
+# use path to user installed gcc instead of simple gcc on mac
+CC = gcc #/usr/local/opt/gcc/bin/gcc-14 
+CXX = g++ #/usr/local/opt/gcc/bin/g++-14

gecatsim/clib_build/MakeWindows64

@@ -0,0 +1,45 @@
+
+all: libcatsim64.dll
+
+include ..\MakeVariables_1
+
+include ..\MakeVariables_3
+
+CXXFLAGS = -O3 -Wall
+CFLAGS = -O3
+
+LFLAGS = -LC:\mingw64\lib -lpthreadGC2_x64
+IFLAGS = -IC:\mingw64\include
+
+p_nlog_inline.o: p_nlog_inline.c
+	gcc -O0 -g -Wall -static -msse -fPIC -c p_nlog_inline.c $(LFLAGS) $(IFLAGS)
+
+
+libcatsim64.dll: $(OBJECTS)
+	@echo ............................................
+	@echo .
+	@echo . Building Windows library ...
+	@echo .
+	@echo .
+	$(CXX) -static-libgcc -static-libstdc++ -o libcatsim64.dll -shared $(OBJECTS) $(LFLAGS) $(IFLAGS)
+	@echo .
+	@echo .
+	@echo .
+	@echo . Done building Windows library.
+	@echo .
+	@echo ............................................
+
+clean:
+	@echo ............................................
+	@echo .
+	@echo . Cleaning ...
+	@echo .
+	@echo .
+	del -f *.o
+	@echo .
+	@echo .
+	@echo . Done cleaning.
+	@echo .
+	@echo ............................................
+
+# DO NOT DELETE

gecatsim/clib_build/Makefile

@@ -0,0 +1,41 @@
+all: libcatsim.so
+
+include ../MakeVariables_1
+include ../MakeVariables_2
+include ../MakeVariables_3
+
+CFLAGS = -fPIC -O3
+CXXFLAGS = -Wall -fPIC -O3
+
+LDFLAGS = -fPIC -lpthread
+
+64bitLibrary = libcatsim.so
+
+libcatsim.so: $(OBJECTS)
+	@echo ............................................
+	@echo .
+	@echo . Building system-specific library ...
+	@echo .
+	@echo .
+	$(CXX) $(CXXFLAGS) -static-libgcc -o $(64bitLibrary) -shared $(OBJECTS) $(LDFLAGS)
+	mv libcatsim.so ../../lib/
+	@echo .
+	@echo .
+	@echo . Done building system-specific library.
+	@echo .
+	@echo ............................................
+
+clean:
+	@echo ............................................
+	@echo .
+	@echo . Cleaning ...
+	@echo .
+	@echo .
+	rm -f *.o
+	@echo .
+	@echo .
+	@echo . Done cleaning.
+	@echo .
+	@echo ............................................
+
+# DO NOT DELETE

gecatsim/clib_build/readme.md

@@ -0,0 +1,13 @@
+# How to compile on Windows
+
+1. unzip `pthreads-2-9-1-release.zip` under `catsim\lib\`
+2. modify lines 10 and 11 in `MakeWindoes64`:
+```
+LFLAGS = -LC:\mingw64\lib -LC:\Users\xxx\software\main-master\catsim\lib -lpthreadGC2_x64
+IFLAGS = -IC:\mingw64\include -IC:\Users\xxx\software\main-master\catsim\lib\Pre-built.2\include
+```
+3. compile using `BuildWin64.bat`
+
+# How to compile on Mac
+
+Due to an issue when running multi-threaded version of ncat projector compiled with `gcc` on mac, we need to first install gcc, then replace `gcc` in `MakeVariable_3` ***and*** `/usr/local/opt/gcc/bin/gcc-14` in MakeMacOS with the path  to real gcc, such as `/usr/local/opt/gcc/bin/gcc-14` and then recompile. Note that the default `gcc` on mac may simply be an alias to `clang`. To verify this, run 'gcc --version' from the command line.

gecatsim/clib_build/src/BaseObject.cpp

@@ -0,0 +1,144 @@
+// Copyright 2020, General Electric Company. All rights reserved. See https://github.com/xcist/code/blob/master/LICENSE
+
+#include "BaseObject.h"
+#include <algorithm>
+
+void BaseObject::WriteVRML(std::ostream& c) {
+}
+
+void BaseObject::PrintMe(std::ostream& c) {
+  c << "Base object data: " << my_ID << "\n";
+  c << "Transform: \n";
+  c << xform;
+  c << "Clipping planes: \n";
+  c << clips;
+  c << "Bounding sphere center: \n";
+  c << boundCenter;
+  c << "\nBounding sphere radius: " << boundRadius << "\n";
+  c << "Material: " << material << "\n";
+  c << "Density: " << density << "\n";
+  c << "Priority: " << priority << "\n";
+}
+
+std::ostream& operator<<(std::ostream& c, BaseObject& p) {
+  p.PrintMe(c);
+  return c;
+}
+
+void BaseObject::UpdateBoundingSphere() {
+  boundRadius = CalculateBoundingRadius()*xform.GetMaxScale();
+  Vec3 iso;
+  boundCenter = xform.Forward(iso);
+  bx = boundCenter.x;
+  by = boundCenter.y;
+  bz = boundCenter.z;
+}
+
+bool BaseObject::BoundarySphereIntersect(float *src, float *direction, float SDD) {
+  bool retval;
+  float x1, y1, z1;
+  float mindist, ip;
+  x1 = src[0] - boundCenter.x;
+  y1 = src[1] - boundCenter.y;
+  z1 = src[2] - boundCenter.z;
+  mindist = x1*x1 + y1*y1 + z1*z1;
+  ip = -(direction[0]*x1+direction[1]*y1+direction[2]*z1);
+  mindist -= ip*ip;
+  retval = ((mindist <= (boundRadius*boundRadius)) && (ip >= 0) && (ip <= SDD));
+  return retval; 
+}
+
+bool BaseObject::Contains(BaseObject* child) {
+  Vec3 tmp;
+  tmp = boundCenter.Subtract(child->boundCenter);
+  double dist;
+  dist = tmp.Norm();
+  return ((dist+child->boundRadius) < boundRadius);
+}
+
+// Calculate the path intersection (includes clipping plane calculations)
+void BaseObject::PathIntersect(float* src, float *direction, IntersectionSet& T) {
+  // Transform the source and unit vector...
+  Vec3 delta(xform.BackwardDelta(Vec3(direction[0],direction[1],direction[2])));
+  Vec3 ct(xform.Backward(Vec3(src[0],src[1],src[2])));
+  // Get the object-path intersection
+  IntersectionSet S;
+  ObjectPathIntersect(ct, delta, S);
+  // Loop over the clip planes
+  for (unsigned i=0;i<clips.size();i++) {
+    clips[i].GetIntersection(Vec3(src[0],src[1],src[2]),Vec3(direction[0],direction[1],direction[2]),S);
+  }
+  // Add these intersections to the master list
+  for (IntersectionSet::iterator j=S.begin(); j!=S.end();j++)
+    T.push_back(*j);
+}
+
+// Calculate a voxel intersection
+IntersectionSet BaseObject::VoxelIntersect(Vec3 src) {
+	return IntersectionSet();
+}
+
+void BaseObject::Material(int str) {
+  material = str;
+}
+
+int BaseObject::Material() {
+  return material;
+}
+
+void BaseObject::Density(double rho) {
+  density = rho;
+}
+
+double BaseObject::Density() {
+  return density;
+}
+
+void BaseObject::Priority(int prio) {
+  priority = prio;
+}
+
+int BaseObject::Priority() {
+  return priority;
+}
+
+void BaseObject::ID(int id) {
+  my_ID = id;
+}
+
+int BaseObject::ID() {
+  return my_ID;
+}
+
+Transformation& BaseObject::Transform() {
+  return xform;
+}
+
+void BaseObject::Transform(Transformation m) {
+  xform = m;
+}
+
+void BaseObject::AddClipPlane(ClipPlane p) {
+  clips.push_back(p);
+}
+
+// Default constructor
+BaseObject::BaseObject() {
+  boundRadius = 0;
+  material = 0;
+  density = 1.0;
+  priority = 0;
+}
+
+BaseObject::~BaseObject() {
+}
+
+Vec3 BaseObject::BoundCenter() {
+  return boundCenter;
+}
+
+double BaseObject::BoundRadius() {
+  return boundRadius;
+}
+
+

gecatsim/clib_build/src/BaseObject.h

@@ -0,0 +1,74 @@
+// Copyright 2020, General Electric Company. All rights reserved. See https://github.com/xcist/code/blob/master/LICENSE
+
+#ifndef BaseObject_h
+#define BaseObject_h
+
+#include <vector>
+#include <iostream>
+#include "MatVec.h"
+#include "Transformation.h"
+#include "ClipPlane.h"
+#include "Intersection.h"
+
+class BaseObject {
+ protected:
+  Transformation xform;
+  ClipPlaneSet clips;
+  int my_ID;
+  int material;
+  double density;
+  int priority;
+  Vec3 boundCenter;
+ public:
+  double boundRadius;
+  float bx, by, bz;
+  // Describe me in VRML syntax
+  virtual void WriteVRML(std::ostream& c);
+  // Describe me to stdout
+  virtual void PrintMe(std::ostream& c);
+  // Calculate the object-path intersection
+  virtual void ObjectPathIntersect(Vec3 src, Vec3 delta, IntersectionSet& T) = 0;
+  // Calculate the object-voxel intersection
+  virtual IntersectionSet ObjectVoxelIntersect(Vec3 src, Vec3 det) = 0;
+  // Returns the bounding radius for this object
+  virtual double CalculateBoundingRadius() = 0;
+  // Updates our bounding sphere calculation
+  void UpdateBoundingSphere();
+  // Test for containment of the bounding boxes
+  bool Contains(BaseObject* child);
+  // Perform the boundary box test
+  bool BoundarySphereIntersect(float *src, float *direction, float SDD);
+  // Calculate the path intersection (includes clipping plane calculations)
+  void PathIntersect(float* src, float* direction, IntersectionSet& T);
+  // Calculate a voxel intersection
+  IntersectionSet VoxelIntersect(Vec3 src);
+  // Set/Get the object material
+  int Material();
+  void Material(int);
+  // Set/Get the density of the object
+  void Density(double rho);
+  double Density(void);
+  // Set/Get the priority of the object
+  void Priority(int prio);
+  int Priority(void);
+  // Set/Get the ID of the object
+  void ID(int id);
+  int ID(void);
+  // Set/Get the objects transform
+  Transformation& Transform();
+  void Transform(Transformation m);
+  // Add a clipping plane (specified by a normal, a minimum distance to the origin, and a point inside the clipping region
+  void AddClipPlane(ClipPlane p);
+  Vec3 BoundCenter();
+  double BoundRadius();
+  // Default constructor
+  BaseObject();
+  virtual ~BaseObject();
+};
+
+typedef std::vector<std::string> MaterialTable;
+
+std::ostream& operator<<(std::ostream& c, BaseObject& p);
+std::ostream& operator<<(std::ostream& c, MaterialTable& p);
+#endif
+