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\BOOKMARK [0][-]{chapter.1}{Introduction}{}
\BOOKMARK [0][-]{chapter.2}{Concepts}{}
\BOOKMARK [1][-]{section.2.1}{Conceptual Overview}{chapter.2}
\BOOKMARK [1][-]{section.2.2}{Phantoms}{chapter.2}
\BOOKMARK [2][-]{subsection.2.2.1}{Phantom File}{section.2.2}
\BOOKMARK [2][-]{subsection.2.2.2}{Phantom Elements}{section.2.2}
\BOOKMARK [2][-]{subsection.2.2.3}{Phantom Size}{section.2.2}
\BOOKMARK [1][-]{section.2.3}{Scanner}{chapter.2}
\BOOKMARK [2][-]{subsection.2.3.1}{Dimensions}{section.2.3}
\BOOKMARK [2][-]{subsection.2.3.2}{Parallel Geometry}{section.2.3}
\BOOKMARK [2][-]{subsection.2.3.3}{Divergent Geometries}{section.2.3}
\BOOKMARK [1][-]{section.2.4}{Reconstruction}{chapter.2}
\BOOKMARK [2][-]{subsection.2.4.1}{Direct Inverse Fourier}{section.2.4}
\BOOKMARK [2][-]{subsection.2.4.2}{Filtered Backprojection}{section.2.4}
\BOOKMARK [1][-]{section.2.5}{Image Comparison}{chapter.2}
\BOOKMARK [0][-]{chapter.3}{The Graphical User Interface}{}
\BOOKMARK [1][-]{section.3.1}{Starting CTSim}{chapter.3}
\BOOKMARK [1][-]{section.3.2}{Quick Start}{chapter.3}
\BOOKMARK [1][-]{section.3.3}{File Types}{chapter.3}
\BOOKMARK [2][-]{subsection.3.3.1}{Phantom}{section.3.3}
\BOOKMARK [2][-]{subsection.3.3.2}{Image}{section.3.3}
\BOOKMARK [2][-]{subsection.3.3.3}{Projection}{section.3.3}
\BOOKMARK [2][-]{subsection.3.3.4}{Plot}{section.3.3}
\BOOKMARK [1][-]{section.3.4}{Global Menu Commands}{chapter.3}
\BOOKMARK [2][-]{subsection.3.4.1}{File - Create Phantom}{section.3.4}
\BOOKMARK [2][-]{subsection.3.4.2}{File - Create Filter}{section.3.4}
\BOOKMARK [2][-]{subsection.3.4.3}{File - Import}{section.3.4}
\BOOKMARK [2][-]{subsection.3.4.4}{File - Preferences}{section.3.4}
\BOOKMARK [2][-]{subsection.3.4.5}{File - Open}{section.3.4}
\BOOKMARK [2][-]{subsection.3.4.6}{File - Save}{section.3.4}
\BOOKMARK [2][-]{subsection.3.4.7}{File - Close}{section.3.4}
\BOOKMARK [2][-]{subsection.3.4.8}{File - Save As}{section.3.4}
\BOOKMARK [2][-]{subsection.3.4.9}{Help - Contents}{section.3.4}
\BOOKMARK [2][-]{subsection.3.4.10}{Help - Tips}{section.3.4}
\BOOKMARK [2][-]{subsection.3.4.11}{Help - Quick Start}{section.3.4}
\BOOKMARK [2][-]{subsection.3.4.12}{Help - About}{section.3.4}
\BOOKMARK [1][-]{section.3.5}{Phantom Menus}{chapter.3}
\BOOKMARK [2][-]{subsection.3.5.1}{Properties}{section.3.5}
\BOOKMARK [2][-]{subsection.3.5.2}{Process - Rasterize}{section.3.5}
\BOOKMARK [2][-]{subsection.3.5.3}{Process - Projections}{section.3.5}
\BOOKMARK [1][-]{section.3.6}{Image Menus}{chapter.3}
\BOOKMARK [2][-]{subsection.3.6.1}{File - Properties}{section.3.6}
\BOOKMARK [2][-]{subsection.3.6.2}{File - Export}{section.3.6}
\BOOKMARK [2][-]{subsection.3.6.3}{View}{section.3.6}
\BOOKMARK [2][-]{subsection.3.6.4}{Image}{section.3.6}
\BOOKMARK [2][-]{subsection.3.6.5}{Filter}{section.3.6}
\BOOKMARK [2][-]{subsection.3.6.6}{Analyze - Plot}{section.3.6}
\BOOKMARK [2][-]{subsection.3.6.7}{Analyze - Compare}{section.3.6}
\BOOKMARK [1][-]{section.3.7}{Projection Menus}{chapter.3}
\BOOKMARK [2][-]{subsection.3.7.1}{File - Properties}{section.3.7}
\BOOKMARK [2][-]{subsection.3.7.2}{Process - Convert Rectangular}{section.3.7}
\BOOKMARK [2][-]{subsection.3.7.3}{Process - Convert Polar}{section.3.7}
\BOOKMARK [2][-]{subsection.3.7.4}{Convert - Convert FFT Polar}{section.3.7}
\BOOKMARK [2][-]{subsection.3.7.5}{Convert - Interpolate to Parallel}{section.3.7}
\BOOKMARK [2][-]{subsection.3.7.6}{Analyze - Plot Histogram}{section.3.7}
\BOOKMARK [2][-]{subsection.3.7.7}{Analyze - Plot T-Theta Sampling}{section.3.7}
\BOOKMARK [2][-]{subsection.3.7.8}{Reconstruct - Filtered Backprojection}{section.3.7}
\BOOKMARK [2][-]{subsection.3.7.9}{Reconstruct - Filtered Backprojection \(Rebin to Parallel\)}{section.3.7}
\BOOKMARK [1][-]{section.3.8}{Plot Menus}{chapter.3}
\BOOKMARK [2][-]{subsection.3.8.1}{File - Properties}{section.3.8}
\BOOKMARK [2][-]{subsection.3.8.2}{View Menu}{section.3.8}
\BOOKMARK [0][-]{chapter.4}{The Command Line Interface}{}
\BOOKMARK [1][-]{section.4.1}{Starting ctsimtext}{chapter.4}
\BOOKMARK [1][-]{section.4.2}{Parallel Processing}{chapter.4}
\BOOKMARK [1][-]{section.4.3}{if1}{chapter.4}
\BOOKMARK [1][-]{section.4.4}{if2}{chapter.4}
\BOOKMARK [1][-]{section.4.5}{ifexport}{chapter.4}
\BOOKMARK [1][-]{section.4.6}{ifinfo}{chapter.4}
\BOOKMARK [1][-]{section.4.7}{phm2pj}{chapter.4}
\BOOKMARK [1][-]{section.4.8}{phm2if}{chapter.4}
\BOOKMARK [1][-]{section.4.9}{pj2if}{chapter.4}
\BOOKMARK [1][-]{section.4.10}{pjinfo}{chapter.4}
\BOOKMARK [1][-]{section.4.11}{pjrec}{chapter.4}
\BOOKMARK [0][-]{chapter.5}{The Web Interface}{}
\BOOKMARK [1][-]{section.5.1}{Overview}{chapter.5}
\BOOKMARK [1][-]{section.5.2}{Requirements}{chapter.5}
\BOOKMARK [1][-]{section.5.3}{Installation}{chapter.5}
\BOOKMARK [0][-]{chapter.6}{Installation}{}
\BOOKMARK [1][-]{section.6.1}{Download}{chapter.6}
\BOOKMARK [1][-]{section.6.2}{Installing Windows Binary}{chapter.6}
\BOOKMARK [1][-]{section.6.3}{Installing Linux RPM}{chapter.6}
\BOOKMARK [1][-]{section.6.4}{Build From Sources}{chapter.6}
\BOOKMARK [2][-]{subsection.6.4.1}{Optional Libraries}{section.6.4}
\BOOKMARK [0][-]{appendix.A}{Algorithms}{}
\BOOKMARK [1][-]{section.A.1}{Phantom Processing}{appendix.A}
\BOOKMARK [1][-]{section.A.2}{Background Processing}{appendix.A}
\BOOKMARK [2][-]{subsection.A.2.1}{Advantages}{section.A.2}
\BOOKMARK [2][-]{subsection.A.2.2}{Disadvantages}{section.A.2}
\BOOKMARK [0][-]{appendix.B}{Simple Graphics Package}{}
\BOOKMARK [1][-]{section.B.1}{Transformation Sequence}{appendix.B}
\BOOKMARK [1][-]{section.B.2}{Functions}{appendix.B}
\BOOKMARK [2][-]{subsection.B.2.1}{Master coordinate functions}{section.B.2}
\BOOKMARK [2][-]{subsection.B.2.2}{Normalized coordinate functions}{section.B.2}
\BOOKMARK [2][-]{subsection.B.2.3}{Master coordinate to World coordinate transformations}{section.B.2}
\BOOKMARK [2][-]{subsection.B.2.4}{Coordinate transformation functions}{section.B.2}
\BOOKMARK [2][-]{subsection.B.2.5}{State functions}{section.B.2}
\BOOKMARK [1][-]{section.B.3}{Coordinate Mapping}{appendix.B}
\BOOKMARK [2][-]{subsection.B.3.1}{Dimensions}{section.B.3}
\BOOKMARK [2][-]{subsection.B.3.2}{Formulas}{section.B.3}
\BOOKMARK [0][-]{appendix*.32}{Bibliography}{}
\BOOKMARK [0][-]{appendix*.32}{Index}{}
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