--- /dev/null
+\chapter{Installation}\index{Installation}%
+\setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
+\setfooter{\thepage}{}{}{}{}{\thepage}%
+
+\section{Download}\label{download}\index{Installation,Download}%
+
+The latest version of CTSim, plus source code, can be accessed from:
+
+\begin{verbatim}
+http://www.ctsim.org
+ftp://ftp.ctsim.org
+\end{verbatim}
+
+It is available in Windows 95/NT/2000 and Linux GUI versions and non-GUI versions.
+
+\section{Installing Linux RPM}\index{Installation,Linux}%
+
+\section{Installing Windows Binary}\index{Installation,Windows}%
+
+\section{Build From Sources}\label{build}\index{Installation,Build}%
+
+See the INSTALL file included in the source distribution for instructions.
+
+\section{Web Requirements}\label{installreq}\index{Installation,Requirements}%
+ \begin{itemize}\itemsep=0pt
+ \item zlib Library (optional)
+ \par Used for PNG file export.
+
+ \item libpng Library (optional)
+ \par Used for PNG file export.
+ \par www.libpng.org
+
+ \item FFTW library (optional)
+ \par Used for frequency-based filtering and fourier transformations of images.
+ \par www.fftw.org
+
+ \item readline library (optional)
+ \par Used for \ctsimtext interactive shell.
+
+ \item dmalloc library (optional)
+ \par Used for debugging memory allocation
+ \par www.dmalloc.com
+
+ \item wxWindows library (optional)
+ \par Used for platform-independent graphical interface. The graphical-shell
+ program \ctsim requires this library.
+ \par www.wxwindows.org
+\end{itemize}
+
--- /dev/null
+\chapter{ctsimtext}\label{ctsimtext}\index{ctsimtext}%
+\setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
+\setfooter{\thepage}{}{}{}{}{\thepage}%
+
+\ctsimtext is a master shell for all of the command-line utilities.
+
+\usage
+\ctsimtext can be executed without any parameters. In that case, \ctsimtext
+offers a command-line to enter the function-names and their parameters. The output of the command is displayed. Further commands may be given to \ctsimtext. The shell is exited by the {\tt quit} command.
+
+\ctsimtext can also be called to execute a single command. This is especially useful for batch files containing multiple \ctsimtext commands. This is invoked by calling \par
+{\tt ctsimtext function-name parameters...}.
+
+The available functions are:
+
+\section{if1}\label{if1}\index{ctsimtext,if1}%
+Perfoms math functions on a single image.
+
+\usage
+\begin{itemize}\itemsep=0pt
+ \item --invert
+ \item --log
+ \item --exp
+ \item --sqr
+ \item --sqrt
+\end{itemize}
+
+\section{if2}\label{if2}\index{ctsimtext,if2}%
+Perfoms math functions on a two images.
+
+\usage
+\begin{itemize}\itemsep=0pt
+ \item --add
+ \item --sub
+ \item --mul
+ \item --comp
+ \item --column-plot
+ \item --row-plot
+\end{itemize}
+
+\section{ifexport}\label{ifexport}\index{ctsimtext,ifexport}%
+Export an imagefile to a standard graphics file.
+
+\usage
+\begin{itemize}\itemsep=0pt
+ \item --format
+ \begin{itemize}\itemsep=0pt
+ \item --pgm
+ \item --pgmasc
+ \item --png
+ \item --png16
+ \end{itemize}
+ \item --center
+ \begin{itemize}\itemsep=0pt
+ \item median
+ \item mode
+ \item mean
+ \end{itemize}
+ \item --auto
+ \begin{itemize}\itemsep=0pt
+ \item --full
+ \item --std0.1
+ \item --std0.5
+ \item --std1
+ \item --std2
+ \item --std3
+ \end{itemize}
+ \item --scale
+ \item --min
+ \item --max
+\end{itemize}
+
+\section{ifinfo}\label{ifinfo}\index{ctsimtext,ifinfo}%
+
+Displays information about an imagefile.
+
+\usage
+\begin{itemize}\itemsep=0pt
+ \item --labels
+ \item --no-labels
+ \item --stats
+ \item --no-stats
+ \item --help
+\end{itemize}
+
+\section{phm2pj}\label{phm2pj}\index{ctsimtext,phm2pj}%
+Simulates collection of X-rays data (projections) around a phantom object.
+
+\usage
+phm2pj projection-file-name number-of-detectors number-of-views [options...]
+\begin{itemize}\itemsep=0pt
+ \item --phantom
+ Select a standard phantom
+ \begin{itemize}\itemsep=0pt
+ \item herman
+ \item herman-b
+ \item shepp-logan
+ \item shepp-logan-b
+ \end{itemize}
+
+ \item --phmfile
+ Load a phantom definition definition
+
+ \item --geometry
+ \begin{itemize}\itemsep=0pt
+ \item parallel
+ \item equiangular
+ \item equilinear
+ \end{itemize}
+
+ \item --nray
+ Number of samples per each detector
+
+ \item --rotangle
+ Sets the rotation amount as a multiple of pi. For parallel geometries use
+a rotation angle of 1 and for equilinear and equiangular geometries use a rotation angle of 2.
+
+ \item --field-of-view
+ Sets the field of view as a ratio of the diameter of the phantom. For parallel geometries, using a value of 1.0 is fine. For other geometies, this should be at least 1.3 to avoid artifacts.
+
+ \item --focal-length
+ Sets the distance of the radiation source and detectors from the center of the object as a ratio of the radius of the object. For parallel geometries, a value of 1.0 is fine. For other geometries, this should be at least 2.0 to avoid artifacts.
+\end{itemize}
+
+The Herman phantom is taken with permission from Gabor Hermans 1980 book\cite{HERMAN80}. The Shepp-Logan phantom was published in 1974\cite{SHEPP74}.
+
+\section{phm2if}\label{phm2if}\index{ctsimtext,phm2if}%
+Converts a geometric phantom object into an imagefile. The size of the
+imagefile in pixels must be specified as well as the number of samples
+to average per pixel.
+
+\usage
+\begin{itemize}\itemsep=0pt
+ \item --nsamples
+\end{itemize}
+
+\section{pj2if}\label{pj2if}\index{ctsimtext,pj2if}%
+Convert a projection file into an imagefile.
+
+\usage
+\begin{itemize}\itemsep=0pt
+\item --help Print brief online help
+\end{itemize}
+
+\section{pjinfo}\label{pjinfo}\index{ctsimtext,pjinfo}%
+Displays information about a projection file.
+
+\usage
+\begin{itemize}\itemsep=0pt
+ \item --binaryheader
+ \item --binaryview
+ \item --startview
+ \item --endview
+ \item --dump
+\end{itemize}
+
+\section{pjrec}\label{pjrec}\index{ctsimtext,pjrec}%
+Reconstructs the interior of an object from a projection file.
+
+\usage
+\begin{twocollist}
+\twocolitemruled{{\bf Parameter}}{{\bf Options}}
+\twocolitem{{\bf --filter}}
+{Selects which filter to apply to each projection. To properly reconstruct an image, this filter should be multiplied
+by the absolute value of distance from zero frequency.
+\begin{itemize}\itemsep=0pt
+\item abs\_bandlimit
+\item abs\_cosine
+\item abs\_hamming
+\end{itemize}
+}
+\twocolitem{{\bf --filter-parameter}}{Sets the alpha level for Hamming
+ window. At setting of 0.54, this equals the Hanning window.}
+
+\twocolitem{{\bf --filter-method}}{Selects the filtering method. For large numbers of detectors, {\tt rfftw} is optimal. For smaller numbers of detectors, {\tt convolution} might be a bit faster.
+\begin{itemize}\itemsep=0pt
+\item convolution
+\item fourier
+\item fourier\_table
+\item fftw
+\item rfftw
+\end{itemize}
+}
+
+\twocolitem{{\bf --filter-generation}}{Selects the filter generation. With convolution, {\tt direct} is the proper method to select. With any of the frequency methods, {\tt inverse-fourier} is the best method.
+\begin{itemize}\itemsep=0pt
+\item direct
+\item inverse-fourier
+\end{itemize}
+}
+\twocolitem{{\bf --interpolation}}{Interpolation technique. {\tt linear} is optimal.
+\begin{itemize}\itemsep=0pt
+\item nearest
+\item linear
+\end{itemize}
+}
+ \twocolitem{{\bf -backprojection}}{Selects the backprojection technique. A setting of {\tt idiff3} is optimal.
+\begin{itemize}\itemsep=0pt
+\item trig
+\item table
+\item diff
+\item diff2
+\item idiff2
+\item idiff3
+\end{itemize}
+}
+\twocolitem{{\bf --zeropad}}{ Zeropad factor. A setting of {\tt 1} is optimal.}
+
+\twocolitem{{\bf --preinterpolate}}{Selects preinterpolation interpolation technique and sets the preinterpolation factor. Currently, this is experimental and does not work well.}
+\end{twocollist}
\include{ctsim-concepts}
-\chapter{Installation}\index{Installation}%
-\setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
-\setfooter{\thepage}{}{}{}{}{\thepage}%
-
-\section{Download}\label{download}\index{Installation,Download}%
-
-The latest version of CTSim, plus source code, can be accessed from:
-
-\begin{verbatim}
-http://www.ctsim.org
-ftp://ftp.ctsim.org
-\end{verbatim}
-
-It is available in Windows 95/NT/2000 and Linux GUI versions and non-GUI versions.
-
-\section{Installing Linux RPM}\index{Installation,Linux}%
-
-\section{Installing Windows Binary}\index{Installation,Windows}%
-
-\section{Build From Sources}\label{build}\index{Installation,Build}%
-
-See the INSTALL file included in the source distribution for instructions.
-
-\section{Web Requirements}\label{installreq}\index{Installation,Requirements}%
- \begin{itemize}\itemsep=0pt
- \item zlib Library (optional)
- \par Used for PNG file export.
-
- \item libpng Library (optional)
- \par Used for PNG file export.
- \par www.libpng.org
-
- \item FFTW library (optional)
- \par Used for frequency-based filtering and fourier transformations of images.
- \par www.fftw.org
-
- \item readline library (optional)
- \par Used for \ctsimtext interactive shell.
-
- \item dmalloc library (optional)
- \par Used for debugging memory allocation
- \par www.dmalloc.com
-
- \item wxWindows library (optional)
- \par Used for platform-independent graphical interface. The graphical-shell
- program \ctsim requires this library.
- \par www.wxwindows.org
-\end{itemize}
-
-\chapter{ctsim - the Graphical User Interface}\label{ctsim}\index{ctsim}%
-\setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
-\setfooter{\thepage}{}{}{}{}{\thepage}%
-
-\ctsim is the graphical shell for the CTSim project. It is
-written using the wxLibrary for cross-platform compatibility with GTK,
-Motif, and Microsoft Windows. It includes all of the functionality of
-the command-line tool {\tt ctsimtext} as well as image processing and visualization features.
-
-\ctsim can open projection files, image files, phantom definition files, and plotfiles.
-
-\usage
-ctsim [OPTIONS] [files to open...]
-
-\chapter{ctsimtext}\label{ctsimtext}\index{ctsimtext}%
-\setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
-\setfooter{\thepage}{}{}{}{}{\thepage}%
-
-\ctsimtext is a master shell for all of the command-line utilities.
-
-\usage
-\ctsimtext can be executed without any parameters. In that case, \ctsimtext
-offers a command-line to enter the function-names and their parameters. The output of the command is displayed. Further commands may be given to \ctsimtext. The shell is exited by the {\tt quit} command.
-
-\ctsimtext can also be called to execute a single command. This is especially useful for batch files containing multiple \ctsimtext commands. This is invoked by calling \par
-{\tt ctsimtext function-name parameters...}.
-
-The available functions are:
-
-\section{if1}\label{if1}\index{ctsimtext,if1}%
-Perfoms math functions on a single image.
-
-\usage
-\begin{itemize}\itemsep=0pt
- \item --invert
- \item --log
- \item --exp
- \item --sqr
- \item --sqrt
-\end{itemize}
-
-\section{if2}\label{if2}\index{ctsimtext,if2}%
-Perfoms math functions on a two images.
-
-\usage
-\begin{itemize}\itemsep=0pt
- \item --add
- \item --sub
- \item --mul
- \item --comp
- \item --column-plot
- \item --row-plot
-\end{itemize}
-
-\section{ifexport}\label{ifexport}\index{ctsimtext,ifexport}%
-Export an imagefile to a standard graphics file.
-
-\usage
-\begin{itemize}\itemsep=0pt
- \item --format
- \begin{itemize}\itemsep=0pt
- \item --pgm
- \item --pgmasc
- \item --png
- \item --png16
- \end{itemize}
- \item --center
- \begin{itemize}\itemsep=0pt
- \item median
- \item mode
- \item mean
- \end{itemize}
- \item --auto
- \begin{itemize}\itemsep=0pt
- \item --full
- \item --std0.1
- \item --std0.5
- \item --std1
- \item --std2
- \item --std3
- \end{itemize}
- \item --scale
- \item --min
- \item --max
-\end{itemize}
-
-\section{ifinfo}\label{ifinfo}\index{ctsimtext,ifinfo}%
-
-Displays information about an imagefile.
-
-\usage
-\begin{itemize}\itemsep=0pt
- \item --labels
- \item --no-labels
- \item --stats
- \item --no-stats
- \item --help
-\end{itemize}
-
-\section{phm2pj}\label{phm2pj}\index{ctsimtext,phm2pj}%
-Simulates collection of X-rays data (projections) around a phantom object.
-
-\usage
-phm2pj projection-file-name number-of-detectors number-of-views [options...]
-\begin{itemize}\itemsep=0pt
- \item --phantom
- Select a standard phantom
- \begin{itemize}\itemsep=0pt
- \item herman
- \item herman-b
- \item shepp-logan
- \item shepp-logan-b
- \end{itemize}
-
- \item --phmfile
- Load a phantom definition definition
-
- \item --geometry
- \begin{itemize}\itemsep=0pt
- \item parallel
- \item equiangular
- \item equilinear
- \end{itemize}
-
- \item --nray
- Number of samples per each detector
-
- \item --rotangle
- Sets the rotation amount as a multiple of pi. For parallel geometries use
-a rotation angle of 1 and for equilinear and equiangular geometries use a rotation angle of 2.
-
- \item --field-of-view
- Sets the field of view as a ratio of the diameter of the phantom. For parallel geometries, using a value of 1.0 is fine. For other geometies, this should be at least 1.3 to avoid artifacts.
-
- \item --focal-length
- Sets the distance of the radiation source and detectors from the center of the object as a ratio of the radius of the object. For parallel geometries, a value of 1.0 is fine. For other geometries, this should be at least 2.0 to avoid artifacts.
-\end{itemize}
-
-The Herman phantom is taken with permission from Gabor Hermans 1980 book\cite{HERMAN80}. The Shepp-Logan phantom was published in 1974\cite{SHEPP74}.
-
-\section{phm2if}\label{phm2if}\index{ctsimtext,phm2if}%
-Converts a geometric phantom object into an imagefile. The size of the
-imagefile in pixels must be specified as well as the number of samples
-to average per pixel.
-
-\usage
-\begin{itemize}\itemsep=0pt
- \item --nsamples
-\end{itemize}
-
-\section{pj2if}\label{pj2if}\index{ctsimtext,pj2if}%
-Convert a projection file into an imagefile.
-
-\usage
-\begin{itemize}\itemsep=0pt
-\item --help Print brief online help
-\end{itemize}
-
-\section{pjinfo}\label{pjinfo}\index{ctsimtext,pjinfo}%
-Displays information about a projection file.
-
-\usage
-\begin{itemize}\itemsep=0pt
- \item --binaryheader
- \item --binaryview
- \item --startview
- \item --endview
- \item --dump
-\end{itemize}
-
-\section{pjrec}\label{pjrec}\index{ctsimtext,pjrec}%
-Reconstructs the interior of an object from a projection file.
-
-\usage
-\begin{twocollist}
-\twocolitemruled{{\bf Parameter}}{{\bf Options}}
-\twocolitem{{\bf --filter}}
-{Selects which filter to apply to each projection. To properly reconstruct an image, this filter should be multiplied
-by the absolute value of distance from zero frequency.
-\begin{itemize}\itemsep=0pt
-\item abs\_bandlimit
-\item abs\_cosine
-\item abs\_hamming
-\end{itemize}
-}
-\twocolitem{{\bf --filter-parameter}}{Sets the alpha level for Hamming
- window. At setting of 0.54, this equals the Hanning window.}
-
-\twocolitem{{\bf --filter-method}}{Selects the filtering method. For large numbers of detectors, {\tt rfftw} is optimal. For smaller numbers of detectors, {\tt convolution} might be a bit faster.
-\begin{itemize}\itemsep=0pt
-\item convolution
-\item fourier
-\item fourier\_table
-\item fftw
-\item rfftw
-\end{itemize}
-}
-
-\twocolitem{{\bf --filter-generation}}{Selects the filter generation. With convolution, {\tt direct} is the proper method to select. With any of the frequency methods, {\tt inverse-fourier} is the best method.
-\begin{itemize}\itemsep=0pt
-\item direct
-\item inverse-fourier
-\end{itemize}
-}
-\twocolitem{{\bf --interpolation}}{Interpolation technique. {\tt linear} is optimal.
-\begin{itemize}\itemsep=0pt
-\item nearest
-\item linear
-\end{itemize}
-}
- \twocolitem{{\bf -backprojection}}{Selects the backprojection technique. A setting of {\tt idiff3} is optimal.
-\begin{itemize}\itemsep=0pt
-\item trig
-\item table
-\item diff
-\item diff2
-\item idiff2
-\item idiff3
-\end{itemize}
-}
-\twocolitem{{\bf --zeropad}}{ Zeropad factor. A setting of {\tt 1} is optimal.}
-
-\twocolitem{{\bf --preinterpolate}}{Selects preinterpolation interpolation technique and sets the preinterpolation factor. Currently, this is experimental and does not work well.}
-\end{twocollist}
-
-\chapter{The Web Browser CGI Interface}\label{webinterface}\index{Web Interface}%
-\setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
-\setfooter{\thepage}{}{}{}{}{\thepage}%
-
-\section{Overview}\index{Web Interface,Overview}%
-The CGI program {\tt ctsim.cgi} takes projections of a standard
-phantom object, performs reconstruction, and then compares the
-rasterized phantom object with the reconstruction. The comparison is
-performed both visually by an image subtraction as well as by standard
-statistics as described by Herman\cite{HERMAN80}.
+\include{ctsim-install}
-\section{Requirements}\index{Web Interface,Requirements}%
- \begin{itemize}\itemsep=0pt
- \item Apache or other CGI compatible web server
+\include{ctsim-gui}
- \item Perl (version 4.0 or higher)
+\include{ctsim-textui}
- \item A client web browser than can display PNG files. Most
- current web browsers support PNG.
- \end{itemize}
+\include{ctsim-web}
\newpage
projects / ctsim.git / commitdiff