From 3df2d0b46d75b796f2d0aeabdd78d60932d884ef Mon Sep 17 00:00:00 2001 From: "Kevin M. Rosenberg" Date: Sat, 27 Jan 2001 04:17:04 +0000 Subject: [PATCH] r449: Broken .tex file into chapters --- doc/tex2rtf/ctsim-gui.tex | 14 ++ doc/tex2rtf/ctsim-install.tex | 49 ++++++ doc/tex2rtf/ctsim-textui.tex | 210 ++++++++++++++++++++++++ doc/tex2rtf/ctsim-web.tex | 20 +++ doc/tex2rtf/ctsim.tex | 295 +--------------------------------- 5 files changed, 297 insertions(+), 291 deletions(-) create mode 100644 doc/tex2rtf/ctsim-gui.tex create mode 100644 doc/tex2rtf/ctsim-install.tex create mode 100644 doc/tex2rtf/ctsim-textui.tex create mode 100644 doc/tex2rtf/ctsim-web.tex diff --git a/doc/tex2rtf/ctsim-gui.tex b/doc/tex2rtf/ctsim-gui.tex new file mode 100644 index 0000000..99bc69d --- /dev/null +++ b/doc/tex2rtf/ctsim-gui.tex @@ -0,0 +1,14 @@ +\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...] + diff --git a/doc/tex2rtf/ctsim-install.tex b/doc/tex2rtf/ctsim-install.tex new file mode 100644 index 0000000..c5cb08d --- /dev/null +++ b/doc/tex2rtf/ctsim-install.tex @@ -0,0 +1,49 @@ +\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} + diff --git a/doc/tex2rtf/ctsim-textui.tex b/doc/tex2rtf/ctsim-textui.tex new file mode 100644 index 0000000..3826c49 --- /dev/null +++ b/doc/tex2rtf/ctsim-textui.tex @@ -0,0 +1,210 @@ +\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} diff --git a/doc/tex2rtf/ctsim-web.tex b/doc/tex2rtf/ctsim-web.tex new file mode 100644 index 0000000..b6ccb31 --- /dev/null +++ b/doc/tex2rtf/ctsim-web.tex @@ -0,0 +1,20 @@ +\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}. + +\section{Requirements}\index{Web Interface,Requirements}% + \begin{itemize}\itemsep=0pt + \item Apache or other CGI compatible web server + + \item Perl (version 4.0 or higher) + + \item A client web browser than can display PNG files. Most + current web browsers support PNG. + \end{itemize} diff --git a/doc/tex2rtf/ctsim.tex b/doc/tex2rtf/ctsim.tex index bda68ad..6b42f8d 100644 --- a/doc/tex2rtf/ctsim.tex +++ b/doc/tex2rtf/ctsim.tex @@ -79,300 +79,13 @@ The \ctsim package has two executable files: the graphical \helprefn{ctsim}{ctsi \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 -- 2.34.1