1 \documentclass[11pt]{report}%
4 \usepackage{fancyheadings}
12 \newcommand{\ctsim}{{\tt CTSim}}
13 \newcommand{\ctsimtext}{{\tt CTSimText}}
14 \newcommand{\usage}{{\bf Usage}{\par}}
16 \newcommand{\commandref}[2]{\helpref{{\tt $\backslash$#1}}{#2}}%
17 \newcommand{\commandrefn}[2]{\helprefn{{\tt $\backslash$#1}}{#2}\index{#1}}%
18 \newcommand{\commandpageref}[2]{\latexignore{\helprefn{{\tt $\backslash$#1}}{#2}}\latexonly{{\tt $\backslash$#1} {\it page \pageref{#2}}}\index{#1}}%
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20 \newcommand{\inioption}[1]{{\bf {\tt #1}}\index{#1}}%
23 %\backgroundcolour{255;255;255}\textcolour{0;0;0}% Has an effect in HTML only
24 \winhelpignore{\title{Manual for CTSim 3.0}%
25 \author{Kevin Rosenberg, M.D.}%
28 \winhelponly{\title{Manual for CTSim 3.0}%
29 \author{by Kevin Rosenberg, M.D.\\$$\image{3cm;3cm}{logo-huge.bmp}$$}%
34 \pagestyle{fancyplain}%
35 \bibliographystyle{plain}%
36 \pagenumbering{roman}%
38 \setheader{{\it CONTENTS}}{}{}{}{}{{\it CONTENTS}}%
39 \setfooter{\thepage}{}{}{}{}{\thepage}%
42 \chapter*{Copyright notice}%
43 \setheader{{\it COPYRIGHT}}{}{}{}{}{{\it COPYRIGHT}}%
44 \setfooter{\thepage}{}{}{}{}{\thepage}%
46 Copyright (c) 1983-2001 Kevin Rosenberg, M.D.
48 Permission to use, copy, modify, and distribute this software and its
49 documentation for any purpose is hereby granted without fee, provided that the
50 above copyright notice, author statement and this permission notice appear in
51 all copies of this software and related documentation.
53 THE SOFTWARE IS PROVIDED ``AS-IS'' AND WITHOUT WARRANTY OF ANY KIND, EXPRESS,
54 IMPLIED OR OTHERWISE, INCLUDING WITHOUT LIMITATION, ANY WARRANTY OF
55 MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.
57 IN NO EVENT SHALL KEVIN ROSENBERG BE LIABLE FOR ANY
58 SPECIAL, INCIDENTAL, INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND, OR
59 ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS,
60 WHETHER OR NOT ADVISED OF THE POSSIBILITY OF DAMAGE, AND ON ANY THEORY
61 OF LIABILITY, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
62 PERFORMANCE OF THIS SOFTWARE.
64 \chapter{Introduction}\label{introduction}%
65 \pagenumbering{arabic}%
66 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
67 \setfooter{\thepage}{}{}{}{}{\thepage}%
69 \winhelponly{$$\image{3cm;3cm}{logo-huge}$$}%
70 \htmlonly{$$\image{3cm;3cm}{logo-huge.gif}$$}%
71 Computed Tomography is a technique for estimating the interior of an object
72 from measurement of radiation collected around the object. This radiation
73 can be either projected through or emitted from the object.
74 \rtfsp\ctsim simulates the process of projecting X-rays through a phantom object.
75 \rtfsp\ctsim can then reconstruct the interior of the object from the projections
76 collected around the phantom object.
78 The \ctsim package has two executable files: the graphical \helprefn{ctsim}{ctsim} and text \helprefn{ctsimtext}{ctsimtext} programs.
80 \chapter{Installation}\index{Installation}%
81 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
82 \setfooter{\thepage}{}{}{}{}{\thepage}%
84 \section{Download}\label{download}\index{Installation,Download}%
86 The latest version of CTSim, plus source code, can be accessed from:
93 It is available in Windows 95/NT/2000 and Linux GUI versions and non-GUI versions.
95 \section{Installing Linux RPM}\index{Installation,Linux}%
97 \section{Installing Windows Binary}\index{Installation,Windows}%
99 \section{Build From Sources}\label{build}\index{Installation,Build}%
101 See the INSTALL file included in the source distribution for instructions.
103 \section{Web Requirements}\label{installreq}\index{Installation,Requirements}%
104 \begin{itemize}\itemsep=0pt
105 \item zlib Library (optional)
106 \par Used for PNG file export.
108 \item libpng Library (optional)
109 \par Used for PNG file export.
112 \item FFTW library (optional)
113 \par Used for frequency-based filtering and fourier transformations of images.
116 \item readline library (optional)
117 \par Used for \ctsimtext interactive shell.
119 \item dmalloc library (optional)
120 \par Used for debugging memory allocation
123 \item wxWindows library (optional)
124 \par Used for platform-independent graphical interface. The graphical-shell
125 program \ctsim requires this library.
126 \par www.wxwindows.org
129 \chapter{ctsim - the Graphical User Interface}\label{ctsim}\index{ctsim}%
130 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
131 \setfooter{\thepage}{}{}{}{}{\thepage}%
133 \ctsim is the graphical shell for the CTSim project. It is
134 written using the wxLibrary for cross-platform compatibility with GTK,
135 Motif, and Microsoft Windows. It includes all of the functionality of
136 the command-line tool {\tt ctsimtext} as well as image processing and visualization features.
138 \ctsim can open projection files, image files, phantom definition files, and plotfiles.
141 ctsim [OPTIONS] [files to open...]
143 \chapter{ctsimtext}\label{ctsimtext}\index{ctsimtext}%
144 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
145 \setfooter{\thepage}{}{}{}{}{\thepage}%
147 \ctsimtext is a master shell for all of the command-line utilities.
150 \ctsimtext can be executed without any parameters. In that case, \ctsimtext
151 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.
153 \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
154 {\tt ctsimtext function-name parameters...}.
156 The available functions are:
158 \section{if1}\label{if1}\index{ctsimtext,if1}%
159 Perfoms math functions on a single image.
162 \begin{itemize}\itemsep=0pt
170 \section{if2}\label{if2}\index{ctsimtext,if2}%
171 Perfoms math functions on a two images.
174 \begin{itemize}\itemsep=0pt
183 \section{ifexport}\label{ifexport}\index{ctsimtext,ifexport}%
184 Export an imagefile to a standard graphics file.
187 \begin{itemize}\itemsep=0pt
189 \begin{itemize}\itemsep=0pt
196 \begin{itemize}\itemsep=0pt
202 \begin{itemize}\itemsep=0pt
215 \section{ifinfo}\label{ifinfo}\index{ctsimtext,ifinfo}%
217 Displays information about an imagefile.
220 \begin{itemize}\itemsep=0pt
228 \section{phm2pj}\label{phm2pj}\index{ctsimtext,phm2pj}%
229 Simulates collection of X-rays data (projections) around a phantom object.
232 phm2pj projection-file-name number-of-detectors number-of-views [options...]
233 \begin{itemize}\itemsep=0pt
235 Select a standard phantom
236 \begin{itemize}\itemsep=0pt
244 Load a phantom definition definition
247 \begin{itemize}\itemsep=0pt
254 Number of samples per each detector
257 Sets the rotation amount as a multiple of pi. For parallel geometries use
258 a rotation angle of 1 and for equilinear and equiangular geometries use a rotation angle of 2.
260 \item --field-of-view
261 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.
264 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.
267 The Herman phantom is taken with permission from Gabor Hermans 1980 book\cite{HERMAN80}. The Shepp-Logan phantom was published in 1974\cite{SHEPP74}.
269 \section{phm2if}\label{phm2if}\index{ctsimtext,phm2if}%
270 Converts a geometric phantom object into an imagefile. The size of the
271 imagefile in pixels must be specified as well as the number of samples
272 to average per pixel.
275 \begin{itemize}\itemsep=0pt
279 \section{pj2if}\label{pj2if}\index{ctsimtext,pj2if}%
280 Convert a projection file into an imagefile.
283 \begin{itemize}\itemsep=0pt
284 \item --help Print brief online help
287 \section{pjinfo}\label{pjinfo}\index{ctsimtext,pjinfo}%
288 Displays information about a projection file.
291 \begin{itemize}\itemsep=0pt
299 \section{pjrec}\label{pjrec}\index{ctsimtext,pjrec}%
300 Reconstructs the interior of an object from a projection file.
304 \twocolitemruled{{\bf Parameter}}{{\bf Options}}
305 \twocolitem{{\bf --filter}}
306 {Selects which filter to apply to each projection. To properly reconstruct an image, this filter should be multiplied
307 by the absolute value of distance from zero frequency.
308 \begin{itemize}\itemsep=0pt
314 \twocolitem{{\bf --filter-parameter}}{Sets the alpha level for Hamming
315 window. At setting of 0.54, this equals the Hanning window.}
317 \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.
318 \begin{itemize}\itemsep=0pt
327 \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.
328 \begin{itemize}\itemsep=0pt
330 \item inverse-fourier
333 \twocolitem{{\bf --interpolation}}{Interpolation technique. {\tt linear} is optimal.
334 \begin{itemize}\itemsep=0pt
339 \twocolitem{{\bf -backprojection}}{Selects the backprojection technique. A setting of {\tt idiff3} is optimal.
340 \begin{itemize}\itemsep=0pt
349 \twocolitem{{\bf --zeropad}}{ Zeropad factor. A setting of {\tt 1} is optimal.}
351 \twocolitem{{\bf --preinterpolate}}{Selects preinterpolation interpolation technique and sets the preinterpolation factor. Currently, this is experimental and does not work well.}
354 \chapter{The Web Browser CGI Interface}\label{webinterface}\index{Web Interface}%
355 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
356 \setfooter{\thepage}{}{}{}{}{\thepage}%
358 \section{Overview}\index{Web Interface,Overview}%
359 The CGI program {\tt ctsim.cgi} takes projections of a standard
360 phantom object, performs reconstruction, and then compares the
361 rasterized phantom object with the reconstruction. The comparison is
362 performed both visually by an image subtraction as well as by standard
363 statistics as described by Herman\cite{HERMAN80}.
365 \section{Requirements}\index{Web Interface,Requirements}%
366 \begin{itemize}\itemsep=0pt
367 \item Apache or other CGI compatible web server
369 \item Perl (version 4.0 or higher)
371 \item A client web browser than can display PNG files. Most
372 current web browsers support PNG.
377 \bibliographystyle{plain}
379 \addcontentsline{toc}{chapter}{Bibliography}
380 \setheader{{\it REFERENCES}}{}{}{}{}{{\it REFERENCES}}%
381 \setfooter{\thepage}{}{}{}{}{\thepage}%
383 \addcontentsline{toc}{chapter}{Index}
384 \setheader{{\it INDEX}}{}{}{}{}{{\it INDEX}} %
385 \setfooter{\thepage}{}{}{}{}{\thepage} %