1 \documentstyle[a4,makeidx,verbatim,texhelp]{report}%
6 \newcommand{\ctsim}{{\tt CTSim}}
7 \newcommand{\ctsimtext}{{\tt CTSimText}}
8 \newcommand{\usage}{{\bf Usage}{\par}}
10 \newcommand{\commandref}[2]{\helpref{{\tt $\backslash$#1}}{#2}}%
11 \newcommand{\commandrefn}[2]{\helprefn{{\tt $\backslash$#1}}{#2}\index{#1}}%
12 \newcommand{\commandpageref}[2]{\latexignore{\helprefn{{\tt $\backslash$#1}}{#2}}\latexonly{{\tt $\backslash$#1} {\it page \pageref{#2}}}\index{#1}}%
13 \newcommand{\indexit}[1]{#1\index{#1}}%
14 \newcommand{\inioption}[1]{{\bf {\tt #1}}\index{#1}}%
17 %\backgroundcolour{255;255;255}\textcolour{0;0;0}% Has an effect in HTML only
18 \winhelpignore{\title{Manual for CTSim 3.0}%
19 \author{Kevin Rosenberg, M.D.}%
22 \winhelponly{\title{Manual for CTSim 3.0}%
23 \author{by Kevin Rosenberg, M.D.\\$$\image{3cm;3cm}{logo-huge.bmp}$$}%
28 \pagestyle{fancyplain}%
29 \bibliographystyle{plain}%
30 \pagenumbering{roman}%
32 \setheader{{\it CONTENTS}}{}{}{}{}{{\it CONTENTS}}%
33 \setfooter{\thepage}{}{}{}{}{\thepage}%
36 \chapter*{Copyright notice}%
37 \setheader{{\it COPYRIGHT}}{}{}{}{}{{\it COPYRIGHT}}%
38 \setfooter{\thepage}{}{}{}{}{\thepage}%
40 Copyright (c) 1983-2001 Kevin Rosenberg, M.D.
42 Permission to use, copy, modify, and distribute this software and its
43 documentation for any purpose is hereby granted without fee, provided that the
44 above copyright notice, author statement and this permission notice appear in
45 all copies of this software and related documentation.
47 THE SOFTWARE IS PROVIDED ``AS-IS'' AND WITHOUT WARRANTY OF ANY KIND, EXPRESS,
48 IMPLIED OR OTHERWISE, INCLUDING WITHOUT LIMITATION, ANY WARRANTY OF
49 MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.
51 IN NO EVENT SHALL KEVIN ROSENBERG BE LIABLE FOR ANY
52 SPECIAL, INCIDENTAL, INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND, OR
53 ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS,
54 WHETHER OR NOT ADVISED OF THE POSSIBILITY OF DAMAGE, AND ON ANY THEORY
55 OF LIABILITY, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
56 PERFORMANCE OF THIS SOFTWARE.
58 \chapter{Introduction}\label{introduction}%
59 \pagenumbering{arabic}%
60 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
61 \setfooter{\thepage}{}{}{}{}{\thepage}%
63 \winhelponly{$$\image{3cm;3cm}{logo-huge}$$}%
64 \htmlonly{$$\image{3cm;3cm}{logo-huge.gif}$$}%
65 Computed Tomography is a technique for estimating the interior of an object
66 from measurement of radiation collected around the object. This radiation
67 can be either projected through or emitted from the object.
68 \rtfsp\ctsim simulates the process of projecting X-rays through a phantom object.
69 \rtfsp\ctsim can then reconstruct the interior of the object from the projections
70 collected around the phantom object.
72 The \ctsim package has two executable files: the graphical \helprefn{ctsim}{ctsim} and text \helprefn{ctsimtext}{ctsimtext} programs.
74 \chapter{Installation}\index{Installation}%
75 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
76 \setfooter{\thepage}{}{}{}{}{\thepage}%
78 \section{Download}\label{download}\index{Installation,Download}%
80 The latest version of CTSim, plus source code, can be accessed from:
87 It is available in Windows 95/NT/2000 and Linux GUI versions and non-GUI versions.
89 \section{Installing Linux RPM}\index{Installation,Linux}%
91 \section{Installing Windows Binary}\index{Installation,Windows}%
93 \section{Build From Sources}\label{build}\index{Installation,Build}%
95 See the INSTALL file included in the source distribution for instructions.
97 \section{Web Requirements}\label{installreq}\index{Installation,Requirements}%
98 \begin{itemize}\itemsep=0pt
99 \item zlib Library (optional)
100 \par Used for PNG file export.
102 \item libpng Library (optional)
103 \par Used for PNG file export.
106 \item FFTW library (optional)
107 \par Used for frequency-based filtering and fourier transformations of images.
110 \item readline library (optional)
111 \par Used for \ctsimtext interactive shell.
113 \item dmalloc library (optional)
114 \par Used for debugging memory allocation
117 \item wxWindows library (optional)
118 \par Used for platform-independent graphical interface. The graphical-shell
119 program \ctsim requires this library.
120 \par www.wxwindows.org
123 \chapter{ctsim - the Graphical User Interface}\label{ctsim}\index{ctsim}%
124 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
125 \setfooter{\thepage}{}{}{}{}{\thepage}%
127 \ctsim is the graphical shell for the CTSim project. It is
128 written using the wxLibrary for cross-platform compatibility with GTK,
129 Motif, and Microsoft Windows. It includes all of the functionality of
130 the command-line tool {\tt ctsimtext} as well as image processing and visualization features.
132 \ctsim can open projection files, image files, phantom definition files, and plotfiles.
135 ctsim [OPTIONS] [files to open...]
137 \chapter{ctsimtext}\label{ctsimtext}\index{ctsimtext}%
138 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
139 \setfooter{\thepage}{}{}{}{}{\thepage}%
141 \ctsimtext is a master shell for all of the command-line utilities.
144 \ctsimtext can be executed without any parameters. In that case, \ctsimtext
145 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.
147 \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
148 {\tt ctsimtext function-name parameters...}.
150 The available functions are:
152 \section{if1}\label{if1}\index{ctsimtext,if1}%
153 Perfoms math functions on a single image.
156 \begin{itemize}\itemsep=0pt
164 \section{if2}\label{if2}\index{ctsimtext,if2}%
165 Perfoms math functions on a two images.
168 \begin{itemize}\itemsep=0pt
177 \section{ifexport}\label{ifexport}\index{ctsimtext,ifexport}%
178 Export an imagefile to a standard graphics file.
181 \begin{itemize}\itemsep=0pt
183 \begin{itemize}\itemsep=0pt
190 \begin{itemize}\itemsep=0pt
196 \begin{itemize}\itemsep=0pt
209 \section{ifinfo}\label{ifinfo}\index{ctsimtext,ifinfo}%
211 Displays information about an imagefile.
214 \begin{itemize}\itemsep=0pt
222 \section{phm2pj}\label{phm2pj}\index{ctsimtext,phm2pj}%
223 Simulates collection of X-rays data (projections) around a phantom object.
226 phm2pj projection-file-name number-of-detectors number-of-views [options...]
227 \begin{itemize}\itemsep=0pt
229 Select a standard phantom
230 \begin{itemize}\itemsep=0pt
238 Load a phantom definition definition
241 \begin{itemize}\itemsep=0pt
248 Number of samples per each detector
251 Sets the rotation amount as a multiple of pi. For parallel geometries use
252 a rotation angle of 1 and for equilinear and equiangular geometries use a rotation angle of 2.
254 \item --field-of-view
255 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.
258 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.
261 The Herman phantom is taken with permission from Gabor Hermans 1980 book\cite{HERMAN80}. The Shepp-Logan phantom was published in 1974\cite{SHEPP74}.
263 \section{phm2if}\label{phm2if}\index{ctsimtext,phm2if}%
264 Converts a geometric phantom object into an imagefile. The size of the
265 imagefile in pixels must be specified as well as the number of samples
266 to average per pixel.
269 \begin{itemize}\itemsep=0pt
273 \section{pj2if}\label{pj2if}\index{ctsimtext,pj2if}%
274 Convert a projection file into an imagefile.
277 \begin{itemize}\itemsep=0pt
280 \section{pjinfo}\label{pjinfo}\index{ctsimtext,pjinfo}%
281 Displays information about a projection file.
284 \begin{itemize}\itemsep=0pt
292 \section{pjrec}\label{pjrec}\index{ctsimtext,pjrec}%
293 Reconstructs the interior of an object from a projection file.
297 \twocolitemruled{{\bf Parameter}}{{\bf Options}}
298 \twocolitem{{\bf --filter}}{Selects which filter to apply to each projection. To properly reconstruct an image, this filter should be multiplied
299 by the absolute value of distance from zero frequency.
300 \begin{itemize}\itemsep=0pt
305 \twocolitem{{\bf --filter-parameter}}{Sets the alpha level for Hamming
306 window. At setting of 0.54, this equals the Hanning window.}
307 \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.
308 \begin{itemize}\itemsep=0pt
315 \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.
316 \begin{itemize}\itemsep=0pt
318 \item inverse-fourier
321 \twocolitem{{\bf --interpolation}}{Interpolation technique. {\tt linear} is optimal.
322 \begin{itemize}\itemsep=0pt
327 \twocolitem{{\bf -backprojection}}{Selects the backprojection technique. A setting of {\tt idiff3} is optimal.
328 \begin{itemize}\itemsep=0pt
337 \twocolitem{{\bf --zeropad}}{ Zeropad factor. A setting of {\tt 1} is optimal.}
339 \twocolitem{{\bf --preinterpolate}}{Selects preinterpolation interpolation technique and sets the preinterpolation factor. Currently, this is experimental and does not work well.}
342 \chapter{The Web Browser CGI Interface}\label{webinterface}\index{Web Interface}%
343 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
344 \setfooter{\thepage}{}{}{}{}{\thepage}%
346 \section{Overview}\index{Web Interface,Overview}%
347 The CGI program {\tt ctsim.cgi} takes projections of a standard
348 phantom object, performs reconstruction, and then compares the
349 rasterized phantom object with the reconstruction. The comparison is
350 performed both visually by an image subtraction as well as by standard
351 statistics as described by Herman\cite{HERMAN80}.
353 \section{Requirements}\index{Web Interface,Requirements}%
354 \begin{itemize}\itemsep=0pt
355 \item Apache or other CGI compatible web server
357 \item Perl (version 4.0 or higher)
359 \item A client web browser than can display PNG files. Most
360 current web browsers support PNG.
365 \bibliographystyle{plain}
367 \addcontentsline{toc}{chapter}{Bibliography}
368 \setheader{{\it REFERENCES}}{}{}{}{}{{\it REFERENCES}}%
369 \setfooter{\thepage}{}{}{}{}{\thepage}%
371 \addcontentsline{toc}{chapter}{Index}
372 \setheader{{\it INDEX}}{}{}{}{}{{\it INDEX}}%
373 \setfooter{\thepage}{}{}{}{}{\thepage}%