1 \documentstyle[a4,makeidx,verbatim,texhelp,fancyhea,mysober,mytitle]{report}%
6 \newcommand{\ctsim}{{\tt CTSim}}
7 \newcommand{\ctsimtext}{{\tt CTSimText}}
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16 %\backgroundcolour{255;255;255}\textcolour{0;0;0}% Has an effect in HTML only
17 \winhelpignore{\title{Manual for CTSim 3.0}%
18 \author{Kevin Rosenberg, M.D.}%
21 \winhelponly{\title{Manual for CTSim 3.0}%
22 \author{by Kevin Rosenberg, M.D.\\$$\image{1cm;0cm}{logo-huge.bmp}$$}%
27 \pagestyle{fancyplain}%
28 \bibliographystyle{plain}%
29 \pagenumbering{roman}%
30 \setheader{{\it CONTENTS}}{}{}{}{}{{\it CONTENTS}}%
31 \setfooter{\thepage}{}{}{}{}{\thepage}%
34 \chapter*{Copyright notice}%
35 \setheader{{\it COPYRIGHT}}{}{}{}{}{{\it COPYRIGHT}}%
36 \setfooter{\thepage}{}{}{}{}{\thepage}%
38 Copyright (c) 1983-2001 Kevin Rosenberg, M.D.
40 Permission to use, copy, modify, and distribute this software and its
41 documentation for any purpose is hereby granted without fee, provided that the
42 above copyright notice, author statement and this permission notice appear in
43 all copies of this software and related documentation.
45 THE SOFTWARE IS PROVIDED ``AS-IS'' AND WITHOUT WARRANTY OF ANY KIND, EXPRESS,
46 IMPLIED OR OTHERWISE, INCLUDING WITHOUT LIMITATION, ANY WARRANTY OF
47 MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.
49 IN NO EVENT SHALL KEVIN ROSENBERG BE LIABLE FOR ANY
50 SPECIAL, INCIDENTAL, INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND, OR
51 ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS,
52 WHETHER OR NOT ADVISED OF THE POSSIBILITY OF DAMAGE, AND ON ANY THEORY
53 OF LIABILITY, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
54 PERFORMANCE OF THIS SOFTWARE.
56 \chapter{Introduction}%
57 \pagenumbering{arabic}%
58 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
59 \setfooter{\thepage}{}{}{}{}{\thepage}%
61 Computed Tomography is a technique for estimating the interior of an object
62 from measurement of radiation collected around the object. This radiation
63 can be either projected through or emitted from the object.
64 \ctsim simulates the process of projecting X-rays through a phantom object.
65 \ctsim can then reconstruct the interior of the object from the projections
66 collected around the phantom object.
68 \chapter{Installation}\index{Installation}%
69 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
70 \setfooter{\thepage}{}{}{}{}{\thepage}%
72 \section{Download}%\index{Installation,Download}%
74 The latest version of CTSim, plus source code, can be accessed from:
81 It is available in Windows 95/NT/2000 and Linux GUI versions and non-GUI versions.
83 \section{Installing Linux RPM}\index{Installation,Linux}%
85 \section{Installing Windows Binary}\index{Installation,Windows}%
87 \section{Build From Sources}%\index{Installation,Build}%
89 See the INSTALL file included in the source distribution for instructions.
91 \section{Requirements}\index{Installation,Build,Requirements}%
92 \begin{itemize}\itemsep=0pt
93 \item zlib Library (optional)
94 \par Used for PNG file export.
96 \item libpng Library (optional)
97 \par Used for PNG file export.
100 \item FFTW library (optional)
101 \par Used for frequency-based filtering and fourier transformations of images.
104 \item readline library (optional)
105 /par Used for {/ctsimtext} interactive shell.
107 \item dmalloc library (optional)
108 \par Used for debugging memory allocation
111 \item wxWindows library (optional)
112 \par Used for platform-independent graphical interface. The graphical-shell
113 program \ctsim requires this library.
114 \par www.wxwindows.org
118 \chapter{ctsim - the Graphical User Interface}%\index{ctsim}%
119 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
120 \setfooter{\thepage}{}{}{}{}{\thepage}%
122 \ctsim\ is the graphical shell for the CTSim project. It is
123 written using the wxLibrary for cross-platform compatibility with GTK,
124 Motif, and Microsoft Windows. It includes all of the functionality of
125 the command-line tool {\tt ctsimtext} as well as image processing and visualization features.
128 ctsim [OPTIONS] [files to open...]
130 \ctsim can open projection files, image files, phantom definition files, and plotfiles.
132 \chapter{ctsimtext - The Command Line Interface}\index{ctsimtext}%
133 \ctsimtext is a master shell for all of the command-line utilities.
134 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
135 \setfooter{\thepage}{}{}{}{}{\thepage}%
139 \ctsimtext can be executed without any parameters. In that case, \ctsimtext
140 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.
142 \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 {\tt ctsimtext function-name parameters...}.
144 The following function names are available:
146 \subsection{if1}\index{Programs,ctsimtext,if1}%
147 Perfoms math functions on a single image.
149 \subsubsection{Usage}%
150 \begin{itemize}\itemsep=0pt
158 \subsection{if2}\index{Programs,ctsimtext,if2}%
159 Perfoms math functions on a two images.
161 \subsubsection{Usage}%
162 \begin{itemize}\itemsep=0pt
171 \subsection{ifinfo}\index{Programs,ctsimtext,ifinfo}%
173 Displays information about an imagefile.
174 \subsubsection{Usage}%
175 \begin{itemize}\itemsep=0pt
183 \subsection{ifexport}\index{Programs,ctsimtext,ifexport}%
184 Export an imagefile to a standard graphics file.
186 \subsubsection{Usage}%
187 \begin{itemize}\itemsep=0pt
189 \begin{itemize}\itemsep=0pt
196 \begin{itemize}\itemsep=0pt
202 \begin{itemize}\itemsep=0pt
215 \subsection{phm2pj}\index{Programs,ctsimtext,phm2pj}%
216 Simulates collection of X-rays data (projections) around a phantom object.
218 \subsubsection{Usage}%
219 phm2pj projection-file-name number-of-detectors number-of-views [options...]
220 \begin{itemize}\itemsep=0pt
222 Select a standard phantom
223 \begin{itemize}\itemsep=0pt
231 Load a phantom definition definition
234 \begin{itemize}\itemsep=0pt
241 Number of samples per each detector
244 Sets the rotation amount as a multiple of pi. For parallel geometries use
245 a rotation angle of 1 and for equilinear and equiangular geometries use a rotation angle of 2.
247 \item --field-of-view
248 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.
251 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.
254 The Herman phantom is taken with permission from Gabor Hermans 1980 book\cite{HERMAN80}. The Shepp-Logan phantom was published in 1974\cite{SHEPP74}.
256 \subsection{phm2if}\index{Programs,ctsimtext,phm2if}%
257 Converts a geometric phantom object into an imagefile. The size of the
258 imagefile in pixels must be specified as well as the number of samples
259 to average per pixel.
261 \subsubsection{Usage}%
262 \begin{itemize}\itemsep=0pt
266 \subsection{pj2if}\index{Programs,ctsimtext,pj2if}%
267 Convert a projection file into an imagefile.
269 \subsubsection{Usage}%
270 \begin{itemize}\itemsep=0pt
273 \subsection{pjinfo}\index{Programs,ctsimtext,pjinfo}%
274 Displays information about a projection file.
276 \subsubsection{Usage}%
277 \begin{itemize}\itemsep=0pt
285 \subsection{pjrec}\index{Programs,ctsimtext,pjrec}%
286 Reconstructs the interior of an object from a projection file.
288 \subsubsection{Usage}%
290 \subsubsection{Parameters}%
291 \begin{itemize}\itemsep=0pt
293 Selects which filter to apply to each projection. To
294 properly reconstruct an image, this filter should be multiplied
295 by the absolute value of distance from zero frequency.
296 \begin{itemize}\itemsep=0pt
303 \item Filter Parameter
304 \par Sets the alpha level for Hamming
305 window. At setting of 0.54, this equals the Hanning window.
308 \begin{itemize}\itemsep=0pt
316 \item Filter Generation
317 \begin{itemize}\itemsep=0pt
319 \item inverse_fourier
323 \begin{itemize}\itemsep=0pt
329 \begin{itemize}\itemsep=0pt
339 \item Preinterpolation Factor
342 \chapter{The Web Browser CGI Interface}\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 For Web Interface
356 \begin{itemize}\itemsep=0pt
357 \item Apache or other CGI compatible web server
359 \item Perl (version 4.0 or higher)
361 \item A client web browser than can display PNG files. Most
362 current web browswer do support PNG.
369 \bibliographystyle{plain}
371 \addcontentsline{toc}{chapter}{Bibliography}
372 \setheader{{\it REFERENCES}}{}{}{}{}{{\it REFERENCES}}%
373 \setfooter{\thepage}{}{}{}{}{\thepage}%
375 \addcontentsline{toc}{chapter}{Index}
376 \setheader{{\it INDEX}}{}{}{}{}{{\it INDEX}}%
377 \setfooter{\thepage}{}{}{}{}{\thepage}%