1 \chapter{The Command Line Interface}\label{ctsimtext}\index{ctsimtext}%
2 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
5 \ctsimtext\ is a master shell for all of the command-line utilities.
7 \usage \ctsimtext\ can be invoked via three different
9 \begin{itemize}\itemsep=0pt
10 \item \ctsimtext\ can executed without any parameters. In that case,
11 \ctsimtext\ offers a command-line to enter the function-names and
12 their parameters. The output of the command is displayed. Further
13 commands may be given to \ctsimtext. The shell is exited by the
14 \texttt{quit} command.
16 \item \ctsimtext\ can also be called to
17 execute a single command. This is especially useful for batch
18 files containing multiple \ctsimtext\ commands. This is invoked by
19 calling\\ \texttt{ctsimtext function-name parameters...}.
21 \item Using operating systems that support soft or hard linking of
22 files (such as UNIX and Linux), the executable file \ctsimtext\ can
23 be linked to the function names. This is automatically done by
24 the installation file for Linux. Thus, to use \ctsimtext\ with the
25 function name \texttt{pjrec}, the below command can be executed:\\
26 \texttt{pjrec parameters...}
30 \section{if1}\label{if1}\index{ctsimtext,if1}%
31 Perfoms math functions on a single image.
34 \begin{itemize}\itemsep=0pt
42 \section{if2}\label{if2}\index{ctsimtext,if2}%
43 Perfoms math functions on a two images.
46 \begin{itemize}\itemsep=0pt
55 \section{ifexport}\label{ifexport}\index{ctsimtext,ifexport}%
56 Export an imagefile to a standard graphics file.
59 \begin{itemize}\itemsep=0pt
61 \begin{itemize}\itemsep=0pt
68 \begin{itemize}\itemsep=0pt
74 \begin{itemize}\itemsep=0pt
87 \section{ifinfo}\label{ifinfo}\index{ctsimtext,ifinfo}%
89 Displays information about an imagefile.
92 \begin{itemize}\itemsep=0pt
100 \section{phm2pj}\label{phm2pj}\index{ctsimtext,phm2pj}%
101 Simulates collection of X-rays data (projections) around a phantom object.
104 phm2pj projection-file-name number-of-detectors number-of-views [options...]
105 \begin{itemize}\itemsep=0pt
107 Select a standard phantom
108 \begin{itemize}\itemsep=0pt
115 Load a phantom definition definition
118 \begin{itemize}\itemsep=0pt
125 Number of samples per each detector
128 Sets the rotation amount as a multiple of pi. For parallel geometries use
129 a rotation angle of 1 and for equilinear and equiangular
130 geometries use a rotation angle of 2. The default is to use to
131 appropriate rotation angle based on the geometry.
134 Sets the field of view as a ratio of the diameter of the phantom.
135 For normal scanning, a value of 1.0 is fine.
138 Sets the length of scanning as a ratio of the view diameter.
139 For normal scanning, a value of 1.0 is fine.
141 \item -\,-focal-length
142 Sets the distance of the radiation source and detectors from the center of the object as a ratio of the radius of the object.
143 For parallel geometries, a value of 1.0 is fine. For other geometries, this should be at least 2.0 to avoid artifacts.
146 The Herman phantom is taken with permission from Gabor Hermans 1980 book\cite{HERMAN80}. The Shepp-Logan phantom was published in 1974\cite{SHEPP74}.
148 \section{phm2if}\label{phm2if}\index{ctsimtext,phm2if}%
149 Converts a geometric phantom object into an imagefile. The size of the
150 imagefile in pixels must be specified as well as the number of samples
151 to average per pixel.
154 \begin{itemize}\itemsep=0pt
159 \section{pj2if}\label{pj2if}\index{ctsimtext,pj2if}%
160 Convert a projection file into an imagefile.
163 \begin{itemize}\itemsep=0pt
164 \item -\,-help Print brief online help
167 \section{pjinfo}\label{pjinfo}\index{ctsimtext,pjinfo}%
168 Displays information about a projection file.
171 \begin{itemize}\itemsep=0pt
172 \item -\,-binaryheader
179 \section{pjrec}\label{pjrec}\index{ctsimtext,pjrec}%
180 Reconstructs the interior of an object from a projection file.
183 \twocolitemruled{\textbf{Parameter}}{\textbf{Options}}
184 \twocolitem{\textbf{-\,-filter}}{Selects which filter to apply to
185 each projection. To properly reconstruct an image, this filter
186 should be multiplied by the absolute value of distance from zero
188 \begin{itemize}\itemsep=0pt
193 } \twocolitem{\textbf{-\,-filter-parameter}}{Sets the alpha level
195 window. At setting of 0.54, this equals the Hanning window.}
197 \twocolitem{\textbf{-\,-filter-method}}{Selects the filtering
198 method. For large numbers of detectors, \texttt{rfftw} is optimal.
199 For smaller numbers of detectors, \texttt{convolution} might be a
201 \begin{itemize}\itemsep=0pt
210 \twocolitem{\textbf{-\,-filter-generation}}{Selects the filter
211 generation. With convolution, \texttt{direct} is the proper method
212 to select. With any of the frequency methods,
213 \texttt{inverse-fourier} is the best method.
214 \begin{itemize}\itemsep=0pt
216 \item inverse-fourier
220 \twocolitem{\textbf{-\,-interpolation}}{Interpolation technique.
221 \texttt{linear} is optimal.
222 \begin{itemize}\itemsep=0pt
229 \twocolitem{\textbf{-\,-backprojection}}{Selects the
230 backprojection technique. A setting of \texttt{idiff} is optimal.
231 \begin{itemize}\itemsep=0pt
239 \twocolitem{\textbf{-\,-zeropad}}{Zeropad factor. A setting of
240 \texttt{1} is optimal.}