doc/ctsim-textui.tex

   1 \chapter{The Command Line Interface}\label{ctsimtext}\index{ctsimtext}%
   2 \setheader{{\it CHAPTER \thechapter}}{}{}{\ctsimheadtitle}{}{{\it CHAPTER \thechapter}}%
   3 \ctsimfooter%
   4
   5 \ctsimtext\ is a master shell for all of the command-line utilities. The
   6 command-line utilities can perform most of the functions of the graphical
   7 shell. These command-line utilities are especially appropriate for use on
   8 systems without graphics, batch files, and parallel processing in a Beowulf
   9 computer cluster.
  10
  11 \usage \ctsimtext\ can be invoked via three different
  12 methods.
  13 \begin{enumerate}\itemsep=3pt
  14 \item \ctsimtext\ can executed without any parameters. In that case,
  15 \ctsimtext\ offers a command-line to enter the function-names and
  16 their parameters. The output of the command is displayed. Further
  17 commands may be given to \ctsimtext. The shell is exited by the
  18 \texttt{quit} command. \ctsimtext\ uses the
  19 \urlref{readline}{http://www.gnu.org} library on UNIX and Linux platforms
  20 to provide for command history processing.
  21
  22 \item \ctsimtext\ can also be called to
  23 execute a single command. This is especially useful for batch
  24 files containing multiple \ctsimtext\ commands. This is invoked by
  25 calling\\ \texttt{ctsimtext function-name parameters...}.
  26
  27 \item Using operating systems that support soft or hard linking of
  28 files (such as UNIX and Linux), the executable file \ctsimtext\ can
  29 be linked to the function names. This is automatically done by
  30 the installation file for Linux. Thus, to use \ctsimtext\ with the
  31 function name \texttt{pjrec}, the below command can be executed:\\
  32 \texttt{pjrec parameters...} \\
  33 as a shortcut rather than the equivalent command \\
  34 \texttt{ctsimtext pjrec parameters...}
  35
  36 \end{enumerate}
  37
  38 \section{Parallel Processing}
  39 \ctsimtext\ can be used to spread it's processing over a cluster. Specifically,
  40 \ctsimtext\ supports the \urlref{LAM}{http://www.mpi.nd.edu/lam} version of
  41 the MPI environment. On platforms with LAM installed, a parallel version of
  42 \ctsimtext\ is created. The name of this program is \texttt{ctsimtext-lam}.
  43 The functions that take advantage of the parallel processing are
  44 \texttt{phm2if}, \texttt{phm2pj}, \texttt{pjrec}.
  45
  46 This parallel processing version has been tested with excellent results on
  47 a 16-CPU \urlref{Beowulf}{http://www.beowulf.org} cluster.
  48
  49
  50 \section{if1}\label{if1}\index{if1}%
  51 Performs math functions on a single image.
  52
  53 \usage
  54 \begin{itemize}\itemsep=0pt
  55   \item \doublehyphen{invert}
  56   \item \doublehyphen{log}
  57   \item \doublehyphen{exp}
  58   \item \doublehyphen{sqr}
  59   \item \doublehyphen{sqrt}
  60 \end{itemize}
  61
  62 \section{if2}\label{if2}\index{if2}%
  63 Performs math functions on a two images.
  64
  65 \usage
  66 \begin{itemize}\itemsep=0pt
  67   \item \doublehyphen{add}
  68   \item \doublehyphen{sub}
  69   \item \doublehyphen{mul}
  70   \item \doublehyphen{comp}
  71   \item \doublehyphen{column-plot}
  72   \item \doublehyphen{row-plot}
  73 \end{itemize}
  74
  75 \section{ifexport}\label{ifexport}\index{ifexport}%
  76 Export an image file to a standard graphics file.
  77
  78 \usage
  79 \begin{itemize}\itemsep=0pt
  80   \item \doublehyphen{format}
  81   \begin{itemize}\itemsep=0pt
  82     \item \texttt{gm}
  83     \item \texttt{pgmasc}
  84     \item \texttt{png}
  85     \item \texttt{png16}
  86   \end{itemize}
  87   \item \doublehyphen{center}
  88   \begin{itemize}\itemsep=0pt
  89     \item \texttt{median}
  90     \item \texttt{mode}
  91     \item \texttt{mean}
  92   \end{itemize}
  93   \item \doublehyphen{auto}
  94   \begin{itemize}\itemsep=0pt
  95      \item \texttt{full}
  96      \item \texttt{std0.1}
  97      \item \texttt{std0.5}
  98      \item \texttt{std1}
  99      \item \texttt{std2}
 100      \item \texttt{std3}
 101   \end{itemize}
 102   \item \doublehyphen{scale}
 103   \item \doublehyphen{min}
 104   \item \doublehyphen{max}
 105 \end{itemize}
 106
 107 \section{ifinfo}\label{ifinfo}\index{ifinfo}%
 108
 109 Displays information about an imagefile.
 110
 111 \usage
 112 \begin{itemize}\itemsep=0pt
 113   \item \doublehyphen{labels}
 114   \item \doublehyphen{no-labels}
 115   \item \doublehyphen{stats}
 116   \item \doublehyphen{no-stats}
 117   \item \doublehyphen{help}
 118 \end{itemize}
 119
 120 \section{phm2pj}\label{phm2pj}\index{phm2pj}%
 121 Simulates collection of X-rays data (projections) around a phantom object.
 122
 123 \usage
 124 \texttt{phm2pj projection-file-name number-of-detectors number-of-views [options...]}
 125
 126 \begin{twocollist}
 127 \twocolitem{\doublehyphen{phantom}}{Select a standard phantom.
 128 \begin{itemize}\itemsep=0pt
 129 \item \texttt{herman}
 130 \item \texttt{shepp-logan}
 131 \item \texttt{unit-pulse}
 132 \end{itemize}
 133 }
 134 \twocolitem{\doublehyphen{phmfile}}{Load a phantom definition definition}
 135
 136 \twocolitem{\doublehyphen{geometry}}{
 137   \begin{itemize}\itemsep=0pt
 138     \item \texttt{parallel}
 139     \item \texttt{equiangular}
 140     \item \texttt{equilinear}
 141   \end{itemize}
 142 }
 143
 144 \twocolitem{\doublehyphen{nray}}{ Number of samples per each detector}
 145
 146 \twocolitem{\doublehyphen{rotangle}}{Sets the rotation amount as a multiple of pi.
 147 For parallel geometries use a rotation angle of \texttt{1} and for equilinear and equiangular
 148 geometries use a rotation angle of \texttt{2}. The default is to use to
 149 appropriate rotation angle based on the geometry.}
 150
 151 \twocolitem{\doublehyphen{view-ratio}}{Sets the field of view as a ratio of the diameter of the phantom.
 152     For normal scanning, a default value of \texttt{1.0} is optimal.}
 153
 154 \twocolitem{\doublehyphen{scan-ratio}}{Sets the length of scanning as a ratio of the view diameter.
 155     For normal scanning, a value of \texttt{1.0} is optimal.}
 156
 157 \twocolitem{\doublehyphen{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.
 158     For parallel geometries, a value of \texttt{1.0} is optimal. For other
 159     geometries, this should be at least \texttt{2.0} to avoid artifacts.}
 160 \end{twocollist}
 161
 162
 163 \section{phm2if}\label{phm2if}\index{phm2if}%
 164 Converts a geometric phantom object into an imagefile. The size of the
 165 imagefile in pixels must be specified as well as the number of samples
 166 to average per pixel.
 167
 168 \usage
 169 \begin{twocollist}
 170   \twocolitem{\doublehyphen{nsamples}}{Number of samples in x \& y directions per pixel}
 171   \twocolitem{\doublehyphen{view-ratio}}{Sets the view ration. For normal scanning,
 172   the default value of \texttt{1.0} is optimal.}
 173 \end{twocollist}
 174
 175 \section{pj2if}\label{pj2if}\index{pj2if}%
 176 Convert a projection file into an imagefile.
 177
 178 \usage
 179 \texttt{pj2if projection-file-name image-file-name x-size ysize [options...]}
 180
 181 \begin{twocollist}
 182 \twocolitem{\doublehyphen{help}}{Print brief online help}
 183 \end{twocollist}
 184
 185 \section{pjinfo}\label{pjinfo}\index{pjinfo}%
 186 Displays information about a projection file.
 187
 188 \usage
 189 \begin{itemize}\itemsep=0pt
 190   \item \doublehyphen{binaryheader}
 191   \item \doublehyphen{binaryview}
 192   \item \doublehyphen{startview}
 193   \item \doublehyphen{endview}
 194   \item \doublehyphen{dump}
 195 \end{itemize}
 196
 197 \section{pjrec}\label{pjrec}\index{pjrec}%
 198 Reconstructs the interior of an object from a projection file.
 199
 200 \begin{twocollist}
 201 \twocolitemruled{\textbf{Parameter}}{\textbf{Options}}
 202 \twocolitem{\doublehyphen{filter}}{Selects which filter to apply to
 203 each projection. To properly reconstruct an image, this filter
 204 should be multiplied by the absolute value of distance from zero
 205 frequency.
 206 \begin{itemize}\itemsep=0pt
 207 \item \texttt{abs\_bandlimit}
 208 \item \texttt{abs\_cosine}
 209 \item \texttt{abs\_hamming}
 210 \end{itemize}
 211 } \twocolitem{\doublehyphen{filter-parameter}}{Sets the alpha level
 212 for Hamming window. At setting of \texttt{0.54}, this equals
 213 the Hanning window.}
 214
 215 \twocolitem{\doublehyphen{filter-method}}{Selects the filtering
 216 method. For large numbers of detectors, \texttt{rfftw} is optimal.
 217 For smaller numbers of detectors, \texttt{convolution} might be a
 218 bit faster.
 219 \begin{itemize}\itemsep=0pt
 220 \item \texttt{convolution}
 221 \item \texttt{fourier}
 222 \item \texttt{fourier-table}
 223 \item \texttt{fftw}
 224 \item \texttt{rfftw}
 225 \item fftw
 226 \item rfftw
 227 \end{itemize}
 228 }
 229
 230 \twocolitem{\doublehyphen{filter-generation}}{Selects the filter
 231 generation. With convolution, \texttt{direct} is the proper method
 232 to select. With any of the frequency methods,
 233 \texttt{inverse-fourier} is the best method.
 234 \begin{itemize}\itemsep=0pt
 235 \item direct
 236 \item inverse-fourier
 237 \end{itemize}
 238 }
 239
 240 \twocolitem{\doublehyphen{interpolation}}{Interpolation technique.
 241 \texttt{linear} is optimal.
 242 \begin{itemize}\itemsep=0pt
 243 \item nearest
 244 \item linear
 245 \item cubic
 246 \end{itemize}
 247 }
 248
 249 \twocolitem{\doublehyphen{backprojection}}{Selects the
 250 backprojection technique. A setting of \texttt{idiff} is optimal.
 251 \begin{itemize}\itemsep=0pt
 252 \item trig
 253 \item table
 254 \item diff
 255 \item idiff
 256 \end{itemize}
 257 }
 258
 259 \twocolitem{\doublehyphen{zeropad}}{Zeropad factor. A setting of
 260 \texttt{1} is optimal.}
 261
 262 \end{twocollist}