X-Git-Url: http://git.kpe.io/?a=blobdiff_plain;f=doc%2Fctsim-textui.tex;h=6a4a67531bb9c47510b5ec0f7564817c0d193f13;hb=befd71a7157339b52a0c40359518d5276b25d127;hp=6f7a5de96bef9aac97a1cb6dd9aa4911c5b4c9af;hpb=ff99ed271fc46136ca6a30221847a54d52ff0de6;p=ctsim.git

diff --git a/doc/ctsim-textui.tex b/doc/ctsim-textui.tex
index 6f7a5de..6a4a675 100644
--- a/doc/ctsim-textui.tex
+++ b/doc/ctsim-textui.tex
@@ -1,28 +1,42 @@
-\chapter{ctsimtext}\label{ctsimtext}\index{ctsimtext}%
+\chapter{The Command Line Interface}\label{ctsimtext}\index{ctsimtext}%
 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
 \setfooter{\thepage}{}{}{}{}{\thepage}%
 
-\ctsimtext\ is a master shell for all of the command-line utilities. 
+\ctsimtext\ is a master shell for all of the command-line utilities.
 
-\usage
-\ctsimtext\ can be executed without any parameters. In that case, \ctsimtext\ 
-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 \texttt{quit} command.
-
-\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
-\texttt{ctsimtext function-name parameters...}.
+\usage \ctsimtext\ can be invoked via three different
+methods.
+\begin{itemize}\itemsep=0pt
+\item \ctsimtext\ can executed without any parameters. In that case,
+\ctsimtext\ 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
+\texttt{quit} command.
+
+\item \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\\ \texttt{ctsimtext function-name parameters...}.
+
+\item Using operating systems that support soft or hard linking of
+files (such as UNIX and Linux), the executable file \ctsimtext\ can
+be linked to the function names. This is automatically done by
+the installation file for Linux. Thus, to use \ctsimtext\ with the
+function name \texttt{pjrec}, the below command can be executed:\\
+\texttt{pjrec parameters...}
 
-The available functions are:
+\end{itemize}
 
 \section{if1}\label{if1}\index{ctsimtext,if1}%
 Perfoms math functions on a single image.
 
 \usage
 \begin{itemize}\itemsep=0pt
-  \item --invert
-  \item --log
-  \item --exp
-  \item --sqr
-  \item --sqrt
+  \item -\,-invert
+  \item -\,-log
+  \item -\,-exp
+  \item -\,-sqr
+  \item -\,-sqrt
 \end{itemize}
 
 \section{if2}\label{if2}\index{ctsimtext,if2}%
@@ -30,12 +44,12 @@ Perfoms math functions on a two images.
 
 \usage
 \begin{itemize}\itemsep=0pt
-  \item --add
-  \item --sub
-  \item --mul
-  \item --comp
-  \item --column-plot
-  \item --row-plot
+  \item -\,-add
+  \item -\,-sub
+  \item -\,-mul
+  \item -\,-comp
+  \item -\,-column-plot
+  \item -\,-row-plot
 \end{itemize}
 
 \section{ifexport}\label{ifexport}\index{ctsimtext,ifexport}%
@@ -45,29 +59,29 @@ Export an imagefile to a standard graphics file.
 \begin{itemize}\itemsep=0pt
   \item --format
   \begin{itemize}\itemsep=0pt
-    \item --pgm
-    \item --pgmasc
-    \item --png
-    \item --png16
+    \item -\,-pgm
+    \item -\,-pgmasc
+    \item -\,-png
+    \item -\,-png16
   \end{itemize}
-  \item --center
+  \item -\,-center
   \begin{itemize}\itemsep=0pt
     \item median
     \item mode
     \item mean
   \end{itemize}
-  \item --auto
+  \item -\,-auto
   \begin{itemize}\itemsep=0pt
-     \item --full
-     \item --std0.1
-     \item --std0.5
-     \item --std1
-     \item --std2
-     \item --std3
+     \item -\,-full
+     \item -\,-std0.1
+     \item -\,-std0.5
+     \item -\,-std1
+     \item -\,-std2
+     \item -\,-std3
   \end{itemize}
-  \item --scale
-  \item --min
-  \item --max
+  \item -\,-scale
+  \item -\,-min
+  \item -\,-max
 \end{itemize}
 
 \section{ifinfo}\label{ifinfo}\index{ctsimtext,ifinfo}%
@@ -76,11 +90,11 @@ Displays information about an imagefile.
 
 \usage
 \begin{itemize}\itemsep=0pt
-  \item --labels
-  \item --no-labels
-  \item --stats
-  \item --no-stats
-  \item --help
+  \item -\,-labels
+  \item -\,-no-labels
+  \item -\,-stats
+  \item -\,-no-stats
+  \item -\,-help
 \end{itemize}
 
 \section{phm2pj}\label{phm2pj}\index{ctsimtext,phm2pj}%
@@ -89,37 +103,44 @@ Simulates collection of X-rays data (projections) around a phantom object.
 \usage
 phm2pj projection-file-name number-of-detectors number-of-views [options...]
 \begin{itemize}\itemsep=0pt
-  \item --phantom
-  Select a standard phantom 
+  \item -\,-phantom
+  Select a standard phantom
   \begin{itemize}\itemsep=0pt
     \item herman
-    \item herman-b
     \item shepp-logan
-    \item shepp-logan-b
+    \item unit-pulse
   \end{itemize}
 
-  \item --phmfile
+  \item -\,-phmfile
   Load a phantom definition definition
 
-  \item --geometry
+  \item -\,-geometry
   \begin{itemize}\itemsep=0pt
     \item parallel
     \item equiangular
     \item equilinear
   \end{itemize}
 
-  \item --nray
+  \item -\,-nray
     Number of samples per each detector
 
-  \item --rotangle
+  \item -\,-rotangle
     Sets the rotation amount as a multiple of pi. For parallel geometries use
-a rotation angle of 1 and for equilinear and equiangular geometries use a rotation angle of 2.
+a rotation angle of 1 and for equilinear and equiangular
+geometries use a rotation angle of 2. The default is to use to
+appropriate rotation angle based on the geometry.
 
-  \item --field-of-view
-    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.
+  \item -\,-view-ratio
+    Sets the field of view as a ratio of the diameter of the phantom.
+    For normal scanning, a value of 1.0 is fine.
 
-  \item --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. For parallel geometries, a value of 1.0 is fine. For other geometries, this should be at least 2.0 to avoid artifacts.
+  \item -\,-scan-ratio
+    Sets the length of scanning as a ratio of the view diameter.
+    For normal scanning, a value of 1.0 is fine.
+
+  \item -\,-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.
+    For parallel geometries, a value of 1.0 is fine. For other geometries, this should be at least 2.0 to avoid artifacts.
 \end{itemize}
 
 The Herman phantom is taken with permission from Gabor Hermans 1980 book\cite{HERMAN80}. The Shepp-Logan phantom was published in 1974\cite{SHEPP74}.
@@ -131,7 +152,8 @@ to average per pixel.
 
 \usage
 \begin{itemize}\itemsep=0pt
-  \item --nsamples
+  \item -\,-nsamples
+  \item -\,-view-ratio
 \end{itemize}
 
 \section{pj2if}\label{pj2if}\index{ctsimtext,pj2if}%
@@ -139,7 +161,7 @@ Convert a projection file into an imagefile.
 
 \usage
 \begin{itemize}\itemsep=0pt
-\item --help    Print brief online help
+\item -\,-help    Print brief online help
 \end{itemize}
 
 \section{pjinfo}\label{pjinfo}\index{ctsimtext,pjinfo}%
@@ -147,31 +169,35 @@ Displays information about a projection file.
 
 \usage
 \begin{itemize}\itemsep=0pt
-  \item --binaryheader
-  \item --binaryview
-  \item --startview
-  \item --endview
-  \item --dump
+  \item -\,-binaryheader
+  \item -\,-binaryview
+  \item -\,-startview
+  \item -\,-endview
+  \item -\,-dump
 \end{itemize}
 
 \section{pjrec}\label{pjrec}\index{ctsimtext,pjrec}%
 Reconstructs the interior of an object from a projection file.
 
-\usage
 \begin{twocollist}
 \twocolitemruled{\textbf{Parameter}}{\textbf{Options}}
-\twocolitem{\textbf{--filter}}{Selects which filter to apply to each projection. To properly reconstruct an image, this filter should be multiplied 
-by the absolute value of distance from zero frequency.
+\twocolitem{\textbf{-\,-filter}}{Selects which filter to apply to
+each projection. To properly reconstruct an image, this filter
+should be multiplied by the absolute value of distance from zero
+frequency.
 \begin{itemize}\itemsep=0pt
 \item abs\_bandlimit
 \item abs\_cosine
 \item abs\_hamming
 \end{itemize}
-}
-\twocolitem{\textbf{\-\-filter-parameter}}{Sets the alpha level for Hamming
+} \twocolitem{\textbf{-\,-filter-parameter}}{Sets the alpha level
+for Hamming
   window. At setting of 0.54, this equals the Hanning window.}
 
-\twocolitem{\textbf{\-\-filter-method}}{Selects the filtering method. For large numbers of detectors, \texttt{rfftw} is optimal. For smaller numbers of detectors, \texttt{convolution} might be a bit faster. 
+\twocolitem{\textbf{-\,-filter-method}}{Selects the filtering
+method. For large numbers of detectors, \texttt{rfftw} is optimal.
+For smaller numbers of detectors, \texttt{convolution} might be a
+bit faster.
 \begin{itemize}\itemsep=0pt
 \item convolution
 \item fourier
@@ -179,31 +205,42 @@ by the absolute value of distance from zero frequency.
 \item fftw
 \item rfftw
 \end{itemize}
-}
-\twocolitem{\textbf{\-\-filter-generation}}{Selects the filter generation. With convolution, \texttt{direct} is the proper method to select. With any of the frequency methods, \texttt{inverse-fourier} is the best method.
-\begin{itemize}\itemsep=0pt
-\item direct
-\item inverse-fourier
-\end{itemize}
-}
-\twocolitem{\textbf{--interpolation}}{Interpolation technique. \texttt{linear} is optimal.
+} \twocolitem{\textbf{-\,-interpolation}}{Interpolation technique.
+\texttt{linear} is optimal.
 \begin{itemize}\itemsep=0pt
 \item nearest
 \item linear
+\item cubic
 \end{itemize}
 }
-\twocolitem{\textbf{-backprojection}}{Selects the backprojection technique. A setting of \texttt{idiff3} is optimal.
+\end{twocollist}
+
+\subsection{Advanced Options}
+
+These options are only visible if \emph{Advanced Options} has been
+selected in the \texttt{File/Preferences} dialog.
+
+\begin{twocollist}
+\twocolitem{\textbf{-\,-backprojection}}{Selects the
+backprojection technique. A setting of \texttt{idiff} is optimal.
 \begin{itemize}\itemsep=0pt
 \item trig
 \item table
 \item diff
-\item diff2
-\item idiff2
-\item idiff3
+\item idiff
 \end{itemize}
 }
-\twocolitem{\textbf{--zeropad}}{Zeropad factor. A setting of \texttt{1} is optimal.}
 
-\twocolitem{\textbf{--preinterpolate}}{Selects preinterpolation interpolation technique and sets the preinterpolation factor. Currently, this is experimental and does not work well.}
-\end{twocollist}
+\twocolitem{\textbf{-\,-zeropad}}{Zeropad factor. A setting of
+\texttt{1} is optimal.}
 
+\twocolitem{\textbf{-\,-filter-generation}}{Selects the filter
+generation. With convolution, \texttt{direct} is the proper method
+to select. With any of the frequency methods,
+\texttt{inverse-fourier} is the best method.
+\begin{itemize}\itemsep=0pt
+\item direct
+\item inverse-fourier
+\end{itemize}
+}
+\end{twocollist}