element-type cx cy dx dy r a
\end{verbatim}
The first entry defines the type of the element, either
-\rtfsp\texttt{rectangle}, \texttt{}, \texttt{triangle},
+\rtfsp\texttt{rectangle}, \texttt{ellipse}, \texttt{triangle},
\rtfsp\texttt{sector}, or \texttt{segment}. \texttt{cx},
\rtfsp\texttt{cy}, \texttt{dx} and \texttt{dy} have different
meanings depending on the element type.
\emph{phantom diameter}. Remember, as mentioned above, the
phantom dimensions are also padded by 1\%.
-The other important geometry variables for scanning objects are the
-\emph{view ratio}, \emph{scan ratio}, and \emph{focal length ratio}.
-These variables are all input into \ctsim\ in terms of ratios rather
-than absolute values.
+The other important geometry variables for scanning phantoms are
+the \emph{view diameter}, \emph{scan diameter}, and \emph{focal
+length}. These variables are all input into \ctsim\ in terms of
+ratios rather than absolute values.
\subsubsection{Phantom Diameter}
\begin{figure}
experimental purposes, it may be desirable to scan an area either
larger or smaller than the \emph{view diameter}. Thus, the concept
of \emph{scan ratio}, \latexonly{$s_r$,}\latexignore{\emph{SR},}
-is born. The scan diameter
+is arises. The scan diameter
\latexonly{$s_d$}\latexignore{\emph{Sd}} is the diameter over
which x-rays are collected and is defined as \latexonly{$$s_d =
v_d s_r$$}\latexignore{\\$$\emph{Sd = Vd x SR}$$\\} By default and
\subsubsection{Detector Array Size}
In general, you do not need to be concerned with the detector
-array size. It is automatically calculated by \ctsim. For those
-interested, this section explains how the detector array size is
-calculated.
+array size. It is automatically calculated by \ctsim. For the
+particularly interested, this section explains how the detector
+array size is calculated.
For parallel geometry, the detector length is equal to the scan
diameter.
cross-platform compatibility. The graphical shell is compatible
with Microsoft Windows, \urlref{GTK}{http://www.gtk.org}, and
\urlref{Motif}{http://www.openmotif.org} graphical environments.
-This graphical includes all of the functionality of the
-command-line interface \helprefn{\ctsimtext}{ctsimtext} as well as
-great image processing and visualization features.
-
-\ctsim\ can open projection files, image files, phantom files, and
-plot files.
\usage \texttt{ctsim [files to open...]}
You can invoke \ctsim\ by itself on the command line, or include
on the command-line any number of files that you want \ctsim\ to
-automatically open.
+automatically open. \ctsim\ can open projection files, image
+files, phantom files, and plot files.
+
\section{File Types Support}
Phantom and plot files are stored as ASCII text. In contrast,
-image and projection files are stored in binary format. \ctsim
-incorporates logic so that binary files are cross-platform
+image and projection files are stored in binary format.
+\ctsim\ incorporates logic so that binary files are cross-platform
compatible between both little and big endian architectures.
\subsection{Phantom}
They can be read and stored on the disk. They are stored as ASCII
files for easy cross-platform support.
+\section{Global Menu Commands}
+These commands are present on the menus for all of the windows of
+\ctsim.
+
+\subsection{Preferences...}
+This command displays a dialog box that allows users to control
+the behavior of \ctsim. These options are saved across \ctsim sessions.
+Under Microsoft Windows environments, they are stored in the registry.
+On UNIX and Linux environments, they are stored in the users home
+directory with the filename of \texttt{.ctsim}.
+
+\begin{description}\itemsep=0pt
+\item[Advanced options] By default, this is turned off in new installations.
+These advanced options are required for normal simulations. When \texttt{Advanced
+Options} is set, \ctsim\ will display more options during scanning of programs and
+the reconstruction of projections.
+
+\item[Ask before deleting new documents] By default, this is turned on in
+new installations. With this option set, \ctsim\ will ask before closing
+documents that have been modified or never saved on disk. By turning off
+this option, \ctsim\ will never ask if you want to save a file -- you'll
+be responsible for saving any files that you create.
+
+\end{description}
+
+\subsection{Open...}
+This command opens a file section dialog box. Of special consideration
+is the \texttt{File Type} combo box on the bottom of the dialog. You need
+to select that to the type of file that you wish to open.
+
+\subsection{Save}
+This command saves the contents of the active window. If the window hasn't
+been named, a dialog box will open asking for the file name to use.
+
+\subsection{Save As...}
+Allows the saving of the contents of a window to any filename.
+
+\subsection{Help}
+This command displays the online help.
+
+\subsection{About}
+This command shows the version number of \ctsim.
+
+
\section{Phantom Menus}
\subsection{Properties}
available when collecting projections are:
\begin{twocollist}
-\twocolitem{\textbf{Geometry}}{
+\twocolitem{\texttt{Geometry}}{
\begin{itemize}\itemsep=0pt
\item Parallel
\item Equiangular
\item Equilinear
\end{itemize}}
-\twocolitem{\textbf{Number of detectors}}{Sets the number of
+\twocolitem{\texttt{Number of detectors}}{Sets the number of
detectors in the detector array.}
-\twocolitem{\textbf{Number of views}}{Sets the number of views
+\twocolitem{\texttt{Number of views}}{Sets the number of views
collected}
-\twocolitem{\textbf{Samples per detector}}{Sets the number of
+\twocolitem{\texttt{Samples per detector}}{Sets the number of
samples collected for each detector}
-\twocolitem{\textbf{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.}
+\twocolitem{\texttt{View Ratio}}{Sets the field of view as a ratio
+of the diameter of the phantom. For normal scanning, use a value of
+\texttt{1.0}.}
-\twocolitem{\textbf{Scan Ratio}}{Sets the length of scanning as a
-ratio of the view diameter. For normal scanning, a value of 1.0 is
-fine.}
+\twocolitem{\texttt{Scan Ratio}}{Sets the length of scanning as a
+ratio of the view diameter. For normal scanning, use a value of \texttt{1.0}.}
-\twocolitem{\textbf{Focal length ratio}}{Sets the distance of the
+\twocolitem{\texttt{Focal length ratio}}{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.}
+For parallel geometries, use a value of \texttt{1.0}. For other
+geometries, this should be at least \texttt{2.0} to avoid artifacts.}
\end{twocollist}
\subsection{Advanced Options}
\begin{twocollist}
\twocolitem{\textbf{Rotation Angle}}{Sets the rotation amount as a
-multiple of pi. For parallel geometries use a rotation angle of 1
+multiple of pi. For parallel geometries use a rotation angle of \texttt{1}
and for equilinear and equiangular geometries use a rotation angle
-of 2. Using any other rotation angle will lead to artifacts.}
+of \texttt{2}. Using any other rotation angle will lead to artifacts.}
\end{twocollist}
These options are for change the intensity scale for viewing the image.
They do not change the image data.
\subsubsection{Set}
+This command brings up a dialog box that allows you to set the lower
+and upper intensities to display.
+
\subsubsection{Auto}
+This command brings up a dialog box that allows \ctsim\ to automatically
+make an intensity scale. The options that \ctsim\ needs to make this
+automatic scale are:
+
+\begin{description}\itemsep=0pt
+\item[Center] This sets the center of the intensity scale. Currently,
+\ctsim\ allows you to use either the mean, mode, or median of the image
+as the center of the intensity scale.
+
+\item[Width] This sets the half-width of the intensity scale. The width
+is specified as a ratio of the standard deviation.
+\end{description}
+
+As an example, if \texttt{median} is selected as the center and
+\texttt{0.5} is selected as the width, the the minimum intensity will
+be \texttt{median - 0.5 x standard deviation} and the maximum will be
+\texttt{median + 0.5 x standard deviation}.
+
\subsubsection{Full}
This resets the intensity scale to the full scale of the image.
and for some commands, also a comparison image.
\subsubsection{Add, Subtract, Multiply, Divide}
+These are simple arithmetic operations. \ctsim\ will display a dialog
+box showing all of the currently opened image files that are the
+same size of the active image. After selecting a compatible image,
+\ctsim\ will perform the arithmetic operation on the two images and
+make a new result image.
\subsubsection{Image Size}
+This command will generate a new window with the current image scaled to
+any size. Currently, \texttt{bilinear} interpolation provides the best
+image quality.
\subsubsection{3-D Conversion}
-Generates a 3-dimensional view of the current phantom.
+Generates a 3-dimensional view of the current phantom. This view can be
+rotated in three dimensions. The left and right arrow control the z-axis
+rotation, the up and down arrows control the x-axis rotation. The y-axis
+rotation is controlled by the \texttt{T} and \texttt{Y} keys. Other options
+include:
+
+\begin{itemize}
+\item Surface plot
+\item Smooth shading
+\item Lighting on or off
+\item Color scale
+\end{itemize}
\subsection{Filter}
These commands filter and modify the image.
\subsubsection{Arithmetic}
+These are simple arithmetic functions that should be self explanatory.
\subsubsection{Frequency Based}
+This commands allow the Fourier and inverse Fourier transformations of
+images. By default, the transformations will automatically convert
+images from Fourier to natural order as expected. For example, \texttt{2-D FFT}
+will transform the points into natural order after the Fourier transform.
+Similarly the inverse, \texttt{2-D IFFT}, will reorder the points from
+natural order to Fourier order before applying the inverse Fourier transformation.
+
+As you would expect, images that undergo frequency filtering will be complex-valued
+images. Normally, only the real component is shown by \ctsim. However, \ctsim\ does
+have options for converting a complex-valued image into a real-valued image via
+the \texttt{Magnitude} and \texttt{Phase} filtering commands.
\subsection{Analyze}
These commands are used for analyzing an image.
\subsubsection{Plotting}
+The commands plot rows and columns of images. There are also commands
+that perform FFT and IFFT transformations prior to plotting.
\subsubsection{Image Comparison}
+This command performs statistical comparisons between two images. An option
+also exists for generating a difference image from the two input images.
+
+There are also commands for plotting rows and columns from two images on
+a single plot. This is quite helpful when comparing a phantom to a reconstruction.
\section{Projection Menus}
\subsection{File - Properties}
+The displayed properties include:
+
+\begin{itemize}
+\item Number of detectors in the projections
+\item Number of views
+\item The variables used when generating the projections from the phantom
+\end{itemize}
\subsection{Process - Convert Polar Dialog}\label{convertpolardialog}
The parameters are \texttt{xsize}, \texttt{ysize}, and \texttt{interpolation}.
\section{Plot Menus}
\subsection{File - Properties}
-
-\subsection{File - Save}
-Plot files can be saved. They are saved in an ASCII text format.
+The displayed properties include
\subsection{View Menu}
-These commands set the scaling for the y-axis.
+These commands set the scaling for the y-axis. They are analogous
+to the options used for setting the intensity scale for images.
\subsubsection{Set}
\subsubsection{Auto}
\subsubsection{Full}
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