-\chapter{ctsim - the Graphical User Interface}\label{ctsim}\index{ctsim}%
-\setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
-\setfooter{\thepage}{}{}{}{}{\thepage}%
+\chapter{The Graphical User Interface}\label{ctsim}\index{ctsim}%
+\setheader{{\it CHAPTER \thechapter}}{}{}{\ctsimheadtitle}{}{{\it CHAPTER \thechapter}}%
+\ctsimfooter%
-\ctsim is the graphical shell for the CTSim project. It is
-written using the wxLibrary for cross-platform compatibility with GTK,
-Motif, and Microsoft Windows. It includes all of the functionality of
-the command-line tool {\tt ctsimtext} as well as image processing and visualization features.
-\ctsim can open projection files, image files, phantom definition files, and plotfiles.
+\section{Overview}
+\ctsim\ is the graphical shell for the CTSim project. It utilizes
+using the \urlref{wxWindows}{http://www.wxwindows.org} library for
+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.
-\usage
-ctsim [OPTIONS] [files to open...]
+\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. \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
+compatible between both little and big endian architectures.
+
+\subsection{Phantom}
+Besides loading phantom files from the disk, the Herman and
+Shepp-Logan phantoms are built-in to \ctsim. Phantom files can be
+read and stored on the disk. However, a text editor is required to
+create and edit these files.
+
+\subsection{Image}
+Image files are 2-dimensional files that store 4-byte floating
+point values. Images files can be either real or complex valued.
+Typically, all images are real except for images that have been
+processed by Fourier transforms. As you might expect,
+complex-valued images are twice the size of real-valued images
+since both a real and imaginary component need to be store.
+
+Images files can also store any number of text labels. \ctsim\ uses
+these labels for storing history information regarding
+the creation and modifications of images.
+
+When complex-valued images are viewed on the screen, only the real
+component is displayed.
+
+\subsection{Projection}
+Projection files are created from Phantom files during the
+projection process. Numerous options are available for the
+creation of the these files. The files are stored in a binary
+format with cross-platform compatibility on little and big endian
+architectures.
+
+\subsection{Plot}
+Plot files are created by \ctsim\ during analysis of image files.
+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}
+Displays the properties of a phantom which includes:
+
+\begin{itemize}\itemsep=0pt
+\item Overall dimensions of a phantom
+\item A list of all component phantom elements
+\end{itemize}
+
+\subsection{Rasterize Dialog}
+This creates an image file from a phantom. Technically, it
+converts the phantom from a vector (infinite resolution) object
+into a 2-dimension array of floating-point pixels. The parameters
+to set are:
+
+\begin{twocollist}
+\twocolitemruled{\textbf{Parameter}}{\textbf{Options}}
+\twocolitem{\texttt{X size}}{Number of columns in image file}
+\twocolitem{\texttt{Y size}}{Number of rows in image file}
+\twocolitem{\texttt{Samples per pixel}}{Numbers of samples taken
+per pixel in both the x and y directions. For example, if the
+\texttt{Samples per pixel} is set to \texttt{3}, then for every
+pixel in the image file 9 samples (3 x 3) are averaged.}
+\end{twocollist}
+
+\subsection{Projection Dialog}
+This creates a projection file from a phantom. The options
+available when collecting projections are:
+
+\begin{twocollist}
+\twocolitem{\texttt{Geometry}}{
+ \begin{itemize}\itemsep=0pt
+ \item Parallel
+ \item Equiangular
+ \item Equilinear
+ \end{itemize}}
+\twocolitem{\texttt{Number of detectors}}{Sets the number of
+detectors in the detector array.}
+
+\twocolitem{\texttt{Number of views}}{Sets the number of views
+collected}
+
+\twocolitem{\texttt{Samples per detector}}{Sets the number of
+samples collected for each detector}
+
+\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{\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{\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, 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 \texttt{1}
+and for equilinear and equiangular geometries use a rotation angle
+of \texttt{2}. Using any other rotation angle will lead to artifacts.}
+\end{twocollist}
+
+
+
+\section{Image Menus}
+\subsection{File - Properties}
+Properties of image files include
+\begin{itemize}\itemsep=0pt
+ \item Whether the image is real or complex valued
+ \item Numeric statistics
+ \item Image file labels
+\end{itemize}
+
+\subsection{File - Export}
+This command allows for exporting image files to a standard
+graphics file format. This is helpful when you want to take an
+image and import it into another application. The current
+\helprefn{intensity scale}{intensityscale} is used when exporting
+the file. The support file formats are:
+
+\begin{description}\itemsep=0pt
+\item[PNG]Portable Network Graphics format. This uses 8-bits or
+256 shades of gray.
+
+\item[PNG-16]This is a 16-bit version of PNG which allows for
+65536 shades of gray.
+\item[PGM]Portable Graymap format. This is a common format used on
+UNIX systems.
+\item[PGM]ASCII version of PGM.
+\end{description}
+
+
+\subsection{View}\label{intensityscale}
+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.
+
+\subsection{Image}
+These commands create a new image based upon the current 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. 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}.
+The \texttt{xsize} and \texttt{ysize} parameters set the size of the
+resulting image file. The \texttt{interpolation} parameter selects the
+interpolation method. Currently, the \texttt{bilinear} option provides
+the highest quality interpolation.
+
+\subsection{Process - Convert FFT Polar Dialog}
+The parameters for this option are the same as \helprefn{Convert
+Polar Dialog}{convertpolardialog}. For this command, though, the
+projections are Fourier transformed prior to conversion to polar
+image.
+
+\subsection{Reconstruct - Filtered Backprojection Dialog}
+This dialog sets the parameters for reconstructing an image from projections
+using the Filtered Backprojection technique.
+
+
+\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.
+\begin{itemize}\itemsep=0pt
+\item abs\_bandlimit
+\item abs\_cosine
+\item abs\_hamming
+\end{itemize}
+} \twocolitem{\textbf{Hamming 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.
+\begin{itemize}\itemsep=0pt
+\item convolution
+\item fourier
+\item fourier\_table
+\item fftw
+\item rfftw
+\end{itemize}
+}
+
+\twocolitem{\textbf{Interpolation}}{Interpolation technique.
+\texttt{cubic} is optimal when many projections are taken and the
+data is smooth. Otherwise, \texttt{linear} gives better results.
+Linear is also much faster than cubic interpolation.
+
+\begin{itemize}\itemsep=0pt
+\item nearest
+\item linear
+\item cubic
+\end{itemize}
+}
+\end{twocollist}
+
+\subsection{Advanced Options}
+
+These options are only visible if \emph{Advanced Options} has been
+selected in the \texttt{File/Preferences} dialog. These parameters
+default to optimal settings and don't need to be adjusted except
+by expert users.
+
+\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 idiff
+\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{Zeropad}}{Zeropad factor when using
+frequency-based filtering. A setting of \texttt{1} is optimal.}
+
+\end{twocollist}
+
+\section{Plot Menus}
+\subsection{File - Properties}
+The displayed properties include the number of curves in the plot
+and the number of points per curve. Additionally, the EZPlot
+commands used to format the plot are displayed.
+
+\subsection{View Menu}
+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}
+This command sets the upper and lower limits for the y-axis.
+
+\subsubsection{Auto}
+This command automatically sets the upper and lower limits for the
+y-axis. Please refer to the \texttt{View - Auto} documentation for
+image files for the details.
+
+\subsubsection{Full}
+The command resets the upper and lower limits of the y-axis to the
+minimum and maximum values of the curves.
projects / ctsim.git / blobdiff