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[ctsim.git] / doc / ctsim-gui.tex

diff --git a/doc/ctsim-gui.tex b/doc/ctsim-gui.tex
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@@ -1,99 +1,295 @@
-\chapter{ctsim - the Graphical User Interface}\label{ctsim}\index{ctsim}% 
+\chapter{The Graphical User Interface}\label{ctsim}\index{ctsim}%

 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%

-\setfooter{\thepage}{}{}{}{}{\thepage}%
+\setfooter{\thepage}{}{}{}{\manver}{\thepage}%
+

 
 \section{Overview}
 
 \section{Overview}

-\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 \ctsimtext\ as well as image processing and visualization features.
+\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.
+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...]}

 
 

-\ctsim\ can open projection files, image files, phantom definition files, and plotfiles.
+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.

 
 

-\usage
-ctsim [OPTIONS] [files to open...]
+\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.

 
 

-\section{Files Supported}

 \subsection{Phantom}
 \subsection{Phantom}

-Phantom files are supported. 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.
- 
+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}
 \subsection{Image}

-Image files are 2-dimensional files stored a 4-byte floating point values.
-They are stored in little-endian format and \ctsim\ incorporates routines
-to read and write files correctly on both big and little endian architextures.
+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.

 
 

-Images files can be either real or complex valued. Typically, all images
-are real except for images that have been processed by Fourier transforms.
+When complex-valued images are viewed on the screen, only the real
+component is displayed.

 
 \subsection{Projection}
 
 \subsection{Projection}

-Projection files are created from Phantom files during the projection process.
-Numerous options are available for creation of the these files.
+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}
 
 \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.
+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{Phantom Menus}
 
 
 \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}
 \subsection{Rasterize Dialog}

-This creates an image file from a phantom. Technically, it converts
-the phantom from a vector (infinite resolution) object into defined resolution
-image. The parameters to set are:
+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:

 
 

-x-size   Number of columns in image file
-y-size   Number of rows in image file
-samples  Numbers of samples taken per pixel in the x and y directions.
-         For example, if the nsamples is set to \texttt{3}, then for every
-         pixel in the image file, 9 samples (3 x 3) are averaged.
+\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}
 
 \subsection{Projection Dialog}

-This creates a projection file from a phantom.
+This creates a projection file from a phantom. The options
+available when collecting projections are:
+
+\begin{twocollist}
+\twocolitem{\textbf{Geometry}}{
+  \begin{itemize}\itemsep=0pt
+    \item Parallel
+    \item Equiangular
+    \item Equilinear
+  \end{itemize}}
+\twocolitem{\textbf{Number of detectors}}{Sets the number of
+detectors in the detector array.}
+
+\twocolitem{\textbf{Number of views}}{Sets the number of views
+collected}
+
+\twocolitem{\textbf{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{\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{\textbf{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.}
+\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
+and for equilinear and equiangular geometries use a rotation angle
+of 2. Using any other rotation angle will lead to artifacts.}
+\end{twocollist}
+
+

 
 \section{Image Menus}
 \subsection{File - Properties}
 Properties of image files include
 
 \section{Image Menus}
 \subsection{File - Properties}
 Properties of image files include

-%\begin{itemize}\itemsep=0
-%\item Whether the image is real or complex valued
-%\item Numeric statistics
-%\item Image file labels
-%\end{itemize}
+\begin{itemize}\itemsep=0pt
+  \item Whether the image is real or complex valued
+  \item Numeric statistics
+  \item Image file labels
+\end{itemize}

 
 

-\subsection{View}
+\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.
 These options are for change the intensity scale for viewing the image.
 They do not change the image data.

+\subsubsection{Set}
+\subsubsection{Auto}
+\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.
 
 
 \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}
+
+\subsubsection{Image Size}
+
+\subsubsection{3-D Conversion}
+Generates a 3-dimensional view of the current phantom.
+

 \subsection{Filter}
 \subsection{Filter}

-These commands filter image.
+These commands filter and modify the image.
+
+\subsubsection{Arithmetic}
+
+\subsubsection{Frequency Based}

 
 

-\subsection{Anaylze}
+\subsection{Analyze}

 These commands are used for analyzing an image.
 
 These commands are used for analyzing an image.
 

+\subsubsection{Plotting}
+
+\subsubsection{Image Comparison}
+

 \section{Projection Menus}
 \section{Projection Menus}

+
+\subsection{File - Properties}
+

 \subsection{Process - Convert Polar Dialog}\label{convertpolardialog}
 The parameters are \texttt{xsize}, \texttt{ysize}, and \texttt{interpolation}.
 \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 
+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}
 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 paramters for this option are the same as 
-\helprefn{convertpolardialog}{Convert Polar Dialog}. For this command,
-though, the projections are Fourier transformed prior to conversion to
-polar image.
+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
 
 \subsection{Reconstruct - Filtered Backprojection Dialog}
 This dialog sets the parameters for reconstructing an image from projections

-using the Filtered Backprojection technique. The parameters are identical
-to those for the \helprefn{pjrec}{pjrec} program.
+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}
 
 \section{Plot Menus}
 \subsection{File - Properties}


@@ -106,4 +302,3 @@ These commands set the scaling for the y-axis.
 \subsubsection{Set}
 \subsubsection{Auto}
 \subsubsection{Full}
 \subsubsection{Set}
 \subsubsection{Auto}
 \subsubsection{Full}

-