-\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}}%
\setfooter{\thepage}{}{}{}{}{\thepage}%
\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 definition files, and plotfiles.
+\ctsim\ can open projection files, image files, phantom files, and
+plot files.
-\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.
+
+\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}
-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}
-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}
-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}
-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}
-\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:
+\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}
-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.
+\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.
+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}
-\subsection{View}
+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}
+\subsubsection{Auto}
+\subsubsection{Full}
+This resets the intensity scale to the full scale of the image.
\subsection{Image}
-These commands create a new 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}
-These commands filter image.
+These commands filter and modify the image.
+
+\subsubsection{Arithmetic}
-\subsection{Anaylze}
+\subsubsection{Frequency Based}
+
+\subsection{Analyze}
+These commands are used for analyzing an image.
+
+\subsubsection{Plotting}
+
+\subsubsection{Image Comparison}
\section{Projection Menus}
+
+\subsection{File - Properties}
+
\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}
-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
\section{Plot Menus}
\subsection{File - Properties}
+
\subsection{File - Save}
Plot files can be saved. They are saved in an ASCII text format.
\subsection{View Menu}
+These commands set the scaling for the y-axis.
\subsubsection{Set}
\subsubsection{Auto}
\subsubsection{Full}
-
projects / ctsim.git / blobdiff