\chapter{The Graphical User Interface}\label{ctsim}\index{ctsim}%
-\setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
+\setheader{{\it CHAPTER \thechapter}}{}{}{\ctsimheadtitle}{}{{\it CHAPTER \thechapter}}%
\ctsimfooter%
-\section{Overview}
+\section{Overview}\index{Graphical shell}
\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...]}
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
-compatible between both little and big endian architectures.
+\section{File Types}\index{File types}
\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
+read and stored on the disk. Phantom files are stored in a simple
+ASCII format. A text editor is required to
create and edit these files.
\subsection{Image}
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.
+since both a real and imaginary component need to be store. When
+complex-valued images are viewed on the screen, only the real
+component is displayed.
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
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 of all windows.
+
+\subsection{File - Create Phantom}\index{Create phantom dialog}
+This command brings up a dialog box showing the phantoms that are preprogrammed
+into \ctsim. After selecting one of these phantoms, the new window with that
+phantom will be generated. The preprogrammed phantoms are:
+
+\begin{twocollist}
+\twocolitem{\textbf{Herman}}{The Herman head phantom\cite{HERMAN80}}
+\twocolitem{\textbf{Shepp-Logan}}{The head phantom of Shepp \& Logan\cite{SHEPP74}}
+\twocolitem{\textbf{Unit pulse}}{A phantom that has a value of \texttt{1} for the
+center of the phantom and \texttt{0} everywhere else.}
+\end{twocollist}
+
+\subsection{File - Create Filter}\index{Create filter dialog}
+This command brings up a dialog box showing the pre-programmed filters
+of \ctsim. This command will create a 2-dimensional image of the selected filter.
+The center of the filter is at the center of the image.
+
+These filters can be created in their natural frequency domain or in their spatial domain.
+\begin{twocollist}
+\twocolitem{\textbf{Filter}}{Selects the filter to generate.}
+\twocolitem{\textbf{Domain}}{Selects either the \texttt{Frequency} or \texttt{Spatial} domains. The filters have the
+frequency domain as their natural domain.}
+\twocolitem{\textbf{X Size}}{Number of columns in the output image.}
+\twocolitem{\textbf{Y Size}}{Number of rows in the output image.}
+\twocolitem{\textbf{Hamming Parameter}}{Sets the parameter for the Hamming filter.}
+\twocolitem{\textbf{Bandwidth}}{Sets the bandwidth of the filter.}
+\twocolitem{\textbf{Axis (input) Scale}}{Sets the scale for the filter input. By default, the input to the filter is
+the distance in pixels from the center of the image. By changing this value, one can set a scale the input to the filter.}
+\twocolitem{\textbf{Filter (output) Scale)}}{Multiplies the output of the filter by this amount. By default, the filter has a maximum
+value of \texttt{1}.}
+\end{twocollist}
+
+\subsection{File - Preferences}\index{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{twocollist}
+\twocolitem{\textbf{Advanced options}}{By default, this is turned off in new installations.
+These advanced options are not required for normal simulations. When \texttt{Advanced
+Options} is set, \ctsim\ will display more options during scanning of programs and
+the reconstruction of projections.}
+
+\twocolitem{\textbf{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{twocollist}
+
+\subsection{File - 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 set the \texttt{File Type} combo box to to the type of file that you wish to open.
+
+\subsection{File - 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{File - Close}
+As one would expect, this closes the active window.
+
+\subsection{File - Save As}
+Allows the saving of the contents of a window to any filename.
+
+\subsection{Help - Contents}
+This command displays the online help.
+
+\subsection{Help - About}
+This command shows the version number of \ctsim.
+
+
\section{Phantom Menus}
\subsection{Properties}
\item A list of all component phantom elements
\end{itemize}
-\subsection{Rasterize Dialog}
+\subsection{Rasterize Dialog}\index{Rasterize}
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
\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
+\twocolitem{\textbf{X size}}{Number of columns in image file}
+\twocolitem{\textbf{Y size}}{Number of rows in image file}
+\twocolitem{\textbf{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.}
+pixel in the image file 9 samples ($3\times3$) are averaged.}
\end{twocollist}
-\subsection{Projection Dialog}
+\subsection{Projection Dialog}\index{Projection collection}
This creates a projection file from a phantom. The options
available when collecting projections are:
\begin{twocollist}
-\twocolitem{\textbf{Geometry}}{
+\twocolitem{\textbf{Geometry}}{Selects the scanner geometry.
\begin{itemize}\itemsep=0pt
- \item Parallel
- \item Equiangular
- \item Equilinear
+ \item \texttt{Parallel}
+ \item \texttt{Equiangular}
+ \item \texttt{Equilinear}
\end{itemize}}
\twocolitem{\textbf{Number of detectors}}{Sets the number of
detectors in the detector array.}
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.}
+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.}
+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
-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.}
+\twocolitem{\textbf{Focal length ratio}}{Sets the distance between the
+radiation source and the center of the phantom as a
+ratio of the radius of the phantom. For parallel geometries, a value
+of \texttt{1.0} is optimal. 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}
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
+ \item Numeric statistics (minimum, maximum, mean, median, mode, and standard deviation)
+ \item History labels (text descriptions of the processing for this image)
\end{itemize}
-\subsection{File - Export}
+\subsection{File - Export}\index{Image 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}
+\begin{twocollist}
+\twocolitem{\textbf{PNG}}{Portable Network Graphics format. This uses 8-bits or
+256 shades of gray.}
+\twocolitem{\textbf{PNG-16}}{This is a 16-bit version of PNG which allows for
+65536 shades of gray.}
+\twocolitem{\textbf{PGM}}{Portable Graymap format. This is a common format used on
+UNIX systems.}
+\twocolitem{\textbf{PGM}}{ASCII version of PGM.}
+\end{twocollist}
\subsection{View}\label{intensityscale}
-These options are for change the intensity scale for viewing the image.
-They do not change the image data.
+These commands are used change the intensity scale for viewing the image.
+These commands do not change the image data. When the minimum intensity is
+set, then the color pure black is assigned to that image intensity. Similarly,
+when the maximum intensity is set, the the color pure white is assigned to that
+image value.
+
\subsubsection{Set}
+This command displays up a dialog box that allows you to set the lower
+and upper intensities to display.
+
\subsubsection{Auto}
+This command displays 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{twocollist}
+\twocolitem{\textbf{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.}
+
+\twocolitem{\textbf{Width}}{This sets the half-width of the intensity scale. The width
+is specified as a ratio of the standard deviation.}
+\end{twocollist}
+
+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 $median - 0.5 \times standard deviation$ and the maximum will be
+$median + 0.5 \times standard deviation$.
+
\subsubsection{Full}
-This resets the intensity scale to the full scale of the image.
+This command 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.
+and for some commands, also upon 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 the selection of 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
+are presented on the \texttt{View} menu and include:
+
+\begin{itemize}
+\item Surface plot versus wireframe
+\item Smooth shading versus flat shading
+\item Lighting on or off
+\item Color scale on or off
+\end{itemize}
-\subsection{Filter}
+\subsection{Filter}\index{Image 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 comparison plotting of rows and columns from two images.
+ 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 Polar Dialog}\label{convertpolardialog}\index{Polar conversion}
+Creates an image file with the polar conversion of the projection data. The options to set are:
+
+\begin{twocollist}
+\twocolitem{\textbf{xsize}}{Number of columns in output image.}
+\twocolitem{\textbf{ysize}}{Number of rows in output image.}
+\twocolitem{\textbf{interpolation}}{Selects the interpolation method.
+Currently, the \texttt{bilinear} option provides the highest
+quality interpolation.}
+\end{twocollist}
\subsection{Process - Convert FFT Polar Dialog}
The parameters for this option are the same as \helprefn{Convert
projections are Fourier transformed prior to conversion to polar
image.
-\subsection{Reconstruct - Filtered Backprojection Dialog}
+\subsection{Reconstruct - Filtered Backprojection Dialog}\index{Reconstruction 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.
+be consist of the the absolute value of distance from zero
+frequency optionally multiplied by a smoothing filter. The optimal
+filters to use are:
\begin{itemize}\itemsep=0pt
-\item abs\_bandlimit
-\item abs\_cosine
-\item abs\_hamming
+\item \texttt{abs\_bandlimit}
+\item \texttt{abs\_cosine}
+\item \texttt{abs\_hamming}
\end{itemize}
} \twocolitem{\textbf{Hamming parameter}}{Sets the alpha level for
Hamming window. At setting of 0.54, this equals the Hanning
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
+\item \texttt{convolution}
+\item \texttt{fourier} - Uses simple Fourier transform.
+\item \texttt{fourier-table} - Optimizes Fourier transform by precalculating trigometric functions.
+\item \texttt{fftw} - Uses complex-valued Fourier transform with the \emph{fftw} library.
+\item \texttt{rfftw} - Uses optimized real/half-complex Fourier transform.
\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.
+\texttt{cubic} is optimal when the
+data is smooth. Smooth data is obtained by taking many projections and/or
+using a smoothing filter. In the absence of smooth data, \texttt{linear} gives better results and
+is many times faster than cubic interpolation.
\begin{itemize}\itemsep=0pt
\item nearest
\subsection{Advanced Options}
These options are only visible if \emph{Advanced Options} has been
-selected in the \texttt{File/Preferences} dialog. These parameters
+selected in the \texttt{File - Preferences} dialog. These parameters
default to optimal settings and don't need to be adjusted except
by expert users.
\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
+\item \texttt{trig} - Use trigometric functions at each image point.
+\item \texttt{table} - Use precalculated trigometric tables.
+\item \texttt{diff} - Use difference method to iterate within image.
+\item \texttt{idiff} - Use integer iteration math.
\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.
+\texttt{inverse-fourier} is the best method.
\begin{itemize}\itemsep=0pt
-\item direct
-\item inverse-fourier
+\item \texttt{direct}
+\item \texttt{inverse-fourier}
\end{itemize}
}
\twocolitem{\textbf{Zeropad}}{Zeropad factor when using
-frequency-based filtering. A setting of \texttt{1} is optimal.}
+frequency-based filtering. A setting of \texttt{1} is optimal whereas
+a setting of \texttt{0} disables zero padding.}
\end{twocollist}
\section{Plot Menus}
\subsection{File - Properties}
+The displayed properties include:
-\subsection{File - Save}
-Plot files can be saved. They are saved in an ASCII text format.
+\begin{itemize}\itemsep=0pt
+\item the number of curves in the plot and the number of points per curve.
+\item the EZPlot commands used to format the plot are displayed.
+\item history labels from the originating image(s) and the plot function
+\end{itemize}
\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}
+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