\ctsimfooter%
-\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
+\section{Overview}\index{Graphical interface}
+\ctsim\ is the graphical shell for the CTSim project. This shell uses
+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 \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
+any number of files that you want \ctsim\ to
automatically open. \ctsim\ can open projection files, image
files, phantom files, and plot files.
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 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
\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.
+files for easy cross-platform support and editing.
\section{Global Menu Commands}
-These commands are present on the menus of all windows.
+These global commands are present on the menus of all windows.
-\subsection{File - Create Phantom}\index{Create phantom dialog}
+\subsection{File - Create Phantom}\label{IDH_DLG_PHANTOM}\index{Dialog!Create phantom}
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:
center of the phantom and \texttt{0} everywhere else.}
\end{twocollist}
-\subsection{File - Create Filter}\index{Create filter dialog}
+\subsection{File - Create Filter}\label{IDH_DLG_FILTER}\index{Dialog!Create filter}
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{Hamming Parameter}}{ This parameter adjusts the smoothing of the Hamming
+filter and can range from \texttt{0} to \texttt{1}.
+At a setting of \texttt{1}, the Hamming filter is the same as the bandlimit filter.
+At a setting of \texttt{0.54}, the Hamming filter is the same as the Hanning
+window.}
\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
+the distance in pixels from the center of the image. By changing this value, one can set a scale the input to the filter.
+For example, if the output image is \texttt{101} pixels and thus the center of the image is at \texttt{(50,50)}, then a pixel
+lying at point \texttt{100,50} would be 50 units from the center of the filter. By applying an \texttt{Axis scale} of
+\texttt{0.1}, then that point would be scaled to 5 units from the center of 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}
+\subsection{File - Preferences}\label{IDH_DLG_PREFERENCES}\index{Dialog!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
+On UNIX and Linux environments, they are stored in the user's 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 required for normal simulations. When \texttt{Advanced
-Options} is set, \ctsim\ will display more options during scanning of programs and
+These advanced options are not required for normal simulations. When \texttt{Advanced
+Options} is set, \ctsim\ will display more options during scanning of phantoms and
the reconstruction of projections.}
\twocolitem{\textbf{Ask before deleting new documents}}{By default, this is turned on in
\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 select that to the type of file that you wish to open.
+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
\item A list of all component phantom elements
\end{itemize}
-\subsection{Rasterize Dialog}\index{Rasterize}
+\subsection{Rasterize Dialog}\label{IDH_DLG_RASTERIZE}\index{Dialog!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
to set are:
\begin{twocollist}
-\twocolitemruled{\textbf{Parameter}}{\textbf{Options}}
\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 ($3\times3$) are averaged.}
+pixel in the image file 9 samples \latexonly{($3\times3$)}\latexignore{(3 x 3)}
+are averaged.}
\end{twocollist}
-\subsection{Projection Dialog}\index{Projection collection}
+\subsection{Projection Dialog}\label{IDH_DLG_PROJECTIONS}\index{Dialog!Projections}
This creates a projection file from a phantom. The options
available when collecting projections are:
\twocolitem{\textbf{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
-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
+\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}
+\textbf{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}
+multiple of \latexonly{$\pi$.}\latexignore{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}
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}\index{Image export}
+\subsection{File - Export}\label{IDH_DLG_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:
+the file. The supported graphic formats are:
\begin{twocollist}
\twocolitem{\textbf{PNG}}{Portable Network Graphics format. This uses 8-bits or
\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.
-\subsubsection{Set}
-This command brings up a dialog box that allows you to set the lower
+\subsection{View}\label{intensityscale}\index{Intensity scale}
+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.
+
+Changing the intensity scale is useful when examining different image features.
+In clinical medicine, the intensity scale is often changed to examine bone
+(high intensity) verses soft-tissue (medium intensity) features.
+
+\subsubsection{Set}\label{IDH_DLG_MINMAX}
+This command displays 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
+\subsubsection{Auto}\label{IDH_DLG_AUTOSCALE}
+This command displays a dialog box that allows \ctsim\ to automatically
+make an intensity scale. The parameters that \ctsim\ needs to make this
automatic scale are:
\begin{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 \texttt{median - 0.5 x standard deviation} and the maximum will be
-\texttt{median + 0.5 x standard deviation}.
+be \latexonly{$median - 0.5 \times standardDeviation$}\latexignore{\emph{median - 0.5 x standardDeviation}}
+and the maximum will be \latexonly{$median + 0.5 \times standardDeviation$.}\latexignore{\emph{
+median + 0.5 x standardDeviation}.}
\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 selecting a compatible image,
+same size as 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.
+This command will generate a new image based on the current image. The new
+image can be scaled to any size. A dialog
+appears asking for the size of the new image. Bilinear interpolation
+is used when calculating the new image.
\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:
+are presented on the \texttt{View} menu and include:
\begin{itemize}
-\item Surface plot
-\item Smooth shading
-\item Lighting on or off
-\item Color scale
+\item Surface plot versus wireframe plot.
+\item Smooth shading versus flat shading.
+\item Lighting on or off.
+\item Color scale on or off.
\end{itemize}
-\subsection{Filter}\index{Image filter}
-These commands filter and modify the image.
+\subsection{Filter}\index{Image!Filter}
+These commands filter and modify the image
\subsubsection{Arithmetic}
-These are simple arithmetic functions that should be self explanatory.
+These commands operate on the image on a pixel-by-pixel basis. The commands
+support both real and complex-valued images. The available arithmetic commards are:
+
+\begin{twocollist}
+ \twocolitem{\textbf{Invert}}{Negate pixel values.}
+ \twocolitem{\textbf{Log}}{Take natural logrithm of pixel values.}
+ \twocolitem{\textbf{Exp}}{Take natural exponent of pixel values.}
+ \twocolitem{\textbf{Square}}{Take square of pixel values.}
+ \twocolitem{\textbf{Square root}}{Take square root of pixel values.}
+\end{twocollist}
+
\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}
+images between Fourier to natural orders 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.
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.
The commands plot rows and columns of images. There are also commands
that perform FFT and IFFT transformations prior to plotting.
-\subsubsection{Image Comparison}
+\subsubsection{Image Comparison}\label{IDH_DLG_COMPARISON}\index{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.
+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.
+
+The three distance measures are:
+
+\begin{twocollist}
+\twocolitem{\textbf{$d$}}{The normalized root mean squared distance measure.}
+\twocolitem{\textbf{$r$}}{The normalized mean absolute distance measure.}
+\twocolitem{\textbf{$e$}}{The worst case distance measure over a \latexonly{$2\times2$}\latexignore{\emph{2 x 2}} pixel area.}
+\end{twocollist}
\section{Projection Menus}
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
+\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}\index{Polar conversion}
+\subsection{Process - Convert Polar Dialog}\label{IDH_DLG_POLAR}\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.
+\twocolitem{\textbf{X Size}}{Number of columns in output image.}
+\twocolitem{\textbf{Y Ssize}}{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
+The parameters for this option are the same as the \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}\index{Reconstruction dialog}
+\subsection{Reconstruct - Filtered Backprojection Dialog}\label{IDH_DLG_RECONSTRUCTION}\index{Dialog!Reconstruction}
This dialog sets the parameters for reconstructing an image from projections
-using the Filtered Backprojection technique.
-
+using the filtered backprojection technique. The parameters available are:
\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 \texttt{abs\_bandlimit}
\item \texttt{abs\_cosine}
\item \texttt{abs\_hamming}
+\item \texttt{abs\_hanning}
\end{itemize}
} \twocolitem{\textbf{Hamming parameter}}{Sets the alpha level for
-Hamming window. At setting of 0.54, this equals the Hanning
+Hamming window. This parameter adjusts the smoothing of the Hamming
+filter and can range from \texttt{0} to \texttt{1}.
+At a setting of \texttt{1}, the Hamming filter is the same as the bandlimit filter.
+At a setting of \texttt{0.54}, the Hamming filter is the same as the Hanning
window.}
+\end{twocollist}
+\begin{twocollist}
\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
+smaller numbers of detectors, \texttt{convolution} can be
faster.
\begin{itemize}\itemsep=0pt
\item \texttt{convolution}
-\item \texttt{fourier}
-\item \texttt{fourier-table}
-\item \texttt{fftw}
-\item \texttt{rfftw}
+\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 also many times faster than cubic interpolation.
\begin{itemize}\itemsep=0pt
\item nearest
}
\end{twocollist}
-\subsection{Advanced Options}
+\textbf{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 \texttt{trig} - Uses trigometric functions at each image point
-\item \texttt{table} - Uses precalculated trigometric tables
-\item \texttt{diff} - Uses difference method to step along image
-\item \texttt{idiff} - Uses integer difference method
+\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 techique.
\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. Settings greater than \texttt{1}
+perform larger amounts of zero padding but without any significant benefit.}
\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.
+The displayed properties include:
+
+\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. They are analogous
projects / ctsim.git / blobdiff