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
\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
+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.}
\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
\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}
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{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 brings up a dialog box that allows you to set the lower
+This command displays 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
+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:
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 $median - 0.5 \times standard deviation$ 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 selecting a compatible image,
+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.
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 Surface plot versus wireframe
+\item Smooth shading versus flat shading
\item Lighting on or off
-\item Color scale
+\item Color scale on or off
\end{itemize}
\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 are simple arithmetic functions that should be self-explanatory.
\subsubsection{Frequency Based}
This commands allow the Fourier and inverse Fourier transformations of
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.
\section{Projection Menus}
\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}
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 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 \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 math.
\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 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