\setheader{{\it Appendix \thechapter}}{}{}{\ctsimheadtitle}{}{{\it Appendix \thechapter}}%
\ctsimfooter%
-
Simple Graphics Package was created in 1980 by Kevin Rosenberg and
-is modelled after the graphics library in Foley and van
+is modelled after the hypothetical graphics library described by Foley and van
Dam\cite{FOLEY82}. It is designed to be platform-independent.
\section{Flowchart}
-Master coordinate (MC) level \\
-$\hspace{3cm} \downarrow$ \\
-Apply \emph{Current transformation matrix} \\
-$\hspace{3cm} \downarrow$ \\
-World coordinate (WC) level \\
-$\hspace{4cm} \downarrow$ \\
-Clipping against Window \\
-$\hspace{3cm} \downarrow$ \\
-Convert to Normalized device coordinates (NDC) \\
-$\hspace{3cm} \downarrow$ \\
-Clipping against Viewport \\
-$\hspace{3cm} \downarrow$ \\
-Convert to Physical device coordinates (PDC) \\
+\parbox{11cm}{
+\centerline{Master coordinate (MC) level}
+\centerline{$\downarrow$}
+\centerline{Apply \emph{Current transformation matrix}}
+\centerline{$\downarrow$}
+\centerline{World coordinate (WC) level}
+\centerline{$\downarrow$}
+\centerline{Clipping against Window}
+\centerline{$\downarrow$}
+\centerline{Convert to Normalized device coordinates (NDC)}
+\centerline{$\downarrow$}
+\centerline{Clipping against Viewport}
+\centerline{$\downarrow$}
+\centerline{Convert to Physical device coordinates (PDC)}
+}
\section{Functions}%
-\subsection{State functions}
-\begin{twocollist}
-\twocolitem{\texttt{eraseWindow()}}{Clears the screen}
-\twocolitem{\texttt{setColor(color)}}{Set current pen color}
-\twocolitem{\texttt{setLinestyle(style)}}{Set current pen style}
-\twocolitem{\texttt{setLinewidth(width)}}{Set current pen width}
-\twocolitem{\texttt{setTextColor(foreground, background)}}{Set text colors}
-\twocolitem{\texttt{setMarker(type, color)}}{Set marker attibutes}
-\twocolitem{\texttt{setRasterOp(rasterOp)}}{Set raster operator}
-\end{twocollist}
-
-
\subsection{Master coordinate functions}
\begin{twocollist}
\twocolitem{\texttt{setWindow(xmin, ymin, xmax, ymax)}}{Set window for world
\twocolitem{\texttt{polylineAbs(x[], y[], n)}}{Draw a series of lines to absolute position}
\twocolitem{\texttt{polylineRel(dx[], dy[], n)}}{Draw series of lines relative to current position}
\twocolitem{\texttt{drawString(str)}}{Draw text string at current positon}
-\twocolitem{\texttt{drawCircle(r}}{Draw circle at current positon}
+\twocolitem{\texttt{drawCircle(r)}}{Draw circle at current positon}
\twocolitem{\texttt{drawArc(r,start,stop)}}{Draw arc with center at current positon}
\twocolitem{\texttt{drawRect(xmin,ymin,xmax,ymax)}}{Draw rectangle}
\end{twocollist}
coordinates}
\end{twocollist}
+\subsection{State functions}
+\begin{twocollist}
+\twocolitem{\texttt{eraseWindow()}}{Clears the screen}
+\twocolitem{\texttt{setColor(color)}}{Set current pen color}
+\twocolitem{\texttt{setLinestyle(style)}}{Set current pen style}
+\twocolitem{\texttt{setLinewidth(width)}}{Set current pen width}
+\twocolitem{\texttt{setTextColor(foreground, background)}}{Set text colors}
+\twocolitem{\texttt{setMarker(type, color)}}{Set marker attibutes}
+\twocolitem{\texttt{setRasterOp(rasterOp)}}{Set raster operator}
+\end{twocollist}
+
\section{Coordinate Mapping}
\subsection{Dimensions}
\subsection{Formulas}
To convert from Master coordinates to World coordinates: \\
-Apply current transformation matrix
+\centerline{Apply \emph{current transformation matrix}}
To convert from WC to NDC:\\
\begin{equation}
object. These reconstructions can be visually and statistically
compared to the original phantom object.
-In order to use \ctsim\ effectively, some knowledge of how \ctsim\
-works and the approach taken is required. \ctsim\ deals with a
+In order to use \ctsim\ effectively, some knowledge of how
+\ctsim\ works and the approach taken is required. \ctsim\ deals with a
variety of object, but the two primary objects that we need to be
concerned with are the \emph{phantom} and the \emph{scanner}.
\latexonly{\begin{equation}s_d = s_r v_r p_d\end{equation}}
\latexignore{\\\centerline{\emph{Sd = Sr x Vr x Pd}}\\}
-Further, $f$ can be defined as \latexonly{$$f = f_r (v_r p_d /
-2)$$}\latexignore{\\$$F = FR x (VR x Pd)$$\\}
+Further, $f$ can be defined as
+\latexonly{\[f = f_r (v_r p_d / 2)\]}
+\latexignore{\\\centerline{\emph{F = FR x (VR x Pd)$$\\}}}
Substituting these equations into \latexignore{the above
equation,}\latexonly{equation~\ref{alphacalc},} We have,
\latexonly{
\begin{eqnarray}
-\alpha &= 2\,\sin^{-1} \frac{s_r v_r p_d / 2}{f_r v_r (p_d / 2)} \nonumber \\
-&= 2\,\sin^{-1} (s_r / f_r)
+\alpha &=& 2\,\sin^{-1} \frac{\displaystyle s_r v_r p_d / 2}{\displaystyle f_r v_r (p_d / 2)} \nonumber \\
+&=& 2\,\sin^{-1} (s_r / f_r)
\end{eqnarray}
} \latexignore{\\\centerline{\emph{\alpha = 2 sin (Sr / Fr)}}\\}
Since in normal scanning $s_r$ = 1, $\alpha$ depends only upon the
-\emph{focal length ratio}.
+\emph{focal length ratio} in normal scanning.
\subsubsection{Detector Array Size}
In general, you do not need to be concerned with the detector
\section{Image Comparison}\index{Image comparison}
Images can be compared statistically. Three measurements can be calculated
by \ctsim. They are taken from the standard measurements used by
-Herman\cite{HERMAN80}.
-$d$ is the normalized root mean squared distance measure,
-$r$ is the normalized mean absolute distance measure,
-and $e$ is the worst case distance measure over a $2\times2$ area.
-
-To compare two images, $A$ and $B$, each of which has $n$ columns and $m$ rows,
-these values are calculated as below.
-
-
-\latexonly{
-\begin{equation}
-d = \sqrt{\frac{\sum_{i=1}^{n}{\sum_{j=1}^{m}{(A_{ij} - B_{ij})^2}}}
- {\sum_{i=1}^{n}{\sum_{j=1}^{m}{(A_{ij} - A^{\_})^2}}}}
-\end{equation}
-\begin{equation}
-r = \max(|A_{ij} - B{ij}|)
-\end{equation}
-}
+Herman\cite{HERMAN80}. They are:
+\begin{description}
+\item[$d$] The normalized root mean squared distance measure.
+\item[$r$] The normalized mean absolute distance measure.
+\item[$e$] The worst case distance measure over a $2\times2$ area.
+\end{description}
+
+These measurements are defined in equations \ref{dequation} through \ref{bigrequation}.
+In these equations, $p$ denotes the phantom image, $r$ denotes the reconstruction
+image, and $\bar{p}$ denotes the average pixel value for $p$. Each of the images have a
+size of $m \times n$. In equation \ref{eequation} $[n/2]$ and $[m/2]$ denote the largest
+integers less than $n/2$ and $m/2$, respectively.
+
+\latexignore{These formulas are shown in the print documentation of \ctsim.}
+\latexonly{\begin{equation}\label{dequation}d = \sqrt{\frac{\displaystyle \sum_{i=1}^{n}{\sum_{j=1}^{m}{(p_{i,j} - r_{i,j})^2}}} {\displaystyle \sum_{i=1}^{n}{\sum_{j=1}^{m}{(p_{i,j} - \bar{p})^2}}}}\end{equation}}
+\latexonly{\begin{equation}\label{requation}r = \frac{\displaystyle \sum_{i=1}^{n}{\sum_{j=1}^{m}{|p_{i,j} - r_{i,j}|}}} {\displaystyle \sum_{i=1}^{n}{\sum_{j=1}^{m}{|p_{i,j}|}}}\end{equation}}
+\latexonly{\begin{equation}\label{eequation}e = \max_{1 \le k \le [n/2] \atop 1 \le l \le [m/2]}(|P_{k,l} - R_{k,l}|)\end{equation}}
+\latexonly{where}
+\latexonly{\begin{equation}\label{bigpequation}P_{k,l} = {\textstyle \frac{1}{4}} (p_{2k,2l} + p_{2k+1,2l} + p_{2k,2j+l} + p_{2k+1,2l+1})\end{equation}}
+\latexonly{\begin{equation}\label{bigrequation}R_{k,l} = \textstyle \frac{1}{4} (r_{2k,2l} + r_{2k+1,2l} + r_{2k,2l+1} + r_{2k+1,2l+1})\end{equation}}
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
The latest version of \ctsim, both executable programs and source code,
can be downloaded from the official
\ctsim\ \urlref{web site}{http://www.ctsim.org}. Additionally, these
- files are also available from the \urlref{FTP site}{ftp://ftp.ctsim.org}.
+ files are also available from the \ctsim\ \urlref{FTP site}{ftp://ftp.ctsim.org}.
\section{Installing Windows Binary}
\section{Installing Linux RPM}
Download the RPM file, then use
-the \texttt{rpm} manager program:\\
+the \texttt{rpm} manager program as follows:\\
\hspace{1cm}\texttt{rpm -Uvh} \emph{ctsim-*.rpm}\\
\ctsim\ and \ctsimtext\ will then be installed in the \texttt{/usr/local/bin}
\subsection{Optional Libraries}%
\begin{itemize}
\item \textbf{wxWindows}\\
- Used for platform-independent graphical interface. The graphical version
+ Used for the platform-independent graphical interface. The graphical version
of \ctsim\ requires this library.\\
\urlref{Web site}{http://www.wxwindows.org}
\item \textbf{FFTW}\\
- Used for fast frequency-based filtering and fourier transformations of images.
+ Used for fast Fourier transformations of projections and images.
Without this library \ctsim\ will use slower, traditional Fourier transformations.\\
\urlref{Web site}{http://www.fftw.org}
\ctsimtext\ is a master shell for all of the command-line utilities. The
command-line utilities can perform most of the functions of the graphical
shell. These command-line utilities are especially appropriate for use on
-systems without graphics, batch files, and parallel processing in a Beowulf
-computer cluster.
+systems without graphical capability, batch files, and parallel processing
+with a Beowulf-type computer cluster.
\usage \ctsimtext\ can be invoked via three different
methods.
commands may be given to \ctsimtext. The shell is exited by the
\texttt{quit} command. \ctsimtext\ uses the
\urlref{readline}{http://www.gnu.org} library on UNIX and Linux platforms
-to provide for command history processing.
+to provide command history processing.
\item \ctsimtext\ can also be called to
execute a single command. This is especially useful for batch
\section{if1}\label{if1}\index{if1}%
-Performs math functions on a single image.
+Performs math functions on a single image. The commands works with
+both real and complex valued images.
\usage
+\texttt{if1 input-filename output-filename [options...]}
+
+\textbf{Options}
\begin{itemize}\itemsep=0pt
- \item \doublehyphen{invert}
- \item \doublehyphen{log}
- \item \doublehyphen{exp}
- \item \doublehyphen{sqr}
- \item \doublehyphen{sqrt}
+ \item \doublehyphen{invert} - Negate pixel values
+ \item \doublehyphen{log} - Take natural logrithm of pixel values
+ \item \doublehyphen{exp} - Take natural exponent of pixel values
+ \item \doublehyphen{sqr} - Take square of pixel values
+ \item \doublehyphen{sqrt} - Take square root of pixel values
\end{itemize}
\section{if2}\label{if2}\index{if2}%
-Performs math functions on a two images.
+Performs math functions on a two images. The command works with both
+real and complex valued images.
\usage
+\texttt{if2 input-filename1 input-filename2 output-filename [options...]}
+
+\textbf{Options}
\begin{itemize}\itemsep=0pt
- \item \doublehyphen{add}
- \item \doublehyphen{sub}
- \item \doublehyphen{mul}
- \item \doublehyphen{comp}
- \item \doublehyphen{column-plot}
- \item \doublehyphen{row-plot}
+ \item \doublehyphen{add} - Add the two images
+ \item \doublehyphen{sub} - Subtract the two images
+ \item \doublehyphen{multiply} - Multiply the two images
+ \item \doublehyphen{divide} - Divide the two images
+ \item \doublehyphen{comp} - Statistically compare the two images
+ \item \doublehyphen{column-plot n} - Plot the values of a particular col
+ \item \doublehyphen{row-plot n} - Plot the values of a particular row
\end{itemize}
\section{ifexport}\label{ifexport}\index{ifexport}%
Export an image file to a standard graphics file.
\usage
+\texttt{ifexport input-filename output-filename -\,-format }\emph{graphic-format} \texttt{ [options...]}
+
+\textbf{Options}
\begin{itemize}\itemsep=0pt
\item \doublehyphen{format}
\begin{itemize}\itemsep=0pt
- \item \texttt{gm}
- \item \texttt{pgmasc}
- \item \texttt{png}
- \item \texttt{png16}
+ \item \texttt{pgm} - Portable graymap format.
+ \item \texttt{pgmasc} - ASCII PGM format.
+ \item \texttt{png} - Portable network graphics format.
+ \item \texttt{png16} - 16-bit PNG format.
\end{itemize}
- \item \doublehyphen{center}
+ \item \doublehyphen{center} - Set center of intensity window.
\begin{itemize}\itemsep=0pt
\item \texttt{median}
\item \texttt{mode}
\item \texttt{mean}
\end{itemize}
- \item \doublehyphen{auto}
+ \item \doublehyphen{auto} - Set half-width of intensity window.
\begin{itemize}\itemsep=0pt
\item \texttt{full}
\item \texttt{std0.1}
\item \texttt{std2}
\item \texttt{std3}
\end{itemize}
- \item \doublehyphen{scale}
- \item \doublehyphen{min}
- \item \doublehyphen{max}
+ \item \doublehyphen{scale} - Set size of output image. A value of
+ \texttt{1} is default and creates an output image the same size as the input image.
+ \item \doublehyphen{min} - Set the minimum intensity value.
+ \item \doublehyphen{max} - Set the maximum intensity value.
\end{itemize}
\section{ifinfo}\label{ifinfo}\index{ifinfo}%
Displays information about an imagefile.
\usage
+\texttt{ifinfo input-filename [options...]}
+
+\textbf{Options}
\begin{itemize}\itemsep=0pt
- \item \doublehyphen{labels}
- \item \doublehyphen{no-labels}
- \item \doublehyphen{stats}
- \item \doublehyphen{no-stats}
- \item \doublehyphen{help}
+ \item \doublehyphen{labels} - Display history labels.
+ \item \doublehyphen{no-labels} - Suppress history labels.
+ \item \doublehyphen{stats} - Display image statistics.
+ \item \doublehyphen{no-stats} - Suppress image statistics.
\end{itemize}
\section{phm2pj}\label{phm2pj}\index{phm2pj}%
Simulates collection of X-rays data (projections) around a phantom object.
\usage
-\texttt{phm2pj projection-file-name number-of-detectors number-of-views [options...]}
+\texttt{phm2pj projection-filename number-detectors number-views [options...]}
\begin{twocollist}
\twocolitem{\doublehyphen{phantom}}{Select a standard phantom.
\item \texttt{unit-pulse}
\end{itemize}
}
-\twocolitem{\doublehyphen{phmfile}}{Load a phantom definition definition}
+\twocolitem{\doublehyphen{phmfile}}{Reads a user-created phantom file.}
-\twocolitem{\doublehyphen{geometry}}{
+\twocolitem{\doublehyphen{geometry}}{Sets the scanner geometry. Valid values are:
\begin{itemize}\itemsep=0pt
\item \texttt{parallel}
\item \texttt{equiangular}
\twocolitem{\doublehyphen{nray}}{ Number of samples per each detector}
-\twocolitem{\doublehyphen{rotangle}}{Sets the rotation amount as a multiple of pi.
+\twocolitem{\doublehyphen{rotangle}}{The rotation angle as a multiple of pi.
For parallel geometries use a rotation angle of \texttt{1} and for equilinear and equiangular
geometries use a rotation angle of \texttt{2}. The default is to use to
appropriate rotation angle based on the geometry.}
\twocolitem{\doublehyphen{view-ratio}}{Sets the field of view as a ratio of the diameter of the phantom.
- For normal scanning, a default value of \texttt{1.0} is optimal.}
+ For normal scanning, the default value of \texttt{1.0} is optimal.}
\twocolitem{\doublehyphen{scan-ratio}}{Sets the length of scanning as a ratio of the view diameter.
- For normal scanning, a value of \texttt{1.0} is optimal.}
+ For normal scanning, the default value of \texttt{1.0} is optimal.}
-\twocolitem{\doublehyphen{focal-length}}{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 \texttt{1.0} is optimal. For other
+\twocolitem{\doublehyphen{focal-length}}{Sets the distance between the radiation source
+ and the center of the object as a ratio of the radius of the object.
+ 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}
\section{phm2if}\label{phm2if}\index{phm2if}%
-Converts a geometric phantom object into an imagefile. The size of the
-imagefile in pixels must be specified as well as the number of samples
-to average per pixel.
+Converts a geometric phantom object into an imagefile.
\usage
+\texttt{phm2if phantom-filename image-filename [options...]}
+
+\textbf{Options}
\begin{twocollist}
\twocolitem{\doublehyphen{nsamples}}{Number of samples in x \& y directions per pixel}
\twocolitem{\doublehyphen{view-ratio}}{Sets the view ration. For normal scanning,
Convert a projection file into an imagefile.
\usage
-\texttt{pj2if projection-file-name image-file-name x-size ysize [options...]}
+\texttt{pj2if projection-filename image-filename x-size y-size [options...]}
+\textbf{Options}
\begin{twocollist}
-\twocolitem{\doublehyphen{help}}{Print brief online help}
+\twocolitem{\doublehyphen{dump}}{Print all projection data to the console.}
\end{twocollist}
\section{pjinfo}\label{pjinfo}\index{pjinfo}%
Displays information about a projection file.
\usage
+\texttt{pjinfo projection-filename [options...]}
+
+\textbf{Options}
\begin{itemize}\itemsep=0pt
- \item \doublehyphen{binaryheader}
- \item \doublehyphen{binaryview}
- \item \doublehyphen{startview}
- \item \doublehyphen{endview}
- \item \doublehyphen{dump}
+ \item \doublehyphen{binaryheader} - Dump the binary header to the standard output.
+ This option is only used when manually creating a composite projection file from
+ several different projection files.
+ \item \doublehyphen{binaryview} - Dump binary view data to the standard output.
+ This option is only used when manually creating a composite projection file from
+ several different projection files.
+ \item \doublehyphen{startview} - Sets starting view to display. Default is \texttt{0}.
+ \item \doublehyphen{endview} - Sets ending view to display. Default is the last view.
+ \item \doublehyphen{dump} - Print all projection data to the console.
\end{itemize}
\section{pjrec}\label{pjrec}\index{pjrec}%
Reconstructs the interior of an object from a projection file.
+\usage
+\texttt{pjrec projection-filename image-filename image-cols image-rows [options...]}
+
+\textbf{Options}
+
\begin{twocollist}
\twocolitemruled{\textbf{Parameter}}{\textbf{Options}}
\twocolitem{\doublehyphen{filter}}{Selects which filter to apply to
bit faster.
\begin{itemize}\itemsep=0pt
\item \texttt{convolution}
-\item \texttt{fourier}
-\item \texttt{fourier-table}
-\item \texttt{fftw}
-\item \texttt{rfftw}
-\item fftw
-\item 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}
}
+\end{twocollist}
+\begin{twocollist}
\twocolitem{\doublehyphen{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
+\item \texttt{direct}
+\item \texttt{inverse-fourier}
\end{itemize}
}
\twocolitem{\doublehyphen{interpolation}}{Interpolation technique.
-\texttt{linear} is optimal.
+\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
-\item linear
-\item cubic
+\item \texttt{nearest}
+\item \texttt{linear}
+\item \texttt{cubic}
\end{itemize}
}
\twocolitem{\doublehyphen{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{\doublehyphen{zeropad}}{Zeropad factor. A setting of
-\texttt{1} is optimal.}
+\texttt{1} is optimal whereas a zeropad of \texttt{0} performs no zeropadding.}
\end{twocollist}
\ctsimfooter%
\section{Overview}
-\ctsim\ can also be executed via a web browser. The CGI program
+\ctsim\ can also be executed via a web browser. The Perl program
\texttt{ctsim.cgi} takes projections of a standard phantom object,
performs reconstruction, and then compares the rasterized phantom
object with the reconstruction. The comparison is performed both
visually by an image subtraction as well as by statistical
analysis.
+The \texttt{ctsim.cgi} program is invoked from the HTML file
+\texttt{simulate.html}.
+
\section{Requirements}
\begin{itemize}\itemsep=0pt
- \item Apache or other CGI compatible web server
+ \item \urlref{Apache}{http://www.apache.org} or other CGI-compatible web server
\item Perl (version 4.0 or higher)
\item A knowledgable system administrator. It is beyond the
scope of this manual to explain the configuration a web server.
\end{itemize}
+
+\section{Installation}
+Installation is rather automatic on Linux and UNIX systems. The
+\texttt{configure} script needs to be given options that specify
+the directory for web pages and for CGI programs.
\setlength{\evensidemargin}{0in}
\setlength{\oddsidemargin}{0in}
-
\latexonly{\includeonly{ctsim-concepts,ctsim-install,ctsim-gui,ctsim-textui,ctsim-web,ctsim-appendix}}
\hyphenation{poly-gon-al}
I hope that you enjoy \ctsim!
-\include{ctsim-concepts}
+%\include{ctsim-concepts}
-\include{ctsim-gui}
+%\include{ctsim-gui}
-\include{ctsim-textui}
+%\include{ctsim-textui}
-\include{ctsim-web}
+%\include{ctsim-web}
-\include{ctsim-install}
+%\include{ctsim-install}
-\include{ctsim-appendix}
+%\include{ctsim-appendix}
\newpage
\nonumber [0]{}
\sum [0]{}
\max [0]{}
+\atop [0]{}
+\setlength [2]{}
+\displaystyle [0]{}
+\textstyle [0]{}
+\[ [0]{}
+\] [0]{}
+\bar [1]{}
+\parbox [2]{}
+\toocomplex [1]{}
projects / ctsim.git / commitdiff