r534: no message

diff --git a/doc/ctsim-concepts.tex b/doc/ctsim-concepts.tex
index 9653a120ead80b7343711c9699b6a87b9dc600f9..21f94ddec9e999d3d39ea3f09613f51bbf824f0d 100644 (file)
--- a/doc/ctsim-concepts.tex
+++ b/doc/ctsim-concepts.tex
@@ -39,7 +39,7 @@ phantom.  Each line contains seven entries, in the following form:
 element-type cx cy dx dy r a
 \end{verbatim}
 The first entry defines the type of the element, either
 element-type cx cy dx dy r a
 \end{verbatim}
 The first entry defines the type of the element, either

-\rtfsp\texttt{rectangle}, \texttt{}, \texttt{triangle},
+\rtfsp\texttt{rectangle}, \texttt{ellipse}, \texttt{triangle},

 \rtfsp\texttt{sector}, or \texttt{segment}. \texttt{cx},
 \rtfsp\texttt{cy}, \texttt{dx} and \texttt{dy} have different
 meanings depending on the element type.
 \rtfsp\texttt{sector}, or \texttt{segment}. \texttt{cx},
 \rtfsp\texttt{cy}, \texttt{dx} and \texttt{dy} have different
 meanings depending on the element type.


@@ -114,10 +114,10 @@ variable is the diameter of the circle surround the phantom, or the
 \emph{phantom diameter}. Remember, as mentioned above, the
 phantom dimensions are also padded by 1\%.
 
 \emph{phantom diameter}. Remember, as mentioned above, the
 phantom dimensions are also padded by 1\%.
 

-The other important geometry variables for scanning objects are the
-\emph{view ratio}, \emph{scan ratio}, and \emph{focal length ratio}.
-These variables are all input into \ctsim\ in terms of ratios rather
-than absolute values.
+The other important geometry variables for scanning phantoms are
+the \emph{view diameter}, \emph{scan diameter}, and \emph{focal
+length}. These variables are all input into \ctsim\ in terms of
+ratios rather than absolute values.

 
 \subsubsection{Phantom Diameter}
 \begin{figure}
 
 \subsubsection{Phantom Diameter}
 \begin{figure}


@@ -165,7 +165,7 @@ By default, the entire \emph{view diameter} is scanned. For
 experimental purposes, it may be desirable to scan an area either
 larger or smaller than the \emph{view diameter}. Thus, the concept
 of \emph{scan ratio}, \latexonly{$s_r$,}\latexignore{\emph{SR},}
 experimental purposes, it may be desirable to scan an area either
 larger or smaller than the \emph{view diameter}. Thus, the concept
 of \emph{scan ratio}, \latexonly{$s_r$,}\latexignore{\emph{SR},}

-is born. The scan diameter
+is arises. The scan diameter

 \latexonly{$s_d$}\latexignore{\emph{Sd}} is the diameter over
 which x-rays are collected and is defined as \latexonly{$$s_d =
 v_d s_r$$}\latexignore{\\$$\emph{Sd = Vd x SR}$$\\} By default and
 \latexonly{$s_d$}\latexignore{\emph{Sd}} is the diameter over
 which x-rays are collected and is defined as \latexonly{$$s_d =
 v_d s_r$$}\latexignore{\\$$\emph{Sd = Vd x SR}$$\\} By default and


@@ -260,9 +260,9 @@ Since in normal scanning $s_r$ = 1, $\alpha$ depends only upon the
 
 \subsubsection{Detector Array Size}
 In general, you do not need to be concerned with the detector
 
 \subsubsection{Detector Array Size}
 In general, you do not need to be concerned with the detector

-array size. It is automatically calculated by \ctsim. For those
-interested, this section explains how the detector array size is
-calculated.
+array size. It is automatically calculated by \ctsim. For the
+particularly interested, this section explains how the detector
+array size is calculated.

 
 For parallel geometry, the detector length is equal to the scan
 diameter.
 
 For parallel geometry, the detector length is equal to the scan
 diameter.

diff --git a/doc/ctsim-gui.tex b/doc/ctsim-gui.tex
index 1353c1a8ed9548041d8651fe5973734dd1a84981..a790baac9839ff0ee9e9f8b81f20aab206fee222 100644 (file)
--- a/doc/ctsim-gui.tex
+++ b/doc/ctsim-gui.tex
@@ -9,24 +9,20 @@ 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.
 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
 
 \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,
 
 \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
+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.
 
 \subsection{Phantom}
 compatible between both little and big endian architectures.
 
 \subsection{Phantom}


@@ -62,6 +58,50 @@ 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.
 
 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 for all of the windows of
+\ctsim.
+
+\subsection{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{description}\itemsep=0pt
+\item[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
+the reconstruction of projections.
+
+\item[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{description}
+
+\subsection{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.
+
+\subsection{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{Save As...}
+Allows the saving of the contents of a window to any filename.
+
+\subsection{Help}
+This command displays the online help.
+
+\subsection{About}
+This command shows the version number of \ctsim.
+
+

 \section{Phantom Menus}
 
 \subsection{Properties}
 \section{Phantom Menus}
 
 \subsection{Properties}


@@ -93,43 +133,42 @@ This creates a projection file from a phantom. The options
 available when collecting projections are:
 
 \begin{twocollist}
 available when collecting projections are:
 
 \begin{twocollist}

-\twocolitem{\textbf{Geometry}}{
+\twocolitem{\texttt{Geometry}}{

   \begin{itemize}\itemsep=0pt
     \item Parallel
     \item Equiangular
     \item Equilinear
   \end{itemize}}
   \begin{itemize}\itemsep=0pt
     \item Parallel
     \item Equiangular
     \item Equilinear
   \end{itemize}}

-\twocolitem{\textbf{Number of detectors}}{Sets the number of
+\twocolitem{\texttt{Number of detectors}}{Sets the number of

 detectors in the detector array.}
 
 detectors in the detector array.}
 

-\twocolitem{\textbf{Number of views}}{Sets the number of views
+\twocolitem{\texttt{Number of views}}{Sets the number of views

 collected}
 
 collected}
 

-\twocolitem{\textbf{Samples per detector}}{Sets the number of
+\twocolitem{\texttt{Samples per detector}}{Sets the number of

 samples collected for each detector}
 
 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{\texttt{View Ratio}}{Sets the field of view as a ratio
+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.}
+\twocolitem{\texttt{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
+\twocolitem{\texttt{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.
 
 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.}
+For parallel geometries, use a value of \texttt{1.0}. 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
 \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
 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}
 
 
 \end{twocollist}
 
 


@@ -166,7 +205,28 @@ UNIX systems.
 These options are for change the intensity scale for viewing the image.
 They do not change the image data.
 \subsubsection{Set}
 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
+and upper intensities to display.
+

 \subsubsection{Auto}
 \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
+automatic scale are:
+
+\begin{description}\itemsep=0pt
+\item[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.
+
+\item[Width] This sets the half-width of the intensity scale. The width
+is specified as a ratio of the standard deviation.
+\end{description}
+
+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}.
+

 \subsubsection{Full}
 This resets the intensity scale to the full scale of the image.
 
 \subsubsection{Full}
 This resets the intensity scale to the full scale of the image.
 


@@ -175,29 +235,74 @@ These commands create a new image based upon the current image,
 and for some commands, also a comparison image.
 
 \subsubsection{Add, Subtract, Multiply, Divide}
 and for some commands, also 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,
+\ctsim\ will perform the arithmetic operation on the two images and
+make a new result image.

 
 \subsubsection{Image Size}
 
 \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}
 
 \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
+include:
+
+\begin{itemize}
+\item Surface plot
+\item Smooth shading
+\item Lighting on or off
+\item Color scale
+\end{itemize}

 
 \subsection{Filter}
 These commands filter and modify the image.
 
 \subsubsection{Arithmetic}
 
 \subsection{Filter}
 These commands filter and modify the image.
 
 \subsubsection{Arithmetic}

+These are simple arithmetic functions that should be self explanatory.

 
 \subsubsection{Frequency Based}
 
 \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}
 
 \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}
 
 \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 plotting rows and columns from two images on
+a single plot. This is quite helpful when comparing a phantom to a reconstruction.

 
 \section{Projection Menus}
 
 \subsection{File - Properties}
 
 \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}.
 
 \subsection{Process - Convert Polar Dialog}\label{convertpolardialog}
 The parameters are \texttt{xsize}, \texttt{ysize}, and \texttt{interpolation}.


@@ -293,12 +398,11 @@ frequency-based filtering. A setting of \texttt{1} is optimal.}
 
 \section{Plot Menus}
 \subsection{File - Properties}
 
 \section{Plot Menus}
 \subsection{File - Properties}

-
-\subsection{File - Save}
-Plot files can be saved. They are saved in an ASCII text format.
+The displayed properties include

 
 \subsection{View Menu}
 
 \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}
 \subsubsection{Auto}
 \subsubsection{Full}
 \subsubsection{Set}
 \subsubsection{Auto}
 \subsubsection{Full}

diff --git a/doc/ctsim.tex b/doc/ctsim.tex
index 2165b15ca4c8abf99c6df22fe174ee04aa5881e2..5a5f7c75d8dd0f9c8a1ca108d08a5e86d2c5a8d9 100644 (file)
--- a/doc/ctsim.tex
+++ b/doc/ctsim.tex
@@ -78,21 +78,21 @@ PERFORMANCE OF THIS SOFTWARE.
 
 
 \centerline{\image{3cm;3cm}{logo-huge.eps}}
 
 
 \centerline{\image{3cm;3cm}{logo-huge.eps}}

-Computed Tomography is
-a technique for estimating the interior of an object from
+Computed Tomography is a technique for estimating the interior of an
+object from

 measurement of radiation collected around the object. This
 radiation can be either projected through or emitted from the
 measurement of radiation collected around the object. This
 radiation can be either projected through or emitted from the

-object. \rtfsp\ctsim\ simulates the process of projecting X-rays
-through a phantom object. \rtfsp\ctsim\ can then reconstruct the
+object. \ctsim\ simulates the process of projecting X-rays
+through a phantom object. \ctsim\ can then reconstruct the

 interior of the object from the projections collected around the
 phantom object.
 
 This manual begins with an introduction into the concepts of
 interior of the object from the projections collected around the
 phantom object.
 
 This manual begins with an introduction into the concepts of

-\rtfsp\ctsim. Then, the graphical shell, \helprefn{ctsim}{ctsim},
-is documented followed the the command-line shell,
-\helprefn{ctsimtext}{ctsimtext}. Finally, the web-based
-\helprefn{interface}{webinterface} is discussed followed by
-\helprefn{installation}{installation} instructions.
+\ctsim. The graphical, \helprefn{ctsim}{ctsim}, and
+command-line, \helprefn{ctsimtext}{ctsimtext}, shells are then
+presented. Finally, the web-based
+\helprefn{interface}{webinterface} and
+\helprefn{installation}{installation} are discussed.

 
 I hope that you enjoy \ctsim!
 
 
 I hope that you enjoy \ctsim!