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[ctsim.git] / doc / ctsim-gui.tex

diff --git a/doc/ctsim-gui.tex b/doc/ctsim-gui.tex
index 8d675de29f81518b0ad58ac0b034f220553023bd..7e0f6d4de0f01ade1dbfc1f9cb53aaad3c0aac72 100644 (file)
--- a/doc/ctsim-gui.tex
+++ b/doc/ctsim-gui.tex
@@ -13,17 +13,18 @@ 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
 great image processing and visualization features.
 
 \ctsim\ can open projection files, image files, phantom files, and

-plotfiles.
+plot files.

 
 

-\usage \texttt{ctsim [files to open...]
+\usage \texttt{ctsim [files to open...]}

 
 You can invoke \ctsim\ by itself on the command line, or include
 
 You can invoke \ctsim\ by itself on the command line, or include

-any number of files that you want \ctsim\ to automatically open.
+on the command-line any number of files that you want \ctsim\ to
+automatically open.

 
 \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\
+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.
 
 incorporates logic so that binary files are cross-platform
 compatible between both little and big endian architectures.
 


@@ -41,9 +42,19 @@ 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.
 
 complex-valued images are twice the size of real-valued images
 since both a real and imaginary component need to be store.
 

+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}
 \subsection{Projection}

-Projection files are created from Phantom files during the projection process.
-Numerous options are available for creation of the these files.
+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
+architectures.

 
 \subsection{Plot}
 Plot files are created by \ctsim\ during analysis of image files.
 
 \subsection{Plot}
 Plot files are created by \ctsim\ during analysis of image files.


@@ -52,6 +63,14 @@ files for easy cross-platform support.
 
 \section{Phantom Menus}
 
 
 \section{Phantom Menus}
 

+\subsection{Properties}
+Displays the properties of a phantom which includes:
+
+\begin{itemize}\itemsep=0pt
+\item Overall dimensions of a phantom
+\item A list of all component phantom elements
+\end{itemize}
+

 \subsection{Rasterize Dialog}
 This creates an image file from a phantom. Technically, it
 converts the phantom from a vector (infinite resolution) object
 \subsection{Rasterize Dialog}
 This creates an image file from a phantom. Technically, it
 converts the phantom from a vector (infinite resolution) object


@@ -59,7 +78,7 @@ into a 2-dimension array of floating-point pixels. The parameters
 to set are:
 
 \begin{twocollist}
 to set are:
 
 \begin{twocollist}

-%\twocolitemruled{\textbf{Parameter}}{\textbf{Options}}
+\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{\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


@@ -69,7 +88,50 @@ pixel in the image file 9 samples (3 x 3) are averaged.}
 \end{twocollist}
 
 \subsection{Projection Dialog}
 \end{twocollist}
 
 \subsection{Projection Dialog}

-This creates a projection file from a phantom.
+This creates a projection file from a phantom. The options
+available when collecting projections are:
+
+\begin{twocollist}
+\twocolitem{\textbf{Geometry}}{
+  \begin{itemize}\itemsep=0pt
+    \item Parallel
+    \item Equiangular
+    \item Equilinear
+  \end{itemize}}
+\twocolitem{\textbf{Number of detectors}}{Sets the number of
+detectors in the detector array.}
+
+\twocolitem{\textbf{Number of views}}{Sets the number of views
+collected}
+
+\twocolitem{\textbf{Samples per detector}}{Sets the number of
+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{\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{\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.}
+\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
+and for equilinear and equiangular geometries use a rotation angle
+of 2. Using any other rotation angle will lead to artifacts.}
+\end{twocollist}
+
+

 
 \section{Image Menus}
 \subsection{File - Properties}
 
 \section{Image Menus}
 \subsection{File - Properties}


@@ -80,21 +142,62 @@ Properties of image files include
   \item Image file labels
 \end{itemize}
 
   \item Image file labels
 \end{itemize}
 

-\subsection{View}
+\subsection{File - 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}
+
+
+\subsection{View}\label{intensityscale}

 These options are for change the intensity scale for viewing the image.
 They do not change the image data.
 These options are for change the intensity scale for viewing the image.
 They do not change the image data.

+\subsubsection{Set}
+\subsubsection{Auto}
+\subsubsection{Full}
+This 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.
 
 
 \subsection{Image}
 These commands create a new image based upon the current image,
 and for some commands, also a comparison image.
 

+\subsubsection{Add, Subtract, Multiply, Divide}
+
+\subsubsection{Image Size}
+
+\subsubsection{3-D Conversion}
+Generates a 3-dimensional view of the current phantom.
+

 \subsection{Filter}
 \subsection{Filter}

-These commands filter image.
+These commands filter and modify the image.

 
 

-\subsection{Anaylze}
+\subsubsection{Arithmetic}
+
+\subsubsection{Frequency Based}
+
+\subsection{Analyze}

 These commands are used for analyzing an image.
 
 These commands are used for analyzing an image.
 

+\subsubsection{Plotting}
+
+\subsubsection{Image Comparison}
+

 \section{Projection Menus}
 \section{Projection Menus}

+
+\subsection{File - Properties}
+

 \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
 \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


@@ -103,10 +206,10 @@ interpolation method. Currently, the \texttt{bilinear} option provides
 the highest quality interpolation.
 
 \subsection{Process - Convert FFT Polar Dialog}
 the highest quality interpolation.
 
 \subsection{Process - Convert FFT Polar Dialog}

-The parameters for this option are the same as
-\helprefn{convertpolardialog}{Convert Polar Dialog}. For this
-command, though, the projections are Fourier transformed prior to
-conversion to polar image.
+The parameters for this option are the same as \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}
 This dialog sets the parameters for reconstructing an image from projections
 
 \subsection{Reconstruct - Filtered Backprojection Dialog}
 This dialog sets the parameters for reconstructing an image from projections