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
-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,
-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.
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}
-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.
\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
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
\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}
\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.
+\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.
+\subsubsection{Add, Subtract, Multiply, Divide}
+
+\subsubsection{Image Size}
+
+\subsubsection{3-D Conversion}
+Generates a 3-dimensional view of the current phantom.
+
\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.
+\subsubsection{Plotting}
+
+\subsubsection{Image Comparison}
+
\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
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
projects / ctsim.git / blobdiff