next up previous


Tracking Target and Spiral Waves with SpiralTrack

Jon Sporring

Introduction

SpiralTrack is program for analyzing the dynamics of target and spiral waves as generated by many physical, biological, and theoretical processes. The theory behind SpiralTrack is described in [#!Tek:Sporring98d!#].

The program is written in Java 1.1.7 and thus requires the java virtual machine version 1.1.7 or higher. The java virtual machine can be obtained on:

http://java.sun.com/products/jdk/

Starting SpiralTrack

SpiralTrack is started by typing the following from a command prompt:
cd SpiralTrack
java Main <imagedir>
where <imagedir> is a directory containing the images to be analyzed. The program can read Jpeg and Gif images, and will sort the list of files in <imagedir> alphabetically. The list obtained is interpreted as the image sequence to analyze. If the program is successfully started, the main window will open together with an output window.

The Main Window

The main window is always open when SpiralTrack is running. The program has three main modes of operations: Test, Start, and Stop. In test mode can the setting of the parameters be controled, and in start mode will the full sequence be analysed for spirals and circular structure. When the program is in stop mode no computation is performed on the images. In Figure 1 is shown a typical example of how the main window can look.
  
Figure 1: The Main Window
\begin{figure}\centerline{\epsfig{file=main.ps,width=8cm}} \end{figure}

The main window controls the calculations performed by SpiralTrack. The interaction with the user is organized in lines. They are:
Directory
 
In the directory field the current directory is shown. If the path is too long, the first part is abbreviated with '...'.
First file
 
The first file field displays the filename of the first file. Clicking on this button, pops up a file dialog window, from which a new first file can be chosen. The first file is not allowed to be alphabetically after last file. A directory change effects the Directory and Last file fields together with all output windows.
Last file
 
The last file field displays the filename of the last file. This field works similarly to the First file field.
Minimum Length
 
When the program is in start mode, the images will be analyzed sequentially. If the previous image did not have an spiral or target center nearby then a new path is initiated. Conversely, all paths that do not have a continuation in the current image of process will be terminated. The minimum length field sets the minimum length a path can have to be taken into consideration. This value is only used in start mode (see below). If it is 1, then it does not have any effect, and all extrema and their paths will be shown.
Measurement scale
 
The measurement scale t controls the degree of Gaussian smoothing of the edge operator. In test mode this parameter effects the black edge lines. The computation time is directly proportional to t, and the smoothing corresponds to smoothing with a Gaussian kernel of variance 2t. I.e. setting this parameter high increases computation time but also reduces the effects of noise. For line structure of width d pixels it is reasonable to set the measurement scale to d2/8.
Integration space-scale
 
The integration space-scale controls the degree of Gaussian smoothing of the spiral centers. In test mode this parameter effects the number and position of the green circles. This parameter is similar to the above. For spirals of wave length d a useful setting is about d2/8.
Integration time-scale
 
The integration time-scale field sets the time-scale parameter a controls the degree of exponential smoothing along time. This is implemented as a first order recursive function using:

Si+1 = I+aSi

where Si is the current sum, and I is the current internal voting image for spirals. For more details on the voting scheme, see [#!Tek:Sporring98d!#]. The implication of the above, is that if a=0 then no smoothing along time is performed, and if a=1 then the smoothing is uniform. In between are exponential filters. This parameter has no effect in test mode.
Action
 
The Action filed allows the user to control the computation state. Three action modes are available. Test mode allows the user to online experiment with some of the parameters. The edges and spiral centers will be shown in all output windows. In start mode will the program evaluate all images in the image sequence and display the paths on the output windows. Paths that has a length less than Minimum length is not displayed, hence there will at least be no paths displayed before as many images as indicated by Mimimum length has been analyzed. Stop mode is the default, and deactivates any computation.
Status
 
This is a message field indicating the status of SpiralTrack. Some possible messages are
Load/Save
 
Pressing either of these two buttons opens a file dialog, and the user may load or save spiral paths. The file format is in Backus-Naur form given by
pathfile = {<comment>}<newline>
``deadPaths''<newline>
{paths}
``alivePaths''<newline>
{paths}

paths = <number of paths><newline>
{<number of coordinates><newline>
{<x><newline>
<y><newline>
<z><newline>
<f><newline>}}
where <comment> is any text (except ``deadPaths''<newline>), <newline> is the newline character, <number of paths> and <number of coordinates> are integers, and <x>, <y>, <z>, and <f> are floats.
New Window/Reset/Quit
 
The new window button opens a new output window. The reset button completely resets SpiralTrack to the initial state. Be warned that all parameter settings are reset. The quit button terminates the program.

The Output Windows

The main purpose of an output window is to show the results of the calculations performed by SpiralTrack. Initially a single output window is opened by SpiralTrack. An example is shown in Figure 2.
  
Figure 2: An Output Window
\begin{figure}\centerline{\epsfig{file=outputwindow.ps,width=8cm}} \end{figure}

An arbitrary number of output windows may be opened by the user.

An output window has the following content:

Top
The image name,
Right
A scrollbar to choose between images from the directory list,
Middle
A graphical display showing the image chosen by the scrollbar and possibly the results of the testing phase or the tracking phase.
Bottom
A close button.
If the directory list is empty, the output window will display the ``No File'' in the image name field.

During testing or tracking is it advantageous to open several output windows and use the scrollbars to examine different images.

In test mode the edges used (black lines) and the centers found (green circles) are shown. In start mode the paths are divided into alive (green) and dead (red), where a path is dead if it does not connect to the image just processed. Both alive and dead paths start with a blue circle and ends with a green or red circle respectively.

Acknowledgement

This program is based on the work described in [#!Tek:Sporring98d!#].

No References!

About this document ...

sporring@diku.dk
next up previous
Flemming
1998-11-20