Bugs

This is the list of known SOM Toolbox bugs. We try to remove the bugs as soon as we can, or otherwise move them to the Annoying Features list.

Bug reports and corrections to the functions are welcome to address somtlbx@mail.cis.hut.fi. Please include at least the following information to the bug report:

  1. In what function did it occure?
  2. What was the error message?
  3. What was the command line?
  4. Was there anything special about the arguments?
  5. Any other information you think might be useful.

Training algorithm reports NaN for quantization error, and does not work!

Symptoms: Training algorithm seems not to work and reports NaN for quantization error, alternatively som_quality reports NaN quantization error and complains about empty data set, even if it isn't.

Explanation: If there really is data in the data set, and they are not all NaN's there might be some Inf's in the data set - this screws up the batch training algorithm and quantization error calculation.

Suggestion: Make sure there aren't any Inf's in the data sets.

Fixing status: I don't really care.


Annoying features

Annoying features are those bugs that we just couldn't or wouldn't fix. It may be that we couldn't find to cause of the problem, we couldn't fix it, or that we thought it was good just the way it was.

Visualization of 1x3 and 3x1 maps doesn't work!

Symptoms: An error occurs or all the nodes have the same color.

Explanation: The routines in som_show.m are based on Matlab's FILL command. This command interpretes the color argument to be a RGB triplet vector instead of a data vector just in this case. Don't use this map grid size.

SOM_SHOW and SOM_PROFILE are slow for large maps!

Symptoms: Visualization is awfully slow!

Explanation: The routines in som_show.m are based on Matlab's FILL, SUBPLOT and COLORBAR commands. Especially the COLORBAR command is very slow in this case. We are planning a customized colorbar function which would be faster. We can't speed up the built-in FILL command itself, so be patient. Draw only some component planes at time. The SOM_PROFILE is based on SUBPLOT. If the map is large there will be a lot of axis objects and this takes time.

The color map is all screwed up!

Symptoms: colormap isn't smooth, but seems to have random colors

Conditions: at least in our SGI workstations with pseudocolor displays

Explanation: some programs steal the colormap rather than use a virtual colormap of theri own, at least Netscape and XEmacs-20.2

Suggestion: if it's Nescape, you can try starting Netscape with the -install option

'Begin' button causes the som_demo to crash

Symptoms: Pushing the 'Begin' button in som_demo.m causes error: '??? Error using ==> local_openfile'

Conditions: som_demo.m is started, a demo selected and the 'Begin' button is pushed

Explanation: Don't know what actually causes the error. It appears both in version 5.0 and 5.2, but not in version 5.1. Strange.

Suggestion: You can run the demos separately: som_demo1, som_demo2, som_demo3, som_demo4.

A zero value changes to a small number eg. 3.47e-17 in the colorbars

Conditions: SOM_SHOW and/or SOM_RECOLORBAR is used in 'denormalized' mode.

Explanation: Denormalization causes this due to limited accuracy of the computer arithmetics. The rounding subfunction round2 returns always three significant digits*exponent

Suggestion: Fix the round2 -subfunction to round near zero values to zero.


somtlbx@mail.cis.hut.fi