databionic-esom-user — Discussion for Databionic ESOM Tools users

Re: [Databionic-ESOM-User] colt 1.2.0.5

[Niko E. <ne...@ne...>]

On Monday 21 January 2008, rde...@it... wrote:
> Hello
>
> I'm working with SOM class, in order to serialize it, if I
> modify it in order to implements Serializable then I have one error
> in

Hello,

as Fabian already said, serialazation was never taken into consideration 
in the design. Hoever, saving and loading maps/bestmatches/etc. is 
already in place, so it probably would be better to extend this 
funktionality, if there is something you are missing. Could you explane 
your use case a bit?

Niko

Re: [Databionic-ESOM-User] colt 1.2.0.5

[<fa...@my...>]

Rafael,

the 1.2.0.5 version is a modification made during the development
of the ESOM tools. The original authors were not interested in
integrating our changes. The complete modified colt can be
checked out from our sourceforge repository by using the module
name "colt" instead of "src" in the instructions on
http://databionic-esom.sourceforge.net/cvs-usage.html

the particular class VectorFunctions is really just a repository for static
functions and should not need to be serialized. even the SOM class
might not be the best to serialize. I have to admit that the code was
not designed with serialization in mind. you are certainly welcome
to suggest modifications. if you want to save a trained map, then
try to serialize the subclasses of the Grid class (but then you need
to serialize the bestmatches separately).

best
fabian

rde...@it... wrote:
> Hello
>
> First of all I'm grateful for your support and for you very good software.
> I'm working with SOM class, in order to serialize it, if I modify it in
> order to implements Serializable then I have one error in
>
> "java.io.NotSerializableException: cern.jet.math.VectorFunctions"
>
> When I try to look for the library "colt 1.2.0.5" in order to find the
> source, however I can not find this library in internet and the last version
> library found is 1.2 and this class doesn't exists. 
>
> My Question, where can I find the source of this files or if it possible to
> make serializable this class without colt modification.
>
> Thanks in advance 
>
> Best Regards Rafael
>
>
>
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[Databionic-ESOM-User] colt 1.2.0.5

[<rde...@it...>]

Hello

First of all I'm grateful for your support and for you very good software.
I'm working with SOM class, in order to serialize it, if I modify it in
order to implements Serializable then I have one error in

"java.io.NotSerializableException: cern.jet.math.VectorFunctions"

When I try to look for the library "colt 1.2.0.5" in order to find the
source, however I can not find this library in internet and the last version
library found is 1.2 and this class doesn't exists. 

My Question, where can I find the source of this files or if it possible to
make serializable this class without colt modification.

Thanks in advance 

Best Regards Rafael

Re: [Databionic-ESOM-User] automated data clustering?

[<fa...@my...>]

Dick,

Prof. Ultsch has developed a method for automated clustering, see

http://www.uni-marburg.de/fb12/datenbionik/pdf/pubs/2005/ultsch05clustering
http://www.uni-marburg.de/fb12/datenbionik/pdf/pubs/2005/ultsch05ustarc

If you contact him directly, he might be willing to share the matlab =20
code with you. I know that a student is working on integrating the =20
method into the ESOM tools but I don't know if and when it would be =20
available.

For the comparison of clusterings or evaluation with know results I =20
recommend to look up measures to compare classifications, for example =20
precision/recall, sensitivity/specificity. you can average these =20
measures over multiple clustering runs. Please be more specific if =20
these general methods do not suffice.

best
fabian

Quoting Greg Dick <gd...@be...>:

> Dear ESOM users,
>
> I am using ESOM to cluster DNA sequences from environmental  =20
> microorganisms, based on genome wide signatures (tetranucleotide  =20
> frequency).  Overall I am very happy with the results and it has  =20
> proven to be an extremely valuable tool for our research group.   =20
> There are two areas that we are hoping to develop further and I am  =20
> curious if anyone has suggestions or comments:
>
> (1) Are there any automated methods for clustering data?  The  =20
> boundaries for our clusters range from obvious to questionable.   =20
> While this variable strength of clustering is useful information in  =20
> itself, we would like to develop an automated method for defining  =20
> clusters in order to avoid potential errors in where we draw the  =20
> lines (it is not always entirely clear how to do so).
>
> (2) Are there statistical tools that have been developed or applied  =20
> to ESOM to evaluate the robustness of clustering (ideally on a  =20
> per-cluster basis)?  We are interested in such an analysis, which  =20
> would either be based on the U-matrix distance structure and/or an  =20
> evaluation of the accuracy of the clustering (for much of our data  =20
> we know the true cluster affiliations).
>
> Any suggestions or references relevant to these areas would be  =20
> greatly appreciated.
>
> Greg Dick
> Postdoctoral Research
> University of California, Berkeley
>
>

Re: [Databionic-ESOM-User] Databionic-ESOM-User Digest, Vol 8, Issue 1

[<al...@de...>]

Dear Greg Dick,

The U-matrix method, devel=ADoped by Ultsch [1], enables =
visualiza=ADtion of the topological relations of the neurons in an =
organized SOM. A gradient image (2D) or a surface plot is generated by =
computing distances between adjacent neurons. High values in the =
U-matrix encode dis=ADsimi=ADlarities between neurons and correspond to =
cluster borders.=20



Some strategies for cluster detection using U-matrix were proposed by =
Costa and Netto [2, 3].=20



Three main algorithms were presented: mathematical morphology derived =
map segmentation [2,3]; a graph partitioning approach [4] and =
contiguity-constrained hierarchical clustering approaches [5, 6]. Both =
algorithms were developed for automatically partitioning and labeling a =
trained SOM network. The first approach uses image processing algorithms =
such as the watershed transform are used to obtain connected regions of =
neurons representing similar stimuli classes. The second approach uses =
rules to partition the map by analyzing inconsistent neighboring =
relations between neurons. Each resulting cluster of neurons is a =
sub-graph that defines, in the input space, complex and non-parametric =
geometries, which approximately describes the shape of the clusters. =
Regarding the last approach, Goncalves et al. [5] presented improvements =
of contiguity-constrained hierarchical clustering approaches using =
validation indexes. =20



I had addressed this problem almost 10 years ago, with papers [7] and =
[8, a extended version of 7]. But there are many recent papers by many =
authors dealing with this problem.=20


Refs:=20


[1]     A. Ultsch, "Self-Organizing Neural Networks for Visualization =
and Classification", In: O. Opitz et al. (Eds). Information and =
Classification, pp.301-306. Springer: Berlin. 1993.

[2]     J. A. F. Costa, and M. L. de Andrade Netto, "Clustering of =
complex shaped data sets via Kohonen maps and mathematical morphology". =
In: Proceedings of the SPIE, Data Mining and Knowledge Discovery. B. =
Dasarathy (Ed.), Vol. 4384, pp. 16-27, 2001.

[3]     J. A. F. Costa, and M. L. de Andrade Netto, "A new =
tree-structured self-organizing map for data analysis". In: Proc. of the =
Intl. Joint Conf. on Neural Networks, Washington, DC, 2001, pp. =
1931-1936.

[4]     J. A. F. Costa, and M. L. de Andrade Netto, "Segmenta=E7=E3o do =
SOM Baseada em Particionamento de Grafos". In: Proc. of Brazilian Neural =
Networks Conference, S=E3o Paulo, Brazil, June, 2003, pp. 301-308 (in =
Portuguese).

[5]     M. Goncalves, M. Netto, J. Zullo, and J.A.F. Costa. "A new =
method for unsupervised classification of remotely sensed images using =
Kohonen self-organizing maps and agglomerative hierarchical clustering =
methods". In: Intl. Journal of Remote Sensing, 2007 (Accepted).

[6]     F. Murtagh, "Interpreting the Kohonen self-organizing feature =
map using contiguity-constrained clustering". Pattern Recognition =
Letters, vol. 16, pp. 399-408.



[7] Costa, J.A.F., & Netto, M. L. A. (1998). "An Approach for Estimating =
the Number of Clusters in Multivariate Data by Self-Organizing Maps". =
In: Anais do V Simp=F3sio Brasileiro de Redes Neurais (SBRN'98), p. =
33-38. Dezembro, Belo Horizonte, MG.=20

[8] Costa, J.A.F., & Netto, M.L.A. (1999). Estimating the Number of =
Clusters in Multivariate Data by Self-Organizing Maps. International =
Journal of Neural Systems, Vol. 9, No. 3, pp. 195-202.  =20



Anyway, there are my doctoral work of 1999 (in portuguese) -> Costa 1999 =
- Classifica=E7=E3o Autom=E1tica e An=E1lise de dados por redes neurais =
auto-organiz=E1veis - link =
http://www.dca.fee.unicamp.br/~marcio/ia004/artigos/Costa_ClassifAutomati=
caPorRedesNeuraisAutoOrg_PhD99.zip



With my best regards, and wishing for all (especially to Dr. Ultsch and =
group) a wonderful new year,=20

Jose Alfredo F. Costa, Prof. Dr.
Federal University, UFRN, Brazil
http://www.dee.ufrn.br/~alfredo



----- Original Message -----=20
From: <dat...@li...>
To: <dat...@li...>
Sent: Friday, December 21, 2007 5:21 PM
Subject: Databionic-ESOM-User Digest, Vol 8, Issue 1


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> Date: Thu, 20 Dec 2007 15:00:31 -0800
> From: "Greg Dick" <gd...@be...>
> Subject: [Databionic-ESOM-User] automated data clustering?
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>=20
> Dear ESOM users,
>=20
> I am using ESOM to cluster DNA sequences from environmental =
microorganisms, based on genome wide signatures (tetranucleotide =
frequency).  Overall I am very happy with the results and it has proven =
to be an extremely valuable tool for our research group.  There are two =
areas that we are hoping to develop further and I am curious if anyone =
has suggestions or comments:
>=20
> (1) Are there any automated methods for clustering data?  The =
boundaries for our clusters range from obvious to questionable.  While =
this variable strength of clustering is useful information in itself, we =
would like to develop an automated method for defining clusters in order =
to avoid potential errors in where we draw the lines (it is not always =
entirely clear how to do so).
>=20
> (2) Are there statistical tools that have been developed or applied to =
ESOM to evaluate the robustness of clustering (ideally on a per-cluster =
basis)?  We are interested in such an analysis, which would either be =
based on the U-matrix distance structure and/or an evaluation of the =
accuracy of the clustering (for much of our data we know the true =
cluster affiliations).
>=20
> Any suggestions or references relevant to these areas would be greatly =
appreciated.
>=20
> Greg Dick
> Postdoctoral Research
> University of California, Berkeley     =20
>=20
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[Databionic-ESOM-User] automated data clustering?

[Greg D. <gd...@be...>]

Dear ESOM users,

I am using ESOM to cluster DNA sequences from environmental =
microorganisms, based on genome wide signatures (tetranucleotide =
frequency).  Overall I am very happy with the results and it has proven =
to be an extremely valuable tool for our research group.  There are two =
areas that we are hoping to develop further and I am curious if anyone =
has suggestions or comments:

(1) Are there any automated methods for clustering data?  The boundaries =
for our clusters range from obvious to questionable.  While this =
variable strength of clustering is useful information in itself, we =
would like to develop an automated method for defining clusters in order =
to avoid potential errors in where we draw the lines (it is not always =
entirely clear how to do so).

(2) Are there statistical tools that have been developed or applied to =
ESOM to evaluate the robustness of clustering (ideally on a per-cluster =
basis)?  We are interested in such an analysis, which would either be =
based on the U-matrix distance structure and/or an evaluation of the =
accuracy of the clustering (for much of our data we know the true =
cluster affiliations).

Any suggestions or references relevant to these areas would be greatly =
appreciated.

Greg Dick
Postdoctoral Research
University of California, Berkeley     =20

Re: [Databionic-ESOM-User] iris data set

[davide c. <daw...@gm...>]

Thank you all for the answers about the size of the map, I have now a
"brighter" idea about ESOM...

> I heard a rumor that someone is implementing U*C for the ESOM
> tools. If you don't want to wait ask Prof. Ultsch for the Matlab version.
>

Mmm, I'll do that for sure, even if I'll have to check if it works in Octave
(I don't have licenses for Matlab)

d

Re: [Databionic-ESOM-User] iris data set

[<fa...@my...>]

Davide,

I disagree with Niko on the size a bit:

you can use 4k neurons for the iris data as long as your starting
radius is large enough not to leave any areas of the map untouched.
I like to compare the size of the map to the resolution of a monitor
that let's you peak into the high dimensional space. the more details
you want, the larger the map should be. with very small datasets
like iris, there is a limit of course where you are simply wasting
computing power and not gaining anything.

it is well known that 2 classes of iris are closer two each other
than to the 3rd. this can also be seen from a PCA projection.
As Niko explained the sliders or retraining on a subset can help
uncover such finer structures.

I heard a rumor that someone is implementing U*C for the ESOM
tools. If you don't want to wait ask Prof. Ultsch for the Matlab version.

fabian


Niko Efthymiou wrote:
> On Friday 12 October 2007, davide cittaro wrote:
>   
>> Hi again,I was trying to better understand how ESOM tools work and
>> perform. I tried with a well-known data set: Iris classification. I
>> used the one provided in Weka, converted in iris.lrn+iris.cls.
>> I tried a standard esom training run, with a 64x64 map, 30 epochs, 31
>> starting radius and default values for all the rest...
>>     
>
> 64x64 is way too large for the iris data set. The set is only 55 samples 
> vs. 4096 neurons...
>
> 24x24 or 16x32 are a starting point. Also don't forget to preprocess the 
> data. ZT and Robust-ZT which are builtin the esom tools are a start, 
> but there might be more sopfisticated transformations.
>
>   
>> I was pretty surprised to see the results. I have a strong evidence
>> that class 1 (iris setosa) is a separated entity (it is surrounded by
>> a circular "mountain") but... Actually the remaining iris classes
>> seems to be in the same group, the lay in the same "plane" or
>> "valley". Selecting datas from class 2 or class 3 makes them visually
>> separated but, I repeat, in the same plane.
>>     
>
> The problem is that class 1 is suroundet by very high "mountains" which 
> hide the fine structures on the map. Try playing with the "clip" slider 
> on the "View" pannel und you will see that the other 2 classes are also 
> seperated by "hills".
>
> What you can do is train a separate ESOM for these. It will probably 
> seperate them.
>
> Also there are some strange outliers in this set, results improve if you 
> remove them.
>
>   
>> Hi again, and sorry for bothering one more time.I've been reading
>> "Emergence in Self Organizing Feature Maps" (Ultsch A.) and I figured
>> out that I may need U*C clustering tools to complete analysis of my
>> data.
>>     
>
> AFAIK, it hasn't been implemented in ESOM-tools. Maybe its in the matlab 
> stuff, but I don't realy know.
>
> Greets Niko
>
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Re: [Databionic-ESOM-User] iris data set

[Niko E. <ne...@Ma...>]

On Friday 12 October 2007, Davide Cittaro wrote:

> Oh great! Thank you! Is there some recommendation about neurons/
> samples ratio?

Well its quite a while.. but avoid too big and too small ones. In 
general you should have more neurons than data points (unless you have 
a great noumber of duplicates). 

As you might know that the height visualized is the average distance of 
a neuron to its direct neighboors.

Niko

Re: [Databionic-ESOM-User] iris data set

[Davide C. <daw...@gm...>]

On Oct 12, 2007, at 9:40 PM, Niko Efthymiou wrote:

> On Friday 12 October 2007, davide cittaro wrote:
>> Hi again,I was trying to better understand how ESOM tools work and
>> perform. I tried with a well-known data set: Iris classification. I
>> used the one provided in Weka, converted in iris.lrn+iris.cls.
>> I tried a standard esom training run, with a 64x64 map, 30 epochs, 31
>> starting radius and default values for all the rest...
>
> 64x64 is way too large for the iris data set. The set is only 55  
> samples
> vs. 4096 neurons...
>
> 24x24 or 16x32 are a starting point. Also don't forget to  
> preprocess the
> data. ZT and Robust-ZT which are builtin the esom tools are a start,
> but there might be more sopfisticated transformations.
>

Oh great! Thank you! Is there some recommendation about neurons/ 
samples ratio?
>
>> Hi again, and sorry for bothering one more time.I've been reading
>> "Emergence in Self Organizing Feature Maps" (Ultsch A.) and I figured
>> out that I may need U*C clustering tools to complete analysis of my
>> data.
>
> AFAIK, it hasn't been implemented in ESOM-tools. Maybe its in the  
> matlab
> stuff, but I don't realy know.

D'oh!
Thank you for the hints and the answers so far.



dawe

Blog http://daweonline.net
Flickr http://flickr.com/photos/daweonline/

Re: [Databionic-ESOM-User] iris data set

[Niko E. <ne...@ne...>]

On Friday 12 October 2007, davide cittaro wrote:
> Hi again,I was trying to better understand how ESOM tools work and
> perform. I tried with a well-known data set: Iris classification. I
> used the one provided in Weka, converted in iris.lrn+iris.cls.
> I tried a standard esom training run, with a 64x64 map, 30 epochs, 31
> starting radius and default values for all the rest...

64x64 is way too large for the iris data set. The set is only 55 samples 
vs. 4096 neurons...

24x24 or 16x32 are a starting point. Also don't forget to preprocess the 
data. ZT and Robust-ZT which are builtin the esom tools are a start, 
but there might be more sopfisticated transformations.

> I was pretty surprised to see the results. I have a strong evidence
> that class 1 (iris setosa) is a separated entity (it is surrounded by
> a circular "mountain") but... Actually the remaining iris classes
> seems to be in the same group, the lay in the same "plane" or
> "valley". Selecting datas from class 2 or class 3 makes them visually
> separated but, I repeat, in the same plane.

The problem is that class 1 is suroundet by very high "mountains" which 
hide the fine structures on the map. Try playing with the "clip" slider 
on the "View" pannel und you will see that the other 2 classes are also 
seperated by "hills".

What you can do is train a separate ESOM for these. It will probably 
seperate them.

Also there are some strange outliers in this set, results improve if you 
remove them.

> Hi again, and sorry for bothering one more time.I've been reading
> "Emergence in Self Organizing Feature Maps" (Ultsch A.) and I figured
> out that I may need U*C clustering tools to complete analysis of my
> data.

AFAIK, it hasn't been implemented in ESOM-tools. Maybe its in the matlab 
stuff, but I don't realy know.

Greets Niko

[Databionic-ESOM-User] U*C clustering

[davide c. <daw...@gm...>]

Hi again, and sorry for bothering one more time.I've been reading "Emergence
in Self Organizing Feature Maps" (Ultsch A.) and I figured out that I may
need U*C clustering tools to complete analysis of my data.
I've tried esomclust in ESOM/bin directory but, after feeding with all
options, I had a "not implemented yet!" error message. Looking in
Cluster.java source I've seen that clustering is missing (substituted by a
dummy algorithm never reached in execution) but then I wonder where the U*C
named in the paper is...

Thanks

d

[Databionic-ESOM-User] iris data set

[davide c. <daw...@gm...>]

Hi again,I was trying to better understand how ESOM tools work and perform.
I tried with a well-known data set: Iris classification. I used the one
provided in Weka, converted in iris.lrn+iris.cls.
I tried a standard esom training run, with a 64x64 map, 30 epochs, 31
starting radius and default values for all the rest...
I was pretty surprised to see the results. I have a strong evidence that
class 1 (iris setosa) is a separated entity (it is surrounded by a circular
"mountain") but... Actually the remaining iris classes seems to be in the
same group, the lay in the same "plane" or "valley". Selecting datas from
class 2 or class 3 makes them visually separated but, I repeat, in the same
plane.


I've been trying to read the publications to better understand how to use
ESOM, but it would be much more helpful if someone posts on this mailing
lists :-)

Thanks

d

[Databionic-ESOM-User] map size?

[davide c. <daw...@gm...>]

Hi all.I'm pretty satisfied with ESOM tools results, even if I still have to
understand which is the "optimal" map (meaning: how can I tell which is the
best map for a data set?).
BTW, is there a "rule of thumb" to decide the map size (x and y dimensions)
or should I use the default 50x82 size?

Thanks

d

[Databionic-ESOM-User] when to stop?

[davide c. <daw...@gm...>]

Hi again, I've somehow solved the clustering problem (and possibly the 3d
visualization), now I have another question for you. How can I evaluate the
"goodness" of a ESOM? And, correlated, how one can choose the max number of
training epochs?

d

Re: [Databionic-ESOM-User] ESOM and Octave

[<fa...@my...>]

Davide,

please try the matlab functions with octave. My guess is that most will
work, but some might need modifications.
Make sure to download the missing *.m files from
http://databionic-esom.sourceforge.net/install.html. They will be
included in an upcoming new version.

The 3D pictures were rendered with a separate tool that is not included
yet. I don't think anyone is working on this at the moment. Matlab can
be used to create 3D pictures as well.

fabian

davide cittaro wrote:
> Hi, I've installed databionic ESOM  on OS X and it works fine
> (although I still have to thoroughly understand it!). I don't have
> MATLAB and I would like to try octave, instead. Can I interface esom
> with octave? 
> Also, how do you plot those wonderful 3d renderings of maps?
>
> thanks
>
> d
>
>  
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>
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> Defy all challenges. Microsoft(R) Visual Studio 2005.
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>   

Re: [Databionic-ESOM-User] what if...

[<fa...@my...>]

Hi,

if you have two valleys separated by a mountain this corresponds to two
clusters on a coarse scale.

Please try to retrain without the points in the mountainous regions as
Christian suggested.

If you want more details than you can find with the sliders you can also
select all points in one valley, save the selection to a new (*.lrn)
file and train a new map only on this data. This will give you the most
detailed view into this region of the data space. Of course you can do
this for each valley.

Please note that normalizing the data and picking a good distance
function is crucial. If you want comparable results to PCA you need to
apply the same normalization, if any. Also note that EM creates clusters
that correspond to possibly overlapping Gaussian distributions in the
high dimensional space. ESOM tries to find clearly separable
non-overlapping clusters.

best
fabian

Christian Stamm wrote:
> Hi davide,
>
> Those results might tell you that there are no separable groups in your
> data. There is a few things you might try to clarify the situation.
>
> First of all use the Clip slider in the view tab to make finer structures
> visible in the existing map. It clips big heights in the U-Matrix, so the
> color gradient will be mapped over lower heights. Structures in those
> might be dominated by the big mountain right now and then become visible.
>
> You should also try and train another map without the suspected outliers,
> just to see what happens. You should also evaluate wether or not they are
> outliers using other methods like scatter plots.
>
> regards,
> Christian
>
>
>
>   
>> Hi againI'm trying to get something out of my ~4000 datapoints in 123
>> attributes. Some clustering techniques (i.e. EM clustering) and other data
>> analysis tools (i.e. PCA) tell me I can divide my dataset in 3 or 4 big
>> "groups".
>> I'm trying now ESOM tools and it looks like I have a mountain and two
>> orthogonal valleys (on a toroid map). On the mountain I have one group
>> (are
>> those all outliers?) in the valleys I have all remaining data. It happens
>> that data that were in the same group in other analysis are still next to
>> each other but, since they are in the same valley (actually a plain under
>> mountains...), I should say that they cannot be clustered with ESOM
>> tools...
>> Do you have any hint to get out this?
>>
>> Thanks
>>
>> d
>> -------------------------------------------------------------------------
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>
>
>
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Re: [Databionic-ESOM-User] what if...

[Christian S. <st...@Ma...>]

Hi davide,

Those results might tell you that there are no separable groups in your
data. There is a few things you might try to clarify the situation.

First of all use the Clip slider in the view tab to make finer structures
visible in the existing map. It clips big heights in the U-Matrix, so the
color gradient will be mapped over lower heights. Structures in those
might be dominated by the big mountain right now and then become visible.

You should also try and train another map without the suspected outliers,
just to see what happens. You should also evaluate wether or not they are
outliers using other methods like scatter plots.

regards,
Christian



> Hi againI'm trying to get something out of my ~4000 datapoints in 123
> attributes. Some clustering techniques (i.e. EM clustering) and other data
> analysis tools (i.e. PCA) tell me I can divide my dataset in 3 or 4 big
> "groups".
> I'm trying now ESOM tools and it looks like I have a mountain and two
> orthogonal valleys (on a toroid map). On the mountain I have one group
> (are
> those all outliers?) in the valleys I have all remaining data. It happens
> that data that were in the same group in other analysis are still next to
> each other but, since they are in the same valley (actually a plain under
> mountains...), I should say that they cannot be clustered with ESOM
> tools...
> Do you have any hint to get out this?
>
> Thanks
>
> d
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2005.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/_______________________________________________
> Databionic-ESOM-User mailing list
> Dat...@li...
> https://lists.sourceforge.net/lists/listinfo/databionic-esom-user
>

[Databionic-ESOM-User] what if...

[davide c. <daw...@gm...>]

Hi againI'm trying to get something out of my ~4000 datapoints in 123
attributes. Some clustering techniques (i.e. EM clustering) and other data
analysis tools (i.e. PCA) tell me I can divide my dataset in 3 or 4 big
"groups".
I'm trying now ESOM tools and it looks like I have a mountain and two
orthogonal valleys (on a toroid map). On the mountain I have one group (are
those all outliers?) in the valleys I have all remaining data. It happens
that data that were in the same group in other analysis are still next to
each other but, since they are in the same valley (actually a plain under
mountains...), I should say that they cannot be clustered with ESOM
tools...
Do you have any hint to get out this?

Thanks

d

[Databionic-ESOM-User] ESOM and Octave

[davide c. <daw...@gm...>]

Hi, I've installed databionic ESOM  on OS X and it works fine (although I
still have to thoroughly understand it!). I don't have MATLAB and I would
like to try octave, instead. Can I interface esom with octave? Also, how do
you plot those wonderful 3d renderings of maps?

thanks

d

Re: [Databionic-ESOM-User] Problem when integrating ESOM with Matlab

[<fa...@my...>]

hm. can't test that right now.
if it doesn't bother you...

fabian

Yok Yen wrote:
> Thanks Fabian,
>
> finally can get it running..
> but a small error pop out at later stage of demo program.
>
> ??? Error using ==> loadumx
> loadumx: could not open file demoComp.umx
>
> Error in ==> esom_matrix at 112
> umx = loadumx(UMxName);
> Error in ==> esom_demo at 96
> cmx = esom_matrix(MatrixFileNamePrefix,OtherFileNames,MatrixType,[],2);
>
> regards,
> yy
>
> On 8/20/07, * Fabian Mörchen* <fa...@my...
> <mailto:fa...@my...>> wrote:
>
>     I uploaded the files manually, not through the source forge system
>     because it takes longer.
>
>     see
>
>     http://databionic-esom.sourceforge.net/missingmfiles.zip
>     <http://databionic-esom.sourceforge.net/missingmfiles.zip>
>
>     fabian
>
>
> ------------------------------------------------------------------------
>
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>   

Re: [Databionic-ESOM-User] Problem when integrating ESOM with Matlab

[Yok Y. <yo...@gm...>]

Thanks Fabian,

finally can get it running..
but a small error pop out at later stage of demo program.

??? Error using =3D=3D> loadumx
loadumx: could not open file demoComp.umx

Error in =3D=3D> esom_matrix at 112
umx =3D loadumx(UMxName);
Error in =3D=3D> esom_demo at 96
cmx =3D esom_matrix(MatrixFileNamePrefix,OtherFileNames,MatrixType,[],2);

regards,
yy

On 8/20/07, Fabian M=F6rchen <fa...@my...> wrote:
>
> I uploaded the files manually, not through the source forge system
> because it takes longer.
>
> see
>
> http://databionic-esom.sourceforge.net/missingmfiles.zip
>
> fabian
>

Re: [Databionic-ESOM-User] Problem when integrating ESOM with Matlab

[<fa...@my...>]

I uploaded the files manually, not through the source forge system
because it takes longer.

see

http://databionic-esom.sourceforge.net/missingmfiles.zip

fabian

Yok Yen wrote:
> Hi Fabian and Flavius,
>
> I am getting the same error as Flavius.
> Fabian, you mentioned the trim(), yes, it is pointing to simulink's
> trim function. And I couldn't find any trim() from the the existing
> esom toolbox.
> Also, you mentioned the zip file in the server for download, I
> couldn't find it.
> The website doesn't show any updated file available since year 2006.
> Could you kindly guide me in downloading the zip file you mentioned?
>
> Latest 	1.0
> <https://sourceforge.net/project/showfiles.php?group_id=127046&package_id=139030&release_id=394537>
> Notes
> <https://sourceforge.net/project/shownotes.php?release_id=394537&group_id=127046>
> (2006-02-18 03:04)
>   	esom-1.0-installer.jar
> <http://downloads.sourceforge.net/databionic-esom/esom-1.0-installer.jar?modtime=1140264890&big_mirror=0>
>   Mirror
> <https://sourceforge.net/project/mirror_picker.php?height=350&width=300&group_id=127046&use_mirror=jaist&filename=esom-1.0-installer.jar>
> 	5833155 	2229
> <https://sourceforge.net/project/stats/detail.php?type=prdownload&group_id=127046&ugn=databionic-esom&package_id=139030&release_id=394537&file_id=894911>
> 	Any 	.jar
>   	esom-1.0.jar
> <http://downloads.sourceforge.net/databionic-esom/esom-1.0.jar?modtime=1140264992&big_mirror=0>
>   Mirror
> <https://sourceforge.net/project/mirror_picker.php?height=350&width=300&group_id=127046&use_mirror=jaist&filename=esom-1.0.jar>
> 	892698 	821
> <https://sourceforge.net/project/stats/detail.php?type=prdownload&group_id=127046&ugn=databionic-esom&package_id=139030&release_id=394537&file_id=894913>
> 	Any 	.jar
>   	esom-1.0-src.tar.gz
> <http://downloads.sourceforge.net/databionic-esom/esom-1.0-src.tar.gz?modtime=1140265006&big_mirror=0>
>   Mirror
> <https://sourceforge.net/project/mirror_picker.php?height=350&width=300&group_id=127046&use_mirror=jaist&filename=esom-1.0-src.tar.gz>
> 	1245795 	718
> <https://sourceforge.net/project/stats/detail.php?type=prdownload&group_id=127046&ugn=databionic-esom&package_id=139030&release_id=394537&file_id=894912>
> 	Any 	Source .gz
>
>
>
> regards,
> yy
>
> On 8/18/07, *Fabian Mörchen* <fa...@my...
> <mailto:fa...@my...> > wrote:
>
>     Flavius,
>
>     >Error in ==> trim at 52
>     >supportMsg = linmodsupported(fcn);
>
>     this error is not from my trim function (which does not even have
>     52 lines)
>
>     you need to make sure that the path to my "trim.m" function
>     is before the simulink path in Matlab's search path.
>
>     if you type "which trim" in matlab it will tell you which version
>     it is currently using.
>
>     another possible solution si to rename trim.m to, e.g., mytrim.m
>     and replace
>     it in loadlrnfast at line 75 and anywhere else in the toolbox
>     where it
>     is used.
>
>     fabian
>
>     Flavius da Luz Gorgonio wrote:
>     > Hi Fabian and Yok,
>     >
>     > I actualized my toolbox with missing files which you send, but the
>     > troubles remains (see below). What can I try now?
>     >
>     > Yok, do you succeeded in completing your work?
>     >
>     > Thanks
>     >
>     > Flavius Gorgônio
>     >
>     >
>     >
>     >>> esom_demo
>     >>>
>     > ??? Error using ==> load_system
>     > There is no system named '4.408357E-001      
>     -7.280088E-002  -2.103747E+000
>     > ' to open.
>     >
>     > Error in ==> simulink\private\fixpt_blks_in_mdl at 38
>     >   load_system(model);
>     >
>     > Error in ==> simulink\private\linmodsupported at 16
>     > if fixpt_blks_in_mdl(model,followLinks)
>     >
>     > Error in ==> trim at 52
>     > supportMsg = linmodsupported(fcn);
>     >
>     > Error in ==> loadlrnfast at 75
>     > while ((length(trim(line))<10) ||
>     strcmp(trim(line),'0.0000000e+000') ||
>     > strcmp(trim(line),'0000000e+000'))
>     >
>     > Error in ==> loadlrn at 56
>     >         [data,names,defined] = loadlrnfast(filename);
>     >
>     > Error in ==> esom_train at 144
>     >     data = loadlrn([prefix, '.lrn']);
>     >
>     > Error in ==> esom_demo at 61
>     > [wts, bm, umx] = esom_train(NOData, prefix, epochs, rows,
>     columns, grid,
>     > radius, learn, algorithm);
>     >
>     >
>     >
>     >
>     >
>     >> Hi,
>     >>
>     >> even if it doesn't look like it this is also an error due to a
>     missing
>     >> file.
>     >> our "trim" function is missing and instead one of the same name in
>     >> simulink is found and used.
>     >>
>     >> I included all missing files that I know about in a *.zip file
>     that is
>     >> linked on
>     >>     http://databionic-esom.sourceforge.net/install.html
>     >> please keep complaining until it works.
>     >>
>     >> When I developed the toolbox I must have had all this code in my
>     >> matlab search p[ath without thinking about it. you guys seem to be
>     >> the first people using the matlab interface (at least the first
>     that ever
>     >> complained).
>     >>
>     >> fabian
>     >>
>     >> Yok Yen wrote:
>     >>
>     >>> I still not able to get esom_demo.m running...
>     >>> The follow error occurs..
>     >>>
>     >>> ??? Error using ==> load_system
>     >>> There is no system named '4.408357E-001    -7.280088E-002
>     >>> -2.103747E+000
>     >>> ' to open.
>     >>>
>     >>> Error in ==> simulink\private\fixpt_blks_in_mdl at 38
>     >>>   load_system(model);
>     >>>
>     >>> Error in ==> simulink\private\linmodsupported at 16
>     >>> if fixpt_blks_in_mdl(model,followLinks)
>     >>>
>     >>> Error in ==> trim at 52
>     >>> supportMsg = linmodsupported(fcn);
>     >>>
>     >>> Error in ==> loadlrnfast at 76
>     >>> while ((length(trim(line))<10) ||
>     strcmp(trim(line),'0.0000000e+000')
>     >>> || strcmp(trim(line),'0000000e+000'))
>     >>>
>     >>> Error in ==> loadlrn at 56
>     >>>         [data,names,defined] = loadlrnfast(filename);
>     >>>
>     >>> Error in ==> esom_train at 144
>     >>>     data = loadlrn([prefix, '.lrn']);
>     >>>
>     >>> Error in ==> esom_demo at 61
>     >>> [wts, bm, umx] = esom_train(NOData, prefix, epochs, rows, columns,
>     >>> grid, radius, learn, algorithm);
>     >>>
>     >>> regards,
>     >>> yok yen
>     >>> On 8/16/07, *Fabian Mörchen* < fa...@my...
>     <mailto:fa...@my...>
>     >>> <mailto:fa...@my... <mailto:fa...@my...>>> wrote:
>     >>>
>     >>>     Yok Yen wrote:
>     >>>     > Hi Fabian,
>     >>>     >
>     >>>     > Thanks for your support.
>     >>>     > I still getting an error while trying to run the esom_demo.m
>     >>>     >
>     >>>     > ??? Undefined command/function 'isnumber'.
>     >>>     >
>     >>>     > Error in ==> loadlrnfast at 69
>     >>>     >         if ~isnumber(t)
>     >>>     >
>     >>>     > Error in ==> loadlrn at 56
>     >>>     >         [data,names,defined] = loadlrnfast(filename);
>     >>>     >
>     >>>     > Error in ==> esom_train at 144
>     >>>     >     data = loadlrn([prefix, '.lrn']);
>     >>>     >
>     >>>     > Error in ==> esom_demo at 61
>     >>>     > [wts, bm, umx] = esom_train(NOData, prefix, epochs,
>     rows, columns,
>     >>>     > grid, radius, learn, algorithm);
>     >>>     >
>     >>>     > regards,
>     >>>     > yok yen
>     >>>     >
>     >>>     > On 8/16/07, *Fabian Mörchen * <fa...@my...
>     <mailto:fa...@my...>
>     >>>     <mailto:fa...@my... <mailto:fa...@my...>>
>     >>>     > <mailto:fa...@my... <mailto:fa...@my...>
>     <mailto:fa...@my... <mailto:fa...@my...>>>> wrote:
>     >>>     >
>     >>>     >     Yok,
>     >>>     >
>     >>>     >     there seem to be some general functions missing.
>     they are
>     >>>     >     attached. I hope to get to create an updated version
>     with
>     >>>     everything
>     >>>     >     some time.
>     >>>     >
>     >>>     >     fabian
>     >>>     >
>     >>>     >     Yok Yen wrote:
>     >>>     >     >
>     >>>     >     > Hi,
>     >>>     >     >
>     >>>     >     > I am trying to integrate ESOM with my matlab problem.
>     >>>     >     > However, it is not successful.
>     >>>     >     > Hope to seek your help in this.
>     >>>     >     > Thanks in advance.
>     >>>     >     >
>     >>>     >     > The errors that shows up when I try to run
>     esom_demo.m are
>     >>> as
>     >>>     >     follows:
>     >>>     >     > 1)
>     >>>     >     > >> esom_demo
>     >>>     >     > ??? Undefined command/function 'tail'.
>     >>>     >     >
>     >>>     >     > Error in ==> addfileext at 29
>     >>>     >     > if ~strcmp(tail(filename,length(ext)),ext)
>     >>>     >     >
>     >>>     >     > Error in ==> savecls at 32
>     >>>     >     > filename = addfileext(filename,'.cls');
>     >>>     >     >
>     >>>     >     > Error in ==> esom_demo at 54
>     >>>     >     > savecls('demo.cls', key, cls);
>     >>>     >     >
>     >>>     >     > 2)
>     >>>     >     > ??? Undefined command/function 'head'.
>     >>>     >     >
>     >>>     >     > Error in ==> loadlrnfast at 60
>     >>>     >     >     tokens = strread(deblank(head(line,-1)),'%s\t');
>     >>>     >     >
>     >>>     >     > Error in ==> loadlrn at 56
>     >>>     >     >         [data,names,defined] = loadlrnfast(filename);
>     >>>     >     >
>     >>>     >     > Error in ==> esom_train at 144
>     >>>     >     >     data = loadlrn([prefix, '.lrn']);
>     >>>     >     >
>     >>>     >     > Error in ==> esom_demo at 61
>     >>>     >     > [wts, bm, umx] = esom_train(NOData, prefix,
>     epochs, rows,
>     >>>     columns,
>     >>>     >     > grid, radius, learn, algorithm);
>     >>>     >     >
>     >>>     >     > regards,
>     >>>     >     > yok yen
>     >>>     >     >
>     >>>     >
>     >>>    
>     ------------------------------------------------------------------------
>
>     >>>     >     >
>     >>>     >     >
>     >>>     >
>     >>>    
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>     >>>     <mailto:Dat...@li...
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>     >>>    
>     https://lists.sourceforge.net/lists/listinfo/databionic-esom-user
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>     >>>     >     <
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Re: [Databionic-ESOM-User] Problem when integrating ESOM with Matlab

[Yok Y. <yo...@gm...>]

Hi Fabian and Flavius,

I am getting the same error as Flavius.
Fabian, you mentioned the trim(), yes, it is pointing to simulink's trim
function. And I couldn't find any trim() from the the existing esom toolbox=
.
Also, you mentioned the zip file in the server for download, I couldn't fin=
d
it.
The website doesn't show any updated file available since year 2006.
Could you kindly guide me in downloading the zip file you mentioned?

Latest 1.0<https://sourceforge.net/project/showfiles.php?group_id=3D127046&=
package_id=3D139030&release_id=3D394537>
Notes<https://sourceforge.net/project/shownotes.php?release_id=3D394537&gro=
up_id=3D127046>
(2006-02-18
03:04)    esom-1.0-installer.jar<http://downloads.sourceforge.net/databioni=
c-esom/esom-1.0-installer.jar?modtime=3D1140264890&big_mirror=3D0>
Mirror<https://sourceforge.net/project/mirror_picker.php?height=3D350&width=
=3D300&group_id=3D127046&use_mirror=3Djaist&filename=3Desom-1.0-installer.j=
ar>
5833155 2229<https://sourceforge.net/project/stats/detail.php?type=3Dprdown=
load&group_id=3D127046&ugn=3Ddatabionic-esom&package_id=3D139030&release_id=
=3D394537&file_id=3D894911>
Any .jar    esom-1.0.jar<http://downloads.sourceforge.net/databionic-esom/e=
som-1.0.jar?modtime=3D1140264992&big_mirror=3D0>
Mirror<https://sourceforge.net/project/mirror_picker.php?height=3D350&width=
=3D300&group_id=3D127046&use_mirror=3Djaist&filename=3Desom-1.0.jar>
892698 821<https://sourceforge.net/project/stats/detail.php?type=3Dprdownlo=
ad&group_id=3D127046&ugn=3Ddatabionic-esom&package_id=3D139030&release_id=
=3D394537&file_id=3D894913>
Any .jar    esom-1.0-src.tar.gz<http://downloads.sourceforge.net/databionic=
-esom/esom-1.0-src.tar.gz?modtime=3D1140265006&big_mirror=3D0>
Mirror<https://sourceforge.net/project/mirror_picker.php?height=3D350&width=
=3D300&group_id=3D127046&use_mirror=3Djaist&filename=3Desom-1.0-src.tar.gz>
1245795 718<https://sourceforge.net/project/stats/detail.php?type=3Dprdownl=
oad&group_id=3D127046&ugn=3Ddatabionic-esom&package_id=3D139030&release_id=
=3D394537&file_id=3D894912>
Any Source .gz

regards,
yy

On 8/18/07, Fabian M=F6rchen <fa...@my...> wrote:
>
> Flavius,
>
> >Error in =3D=3D> trim at 52
> >supportMsg =3D linmodsupported(fcn);
>
> this error is not from my trim function (which does not even have 52
> lines)
>
> you need to make sure that the path to my "trim.m" function
> is before the simulink path in Matlab's search path.
>
> if you type "which trim" in matlab it will tell you which version
> it is currently using.
>
> another possible solution si to rename trim.m to, e.g., mytrim.m and
> replace
> it in loadlrnfast at line 75 and anywhere else in the toolbox where it
> is used.
>
> fabian
>
> Flavius da Luz Gorgonio wrote:
> > Hi Fabian and Yok,
> >
> > I actualized my toolbox with missing files which you send, but the
> > troubles remains (see below). What can I try now?
> >
> > Yok, do you succeeded in completing your work?
> >
> > Thanks
> >
> > Flavius Gorg=F4nio
> >
> >
> >
> >>> esom_demo
> >>>
> > ??? Error using =3D=3D> load_system
> > There is no system named '4.408357E-001       -7.280088E-002  -
> 2.103747E+000
> > ' to open.
> >
> > Error in =3D=3D> simulink\private\fixpt_blks_in_mdl at 38
> >   load_system(model);
> >
> > Error in =3D=3D> simulink\private\linmodsupported at 16
> > if fixpt_blks_in_mdl(model,followLinks)
> >
> > Error in =3D=3D> trim at 52
> > supportMsg =3D linmodsupported(fcn);
> >
> > Error in =3D=3D> loadlrnfast at 75
> > while ((length(trim(line))<10) || strcmp(trim(line),'0.0000000e+000') |=
|
> > strcmp(trim(line),'0000000e+000'))
> >
> > Error in =3D=3D> loadlrn at 56
> >         [data,names,defined] =3D loadlrnfast(filename);
> >
> > Error in =3D=3D> esom_train at 144
> >     data =3D loadlrn([prefix, '.lrn']);
> >
> > Error in =3D=3D> esom_demo at 61
> > [wts, bm, umx] =3D esom_train(NOData, prefix, epochs, rows, columns, gr=
id,
> > radius, learn, algorithm);
> >
> >
> >
> >
> >
> >> Hi,
> >>
> >> even if it doesn't look like it this is also an error due to a missing
> >> file.
> >> our "trim" function is missing and instead one of the same name in
> >> simulink is found and used.
> >>
> >> I included all missing files that I know about in a *.zip file that is
> >> linked on
> >>     http://databionic-esom.sourceforge.net/install.html
> >> please keep complaining until it works.
> >>
> >> When I developed the toolbox I must have had all this code in my
> >> matlab search p[ath without thinking about it. you guys seem to be
> >> the first people using the matlab interface (at least the first that
> ever
> >> complained).
> >>
> >> fabian
> >>
> >> Yok Yen wrote:
> >>
> >>> I still not able to get esom_demo.m running...
> >>> The follow error occurs..
> >>>
> >>> ??? Error using =3D=3D> load_system
> >>> There is no system named '4.408357E-001    -7.280088E-002
> >>> -2.103747E+000
> >>> ' to open.
> >>>
> >>> Error in =3D=3D> simulink\private\fixpt_blks_in_mdl at 38
> >>>   load_system(model);
> >>>
> >>> Error in =3D=3D> simulink\private\linmodsupported at 16
> >>> if fixpt_blks_in_mdl(model,followLinks)
> >>>
> >>> Error in =3D=3D> trim at 52
> >>> supportMsg =3D linmodsupported(fcn);
> >>>
> >>> Error in =3D=3D> loadlrnfast at 76
> >>> while ((length(trim(line))<10) || strcmp(trim(line),'0.0000000e+000')
> >>> || strcmp(trim(line),'0000000e+000'))
> >>>
> >>> Error in =3D=3D> loadlrn at 56
> >>>         [data,names,defined] =3D loadlrnfast(filename);
> >>>
> >>> Error in =3D=3D> esom_train at 144
> >>>     data =3D loadlrn([prefix, '.lrn']);
> >>>
> >>> Error in =3D=3D> esom_demo at 61
> >>> [wts, bm, umx] =3D esom_train(NOData, prefix, epochs, rows, columns,
> >>> grid, radius, learn, algorithm);
> >>>
> >>> regards,
> >>> yok yen
> >>> On 8/16/07, *Fabian M=F6rchen* <fa...@my...
> >>> <mailto:fa...@my...>> wrote:
> >>>
> >>>     Yok Yen wrote:
> >>>     > Hi Fabian,
> >>>     >
> >>>     > Thanks for your support.
> >>>     > I still getting an error while trying to run the esom_demo.m
> >>>     >
> >>>     > ??? Undefined command/function 'isnumber'.
> >>>     >
> >>>     > Error in =3D=3D> loadlrnfast at 69
> >>>     >         if ~isnumber(t)
> >>>     >
> >>>     > Error in =3D=3D> loadlrn at 56
> >>>     >         [data,names,defined] =3D loadlrnfast(filename);
> >>>     >
> >>>     > Error in =3D=3D> esom_train at 144
> >>>     >     data =3D loadlrn([prefix, '.lrn']);
> >>>     >
> >>>     > Error in =3D=3D> esom_demo at 61
> >>>     > [wts, bm, umx] =3D esom_train(NOData, prefix, epochs, rows,
> columns,
> >>>     > grid, radius, learn, algorithm);
> >>>     >
> >>>     > regards,
> >>>     > yok yen
> >>>     >
> >>>     > On 8/16/07, *Fabian M=F6rchen * <fa...@my...
> >>>     <mailto:fa...@my...>
> >>>     > <mailto:fa...@my... <mailto:fa...@my...>>> wrote:
> >>>     >
> >>>     >     Yok,
> >>>     >
> >>>     >     there seem to be some general functions missing. they are
> >>>     >     attached. I hope to get to create an updated version with
> >>>     everything
> >>>     >     some time.
> >>>     >
> >>>     >     fabian
> >>>     >
> >>>     >     Yok Yen wrote:
> >>>     >     >
> >>>     >     > Hi,
> >>>     >     >
> >>>     >     > I am trying to integrate ESOM with my matlab problem.
> >>>     >     > However, it is not successful.
> >>>     >     > Hope to seek your help in this.
> >>>     >     > Thanks in advance.
> >>>     >     >
> >>>     >     > The errors that shows up when I try to run esom_demo.m ar=
e
> >>> as
> >>>     >     follows:
> >>>     >     > 1)
> >>>     >     > >> esom_demo
> >>>     >     > ??? Undefined command/function 'tail'.
> >>>     >     >
> >>>     >     > Error in =3D=3D> addfileext at 29
> >>>     >     > if ~strcmp(tail(filename,length(ext)),ext)
> >>>     >     >
> >>>     >     > Error in =3D=3D> savecls at 32
> >>>     >     > filename =3D addfileext(filename,'.cls');
> >>>     >     >
> >>>     >     > Error in =3D=3D> esom_demo at 54
> >>>     >     > savecls('demo.cls', key, cls);
> >>>     >     >
> >>>     >     > 2)
> >>>     >     > ??? Undefined command/function 'head'.
> >>>     >     >
> >>>     >     > Error in =3D=3D> loadlrnfast at 60
> >>>     >     >     tokens =3D strread(deblank(head(line,-1)),'%s\t');
> >>>     >     >
> >>>     >     > Error in =3D=3D> loadlrn at 56
> >>>     >     >         [data,names,defined] =3D loadlrnfast(filename);
> >>>     >     >
> >>>     >     > Error in =3D=3D> esom_train at 144
> >>>     >     >     data =3D loadlrn([prefix, '.lrn']);
> >>>     >     >
> >>>     >     > Error in =3D=3D> esom_demo at 61
> >>>     >     > [wts, bm, umx] =3D esom_train(NOData, prefix, epochs, row=
s,
> >>>     columns,
> >>>     >     > grid, radius, learn, algorithm);
> >>>     >     >
> >>>     >     > regards,
> >>>     >     > yok yen
> >>>     >     >
> >>>     >
> >>>
> ------------------------------------------------------------------------
> >>>     >     >
> >>>     >     >
> >>>     >
> >>>
> -------------------------------------------------------------------------
> >>>     >     > This SF.net email is sponsored by: Splunk Inc.
> >>>     >     > Still grepping through log files to find problems?  Stop.
> >>>     >     > Now Search log events and configuration files using AJAX
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> >>>     >     >
> >>>     >
> >>>
> ------------------------------------------------------------------------
> >>>     >     >
> >>>     >     > _______________________________________________
> >>>     >     > Databionic-ESOM-User mailing list
> >>>     >     > Dat...@li...
> >>>     <mailto:Dat...@li...>
> >>>     >     <mailto:Dat...@li...
> >>>     <mailto:Dat...@li...>>
> >>>     >     >
> >>>     >
> >>>     https://lists.sourceforge.net/lists/listinfo/databionic-esom-user
> >>>     >     <
> >>>     https://lists.sourceforge.net/lists/listinfo/databionic-esom-user=
>
> >>>     >     >
> >>>     >
> >>>     >
> >>>     >
> >>>
> -------------------------------------------------------------------------
> >>>     >     This SF.net email is sponsored by: Splunk Inc.
> >>>     >     Still grepping through log files to find problems?  Stop.
> >>>     >     Now Search log events and configuration files using AJAX an=
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> a
> >>>     >     browser.
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> >>>     >     _______________________________________________
> >>>     >     Databionic-ESOM-User mailing list
> >>>     >     Dat...@li...
> >>>     <mailto:Dat...@li...>
> >>>     >     <mailto:Dat...@li...
> >>>     <mailto:Dat...@li...>>
> >>>     >
> >>>     https://lists.sourceforge.net/lists/listinfo/databionic-esom-user
> >>>     >
> >>>     >
> >>>     >
> >>>     >
> >>>
> ------------------------------------------------------------------------
> >>>     >
> >>>     >
> >>>
> -------------------------------------------------------------------------
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> >>>     > This SF.net email is sponsored by: Splunk Inc.
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> >>>
> ------------------------------------------------------------------------
> >>>     >
> >>>     > _______________________________________________
> >>>     > Databionic-ESOM-User mailing list
> >>>     > Dat...@li...
> >>>     <mailto:Dat...@li...>
> >>>     >
> >>>     https://lists.sourceforge.net/lists/listinfo/databionic-esom-user
> >>>     <https://lists.sourceforge.net/lists/listinfo/databionic-esom-use=
r
> >
> >>>     >
> >>>
> >>>
> >>>
> -------------------------------------------------------------------------
> >>>     This SF.net email is sponsored by: Splunk Inc.
> >>>     Still grepping through log files to find problems?  Stop.
> >>>     Now Search log events and configuration files using AJAX and a
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> >>>     Dat...@li...
> >>>     <mailto:Dat...@li...>
> >>>     https://lists.sourceforge.net/lists/listinfo/databionic-esom-user
> >>>
> >>>
> >>>
> >>>
> ------------------------------------------------------------------------
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> >>>
> -------------------------------------------------------------------------
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> >>> Still grepping through log files to find problems?  Stop.
> >>> Now Search log events and configuration files using AJAX and a
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> ------------------------------------------------------------------------
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> >>> https://lists.sourceforge.net/lists/listinfo/databionic-esom-user
> >>>
> >>>
> >>
> -------------------------------------------------------------------------
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.
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> >>
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>

Re: [Databionic-ESOM-User] Problem when integrating ESOM with Matlab

[<fa...@my...>]

Flavius,

>Error in ==> trim at 52
>supportMsg = linmodsupported(fcn);

this error is not from my trim function (which does not even have 52 lines)

you need to make sure that the path to my "trim.m" function
is before the simulink path in Matlab's search path.

if you type "which trim" in matlab it will tell you which version
it is currently using.

another possible solution si to rename trim.m to, e.g., mytrim.m and replace
it in loadlrnfast at line 75 and anywhere else in the toolbox where it
is used.

fabian

Flavius da Luz Gorgonio wrote:
> Hi Fabian and Yok,
>
> I actualized my toolbox with missing files which you send, but the
> troubles remains (see below). What can I try now?
>
> Yok, do you succeeded in completing your work?
>
> Thanks
>
> Flavius Gorgônio
>
>
>   
>>> esom_demo
>>>       
> ??? Error using ==> load_system
> There is no system named '4.408357E-001	-7.280088E-002	-2.103747E+000
> ' to open.
>
> Error in ==> simulink\private\fixpt_blks_in_mdl at 38
>   load_system(model);
>
> Error in ==> simulink\private\linmodsupported at 16
> if fixpt_blks_in_mdl(model,followLinks)
>
> Error in ==> trim at 52
> supportMsg = linmodsupported(fcn);
>
> Error in ==> loadlrnfast at 75
> while ((length(trim(line))<10) || strcmp(trim(line),'0.0000000e+000') ||
> strcmp(trim(line),'0000000e+000'))
>
> Error in ==> loadlrn at 56
>         [data,names,defined] = loadlrnfast(filename);
>
> Error in ==> esom_train at 144
>     data = loadlrn([prefix, '.lrn']);
>
> Error in ==> esom_demo at 61
> [wts, bm, umx] = esom_train(NOData, prefix, epochs, rows, columns, grid,
> radius, learn, algorithm);
>
>   
>
>
>   
>> Hi,
>>
>> even if it doesn't look like it this is also an error due to a missing
>> file.
>> our "trim" function is missing and instead one of the same name in
>> simulink is found and used.
>>
>> I included all missing files that I know about in a *.zip file that is
>> linked on
>>     http://databionic-esom.sourceforge.net/install.html
>> please keep complaining until it works.
>>
>> When I developed the toolbox I must have had all this code in my
>> matlab search p[ath without thinking about it. you guys seem to be
>> the first people using the matlab interface (at least the first that ever
>> complained).
>>
>> fabian
>>
>> Yok Yen wrote:
>>     
>>> I still not able to get esom_demo.m running...
>>> The follow error occurs..
>>>
>>> ??? Error using ==> load_system
>>> There is no system named '4.408357E-001    -7.280088E-002
>>> -2.103747E+000
>>> ' to open.
>>>
>>> Error in ==> simulink\private\fixpt_blks_in_mdl at 38
>>>   load_system(model);
>>>
>>> Error in ==> simulink\private\linmodsupported at 16
>>> if fixpt_blks_in_mdl(model,followLinks)
>>>
>>> Error in ==> trim at 52
>>> supportMsg = linmodsupported(fcn);
>>>
>>> Error in ==> loadlrnfast at 76
>>> while ((length(trim(line))<10) || strcmp(trim(line),'0.0000000e+000')
>>> || strcmp(trim(line),'0000000e+000'))
>>>
>>> Error in ==> loadlrn at 56
>>>         [data,names,defined] = loadlrnfast(filename);
>>>
>>> Error in ==> esom_train at 144
>>>     data = loadlrn([prefix, '.lrn']);
>>>
>>> Error in ==> esom_demo at 61
>>> [wts, bm, umx] = esom_train(NOData, prefix, epochs, rows, columns,
>>> grid, radius, learn, algorithm);
>>>
>>> regards,
>>> yok yen
>>> On 8/16/07, *Fabian Mörchen* <fa...@my...
>>> <mailto:fa...@my...>> wrote:
>>>
>>>     Yok Yen wrote:
>>>     > Hi Fabian,
>>>     >
>>>     > Thanks for your support.
>>>     > I still getting an error while trying to run the esom_demo.m
>>>     >
>>>     > ??? Undefined command/function 'isnumber'.
>>>     >
>>>     > Error in ==> loadlrnfast at 69
>>>     >         if ~isnumber(t)
>>>     >
>>>     > Error in ==> loadlrn at 56
>>>     >         [data,names,defined] = loadlrnfast(filename);
>>>     >
>>>     > Error in ==> esom_train at 144
>>>     >     data = loadlrn([prefix, '.lrn']);
>>>     >
>>>     > Error in ==> esom_demo at 61
>>>     > [wts, bm, umx] = esom_train(NOData, prefix, epochs, rows, columns,
>>>     > grid, radius, learn, algorithm);
>>>     >
>>>     > regards,
>>>     > yok yen
>>>     >
>>>     > On 8/16/07, *Fabian Mörchen * <fa...@my...
>>>     <mailto:fa...@my...>
>>>     > <mailto:fa...@my... <mailto:fa...@my...>>> wrote:
>>>     >
>>>     >     Yok,
>>>     >
>>>     >     there seem to be some general functions missing. they are
>>>     >     attached. I hope to get to create an updated version with
>>>     everything
>>>     >     some time.
>>>     >
>>>     >     fabian
>>>     >
>>>     >     Yok Yen wrote:
>>>     >     >
>>>     >     > Hi,
>>>     >     >
>>>     >     > I am trying to integrate ESOM with my matlab problem.
>>>     >     > However, it is not successful.
>>>     >     > Hope to seek your help in this.
>>>     >     > Thanks in advance.
>>>     >     >
>>>     >     > The errors that shows up when I try to run esom_demo.m are
>>> as
>>>     >     follows:
>>>     >     > 1)
>>>     >     > >> esom_demo
>>>     >     > ??? Undefined command/function 'tail'.
>>>     >     >
>>>     >     > Error in ==> addfileext at 29
>>>     >     > if ~strcmp(tail(filename,length(ext)),ext)
>>>     >     >
>>>     >     > Error in ==> savecls at 32
>>>     >     > filename = addfileext(filename,'.cls');
>>>     >     >
>>>     >     > Error in ==> esom_demo at 54
>>>     >     > savecls('demo.cls', key, cls);
>>>     >     >
>>>     >     > 2)
>>>     >     > ??? Undefined command/function 'head'.
>>>     >     >
>>>     >     > Error in ==> loadlrnfast at 60
>>>     >     >     tokens = strread(deblank(head(line,-1)),'%s\t');
>>>     >     >
>>>     >     > Error in ==> loadlrn at 56
>>>     >     >         [data,names,defined] = loadlrnfast(filename);
>>>     >     >
>>>     >     > Error in ==> esom_train at 144
>>>     >     >     data = loadlrn([prefix, '.lrn']);
>>>     >     >
>>>     >     > Error in ==> esom_demo at 61
>>>     >     > [wts, bm, umx] = esom_train(NOData, prefix, epochs, rows,
>>>     columns,
>>>     >     > grid, radius, learn, algorithm);
>>>     >     >
>>>     >     > regards,
>>>     >     > yok yen
>>>     >     >
>>>     >
>>>     ------------------------------------------------------------------------
>>>     >     >
>>>     >     >
>>>     >
>>>     -------------------------------------------------------------------------
>>>     >     > This SF.net email is sponsored by: Splunk Inc.
>>>     >     > Still grepping through log files to find problems?  Stop.
>>>     >     > Now Search log events and configuration files using AJAX and
>>> a
>>>     >     browser.
>>>     >     > Download your FREE copy of Splunk now >>
>>>     http://get.splunk.com/ <http://get.splunk.com/>
>>>     >     >
>>>     >
>>>     ------------------------------------------------------------------------
>>>     >     >
>>>     >     > _______________________________________________
>>>     >     > Databionic-ESOM-User mailing list
>>>     >     > Dat...@li...
>>>     <mailto:Dat...@li...>
>>>     >     <mailto:Dat...@li...
>>>     <mailto:Dat...@li...>>
>>>     >     >
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