siRelax
- Olivier Coulon
- Posts: 176
- Joined: Fri Feb 27, 2004 11:48 am
- Location: MeCA research group, Institut de Neurosciences de La Timone, Marseille, France
- Contact:
siRelax
Hi there,
I suppose my question is mostly for Denis here (again ).
I am trying to use the siRelax command and I have a few questions about the parameter file.
I am building a parameter file using the siRelax.stx syntax, found in sigraph-main/shared/config/
You (Denis) once told me that I could give several graphs instead of one as an input. Should I just consider that the graphFile attribute is a vector of strings, then ?
What about the labelsMapFile attribute ? It is irrelevant for my process, but it has a default value. Should I just ignore it and consider that my models will never use it ? Is it looked for during the relaxation ? (I just want to make sure that it will not disturb the minimisation in a way I don't understand).
That's all for now, thank you very much in advance.
Olivier
I suppose my question is mostly for Denis here (again ).
I am trying to use the siRelax command and I have a few questions about the parameter file.
I am building a parameter file using the siRelax.stx syntax, found in sigraph-main/shared/config/
You (Denis) once told me that I could give several graphs instead of one as an input. Should I just consider that the graphFile attribute is a vector of strings, then ?
What about the labelsMapFile attribute ? It is irrelevant for my process, but it has a default value. Should I just ignore it and consider that my models will never use it ? Is it looked for during the relaxation ? (I just want to make sure that it will not disturb the minimisation in a way I don't understand).
That's all for now, thank you very much in advance.
Olivier
Olivier Coulon
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org
- riviere
- Site Admin
- Posts: 1361
- Joined: Tue Jan 06, 2004 12:21 pm
- Location: CEA NeuroSpin, Saint Aubin, France
- Contact:
Hi Olivier,
Yes, the relaxation process has been modified to accept several graphs as input. The parameters format doesn't currently allow vectors of strings (this limitation will disapear when we use XML parameter files, soon), so you have to separate filenames by a '|' (pipe character):
All graphs are concatenated into a single one.
labelsMapFile specifies a translation file for labels, it is common to many cortical folds algorithms, but in your case it won't be used. In siRelax, I guess it is only useful when initializing labels with existing values (before starting the relaxation) if it is even used at all...
During the relaxation, labels are taken from the model graph.
Denis
Yes, the relaxation process has been modified to accept several graphs as input. The parameters format doesn't currently allow vectors of strings (this limitation will disapear when we use XML parameter files, soon), so you have to separate filenames by a '|' (pipe character):
Code: Select all
graphFile toto.arg|tutu.arg|ploplo.arg
labelsMapFile specifies a translation file for labels, it is common to many cortical folds algorithms, but in your case it won't be used. In siRelax, I guess it is only useful when initializing labels with existing values (before starting the relaxation) if it is even used at all...
During the relaxation, labels are taken from the model graph.
Denis
- Olivier Coulon
- Posts: 176
- Joined: Fri Feb 27, 2004 11:48 am
- Location: MeCA research group, Institut de Neurosciences de La Timone, Marseille, France
- Contact:
Thank you Denis.
Olivier Coulon
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org
- Olivier Coulon
- Posts: 176
- Joined: Fri Feb 27, 2004 11:48 am
- Location: MeCA research group, Institut de Neurosciences de La Timone, Marseille, France
- Contact:
HI,
I am back with some more problems.
When I call :
I get the following message :
I used the syntax defined by the file : sigraph-main/shared/config/siRelax.stx
and my parameter file looks like that :
As far as I understand, a 'label' attribute is expected which does not appear in the syntax. Any idea about what's wrong ?
Yhanks in advance,
Olivier
I am back with some more problems.
When I call :
Code: Select all
siRelax paramFile.tree
Code: Select all
missing semantic attribute label
terminate called after throwing an instance of 'carto::invalid_format_error'
what() : missing semantic attribute label
and my parameter file looks like that :
Code: Select all
*BEGIN TREE siRelax
modelFile (path)/functionalsketchmodel.arg
graphFile (path)/graph1.arg|(path)/graph2.arg|...
output /home/olivier/data/spmt-stats/labelled.arg
save 1
temp 20000.0
mode gibbs
rate 0.99
tempICM 1000.0
gibbsChange 1
verbose 1
plotfile /home/olivier/data/spmt-stats/energy.log
*END
Yhanks in advance,
Olivier
Olivier Coulon
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org
- Olivier Coulon
- Posts: 176
- Joined: Fri Feb 27, 2004 11:48 am
- Location: MeCA research group, Institut de Neurosciences de La Timone, Marseille, France
- Contact:
Yes, that's what it was, I don't use the label attribute and I did not realise it was mandatory in the nodes of the model graph.
As always : thank you Denis,
Olivier
As always : thank you Denis,
Olivier
Olivier Coulon
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org
- Olivier Coulon
- Posts: 176
- Joined: Fri Feb 27, 2004 11:48 am
- Location: MeCA research group, Institut de Neurosciences de La Timone, Marseille, France
- Contact:
tree files that define models for siRelax
Hi there,
what are the syntax files for tree files that define models (for siRelax) ?
I looked in the siRelax/main/shared/ directory but still can't find one ?
Thanks ,
Olivier
what are the syntax files for tree files that define models (for siRelax) ?
I looked in the siRelax/main/shared/ directory but still can't find one ?
Thanks ,
Olivier
Olivier Coulon
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org
- Olivier Coulon
- Posts: 176
- Joined: Fri Feb 27, 2004 11:48 am
- Location: MeCA research group, Institut de Neurosciences de La Timone, Marseille, France
- Contact:
Me again,
I found it in :
shared/main/nomenclature/syntax/adap.stx
Sorry about the previous question, I should have looked there before...
Olivier
I found it in :
shared/main/nomenclature/syntax/adap.stx
Sorry about the previous question, I should have looked there before...
Olivier
Olivier Coulon
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org
- Olivier Coulon
- Posts: 176
- Joined: Fri Feb 27, 2004 11:48 am
- Location: MeCA research group, Institut de Neurosciences de La Timone, Marseille, France
- Contact:
Hello Denis and others,
some more questions about siRelax :
- every N iterations, with N a parameter, the annealing does three "special" iterations :
Void pass
CONN_VOID
CONNECT
What are those ? I can't figure out what they do. Is there a way to turn those "extensions" off ?
Thanks in advance,
Olivier
some more questions about siRelax :
- every N iterations, with N a parameter, the annealing does three "special" iterations :
Void pass
CONN_VOID
CONNECT
What are those ? I can't figure out what they do. Is there a way to turn those "extensions" off ?
Thanks in advance,
Olivier
Olivier Coulon
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org
- Jean-Francois Mangin
- Posts: 337
- Joined: Mon Mar 01, 2004 10:24 am
- Location: Neurospin, CEA, France
- Contact:
Well,
the annealing schedule dedicated to the sulci is not based on a standard Gibbs sampling. It is a bit tricky to explain in a few words but we added some iterations inspired from some other dynamics usually used to sample phase transitions of spin glasses. Practically, these specific iterations consists in looping on the labels (sulci): for each label, we consider the following transitions: turn the whole label to unknown, turn one of the connected components of the label to unknown. The idea is to get rid of the local minima related to the fact that a label can be made up of a a lot of nodes. Therefore, local modifications of one single node fail at discovering a way to escape. With a more intuitive language, a wrong choice for a sulcus can nor be removed easily one node after another. In return, globally, mistakes are easier to detect.
A last point, this dynamics means our algorithm is not a conventional annealing. The transitions, indeed, are nor reversible.
I do not know where is the mecanism to turn that off. Knowing Denis'habit, I would gamble on a configuration file with the tree/graph format. Denis is skiing this week...
the annealing schedule dedicated to the sulci is not based on a standard Gibbs sampling. It is a bit tricky to explain in a few words but we added some iterations inspired from some other dynamics usually used to sample phase transitions of spin glasses. Practically, these specific iterations consists in looping on the labels (sulci): for each label, we consider the following transitions: turn the whole label to unknown, turn one of the connected components of the label to unknown. The idea is to get rid of the local minima related to the fact that a label can be made up of a a lot of nodes. Therefore, local modifications of one single node fail at discovering a way to escape. With a more intuitive language, a wrong choice for a sulcus can nor be removed easily one node after another. In return, globally, mistakes are easier to detect.
A last point, this dynamics means our algorithm is not a conventional annealing. The transitions, indeed, are nor reversible.
I do not know where is the mecanism to turn that off. Knowing Denis'habit, I would gamble on a configuration file with the tree/graph format. Denis is skiing this week...
- Olivier Coulon
- Posts: 176
- Joined: Fri Feb 27, 2004 11:48 am
- Location: MeCA research group, Institut de Neurosciences de La Timone, Marseille, France
- Contact:
Thanks Jeff,
there is a parameter file for siRelax that can be used to define all options. That is what I am using. And there seems to be a way to turn off the aznnealing extension but I do not know the exact syntax for that. Since Denis generates the parameter file "on the fly" in the Brainvisa recognition process, I do not have any example showing how to define each parameter. Anyway, little by little I understand.
I would also know how to set the 'unknown' label to another value ('0'). It is possible as an option but I don't know how to set it up in the parameter file. Maybe you know ?
I don't think you should let Denis go skiing, it's a very dangerous activity and he is very precious to me at the moment
Thanks for your answer,
Olivier
there is a parameter file for siRelax that can be used to define all options. That is what I am using. And there seems to be a way to turn off the aznnealing extension but I do not know the exact syntax for that. Since Denis generates the parameter file "on the fly" in the Brainvisa recognition process, I do not have any example showing how to define each parameter. Anyway, little by little I understand.
I would also know how to set the 'unknown' label to another value ('0'). It is possible as an option but I don't know how to set it up in the parameter file. Maybe you know ?
I don't think you should let Denis go skiing, it's a very dangerous activity and he is very precious to me at the moment
Thanks for your answer,
Olivier
Olivier Coulon
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org
- Jean-Francois Mangin
- Posts: 337
- Joined: Mon Mar 01, 2004 10:24 am
- Location: Neurospin, CEA, France
- Contact:
- Olivier Coulon
- Posts: 176
- Joined: Fri Feb 27, 2004 11:48 am
- Location: MeCA research group, Institut de Neurosciences de La Timone, Marseille, France
- Contact:
It's alright Jeff, don't bother looking for oàne. I can see what the brainvisa process is generating, my only problem is that it is using a lot of default values so not all the options are explicitely set up. I guess I have to wait for Denis' return.
thanks a lot,
Olivier
thanks a lot,
Olivier
Olivier Coulon
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org
- riviere
- Site Admin
- Posts: 1361
- Joined: Tue Jan 06, 2004 12:21 pm
- Location: CEA NeuroSpin, Saint Aubin, France
- Contact:
Hi,
I'm back (in one piece, nothing broken!)...
The process in BrainVisa only uses a simplified mode of siRelax: it doesn't feed some parameters which have a default value in siRelax.
You already have found the list of parameters in sigraph/shared/config/siRelax.cfg: here you need to specify voidMode, voidLabel and/or voidOccurency. You can use:
I don't know if the default void passes are of any interest for your application or not - they may be.
Trick: in Anatomist, there is a recognition module which performs the relaxation with a colored 3D display while it runs. The configuration panel for it shows a (quite) complete set of options and basic help on tooltips. To use it, load in Anatomist both a data graph and a model graph, make a fusion with them (FusionGraph), and then on the new object (AFGRAPH), you can get the annealing panel.
Does it help ?
Denis
I'm back (in one piece, nothing broken!)...
The process in BrainVisa only uses a simplified mode of siRelax: it doesn't feed some parameters which have a default value in siRelax.
You already have found the list of parameters in sigraph/shared/config/siRelax.cfg: here you need to specify voidMode, voidLabel and/or voidOccurency. You can use:
Code: Select all
voidMode NONE
voidLabel 0
Trick: in Anatomist, there is a recognition module which performs the relaxation with a colored 3D display while it runs. The configuration panel for it shows a (quite) complete set of options and basic help on tooltips. To use it, load in Anatomist both a data graph and a model graph, make a fusion with them (FusionGraph), and then on the new object (AFGRAPH), you can get the annealing panel.
Does it help ?
Denis