editor I/O issue

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editor I/O issue

Davide Punzo
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Hi Steve, Jc and Andras,

I'd like to have your feedback regarding how to fix my issue to feed the editor module with
my vtkMRMLAstroVolume nodes (child of vtkMRMLScalarVolume).
I didn't check in detail the code of the Segmentation Editor, but I can imagine that there will be
similar issues.

issues:
1) Give as input to the editor module child class of ScalarVolume.
2) create child class of vtkMRMLLabelMapVolumeNode in
https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/EditorLib/HelperBox.py#L101-L119
3) I/O problem for the modelMaker.  http://wiki.slicer.org/slicerWiki/index.php/Documentation/Labs/CLIInfrastructureCleanupAndRefactoring

my proposed solutions:
1) having an attribute in vtkMRMLScalarVolume: hasScalarVolumeProprieties (true/false).
     Using this attribute in the editor module at this line
     https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/Editor/Editor.py#L184
     we can choose if the node is a valid input.
     
2) having a a virtual method CreateLabelMapVolume in vtkMRMLScalarVolume.
   This method will be used in
 https://github.com/Slicer/Slicer/blob/master/Modules/Loadable/Volumes/Logic/vtkSlicerVolumesLogic.cxx#L865-L888
   So it will be vtkNew<vtkMRMLLabelMapVolumeNode> labelNode; ->
   vtkSmartpointer<vtkMRMLLabelMapVolumeNode> labelNode = volumeNode->CreateLabelMapVolume();

3) rewrite ModelMaker as a Loadable module in C++.

Cheers,
Davide.
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Re: editor I/O issue

lasso2
Hi Davide,

Description of the issues is very short but not very clear. Some more details would help. Anyway, I can comment on the recommended solutions:

1. The fact that you have an object of vtkMRMLScalarVolume or derived type should mean that it has scalar volume properties. Adding 'hasScalarVolumeProprieties' property should not be necessary. If the problem is that you cannot select an astro volume in the editor then there could be many solutions for that: you could register additional node types to be shown in the editor widget; change the editor widget to just not show any labelmap volumes; .... I could even imagine revisiting volume class hierarchy, as it doesn't make much sense that all volumes are derived from scalar volume node (even vector and tensor volume nodes). Note that the Editor that is currently in the core is not developed any further. Enhancements are made in the new Segment Editor module (currently packaged in SlicerRT extension, will be merged into the core around the project week).

2. While some MRML nodes contain basic processing and convenience methods, MRML nodes main role is data storage. What would be the advantage of moving the labelmap converter convenience function from logic class to MRML node class?

3. Model maker is an important example of processing labelmaps and creating model output. Rewriting the module would be considerable effort spent on a workaround instead of addressing the real issue.

Andras

-----Original Message-----
From: slicer-devel [mailto:[hidden email]] On Behalf Of Davide Punzo
Sent: May 30, 2016 2:35 PM
To: SPL Slicer Devel <[hidden email]>
Subject: [slicer-devel] editor I/O issue

Hi Steve, Jc and Andras,

I'd like to have your feedback regarding how to fix my issue to feed the editor module with my vtkMRMLAstroVolume nodes (child of vtkMRMLScalarVolume).
I didn't check in detail the code of the Segmentation Editor, but I can imagine that there will be similar issues.

issues:
1) Give as input to the editor module child class of ScalarVolume.
2) create child class of vtkMRMLLabelMapVolumeNode in
https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/EditorLib/HelperBox.py#L101-L119
3) I/O problem for the modelMaker.
http://wiki.slicer.org/slicerWiki/index.php/Documentation/Labs/CLIInfrastructureCleanupAndRefactoring

my proposed solutions:
1) having an attribute in vtkMRMLScalarVolume: hasScalarVolumeProprieties (true/false).
     Using this attribute in the editor module at this line
   
https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/Editor/Editor.py#L184
     we can choose if the node is a valid input.
     
2) having a a virtual method CreateLabelMapVolume in vtkMRMLScalarVolume.
   This method will be used in

https://github.com/Slicer/Slicer/blob/master/Modules/Loadable/Volumes/Logic/vtkSlicerVolumesLogic.cxx#L865-L888
   So it will be vtkNew<vtkMRMLLabelMapVolumeNode> labelNode; ->
   vtkSmartpointer<vtkMRMLLabelMapVolumeNode> labelNode =
volumeNode->CreateLabelMapVolume();

3) rewrite ModelMaker as a Loadable module in C++.

Cheers,
Davide.



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Re: editor I/O issue

Davide Punzo
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This post was updated on .
Hi Andras,

thanks for the reply. Sorry I forgot you were not at the developer hangout when I showed the issue.

The main issue is that I'd like to use my astroVolume class (child of ScalarVolume) and AstroLabelMapVolume (child of LabelMapVolume) in the editor module.

On the other hand, if the segmentation Module will replace the editor one, I should take look in detail
to the code of the segmetation module (I thought the segmetation Module will be an addon, not a
replecement, respect to the editor one).


 
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Re: editor I/O issue

pinter
In reply to this post by lasso2
Hi Davide,

It would help a lot if you let us know what is the extra feature in your Astro labelmap class.

To make it clear, the Segment Editor module will be an "addon", but what Andras said about the Editor module being kind of frozen still stands. That is the reason why we decided to completely implement Editor, as its use cases apparently overgrew the design, and it has been increasingly hard to change, i.e. a minor fix mostly introduced regressions and it has proven to be hard to maintain.

The Segment Editor module uses the Segmentations infrastructure, which is basically a new type of MRML node and a module with the same name with all the Slicer-specific features you can imagine (widgets, storage, display, displayable managers, algorithm classes, converters, etc.). For further explanation I suggest you look at the slides referenced from the bottom of the project page about integrating it into Slicer core:
http://www.na-mic.org/Wiki/index.php/2016_Summer_Project_Week/Segmentations_Integration

Segmentations will coexist with the current LabelMapVolumeNode + Editor + ModelMaker ecosystem, but it offers more flexibility, easier usage, and many extra features. The presentation I referred to above should make it clearer than this short description, so please go through that.

Also I would be really interested in the reason you subclassed labelmap to an "astro labelmap".

Cheers,
csaba

-----Original Message-----
From: slicer-devel [mailto:[hidden email]] On Behalf Of Davide Punzo
Sent: May 30, 2016 15:26
To: SPL Slicer Devel <[hidden email]>
Subject: Re: [slicer-devel] editor I/O issue

Hi Andras,

thanks for the reply. Sorry I forgot you were not at the developer hangout when I showed the issue.

The main issue is that I'd like to use my astroVolume class and AstroLabelMapVolume in the editor.

On the other hand, if the segmentation Module will replace the editor one, I should take look in detail to the code of the segmetation module (I thought the segmetation Module will be an addon, not a replecement, respect to the editor one).


 



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Re: editor I/O issue

Davide Punzo
Hi Csaba,

thanks for the detailed info.

I already donwloded SlicerRT and I looked at the source code (however, not
in detail yet).

In the Seggmentation Editor I could load my AstroVolume. However, I still
have the issue that
the segmentation node will miss my "astro features".

The use of AstroLabelMap is due for these two reasons:

1) it uses the vtkMRMLAstroVolumeStorageNode (read and write to FITS format
file, astronomical format file).
2) It uses the vtkMRMLAstroLabelMapVolumeDisplayNode in which are stored
attributes and methods related
    to the astronomical world coordinate system (needed to display them on
DataProbe, etc.).

However the vtkImageData stored in a AstroLabelMap are the same type of a
LabelMap (as well in
the AstroVolume the data are same typo of a ScalarVolume).

Therefore, the Astro "attributes" are not "required" by the editor or
segmentation editor.
However, the point is that I'd like to be able to do these two workflows:
A)
1)  load my astroVolume as masterVolume
2)  I create a mask (segmentation) interacting with the editors ->
AstroLabelMap
3)  reuse it for other purpose or resave it as a FITS file.

B)
1) load a AstroLabelMap (from fits file)
2) change it with the editors
3) reuse it for other purpose or resave it as a FITS file.

Davide.







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Re: editor I/O issue

Davide Punzo
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Re: editor I/O issue

Davide Punzo
I geuss converting AstroLabelMap to LabelMap or SegmentationNode and
viceversa should be possible. However, I'd like to avoid to copy the data
many times



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Re: editor I/O issue

pinter
In reply to this post by Davide Punzo
Hi Davide,

Thanks a lot for the explanation, the use cases are especially helpful!

If you write an IO plugin that can load a FITS file to segmentation and save a segmentation to FITS files, then you can select it in the drop-down when loading and writing. See an example here for loading:
https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/src/VffFileReader

I think adding extra formats to save/load existing MRML types is possible by storage nodes as well, but I'm not completely sure about that.

csaba

-----Original Message-----
From: slicer-devel [mailto:[hidden email]] On Behalf Of Davide Punzo
Sent: May 30, 2016 16:08
To: SPL Slicer Devel <[hidden email]>
Subject: Re: [slicer-devel] editor I/O issue

Hi Csaba,

thanks for the detailed info.

I already donwloded SlicerRT and I looked at the source code (however, not in detail yet).

In the Seggmentation Editor I could load my AstroVolume. However, I still have the issue that the segmentation node will miss my "astro features".

The use of AstroLabelMap is due for these two reasons:

1) it uses the vtkMRMLAstroVolumeStorageNode (read and write to FITS format file, astronomical format file).
2) It uses the vtkMRMLAstroLabelMapVolumeDisplayNode in which are stored attributes and methods related
    to the astronomical world coordinate system (needed to display them on DataProbe, etc.).

However the vtkImageData stored in a AstroLabelMap are the same type of a LabelMap (as well in the AstroVolume the data are same typo of a ScalarVolume).

Therefore, the Astro "attributes" are not "required" by the editor or segmentation editor.
However, the point is that I'd like to be able to do these two workflows:
A)
1)  load my astroVolume as masterVolume
2)  I create a mask (segmentation) interacting with the editors -> AstroLabelMap
3)  reuse it for other purpose or resave it as a FITS file.

B)
1) load a AstroLabelMap (from fits file)
2) change it with the editors
3) reuse it for other purpose or resave it as a FITS file.

Davide.







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Re: editor I/O issue

Davide Punzo
ok,

what I do at the moment using my astroReader and storing classes:
is that I load from FITS to AstroVolume (if is data) or to AstroLabelMap (if
it a segmentation) and viceversa for saving.

Of course I can decide to load and save FITS segmentation in a
vtkMRMLSegmentationNode, but then I'll lose the information and the methods
relative to the astronomical World Coordinates System (which I need when I
visualize it!!!!!).

So, I'd like still to load the FITS file into my AstroLabelMap node.

I don't know, my prefered solution will be something like this (this is very
hypotetical):

1) I write my AstroSegmetationNode (child of SegmetationNode).

2) I load/save the data there (instead of the AstroLabelMap).

3) instead to create always a vtkMRMLSegmentationNode here
https://github.com/SlicerRt/SlicerRT/blob/master/SegmentEditor/SegmentEditor.py#L104

we could have a virtual method createSegmetationNode in the ScalarVolume
similar to this one
https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Core/vtkMRMLScalarVolumeNode.h#L68

then use it to create the segemtation node desired.

4) when passing the Segmetation Node to the modelMaker downcast it so there
will be no problem with the CLI I/O issue.

this is very hypotetical, let me a couple of days to study your code, to see
if it will work (and of course if for you is an accetable solution).

Davide.




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Re: editor I/O issue

Davide Punzo
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In reply to this post by pinter
ok,

what I do at the moment using my astroReader and storing classes:
is that I load from FITS to AstroVolume (if is data) or to AstroLabelMap (if it a segmentation) and viceversa for saving.

Of course I can decide to load and save FITS segmentation in a vtkMRMLSegmentationNode, but then I'll lose the information and the methods relative to the astronomical World Coordinates System (which I need when I visualize it!!!!!).

So, I'd like still to load the FITS file into my AstroLabelMap node.

I don't know, my prefered solution will be something like this (this is very hypotetical):

1) I write my AstroSegmetationNode (child of SegmetationNode).

2) I load/save the data there (instead of the AstroLabelMap).

3) instead to create always a vtkMRMLSegmentationNode here
https://github.com/SlicerRt/SlicerRT/blob/master/SegmentEditor/SegmentEditor.py#L104

we could have a virtual method createSegmetationNode in the ScalarVolume similar to this one
https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Core/vtkMRMLScalarVolumeNode.h#L68

then use it to create the segemtation node desired.

4) when passing the Segmetation Node to the modelMaker downcast it so there will be no problem with the CLI I/O issue.

this is very hypotetical, let me a couple of days to study your code, to see if it will work (and of course if for you is an accetable solution).

Davide.
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Re: editor I/O issue

pinter
In reply to this post by Davide Punzo
Hi Davide,

It would be great to understand more about the astronomical coordinate system. Maybe we could talk more about this at the project week. Or if you have some material summarizing it briefly I could look at that.

Steps 1-3 sound reasonable, we should talk about this more. Alternatively you can stick to the Editor module, whichever seems to satisfy your needs more. However,

4. The whole point of Segmentations is that it does the conversion itself, you don't need to use external converters such as ModelMaker! Please go through those slides I referred to so that you see what the whole infrastructure is for (the gist are slides 3-12 = 10 slides).

Once I know the additional information the extra coordinate system provides I can help you figure out whether it can be done with Segmentations, and if yes then how. My vague idea (without knowing these) is that we could create an alternative display pipeline for your subclass to accommodate this extra information. Or if not then we could stick to the labelmap approach, but then you'll face those difficulties you mentioned (using it with Editor and ModelMaker).

csaba

-----Original Message-----
From: slicer-devel [mailto:[hidden email]] On Behalf Of Davide Punzo
Sent: May 30, 2016 16:46
To: SPL Slicer Devel <[hidden email]>
Subject: Re: [slicer-devel] editor I/O issue

ok,

what I do at the moment using my astroReader and storing classes:
is that I load from FITS to AstroVolume (if is data) or to AstroLabelMap (if it a segmentation) and viceversa for saving.

Of course I can decide to load and save FITS segmentation in a vtkMRMLSegmentationNode, but then I'll lose the information and the methods relative to the astronomical World Coordinates System (which I need when I visualize it!!!!!).

So, I'd like still to load the FITS file into my AstroLabelMap node.

I don't know, my prefered solution will be something like this (this is very
hypotetical):

1) I write my AstroSegmetationNode (child of SegmetationNode).

2) I load/save the data there (instead of the AstroLabelMap).

3) instead to create always a vtkMRMLSegmentationNode here
https://github.com/SlicerRt/SlicerRT/blob/master/SegmentEditor/SegmentEditor.py#L104

we could have a virtual method createSegmetationNode in the ScalarVolume similar to this one
https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Core/vtkMRMLScalarVolumeNode.h#L68

then use it to create the segemtation node desired.

4) when passing the Segmetation Node to the modelMaker downcast it so there will be no problem with the CLI I/O issue.

this is very hypotetical, let me a couple of days to study your code, to see if it will work (and of course if for you is an accetable solution).

Davide.




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Re: editor I/O issue

Davide Punzo
Hi Csaba,

1-3: ok thanks. It will be nice if we can talk about it even earlier than
the slicer meeting. Please, let me know
if you are available for a videocall and when it suits your agenda. Thank
you!

4: that it is great!!!!! ( as I said I looked at your code not too much in
detail yet). Then, with the Segmetation Module there will be no more the CLI
I/O issue!!!

I don't have a real documentation about the WCS, however they are attributes
and methods of the Display classes

https://github.com/Punzo/SlicerAstro/blob/master/AstroVolume/MRML/vtkMRMLAstroLabelMapVolumeDisplayNode.h#L63-L158

to display the coordinates (the coordinates system is a non-linear system
which depends on each datacube)
as shown here
https://github.com/Punzo/SlicerAstro/wiki/SlicerAstroModules#astrodataprobe 

Davide.



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Re: editor I/O issue

Davide Punzo
This post has NOT been accepted by the mailing list yet.
In reply to this post by pinter
Hi Csaba,

1-3: ok thanks. It will be nice if we can talk about it even earlier than the slicer meeting. Please, let me know
if you are available for a videocall and when it suits your agenda. Thank you!

4: that it is great!!!!! ( as I said I looked at your code not too much in detail yet). Then, with the Segmetation Module there will be no more the CLI I/O issue!!!

I don't have a real documentation about the WCS, however they are attributes and methods of the Display classes

https://github.com/Punzo/SlicerAstro/blob/master/AstroVolume/MRML/vtkMRMLAstroLabelMapVolumeDisplayNode.h#L63-L158

to display the coordinates (the coordinates system is a non-linear system which depends on each datacube)
as shown here
https://github.com/Punzo/SlicerAstro/wiki/SlicerAstroModules#astrodataprobe 

Davide.
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Re: editor I/O issue

pinter
In reply to this post by Davide Punzo
Hi Davide,

Thanks for the information, it is somewhat clearer now!

We can have a skype or hangouts call about this, but I think we should involve other stakeholders too. Please consult with any colleague you'd like to attend the meeting and suggest a few time slots.
I and Andras will choose one that works for us. If I see correctly that you're in the Netherlands then we have a 6-hour difference, so what's morning for us is afternoon for you.

Cheers,
csaba


-----Original Message-----
From: slicer-devel [mailto:[hidden email]] On Behalf Of Davide Punzo
Sent: May 30, 2016 17:18
To: SPL Slicer Devel <[hidden email]>
Subject: Re: [slicer-devel] editor I/O issue

Hi Csaba,

1-3: ok thanks. It will be nice if we can talk about it even earlier than the slicer meeting. Please, let me know if you are available for a videocall and when it suits your agenda. Thank you!

4: that it is great!!!!! ( as I said I looked at your code not too much in detail yet). Then, with the Segmetation Module there will be no more the CLI I/O issue!!!

I don't have a real documentation about the WCS, however they are attributes and methods of the Display classes

https://github.com/Punzo/SlicerAstro/blob/master/AstroVolume/MRML/vtkMRMLAstroLabelMapVolumeDisplayNode.h#L63-L158

to display the coordinates (the coordinates system is a non-linear system which depends on each datacube) as shown here https://github.com/Punzo/SlicerAstro/wiki/SlicerAstroModules#astrodataprobe 

Davide.



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Re: editor I/O issue

Davide Punzo
Hi Csaba,

at the moment I am in Noth Carolina at the kitware offices. So no time zone
issues.

I think the best is that I go through the Segmentation classes
implementation,
so I'll have clearer ideas and then have the videocall.
At the moment I have to fix a couple of problems to upload SlicerAstro in
the extension repository.

Therefore, maybe the best is on Friday (any time for me).
I don't know if Jc and Steve may be interested in following this.

Another option may be to talk in
the developer hangout next Tuesday.

Cheers,

Davide.



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Re: editor I/O issue

Davide Punzo
This post has NOT been accepted by the mailing list yet.
This post was updated on .
In reply to this post by pinter
Hi Csaba,

at the moment I am in Noth Carolina at the kitware offices. So no big time zone issues.

I think the best is that I go through the Segmentation classes implementation,
so I'll have clearer ideas and then have the videocall.
At the moment I have to fix a couple of problems to upload SlicerAstro in the extension repository.

Therefore, maybe the best is on Friday (any time for me).
I don't know if Jc and Steve may be interested in following this.

Another option may be to talk in
the developer hangout next Tuesday.

Thanks,

Cheers,

Davide.
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Re: editor I/O issue

pinter
In reply to this post by Davide Punzo
Hi Davide,

The Segmentations implementation itself consists of 40 C++ classes and 12 python files (only the source code is over 1MB), so I'd advise against going through the code.
What I suggest is the same as before: please look at the presentation I made that explains the mechanism
https://www.slicer.org/slicerWiki/index.php/File:20160526_Segmentations.pptx
Also looking at the labs page [1] and the module wiki page [2] could be useful.

For me the developer hangout would be somewhat better.

Cheers,
csaba

[1] https://www.slicer.org/slicerWiki/index.php/Documentation/Labs/Segmentations
[2] https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Segmentations


-----Original Message-----
From: slicer-devel [mailto:[hidden email]] On Behalf Of Davide Punzo
Sent: May 31, 2016 18:04
To: SPL Slicer Devel <[hidden email]>
Subject: Re: [slicer-devel] editor I/O issue

Hi Csaba,

at the moment I am in Noth Carolina at the kitware offices. So no time zone issues.

I think the best is that I go through the Segmentation classes implementation, so I'll have clearer ideas and then have the videocall.
At the moment I have to fix a couple of problems to upload SlicerAstro in the extension repository.

Therefore, maybe the best is on Friday (any time for me).
I don't know if Jc and Steve may be interested in following this.

Another option may be to talk in
the developer hangout next Tuesday.

Cheers,

Davide.



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Re: editor I/O issue

pinter
Sorry, 52 C++ classes in addition to the 12 python files :)

-----Original Message-----
From: slicer-devel [mailto:[hidden email]] On Behalf Of Csaba Pinter
Sent: May 31, 2016 18:22
To: Davide Punzo <[hidden email]>; SPL Slicer Devel <[hidden email]>
Subject: Re: [slicer-devel] editor I/O issue

Hi Davide,

The Segmentations implementation itself consists of 40 C++ classes and 12 python files (only the source code is over 1MB), so I'd advise against going through the code.
What I suggest is the same as before: please look at the presentation I made that explains the mechanism https://www.slicer.org/slicerWiki/index.php/File:20160526_Segmentations.pptx
Also looking at the labs page [1] and the module wiki page [2] could be useful.

For me the developer hangout would be somewhat better.

Cheers,
csaba

[1] https://www.slicer.org/slicerWiki/index.php/Documentation/Labs/Segmentations
[2] https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Segmentations


-----Original Message-----
From: slicer-devel [mailto:[hidden email]] On Behalf Of Davide Punzo
Sent: May 31, 2016 18:04
To: SPL Slicer Devel <[hidden email]>
Subject: Re: [slicer-devel] editor I/O issue

Hi Csaba,

at the moment I am in Noth Carolina at the kitware offices. So no time zone issues.

I think the best is that I go through the Segmentation classes implementation, so I'll have clearer ideas and then have the videocall.
At the moment I have to fix a couple of problems to upload SlicerAstro in the extension repository.

Therefore, maybe the best is on Friday (any time for me).
I don't know if Jc and Steve may be interested in following this.

Another option may be to talk in
the developer hangout next Tuesday.

Cheers,

Davide.



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Re: editor I/O issue

Davide Punzo
yeap, exactly  

thanks again for the link and the info.

Ok then I'll ask if there will be a free slot at the next hangout.

Davide.



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Re: editor I/O issue

Davide Punzo
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In reply to this post by pinter
yeap, exactly  

thanks again for the link and the info.

Ok then I'll ask if there will be a free slot at the next hangout.

Davide.
12