Please update nipype with slicer support #218
Conversation
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we'll tackle this at the sprint tomorrow. |
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Merging it will not be a big problem. The problem is how to maintain it.
I would like to start with 1. Any ideas how can I get the list of all SEM command lines (both slicer and BRAINS)? |
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Do you just need a list or the programs themselves as they currently stand? To get the programs themselves: |
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Thanks. Is there another way to get the list of all SEM tools other than listing a directory? |
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Do you mean another way to do it from a program, that you want me to add a current list of the program names here, or something else? |
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Chris, What do you mean by all SEM tools? This is similar to asking for all tools that can read nifti image files. Keep in mind that the SEM command line parser is gainging popularity From todays build of Slicer4, here are the names of the tools that are SEM ./Applications/CLI/Add/Add.xml Does this help? Hans J. Johnson -----Original Message----- Thanks. Is there another way to get the list of all SEM tools other than Reply to this email directly or view it on GitHub: |
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I am glad that SEM command line parser is gainging popularity outside of slicer, but for now we should focus on Slicer. So far I was getting the XML files through calling "Slicer --launch <module_name> --xml", but for this I need the names of all modules. I am not keen on hardcoding them. I would prefer to get them from Slicer somehow. I'll look into listing the plugins directory first. |
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JC, Is there an easy way (or could there be added) to get a listing of all CLI "Slicer --no-splash --list-plugins" Would this be an easy addition? Thanks, Hans J. Johnson -----Original Message----- I am glad that SEM command line parser is gainging popularity outside of So far I was getting the XML files through calling "Slicer --launch Reply to this email directly or view it on GitHub: |
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@chris, @hans : what's the status of this? i think this is a good use case where you want to include the python files for a particular version of slicer/brains in the library. this goes back to a discussion we had at the sprint that one should be able to install nipype and create nipype interface objects without having the underlying software installed on the system. this is especially important for clusters, where a client can create a workflow and execute it remotely on the grid. proposed solution: include the generated python files for slicer/brains in the repo. future: if we want a more dynamic approach we will get to it in a future version of nipype when we don't write any wrappers :) |
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Ok - this definitely will be easiest. I will use Slicer4 trunk and the list provided by Hans. |
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I have problems building newest slicer In file included from /usr/include/c++/4.5/bits/stl_iterator.h:64:0, Where should I look for help? Slicer dev mailing list? |
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The slicer dev mailing list or the bug tracker: -Mark On 9/22/11 12:53 PM, "Chris Filo Gorgolewski"
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I managed to build slicer4! Yay! with the flag you have provided BRAINS gets build as well, but not in the same folders as Slicer (Slicer-build) but into SlicerBRAINSTools-build. Maybe this is the reason why SLicer4 does not see those modules: |
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Congratulations on building Slicer4! You currently have to give it the full path to the CLI you¹re launching. There¹s a bug filed here: http://www.na-mic.org/Bug/view.php?id=1455 -Mark On 9/24/11 7:52 AM, "Chris Filo Gorgolewski"
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I was quite excited to see that this bug has been fixed, so I have updated my sources and rebuild slicer. Unfortunately this functionality still does not seem to work. Despite the fact a module (for example "Add") is loaded when you run GUI: When I try to use the "--launch" parameter id does not work. Before I post it back to Slicer bug tracker I would like to make sure I'm not making any silly mistakes. |
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Looks like that bug has been re-opened, so I guess it¹s not fixed. -Mark On 11/11/11 4:14 AM, "Chris Filo Gorgolewski"
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Chris, this is a separate issue from what you would like to have fixed. See earlier comments from JC on that bug report. The bug is about the situation where you have one plugin calling another from within CLI by using system(): Slicer --launch <full_path_to_plugin1> in plugin1.cxx you have system('<just_name_of_plugin2>') What you want to have fixed (and I would like it fixed too) is Slicer --launch <just_name_of_plugin1> |
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oops, looks like whatever is in < ... > brackets is discarded from comments! Let me repost: The bug is about the situation where you have one plugin calling another from within CLI by using system(): Slicer --launch full_path_to_plugin1 in plugin1.cxx you have system(just_name_of_plugin2) What you want to have fixed (and I would like it fixed too) is Slicer --launch just_name_of_plugin1 |
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Thanks for letting us know Andrey. The summary and description of bug are very ambiguous. I'm even afraid that if I would open a new bug to fix our problem it would be flagged as a duplicate of this one! Shall we report one anyway? BTW if not using Slicer executable - what is the normal way to call CLI modules now? |
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I suggest you submit a separate bug report and mark it as "related" to the existing one. I do think this is a separate issue, but JC will know better. FYI, we are working towards RSNA deadline right now, and this bug is not in a critical path. So I would expect this bug could be addressed December or in January during NAMIC programming week. |
Chris,
We are trying to integrate SEM compatible tools from Slicer with nipype. I had this working nicely back in June, but so much has happened with nipype since then that we have fallen out of sync.
This pull request simply rebases the slicer branch on the latest master as of today. We would like to work on getting this integrated with Slicer, and then address generating all the .py files automatically once Slicer4 starts to settle down.
I have been working on improving the SEM system, and I have kept nipype integration as one of the desired goals.
The sooner this branch can make it into nipype master, the more extensively we can test it.
Thanks,
Hans