Official Slicer CLI docker image?

classic Classic list List threaded Threaded
8 messages Options
Reply | Threaded
Open this post in threaded view
|

Official Slicer CLI docker image?

andrey.fedorov
Hi,

is there an official image of 3D Slicer that would expose Slicer command line to allow running Slicer CLIs using Docker? 

This would be helpful for the users who put together pipelines out of "dockerized tools", which is very fashionable these days (at least in some sub-communities). This should not be hard at all to do for Slicer CLIs.

It looks like we have an organization, and several images, but none of these seems to be exposing command line tools, and also they are not documented and are not linked to Dockerfiles.


If we already have a Slicer build, we could just add an entrypoint to pass the command line parameters and perhaps add an option that would list all CLIs available. Would be great to get Kitware thoughts on this.

AF

_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ
Reply | Threaded
Open this post in threaded view
|

Re: Official Slicer CLI docker image?

Steve Pieper-2
Hi Andrey - 

I agree, it would be helpful to make a set of user-facing docker tools.  I think the current ones in dockerhub/slicer are mostly related to building slicer.

I recently made a set that follow the pattern of the dit4c Dockerfiles and expose the noVNC interface, which I find very useful.



I've been thinking we could expose variants that have different extensions and tools pre-installed and configured.  For example my slicer-chronicle one is preconfigured to listen for jobs to execute in response to database triggers.

I'll be interested to hear what others have in mind.

Best,
Steve

On Wed, Feb 15, 2017 at 3:07 PM, Andrey Fedorov <[hidden email]> wrote:
Hi,

is there an official image of 3D Slicer that would expose Slicer command line to allow running Slicer CLIs using Docker? 

This would be helpful for the users who put together pipelines out of "dockerized tools", which is very fashionable these days (at least in some sub-communities). This should not be hard at all to do for Slicer CLIs.

It looks like we have an organization, and several images, but none of these seems to be exposing command line tools, and also they are not documented and are not linked to Dockerfiles.


If we already have a Slicer build, we could just add an entrypoint to pass the command line parameters and perhaps add an option that would list all CLIs available. Would be great to get Kitware thoughts on this.

AF

_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ


_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ
Reply | Threaded
Open this post in threaded view
|

Re: Official Slicer CLI docker image?

andrey.fedorov
In reply to this post by andrey.fedorov
I personally think that being able to access CLIs is the most basic use case. I could probably set it up myself, but since I would be passing that link around, it would be nice if the images were provided under the official Slicer organization and not under my personal account.

On Wed, Feb 15, 2017 at 3:20 PM, Steve Pieper <[hidden email]> wrote:
Hi Andrey - 

I agree, it would be helpful to make a set of user-facing docker tools.  I think the current ones in dockerhub/slicer are mostly related to building slicer.

I recently made a set that follow the pattern of the dit4c Dockerfiles and expose the noVNC interface, which I find very useful.



I've been thinking we could expose variants that have different extensions and tools pre-installed and configured.  For example my slicer-chronicle one is preconfigured to listen for jobs to execute in response to database triggers.

I'll be interested to hear what others have in mind.

Best,
Steve

On Wed, Feb 15, 2017 at 3:07 PM, Andrey Fedorov <[hidden email]> wrote:
Hi,

is there an official image of 3D Slicer that would expose Slicer command line to allow running Slicer CLIs using Docker? 

This would be helpful for the users who put together pipelines out of "dockerized tools", which is very fashionable these days (at least in some sub-communities). This should not be hard at all to do for Slicer CLIs.

It looks like we have an organization, and several images, but none of these seems to be exposing command line tools, and also they are not documented and are not linked to Dockerfiles.


If we already have a Slicer build, we could just add an entrypoint to pass the command line parameters and perhaps add an option that would list all CLIs available. Would be great to get Kitware thoughts on this.

AF

_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ



_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ
Reply | Threaded
Open this post in threaded view
|

Re: Official Slicer CLI docker image?

Matt McCormick
Hi,

The slicer images on DockerHub are configured here:

  https://github.com/thewtex/SlicerDocker

This is currently in my GitHub user account, but I would be happy if
these were transferred to the Slicer/ GitHub organization.


The images are separated to effectively build, test, and run Slicer
and Slicer extensions.


For an example of how to use the images to build and test an
extension, see the TravisCI configuration in this repository:

  https://github.com/KitwareMedical/SlicerITKUltrasound


To see how it can be used to build and test Slicer itself, see the
CircleCI configuration on the Slicer GitHub repository:

  https://github.com/Slicer/Slicer

and a detailed description is in this article:

  https://blog.kitware.com/3d-slicer-improves-testing-for-pull-requests-using-docker-and-circleci/


These images are also built with web noVNC support. More details here:

   https://github.com/thewtex/docker-opengl

HTH,
Matt

On Wed, Feb 15, 2017 at 3:25 PM, Andrey Fedorov
<[hidden email]> wrote:

> I personally think that being able to access CLIs is the most basic use
> case. I could probably set it up myself, but since I would be passing that
> link around, it would be nice if the images were provided under the official
> Slicer organization and not under my personal account.
>
> On Wed, Feb 15, 2017 at 3:20 PM, Steve Pieper <[hidden email]> wrote:
>>
>> Hi Andrey -
>>
>> I agree, it would be helpful to make a set of user-facing docker tools.  I
>> think the current ones in dockerhub/slicer are mostly related to building
>> slicer.
>>
>> I recently made a set that follow the pattern of the dit4c Dockerfiles and
>> expose the noVNC interface, which I find very useful.
>>
>> https://hub.docker.com/u/stevepieper/
>>
>> https://github.com/pieper/SlicerDockers
>>
>> I've been thinking we could expose variants that have different extensions
>> and tools pre-installed and configured.  For example my slicer-chronicle one
>> is preconfigured to listen for jobs to execute in response to database
>> triggers.
>>
>> I'll be interested to hear what others have in mind.
>>
>> Best,
>> Steve
>>
>> On Wed, Feb 15, 2017 at 3:07 PM, Andrey Fedorov <[hidden email]>
>> wrote:
>>>
>>> Hi,
>>>
>>> is there an official image of 3D Slicer that would expose Slicer command
>>> line to allow running Slicer CLIs using Docker?
>>>
>>> This would be helpful for the users who put together pipelines out of
>>> "dockerized tools", which is very fashionable these days (at least in some
>>> sub-communities). This should not be hard at all to do for Slicer CLIs.
>>>
>>> It looks like we have an organization, and several images, but none of
>>> these seems to be exposing command line tools, and also they are not
>>> documented and are not linked to Dockerfiles.
>>>
>>> https://hub.docker.com/u/slicer/
>>>
>>> If we already have a Slicer build, we could just add an entrypoint to
>>> pass the command line parameters and perhaps add an option that would list
>>> all CLIs available. Would be great to get Kitware thoughts on this.
>>>
>>> AF
>>>
>>> _______________________________________________
>>> slicer-devel mailing list
>>> [hidden email]
>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
>>> To unsubscribe: send email to [hidden email] with
>>> unsubscribe as the subject
>>>
>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ
>>
>>
>
>
> _______________________________________________
> slicer-devel mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
> To unsubscribe: send email to [hidden email] with
> unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ
_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ
Reply | Threaded
Open this post in threaded view
|

Fwd: Official Slicer CLI docker image?

Dzenan Zukic
In reply to this post by andrey.fedorov
Forwarding reply from a colleague.

---------- Forwarded message ----------
From: Deepak Chittajallu <[hidden email]>
Date: Wed, Feb 15, 2017 at 5:00 PM


slicer_cli_web plugins (see Docker file of this example plugin) aka derivative docker images can derive from the girder/slicer_cli_web docker image and use this entrypoint to list the CLI inside.

Wonder if this is what he is referring to?

But i agree all this is not well documented yet.

Regards,
Deepak

On Wed, Feb 15, 2017 at 3:08 PM, Dzenan Zukic <[hidden email]> wrote:

---------- Forwarded message ----------
From: Andrey Fedorov <[hidden email]>
Date: Wed, Feb 15, 2017 at 3:07 PM
Subject: [slicer-devel] Official Slicer CLI docker image?
To: SPL Slicer Devel <[hidden email]>


Hi,

is there an official image of 3D Slicer that would expose Slicer command line to allow running Slicer CLIs using Docker? 

This would be helpful for the users who put together pipelines out of "dockerized tools", which is very fashionable these days (at least in some sub-communities). This should not be hard at all to do for Slicer CLIs.

It looks like we have an organization, and several images, but none of these seems to be exposing command line tools, and also they are not documented and are not linked to Dockerfiles.


If we already have a Slicer build, we could just add an entrypoint to pass the command line parameters and perhaps add an option that would list all CLIs available. Would be great to get Kitware thoughts on this.

AF

_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ




--
Deepak Roy Chittajallu, Ph.D.
R&D Engineer, Medical Computing Team
Kitware Inc, Carrboro, NC, USA


_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ
Reply | Threaded
Open this post in threaded view
|

Re: Fwd: Official Slicer CLI docker image?

andrey.fedorov
Dzenan,

thanks!

looking at https://github.com/girder/slicer_cli_web - it builds
SlicerExecutionModel, but I don't see it building Slicer CLIs. Is it
done somewhere else, or am I missing something?

Another thought, the docker container I am thinking of doesn't even
need to build anything - it can simply use the nightly build of
Slicer, and just provide a mechanism to run CLIs in a
platform-independent fashion.

AF

On Thu, Feb 16, 2017 at 4:39 PM, Dzenan Zukic <[hidden email]> wrote:

> Forwarding reply from a colleague.
>
> ---------- Forwarded message ----------
> From: Deepak Chittajallu <[hidden email]>
> Date: Wed, Feb 15, 2017 at 5:00 PM
>
> slicer_cli_web has a docker image that builds ITK 4.10 and slicer execution
> model inside and also provides an entrypoint to list slicer CLI inside.
>
> slicer_cli_web plugins (see Docker file of this example plugin) aka
> derivative docker images can derive from the girder/slicer_cli_web docker
> image and use this entrypoint to list the CLI inside.
>
> Wonder if this is what he is referring to?
>
> But i agree all this is not well documented yet.
>
> Regards,
> Deepak
>
> On Wed, Feb 15, 2017 at 3:08 PM, Dzenan Zukic <[hidden email]>
> wrote:
>>
>>
>> ---------- Forwarded message ----------
>> From: Andrey Fedorov <[hidden email]>
>> Date: Wed, Feb 15, 2017 at 3:07 PM
>> Subject: [slicer-devel] Official Slicer CLI docker image?
>> To: SPL Slicer Devel <[hidden email]>
>>
>>
>> Hi,
>>
>> is there an official image of 3D Slicer that would expose Slicer command
>> line to allow running Slicer CLIs using Docker?
>>
>> This would be helpful for the users who put together pipelines out of
>> "dockerized tools", which is very fashionable these days (at least in some
>> sub-communities). This should not be hard at all to do for Slicer CLIs.
>>
>> It looks like we have an organization, and several images, but none of
>> these seems to be exposing command line tools, and also they are not
>> documented and are not linked to Dockerfiles.
>>
>> https://hub.docker.com/u/slicer/
>>
>> If we already have a Slicer build, we could just add an entrypoint to pass
>> the command line parameters and perhaps add an option that would list all
>> CLIs available. Would be great to get Kitware thoughts on this.
>>
>> AF
>>
>> _______________________________________________
>> slicer-devel mailing list
>> [hidden email]
>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
>> To unsubscribe: send email to [hidden email] with
>> unsubscribe as the subject
>>
>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ
>>
>
>
>
> --
> Deepak Roy Chittajallu, Ph.D.
> R&D Engineer, Medical Computing Team
> Kitware Inc, Carrboro, NC, USA
> URL: http://www.drchittajallu.info
> Linkedin: https://www.linkedin.com/in/cdeepakroy
>
>
> _______________________________________________
> slicer-devel mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
> To unsubscribe: send email to [hidden email] with
> unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ
_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ
Reply | Threaded
Open this post in threaded view
|

Re: Fwd: Official Slicer CLI docker image?

Dzenan Zukic
In reply to this post by Dzenan Zukic
Hi Andrey,

slicer_cli_web is supposed to be a base image for custom CLI development. This is to ease repackaging algorithms from Slicer CLI format into web back-end friendly format. It does not contain any CLIs itself.

Regards

Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Thu, Feb 16, 2017 at 4:46 PM, Andrey Fedorov <[hidden email]> wrote:
Dzenan,

thanks!

looking at https://github.com/girder/slicer_cli_web - it builds
SlicerExecutionModel, but I don't see it building Slicer CLIs. Is it
done somewhere else, or am I missing something?

Another thought, the docker container I am thinking of doesn't even
need to build anything - it can simply use the nightly build of
Slicer, and just provide a mechanism to run CLIs in a
platform-independent fashion.

AF

On Thu, Feb 16, 2017 at 4:39 PM, Dzenan Zukic <[hidden email]> wrote:
> Forwarding reply from a colleague.
>
> ---------- Forwarded message ----------
> From: Deepak Chittajallu <[hidden email]>
> Date: Wed, Feb 15, 2017 at 5:00 PM
>
> slicer_cli_web has a docker image that builds ITK 4.10 and slicer execution
> model inside and also provides an entrypoint to list slicer CLI inside.
>
> slicer_cli_web plugins (see Docker file of this example plugin) aka
> derivative docker images can derive from the girder/slicer_cli_web docker
> image and use this entrypoint to list the CLI inside.
>
> Wonder if this is what he is referring to?
>
> But i agree all this is not well documented yet.
>
> Regards,
> Deepak
>
> On Wed, Feb 15, 2017 at 3:08 PM, Dzenan Zukic <[hidden email]>
> wrote:
>>
>>
>> ---------- Forwarded message ----------
>> From: Andrey Fedorov <[hidden email]>
>> Date: Wed, Feb 15, 2017 at 3:07 PM
>> Subject: [slicer-devel] Official Slicer CLI docker image?
>> To: SPL Slicer Devel <[hidden email]>
>>
>>
>> Hi,
>>
>> is there an official image of 3D Slicer that would expose Slicer command
>> line to allow running Slicer CLIs using Docker?
>>
>> This would be helpful for the users who put together pipelines out of
>> "dockerized tools", which is very fashionable these days (at least in some
>> sub-communities). This should not be hard at all to do for Slicer CLIs.
>>
>> It looks like we have an organization, and several images, but none of
>> these seems to be exposing command line tools, and also they are not
>> documented and are not linked to Dockerfiles.
>>
>> https://hub.docker.com/u/slicer/
>>
>> If we already have a Slicer build, we could just add an entrypoint to pass
>> the command line parameters and perhaps add an option that would list all
>> CLIs available. Would be great to get Kitware thoughts on this.
>>
>> AF
>>
>> _______________________________________________
>> slicer-devel mailing list
>> [hidden email]
>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
>> To unsubscribe: send email to [hidden email] with
>> unsubscribe as the subject
>>
>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ
>>
>
>
>
> --
> Deepak Roy Chittajallu, Ph.D.
> R&D Engineer, Medical Computing Team
> Kitware Inc, Carrboro, NC, USA
> URL: http://www.drchittajallu.info
> Linkedin: https://www.linkedin.com/in/cdeepakroy
>
>
> _______________________________________________
> slicer-devel mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
> To unsubscribe: send email to [hidden email] with
> unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ


_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ
Reply | Threaded
Open this post in threaded view
|

Re: Fwd: Official Slicer CLI docker image?

Steve Pieper-2
Hi Andrey - 

Once you have slicer installed in a docker it's very easy to run CLIs like this:

docker run -it stevepieper/slicer /opt/slicer/Slicer --launch ExecutionModelTour

With the -v flag you can also mount specific directories in the docker instance to easily pass files back and forth.

It's very easy to make them with whatever version of slicer plus extensions you want to expose.

-Steve

On Thu, Feb 16, 2017 at 4:50 PM, Dzenan Zukic <[hidden email]> wrote:
Hi Andrey,

slicer_cli_web is supposed to be a base image for custom CLI development. This is to ease repackaging algorithms from Slicer CLI format into web back-end friendly format. It does not contain any CLIs itself.

Regards

Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Thu, Feb 16, 2017 at 4:46 PM, Andrey Fedorov <[hidden email]> wrote:
Dzenan,

thanks!

looking at https://github.com/girder/slicer_cli_web - it builds
SlicerExecutionModel, but I don't see it building Slicer CLIs. Is it
done somewhere else, or am I missing something?

Another thought, the docker container I am thinking of doesn't even
need to build anything - it can simply use the nightly build of
Slicer, and just provide a mechanism to run CLIs in a
platform-independent fashion.

AF

On Thu, Feb 16, 2017 at 4:39 PM, Dzenan Zukic <[hidden email]> wrote:
> Forwarding reply from a colleague.
>
> ---------- Forwarded message ----------
> From: Deepak Chittajallu <[hidden email]>
> Date: Wed, Feb 15, 2017 at 5:00 PM
>
> slicer_cli_web has a docker image that builds ITK 4.10 and slicer execution
> model inside and also provides an entrypoint to list slicer CLI inside.
>
> slicer_cli_web plugins (see Docker file of this example plugin) aka
> derivative docker images can derive from the girder/slicer_cli_web docker
> image and use this entrypoint to list the CLI inside.
>
> Wonder if this is what he is referring to?
>
> But i agree all this is not well documented yet.
>
> Regards,
> Deepak
>
> On Wed, Feb 15, 2017 at 3:08 PM, Dzenan Zukic <[hidden email]>
> wrote:
>>
>>
>> ---------- Forwarded message ----------
>> From: Andrey Fedorov <[hidden email]>
>> Date: Wed, Feb 15, 2017 at 3:07 PM
>> Subject: [slicer-devel] Official Slicer CLI docker image?
>> To: SPL Slicer Devel <[hidden email]>
>>
>>
>> Hi,
>>
>> is there an official image of 3D Slicer that would expose Slicer command
>> line to allow running Slicer CLIs using Docker?
>>
>> This would be helpful for the users who put together pipelines out of
>> "dockerized tools", which is very fashionable these days (at least in some
>> sub-communities). This should not be hard at all to do for Slicer CLIs.
>>
>> It looks like we have an organization, and several images, but none of
>> these seems to be exposing command line tools, and also they are not
>> documented and are not linked to Dockerfiles.
>>
>> https://hub.docker.com/u/slicer/
>>
>> If we already have a Slicer build, we could just add an entrypoint to pass
>> the command line parameters and perhaps add an option that would list all
>> CLIs available. Would be great to get Kitware thoughts on this.
>>
>> AF
>>
>> _______________________________________________
>> slicer-devel mailing list
>> [hidden email]
>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
>> To unsubscribe: send email to [hidden email] with
>> unsubscribe as the subject
>>
>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ
>>
>
>
>
> --
> Deepak Roy Chittajallu, Ph.D.
> R&D Engineer, Medical Computing Team
> Kitware Inc, Carrboro, NC, USA
> URL: http://www.drchittajallu.info
> Linkedin: https://www.linkedin.com/in/cdeepakroy
>
>
> _______________________________________________
> slicer-devel mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
> To unsubscribe: send email to [hidden email] with
> unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ


_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ


_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ