mrpeek: a sixel-based terminal image viewer for MRtrix3

[jdtournier]

Guidelines

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Project info

mrpeek: a sixel-based terminal image viewer for MRtrix3:

Project lead:

• J-Donald Tournier @jdtournier
• Daan Christiaens @dchristiaens
• Max Pietsch: @maxpietsch

Timezone: London UTC+1

Hub: Europe, Middle East and Africa

Description:

Displaying images on a remote server is very difficult / impossible currently using MRtrix3's mrview, due the incompatibility of OpenGL 3+ with X11 forwarding (see here for details). It will be some time before the technology is updated to fix this.

In the meantime, @wasserth's niicat project shows that it is possible to allow some (limited) display functionality using sixel. The libsixel project provides an implementation that seems like a good starting point for a C++ command.

The aim of this project is to create a simple command for interactive display of MR images within the terminal, build on the MRtrix3 codebase, so that it can be used for quick inspection of images both locally and remotely.

If successful, changes will be included in a future update to the MRtrix3 software. Contributors will be included in the built-in git contribution statistics. We additionally credit contributors by showing their avatar at the bottom of the MRtrix3 website front page, and in the changelog as reported on the community forum (example).

Link to project: MRtrix3/mrtrix3#2079

Mattermost handle: jdtournier

Goals for the OHBM Brainhack

The range of possible milestones are presented in MRtrix3/mrtrix3#2079. The minimum requirements for the Hackathon would be:

• extract a given slice of interest and render it to the terminal using libsixel
  • implement options or other user controls to select the slice of interest, projection (axial/sagittal/coronal), and brightness/control
• implement real-time interaction based on keyboard input
  • implement real-time interaction based on mouse input

Good first issues:

• Install MRtrix3 from source and set up an external linked module to create your own app
• build a simple MRtrix3 app that can loop over a single slice of an image and extract the intensities (inspired by e.g. MRtrix3's mrcolour)
• install libsixel and add it as a dependency to your project (by editing your config file if needed)
• work out how to feed the image intensities from the input data in a format suitable for libsixel, and display to the terminal

Skills:

Some experience with C++ is essential for this project. Experience with git and Unix in general would be advantageous. The pace of the project will however be tailored to the skillset of team members. No prior expectations are set on the quantity of team members.

Chat channel: hbmhack-mrpeek

Video Channel

Please have a look at the Mattermost channel(pinned posts) for the URL of the video channel, or alternatively, please contact to @jdtournier on Mattermost.

Image for the OHBM brainhack website

Project submission

Submission checklist

Once the issue is submitted, please check items in this list as you add under 'Additional project info'

Please include the following above (all required):

• [x] Link to your project: could be a code repository, a shared document, etc. See here
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• [x] Goals for the OHBM Brainhack: describe what you want to achieve during this brainhack. See here.
• [x] Flesh out at least 2 "good first issues": those are tasks that do not require any prior knowledge about your project, could be defined as issues in a GitHub repository, or in a shared document, cf here.
• [x] Skills: list skills that would be particularly suitable for your project. We ask you to include at least one non-coding skill, cf. here.
• [x] Chat channel: A link to a chat channel that will be used during the OHBM Brainhack. This can be an existing channel or a new one. We recommend using the Brainhack space on mattermost, cf. here.
• [x] Video channel: Please create a video channel that will be used during the OHBM Brainhack and share it in your chat channel above. This can be an existing channel or a new one. For instance a jitsi meet room, cf. here.
• [x] Provide an image of your project for the OHBM brainhack website

You can also include information about (all optional):

• [x] Number of participants, cf. here
• [ ] Twitter-size summary of your project pitch, cf. here
• [ ] Set up a kanban board on your repository to better divide the work and keep track of things, cf here
• [ ] Project snippet for the OHBM Brainhack website, cf. here

We would like to think about how you will credit and onboard new members to your project. We recommend reading references from this section. If you'd like to share your thoughts with future project participants, you can include information about (recommended):

• [x] Specify how will you acknowledge contributions (e.g. listing members on a contributing page).
• [ ] Provide links to onboarding documents if you have some.

[welcome[bot]]

(Image: CC-BY license, The Turing Way Community, & Scriberia. Zenodo. http://doi.org/10.5281/zenodo.3332808) :tada: Welcome to the 2020 OHBM Hackathon! :tada: We're really excited to have your input on this repository and welcome your idea! :sparkling_heart: If you haven't done so already, please make sure you check out our Code of Conduct. Did you issue a new hackathon project? Please check if you have provided all relevant information and an image for the website.

[Remi-Gau]

hey @jdtournier

As you seem to have project leads in several hubs, should I put you down for project pitches in both hubs (meaning will there be some who can pitch live for both hubs)?

[Remi-Gau]

Oops sorry that was a mishap my part.

[jdtournier]

We're discussing the live pitch issue right now. I'm unlikely to be able to do it myself due to home schooling duties...

On a different note: I'm a bit confused about the advice regarding the video channel. I'm assuming we're free to choose whatever we want, so I've set up a Google Meet for that. But are we to show the details of the channel here, or keep them hidden as a comment, or only show the channel on the mattermost channel?

[jdtournier]

OK, we've decided to limit this to the Europe, Middle East & Africe time zone to avoid too many clashes... I've updated the description to match, I assume we'll also need to remove the corresponding label?

[Remi-Gau]

On a different note: I'm a bit confused about the advice regarding the video channel. I'm assuming we're free to choose whatever we want, so I've set up a Google Meet for that. But are we to show the details of the channel here, or keep them hidden as a comment, or only show the channel on the mattermost channel?

Sorry about the confusion. You are free to use whatever means you want. :+1:

And yes the best is to just put the video channel link in your mattermost channel and leave them out of the issue all together. Sorry we are sort of course correcting as we go. We promise that for the next pandemic, we will be ready. :wink:

[Remi-Gau]

OK, we've decided to limit this to the Europe, Middle East & Africe time zone to avoid too many clashes... I've updated the description to match, I assume we'll also need to remove the corresponding label?

Done it for you.

But if you want you can mention where each project lead is situated if that can help some attendees get in touch with them in their hub.

[jdtournier]

OK, video channel section removed - I assume there's no point in it being here any more.

All our project leads for this project are actually in UK / Germany, so all in Europe hub. I've taken @Lestropie off at his request even though he's keen to drop in unofficially when possible, but he'll have his own project to deal with.

[jdtournier]

Otherwise, I reckon this is good to go? I'm not sure we need to set up the Twitter snippet if we're happy with the default?

We might set up a separate repo and issue track / project board from there, but again, I assume this is something we can do from the mattermost channel, right?

[jdtournier]

I'm also a bit unclear about the onboarding process. I assume interested users will contact us on the mattermost channel, and if we're all happy, they're in, right? Is there a more formal process we should follow here?

[Remi-Gau]

Otherwise, I reckon this is good to go? I'm not sure we need to set up the Twitter snippet if we're happy with the default?

We want to try to tweet about every project to give them more visibility but we are bit short-staffed on that end. Let's see how much we can do.

We might set up a separate repo and issue track / project board from there, but again, I assume this is something we can do from the mattermost channel, right?

Yes definitely. In your own time. We are just making suggestions on possible workflows that might help people work together remotely. Not everyone knows about project boards and so on. :-)

[jdtournier]

We want to try to tweet about every project to give them more visibility but we are bit short-staffed on that end. Let's see how much we can do.

We'll be tweeting it out from our side anyway, so you can always just retweet that if you're short on time! I assume there's a hashtag I can use to get your attention?

Otherwise, please consider this project ready for submission!

[Remi-Gau]

I'm also a bit unclear about the onboarding process. I assume interested users will contact us on the mattermost channel, and if we're all happy, they're in, right? Is there a more formal process we should follow here?

Would this answer in our FAQ help?

https://ohbm.github.io/hackathon2020/FAQ/#If%20you%20are%20attending%20the%20OHBM%20brainhack%208

Let me know because it can help me rephrase for other people. :pray:

[jdtournier]

OK, it helps in that it's clear it's a pretty informal process. They contact us, we discuss. If that's all it is, that's fine. I was just concerned that there was a more formal aspect to it that I'd missed - maybe there's a requirement on our side to vet applicants, and report back to the organisers who is taking part in our project, etc. If that's not the case, that's no problem. :+1:

[Remi-Gau]

We want to try to tweet about every project to give them more visibility but we are bit short-staffed on that end. Let's see how much we can do.

We'll be tweeting it out from our side anyway, so you can always just retweet that if you're short on time! I assume there's a hashtag I can use to get your attention?

Awesome. This is our twitter handle: @OhbmOpen And the hashtags we have been using.

OHBMHackathon #OHBM2020 #Brainhack

Otherwise, please consider this project ready for submission!

Goodie. You're in. I think the project monitors will do another cross-check with you. One again a bit short-staffed and hard to keep track of everything.

[Remi-Gau]

OK, it helps in that it's clear it's a pretty informal process. They contact us, we discuss. If that's all it is, that's fine. I was just concerned that there was a more formal aspect to it that I'd missed - maybe there's a requirement on our side to vet applicants, and report back to the organisers who is taking part in our project, etc. If that's not the case, that's no problem. +1

No it is very much self managed. :wink:

Though we would love for you to keep track of who helped you. Our grand idea would be to have at least one post-hacakthon tweet explaining the progress made and with the twitter handles of all the contributors of that project on that hackathon.

[jdtournier]

All good, thanks!

[jdtournier]

Sorry, can I just confirm that this project is submitted? Do I need to do anything else? I need to run some errands now, so won't be available later to fix anything if needed...

[Remi-Gau]

Yup project is submitted. You are all set.

There might be some post-submission checks but you are good to go. :+1:

[jdtournier]

Great to hear, thanks for confirming!

[complexbrains]

Dear @jdtournier May I ask you to share your Video channel info at your Mattermost channel and pin it to the channel, please? Could you please let us know regarding completion of this then we will complete the revision. Thank you 🤗

[jdtournier]

Done. At least I think I've done this right... https://mattermost.brainhack.org/brainhack/channels/hbmhack-mrpeek

[complexbrains]

Thank you @jdtournier Your project seems ready to go! Welcome aboard! :hugs: 🎊

[cmaumet]

Hi @jdtournier! Thanks a lot for your project. Unless I am mistaken, In think that your project co-lead (Daan Christiaens) is not registered yet to the event. Can you please ask them to register or list them as project collaborators if they are not joining the event? Thank you!

[dchristiaens]

I signed up this morning.

[cmaumet]

Thank you @dchristiaens! All good now :D