Hackathon November 2021
This is the first of the two hackathons co-organized by
PET++,
CCP SyneRBI and
CCPi.
Goal
The goal is to implement selected randomized algorithms in CIL (eg SAGA, SVRG) and test them on a toy dataset jointly with already implemented algorithms (eg SPDHG). There will also be a group working on subset data structures in STIR to enable efficient computation on subsets.
Venue
The hackathon begins by two in-person days at STFC Cosener’s house in Abingdon, Tuesday 23rd November – Wednesday 24th, and then follow online Thursday 25 - Friday 26. Detailed planning below.
Resources
The algorithms will be implemented in CIL, a software developped by
CCPi Tomographic Imaging. If not already familiar with CIL, hackathon participants are encouraged to go through the following resources before the hackathon:
Planning
If you would like to listen to the presentations, please contact Claire Delplancke (
cd902@bath.ac.uk) to get the zoom link.
Tuesday 23
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14:00-16:00 |
Presentations |
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14:00 |
Introduction (Claire Delplancke) |
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14:10 |
Gradient-based stochastic algorithms: SAGA (Robbie Twyman), SVREM (Zeljko Kereta), accelerated algorithms (Junqi Tang) |
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15:40 |
CIL interface for subsets (Edoardo Pasca) |
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15:50 |
General overview of STIR subsets (Kris Thielemans) |
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16:10 |
Coffee break |
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16:30-18:00 |
Group work |
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19:00 |
Dinner in Abingdon |
Wednesday 24
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9:30 |
Progress report |
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9:40 |
Group work |
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11:00 |
Coffee break |
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12:20 |
Progress report |
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12:30 |
Lunch |
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13:30 |
Group work |
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15:00 |
Progress report and planning for the rest of the week |
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15:30 |
Coffee break |
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16:00 |
End of in-person event |
Contact
Contact Claire Delplancke (
cd902@bath.ac.uk) for any information.
Hackathon April 2022
This is the second of the two hackathons co-organized by
PET++,
CCP SyneRBI and
CCPi.
Goal
The goal is to establish a framework for benchmarking numerous state-of-the-art iterative algorithms for PET reconstruction and CT reconstruction, with a focus on randomized subset algorithms. In the previous hackathon, we have focused on implementing the selected algorithms in CIL (eg SGD, SAGA, SVRG, SPDHG, and accelerated methods) and have tested them on a toy 2D CT example. In this hackathon, we will seek to make the next step for evaluating the implemented stochastic optimization algorithms on large-scale CT and PET 3D reconstructions on real datasets.
Date and venue
The hackathon will take place on April 4-7, at Centre for Mathematical Sciences (CMS), University of Cambridge, with certain parts, notably introduction, progress updates and conclusions, earmarked for remote attendance. We will start at 1:30 pm on Monday at the room MR13 of CMS and end at 4pm on Thursday April.
Contact
Please contact local organizer Junqi Tang (
jt814@cam.ac.uk) if you would like to join in person or remotely. The event is free and a number of rooms has been booked for us at Churchill College which is nearby CMS.
Detailed goals
Specific goals are:
- Agree on a suitable evaluation strategy, including metrics for image quality and algorithm performance (run-time, memory etc), taking into account parameter selection for algorithms
- Agree on suitable data sets for evaluation
- Implement quality metrics (e.g. based on tools from scikit-rt)
- Implement a framework to organize the data and the experiments, for example with Hydra
- Initial implementation of evaluation framework on a cluster (STFC or even distributed)
- Investigate feasibility of scope of evaluation
How to join
In-person: room MR13, Centre for Mathematical Sciences, Cambridge. Travel and accomodation funding is available.
Remotely: remote attendance will be possible in the time slots highlighted in yellow in the planning below, with this
zoom link.
Meeting ID: 974 3480 1191
Passcode: 380697
Please confirm your attendance if you’re interested in joining us (remotely or in person) beyond the first day.
Planning
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Monday 4
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12:00-13:30
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Lunch
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13:30-14:00
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Opening (hybrid)
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Presentation: stochastic algorithms implemented in last hackathon (Claire Delplancke)
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14:00-14:45
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Discussion about PET quality
metrics (hybrid)
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Presentations: Robbie Twyman (15 min),
Georg Schramm (5 min)
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14:45-15:30
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Discussion about CT quality
metrics (hybrid)
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Presentation: Jakob S. Jørgensen
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15:30-16:00
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Coffee break
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16:00-17:00
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Recap of discussion:
what needs to be implemented? + experiments management (hybrid)
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Presentations: Imraj Singh on Hydra
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17:00-18:00
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organization of following days
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Tuesday 5 - Wednesday 6
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9:30
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Brief progress report
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9:40
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Group work
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11:00
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Coffee break
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11:30
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Group work
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12:30
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Lunch
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13:30-14:30
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Progress report (hybrid)
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14:30
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Group work
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15:30
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Coffee break
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16:00 - 18:00
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Group work
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Thursday 7
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9:30
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Brief progress report
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9:40
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Group work
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11:00
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Coffee break
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11:30
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Group work
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12:30
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Lunch
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13:30-15:30
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Conclusions and planning
(hybrid)
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15:30
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Coffee break
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16:00
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End of event
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© 2019-22 PET++ team - last updated: March 2022