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This is a Developer Mailing list for CCP SyneRBI (Collaborative Computational Project on Synergistic Reconstruction for Biomedical Imaging).

web: http://www.ccpsynerbi.ac.uk
code: https://github.com/SynerBI/SIRF

The main mailing lists are actually

This group (ccp-petmr-codebot@googlegroups.com) sends daily digests to the DEVEL JISCMail list.

Due to various nuances, it has been set up in such a way that GitHub notifications are sent to ccp.petmr.devel@gmail.com, which in turn forwards to ccp-petmr-codebot@googlegroups.com, which finally sends daily digests to SYNERBI-DEVEL@jiscmail.ac.uk.

If you would like any other integration service (similar to GitHub's notifications) to be posted to JISCMail lists via ccp.petmr.devel@gmail.com - simply email the latter.

--
Casper

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Dimitra-Kyriakopoulou17

12:55 PM

[SyneRBI/SIRF] Hackathon Project 8: Expose CUDA-managed STIR image and acquisition queries in sirf.STIR (continuation of the image stage) (PR #1381)

Dimitra-Kyriakopoulou left a comment (SyneRBI/SIRF#1381) Dear Professor @KrisThielemans , THANK YOU

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[SyneRBI/SIRF] Hackathon Project 8: Expose CUDA-managed STIR image and acquisition queries in sirf.STIR (continuation of the image stage) (PR #1381)

Dimitra-Kyriakopoulou left a comment (SyneRBI/SIRF#1381) Dear Professor @KrisThielemans , THANK YOU

12:55 PM

Dimitra-Kyriakopoulou7

7:07 AM

[SyneRBI/SIRF] Hackathon project8: Expose CUDA-managed STIR image queries in sirf.STIR (PR #1380)

Closed #1380. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving

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[SyneRBI/SIRF] Hackathon project8: Expose CUDA-managed STIR image queries in sirf.STIR (PR #1380)

Closed #1380. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving

7:07 AM

Kris Thielemans

Mar 13

[SyneRBI/SIRF] torch interface: 2 PET tests causing a segfault on GHA (Issue #1382)

KrisThielemans created an issue (SyneRBI/SIRF#1382) See #1305 (review)_ — Reply to this email

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[SyneRBI/SIRF] torch interface: 2 PET tests causing a segfault on GHA (Issue #1382)

KrisThielemans created an issue (SyneRBI/SIRF#1382) See #1305 (review)_ — Reply to this email

Mar 13

Mar 13

[SyneRBI/SIRF] Adding PyTorch functionality to SIRF (PR #1305)

@KrisThielemans approved this pull request. We have 2 PET tests causing a segfault on GHA:

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[SyneRBI/SIRF] Adding PyTorch functionality to SIRF (PR #1305)

@KrisThielemans approved this pull request. We have 2 PET tests causing a segfault on GHA:

Mar 13

Evgueni Ovtchinnikov11

Mar 12

[SyneRBI/SIRF] Updates for mixed data algebra based on __array_priority__. (PR #1373)

Merged #1373 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

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[SyneRBI/SIRF] Updates for mixed data algebra based on __array_priority__. (PR #1373)

Merged #1373 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

Mar 12

Kris Thielemans10

Mar 12

[SyneRBI/SIRF] backwards incompatibility: algebraic operations with numpy arrays now fail (Issue #1357)

Closed #1357 as completed via #1373. — Reply to this email directly, view it on GitHub, or

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[SyneRBI/SIRF] backwards incompatibility: algebraic operations with numpy arrays now fail (Issue #1357)

Closed #1357 as completed via #1373. — Reply to this email directly, view it on GitHub, or

Mar 12

Dimitra-Kyriakopoulou9

Mar 12

[SyneRBI/SIRF] SIRF #1357 (PR #1378)

KrisThielemans left a comment (SyneRBI/SIRF#1378) no problem. Closing this. — Reply to this email

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[SyneRBI/SIRF] SIRF #1357 (PR #1378)

KrisThielemans left a comment (SyneRBI/SIRF#1378) no problem. Closing this. — Reply to this email

Mar 12

Evgueni Ovtchinnikov7

Mar 12

[SyneRBI/SIRF] sirf.Reg.ImageData.asarray() fix (PR #1376)

evgueni-ovtchinnikov left a comment (SyneRBI/SIRF#1376) @KrisThielemans To clean up the history, I

unread,

[SyneRBI/SIRF] sirf.Reg.ImageData.asarray() fix (PR #1376)

evgueni-ovtchinnikov left a comment (SyneRBI/SIRF#1376) @KrisThielemans To clean up the history, I

Mar 12

Casper da Costa-Luis2

Mar 11

[SyneRBI/PETRIC-backend] PETRIC2: final ranking & leaderboard (PR #8)

Merged #8 into main. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

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[SyneRBI/PETRIC-backend] PETRIC2: final ranking & leaderboard (PR #8)

Merged #8 into main. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

Mar 11

Vaggelis Papoutsellis

Mar 11

[SyneRBI/SIRF] Partitioner crashes kernel (Issue #1379)

epapoutsellis created an issue (SyneRBI/SIRF#1379) When I am trying to partition the petric data

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[SyneRBI/SIRF] Partitioner crashes kernel (Issue #1379)

epapoutsellis created an issue (SyneRBI/SIRF#1379) When I am trying to partition the petric data

Mar 11

Casper da Costa-Luis13

Mar 11

[SyneRBI/SIRF-Contribs] Hackathon projects (Discussion #31)

Deep Image Prior — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving

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[SyneRBI/SIRF-Contribs] Hackathon projects (Discussion #31)

Deep Image Prior — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving

Mar 11

Feb 27

[SyneRBI/SIRF-Exercises] Mcir cil (PR #204)

Merged #204 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

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[SyneRBI/SIRF-Exercises] Mcir cil (PR #204)

Merged #204 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

Feb 27

Feb 26

[SyneRBI/SIRF] Memory not freed up after deleting linear acquisition model (Issue #1377)

KrisThielemans left a comment (SyneRBI/SIRF#1377) @evgueni-ovtchinnikov how does

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[SyneRBI/SIRF] Memory not freed up after deleting linear acquisition model (Issue #1377)

KrisThielemans left a comment (SyneRBI/SIRF#1377) @evgueni-ovtchinnikov how does

Feb 26

Feb 25

[SyneRBI/SIRF-Exercises] Revise cloud instance usage instructions (PR #269)

Removed outdated information closes #268 You can view, comment on, or merge this pull request online

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[SyneRBI/SIRF-Exercises] Revise cloud instance usage instructions (PR #269)

Removed outdated information closes #268 You can view, comment on, or merge this pull request online

Feb 25

Feb 25

[SyneRBI/SIRF-Exercises] Docs referring to Azure are very outdated (Issue #268)

paskino created an issue (SyneRBI/SIRF-Exercises#268) We have these docs https://github.com/SyneRBI/

unread,

[SyneRBI/SIRF-Exercises] Docs referring to Azure are very outdated (Issue #268)

paskino created an issue (SyneRBI/SIRF-Exercises#268) We have these docs https://github.com/SyneRBI/

Feb 25

Edoardo Pasca17

Feb 20

[SyneRBI/SIRF] Poisson Log Likelihood ObjectiveFunction `gradient` with and without `out` parameter has larger difference than expected (Issue #1349)

evgueni-ovtchinnikov left a comment (SyneRBI/SIRF#1349) For each i, x_out is overwritten showing us

unread,

[SyneRBI/SIRF] Poisson Log Likelihood ObjectiveFunction `gradient` with and without `out` parameter has larger difference than expected (Issue #1349)

evgueni-ovtchinnikov left a comment (SyneRBI/SIRF#1349) For each i, x_out is overwritten showing us

Feb 20

Evgueni Ovtchinnikov15

Feb 17

[SyneRBI/SIRF] Implement adding Hessian diagonal in SIRF (PR #1370)

KrisThielemans left a comment (SyneRBI/SIRF#1370) Good idea. I suggest to use $$ H_{ii} \approx \frac

unread,

[SyneRBI/SIRF] Implement adding Hessian diagonal in SIRF (PR #1370)

KrisThielemans left a comment (SyneRBI/SIRF#1370) Good idea. I suggest to use $$ H_{ii} \approx \frac

Feb 17

Evgueni Ovtchinnikov

Feb 16

[SyneRBI/SIRF] The return value of `sirf.Reg.ImageData.asarray()` is wrong. (Issue #1375)

evgueni-ovtchinnikov created an issue (SyneRBI/SIRF#1375) The following code data_path =

unread,

[SyneRBI/SIRF] The return value of `sirf.Reg.ImageData.asarray()` is wrong. (Issue #1375)

evgueni-ovtchinnikov created an issue (SyneRBI/SIRF#1375) The following code data_path =

Feb 16

Casper da Costa-Luis4

Feb 16

[SyneRBI/SIRF-SuperBuild] use startup hooks (PR #985)

KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#985) Looks like a good idea to me. I'll

unread,

[SyneRBI/SIRF-SuperBuild] use startup hooks (PR #985)

KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#985) Looks like a good idea to me. I'll

Feb 16

Casper da Costa-Luis8

Feb 16

[SyneRBI/PETRIC-backend] docker improvements (PR #7)

Merged #7 into main. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

unread,

[SyneRBI/PETRIC-backend] docker improvements (PR #7)

Merged #7 into main. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

Feb 16

Kris Thielemans2

Feb 12

[SyneRBI/SIRF-SuperBuild] Update README with Jupyter password details (PR #984)

Merged #984 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

unread,

[SyneRBI/SIRF-SuperBuild] Update README with Jupyter password details (PR #984)

Merged #984 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

Feb 12

Kris Thielemans2

Feb 12

[SyneRBI/SIRF] occasional (ignored) exception AttributeError: 'NoneType' object has no attribute 'deleteDataHandle' (Issue #1374)

KrisThielemans left a comment (SyneRBI/SIRF#1374) Suggested steps: do we have any of this when

unread,

[SyneRBI/SIRF] occasional (ignored) exception AttributeError: 'NoneType' object has no attribute 'deleteDataHandle' (Issue #1374)

KrisThielemans left a comment (SyneRBI/SIRF#1374) Suggested steps: do we have any of this when

Feb 12

Casper da Costa-Luis

Feb 5

[SyneRBI/PETRIC-backend] Release v1 - PETRIC

PETRIC Repository: SyneRBI/PETRIC-backend · Tag: v1 · Commit: 2aa7a44 · Released by: casperdcl

unread,

[SyneRBI/PETRIC-backend] Release v1 - PETRIC

PETRIC Repository: SyneRBI/PETRIC-backend · Tag: v1 · Commit: 2aa7a44 · Released by: casperdcl

Feb 5

Evgueni Ovtchinnikov5

Feb 5

Re: [SyneRBI/SIRF] [FIX] Constructing STIR Image from Acq Data with nx, ny should use Acq data (#231)

paskino left a comment (SyneRBI/SIRF#231) Closing as the functionality has been merged via #1364 —

unread,

Re: [SyneRBI/SIRF] [FIX] Constructing STIR Image from Acq Data with nx, ny should use Acq data (#231)

paskino left a comment (SyneRBI/SIRF#231) Closing as the functionality has been merged via #1364 —

Feb 5

Feb 5

[SyneRBI/SIRF-SuperBuild] Error building Tomophantom (Issue #932)

paskino left a comment (SyneRBI/SIRF-SuperBuild#932) Currently TomoPhantom is not a dependency

unread,

[SyneRBI/SIRF-SuperBuild] Error building Tomophantom (Issue #932)

paskino left a comment (SyneRBI/SIRF-SuperBuild#932) Currently TomoPhantom is not a dependency

Feb 5

Kris Thielemans6

Feb 5

[SyneRBI/SIRF] Python: modify some DataContainer methods to fall back to numpy (Issue #1334)

Closed #1334 as completed. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

unread,

[SyneRBI/SIRF] Python: modify some DataContainer methods to fall back to numpy (Issue #1334)

Closed #1334 as completed. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

Feb 5

Casper da Costa-Luis

Feb 3

[SyneRBI/SIRF-Contribs] SIRF RDP (Issue #30)

casperdcl created an issue (SyneRBI/SIRF-Contribs#30) Follow-up to #28, simplify MaGeZ after SyneRBI/

unread,

[SyneRBI/SIRF-Contribs] SIRF RDP (Issue #30)

casperdcl created an issue (SyneRBI/SIRF-Contribs#30) Follow-up to #28, simplify MaGeZ after SyneRBI/

Feb 3

Casper da Costa-Luis29

Feb 3

[SyneRBI/SIRF-Contribs] MaGeZ (PR #28)

@evgueni-ovtchinnikov commented on this pull request. In src/Python/sirf/contrib/MaGeZ/main.py: >

unread,

[SyneRBI/SIRF-Contribs] MaGeZ (PR #28)

@evgueni-ovtchinnikov commented on this pull request. In src/Python/sirf/contrib/MaGeZ/main.py: >

Feb 3

Kris Thielemans

Feb 1

[SyneRBI/SIRF-SuperBuild] update to NiftyReg 2.0.0 (Issue #983)

KrisThielemans created an issue (SyneRBI/SIRF-SuperBuild#983) NiftyReg v2.0.0 has seen major updates,

unread,

[SyneRBI/SIRF-SuperBuild] update to NiftyReg 2.0.0 (Issue #983)

KrisThielemans created an issue (SyneRBI/SIRF-SuperBuild#983) NiftyReg v2.0.0 has seen major updates,

Feb 1

Kris Thielemans

Jan 29

[SyneRBI/SIRF] Make template for ListmodeToSinograms optional (Issue #1372)

KrisThielemans created an issue (SyneRBI/SIRF#1372) Since STIR 6.3, LmToProjData no longer requires a

unread,

[SyneRBI/SIRF] Make template for ListmodeToSinograms optional (Issue #1372)

KrisThielemans created an issue (SyneRBI/SIRF#1372) Since STIR 6.3, LmToProjData no longer requires a

Jan 29

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