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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.

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Casper

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Casper da Costa-Luis17

11:59 AM

[SyneRBI/SIRF-SuperBuild] CIL & deps: move to conda (PR #994)

@paskino pushed 1 commit. 575ca86 force USE_SYSTEM_HDF5=OFF on CI workflow — View it on GitHub or

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[SyneRBI/SIRF-SuperBuild] CIL & deps: move to conda (PR #994)

@paskino pushed 1 commit. 575ca86 force USE_SYSTEM_HDF5=OFF on CI workflow — View it on GitHub or

11:59 AM

10:10 AM

[SyneRBI/SIRF] Add tests for asarray method in test_algebra.py (PR #1399)

@paskino pushed 1 commit. 8690046 Remove unnecessary variable assignments in tests — View it on

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[SyneRBI/SIRF] Add tests for asarray method in test_algebra.py (PR #1399)

@paskino pushed 1 commit. 8690046 Remove unnecessary variable assignments in tests — View it on

10:10 AM

9:47 AM

[SyneRBI/SIRF] MR specific test in `xSTIR/pSTIR/test` (Issue #1398)

paskino created an issue (SyneRBI/SIRF#1398) Why is there this test in the PET directory? https://

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[SyneRBI/SIRF] MR specific test in `xSTIR/pSTIR/test` (Issue #1398)

paskino created an issue (SyneRBI/SIRF#1398) Why is there this test in the PET directory? https://

9:47 AM

Kris Thielemans8

8:46 AM

Re: [SyneRBI/SIRF-SuperBuild] Conda (#112)

Closed #112. — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications

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Re: [SyneRBI/SIRF-SuperBuild] Conda (#112)

Closed #112. — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications

8:46 AM

Evgueni Ovtchinnikov

May 6

[SyneRBI/SIRF] Release v3.10.0 - Release 3.10.0

Release 3.10.0 Repository: SyneRBI/SIRF · Tag: v3.10.0 · Commit: 7f3cdcb · Released by: evgueni-

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[SyneRBI/SIRF] Release v3.10.0 - Release 3.10.0

Release 3.10.0 Repository: SyneRBI/SIRF · Tag: v3.10.0 · Commit: 7f3cdcb · Released by: evgueni-

May 6

Kris Thielemans3

May 5

[SyneRBI/SIRF] hkem example needs cgitb (causing ctest failure) (Issue #1395)

Closed #1395 as completed via 724d102. — Reply to this email directly, view it on GitHub, or

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[SyneRBI/SIRF] hkem example needs cgitb (causing ctest failure) (Issue #1395)

Closed #1395 as completed via 724d102. — Reply to this email directly, view it on GitHub, or

May 5

Evgueni Ovtchinnikov3

May 5

[SyneRBI/SIRF] Remove cgitb (PR #1397)

Merged #1397 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. Triage

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[SyneRBI/SIRF] Remove cgitb (PR #1397)

Merged #1397 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. Triage

May 5

Evgueni Ovtchinnikov3

Apr 30

[SyneRBI/SIRF] Prepares Release 3.10.0 (PR #1396)

Merged #1396 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. Triage

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[SyneRBI/SIRF] Prepares Release 3.10.0 (PR #1396)

Merged #1396 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. Triage

Apr 30

Casper da Costa-Luis8

Apr 28

[SyneRBI/SIRF] handle conveniences (PR #1390)

Merged #1390 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. Triage

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[SyneRBI/SIRF] handle conveniences (PR #1390)

Merged #1390 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. Triage

Apr 28

Casper da Costa-Luis3

Apr 27

[SyneRBI/SIRF-SuperBuild] bump CIL deps (Issue #993)

KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#993) I don't know what TomoPhantom depends

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[SyneRBI/SIRF-SuperBuild] bump CIL deps (Issue #993)

KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#993) I don't know what TomoPhantom depends

Apr 27

Apr 21

Re: [SyneRBI/SIRF-SuperBuild] Fix failing CIL unittests (Issue #987)

Closed #987 as completed via #989. — Reply to this email directly, view it on GitHub, or unsubscribe.

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Re: [SyneRBI/SIRF-SuperBuild] Fix failing CIL unittests (Issue #987)

Closed #987 as completed via #989. — Reply to this email directly, view it on GitHub, or unsubscribe.

Apr 21

Apr 21

[SyneRBI/SIRF-SuperBuild] CI: docker tests fail because Gadgetron is not running (Issue #991)

Closed #991 as completed via #989. — Reply to this email directly, view it on GitHub, or unsubscribe.

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[SyneRBI/SIRF-SuperBuild] CI: docker tests fail because Gadgetron is not running (Issue #991)

Closed #991 as completed via #989. — Reply to this email directly, view it on GitHub, or unsubscribe.

Apr 21

Edoardo Pasca16

Apr 21

[SyneRBI/SIRF-SuperBuild] update CIL branch for testing (PR #989)

Merged #989 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

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[SyneRBI/SIRF-SuperBuild] update CIL branch for testing (PR #989)

Merged #989 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

Apr 21

Evgueni Ovtchinnikov2

Apr 21

[SyneRBI/SIRF] Exception in function `Handle.__del__` (Issue #1393)

Closed #1393 as completed via #1394. — Reply to this email directly, view it on GitHub, or

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[SyneRBI/SIRF] Exception in function `Handle.__del__` (Issue #1393)

Closed #1393 as completed via #1394. — Reply to this email directly, view it on GitHub, or

Apr 21

Evgueni Ovtchinnikov3

Apr 21

[SyneRBI/SIRF] Fixed Handle.__del__. (PR #1394)

Merged #1394 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

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[SyneRBI/SIRF] Fixed Handle.__del__. (PR #1394)

Merged #1394 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

Apr 21

Evgueni Ovtchinnikov2

Apr 16

[SyneRBI/SIRF] Release 3.9.0 checklist (Issue #1341)

Closed #1341 as completed. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

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[SyneRBI/SIRF] Release 3.9.0 checklist (Issue #1341)

Closed #1341 as completed. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

Apr 16

Casper da Costa-Luis5

Apr 13

[SyneRBI/SIRF] minor tidy (PR #1389)

Merged #1389 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

unread,

[SyneRBI/SIRF] minor tidy (PR #1389)

Merged #1389 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

Apr 13

Evgueni Ovtchinnikov

Apr 7

[SyneRBI/SIRF] Release 3.10.0 Checklist (Issue #1392)

evgueni-ovtchinnikov created an issue (SyneRBI/SIRF#1392) Release Checklist Set version variable of

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[SyneRBI/SIRF] Release 3.10.0 Checklist (Issue #1392)

evgueni-ovtchinnikov created an issue (SyneRBI/SIRF#1392) Release Checklist Set version variable of

Apr 7

Kris Thielemans4

Apr 7

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

casperdcl left a comment (SyneRBI/SIRF#1374) likely fixed by #1388 — Reply to this email directly,

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

casperdcl left a comment (SyneRBI/SIRF#1374) likely fixed by #1388 — Reply to this email directly,

Apr 7

Apr 2

[SyneRBI/SIRF-SuperBuild] CI: `TORCH_TEST_PYTHON` fail (Issue #992)

paskino created an issue (SyneRBI/SIRF-SuperBuild#992) Currently with master, the CI fails because of

unread,

[SyneRBI/SIRF-SuperBuild] CI: `TORCH_TEST_PYTHON` fail (Issue #992)

paskino created an issue (SyneRBI/SIRF-SuperBuild#992) Currently with master, the CI fails because of

Apr 2

Apr 1

[SyneRBI/SIRF-SuperBuild] CMake: `External_HDF5.cmake` need to escape strings in `HDF5_CMAKE_ARGS` (Issue #990)

KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#990) yes indeed. If it's with external

unread,

[SyneRBI/SIRF-SuperBuild] CMake: `External_HDF5.cmake` need to escape strings in `HDF5_CMAKE_ARGS` (Issue #990)

KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#990) yes indeed. If it's with external

Apr 1

Mar 31

[SyneRBI/SIRF] Separate PET and MR unit test for test_asarray (Issue #1391)

paskino created an issue (SyneRBI/SIRF#1391) The PET and MR unit tests are run in the same function

unread,

[SyneRBI/SIRF] Separate PET and MR unit test for test_asarray (Issue #1391)

paskino created an issue (SyneRBI/SIRF#1391) The PET and MR unit tests are run in the same function

Mar 31

Kris Thielemans5

Mar 30

[SyneRBI/SIRF] expose STIR.GeneralisedPrior.compute_Hessian_diagonal and new priors (Issue #1350)

paskino left a comment (SyneRBI/SIRF#1350) closed by #1370 — Reply to this email directly, view it on

unread,

[SyneRBI/SIRF] expose STIR.GeneralisedPrior.compute_Hessian_diagonal and new priors (Issue #1350)

paskino left a comment (SyneRBI/SIRF#1350) closed by #1370 — Reply to this email directly, view it on

Mar 30

Mar 30

Re: [SyneRBI/SIRF-SuperBuild] Cannot build master on CI (Issue #987)

paskino left a comment (SyneRBI/SIRF-SuperBuild#987) TODO: @paskino to open a PR for this on a

unread,

Re: [SyneRBI/SIRF-SuperBuild] Cannot build master on CI (Issue #987)

paskino left a comment (SyneRBI/SIRF-SuperBuild#987) TODO: @paskino to open a PR for this on a

Mar 30

Mar 27

[SyneRBI/SIRF] get from buffer (#717)

KrisThielemans left a comment (SyneRBI/SIRF#717) resolved by all our asarray() updates — Reply to

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[SyneRBI/SIRF] get from buffer (#717)

KrisThielemans left a comment (SyneRBI/SIRF#717) resolved by all our asarray() updates — Reply to

Mar 27

Evgueni Ovtchinnikov2

Mar 27

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

Closed #1375 as completed via #1376. — Reply to this email directly, view it on GitHub, or

unread,

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

Closed #1375 as completed via #1376. — Reply to this email directly, view it on GitHub, or

Mar 27

Evgueni Ovtchinnikov27

Mar 27

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

Merged #1376 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

unread,

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

Merged #1376 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

Mar 27

Casper da Costa-Luis11

Mar 27

[SyneRBI/SIRF] `Handle` everything (PR #1388)

Merged #1388 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

unread,

[SyneRBI/SIRF] `Handle` everything (PR #1388)

Merged #1388 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

Mar 27

Casper da Costa-Luis3

Mar 27

[SyneRBI/SIRF] swig: Handle wrapper (Issue #1384)

Closed #1384 as completed via fdcd949. — Reply to this email directly, view it on GitHub, or

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[SyneRBI/SIRF] swig: Handle wrapper (Issue #1384)

Closed #1384 as completed via fdcd949. — Reply to this email directly, view it on GitHub, or

Mar 27

Edoardo Pasca10

Mar 26

[SyneRBI/SIRF-Exercises] Update reconstruct_measured_data.ipynb (PR #261)

Merged #261 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

unread,

[SyneRBI/SIRF-Exercises] Update reconstruct_measured_data.ipynb (PR #261)

Merged #261 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

Mar 26

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