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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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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

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[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

Edoardo Pasca11

Apr 2

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

@paskino pushed 3 commits. dfc8352 revert to using CIL numpy-2 branch ded137e revert add cat of

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

@paskino pushed 3 commits. dfc8352 revert to using CIL numpy-2 branch ded137e revert add cat of

Apr 2

Apr 2

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

paskino created an issue (SyneRBI/SIRF-SuperBuild#991) On the docker CI there is a unittest error due

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

paskino created an issue (SyneRBI/SIRF-SuperBuild#991) On the docker CI there is a unittest error due

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

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[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

Casper da Costa-Luis3

Mar 31

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

@KrisThielemans approved this pull request. ok, but now might be a good time to add a little bit of

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

@KrisThielemans approved this pull request. ok, but now might be a good time to add a little bit of

Mar 31

Casper da Costa-Luis3

Mar 31

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

@KrisThielemans approved this pull request. — Reply to this email directly, view it on GitHub, or

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

@KrisThielemans approved this pull request. — Reply to this email directly, view it on GitHub, or

Mar 31

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

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[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

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[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

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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

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[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

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[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

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[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

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[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

Mar 26

[SyneRBI/SIRF-Exercises] notebook: `reconstruc_measured_data` does not work if the data is not in the working directory (Issue #260)

Closed #260 as completed via #261. — Reply to this email directly, view it on GitHub, or unsubscribe.

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[SyneRBI/SIRF-Exercises] notebook: `reconstruc_measured_data` does not work if the data is not in the working directory (Issue #260)

Closed #260 as completed via #261. — Reply to this email directly, view it on GitHub, or unsubscribe.

Mar 26

Kris Thielemans2

Mar 26

[SyneRBI/SIRF-Exercises] gaussian_filter deperecation warning (Issue #198)

Closed #198 as completed via #251. — Reply to this email directly, view it on GitHub, or unsubscribe.

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[SyneRBI/SIRF-Exercises] gaussian_filter deperecation warning (Issue #198)

Closed #198 as completed via #251. — Reply to this email directly, view it on GitHub, or unsubscribe.

Mar 26

Kris Thielemans10

Mar 26

[SyneRBI/SIRF-Exercises] Minor fixes (PR #251)

Merged #251 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

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[SyneRBI/SIRF-Exercises] Minor fixes (PR #251)

Merged #251 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

Mar 26

Casper da Costa-Luis

Mar 26

[SyneRBI/SIRF-SuperBuild] VM: build from docker (Issue #988)

casperdcl created an issue (SyneRBI/SIRF-SuperBuild#988) Explore building the VM from Docker (so no

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[SyneRBI/SIRF-SuperBuild] VM: build from docker (Issue #988)

casperdcl created an issue (SyneRBI/SIRF-SuperBuild#988) Explore building the VM from Docker (so no

Mar 26

Evgueni Ovtchinnikov2

Mar 26

[SyneRBI/SIRF] Implement the computation of the diagonal of RDP Hessian in SIRF. (Issue #1369)

Closed #1369 as completed via #1370. — Reply to this email directly, view it on GitHub, or

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[SyneRBI/SIRF] Implement the computation of the diagonal of RDP Hessian in SIRF. (Issue #1369)

Closed #1369 as completed via #1370. — Reply to this email directly, view it on GitHub, or

Mar 26

Evgueni Ovtchinnikov26

Mar 26

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

Merged #1370 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

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

Merged #1370 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

Mar 26

Mar 25

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

Closed #1377 as completed via #1387. — Reply to this email directly, view it on GitHub, or

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

Closed #1377 as completed via #1387. — Reply to this email directly, view it on GitHub, or

Mar 25

Evgueni Ovtchinnikov4

Mar 25

[SyneRBI/SIRF] Fix STIR.AcquisitionModel base (missing `__del__`). (PR #1387)

Merged #1387 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

unread,

[SyneRBI/SIRF] Fix STIR.AcquisitionModel base (missing `__del__`). (PR #1387)

Merged #1387 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

Mar 25

Mar 24

[SyneRBI/SIRF] Relax Hessian diagonal test tolerance to 2% (PR #1386)

Summary Relaxes the Hessian_diagonal_test tolerance from 1% to 2% to fix CI failure The one-sided

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[SyneRBI/SIRF] Relax Hessian diagonal test tolerance to 2% (PR #1386)

Summary Relaxes the Hessian_diagonal_test tolerance from 1% to 2% to fix CI failure The one-sided

Mar 24

Kris Thielemans10

Mar 24

Re: [SyneRBI/SIRF] Add numerical test for Hessian diagonal (PR #1385)

KrisThielemans left a comment (SyneRBI/SIRF#1385) thanks! — Reply to this email directly, view it on

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Re: [SyneRBI/SIRF] Add numerical test for Hessian diagonal (PR #1385)

KrisThielemans left a comment (SyneRBI/SIRF#1385) thanks! — Reply to this email directly, view it on

Mar 24

Mar 23

[SyneRBI/SIRF-SuperBuild] Build of ASTRA on Ubuntu 22.04 fails (Issue #802)

wjp left a comment (SyneRBI/SIRF-SuperBuild#802) Hi Edoardo, I realize this is an old issue, but I

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[SyneRBI/SIRF-SuperBuild] Build of ASTRA on Ubuntu 22.04 fails (Issue #802)

wjp left a comment (SyneRBI/SIRF-SuperBuild#802) Hi Edoardo, I realize this is an old issue, but I

Mar 23

Casper da Costa-Luis15

Mar 19

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

Merged!! — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this

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

Merged!! — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this

Mar 19

Mar 19

[SyneRBI/SIRF-SuperBuild] Apple Silicon (M-series) + VS Code devcontainer: severe slowdown / hangs when using prebuilt Ubuntu/x86_64 image (Issue #986)

epapoutsellis left a comment (SyneRBI/SIRF-SuperBuild#986) For CIL there is no problem at all once

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[SyneRBI/SIRF-SuperBuild] Apple Silicon (M-series) + VS Code devcontainer: severe slowdown / hangs when using prebuilt Ubuntu/x86_64 image (Issue #986)

epapoutsellis left a comment (SyneRBI/SIRF-SuperBuild#986) For CIL there is no problem at all once

Mar 19

Kris Thielemans

Mar 18

[SyneRBI/SIRF] extra options for STIR.AcquisitionData.create_uniform_image (Issue #1383)

KrisThielemans created an issue (SyneRBI/SIRF#1383) At the moment, we have https://github.com/SyneRBI

unread,

[SyneRBI/SIRF] extra options for STIR.AcquisitionData.create_uniform_image (Issue #1383)

KrisThielemans created an issue (SyneRBI/SIRF#1383) At the moment, we have https://github.com/SyneRBI

Mar 18

Kris Thielemans2

Mar 18

[SyneRBI/SIRF-Exercises] add packages etc for OpenGATE (PR #271)

KrisThielemans left a comment (SyneRBI/SIRF-Exercises#271) creation error $5 -c echo Container

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[SyneRBI/SIRF-Exercises] add packages etc for OpenGATE (PR #271)

KrisThielemans left a comment (SyneRBI/SIRF-Exercises#271) creation error $5 -c echo Container

Mar 18

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