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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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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

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[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 Ovtchinnikov6

Feb 18

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

@evgueni-ovtchinnikov commented on this pull request. In src/Registration/pReg/Reg.py: > @@ -567,7

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

@evgueni-ovtchinnikov commented on this pull request. In src/Registration/pReg/Reg.py: > @@ -567,7

Feb 18

Feb 17

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

@KrisThielemans commented on this pull request. In cmake/sirf.__init__.py.in: > +# import sirf.

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

@KrisThielemans commented on this pull request. In cmake/sirf.__init__.py.in: > +# import sirf.

Feb 17

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

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[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 =

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[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

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[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

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[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

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[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

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[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

Evgueni Ovtchinnikov9

Feb 11

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

@KrisThielemans commented on this pull request. In src/common/Utilities.py: > @@ -790,24 +790,47 @

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

@KrisThielemans commented on this pull request. In src/common/Utilities.py: > @@ -790,24 +790,47 @

Feb 11

Casper da Costa-Luis

Feb 5

[SyneRBI/PETRIC-backend] Release v1 - PETRIC

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

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[SyneRBI/PETRIC-backend] Release v1 - PETRIC

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

Feb 5

Kris Thielemans9

Feb 5

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

Reopened #1357. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving

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

Reopened #1357. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving

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 —

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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

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[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

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[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/

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[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: >

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[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,

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[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

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[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

Casper da Costa-Luis2

Jan 29

[SyneRBI/SIRF-SuperBuild] pip install sirf-contrib (Issue #981)

Closed #981 as completed via 4e307d6. — Reply to this email directly, view it on GitHub, or

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[SyneRBI/SIRF-SuperBuild] pip install sirf-contrib (Issue #981)

Closed #981 as completed via 4e307d6. — Reply to this email directly, view it on GitHub, or

Jan 29

Casper da Costa-Luis5

Jan 29

[SyneRBI/SIRF-SuperBuild] bump sirf.contrib (PR #982)

Merged #982 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

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[SyneRBI/SIRF-SuperBuild] bump sirf.contrib (PR #982)

Merged #982 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

Jan 29

Casper da Costa-Luis3

Jan 29

[SyneRBI/SIRF] allow namespace packages (PR #1371)

Merged #1371 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

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[SyneRBI/SIRF] allow namespace packages (PR #1371)

Merged #1371 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

Jan 29

Casper da Costa-Luis2

Jan 29

[SyneRBI/SIRF-Contribs] make pip-installable (PR #29)

Merged #29 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

unread,

[SyneRBI/SIRF-Contribs] make pip-installable (PR #29)

Merged #29 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

Jan 29

Evgueni Ovtchinnikov

Jan 26

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

evgueni-ovtchinnikov created an issue (SyneRBI/SIRF#1369) — Reply to this email directly, view it on

unread,

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

evgueni-ovtchinnikov created an issue (SyneRBI/SIRF#1369) — Reply to this email directly, view it on

Jan 26

Kris Thielemans2

Jan 25

[SyneRBI/SIRF-Contribs] LBFGSPC implementation and scipy callback vs CIL Algorithm callback (Issue #24)

Closed #24 as completed via #27. — Reply to this email directly, view it on GitHub, or unsubscribe.

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[SyneRBI/SIRF-Contribs] LBFGSPC implementation and scipy callback vs CIL Algorithm callback (Issue #24)

Closed #24 as completed via #27. — Reply to this email directly, view it on GitHub, or unsubscribe.

Jan 25

Kris Thielemans6

Jan 25

[SyneRBI/SIRF-Contribs] LBFGSBPC callbacks (PR #27)

Merged #27 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

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[SyneRBI/SIRF-Contribs] LBFGSBPC callbacks (PR #27)

Merged #27 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

Jan 25

Jan 23

[SyneRBI/SIRF-Contribs] partitioner code from CIL (Issue #19)

Closed #19 as completed via 80efdd6. — Reply to this email directly, view it on GitHub, or

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[SyneRBI/SIRF-Contribs] partitioner code from CIL (Issue #19)

Closed #19 as completed via 80efdd6. — Reply to this email directly, view it on GitHub, or

Jan 23

Evgueni Ovtchinnikov8

Jan 19

[SyneRBI/SIRF] Creating compatible ImageData from AcquisitionData and voxels grid dimensions x and y (PR #1364)

Merged #1364 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

unread,

[SyneRBI/SIRF] Creating compatible ImageData from AcquisitionData and voxels grid dimensions x and y (PR #1364)

Merged #1364 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

Jan 19

Evgueni Ovtchinnikov20

Jan 15

[SyneRBI/SIRF] Extends SIRF data algebra possible operands to numpy arrays (PR #1358)

Merged #1358 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

unread,

[SyneRBI/SIRF] Extends SIRF data algebra possible operands to numpy arrays (PR #1358)

Merged #1358 into master. — Reply to this email directly, view it on GitHub, or unsubscribe. You are

Jan 15

Jan 15

[SyneRBI/SIRF] README and installation (Issue #1361)

KrisThielemans left a comment (SyneRBI/SIRF#1361) I have updated the wiki somewhat to remove obsolete

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[SyneRBI/SIRF] README and installation (Issue #1361)

KrisThielemans left a comment (SyneRBI/SIRF#1361) I have updated the wiki somewhat to remove obsolete

Jan 15

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