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Today's topic summary
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URL:
https://groups.google.com/forum/?utm_source=digest&utm_medium=email#!forum/ccp-petmr-codebot/topics
- [SyneRBI/SIRF-Exercises] registration demo question (#44) [8 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/aaeb271505520804
- [SyneRBI/SIRF] print projdatainfo (#703) [3 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/9218de44830e84ff
- [SyneRBI/SIRF-SuperBuild] disable hdf5 by default (#407) [4 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/78ff0c004cb60039
- [SyneRBI/SIRF-SuperBuild] update STIR tag to release_4 (#406) [1 Update]
http://groups.google.com/group/ccp-petmr-codebot/t/e1ae2cac2836eee3
- [SyneRBI/SIRF-Exercises] some notebooks require tdqm (#41) [2 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/8d65a64735d817b3
- [SyneRBI/SIRF-Exercises] Brainweb-single_slice_motion problems (#48) [12 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/c544e1c89acb191f
- [SyneRBI/SIRF-Exercises] fixes python2 makedirs(exist_ok) (#47) [4 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/dde84d68278bb428
- [SyneRBI/SIRF-Exercises] synergistic/BrainWeb-single_slice_motion.ipynb fails on python 2 due to os.makedirs (#46) [3 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/b5d17c6eb5339ed3
- [SyneRBI/SIRF-Exercises] Can no longer install numba with python 2 (#45) [7 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/323da11e52b7e061
- [SyneRBI/SIRF-Exercises] No need for numba (#49) [6 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/57ceff552d169d1c
- [SyneRBI/SIRF-Exercises] de_Pierro_MAPEM.ipynb refers to non-existing notebook (#50) [2 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/11cd0f271e6ee1ee
- [SyneRBI/SIRF-Exercises] dePierro MAPEM point to correct page (#51) [2 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/1cbd8bed434d2d6
- [SyneRBI/SIRF] resampler.process deprecation (#700) [10 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/f56a08925221c41
- [SyneRBI/SIRF-Exercises] Cropping with SIRF <= v2.1.0 (#52) [2 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/68a3ccc91568f781
- [SyneRBI/SIRF] remove NiftyResample::process deprecation, improve documentation (#702) [1 Update]
http://groups.google.com/group/ccp-petmr-codebot/t/93f0b83bab34ede4
- [SyneRBI/SIRF] using process() and uniformity of class interfaces (#701) [1 Update]
http://groups.google.com/group/ccp-petmr-codebot/t/4a09408dea358325
- [SyneRBI/SyneRBI_VM] use Ubuntu 20.04 from > 2.2 release (#167) [1 Update]
http://groups.google.com/group/ccp-petmr-codebot/t/75f7683542aa3aaf
- [SyneRBI/SIRF-Exercises] Transition to SynerBI (#43) [1 Update]
http://groups.google.com/group/ccp-petmr-codebot/t/5cfceb9283dd3e17
- [SyneRBI/SIRF-Exercises] Transition to SynerBI (#43) [1 Update]
http://groups.google.com/group/ccp-petmr-codebot/t/1956d7aaa10216df
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Topic: [SyneRBI/SIRF-Exercises] registration demo question (#44)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/aaeb271505520804
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From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 02:08AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41a681a906866
Just tried with 2.2.0-rc.1 VM.
The registration demo works, but it seems a bit strange. Initial display of images is
---------- 2 of 8 ----------
From: Richard Brown <[log in to unmask]>
Date: Jun 04 04:48AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/42327cf644a94
Looking into it, the two images have vastly different `qto_ijk` matrices:
```
[4.06,0,0,-128] [-4.06,0,0,-0]
[0,4.06,0,-128] [0,0,4.06,256]
---------- 3 of 8 ----------
From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 06:44AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/42976fe304200
> it looks like the first is RAS, whilst the second is LSI.
ok
> This comes back to the bigger question we've had a few times over what `as_array` should really do. As-is or LPS?
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From: Richard Brown <[log in to unmask]>
Date: Jun 04 07:28AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/42be347923e20
> Otherwise performance penalty will be terrible.
I'm not sure that's true.
The displacements do look confusing. But I suspect they're correct, since they mostly encode a translation (the `cmap`
---------- 5 of 8 ----------
From: Richard Brown <[log in to unmask]>
Date: Jun 04 07:32AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/42c171432b548
Copying in the displacements for future reference
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---------- 6 of 8 ----------
From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 07:59AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/42d92700ea4bb
ok. agreed. if you look at the scales, they look fine. sorry.
Obviously, if you reorient the image, and get a different deformation field out, we're in trouble.
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---------- 7 of 8 ----------
From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 12:46PM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/43d386bc3ad87
> > Otherwise performance penalty will be terrible.
> I'm not sure that's true.
At the moment, `as_array` is a straightforward copy. if we reorient, it's going to be a bunch of nested loops.
---------- 8 of 8 ----------
From: Richard Brown <[log in to unmask]>
Date: Jun 04 01:11PM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/43e9a73e118de
I'm afraid not (on the `NiftiImageData` side):
https://github.com/SyneRBI/SIRF/blob/913b422d0f32852bcd421115de37f2fdd9be0b41/src/Registration/cReg/cReg.cpp#L303-L311
I don't believe this to be
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Topic: [SyneRBI/SIRF] print projdatainfo (#703)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/9218de44830e84ff
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From: Richard Brown <[log in to unmask]>
Date: Jun 04 09:15AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/431b48b12acd3
Ability to print AcqData info.
You can view, comment on, or merge this pull request online at:
https://github.com/SyneRBI/SIRF/pull/703
-- Commit Summary --
* print projdatainfo
---------- 2 of 3 ----------
From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 09:48AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/4337fa7f2ce4c
@KrisThielemans requested changes on this pull request.
Great. Very useful. As opposed to printing, I'd return a string though. Then the user can print it or parse.
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From: Richard Brown <[log in to unmask]>
Date: Jun 04 09:52AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/433b89453bc90
@rijobro pushed 1 commit.
a014c773639bfaca4ac730421aa8eb47c27dc126 return info as string
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Topic: [SyneRBI/SIRF-SuperBuild] disable hdf5 by default (#407)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/78ff0c004cb60039
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---------- 1 of 4 ----------
From: Richard Brown <[log in to unmask]>
Date: Jun 04 08:03AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/42dbfdbc57e39
In spite of https://github.com/SyneRBI/SIRF-SuperBuild/pull/404, STIR HDF5 support still being built on PRs, causing them to fail:
---------- 2 of 4 ----------
From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 08:45AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/43014c2742b2f
There has never been a `DISABLE_HDF5_SUPPORT` as far as I can see. It certainly is `DISABLE_HDF5` in STIR `release_4` branch (it isn't yet anywhere else I believe).
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---------- 3 of 4 ----------
From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 08:46AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/4301adb247010
please remove the `*SUPPORT` variable therefore
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From: Richard Brown <[log in to unmask]>
Date: Jun 04 08:49AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/430449e3df35d
@rijobro pushed 1 commit.
121505203c3f0f52359e2f6f571cd8426b28077e remove variable STIR_DISABLE_HDF5_SUPPORT
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============================================================================
Topic: [SyneRBI/SIRF-SuperBuild] update STIR tag to release_4 (#406)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/e1ae2cac2836eee3
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From: Richard Brown <[log in to unmask]>
Date: Jun 04 08:03AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/42dcae79f2a8d
Travis currently not happy. Will hopefully be fixed with #407.
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Topic: [SyneRBI/SIRF-Exercises] some notebooks require tdqm (#41)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/8d65a64735d817b3
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From: Casper da Costa-Luis <[log in to unmask]>
Date: Jun 04 07:26AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/42bbef1659c97
Closed #41.
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From: Casper da Costa-Luis <[log in to unmask]>
Date: Jun 04 07:26AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/42bbf17a77119
probably best to merge this issue with #40
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Topic: [SyneRBI/SIRF-Exercises] Brainweb-single_slice_motion problems (#48)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/c544e1c89acb191f
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From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 02:53AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41cdc13f075e7
Images loaded look like this
Motion states and sinos look empty.
It uses
---------- 2 of 12 ----------
From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 02:58AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41d25122fefe6
same for `Brainweb` notebook
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From: Richard Brown <[log in to unmask]>
Date: Jun 04 03:05AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41d837ab0b364
@casperdcl is this related to https://github.com/casperdcl/brainweb/issues/1?
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From: Casper da Costa-Luis <[log in to unmask]>
Date: Jun 04 03:10AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41dc39a15b1cc
:eyes: looks like it; never been able to reproduce this - would be great if you can. Are you running this on windows?
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---------- 5 of 12 ----------
From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 03:11AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41ddab0c45f0f
This is on our new VM (ubuntu 18.04, but python 2).
https://zenodo.org/record/3874226#.XtgnuGhKh6o
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From: Casper da Costa-Luis <[log in to unmask]>
Date: Jun 04 03:24AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41e910fb806c0
Ooh nice. Will try to reproduce... Which ova? 2.0, 2.1, or 2.2-rc.1?
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From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 03:26AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41ea1ee34235b
2.2-rc.1. I'm not sure what happens with the previous ones (but should have been fine)
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From: Richard Brown <[log in to unmask]>
Date: Jun 04 03:41AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41f7776ad6c4e
Blank with python2, normal with python3 if that helps narrow things down for you.
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From: Casper da Costa-Luis <[log in to unmask]>
Date: Jun 04 05:41AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/42606211d6267
fixed in `brainweb>=1.5.1`
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From: Richard Brown <[log in to unmask]>
Date: Jun 04 07:08AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/42ac8b887854d
Sure?
---------- 11 of 12 ----------
From: Richard Brown <[log in to unmask]>
Date: Jun 04 07:10AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/42ae8412372be
ah, it was reusing pre-downloaded data. deleted the working folder and it seems to be working.
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From: Casper da Costa-Luis <[log in to unmask]>
Date: Jun 04 07:25AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/42bb385c98239
Closed #48.
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Topic: [SyneRBI/SIRF-Exercises] fixes python2 makedirs(exist_ok) (#47)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/dde84d68278bb428
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---------- 1 of 4 ----------
From: Richard Brown <[log in to unmask]>
Date: Jun 04 02:50AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41cb35fe0d80c
fixes https://github.com/SyneRBI/SIRF-Exercises/issues/46
You can view, comment on, or merge this pull request online at:
https://github.com/SyneRBI/SIRF-Exercises/pull/47
-- Commit Summary
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From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 02:57AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41d17e9a3fa87
same for `Brainweb` (also for numba)
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From: Richard Brown <[log in to unmask]>
Date: Jun 04 03:03AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41d6679b20645
@rijobro pushed 1 commit.
c5f9013f1ae7377e4e4be82aef04243399ad1169 fix brainweb py2 makedirs exist_ok
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From: Richard Brown <[log in to unmask]>
Date: Jun 04 06:30AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/428b6c4b37179
Merged #47 into master.
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Topic: [SyneRBI/SIRF-Exercises] synergistic/BrainWeb-single_slice_motion.ipynb fails on python 2 due to os.makedirs (#46)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/b5d17c6eb5339ed3
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---------- 1 of 3 ----------
From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 02:44AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41c5d099ee8cd
code is
```python
if not path.isdir(data_path):
os.makedirs(data_path, exist_ok=True)
```
This fails on Python 2 as `exist_ok` didn't exist (...). However, it seems unnecessary as we check
---------- 2 of 3 ----------
From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 02:56AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41d09e295160f
same for Brainweb
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From: Richard Brown <[log in to unmask]>
Date: Jun 04 06:30AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/428b694ff7de1
Closed #46 via #47.
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Topic: [SyneRBI/SIRF-Exercises] Can no longer install numba with python 2 (#45)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/323da11e52b7e061
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---------- 1 of 7 ----------
From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 02:35AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41bdd4c06a9d1
The synergistic demos use brainweb, which starts by using `pip install numba`. That now fails
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From: Casper da Costa-Luis <[log in to unmask]>
Date: Jun 04 02:48AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41c9292f2aa7b
I think `numba` is a leftover from some performance hacks @rijobro was trying - looks like it can be removed.
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From: Richard Brown <[log in to unmask]>
Date: Jun 04 02:59AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41d2eb0ae6060
yeah, it looks like it wasn't actually being used in the notebook. It is, however, used in a few others (but not `pip` installed):
---------- 4 of 7 ----------
From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 03:09AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41db4e83ce0bb
Serves us right from not upgrading to Python 3. @paskino, this will have to be a priority after 2.2 (unless it's a matter of dropping in ubuntu 20.04, but that seems unlikely!)
I suggest to move
---------- 5 of 7 ----------
From: Casper da Costa-Luis <[log in to unmask]>
Date: Jun 04 03:11AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41dd4bfb14ddd
How much of a speedup does it really give in those notebooks? May just be better to leave it out...
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From: Richard Brown <[log in to unmask]>
Date: Jun 04 04:22AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/421b0cc37e379
Comment from a notebook says
> Using jit gets computation time from 90 secs to 2!
So I'm inclined to comment it out rather than delete.
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---------- 7 of 7 ----------
From: Richard Brown <[log in to unmask]>
Date: Jun 04 06:30AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/428b0dda7bac3
Closed #45 via #49.
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Topic: [SyneRBI/SIRF-Exercises] No need for numba (#49)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/57ceff552d169d1c
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---------- 1 of 6 ----------
From: Richard Brown <[log in to unmask]>
Date: Jun 04 02:53AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41ce041b6709b
fixes https://github.com/SyneRBI/SIRF-Exercises/issues/45
You can view, comment on, or merge this pull request online at:
https://github.com/SyneRBI/SIRF-Exercises/pull/49
-- Commit Summary
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From: Richard Brown <[log in to unmask]>
Date: Jun 04 03:02AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41d55a6fe46e5
@rijobro pushed 1 commit.
a45e419e0f60dca15f41cacb8d4b51fcbf722cc1 no numba in brainweb either
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From: Richard Brown <[log in to unmask]>
Date: Jun 04 03:29AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41ed5e40c81f0
@rijobro pushed 1 commit.
7c66536d660dd2d7f9ef71db66c3ab10ef52a4cb comma
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From: Richard Brown <[log in to unmask]>
Date: Jun 04 04:26AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/421e80a399d54
@rijobro pushed 1 commit.
c31f7cd5a8fa5e6e5c532c7dc360c9e256439729 comment out jit
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From: Richard Brown <[log in to unmask]>
Date: Jun 04 06:28AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/4289d1fba8533
@rijobro pushed 1 commit.
3c4dd5e08510622530667a412dc0fa9724eca40a undo python3 changes
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From: Richard Brown <[log in to unmask]>
Date: Jun 04 06:30AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/428b0bb7059f7
Merged #49 into master.
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Topic: [SyneRBI/SIRF-Exercises] de_Pierro_MAPEM.ipynb refers to non-existing notebook (#50)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/11cd0f271e6ee1ee
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---------- 1 of 2 ----------
From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 03:00AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41d42dd5bab10
It instructs to run the `generate_data` notebook but that no longer exists
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From: Richard Brown <[log in to unmask]>
Date: Jun 04 06:17AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/42803d0cbaf07
Closed #50 via #51.
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Topic: [SyneRBI/SIRF-Exercises] dePierro MAPEM point to correct page (#51)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/1cbd8bed434d2d6
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---------- 1 of 2 ----------
From: Richard Brown <[log in to unmask]>
Date: Jun 04 04:27AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/421fa0e70ba3e
fixes https://github.com/SyneRBI/SIRF-Exercises/issues/45
You can view, comment on, or merge this pull request online at:
https://github.com/SyneRBI/SIRF-Exercises/pull/51
-- Commit Summary
---------- 2 of 2 ----------
From: Richard Brown <[log in to unmask]>
Date: Jun 04 06:17AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/428039896d3d3
Merged #51 into master.
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Topic: [SyneRBI/SIRF] resampler.process deprecation (#700)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/f56a08925221c41
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---------- 1 of 10 ----------
From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 02:17AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41ae4e1f5ad2b
SIRF-exercises registration demo does
```python
resampler = Reg.NiftyResample()
resampler.set_reference_image(ref)
resampler.set_floating_image(flo)
resampler.add_transformation(tm)
---------- 2 of 10 ----------
From: Richard Brown <[log in to unmask]>
Date: Jun 04 02:42AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41c448833c19a
Hum, two possible solutions:
1. Un-deprecate the `process` methods
2. In this example, replace `process()` with `forward(flo)`.
3. See bottom
Personally, between the first two, I'm in favour
---------- 3 of 10 ----------
From: Biguri <[log in to unmask]>
Date: Jun 04 02:46AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/41c77158917d3
@rijobro just nitpicking: `process` does not only work for `forward` right? It may not return the `adjoint(reg)` but it does return the DVFs to do so, am I correct?
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From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 03:53AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/42022772e23b0
@AnderBiguri this is the resampler. it doesn't return a DVF (that's the job of the registration)
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From: Richard Brown <[log in to unmask]>
Date: Jun 04 03:53AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/42024a903ec3b
Not sure what you mean, can you give an example? The DVFs are the same regardless of forward/adjoint.
Anyway, I'm fairly sure that under the hood, `process` simply calls `forward`.
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---------- 6 of 10 ----------
From: Biguri <[log in to unmask]>
Date: Jun 04 03:55AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/420371891ddf6
@KrisThielemans @rijobro let me go and buy stronger coffee, completely misread all this. Sorry!
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From: Richard Brown <[log in to unmask]>
Date: Jun 04 03:55AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/42038d505e67f
https://github.com/SyneRBI/SIRF/blob/225d6211a8e6adc02d859978764d062a70f36806/src/Registration/cReg/NiftyResample.cpp#L190-L194
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---------- 8 of 10 ----------
From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 04:30AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/42225719cbdd1
Obviously, all this `forward` `backward` terminology is incredibly confusing in registration. (Most people will think that `backward` is the inverse of course). Not much we can do about that, except
---------- 9 of 10 ----------
From: Richard Brown <[log in to unmask]>
Date: Jun 04 05:24AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/42517afa9eaa7
PR to un-deprecate `process` and improve doc in UserGuide.
For what it's worth, I think this is a pretty good warning!
```
DeprecatedWarning: process is deprecated as of 2.1.0.
---------- 10 of 10 ----------
From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 05:59AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/4270842e59da6
Sure, that warning is crystal clear. It's the cruft around it that more distracting than anything else. Anyway. not our issue.
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============================================================================
Topic: [SyneRBI/SIRF-Exercises] Cropping with SIRF <= v2.1.0 (#52)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/68a3ccc91568f781
============================================================================
---------- 1 of 2 ----------
From: Richard Brown <[log in to unmask]>
Date: Jun 04 05:28AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/42551b3276514
The following was in this notebook as a workaround for older versions of SIRF: https://github.com/SyneRBI/SIRF-Exercises/blob/master/notebooks/Synergistic/BrainWeb.ipynb
I don't really want it in
---------- 2 of 2 ----------
From: Richard Brown <[log in to unmask]>
Date: Jun 04 05:28AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/42552de5cdac4
Closed #52.
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============================================================================
Topic: [SyneRBI/SIRF] remove NiftyResample::process deprecation, improve documentation (#702)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/93f0b83bab34ede4
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---------- 1 of 1 ----------
From: Richard Brown <[log in to unmask]>
Date: Jun 04 05:23AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/4250a9faee32b
fixes https://github.com/SyneRBI/SIRF/issues/700
You can view, comment on, or merge this pull request online at:
https://github.com/SyneRBI/SIRF/pull/702
-- Commit Summary --
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Topic: [SyneRBI/SIRF] using process() and uniformity of class interfaces (#701)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/4a09408dea358325
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---------- 1 of 1 ----------
From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 04:22AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/421b9b8246b5e
It makes it far easier to the user if most classes act the same. The `set_input();process();get_output()` terminology was suggested by @ckolbPTB as a generic way of doing things (for `sirf.STIR` to be
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Topic: [SyneRBI/SyneRBI_VM] use Ubuntu 20.04 from > 2.2 release (#167)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/75f7683542aa3aaf
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---------- 1 of 1 ----------
From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 03:52AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/42014124a4072
@paskino, we have multiple problems with the SIRF-exercises. want to give this a go if it happens to work already?
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============================================================================
Topic: [SyneRBI/SIRF-Exercises] Transition to SynerBI (#43)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/5cfceb9283dd3e17
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---------- 1 of 1 ----------
From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 01:53AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/4199034bd470f
Closed #43.
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Topic: [SyneRBI/SIRF-Exercises] Transition to SynerBI (#43)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/1956d7aaa10216df
============================================================================
---------- 1 of 1 ----------
From: Kris Thielemans <[log in to unmask]>
Date: Jun 04 01:53AM -0700
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/4199006fe3ece
repo has transitioned. We could update header of all the notebooks, but I suggest we do that as we go.
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