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Kris Thielemans <[log in to unmask]>: Jun 04 02:08AM -0700 Just tried with 2.2.0-rc.1 VM.   The registration demo works, but it seems a bit strange. Initial display of images is ...more

Richard Brown <[log in to unmask]>: Jun 04 04:48AM -0700 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] ...more

Kris Thielemans <[log in to unmask]>: Jun 04 06:44AM -0700 > 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? ...more

Richard Brown <[log in to unmask]>: Jun 04 07:28AM -0700 > 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` ...more

Richard Brown <[log in to unmask]>: Jun 04 07:32AM -0700 Copying in the displacements for future reference      -- You are receiving this ...more

Kris Thielemans <[log in to unmask]>: Jun 04 07:59AM -0700 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.   -- You are receiving this ...more

Kris Thielemans <[log in to unmask]>: Jun 04 12:46PM -0700 > > 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. ...more

Richard Brown <[log in to unmask]>: Jun 04 01:11PM -0700 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 ...more

Richard Brown <[log in to unmask]>: Jun 04 09:15AM -0700 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 ...more

Kris Thielemans <[log in to unmask]>: Jun 04 09:48AM -0700 @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.       -- You are receiving ...more

Richard Brown <[log in to unmask]>: Jun 04 09:52AM -0700 @rijobro pushed 1 commit.   a014c773639bfaca4ac730421aa8eb47c27dc126 return info as string     -- You are receiving this because you are subscribed to this thread. View it on GitHub: ...more

Richard Brown <[log in to unmask]>: Jun 04 08:03AM -0700 In spite of https://github.com/SyneRBI/SIRF-SuperBuild/pull/404, STIR HDF5 support still being built on PRs, causing them to fail: ...more

Kris Thielemans <[log in to unmask]>: Jun 04 08:45AM -0700 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).   -- You are receiving this ...more

Kris Thielemans <[log in to unmask]>: Jun 04 08:46AM -0700 please remove the `*SUPPORT` variable therefore   -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: ...more

Richard Brown <[log in to unmask]>: Jun 04 08:49AM -0700 @rijobro pushed 1 commit.   121505203c3f0f52359e2f6f571cd8426b28077e remove variable STIR_DISABLE_HDF5_SUPPORT     -- You are receiving this because you are subscribed to this thread. ...more

Richard Brown <[log in to unmask]>: Jun 04 08:03AM -0700 Travis currently not happy. Will hopefully be fixed with #407.   -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: ...more

Casper da Costa-Luis <[log in to unmask]>: Jun 04 07:26AM -0700 Closed #41.   -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: ...more

Casper da Costa-Luis <[log in to unmask]>: Jun 04 07:26AM -0700 probably best to merge this issue with #40   -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: ...more

Kris Thielemans <[log in to unmask]>: Jun 04 02:53AM -0700 Images loaded look like this  Motion states and sinos look empty.   It uses ...more

Kris Thielemans <[log in to unmask]>: Jun 04 02:58AM -0700 same for `Brainweb` notebook   -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: ...more

Richard Brown <[log in to unmask]>: Jun 04 03:05AM -0700 @casperdcl is this related to https://github.com/casperdcl/brainweb/issues/1?   -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on ...more

Casper da Costa-Luis <[log in to unmask]>: Jun 04 03:10AM -0700 :eyes: looks like it; never been able to reproduce this - would be great if you can. Are you running this on windows?   -- You are receiving this because you are subscribed to this thread. ...more

Kris Thielemans <[log in to unmask]>: Jun 04 03:11AM -0700 This is on our new VM (ubuntu 18.04, but python 2). https://zenodo.org/record/3874226#.XtgnuGhKh6o   -- You are receiving this because you are subscribed to this thread. Reply to this email ...more

Casper da Costa-Luis <[log in to unmask]>: Jun 04 03:24AM -0700 Ooh nice. Will try to reproduce... Which ova? 2.0, 2.1, or 2.2-rc.1?   -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: ...more

Kris Thielemans <[log in to unmask]>: Jun 04 03:26AM -0700 2.2-rc.1. I'm not sure what happens with the previous ones (but should have been fine)   -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view ...more

Richard Brown <[log in to unmask]>: Jun 04 03:41AM -0700 Blank with python2, normal with python3 if that helps narrow things down for you.   -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on ...more

Casper da Costa-Luis <[log in to unmask]>: Jun 04 05:41AM -0700 fixed in `brainweb>=1.5.1`   -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: ...more

Richard Brown <[log in to unmask]>: Jun 04 07:08AM -0700 Sure?    ...more

Richard Brown <[log in to unmask]>: Jun 04 07:10AM -0700 ah, it was reusing pre-downloaded data. deleted the working folder and it seems to be working.   -- You are receiving this because you are subscribed to this thread. Reply to this email directly ...more

Casper da Costa-Luis <[log in to unmask]>: Jun 04 07:25AM -0700 Closed #48.   -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: ...more

Richard Brown <[log in to unmask]>: Jun 04 02:50AM -0700 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 ...more

Kris Thielemans <[log in to unmask]>: Jun 04 02:57AM -0700 same for `Brainweb` (also for numba)   -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: ...more

Richard Brown <[log in to unmask]>: Jun 04 03:03AM -0700 @rijobro pushed 1 commit.   c5f9013f1ae7377e4e4be82aef04243399ad1169 fix brainweb py2 makedirs exist_ok     -- You are receiving this because you are subscribed to this thread. ...more

Richard Brown <[log in to unmask]>: Jun 04 06:30AM -0700 Merged #47 into master.   -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: ...more

Kris Thielemans <[log in to unmask]>: Jun 04 02:44AM -0700 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 ...more

Kris Thielemans <[log in to unmask]>: Jun 04 02:56AM -0700 same for Brainweb   -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: ...more

Richard Brown <[log in to unmask]>: Jun 04 06:30AM -0700 Closed #46 via #47.   -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: ...more

Kris Thielemans <[log in to unmask]>: Jun 04 02:35AM -0700 The synergistic demos use brainweb, which starts by using `pip install numba`. That now fails     -- You are receiving this because you are subscribed to this thread. Reply to this email directly ...more

Casper da Costa-Luis <[log in to unmask]>: Jun 04 02:48AM -0700 I think `numba` is a leftover from some performance hacks @rijobro was trying - looks like it can be removed.   -- You are receiving this because you are subscribed to this thread. ...more

Richard Brown <[log in to unmask]>: Jun 04 02:59AM -0700 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): ...more

Kris Thielemans <[log in to unmask]>: Jun 04 03:09AM -0700 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 ...more

Casper da Costa-Luis <[log in to unmask]>: Jun 04 03:11AM -0700 How much of a speedup does it really give in those notebooks? May just be better to leave it out...   -- You are receiving this because you are subscribed to this thread. Reply to this email ...more

Richard Brown <[log in to unmask]>: Jun 04 04:22AM -0700 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.   -- You are receiving this because you are subscribed to ...more

Richard Brown <[log in to unmask]>: Jun 04 06:30AM -0700 Closed #45 via #49.   -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: ...more

Richard Brown <[log in to unmask]>: Jun 04 02:53AM -0700 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 ...more

Richard Brown <[log in to unmask]>: Jun 04 03:02AM -0700 @rijobro pushed 1 commit.   a45e419e0f60dca15f41cacb8d4b51fcbf722cc1 no numba in brainweb either     -- You are receiving this because you are subscribed to this thread. View it on GitHub: ...more

Richard Brown <[log in to unmask]>: Jun 04 03:29AM -0700 @rijobro pushed 1 commit.   7c66536d660dd2d7f9ef71db66c3ab10ef52a4cb comma     -- You are receiving this because you are subscribed to this thread. View it on GitHub: ...more

Richard Brown <[log in to unmask]>: Jun 04 04:26AM -0700 @rijobro pushed 1 commit.   c31f7cd5a8fa5e6e5c532c7dc360c9e256439729 comment out jit     -- You are receiving this because you are subscribed to this thread. View it on GitHub: ...more

Richard Brown <[log in to unmask]>: Jun 04 06:28AM -0700 @rijobro pushed 1 commit.   3c4dd5e08510622530667a412dc0fa9724eca40a undo python3 changes     -- You are receiving this because you are subscribed to this thread. View it on GitHub: ...more

Richard Brown <[log in to unmask]>: Jun 04 06:30AM -0700 Merged #49 into master.   -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: ...more

Kris Thielemans <[log in to unmask]>: Jun 04 03:00AM -0700 It instructs to run the `generate_data` notebook but that no longer exists   -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: ...more

Richard Brown <[log in to unmask]>: Jun 04 06:17AM -0700 Closed #50 via #51.   -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: ...more

Richard Brown <[log in to unmask]>: Jun 04 04:27AM -0700 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 ...more

Richard Brown <[log in to unmask]>: Jun 04 06:17AM -0700 Merged #51 into master.   -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: ...more

Kris Thielemans <[log in to unmask]>: Jun 04 02:17AM -0700 SIRF-exercises registration demo does ```python resampler = Reg.NiftyResample() resampler.set_reference_image(ref) resampler.set_floating_image(flo) resampler.add_transformation(tm) ...more

Richard Brown <[log in to unmask]>: Jun 04 02:42AM -0700 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 ...more

Biguri <[log in to unmask]>: Jun 04 02:46AM -0700 @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?   -- You are receiving this ...more

Kris Thielemans <[log in to unmask]>: Jun 04 03:53AM -0700 @AnderBiguri this is the resampler. it doesn't return a DVF (that's the job of the registration)   -- You are receiving this because you are subscribed to this thread. Reply to this email directly ...more

Richard Brown <[log in to unmask]>: Jun 04 03:53AM -0700 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`.   -- ...more

Biguri <[log in to unmask]>: Jun 04 03:55AM -0700 @KrisThielemans @rijobro let me go and buy stronger coffee, completely misread all this. Sorry!     -- You are receiving this because you are subscribed to this thread. Reply to this email ...more

Richard Brown <[log in to unmask]>: Jun 04 03:55AM -0700 https://github.com/SyneRBI/SIRF/blob/225d6211a8e6adc02d859978764d062a70f36806/src/Registration/cReg/NiftyResample.cpp#L190-L194   -- You are receiving this because you are subscribed to this ...more

Kris Thielemans <[log in to unmask]>: Jun 04 04:30AM -0700 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 ...more

Richard Brown <[log in to unmask]>: Jun 04 05:24AM -0700 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. ...more

Kris Thielemans <[log in to unmask]>: Jun 04 05:59AM -0700 Sure, that warning is crystal clear. It's the cruft around it that more distracting than anything else. Anyway. not our issue.   -- You are receiving this because you are subscribed to this thread. ...more

Richard Brown <[log in to unmask]>: Jun 04 05:28AM -0700 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 ...more

Richard Brown <[log in to unmask]>: Jun 04 05:28AM -0700 Closed #52.   -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: ...more

Richard Brown <[log in to unmask]>: Jun 04 05:23AM -0700 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 -- ...more

Kris Thielemans <[log in to unmask]>: Jun 04 04:22AM -0700 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 ...more

Kris Thielemans <[log in to unmask]>: Jun 04 03:52AM -0700 @paskino, we have multiple problems with the SIRF-exercises. want to give this a go if it happens to work already?   -- You are receiving this because you are subscribed to this thread. ...more

Kris Thielemans <[log in to unmask]>: Jun 04 01:53AM -0700 Closed #43.   -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: ...more

Kris Thielemans <[log in to unmask]>: Jun 04 01:53AM -0700 repo has transitioned. We could update header of all the notebooks, but I suggest we do that as we go.   -- You are receiving this because you are subscribed to this thread. Reply to this email ...more

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