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Kris Thielemans <[log in to unmask]>: May 10 01:07PM -0700
@evgueni-ovtchinnikov, can you make these changes on the MATLAB demos please? Thanks! -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it ...more |
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Kris Thielemans <[log in to unmask]>: May 10 10:25AM -0700
@evgueni-ovtchinnikov, this all works fine. thanks! Could you rename `set_alpha_ramp` to `set_alpha_cosine_window`? Add some doc for the class like: ``` This is an implementation of the 2D FBP ...more |
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Kris Thielemans <[log in to unmask]>: May 10 05:29AM -0700
for the course, we've decided on jupyter notebooks (assuming it all works!). That will lead to duplication of demos and therefore bugs. One solution might be to swap to jupyter notebooks and tell ...more |
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Edoardo Pasca <[log in to unmask]>: May 10 07:21AM -0700
And I've made a script to convert spyder scripts to jupyter notebooks! We can close the circle. -- You are receiving this because you are subscribed to this thread. Reply to this email directly ...more |
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Kris Thielemans <[log in to unmask]>: May 10 07:23AM -0700
:-) I knew you were not a copy-paste guy. will be interesting to see the output... Note that there are some fixes on the demos already. -- You are receiving this because you are subscribed to ...more |
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Edoardo Pasca <[log in to unmask]>: May 10 08:35AM -0700
After the first file I painstakingly translated I went for the more interesting way. Which enabled me to update the notebook you've updated! I've got a question: it seems that you need to run the ...more |
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Kris Thielemans <[log in to unmask]>: May 10 03:49PM
great. RE the PET interactive ones question, does each notebook run with its own kernel? If not, I'd rather avoid it. It otherwise would become a very large notebook. Maybe we could put some stuff ...more |
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Edoardo Pasca <[log in to unmask]>: May 10 04:14PM
they are here https://github.com/CCPPETMR/SIRF-Exercises/tree/notebook Yes, each notebook runs on a different kernel, and to make a notebook connect to another kernel is quite a ...more |
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evgueni-ovtchinnikov <[log in to unmask]>: May 10 04:08AM -0700
1. corrected 2. need your data to debug 3. slice number means its number in the whole set of slices wherever they come from (different z, different repetition etc.) - do not see how to label slices ...more |
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David Atkinson <[log in to unmask]>: May 10 04:44AM -0700
1. corrected - Thanks 2. need your data to debug - run siemens_to_ismrmrd on this 3D dataset to generate an input h5 file: ...more |
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evgueni-ovtchinnikov <[log in to unmask]>: May 10 05:36AM -0700
2. I do not have siemens_to_ismrmrd - can you not just let me have m3d.h5? By the way, what makes you think the reconstruction succeeded? Can you print image_data.number() and image_data.norm()? ...more |
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Kris Thielemans <[log in to unmask]>: May 10 05:51AM -0700
2. for the data, you have siemens_to_ismrmrd on the VM. would that be ok? 3. let's definitely discuss, but I suppose that the data issue needs to be fixed before the course. can just as well adjust ...more |
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evgueni-ovtchinnikov <[log in to unmask]>: May 10 03:04PM
2. the error is due to failure to read the saved image - have no idea why. for now commented out the reading. 3. the point is - how to adjust. i considered David's suggestions and pointed out at ...more |
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Kris Thielemans <[log in to unmask]>: May 10 07:29AM -0700
Due to #157 we have to rely on latest STIR, so this could be done now. @evgueni-ovtchinnikov, please assign to feasible milestone (I'm not sure how much effort this is). -- You are receiving this ...more |
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evgueni-ovtchinnikov <[log in to unmask]>: May 10 02:38AM -0700
``` VER=1.1.0-rc.1 ``` 1. SIRF - [ ] update `CHANGES.md` - [ ] update `NOTICE.txt` - [ ] update version numbers in [SIRF/CMakeLists.txt](CMakeLists.txt) - [ ] update version numbers in ...more |
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Kris Thielemans <[log in to unmask]>: May 10 02:29PM
@paskino, @evgueni-ovtchinnikov, can we start completing some of the trivial ones? No tagging etc yet. -- You are receiving this because you are subscribed to this thread. Reply to this email ...more |
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Kris Thielemans <[log in to unmask]>: May 10 04:51AM -0700
confirmed that this is still the case. This must be a STIR bug. -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: ...more |
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Kris Thielemans <[log in to unmask]>: May 10 07:21AM -0700
fixed on STIR master at https://github.com/UCL/STIR/commit/cc7c16451abe1af7d0c02cc790f5d0752c2a7b68. We therefore need to bump the `default_STIR_TAG` in the superbuild -- You are receiving ...more |
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evgueni-ovtchinnikov <[log in to unmask]>: May 10 03:41AM -0700
grayscale plotting enabled -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: ...more |
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evgueni-ovtchinnikov <[log in to unmask]>: May 10 03:41AM -0700
Closed #168. -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/CCPPETMR/SIRF/issues/168#event-1619523724 ...more |
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evgueni-ovtchinnikov <[log in to unmask]>: May 10 02:21AM -0700
to show the boundary between repetitions - say, for the range (250,254) all data would be zeros except encoding - not very illuminative docstrings corrected -- You are receiving this because you ...more |
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evgueni-ovtchinnikov <[log in to unmask]>: May 10 09:21AM
Closed #166. -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/CCPPETMR/SIRF/issues/166#event-1619392919 ...more |
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David Atkinson <[log in to unmask]>: May 10 02:41AM -0700
This range sets the variable 'where' which then affects a number of print statements but not any numerical output? At first sight the docstring is confusing - to me it implies the range of phase ...more |
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evgueni-ovtchinnikov <[log in to unmask]>: May 10 02:51AM -0700
Yes, you are right, no data is affected. To remind you, the docstring says: -r <rnge>, --range=<rnge> range of readouts to examine as string '(a,b)' If you find 'readouts to examine' not clear ...more |
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