Skip to content

Support for input from PENNPET Explorer#1028

Merged
KrisThielemans merged 31 commits intoUCL:masterfrom
NikEfth:upenn_io
May 14, 2022
Merged

Support for input from PENNPET Explorer#1028
KrisThielemans merged 31 commits intoUCL:masterfrom
NikEfth:upenn_io

Conversation

@NikEfth
Copy link
Copy Markdown
Collaborator

@NikEfth NikEfth commented Apr 26, 2022

Successful unlisting of UPENN acquired data
Support for the 5-ring variant (with gaps)

Copy link
Copy Markdown
Collaborator

@KrisThielemans KrisThielemans left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

house-keeping comments. I didn't really check the actual code. Some general comments

  • license info is sometimes LGPL
  • copyright/authorship header is sometimes out-of-date
  • we should never call std::exit in library functions, as that will crash python etc. Call error() instead

Comment thread src/IO/InputStreamWithRecordsFromUPENN.cxx
Comment thread src/IO/InputStreamWithRecordsFromUPENN.cxx
Comment thread src/IO/InputStreamWithRecordsFromUPENN.cxx Outdated
Comment thread src/IO/InputStreamWithRecordsFromUPENNbin.cxx Outdated
Comment thread src/IO/InputStreamWithRecordsFromUPENNtxt.cxx Outdated
Comment thread src/listmode_buildblock/CListModeDataPENN.cxx Outdated
Comment thread src/listmode_buildblock/CListModeDataPENN.cxx Outdated
Comment thread src/listmode_buildblock/CListRecordPENN.cxx Outdated
Comment thread src/listmode_buildblock/CListRecordPENN.cxx Outdated
Comment thread src/utilities/UPENN/CMakeLists.txt Outdated
NikEfth and others added 7 commits April 26, 2022 23:47
Co-authored-by: Kris Thielemans <[email protected]>
Co-authored-by: Kris Thielemans <[email protected]>
*. Fixed: 
  - License is somethings LGPL
  - copyright / authorship 
  - use error() instead of std::exit()
  - Some variables were shadowed. 
  - Added doxygen comments. 
  - Clean up
@KrisThielemans
Copy link
Copy Markdown
Collaborator

could you "resolve" comments when addressed? Makes it easier for me to find what I still need to look at. sorry

@NikEfth
Copy link
Copy Markdown
Collaborator Author

NikEfth commented Apr 27, 2022

I applied your comments.

@KrisThielemans
Copy link
Copy Markdown
Collaborator

thanks. could you take a look at why the CI tests fail?

@NikEfth
Copy link
Copy Markdown
Collaborator Author

NikEfth commented Apr 27, 2022

WARNING: Scanner UPENN_5rings: inconsistent transaxial block info

@NikEfth
Copy link
Copy Markdown
Collaborator Author

NikEfth commented Apr 27, 2022

The test_Scanner passes at my PC, now.

* The utility can also decompress on-the-fly, introduce gaps
Comment thread src/test/test_Scanner.cxx
@KrisThielemans
Copy link
Copy Markdown
Collaborator

I see you've introduced a new "module" concept. I have no idea what that is supposed to be unfortunately and am therefore reluctant. (I see that by using num*modules=0 by default, it doesn't change other scanners, but that doesn't help me understand what this is supposed to be).

Also, I don't see what is different between this scanner and others? I appreciate that you probably want to have gaps between buckets and not blocks, but maybe you can fake this at the moment by saying that one STIR block is the actual physical bucket?

Copy link
Copy Markdown
Collaborator

@KrisThielemans KrisThielemans left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

some more house-keeping but nearly done, except for Scanner mods, which I don't understand yet.

Note that probably all doxygen ingroup statements should be listmode, not IO``

Could you try to group updates in as few commits as possible. Also, ideally only push when done (to avoid multiple CI runs).

Comment thread src/IO/InputStreamWithRecordsFromUPENN.cxx
Comment thread src/IO/InputStreamWithRecordsFromUPENNbin.cxx Outdated
Comment thread src/IO/InputStreamWithRecordsFromUPENNbin.cxx Outdated
Comment thread src/IO/InputStreamWithRecordsFromUPENNbin.cxx Outdated
Comment thread src/IO/InputStreamWithRecordsFromUPENNtxt.cxx
Comment thread src/IO/InputStreamWithRecordsFromUPENNtxt.cxx Outdated
Comment thread src/IO/InputStreamWithRecordsFromUPENNtxt.cxx Outdated
Comment thread src/include/stir/IO/InputStreamWithRecordsFromUPENNbin.inl Outdated
Comment thread src/include/stir/listmode/CListModeDataPENN.h Outdated
Comment thread src/listmode_buildblock/CListModeDataPENN.cxx Outdated
NikEfth and others added 7 commits May 12, 2022 11:06
This reverts commit 17993b7.
* Reverted the Scanner mods (I don't really like the current scanner descriptions)
* Pass test_Scanner
* Updated and faster conv_UPENN_projdata_to_STIR
* fixed in IO
Copy link
Copy Markdown
Collaborator

@KrisThielemans KrisThielemans left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

it's looking good!

There's 2-3 unresolved very comments left (clock on the "conversations" in "Files changed").

squash-merge this ok?

Comment thread src/listmode_buildblock/CListModeDataPENN.cxx Outdated
Comment thread src/test/test_Scanner.cxx
@NikEfth
Copy link
Copy Markdown
Collaborator Author

NikEfth commented May 13, 2022

I don't see any other comments.
squash works for me.

Comment thread src/include/stir/IO/PENNListmodeInputFileFormat.h Outdated
Comment thread src/include/stir/IO/InputStreamWithRecordsFromUPENNbin.inl Outdated
@KrisThielemans KrisThielemans merged commit 2fd9083 into UCL:master May 14, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants