[SyneRBI/SIRF] Continue working on moving Challenge data preparation utilities to SIRF. (PR #1266)
Evgueni Ovtchinnikov
Changes in this pull request
Testing performed
Related issues
PR #1241
Checklist before requesting a review
- I have performed a self-review of my code
- I have added docstrings/doxygen in line with the guidance in the developer guide
- I have implemented unit tests that cover any new or modified functionality
- The code builds and runs on my machine
- CHANGES.md has been updated with any functionality change
Contribution Notes
Please read and adhere to the contribution guidelines.
Please tick the following:
- The content of this Pull Request (the Contribution) is intentionally submitted for inclusion in SIRF (the Work) under the terms and conditions of the Apache-2.0 License.
You can view, comment on, or merge this pull request online at:
https://github.com/SyneRBI/SIRF/pull/1266
Commit Summary
- c25c1e0 started moving Challenge nema-data utilities to SIRF
- a2691ac reimplemented two nema data processing functions in SIRF (C++)
- df408d2 moved the functions of the previous commit to more sensible places
- f7c417d added C++ code for testing ScatterEstimator in test7.cpp
- e6300c7 rewrote all my Challenge functions in C++, hit incompatible proj data bug [ci skip]
- ab00641 fixed incompatible proj data bug
- a5e8ba0 added simpler set up for PETAcquisitionSensitivityModel
- c4b254c implemented Python interface for sinograms_and_randoms_from_listmode
- 83fbbd0 implemented Python interface to compute_ac_factors (not tested yet)
- ea6a736 fixed typos in STIR.py lines 1740 and 1741
- de8e615 interfaced all C++ nema-data utilities in SIRF into Python
- e40bdc1 made some corrections/amendments suggested by KT
- 4db5527 attended to Codacy issues
- 8866464 removed hardwired prompts prefix from prompts and randoms computation code
- 61a60f9 documented the type of objects returned by compute_attenuation_factors() [ci skip]
- a7b4756 removed unused import of existing_filepath from test_data_preparation.py
- 413808f compute_ac_factors now gets PETAcquisitionModel as an argument
- b5a4b8d removed commented-out member function of ListmodeToSinograms
- 1b30b55 attended to reviewers remarks on computing attenuation factors
- d2585d9 simplified compute_ac_factors methods (C++/C/Python)
- 85ebbde attended to reviewer's comments and suggestions
- d43062e updated CHANGES.md
- 7e44d4e added methods for computing prompts only from list-mode data
- fc7eda8 corrected the return of prompts_from_listmpde [ci skip]
- e8b4388 added modality() method to AcquisitionData objects
- d4dcb6e commented out no longer used functions
File Changes
(13 files)
- M CHANGES.md (5)
- M examples/Python/PET/acquisition_model.py (1)
- A examples/Python/PET/test_data_preparation.py (74)
- M examples/Python/SPECT/acquisition_model.py (2)
- M src/iUtilities/include/sirf/iUtilities/DataHandle.h (17)
- M src/xSTIR/cSTIR/cstir.cpp (55)
- M src/xSTIR/cSTIR/cstir_p.cpp (2)
- M src/xSTIR/cSTIR/include/sirf/STIR/cstir.h (12)
- M src/xSTIR/cSTIR/include/sirf/STIR/stir_data_containers.h (5)
- M src/xSTIR/cSTIR/include/sirf/STIR/stir_x.h (834)
- M src/xSTIR/cSTIR/tests/CMakeLists.txt (6)
- A src/xSTIR/cSTIR/tests/test7.cpp (151)
- M src/xSTIR/pSTIR/STIR.py (44)
Patch Links:
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Evgueni Ovtchinnikov
@evgueni-ovtchinnikov pushed 2 commits.
- 4ef1fbb commented out no longer used functions in stir_x.h
- 118f4f0 removed commented out lines confusing Codacy
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Kris Thielemans
I won't have time to review this today, but I think you've addressed my main concerns, so go ahead when you're ready.
Given the tortuous history here, I suggest a squash-merge, but please edit the commit message such that it not just a list of all the attempts, but an overall conclusion. (Note that I see you're adding modality, which is great, so add that to the CHANGES.md).
thanks!
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Kris Thielemans
looks like you still need to remove examples/Python/PET/test_data_preparation.py
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Evgueni Ovtchinnikov
@evgueni-ovtchinnikov pushed 2 commits.
- 5444647 removed outdated PET/test_data_preparation.py [ci skip]
- 99314f3 updated CHANGES.md [ci skip]
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Evgueni Ovtchinnikov
Merged #1266 into master.
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