Radionuclide code improvements #1026
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It seems that I've been a bit too enthusiastic with adding even for the tests where Appveyor (i.e. no JSON) is failing with https://ci.appveyor.com/project/KrisThielemans/stir/builds/43273181/job/r0j359avdtqrl8iw#L133 and also has warnings about unused variables. |
- better handling of defaults in RadionuclideDB ("default" or "")
- more checks/info when JSON support is disabled
- more information when JSON parsing failed
- more doxygen
this will likely fail because of 2 reasons: - modality keyword problems - when test code is run before install, it won't find the JSON files
changed keV and branching_ratio
ctest can be run before installation, so we need to set the STIR_CONFIG_DIR environment variable to where the JSON files are in the source directory
Calling error() was too drastic as most files will not have the necessary info. Instead use warning() and return default-constructed Radionuclide (i.e. set the "unknown")
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when parsing output of list_projdata_info, explicitly look for the "sum". This solves a problem when info() statements throw up lots of other things.
The database now contains multiple decays per radioisotope. This will allow having multiple gamma energies for one radionuclide.
As we include nlohmann/json.hpp in RadionuclideDB.h, it needs to be a public dependency.
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@danieldeidda I've changed the database format rather drastically. I think this makes more sense and is more extendible. Obviously that needed code changes. Could you have a look please? (I've added a test on Y90, so that seems to work ok). |
awk processing depended on info statements. Now only look at lines that contain min/max
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@danieldeidda let me know if you tested it. I'd like to merge this tomorrow or the day after. |
set verbosity level if info() statements to 3, to avoid too much output
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Merging as tests work, @danieldeidda please create a new issue etc if you discover any problems. |
I created a test for Radionuclide code and then had to fix various things to get it to work/understand.
The test fails locally because the JSON file has
PETandnucmedbutImagingModalityusesPTandNMas strings. We could fix this in the code or the JSON file. Not sure what the best option is. @danieldeidda ?In addition, I think this will fail on Github Actions etc as the test code is run before install, so it won't find the JSON files.