TOF

[ALEXJAZZ008008]

partially addresses issues in #315 and #390

[KrisThielemans]

Looks good to me! Hopefully you're getting better results now...

I think we'll need to do the same as in STIR: get_num_sinograms is as it is now, but add get_num_non_TOF_sinograms (in SIRF with capital, as we're using get_num_TOF_bins). Will need some doxygen on the C++-side then to clarify. Will also need to be exposed to Python and MATLAB (with appropriate doc).

I found a few other places where the documentation will have to say something like number of (non-TOF) sinograms. Search for TOF in:

• src/xSTIR/mSTIR/+sirf/+STIR/AcquisitionData.m
• examples/Python/PET/input_output.py
• examples/Matlab/PET/acquisition_data_from_scanner_info.m

@evgueni-ovtchinnikov, could you help with that?

This isn't urgent of course, as we cannot merge this until STIR TOF has been merged.

Potential strategy: add dummy TOF functions (get_num_tof_poss and get_num_non_tof_sinograms) on STIR master, such that this could be merged already. Good idea?

[KrisThielemans]

will have to modify .travis.yml to use the TOF STIR branch I guess

[KrisThielemans]

Potential strategy: add dummy TOF functions (get_num_tof_poss and get_num_non_tof_sinograms) on STIR master, such that this could be merged already. Good idea?

I am doing this on release_4. UCL/STIR#762

This should allow us to merge this SIRF PR

[KrisThielemans]

UCL/STIR#762 is merged on STIR release_4. This now needs to be merged to master. I've pushed my updates here already anyway, so expect the Travis job that uses STIR master to fail. Otherwise, I think this is ready.

[KrisThielemans]

Happy to say that all builds succeeded, except when DEVEL_BUILD=ON.

Of course, none of the builds actually test TOF functionality.

[KrisThielemans]

pending UCL/STIR#764

[KrisThielemans]

This should be fine now but running one more check.

@evgueni-ovtchinnikov do we need any (urgent) changes on the MATLAB side?

[KrisThielemans]

@evgueni-ovtchinnikov I'll merge this. Please make any urgent changes for MATLAB separately. Otherwise, add them to #555

[evgueni-ovtchinnikov]

@KrisThielemans MATLAB scripts run ok except for osem_reconstruction.m (cf. #687) and reconstruct_from_listmode.m, which throws ChainedBinNormalisation: both first and second have a calibration. The factor would be applied twice (and so does respective Python script).

[KrisThielemans]

@danieldeidda This will be due to UCL/STIR#672 I guess. this shouldn't have happened I believe

[danieldeidda]

Mh yes definetely because of UCL/STIR#672

[danieldeidda]

@danieldeidda This will be due to UCL/STIR#672 I guess. this shouldn't have happened I believe

I think the problem is that I check that calib_factor>0 but than set it to one for ECAT etc.

[KrisThielemans]

@evgueni-ovtchinnikov could you confirm which commit you are on in STIR when this happens? We think that it shouldn't happen (on current master). (you could go to sources/STIR and go git log for instance)

[KrisThielemans]

@evgueni-ovtchinnikov also, can you give some more output to tell us when this happened

[evgueni-ovtchinnikov]

commit fe1af133aee5c44ce9fecd50993612f47d274b44
Merge: e6d40fe 9eb4aef
Author: Kris Thielemans KrisThielemans@users.noreply.github.com
Date: Tue Jan 5 20:13:13 2021 +0000

Merge pull request #787 from danieldeidda/isotopeInInterfile785

fixes #785: moving isotope name to `InterfileHeader`

[evgueni-ovtchinnikov]

reconstruct_from_listmode
loading miutilities library...
loading msirf library...
loading mstir library...

WARNING: KeyParser: keyword 'isotope name' already registered for parsing, overwriting previous value

WARNING: KeyParser: keyword '%comment' already registered for parsing, overwriting previous value
LmToProjData NOT Using FRAME_BASED_DT_CORR
converting raw data to sinograms...

Processing time frame 1

500000 events stored
1000000 events stored
1500000 events stored
Number of prompts stored in this time period : 1560300
Number of delayeds stored in this time period: 0
Last stored event was recorded before time-tick at 50 secs
Total number of counts (either prompts/trues/delayeds) stored: 1560300

This took 4.34375s CPU time.
estimating randoms...
processed frame 1
Last stored event was recorded after time-tick at 49.999 secs
Total number of prompts/trues/delayed stored: 410099

This took 2.40625s CPU time.
Starting iteration 1 KL 247.329
Starting iteration 2 KL 18.2321
Starting iteration 3 KL 0.663053
Starting iteration 4 KL 0.0278851
Starting iteration 5 KL 0.00129212
Starting iteration 6 KL 4.15109e-05
Starting iteration 7 KL 2.26989e-06
Starting iteration 8 KL 3.85613e-08
Starting iteration 9 KL 4.10926e-09
Starting iteration 10 KL 5.79696e-10
CPU time 42.9844 secs
acquisition data dimensions: 344 x 126 x 357 x 1
image dimensions: 127 x 127 x 127
applying attenuation (please wait, may take a while)...

ERROR: ChainedBinNormalisation: both first and second have a calibration factor. The factor would be applied twice
??? ??? ChainedBinNormalisation: both first and second have a calibration factor. The factor would be applied twice exception thrown at line 457 of C:\Users\wps46139\Documents\GitHub\build\SIRF-SuperBuild\sources\SIRF\src\xSTIR\cSTIR\cstir.cpp,
the reconstruction engine output may provide more information
error id is AcquisitionSensitivityModel:ctor:error

[danieldeidda]

@KrisThielemans MATLAB scripts run ok except for osem_reconstruction.m (cf. #687) and reconstruct_from_listmode.m, which throws ChainedBinNormalisation: both first and second have a calibration. The factor would be applied twice (and so does respective Python script).

The issue has been fixed by UCL/STIR#800