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Modifications for psmr2024#1430

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NikEfth wants to merge 83 commits intomasterUCL/STIR:masterfrom modifications_for_psmr2024UCL/STIR:modifications_for_psmr2024Copy head branch name to clipboard

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Commits on Mar 26, 2024

• Adding support for singleTOF scanner.

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Commits on May 15, 2024

• Fast reconstruction for LAFOV scanners

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Commits on May 16, 2024

• Update src/buildblock/ProjDataInfo.cxx

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• Update src/include/stir/ProjDataInfo.inl

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• Update src/recon_buildblock/ProjMatrixByBin.cxx

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• Minor fixes and comments.

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• Minor fixes and executable to cache listmode files without reconstruction

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• Update CMakeLists.txt

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• Update src/IO/InterfileHeader.cxx

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• Minor fixes

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• Merge branch 'master' into modifications_for_psmr2024

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• Split GeneralisedPriorTests into several classes

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• fix abs() bug for RDP and slightly cleaner code

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• change RDP Hessian behaviour at 0,0 when epsilon==0

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• extra tests for the Relative Difference Prior

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• make epsilon in numerical test for prior gradient a bit smaller

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• fix and document RDP large limit test for numerical error

  

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• update RDP doc [ci skip]

  

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• increase numerical precision of priors

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• [GHA] remove explicit setting of xcode version

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• update Byte Order compile-time checks

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• fix white-space

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• List-mode objective function: always uses OpenMP for gradient

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• use more local variables in LM_distributable_computation

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• prepare LM_distributable function for Hessian

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• minor clean-up and clarifications

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• LM_listmode_function: implement Hessian and move functions

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• fix error when OpenMP is not present

  

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• Add compute_gradient* (as opposed to only subset)

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• Move common test to ObjectiveFunctionTests

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• add numerical test for accumulate_Hessian_times_input

  

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• fix sign of LM Hessian

  

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• LM obj-fun: add value() and tests

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• LM objfun tests slightly better diagnostics

  

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• [GHA] upload ctest artefact if failure

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• add "increment" test for gradient (enabled for LM data)

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• [GHA] disabled LM objfunc test on MacOS

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• fix return value FastErf::get_maximum_sample_value

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• [CMake] force C++ version for more recent ROOT

  

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• update to 6.1 and minor doc improvements

  

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• minor changes preparing for 6.1

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• Changing all occurrences of abs() to std::abs() (#1425)

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• add TOF loop in computation of Hessian for projdata

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• fix set_up of norm in TOF ProjData gradient

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• small rationalising of warnings

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• let git blame ignore some maintenance commits

  

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• updates to release notes

  

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• update CITATION.cff according to git-fame

  

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• small change to credits

  

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• update history for release 6.1

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• change comment to avoid confusing doxygen [ci skip]

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• Merge remote-tracking branch 'refs/remotes/origin/modifications_for_psmr2024' into modifications_for_psmr2024

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Commits on May 17, 2024

• New utility to convert ProjData to FanProjData3D.

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• Added option to load the model fanprojdata from the disk.

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• Update src/buildblock/Scanner.cxx

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• Fixes for test_time_of_flight.

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• minor fix

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• Fix to pass recon tests

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• find ML normalization from listmode data.

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• Parallelization changes and labels

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• Important fix.

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• OpenMP parallelise Array::sum/find_max/find_min

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• parallelise some functions in ML_norm

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• ML_norm estimation: avoid doing some block calculations if !do_block

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• some ML_norm parallelisations

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• set KL_threshold to avoid problems

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Commits on May 18, 2024

• More parallelization.

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• small fix

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• fixes minor

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• parallellized apply_geo_norm

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• Fix single TOF position

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• Print TOF

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• extra documentation for ML_estimate_component_based_normalisation

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• [SWIG] expose ML_estimate etc.

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• remove hard-wired 50 threads

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• Some restructuring, needed.

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• Merge remote-tracking branch 'refs/remotes/origin/modifications_for_psmr2024' into modifications_for_psmr2024

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Commits on May 19, 2024

• fix writing of single-TOF bin data

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• another fix on tof data

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Commits on Jun 1, 2024

• Merge remote-tracking branch 'origin/master' into modifications_for_psmr2024

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• fix Interfile writing of TOF data with 1 TOF bin

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• replace std::cout calls with info()

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Commits on Jun 12, 2024

• Merge remote-tracking branch 'origin/master' into modifications_for_psmr2024

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