STIR: Software for Tomographic Image Reconstruction

These notes only describe a summary of the changes. Please check documentation/release_4.1.htm

• Almost all modifications and additions since version 0.92 in 2001 are now licensed under the Apache 2.0 license as opposed to the (L)GPL.
• Reading of GE HDF5 data (GE fileformat RDF 9) for the GE Signa PET/MR and recent GE PET/CT scanners (but depending on their software version). We currently read listmode, sinograms and calibration files (except for the WCC (well-counter calibration) files). This code is TOF-ready, but TOF is not enabled pending merge of the TOF Pull Request. Therefore, all reconstructions will be non-TOF.
• Addition of the Relative Difference Prior [J. Nuyts, et al., 2002].
• Interfile and ITK image IO now understand some date/time fields. This required a change to our Interfile version specification to be able to handle time-zones. These can now be added via the same suffix as used by DICOM, e.g. 10:01:01.00+0130.
• NiftyPET's GPU projectors have been wrapped.
• stir_math now supports the --output-format option for dynamic and parametric images as well. (An example file using the Multi format is given in the examples/samples folder).
• Added a utility list_lm_info - A new script create_fdef_from_listmode.sh that can be used to create a single-time frame definition file for a given listmode file.
• Implementation of ax+by methods xapyb and sapyb where a and b can be scalar or vector types.
• The LmToProjData hierarchy has a new member function set_up(), and more set_*functions, such that it can be used without parsing.

• Modification of log-likelihood computation to use more doubles, improving numerical stability, see PR 528.
• Reconstruction algorithms perform now more checks during set_up() etc. However, this means that you have to call set_up() also for analytic reconstruction algorithms. (This was already documented, but not yet enforced).
• copy energy information from the template in the forward_project utility.
• PET scatter improvements:
  • the scatter estimation parsing now prefers specifying normalisation and attenuation via two separate keywords (as opposed to via a chained bin normalisation), (keyword normalisation type) and the attenuation factors. Check the updated sample file. The old parsing keyword Bin normalisation type will still work but is deprecated and will be removed in a future version.
    • scatter estimation uses now more defaults such that you need to have less files.
    • ScatterEstimation has now many more set* functions such that most (all?) parameters can be set from C++/Python (i.e. without parsing).
• The SinglesRates hierarchy has been revised. The SinglesRates classes assumed that stored singles were rates but in practice were totals-per-time-interval (for both ECAT7 and RDF9). It is convenient to be able to access totals and rates, so SinglesRates has now get_singles (returning the singles in the time interval) and get_singles_rates (returning the rate per second). Due to the previous confusion, "client"-code will need to be adapted to use either get_singles or get_singles_rate, depending on what is needed