Merge pull request #1433 from KrisThielemans/gitFameUpdates

updates to CITATION, git fame etc for release 6.1

Author: KrisThielemans

.git-blame-ignore-revs

@@ -0,0 +1,8 @@
+# change to Apache 2.0 license
+47d1aa5f302c5b6b579de176535e01aa97d1ff27
+# run clang-tidy --modernize-use-override
+8af125617a113724f52d26e991bfc6c36abb952f
+# manual fixes in stir_experimental and clang-tidy modernize-use-override
+c5a1c6bc29d3f24d8fdb5c198946ec9580947257
+# stir_maintenance run pre-commit
+88f4ce70929a41c745fc39030e90c87bfaf046b7

.mailmap

@@ -37,6 +37,7 @@ Matthias Ehrhardt <m.ehrhardt@bath.ac.uk> <m.ehrhardt@bath.ac.uk>
 Matthias Ehrhardt <m.ehrhardt@bath.ac.uk> <m.j.ehrhardt@damtp.cam.ac.uk>
 Nikos Efthimiou <nikos.efthimiou@gmail.com> <nikos.efthimiou@gmail.com>
 Nikos Efthimiou <nikos.efthimiou@gmail.com> <NikEfth@users.noreply.github.com>
+Nikos Efthimiou <nikos.efthimiou@gmail.com> <n.efthymiou@hull.ac.uk>
 Ottavia Bertolli <ottavia.bertolli.13@ucl.ac.uk>
 Palak Wadhwa <pwadhwa351@gmail.com> <38861704+pwadhwa351@users.noreply.github.com>
 Palak Wadhwa <pwadhwa351@gmail.com> <medpwad@leeds.ac.uk>

CITATION.cff

@@ -32,31 +32,31 @@ authors:
     - family-names: Jehl
       given-names:  Markus
       affiliation:  Positrigo
+    - family-names: Borgeaud
+      given-names:  Tim
+      affiliation:  Hammersmith Imanet Ltd
     - family-names: Strugari
       given-names:  Matthew
       affiliation:  Dalhousie University (Canada)
     - family-names: Khateri
       given-names:  Parisa
       affiliation:  ETH Zuerich
-    - family-names: Beisel
-      given-names:  Tobias
     - family-names: Wadhwa
       given-names:  Palak
       affiliation:  University of Leeds (UK)
-    - family-names: Borgeaud
-      given-names:  Tim
-      affiliation:  Hammersmith Imanet Ltd
+    - family-names: Beisel
+      given-names:  Tobias
     - family-names: Emond
       given-names:  Elise
       affiliation:  University College London
-    - family-names: Jacobson
-      given-names:  Matthew
     - family-names: Gillman
       given-names:  Ashley
       orcid:        'https://orcid.org/0000-0001-9130-1092'
       affiliation:  >-
         Commonwealth Scientific and Industrial Research
         Organisation, and University of Queensland
+    - family-names: Jacobson
+      given-names:  Matthew
     - family-names: Zverovich
       given-names:  Alexey
       affiliation:  Brunel University (UK)
@@ -113,6 +113,9 @@ authors:
     - family-names: Valente
       given-names:  Patrick
       affiliation:  Brunel University (UK)
+    - family-names: Jurjew
+      given-names:  Nicole
+      affiliation:  University College London
     - family-names: Ovtchinnikov
       given-names:  Evgueni
       orcid:        'https://orcid.org/0000-0002-9359-6514'
@@ -127,9 +130,6 @@ authors:
     - family-names: Belluzzo
       given-names:  Damiano
       affiliation:  Hospedale San Raffaele Milano (Italy)
-    - family-names: Jurjew
-      given-names:  Nicole
-      affiliation:  University College London
     - family-names: Ching
       given-names:  Daniel
     - family-names: Hague
@@ -178,10 +178,14 @@ authors:
 identifiers:
     - type: doi
       value: 10.1088/0031-9155/57/4/867
+    - type: doi
+      value: 10.3389/fnume.2023.1134774
     - type: doi
       value: 10.1186/s40658-019-0248-9
     - type: doi
       value: 10.3390/jimaging8060172
+    - type: doi
+      value: 10.1088/1361-6560/aaf9b9
     - type: doi
       value: 10.1109/NSSMIC.2018.8824341
     - type: doi

documentation/credits.htm

@@ -116,9 +116,9 @@ <h2>contributions since the PARAPET EU project (April 2000)</h2>
     Roethlisberger, Michael
 
 16. Positrigo, Switserland
-    SWIG improvements and "blocks on cylindrical" testing
-    Mikhaylova, Ekaterina
+    SWIG improvements, "blocks on cylindrical" testing and fixes
     Jehl, Markus
+    Mikhaylova, Ekaterina
     Fisher, Jannis
 
 17. National Physical Laboratory, UK
@@ -132,7 +132,8 @@ <h2>contributions since the PARAPET EU project (April 2000)</h2>
 
 19. University College London, UK
     (2013-2024)
-    scatter updates, dynamic data updates, OPENMP, PLS, RDP etc priors, reconstruction hierarchy, Siemens ECAT8 support etc
+    scatter updates, dynamic data updates, OPENMP, PLS, RDP etc priors, reconstruction hierarchy, Siemens ECAT8 support,
+    TOF support, parallelproj integration etc
     pinhole SPECT modelling
     help with integration and general maintenance
     Brown, Richard

documentation/history.htm

@@ -11,6 +11,7 @@ <h1>History of public releases of the STIR software</h1>
 The following links give you a summary what has changed. However,
 the ChangeLog is the definite (but tedious) information.
 <ul >
+<li><a href="release_6.1.htm">version 6.1.0 (dated 16 May 2024)</a></li>
 <li><a href="release_6.0.htm">version 6.0.0 (dated 07 February 2024)</a></li>
 <li><a href="release_5.2.htm">version 5.2.0 (dated 30 October 2023)</a></li>
 <li><a href="release_5.1.htm">version 5.1.2 (dated 10 September 2023)</a></li>
@@ -49,7 +50,7 @@ <h1>History of public releases of the PARAPET software</h1>
 
 <!-- Created: Wed Jul 19 16:03:02 BST 2000 -->
 <!-- hhmts start -->
-Last modified: 7 February 2024
+Last modified: 16 May 2024
 <!-- hhmts end -->
   </body>
 </html>

documentation/release_6.1.htm

@@ -29,7 +29,7 @@ <h2>Overall summary</h2>
 <h2>Patch release info</h2>
 <ul>
   <li>
-    6.1.0 released 15/05/2024<br>
+    6.1.0 released 16/05/2024<br>
     <a href="https://github.com/UCL/STIR/milestone/10">GitHub Milestone 6.1</a>
   </li>
   <!--
@@ -88,9 +88,17 @@ <h3>Bug fixes</h3>
   </li>
   <li>
       Our checks for determining system byte-order were out-of-date and in particular did not work on MacOS 14 on ARM.
-      We now use CMake's <code>CMAKE_CXX_BYTE_ORDER</code> (available since CMake 3.20).
-      See <a href=https://github.com/UCL/STIR/pull/1412>PR #1412</a>.
+      We now use CMake's <code>CMAKE_CXX_BYTE_ORDER</code> (available since CMake 3.20). This could potentially affect reading of list-mode data
+      (which would otherwise be garbled).
+      <br>
+      Fixed in <a href=https://github.com/UCL/STIR/pull/1412>PR #1412</a>.
   </li>
+  <li>
+    The listmode objective function did not loop over TOF bins when computing the Hessian. This would give different results in OSSPS
+    for computing the "denominator".
+    <br>
+    Fixed in <a href=https://github.com/UCL/STIR/pull/1427>issue #1427</a>.
+    </li>
 </ul>
 
 <h3>Known problems</h3>
@@ -108,10 +116,16 @@ <h3>Backward incompatibities</h3>
     </li>
 </ul>
 
-<h3>New functionality</h3>
+<h3>Bug fixes</h3>
 <ul>
-<li>
-</li>
+  <li>
+    <code>PoissonLogLikelihoodWithLinearModelForMeanAndProjData</code> had a (minor?) problem with TOF data
+    that when computing the gradient, the normalisation object was not set-up with the TOF data,
+    but non-TOF instead. This did not happen in our normal reconstruction code, and would have thrown an error
+    if it occured.
+    <br>
+    Fixed in <a href=https://github.com/UCL/STIR/pull/1427>issue #1427</a>.
+  </li>
 </ul>
 
 

scripts/maintenance/git-fame.sh

@@ -17,6 +17,7 @@
 # Note that various files were apparently not in git before 2003 (rel_1_10) (they were in CVS).
 # Also, some files did not have correct authorship.
 # The output therefore needs manual ordering (see below)
+git config --local blame.ignoreRevsFile .git-blame-ignore-revs
 git fame -wMC  --excl '\.(eps|root|ahv|hv|v|hs|s|scan|l|hdr|rtf|gz|if|pdf|safir|options|png|cls|sty)$|external_helpers|crystal_map|collimator.*txt|Doxyfile.in|LICENSE.txt|LICENSES' \
   | tee git-fame-output.txt
 exit

scripts/maintenance/make_distribution.sh

@@ -64,7 +64,7 @@ set -e
 #fi
 
 
-read -p "Did you update CMakeLists.txt, version numbers in \*tex files, documentation/history.htm, .zenodo.json? (press Ctrl-C if not)"
+read -p "Did you update CMakeLists.txt, version numbers in \*tex files, documentation/history.htm, CITATION.cff? (press Ctrl-C if not)"
 
 mkdir -p ${DISTRIB}
 cd ${DISTRIB}