reading of PETSIRD list-mode function by KrisThielemans · Pull Request #1604 · UCL/STIR

KrisThielemans · 2025-07-16T13:22:37Z

WIP

…its from classes

…D listmode data classes.

… information.

STIR no longer vendors PETSIRD as a submodule. PETSIRD integration is expected via an external installation using find_package(PETSIRD).

Introduced generic tests

1. Figuring out flattened geometries from STIR2PETSIRD converter. 2. Fixing detection efficiency lookup in BinNormalisationFromPETSIRD. Still some normalisation issues to be resolved. 3. Get / Set positions for PETSIRD Listmode data.

KrisThielemans

This is mostly clean. thanks! A lot of my comments are housekeeping, but there are some important ones. Major thing is to keep this PR separate from other things (I won't accept this PR with them...), for example:

there are some changes here for set_proj_data_info which probably came from another PR. Maybe they'll disappear when you merge master here
there are changes here to cope with even number of TOF bins. They might be good, but it doesn't have anything to do with PETSIRD.
there's some changes in find_basic_vs_nums... which don't belong here
I see no reason to make InputFormat::can_read non-const. If this is really required for PETSIRD, please explain. We should then work around it.

I guess the BinNormalisation isn't finished yet. I would suggest we currently call error and do it in a separate PR.

KrisThielemans · 2026-03-04T08:04:30Z

.github/workflows/build-petsird-stir.yml

+            ref: fix/cmake-export
+            path: PETSIRD
+
+        - name: Checkout Yardl (main)


we can use yardl 0.6.6 now, no need to self-build

KrisThielemans · 2026-03-04T08:08:58Z

src/buildblock/PETSIRDInfo.cxx

+    return false;
+  };
+
+  std::vector<petsird::ReplicatedDetectorModule> replicated_module_list


why the copy? Can be const auto&?

KrisThielemans · 2026-03-04T08:09:21Z

src/buildblock/PETSIRDInfo.cxx

+void
+PETSIRDInfo::figure_out_block_angles(std::set<float>& unique_angle_modules, const int rot_axis)
+{
+  std::vector<petsird::ReplicatedDetectorModule> replicated_module_list


KrisThielemans · 2026-03-04T08:14:41Z

src/buildblock/PETSIRDInfo.cxx

+  // const int num_ax = blocks_per_bucket_axial * num_axial_crystals_per_block;
+  // const int num_tang = blocks_per_bucket_transaxial * num_trans_crystals_per_block;
+
+  std::cerr << "Tile size (groupSize) = " << groupSize << "\n";


will want to comment this out, or replace with an info call at high verbosity (and sensible text)

KrisThielemans · 2026-03-04T08:15:51Z

src/buildblock/PETSIRDInfo.cxx

+      std::cerr << "Map size mismatch!\n"
+                << "Forward size: " << petsird_to_stir->size() << "\n"
+                << "Reverse size: " << stir_to_petsird->size() << std::endl;
+      error("Forward and reverse maps differ in size");


merge all of that, e.g. using fmt::format as we cannot see stderr in ython for instance

KrisThielemans · 2026-03-04T09:16:30Z

src/recon_test/test_blocks_on_cylindrical_projectors.cxx

  //    rotate by 30 degrees
  phi2 = 30 * _PI / 180;
-  VoxelsOnCartesianGrid<float> image2 = *image.get_empty_copy();
+  VoxelsOnCartesianGrid<float> image2(image); // = *image.get_empty_copy();


changes from other PR?

KrisThielemans · 2026-03-04T09:17:53Z

src/swig/Makefile

-# This is a temporary makefile used for development only.
-# Do not use. Instead, use CMake for building
-SWIG=swig
+# CMAKE generated file: DO NOT EDIT!


certainly cannot have this. We should probably just delete this file (but not in this PR)

KrisThielemans · 2026-03-04T09:18:58Z

.travis.yml

     - *addons_apt_packages
     - [g++-6]
-   env: EXTRA_BUILD_FLAGS="-DDISABLE_CERN_ROOT=1 -DSTIR_OPENMP:BOOL=OFF" CC=gcc-6 CXX=g++-6
+   env: EXTRA_BUILD_FLAGS="-DDISABLE_CERN_ROOT=1 -DSTIR_OPENMP:BOOL=OFF -DDISABLE_PETSIRD:BOOL=ON" CC=gcc-6 CXX=g++-6


forget about .travis.yml, we should delete this file (but not in this PR)

KrisThielemans · 2026-03-04T09:20:13Z

CMakeLists.txt

+    if(TARGET PETSIRD::petsird)
+      get_target_property(_petsird_libs PETSIRD::petsird INTERFACE_LINK_LIBRARIES)
+
+      # --- HDF5 ---
+      if(_petsird_libs MATCHES "HDF5::")
+        if(DISABLE_HDF5)
+          message(STATUS "PETSIRD was built with HDF5 → forcing DISABLE_HDF5=OFF")
+          set(DISABLE_HDF5 OFF CACHE BOOL "disable use of HDF5 libraries" FORCE)
+        endif()
+      endif()
+
+      # --- nlohmann_json (optional but recommended) ---
+      if(_petsird_libs MATCHES "nlohmann_json::")
+        if(DISABLE_NLOHMANN_JSON)
+          message(STATUS "PETSIRD was built with nlohmann_json → forcing DISABLE_NLOHMANN_JSON=OFF")
+          set(DISABLE_NLOHMANN_JSON OFF CACHE BOOL "disable use of nlohmann JSON libraries" FORCE)
+        endif()
+      endif()


I see no reason to do this. It might be that PETSIRD has it, but someone doesn't want to have it in STIR for whatever reason. Let's just cut this

KrisThielemans · 2026-03-04T09:21:03Z

.appveyor.yml

  - mkdir install
  - cd build
-  - cmake .. -GNinja -DCMAKE_C_COMPILER="cl.exe" -DCMAKE_CXX_COMPILER="cl.exe" -DCMAKE_INSTALL_PREFIX="C:\projects\stir\install" -DCMAKE_BUILD_TYPE=%CONFIGURATION%  -DCMAKE_CONFIGURATION_TYPES=%CONFIGURATION% -DSTIR_OPENMP:BOOL=ON -DBUILD_DOCUMENTATION:BOOL=OFF -DBUILD_SWIG_PYTHON:BOOL=ON -DPython_EXECUTABLE=%CONDA_PREFIX%\python.exe -DCMAKE_PREFIX_PATH:PATH="%CONDA_PREFIX%"
+  - cmake .. -GNinja -DCMAKE_C_COMPILER="cl.exe" -DCMAKE_CXX_COMPILER="cl.exe" -DCMAKE_INSTALL_PREFIX="C:\projects\stir\install" -DCMAKE_BUILD_TYPE=%CONFIGURATION%  -DCMAKE_CONFIGURATION_TYPES=%CONFIGURATION% -DSTIR_OPENMP:BOOL=ON -DBUILD_DOCUMENTATION:BOOL=OFF -DDISABLE_PETSIRD:BOOL=ON -DBUILD_SWIG_PYTHON:BOOL=ON -DPython_EXECUTABLE=%CONDA_PREFIX%\python.exe -DCMAKE_PREFIX_PATH:PATH="%CONDA_PREFIX%"


hopefully no need for an explicit DISABLE_PETSIRD. Logic should be that it still works if it's not found

KrisThielemans · 2026-03-04T11:00:36Z

You van have mutable members Kris

________________________________ From: Nikos Efthimiou ***@***.***> Sent: Wednesday, March 4, 2026 10:02:46 AM To: UCL/STIR ***@***.***> Cc: Kris Thielemans ***@***.***>; Author ***@***.***> Subject: Re: [UCL/STIR] reading of PETSIRD list-mode function (PR #1604) ⚠ Caution: External sender @NikEfth commented on this pull request.

________________________________ In src/include/stir/IO/InputFileFormat.h<#1604 (comment)>:

@@ -46,7 +46,7 @@ class InputFileFormat

{ return this->actual_can_read(signature, input); } - virtual bool can_read(const FileSignature& signature, const std::string& filename) const + virtual bool can_read(const FileSignature& signature, const std::string& filename) This was necessary to support both the HDF5 and binary versions of PETSIRD. I could not think another way arround it. — Reply to this email directly, view it on GitHub<#1604 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABQRIHMFCYAB5WGTRVX5QVT4O75MNAVCNFSM6AAAAACBU47CHKVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMZTQOBYGM4DKOJQHE>. You are receiving this because you authored the thread.Message ID: ***@***.***>

KrisThielemans and others added 13 commits July 14, 2025 17:54

add PETSIRD submodule

5a85ad6

* Initial commit that adds PETSIRD support in CMake configuration

561616e

WIP: Subclass CListModeDataSAFIR from CListModeDataBasedOnCoordinateMap.

d6c218a

Update .gitmodules

8ff962a

Remove PETSIRD submodule from .gitmodules

557cf97

Fix the include and link paths

493a0c0

* Minor fix

27ec9f4

creating classes for LM PETSIRD, mainly a copy at this stage

0e0b71b

move cmake importing of sird into lmbuildblock remove: unnecessary b…

6d00cde

…its from classes

correct cmake importing of sird into lmbuildblock. can import binary/

0f9deb2

started reading info from header

3550178

Work in separating the SAFIR from the BasedOnCoordinateMAP and PETSIR…

32daa97

…D listmode data classes.

Merge branch 'PETSIRD' of github.com:UCL/STIR into PETSIRD

b874c8e

KrisThielemans self-assigned this Jul 16, 2025

NikEfth and others added 16 commits July 16, 2025 11:03

Important fix in CListModeDataPETSIRD.inl

ba44a95

* Fixes and interface clean up

0ff78b1

Removed constructor.

f6de251

reading header and extracting scanner info

43febf1

Fixed registries! :)

12e6f57

Merge branch 'PETSIRD' of github.com:UCL/STIR into PETSIRD

828817e

Updates on the interface and CMake

4897222

Compiles and LInks

ddc06a5

Finished all the infrastrucure. We can now focus on reading events,

3a4ee34

reading header and extracting averag position of each detector

d7a00cc

Finalizing the Interface with PETSIRD.

32c3144

Trying to figure out how the scanner looks like.

4b39461

Create ProjDataInfoBlocksOnCylindricalNoArcCorr from PETSIRD

5499245

Merge remote-tracking branch 'origin/master' into PETSIRD

d029d0d

* Clean up the code that creates a Scanner object from PETSRID header…

d00e987

… information.

* Stop testing for PETSIRD

d0e46a4

NikEfth marked this pull request as ready for review December 22, 2025 14:34

NikEfth added 6 commits December 22, 2025 15:35

pre-commit

0320b3c

Drop one more const

dc24acf

Drop one more const

76488af

Merge branch 'PETSIRD' of github.com:UCL/STIR into PETSIRD

b63eaa7

pre-commit

9fae5ea

Fix yml syntax error in build-test.yml

c47bdc3

NikEfth marked this pull request as draft December 23, 2025 08:38

NikEfth added 2 commits December 23, 2025 10:20

Fix memory leak from repeated ProjDataInfo::clone() calls

42104a5

Memory leak fixes.

149fb55

NikEfth added the enhancement label Dec 23, 2025

NikEfth added 17 commits December 23, 2025 11:48

Merge branch 'fix/scatter-clone-memleak' into PETSIRD

360b3df

Remove PETSIRD submodule and decouple PETSIRD from STIR

4386308

STIR no longer vendors PETSIRD as a submodule. PETSIRD integration is expected via an external installation using find_package(PETSIRD).

Successfully links to PETSIRD.

fdf4a62

Finally, STIR->PETSIRD map works as expected.

a9cbff5

CI file that will build PETSIRD-STIR using GitHub Actions.

ee8b22e

CI builds PETSIRD

b6f8d7c

Successfully builds and links against PETSIRD in CI.

0031d23

Work on tests.

51eeb6c

pre-commit

ed233bb

Don't build documentation in CI workflow

51d5c43

Moved PETISDInfo helpers to detail folder

5d93eca

Introduced generic tests

pre-commit

1a20b7d

Commented out unused variables.

36d9091

I think I guard against some issues with the PETSIRD header.

315ee3e

pre-commit

2ef68ab

New functionalities:

e818ce2

1. Figuring out flattened geometries from STIR2PETSIRD converter. 2. Fixing detection efficiency lookup in BinNormalisationFromPETSIRD. Still some normalisation issues to be resolved. 3. Get / Set positions for PETSIRD Listmode data.

Trying to fix the normalization issue observed in PETSIRD.

e46d43f

KrisThielemans commented Mar 4, 2026

View reviewed changes

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

reading of PETSIRD list-mode function#1604

reading of PETSIRD list-mode function#1604
KrisThielemans wants to merge 101 commits intomasterfrom
PETSIRD

KrisThielemans commented Jul 16, 2025

Uh oh!

KrisThielemans left a comment

Uh oh!

KrisThielemans Mar 4, 2026

Uh oh!

KrisThielemans Mar 4, 2026

Uh oh!

KrisThielemans Mar 4, 2026

Uh oh!

KrisThielemans Mar 4, 2026

Uh oh!

KrisThielemans Mar 4, 2026

Uh oh!

KrisThielemans Mar 4, 2026

Uh oh!

KrisThielemans Mar 4, 2026

Uh oh!

KrisThielemans Mar 4, 2026

Uh oh!

KrisThielemans Mar 4, 2026

Uh oh!

KrisThielemans Mar 4, 2026

Uh oh!

KrisThielemans commented Mar 4, 2026 via email

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

5 participants

Conversation

KrisThielemans commented Jul 16, 2025

Uh oh!

KrisThielemans left a comment

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

KrisThielemans commented Mar 4, 2026 via email

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

5 participants