Simset input by NikEfth · Pull Request #1678 · UCL/STIR

NikEfth · 2026-02-18T11:47:57Z

Changes in this pull request

This PR add support for SimSET history files.

In order to make this run you need to link to SimSET.
Apply this patch to SimSET and recompile.
This will crate a lib file that you can point to at CMake.

Testing performed

Related issues

Checklist before requesting a review

[] I have performed a self-review of my code
[] I have added docstrings/doxygen in line with the guidance in the developer guide
[] I have implemented unit tests that cover any new or modified functionality (if applicable)
The code builds and runs on my machine (in the past)
[] documentation/release_XXX.md has been updated with any functionality change (if applicable)

Contribution Notes

Please tick the following:

The content of this Pull Request (the Contribution) is intentionally submitted for inclusion in STIR (the Work) under the terms and conditions of the Apache-2.0 License.
I (or my institution) have signed the STIR Contribution License Agreement (not required for small changes).

There is a weird point, as in order to get to the version I need to skip to byte 32 and read it as big endian. The header kind and header size are read correctly, as little endians in the right place. In the print_header I cannot any relevant process.

Progress on matters of initialisations using SimSET headers. Next step, initialise the history header and get events.

Trying to guess the scanner.

Test pending. Todo: fix the signature. Now it is always on.

I am trying to make the old simSET example to work. Had to modify slightly the binning module to match with STIR scanner template. But the error of the different axial length persists. I am trying to guess the geometry with even fewer data.

Fixed the mCT block config

KrisThielemans

some initial comments. What's in the SimSET.tar.gz? Can't check in source code.

src/cmake/STIRConfig.cmake.in

KrisThielemans · 2026-02-18T13:44:54Z

src/include/stir/IO/SimSETListmodeInputFileFormat.h

+
+#endif
+
+// This is an alternative version of the is_SimSET_signature.


shouldn't be here

I will have removed it by the end of this PR

src/include/stir/listmode/CListEventCylindricalScannerWithDiscreteDetectors.inl

src/include/stir/listmode/CListModeDataSimSET.h

src/include/stir/listmode/CListRecordSimSET.h

src/IO/IO_registries.cxx

KrisThielemans · 2026-02-18T13:53:10Z

src/listmode_buildblock/CMakeLists.txt

 endif()

+if (HAVE_SIMSET)
+	list(APPEND ${dir_LIB_SOURCES}


will probably need changing

KrisThielemans · 2026-02-18T13:53:53Z

src/listmode_buildblock/LmToProjData.cxx

      // uncompressed bins in a compressed bin

-      const float bin_value = 1.f / bin_efficiency;
+      const float bin_value = uncompressed_bin.get_bin_value() / bin_efficiency;


this seems dangerous for backwards compatibility and will need careful checking

The problem is that SimSET events carry can carry weights and we need those.

Either in the cylidrical or the blocks geometry, I am not 100% sure in which the weights were applicable.

KrisThielemans · 2026-02-18T13:54:43Z

src/SimSET/examples/template_bin.rec

 # NOTE: Take note if you are setting min_td and max_td to any value less than the radius of your object cylinder.
 # num_td_bins needs to be odd for STIR, and the range needs to be symmetric
-INT     num_td_bins             =       287
+INT     num_td_bins             =       288


see comment above. For even-sized, I seem to recall there was a difference between SimSET and STIR conventions

Probably. But that is why the TOF modification from PETSIRD is relevant, here. IDK what to do. Bring that over and resolve the conflict later? Which one will be merged first?

This has nothing to do with TOF. It is tangential positions.

In any case, and "even TOF" mods should not be in either of these PRs, so they should be independent. To be discussed tomorrow what we do with the even TOF bins (with @danieldeidda)

oops.. I missread. Let's keep this open I don't remeber right now.

src/CMakeLists.txt

NikEfth · 2026-03-04T00:01:28Z

OK, solid progress on this one. We are able to compile the latest master with SimSET support. I have not tested yet.

KrisThielemans

some house-keeping comments, nothing really regarding functionality.

I suggest moving most (all?) of .inl to .cxx to .cxx. There seems to be no reason to think any compiler will be able to inline all of that code (and the remaining ones are probably hardly ever used anyway)

examples/samples/simset_header.hsim

KrisThielemans · 2026-03-04T07:15:54Z

src/cmake/FindSIMSET.cmake

+    target_compile_definitions(SIMSET::simset INTERFACE DARWIN MAC_10 GEN_UNIX arm64)
+    elseif(UNIX)
+      target_compile_definitions(SIMSET::simset INTERFACE GEN_UNIX)
+      elseif(WIN32)
+        target_compile_definitions(SIMSET::simset INTERFACE WIN32)
+        endif()


fix indentation, but I'm hoping we don't need these (They are needed for Simset compilation, but do we need it for the Simset headers?) Add a comment if so.

Photon.h uses types like LbFourByte, LbUsFourByte, etc. Those are defined in SimSET’s LbTypes.h inside an OS-specific #if ... #elif ... block. If none of the expected platform macros are defined, you get “unknown type name LbFourByte” (or even #error you have not declared an OS-dependent clause). This can be changed in the SimSET code. No super hard, but we need to wait until the public version.

src/cmake/FindSIMSET.cmake

src/include/stir/IO/InputStreamFromSimSET.h

src/include/stir/IO/InputStreamFromSimSET.inl

src/IO/CMakeLists.txt

src/listmode_buildblock/CListModeDataSimSET.cxx

KrisThielemans · 2026-03-04T07:44:51Z

src/listmode_buildblock/CListModeDataSimSET.cxx

+START_NAMESPACE_STIR
+
+//! N.E: Large parts adapted from phgbin and functions called by it;
+CListModeDataSimSET::CListModeDataSimSET(const std::string& _hsimset_filename)


either we move all/most of this into open_lm_file (which could be useful if at some point we want to be able to call it from somewhere else), or we delete open_lm_file

src/listmode_buildblock/CMakeLists.txt

NikEfth and others added 30 commits March 15, 2019 09:03

Initial commit

ba67dd4

Process filesignature.

f8d260f

There is a weird point, as in order to get to the version I need to skip to byte 32 and read it as big endian. The header kind and header size are read correctly, as little endians in the right place. In the print_header I cannot any relevant process.

Linking to SimSET and Several initialisations working

74cdaba

Progress on matters of initialisations using SimSET headers. Next step, initialise the history header and get events.

Fixed issues with the extern global variables in SimSET

cf9cfee

Trying to guess the scanner.

CListModeSimSET tries to guess the scanner.

5d705c9

Ignore energy resolution, if has not been set in Scanner template

16469c9

Unlisting and recon seem to be working.

dc9bd77

Test pending. Todo: fix the signature. Now it is always on.

Creating the test for the SimSET interface

bb57c02

Doxygen groups fixed

37dfbc6

Partial support of simplePET

104b91c

I am trying to make the old simSET example to work. Had to modify slightly the binning module to match with STIR scanner template. But the error of the different axial length persists. I am trying to guess the geometry with even fewer data.

Fixed reset() and re-positioning

14741bc

Fixed mCT

a34e965

Fixed the mCT block config

6c5ca20

Merge pull request #10 from txusser/simset_input

fc4c496

Fixed the mCT block config

more documentation, clean up and signature fix

be270a6

More documentation and clean up

57e7c86

Addition of energy window

ef5cf8a

Read the detector history.

406bc4c

Take into account count weights

60d57dc

fix to post_normalisation

489fd07

Corrections at decay and multiples

47906c6

Corrections for randoms

1e3c21b

Merge branch 'tof_sino_UCL' into simset_input

c46110f

TOF installed

4011356

Addition of TOF mashing factor and SimSET header

6c841e3

fix on signature reading

80e9ee0

Merge branch 'tof_sino_UCL' into simset_input

fd62713

small fix

1191f8e

Merge branch 'tof_sino_UCL' into simset_input

1946191

documentation

3611e07

NikEfth and others added 4 commits April 13, 2020 11:58

Remove comparison with SimSET TOF information

51579bd

TOF mods

d20194c

Merge remote-tracking branch 'upstream/master' into simset_input

d78a027

Pre-commit

807987a

NikEfth requested a review from KrisThielemans February 18, 2026 13:15

NikEfth added enhancement in-progress labels Feb 18, 2026

NikEfth marked this pull request as draft February 18, 2026 13:16

CODACY

46bc103

KrisThielemans requested changes Feb 18, 2026

View reviewed changes

KrisThielemans self-assigned this Feb 18, 2026

NikEfth added 2 commits March 4, 2026 00:31

Compiles and Links once more.

3dd7fd6

Address comments from github

0342e78

KrisThielemans requested changes Mar 4, 2026

View reviewed changes

NikEfth added 4 commits March 4, 2026 11:22

Comment resolved.

9923519

Comments and house-keeping

64131e3

Build, and reads the simset headers.

4d5c3a2

pre-commit

8ffd393


		#endif

		// This is an alternative version of the is_SimSET_signature.

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NikEfth commented Feb 18, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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NikEfth commented Mar 4, 2026

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NikEfth commented Feb 18, 2026 •

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