SWIG: expose more LOR and listmode classes

examples/python/listmode_loop_demo.py

@@ -0,0 +1,43 @@
+# Demo how to use STIR from Python to access events in a list-mode file
+
+# Copyright 2023 - University College London
+# This file is part of STIR.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+# See STIR/LICENSE.txt for details
+
+#%% Initial imports
+import stir
+
+#%% read file
+filename = '20170809_NEMA_60min_UCL.l.hdr'
+# example using the hroot file in recon_test_pack, which needs some env variables to be set
+#import os
+#os.environ["INPUT_ROOT_FILE"]="test_PET_GATE.root"
+#os.environ["EXCLUDE_SCATTERED"] = "1"
+#os.environ["EXCLUDE_RANDOM"] = "0"
+#filename = "root_header.hroot"
+
+lm=stir.ListModeData.read_from_file(filename)
+# could print some exam info
+# print(lm.get_exam_info().parameter_info())
+proj_data_info = lm.get_proj_data_info()
+# could print some geometric info
+#print(proj_data_info.parameter_info())
+
+#%% loop over first few events and print some information
+# create some variables for re-use in the loop
+record = lm.get_empty_record()
+b = stir.Bin()
+for i in range(50):
+    lm.get_next_record(record)
+    if (record.is_time()):
+        print(f"Time: {record.time().get_time_in_millisecs()}")
+    if (record.is_event()):
+        event = record.event()
+        lor = event.get_LOR()
+        event.get_bin(b, proj_data_info);
+        # TODO We can will be able to simply print bin once STIR_TOF is on
+        print(f"Event: p/d: {event.is_prompt()} LOR: {[lor.p1(), lor.p2()]}, ",
+              f"bin: s:{b.segment_num}, a: {b.axial_pos_num}, v: {b.view_num}, t:{b.tangential_pos_num}")

src/include/stir/LORCoordinates.h

@@ -161,7 +161,12 @@ class LORCylindricalCoordinates_z_and_radius
 template <class coordT>
 class LORInCylinderCoordinates : public LOR<coordT>
 {
+#ifdef SWIG
+  // SWIG needs this typedef to be public
+ public:
+#endif
   typedef  LORInCylinderCoordinates<coordT> self_type;
+ private:
   void check_state() const
   {
     assert(_radius>0);
@@ -217,16 +222,14 @@ class LORInCylinderCoordinates : public LOR<coordT>
   inline
     LORInCylinderCoordinates(const LORInAxialAndSinogramCoordinates<coordT>&);
 
+#if 0
+  // disabled as would need radius argument as well, but currently not needed
   inline
     LORInCylinderCoordinates(const LORAs2Points<coordT>&);
+#endif
 
-  virtual
-#ifndef STIR_NO_COVARIANT_RETURN_TYPES
-    self_type* 
-#else
-      LOR<coordT>*
-#endif    
-    clone() const { return new self_type(*this); }
+  self_type* clone() const override
+  { return new self_type(*this); }
 
   virtual
     Succeeded
@@ -259,6 +262,10 @@ class LORInCylinderCoordinates : public LOR<coordT>
 template <class coordT>
 class LORAs2Points : public LOR<coordT>
 {
+#ifdef SWIG
+  // SWIG needs this typedef to be public
+ public:
+#endif
   typedef LORAs2Points<coordT> self_type;
  public:
   const CartesianCoordinate3D<coordT>& p1() const { return _p1; }
@@ -282,13 +289,8 @@ class LORAs2Points : public LOR<coordT>
   inline
     LORAs2Points(const LORInAxialAndNoArcCorrSinogramCoordinates<coordT>&);
 
-  virtual
-#ifndef STIR_NO_COVARIANT_RETURN_TYPES
-    self_type* 
-#else
-      LOR<coordT>*
-#endif
-      clone() const { return new self_type(*this); }
+  self_type* clone() const override
+  { return new self_type(*this); }
 
   virtual
     Succeeded
@@ -326,7 +328,12 @@ class LORInAxialAndSinogramCoordinates
   : public LOR<coordT>, private LORCylindricalCoordinates_z_and_radius<coordT>
 {
  private:
+#ifdef SWIG
+  // SWIG needs this typedef to be public
+ public:
+#endif
   typedef LORInAxialAndSinogramCoordinates<coordT> self_type;
+ private:
   typedef LORCylindricalCoordinates_z_and_radius<coordT> private_base_type;
   // sorry: has to be first to give the compiler a better chance of inlining
   void check_state() const
@@ -371,18 +378,13 @@ class LORInAxialAndSinogramCoordinates
   inline
     LORInAxialAndSinogramCoordinates(const LORInAxialAndNoArcCorrSinogramCoordinates<coordT>&);
 
-#if __cplusplus>= 201103L
+#if 0
   inline
     LORInAxialAndSinogramCoordinates(const LORAs2Points<coordT>&);
 #endif
 
-  virtual
-#ifndef STIR_NO_COVARIANT_RETURN_TYPES
-    self_type* 
-#else
-      LOR<coordT>*
-#endif
-      clone() const { return new self_type(*this); }
+  self_type* clone() const override
+  { return new self_type(*this); }
 
   void reset(coordT radius=1)
     {
@@ -506,18 +508,13 @@ class LORInAxialAndNoArcCorrSinogramCoordinates
   inline
   LORInAxialAndNoArcCorrSinogramCoordinates(const LORInAxialAndSinogramCoordinates<coordT>&);
 
-#if __cplusplus>= 201103L
+#if 0
   inline
     LORInAxialAndNoArcCorrSinogramCoordinates(const LORAs2Points<coordT>&);
 #endif
 
-  virtual
-#ifndef STIR_NO_COVARIANT_RETURN_TYPES
-    self_type* 
-#else
-      LOR<coordT>*
-#endif
-      clone() const { return new self_type(*this); }
+  self_type* clone() const override
+  { return new self_type(*this); }
 
   virtual
     Succeeded

src/include/stir/LORCoordinates.inl

@@ -269,7 +269,7 @@ LORInAxialAndNoArcCorrSinogramCoordinates(const LORInAxialAndSinogramCoordinates
   check_state();
 }
 
-#if __cplusplus>= 201103L
+#if 0
 template <class coordT>
 LORInAxialAndSinogramCoordinates<coordT>::
 LORInAxialAndSinogramCoordinates(const LORAs2Points<coordT>& coords)

src/include/stir/listmode/CListRecord.h

@@ -23,7 +23,7 @@
 #ifndef __stir_listmode_CListRecord_H__
 #define __stir_listmode_CListRecord_H__
 
-#include "ListRecord.h"
+#include "stir/listmode/ListRecord.h"
 
 START_NAMESPACE_STIR
 class Bin;

src/include/stir/listmode/ListEvent.h

@@ -24,8 +24,6 @@
 #ifndef __stir_listmode_ListEvent_H__
 #define __stir_listmode_ListEvent_H__
 
-#include "stir/round.h"
-#include "stir/Succeeded.h"
 #include "stir/Bin.h"
 #include "stir/ProjDataInfo.h"
 #include "stir/CartesianCoordinate3D.h"

src/include/stir/listmode/ListRecord.h

@@ -24,9 +24,8 @@
 #ifndef __stir_listmode_ListRecord_H__
 #define __stir_listmode_ListRecord_H__
 
-#include "ListEvent.h"
-#include "ListTime.h"
-#include "stir/Succeeded.h"
+#include "stir/listmode/ListEvent.h"
+#include "stir/listmode/ListTime.h"
 
 START_NAMESPACE_STIR
 

src/swig/CMakeLists.txt

@@ -108,6 +108,7 @@ set(swig_stir_dependencies
   stir_objectivefunctions.i
   stir_priors.i
   stir_projdata.i
+  stir_listmode.i
   stir_projectors.i
   stir_reconstruction.i
   stir_shapes.i

src/swig/stir.i

@@ -70,8 +70,12 @@
  #include "stir/recon_buildblock/BinNormalisationFromProjData.h"
  #include "stir/recon_buildblock/BinNormalisationFromAttenuationImage.h"
  #include "stir/recon_buildblock/TrivialBinNormalisation.h"
- #include "stir/listmode/LmToProjData.h"
+ #include "stir/listmode/ListRecord.h"
+ #include "stir/listmode/ListEvent.h"
+ #include "stir/listmode/CListRecord.h"
  #include "stir/listmode/ListModeData.h"
+ #include "stir/listmode/CListModeData.h"
+ #include "stir/listmode/LmToProjData.h"
 
 #include "stir/CartesianCoordinate2D.h"
 #include "stir/CartesianCoordinate3D.h"
@@ -908,9 +912,6 @@ namespace std {
 %shared_ptr(stir::ParsingObject);
 
 %shared_ptr(stir::Verbosity);
-%shared_ptr(stir::LORAs2Points<float>);
-%shared_ptr(stir::LOR<float>);
-%shared_ptr(stir::LORInAxialAndNoArcCorrSinogramCoordinates<float>);
 
 //  William S Fulton trick for passing templates (with commas) through macro arguments
 // (already defined in swgmacros.swg)
@@ -951,30 +952,14 @@ ADD_REPR(stir::Succeeded, %arg($self->succeeded() ? "yes" : "no"));
 %include "stir/ByteOrder.h"
 
 %include "stir_coordinates.i"
-
-#if 0
- // TODO enable this in STIR version 6 (breaks backwards compatibility
-%attributeref(stir::LORInAxialAndNoArcCorrSinogramCoordinates<float>, float, z1);
-%attributeref(stir::LORInAxialAndNoArcCorrSinogramCoordinates<float>, float, z2);
-%attributeref(stir::LORInAxialAndNoArcCorrSinogramCoordinates<float>, float, beta);
-%attributeref(stir::LORInAxialAndNoArcCorrSinogramCoordinates<float>, float, phi);
-#else
-%ignore *::z1() const;
-%ignore *::z2() const;
-%ignore *::beta() const;
-%ignore *::phi() const;
-#endif
-%ignore *::check_state;
-%include "stir/LORCoordinates.h"
-
-%template(FloatLOR) stir::LOR<float>;
-%template(FloatLORInAxialAndNoArcCorrSinogramCoordinates) stir::LORInAxialAndNoArcCorrSinogramCoordinates<float>;
+%include "stir_LOR.i"
 
 %include "stir_array.i"
 %include "stir_exam.i"
 
 %shared_ptr(stir::DataSymmetriesForViewSegmentNumbers);
 %include "stir_projdata.i"
+%include "stir_listmode.i"
 %include "stir/DataSymmetriesForViewSegmentNumbers.h"
 
 %include "stir_voxels.i"
@@ -1009,10 +994,6 @@ ADD_REPR(stir::Succeeded, %arg($self->succeeded() ? "yes" : "no"));
 %include "stir/multiply_crystal_factors.h"
 %include "stir/decay_correction_factor.h"
 
-%rename (set_template_proj_data_info) *::set_template_proj_data_info_sptr;
-%shared_ptr(stir::LmToProjData);
-%include "stir/listmode/LmToProjData.h"
-
 %shared_ptr(stir::ScatterSimulation);
 %shared_ptr(stir::RegisteredParsingObject<stir::SingleScatterSimulation,
   stir::ScatterSimulation, stir::ScatterSimulation>);
@@ -1031,18 +1012,6 @@ ADD_REPR(stir::Succeeded, %arg($self->succeeded() ? "yes" : "no"));
 %shared_ptr(stir::CreateTailMaskFromACFs);
 %include "stir/scatter/CreateTailMaskFromACFs.h"
 
-%shared_ptr(stir::ListModeData);
-%include "stir/listmode/ListModeData.h"
-
-%extend stir::ListModeData {
-  static shared_ptr<stir::ListModeData> read_from_file(const std::string& filename)
-    {
-      using namespace stir;
-      shared_ptr<ListModeData> ret(read_from_file<ListModeData>(filename));
-      return ret;
-    }
-}
-
 %shared_ptr(stir::FanProjData);
 %shared_ptr(stir::GeoData3D);
 %ignore operator<<;

src/swig/stir_LOR.i

@@ -0,0 +1,49 @@
+/*
+    Copyright (C) 2023 University College London
+    Copyright (C) 2022 National Physical Laboratory
+    This file is part of STIR.
+
+    SPDX-License-Identifier: Apache-2.0
+
+    See STIR/LICENSE.txt for details
+*/
+/*!
+  \file
+  \brief Interface file for SWIG: stir::LOR and derived classes
+
+  \author Kris Thielemans
+  \author Daniel Deidda
+*/
+
+%shared_ptr(stir::LOR<float>);
+%shared_ptr(stir::LORAs2Points<float>);
+%shared_ptr(stir::LORInAxialAndNoArcCorrSinogramCoordinates<float>);
+%shared_ptr(stir::LORInAxialAndSinogramCoordinates<float>);
+%shared_ptr(stir::PointOnCylinder<float>);
+%shared_ptr(stir::LORInCylinderCoordinates<float>);
+
+#if 0
+ // TODO enable this in STIR version 6 (breaks backwards compatibility
+%attributeref(stir::LORInAxialAndNoArcCorrSinogramCoordinates<float>, float, z1);
+%attributeref(stir::LORInAxialAndNoArcCorrSinogramCoordinates<float>, float, z2);
+%attributeref(stir::LORInAxialAndNoArcCorrSinogramCoordinates<float>, float, beta);
+%attributeref(stir::LORInAxialAndNoArcCorrSinogramCoordinates<float>, float, phi);
+#else
+%ignore *::z1() const;
+%ignore *::z2() const;
+%ignore *::beta() const;
+%ignore *::phi() const;
+#endif
+%ignore *::check_state;
+
+%attributeref(stir::PointOnCylinder<float>, float, z);
+%attributeref(stir::PointOnCylinder<float>, float, psi);
+
+%include "stir/LORCoordinates.h"
+
+%template(LOR) stir::LOR<float>;
+%template(LORInAxialAndNoArcCorrSinogramCoordinates) stir::LORInAxialAndNoArcCorrSinogramCoordinates<float>;
+%template(LORAs2Points) stir::LORAs2Points<float>;
+%template(LORInAxialAndSinogramCoordinates) stir::LORInAxialAndSinogramCoordinates<float>;
+%template(PointOnCylinder) stir::PointOnCylinder<float>;
+%template(LORInCylinderCoordinates) stir::LORInCylinderCoordinates<float>;