Merge pull request #61 from KrisThielemans/merge_master_to_TOF_2024_0…

…1_02

Merge master to TOF 2024 01 02

documentation/STIR-developers-overview.tex

@@ -1261,8 +1261,21 @@ \section{
 # add my include directory to compiler switches (or better: use target_include_directories)
 include_directories(include)
 
-# check CMakeLists in next directories
-add_subdirectory(buildblock my_buildblock)
+# check CMakeLists in next directory
+# note: 2nd argument needs to have different name than any of the existing STIR libraries
+add_subdirectory(${STIR_LOCAL}/buildblock my_buildblock)
+
+# add registries (if you have any)
+list(APPEND STIR_REGISTRIES 
+  ${STIR_LOCAL}/buildblock/my_registries.cxx)
+
+# add to list of libraries to include in linking
+list(APPEND STIR_LIBRARIES my_buildblock)
+
+# copy variables to PARENT_SCOPE
+SET( STIR_REGISTRIES ${STIR_REGISTRIES} PARENT_SCOPE)
+SET( STIR_LIBRARIES ${STIR_LIBRARIES} PARENT_SCOPE)
+
 \end{verbatim}
 where \textbf{buildblock} is the name of your subdirectory and \textbf{my\_buildblock} is a name for the
 sub-directory where CMake will build the files (make sure the latter is different from any
@@ -1286,12 +1299,6 @@ \section{
 # declare dependencies on other STIR libraries, for instance
 target_link_libraries($(dir) PUBLIC buildblock)
 
-# add to list of libraries for STIR to include in linking
-list(APPEND STIR_LIBRARIES $(dir))
-
-# add source file for registries (if you have one)
-list(APPEND STIR_REGISTRIES my_registry)
-
 include(stir_lib_target)
 \end{verbatim}
 
@@ -1311,7 +1318,7 @@ \section{
 #include "myOutputFileFormat.h"
 static myOutputFileFormat::RegisterIt dummy1;
 \end{verbatim}
-If you add that to the \texttt{STIR\_REGISTRIES} variable in your \textbf{CMakeLists.txt}
+If you add that to the \texttt{STIR\_REGISTRIES} variable in your \textbf{extra\_stir\_dirs.cmake}
 as above, everything should work as expected.
 
 \section{Contributing to STIR}

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/buildblock/RadionuclideDB.cxx

@@ -130,7 +130,7 @@ get_radionuclide_from_json(ImagingModality rmodality, const std::string &rname)
     case ImagingModality::NM:
       modality_string = "nucmed"; break;
     default:
-      warning("RadionuclideDB::get_radionuclide_from_json called with unknown modality. Returning \"unknown\" radionuclide.");
+      warning(std::string("RadionuclideDB::get_radionuclide_from_json called with unknown modality. Returning \"unknown\" radionuclide."));
       return Radionuclide();
     }
 
@@ -151,7 +151,7 @@ get_radionuclide_from_json(ImagingModality rmodality, const std::string &rname)
 
   if (rnuclide_entry == all_nuclides.end())
     {
-      warning("RadionuclideDB: radionuclide " + rname + " not found in JSON database. Returning \"unknown\" radionuclide.");
+      warning(std::string("RadionuclideDB: radionuclide " + rname + " not found in JSON database. Returning \"unknown\" radionuclide."));
       return Radionuclide();
     }
 
@@ -180,7 +180,7 @@ get_radionuclide_from_json(ImagingModality rmodality, const std::string &rname)
 
   if (decay_entry == decays.end())
     {
-      warning("RadionuclideDB: radionuclide " + rname + ": modality " + modality_string + " not found in JSON database. Returning \"unknown\" radionuclide.");
+      warning(std::string("RadionuclideDB: radionuclide " + rname + ": modality " + modality_string + " not found in JSON database. Returning \"unknown\" radionuclide."));
       return Radionuclide();
     }
 
@@ -240,7 +240,7 @@ get_radionuclide(ImagingModality rmodality, const std::string& rname)
         return get_radionuclide(rmodality, "^99m^Technetium");
       else
         {
-          warning("RadioNuclideDB::get_radionuclide: unknown modality. Returning \"unknown\" radionuclide.");
+          warning(std::string("RadioNuclideDB::get_radionuclide: unknown modality. Returning \"unknown\" radionuclide."));
           return Radionuclide();
         }
     }
@@ -256,7 +256,7 @@ get_radionuclide(ImagingModality rmodality, const std::string& rname)
     if(rmodality.get_modality()==ImagingModality::PT){
         if (rname != "^18^Fluorine")
           {
-            warning("RadioNuclideDB::get_radionuclide: since STIR was compiled without nlohmann-json-dev, We only have information for ^18^Fluorine for the PET modality. Returning \"unknown\" radionuclide.");
+            warning(std::string("RadioNuclideDB::get_radionuclide: since STIR was compiled without nlohmann-json-dev, We only have information for ^18^Fluorine for the PET modality. Returning \"unknown\" radionuclide."));
             return Radionuclide();
           }
 
@@ -268,7 +268,7 @@ get_radionuclide(ImagingModality rmodality, const std::string& rname)
     }else if(rmodality.get_modality()==ImagingModality::NM){
         if (rname != "^99m^Technetium")
           {
-            warning("RadioNuclideDB::get_radionuclide: since STIR was compiled without nlohmann-json-dev, We only have information for ^99m^Technetium for the NM modality. Returning \"unknown\" radionuclide.");
+            warning(std::string("RadioNuclideDB::get_radionuclide: since STIR was compiled without nlohmann-json-dev, We only have information for ^99m^Technetium for the NM modality. Returning \"unknown\" radionuclide."));
             return Radionuclide();
           }
 
@@ -280,7 +280,7 @@ get_radionuclide(ImagingModality rmodality, const std::string& rname)
     }
     else
       {
-        warning("RadioNuclideDB::get_radionuclide: unknown modality. Returning \"unknown\" radionuclide.");
+        warning(std::string("RadioNuclideDB::get_radionuclide: unknown modality. Returning \"unknown\" radionuclide."));
         return Radionuclide();
       }
 

src/include/stir/LORCoordinates.h

@@ -169,7 +169,12 @@ 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);
@@ -233,16 +238,14 @@ 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
@@ -275,6 +278,10 @@ 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; }
@@ -297,14 +304,6 @@ 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); }
 
   //! \copybrief LOR::is_swapped()
   /*! In this class, this currently always return \c false. You can swap the points if
@@ -315,6 +314,9 @@ class LORAs2Points : public LOR<coordT>
       return false;
     }
 
+  self_type* clone() const override
+  { return new self_type(*this); }
+
   virtual
     Succeeded
     change_representation(LORInCylinderCoordinates<coordT>&,
@@ -351,7 +353,12 @@ 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
@@ -398,18 +405,13 @@ 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)
     {
@@ -537,18 +539,13 @@ 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

@@ -285,7 +285,7 @@ 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

@@ -27,7 +27,7 @@
 #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/include/stir/recon_buildblock/SqrtHessianRowSum.h

@@ -112,9 +112,9 @@ class SqrtHessianRowSum:
     void compute_approximate_Hessian_row_sum();
 
 protected:
+    bool _already_setup = false;
 
 private:
-    bool _already_setup = false;
 
     //! Objective function object
     shared_ptr<GeneralisedObjectiveFunction<TargetT> >  objective_function_sptr;

src/include/stir/scatter/ScatterEstimation.h

@@ -291,10 +291,11 @@ class ScatterEstimation: public ParsingObject
 
     std::string output_additive_estimate_prefix;
 
-private:
     //! variable to check if we have called set_up()
     bool _already_setup;
 
+private:
+
     //! attenuation in 3D
     shared_ptr<BinNormalisation>  atten_norm_3d_sptr;
 

src/include/stir/scatter/ScatterSimulation.h

@@ -435,6 +435,7 @@ class ScatterSimulation : public RegisteredObject<ScatterSimulation>
     int downsample_scanner_dets;
 
     bool downsample_scanner_bool;
+    bool _already_set_up;
 
  private:
     int total_detectors;
@@ -446,7 +447,6 @@ class ScatterSimulation : public RegisteredObject<ScatterSimulation>
     // numbers that we don't want to recompute all the time
     mutable float detector_efficiency_no_scatter;
 
-    bool _already_set_up;
 
     //! a function that checks if image sizes are ok
     /*! It will call \c error() if not.

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