Modifications for psmr2024

recon_test_pack/root_header.hroot

@@ -14,6 +14,7 @@ View offset (degrees)					 := 0
 Maximum number of (unmashed) TOF time bins := 5
 Size of unmashed TOF time bins (ps)        := 820.0
 TOF timing resolution (ps)                 := 400.0
+TOF mashing factor:= 1
 
 GATE scanner type := GATE_Cylindrical_PET
 GATE_Cylindrical_PET Parameters :=

src/IO/InterfileHeader.cxx

@@ -612,19 +612,19 @@ InterfilePDFSHeader::InterfilePDFSHeader()
   reference_energy = -1.f;
   add_key("Reference energy (in keV)", &reference_energy);
 
-  max_num_timing_poss = -1;
+  max_num_timing_poss = 1;
   add_key("Maximum number of (unmashed) TOF time bins", &max_num_timing_poss);
 #if STIR_VERSION < 070000
   add_alias_key("Maximum number of (unmashed) TOF time bins", "Number of TOF time bins");
 #endif
   timing_poss_sequence.clear();
   add_key("TOF bin order", &timing_poss_sequence);
-  size_of_timing_pos = -1.f;
+  size_of_timing_pos = 0.0f;
   add_key("Size of unmashed TOF time bins (ps)", &size_of_timing_pos);
 #if STIR_VERSION < 070000
   add_alias_key("Size of unmashed TOF time bins (ps)", "Size of timing bin (ps)");
 #endif
-  timing_resolution = -1.f;
+  timing_resolution = 0.0f;
   add_key("TOF timing resolution (ps)", &timing_resolution);
 #if STIR_VERSION < 070000
   add_alias_key("TOF timing resolution (ps)", "timing resolution (ps)");

src/IO/interfile.cxx

@@ -1201,7 +1201,7 @@ write_basic_interfile_PDFS_header(const string& header_file_name, const string&
 
   // it's PET data if we get here
   // N.E. Added timing locations
-  const bool is_TOF = pdfs.get_proj_data_info_sptr()->get_num_tof_poss() > 1;
+  const bool is_TOF = pdfs.get_proj_data_info_sptr()->is_tof_data();
   output_header << "number of dimensions := " + std::to_string(is_TOF ? 5 : 4) + "\n";
 
   // TODO support more ?
@@ -1225,12 +1225,16 @@ write_basic_interfile_PDFS_header(const string& header_file_name, const string&
      */
       {
         case ProjDataFromStream::Segment_View_AxialPos_TangPos: {
+          if (is_TOF) // TOF data with 1 timing position
+            order_of_timing_poss = 5;
           order_of_segment = 4;
           order_of_view = 3;
           order_of_z = 2;
           break;
         }
         case ProjDataFromStream::Segment_AxialPos_View_TangPos: {
+          if (is_TOF) // TOF data with 1 timing position
+            order_of_timing_poss = 5;
           order_of_segment = 4;
           order_of_view = 2;
           order_of_z = 3;
@@ -1252,8 +1256,7 @@ write_basic_interfile_PDFS_header(const string& header_file_name, const string&
     if (order_of_timing_poss > 0)
       {
         output_header << "matrix axis label [" << order_of_timing_poss << "] := timing positions\n";
-        output_header << "!matrix size [" << order_of_timing_poss << "] := " << pdfs.get_timing_poss_sequence_in_stream().size()
-                      << "\n";
+        output_header << "!matrix size [" << order_of_timing_poss << "] := " << pdfs.get_num_tof_poss() << "\n";
       }
 
     output_header << "matrix axis label [" << order_of_segment << "] := segment\n";

src/buildblock/FilePath.cxx

@@ -72,7 +72,7 @@ FilePath::is_directory() const
   struct stat info;
 
   if (stat(my_string.c_str(), &info) != 0)
-    error(boost::format("FilePath: Cannot access %1%.") % my_string);
+    warning(boost::format("FilePath: Cannot access %1%.") % my_string);
   else if (info.st_mode & S_IFDIR)
     return true;
 #endif
@@ -92,7 +92,7 @@ FilePath::is_regular_file() const
   struct stat info;
 
   if (stat(my_string.c_str(), &info) != 0)
-    error(boost::format("FilePath: Cannot access %1%.") % my_string);
+    warning(boost::format("FilePath: Cannot access %1%.") % my_string);
   else if (info.st_mode & S_IFREG)
     return true;
 #endif