fix RDF9 import of non-TOF data

KrisThielemans · KrisThielemans · commit a88ccdea60b0 · 2024-09-04T17:08:20.000+01:00
also avoid hard-wired length of manufacturer etc dataset, which can cause problems
diff --git a/src/IO/GEHDF5Wrapper.cxx b/src/IO/GEHDF5Wrapper.cxx
@@ -65,6 +65,17 @@ read_float(const H5::H5File& file, const std::string& dataset)
   return tmp;
 }
 
+static std::string
+read_string(const H5::H5File& file, const std::string& dataset)
+{
+  H5::DataSet ds = file.openDataSet(dataset.c_str());
+  H5::StrType datatype = ds.getStrType();
+
+  std::string value;
+  ds.read(value, datatype);
+  return value;
+}
+
 bool
 GEHDF5Wrapper::check_GE_signature(const std::string& filename)
 {
@@ -90,13 +101,7 @@ GEHDF5Wrapper::check_GE_signature(H5::H5File& file)
   if (file.getId() == -1)
     error("File is not open. Aborting");
 
-  H5::StrType vlst(
-      0,
-      37); // 37 here is the length of the string (PW got it from the text file generated by list2txt with the LIST000_decomp.BLF
-  std::string read_str_manufacturer;
-
-  H5::DataSet dataset2 = file.openDataSet("/HeaderData/ExamData/manufacturer");
-  dataset2.read(read_str_manufacturer, vlst);
+  std::string read_str_manufacturer = read_string(file, "/HeaderData/ExamData/manufacturer");
 
   if (read_str_manufacturer == "GE MEDICAL SYSTEMS")
     {
@@ -277,14 +282,7 @@ GEHDF5Wrapper::open(const std::string& filename)
 shared_ptr<Scanner>
 GEHDF5Wrapper::get_scanner_from_HDF5()
 {
-  std::string read_str_scanner;
-  H5::StrType vlst(
-      0,
-      37); // 37 here is the length of the string (PW got it from the text file generated by list2txt with the LIST000_decomp.BLF
-
-  H5::DataSet dataset = file.openDataSet("/HeaderData/ExamData/scannerDesc");
-  dataset.read(read_str_scanner, vlst);
-
+  std::string read_str_scanner = read_string(this->file, "/HeaderData/ExamData/scannerDesc");
   float effective_ring_diameter;
   int num_transaxial_blocks_per_bucket = 0;
   int num_axial_blocks_per_bucket = 0;
@@ -425,6 +423,11 @@ GEHDF5Wrapper::initialise_proj_data_info_from_HDF5()
 {
   shared_ptr<Scanner> scanner_sptr = get_scanner_from_HDF5();
 
+  // TODO get TOF mashing when reading sinos as TOF
+  const auto num_tof_bins = read_dataset_uint32("/HeaderData/Sorter/numTOF_bins");
+  if (num_tof_bins > 1)
+    warning("GE RDF data currently still read as non-TOF");
+
   this->proj_data_info_sptr
       = ProjDataInfo::construct_proj_data_info(scanner_sptr,
                                                /*span*/ 2,
@@ -654,11 +657,20 @@ GEHDF5Wrapper::initialise_proj_data(const unsigned int view_num)
   if (view_num == 0 || view_num > static_cast<unsigned>(this->get_scanner_sptr()->get_num_detectors_per_ring() / 2))
     error("internal error in GE HDF5 code: view number " + std::to_string(view_num) + " is incorrect");
 
+  const auto num_tof_bins = read_dataset_uint32("/HeaderData/Sorter/numTOF_bins");
+
   if (rdf_ver == 9)
     {
-      m_address = "/SegmentData/Segment2/3D_TOF_Sinogram/view" + std::to_string(view_num);
-
-      m_dataset_sptr.reset(new H5::DataSet(file.openDataSet(m_address)));
+      if (num_tof_bins > 1)
+        {
+          m_address = "/SegmentData/Segment2/3D_TOF_Sinogram/view" + std::to_string(view_num);
+          m_dataset_sptr.reset(new H5::DataSet(file.openDataSet(m_address)));
+        }
+      else
+        {
+          m_address = "/SegmentData/Segment2/3D_Sinogram/view" + std::to_string(view_num);
+          m_dataset_sptr.reset(new H5::DataSet(file.openDataSet(m_address)));
+        }
       m_dataspace = m_dataset_sptr->getSpace();
       // Create an array to host the size of the dimensions
       const int rank = m_dataspace.getSimpleExtentNdims();
@@ -673,13 +685,7 @@ GEHDF5Wrapper::initialise_proj_data(const unsigned int view_num)
       // AB for signa, these where [1981,27,357] and [45,448,357]
       m_NX_SUB = dims[0]; // hyperslab dimensions
       m_NY_SUB = dims[1];
-      m_NZ_SUB = dims[2];
-#if 0
-        // AB todo: ??? why are these different?
-        m_NX = 45;        // output buffer dimensions
-        m_NY = 448;
-        m_NZ = 357;
-#endif
+      m_NZ_SUB = rank > 2 ? dims[2] : 1;
     }
   else
     return Succeeded::no;
@@ -831,7 +837,6 @@ GEHDF5Wrapper::read_sinogram(Array<3, unsigned char>& output,
                 }
             }
         }
-      output.release_data_ptr();
     }
 
   return Succeeded::yes;
