diff --git a/documentation/release_6.3.htm b/documentation/release_6.3.htm
index fc818f8db..43342331f 100644
--- a/documentation/release_6.3.htm
+++ b/documentation/release_6.3.htm
@@ -25,6 +25,11 @@ New functionality
is disabled for backwards compatibility.
PR #1291
+
+ Data from GE Discovery MI systems in RDF9 should now be readable. TOF information on these scanners has also been added.
+ However, projection data is currently still always returned as non-TOF (but list-mode data is read as TOF).
+ PR #1503
+
diff --git a/src/IO/GEHDF5Wrapper.cxx b/src/IO/GEHDF5Wrapper.cxx
index 45978ba2e..bc6abad67 100644
--- 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
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_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(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;
diff --git a/src/buildblock/Scanner.cxx b/src/buildblock/Scanner.cxx
index 2f48f1438..e8341af61 100644
--- a/src/buildblock/Scanner.cxx
+++ b/src/buildblock/Scanner.cxx
@@ -864,9 +864,10 @@ Scanner::Scanner(Type scanner_type)
1,
0.0944F, // energy resolution from Hsu et al. 2017
511.F,
- (short int)(0),
- (float)(0), // TODO
- (float)(0));
+ (short int)(2 * 188 + 1), // from RDF file
+ (float)(13), // from RDF file
+ (float)(375.4) // Hsu et al.
+ );
break;
case DiscoveryMI4ring: // This is the 4-ring DMI
@@ -895,9 +896,10 @@ Scanner::Scanner(Type scanner_type)
1,
0.0944F, // energy resolution from Hsu et al. 2017
511.F,
- (short int)(0),
- (float)(0), // TODO
- (float)(0));
+ (short int)(2 * 188 + 1), // from RDF file
+ (float)(13), // from RDF file
+ (float)(375.4) // Hsu et al.
+ );
break;
case DiscoveryMI5ring: // This is the 5-ring DMI
@@ -926,9 +928,42 @@ Scanner::Scanner(Type scanner_type)
1,
0.0944F, // energy resolution from Hsu et al. 2017
511.F,
- (short int)(0),
- (float)(0), // TODO
- (float)(0));
+ (short int)(2 * 188 + 1), // from RDF file
+ (float)(13), // from RDF file
+ (float)(375.4) // Hsu et al.
+ );
+ break;
+
+ case DiscoveryMI6ring: // This is the 6-ring DMI
+ // as above, but one extra block
+ // Hsu et al. 2017 JNM
+ // crystal size 3.95 x 5.3 x 25
+ set_params(DiscoveryMI6ring,
+ string_list("GE Discovery MI 6 rings",
+ "Discovery MI6",
+ "Discovery MI"), // needs to include last value as used by GE in RDF files
+ 54,
+ 415,
+ 401, // TODO should compute num_arccorrected_bins from effective_FOV/default_bin_size
+ 2 * 272,
+ 380.5F - 9.4F, // TODO inner_ring_radius and DOI, currently set such that effective ring-radius is correct
+ 9.4F, // TODO DOI
+ 5.52296F, // ring-spacing
+ 2.206F, // TODO currently using the central bin size default bin size. GE might be using something else
+ static_cast(-4.399 * _PI / 180), // TODO check sign
+ 6,
+ 4,
+ 9,
+ 4,
+ 1,
+ 1,
+ 1,
+ 0.0944F, // energy resolution from Hsu et al. 2017
+ 511.F,
+ (short int)(2 * 188 + 1), // from RDF file
+ (float)(13), // from RDF file
+ (float)(375.4) // Hsu et al.
+ );
break;
case HZLR:
diff --git a/src/include/stir/Scanner.h b/src/include/stir/Scanner.h
index e5b7332bd..5b2210c69 100644
--- a/src/include/stir/Scanner.h
+++ b/src/include/stir/Scanner.h
@@ -165,6 +165,7 @@ class Scanner
DiscoveryMI3ring,
DiscoveryMI4ring,
DiscoveryMI5ring,
+ DiscoveryMI6ring,
HZLR,
RATPET,
PANDA,