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GE Discovery MI updates #1503

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merged 3 commits into from
Sep 4, 2024
Merged

GE Discovery MI updates #1503

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c6adcbb
add GE DMI TOF info and 6-ring version
KrisThielemans Sep 4, 2024
a88ccde
fix RDF9 import of non-TOF data
KrisThielemans Sep 4, 2024
66c60da
updated release notes [ci skip]
KrisThielemans Sep 4, 2024
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5 changes: 5 additions & 0 deletions documentation/release_6.3.htm
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,11 @@ <h3>New functionality</h3>
is disabled for backwards compatibility.<br>
<a href=https://github.com/UCL/STIR/pull/1291>PR #1291</a>
</li>
<li>
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).<br>
<a href=https://github.com/UCL/STIR/pull/1503>PR #1503</a>
</li>
</ul>


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57 changes: 31 additions & 26 deletions src/IO/GEHDF5Wrapper.cxx
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Expand Up @@ -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)
{
Expand All @@ -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")
{
Expand Down Expand Up @@ -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;
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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();
Expand All @@ -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;
Expand Down Expand Up @@ -831,7 +837,6 @@ GEHDF5Wrapper::read_sinogram(Array<3, unsigned char>& output,
}
}
}
output.release_data_ptr();
}

return Succeeded::yes;
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53 changes: 44 additions & 9 deletions src/buildblock/Scanner.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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<float>(-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:

Expand Down
1 change: 1 addition & 0 deletions src/include/stir/Scanner.h
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Original file line number Diff line number Diff line change
Expand Up @@ -165,6 +165,7 @@ class Scanner
DiscoveryMI3ring,
DiscoveryMI4ring,
DiscoveryMI5ring,
DiscoveryMI6ring,
HZLR,
RATPET,
PANDA,
Expand Down