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Change prefix from PETAcquisitionData to STIRAcquisitionData. #1146

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merged 4 commits into from
Nov 17, 2022
Merged

Change prefix from PETAcquisitionData to STIRAcquisitionData. #1146

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2daf037
PETAcquisitionData -> STIRAcquisitionData, fixes #1126
evgueni-ovtchinnikov Nov 14, 2022
152ddcd
backward compatibility typedefs only used if SIRF version < 4.0.0
evgueni-ovtchinnikov Nov 17, 2022
02d3d5e
trying to fix build error (no version.h)
evgueni-ovtchinnikov Nov 17, 2022
0daf83b
[ci skip] updated CHANGES.md
evgueni-ovtchinnikov Nov 17, 2022
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1 change: 1 addition & 0 deletions CHANGES.md
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
- Added support for spiral trajectories that are pre-computed by the user by exposing a setter.
- Writing MR images to `.dcm` files quick-fixed. For proper fix, help from Gadgetron team will be sought after moving to using Gadgetron 4.
- Use C++ 17 if Gadgetron-support is enabled
- Renamed PETAcquisitionData and derived classes to STIRAcquisitionData* as STIR now supports SPECT in addition to PET modality. Backward compatibility ensured by defining old nomenclature via typedefs until the release of SIRF 4.

* Documentation
- revision of READMEs for the examples
Expand Down
80 changes: 40 additions & 40 deletions src/xSTIR/cSTIR/cstir.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -308,11 +308,11 @@ void* cSTIR_objectFromFile(const char* name, const char* filename)
}
if (sirf::iequals(name, "AcquisitionData")) {

std::shared_ptr<PETAcquisitionData> sptr;
if (PETAcquisitionData::storage_scheme().compare("file") == 0)
sptr.reset(new PETAcquisitionDataInFile(filename));
std::shared_ptr<STIRAcquisitionData> sptr;
if (STIRAcquisitionData::storage_scheme().compare("file") == 0)
sptr.reset(new STIRAcquisitionDataInFile(filename));
else
sptr.reset(new PETAcquisitionDataInMemory(filename));
sptr.reset(new STIRAcquisitionDataInMemory(filename));
return newObjectHandle(sptr);
}
if (sirf::iequals(name, "ListmodeToSinograms")) {
Expand Down Expand Up @@ -415,7 +415,7 @@ void* cSTIR_scatterSimulatorFwdReplace
try {
auto& am = objectFromHandle<PETSingleScatterSimulator>(ptr_am);
auto& id = objectFromHandle<STIRImageData>(ptr_im);
auto& ad = objectFromHandle<PETAcquisitionData>(ptr_ad);
auto& ad = objectFromHandle<STIRAcquisitionData>(ptr_ad);
am.forward(ad, id);
return new DataHandle;
}
Expand All @@ -429,7 +429,7 @@ void* cSTIR_setupScatterSimulator
try {
auto& am = objectFromHandle<PETSingleScatterSimulator>(ptr_am);
SPTR_FROM_HANDLE(STIRImageData, id, ptr_im);
SPTR_FROM_HANDLE(PETAcquisitionData, ad, ptr_ad);
SPTR_FROM_HANDLE(STIRAcquisitionData, ad, ptr_ad);
am.set_up(ad, id);
return new DataHandle;
}
Expand Down Expand Up @@ -521,7 +521,7 @@ void* cSTIR_createPETAcquisitionSensitivityModel
try {
shared_ptr<PETAcquisitionSensitivityModel> sptr;
if (sirf::iequals(src, "s")) {
PETAcquisitionData& ad = objectFromHandle<PETAcquisitionData>(ptr_src);
STIRAcquisitionData& ad = objectFromHandle<STIRAcquisitionData>(ptr_src);
sptr.reset(new PETAcquisitionSensitivityModel(ad));
}
else if (sirf::iequals(src, "n")) {
Expand Down Expand Up @@ -568,7 +568,7 @@ void* cSTIR_setupAcquisitionSensitivityModel(void* ptr_sm, void* ptr_ad)
try {
PETAcquisitionSensitivityModel& sm =
objectFromHandle<PETAcquisitionSensitivityModel>(ptr_sm);
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_ad, ptr_ad);
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_ad, ptr_ad);
sm.set_up(sptr_ad->get_exam_info_sptr(),
sptr_ad->get_proj_data_info_sptr()->create_shared_clone());
return (void*) new DataHandle;
Expand All @@ -583,7 +583,7 @@ void* cSTIR_applyAcquisitionSensitivityModel
try {
PETAcquisitionSensitivityModel& sm =
objectFromHandle<PETAcquisitionSensitivityModel>(ptr_sm);
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_ad, ptr_ad);
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_ad, ptr_ad);

if (sirf::iequals(job, "fwd"))
return newObjectHandle(sm.forward(*sptr_ad));
Expand All @@ -606,7 +606,7 @@ void* cSTIR_setupAcquisitionModel(void* ptr_am, void* ptr_dt, void* ptr_im)
try {
//writeText("setting up acquisition model\n");
AcqMod3DF& am = objectFromHandle<AcqMod3DF>(ptr_am);
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_dt, ptr_dt);
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_dt, ptr_dt);
SPTR_FROM_HANDLE(STIRImageData, sptr_id, ptr_im);
am.set_up(sptr_dt, sptr_id);
return (void*) new DataHandle;
Expand Down Expand Up @@ -653,7 +653,7 @@ void* cSTIR_acquisitionModelFwdReplace
try {
AcqMod3DF& am = objectFromHandle<AcqMod3DF>(ptr_am);
STIRImageData& id = objectFromHandle<STIRImageData>(ptr_im);
PETAcquisitionData& ad = objectFromHandle<PETAcquisitionData>(ptr_ad);
STIRAcquisitionData& ad = objectFromHandle<STIRAcquisitionData>(ptr_ad);
am.forward(ad, id, subset_num, num_subsets, num_subsets > 1);
return new DataHandle;
}
Expand All @@ -666,7 +666,7 @@ void* cSTIR_acquisitionModelBwd(void* ptr_am, void* ptr_ad,
{
try {
AcqMod3DF& am = objectFromHandle<AcqMod3DF>(ptr_am);
PETAcquisitionData& ad = objectFromHandle<PETAcquisitionData>(ptr_ad);
STIRAcquisitionData& ad = objectFromHandle<STIRAcquisitionData>(ptr_ad);
return newObjectHandle(am.backward(ad, subset_num, num_subsets));
}
CATCH;
Expand All @@ -691,7 +691,7 @@ void* cSTIR_acquisitionModelBwdReplace(void* ptr_am, void* ptr_ad,
{
try {
AcqMod3DF& am = objectFromHandle<AcqMod3DF>(ptr_am);
PETAcquisitionData& ad = objectFromHandle<PETAcquisitionData>(ptr_ad);
STIRAcquisitionData& ad = objectFromHandle<STIRAcquisitionData>(ptr_ad);
STIRImageData& id = objectFromHandle<STIRImageData>(ptr_im);
am.backward(id, ad, subset_num, num_subsets);
return new DataHandle;
Expand All @@ -716,9 +716,9 @@ cSTIR_setAcquisitionDataStorageScheme(const char* scheme)
{
try {
if (scheme[0] == 'f' || strcmp(scheme, "default") == 0)
PETAcquisitionDataInFile::set_as_template();
STIRAcquisitionDataInFile::set_as_template();
else
PETAcquisitionDataInMemory::set_as_template();
STIRAcquisitionDataInMemory::set_as_template();
return (void*)new DataHandle;
}
CATCH;
Expand All @@ -729,15 +729,15 @@ void*
cSTIR_getAcquisitionDataStorageScheme()
{
return charDataHandleFromCharData
(PETAcquisitionData::storage_scheme().c_str());
(STIRAcquisitionData::storage_scheme().c_str());
}

extern "C"
void* cSTIR_acquisitionDataFromTemplate(void* ptr_t)
{
try {
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_t, ptr_t);
std::shared_ptr<PETAcquisitionData> sptr(sptr_t->new_acquisition_data());
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_t, ptr_t);
std::shared_ptr<STIRAcquisitionData> sptr(sptr_t->new_acquisition_data());
return newObjectHandle(sptr);
}
CATCH;
Expand All @@ -747,8 +747,8 @@ extern "C"
void* cSTIR_cloneAcquisitionData(void* ptr_ad)
{
try {
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_ad, ptr_ad);
std::shared_ptr<PETAcquisitionData> sptr(sptr_ad->clone());
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_ad, ptr_ad);
std::shared_ptr<STIRAcquisitionData> sptr(sptr_ad->clone());
return newObjectHandle(sptr);
}
CATCH;
Expand All @@ -765,8 +765,8 @@ const int num_tof_bins_to_combine
)
{
try {
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_t, ptr_t);
std::shared_ptr<PETAcquisitionData> sptr =
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_t, ptr_t);
std::shared_ptr<STIRAcquisitionData> sptr =
sptr_t->single_slice_rebinned_data(
num_segments_to_combine,
num_views_to_combine,
Expand All @@ -788,15 +788,15 @@ void* cSTIR_acquisitionDataFromScannerInfo
stir::shared_ptr<ExamInfo> sptr_ei(new ExamInfo());
sptr_ei->imaging_modality = ImagingModality::PT;
stir::shared_ptr<stir::ProjDataInfo> sptr_pdi =
PETAcquisitionData::proj_data_info_from_scanner
STIRAcquisitionData::proj_data_info_from_scanner
(scanner, span, max_ring_diff, view_mash_factor);
#if STIR_VERSION >= 050000
sptr_pdi->set_tof_mash_factor(tof_mash_factor);
#endif
PETAcquisitionDataInFile::init();
std::shared_ptr<PETAcquisitionData> sptr_t =
PETAcquisitionData::storage_template();
std::shared_ptr<PETAcquisitionData> sptr(sptr_t->same_acquisition_data
STIRAcquisitionDataInFile::init();
std::shared_ptr<STIRAcquisitionData> sptr_t =
STIRAcquisitionData::storage_template();
std::shared_ptr<STIRAcquisitionData> sptr(sptr_t->same_acquisition_data
(sptr_ei, sptr_pdi));
sptr->fill(0.0f);
return newObjectHandle(sptr);
Expand All @@ -809,7 +809,7 @@ void* cSTIR_getAcquisitionDataDimensions(const void* ptr_acq, size_t ptr_dim)
{
try {
int* dim = (int*)ptr_dim;
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_ad, ptr_acq);
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_ad, ptr_acq);
dim[0] = sptr_ad->get_num_tangential_poss();
dim[1] = sptr_ad->get_num_views();
dim[2] = sptr_ad->get_num_non_TOF_sinograms();
Expand All @@ -824,7 +824,7 @@ void* cSTIR_getAcquisitionData(const void* ptr_acq, size_t ptr_data)
{
try {
float* data = (float*)ptr_data;
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_ad, ptr_acq);
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_ad, ptr_acq);
if (sptr_ad->is_empty())
return DataHandle::error_handle(
"Failed to get acquisition data: dealing with empty template?",
Expand All @@ -839,7 +839,7 @@ extern "C"
void* cSTIR_fillAcquisitionData(void* ptr_acq, float v)
{
try {
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_ad, ptr_acq);
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_ad, ptr_acq);
sptr_ad->fill(v);
return (void*)new DataHandle;
}
Expand All @@ -851,8 +851,8 @@ void* cSTIR_fillAcquisitionDataFromAcquisitionData
(void* ptr_acq, const void* ptr_from)
{
try {
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_ad, ptr_acq);
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_from, ptr_from);
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_ad, ptr_acq);
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_from, ptr_from);
sptr_ad->fill(*sptr_from);
return (void*)new DataHandle;
}
Expand All @@ -863,7 +863,7 @@ extern "C"
void* cSTIR_setAcquisitionData(void* ptr_acq, size_t ptr_data)
{
try {
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_ad, ptr_acq);
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_ad, ptr_acq);
float *data = (float *)ptr_data;
sptr_ad->fill_from(data);
return (void*)new DataHandle;
Expand All @@ -875,7 +875,7 @@ extern "C"
void* cSTIR_writeAcquisitionData(void* ptr_acq, const char* filename)
{
try {
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_ad, ptr_acq);
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_ad, ptr_acq);
sptr_ad->write(filename);
return (void*)new DataHandle;
}
Expand All @@ -886,7 +886,7 @@ extern "C"
void* cSTIR_get_ProjDataInfo(void* ptr_acq)
{
try {
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_ad, ptr_acq);
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_ad, ptr_acq);
return charDataHandleFromCharData(
sptr_ad->get_proj_data_info_sptr()->parameter_info().c_str());
}
Expand All @@ -897,10 +897,10 @@ extern "C"
void* cSTIR_get_subset(void* ptr_acq, int nv, size_t ptr_views)
{
try {
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_ad, ptr_acq);
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_ad, ptr_acq);
int* ptr_v = (int*)ptr_views;
std::vector<int> v(ptr_v, ptr_v + nv);
std::shared_ptr<PETAcquisitionData> sptr = std::move(sptr_ad->get_subset(v));
std::shared_ptr<STIRAcquisitionData> sptr = std::move(sptr_ad->get_subset(v));
return newObjectHandle(sptr);
}
CATCH;
Expand Down Expand Up @@ -1248,7 +1248,7 @@ void* cSTIR_ImageData_move_to_scanner_centre(void* im_ptr, const void* acq_data_
{
try {
STIRImageData& im = objectFromHandle<STIRImageData>(im_ptr);
PETAcquisitionData& ad = objectFromHandle<PETAcquisitionData>(acq_data_ptr);
STIRAcquisitionData& ad = objectFromHandle<STIRAcquisitionData>(acq_data_ptr);
im.move_to_scanner_centre(ad);

return static_cast<void*>(new DataHandle);
Expand All @@ -1261,7 +1261,7 @@ extern "C"
void* cSTIR_imageFromAcquisitionData(void* ptr_ad)
{
try {
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_ad, ptr_ad);
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_ad, ptr_ad);
shared_ptr<STIRImageData> sptr(new STIRImageData(*sptr_ad));
return newObjectHandle(sptr);
}
Expand All @@ -1272,7 +1272,7 @@ extern "C"
void* cSTIR_imageFromAcquisitionDataAndNxNy(void* ptr_ad, int nx, int ny)
{
try {
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_ad, ptr_ad);
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_ad, ptr_ad);
STIRImageData id(*sptr_ad);
int dim[3];
float vs[3];
Expand Down
20 changes: 10 additions & 10 deletions src/xSTIR/cSTIR/cstir_p.cpp
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Expand Up @@ -97,7 +97,7 @@ wrongFloatParameterValue
void*
sirf::cSTIR_AcquisitionDataParameter(void* hp, const char* name)
{
PETAcquisitionData& ad = objectFromHandle<PETAcquisitionData>(hp);
STIRAcquisitionData& ad = objectFromHandle<STIRAcquisitionData>(hp);
if (sirf::iequals(name, "tof_mash_factor"))
return dataHandle<int>(ad.get_tof_mash_factor());
else
Expand Down Expand Up @@ -136,7 +136,7 @@ sirf::cSTIR_setListmodeToSinogramsParameter(void* hp, const char* name, const vo
else if (sirf::iequals(name, "template_file"))
lm2s.set_template(charDataFromHandle(hv));
else if (sirf::iequals(name, "template"))
lm2s.set_template(objectFromHandle<PETAcquisitionData>(hv));
lm2s.set_template(objectFromHandle<STIRAcquisitionData>(hv));
else
return parameterNotFound(name, __FILE__, __LINE__);
return new DataHandle;
Expand Down Expand Up @@ -360,11 +360,11 @@ sirf::cSTIR_setAcquisitionModelParameter
{
AcqMod3DF& am = objectFromHandle< AcqMod3DF >(hp);
if (sirf::iequals(name, "additive_term")) {
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_ad, hv);
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_ad, hv);
am.set_additive_term(sptr_ad);
}
else if (sirf::iequals(name, "background_term")) {
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_ad, hv);
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_ad, hv);
am.set_background_term(sptr_ad);
}
else if (sirf::iequals(name, "asm")) {
Expand Down Expand Up @@ -565,12 +565,12 @@ sirf::cSTIR_setScatterEstimatorParameter

if (sirf::iequals(name, "setInput"))
{
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_pd, hv);
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_pd, hv);
obj.set_input_sptr(sptr_pd);
}
else if (sirf::iequals(name, "setRandoms"))
{
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_pd, hv);
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_pd, hv);
obj.set_background_sptr(sptr_pd);
}
else if (sirf::iequals(name, "setAttenuationImage"))
Expand All @@ -580,7 +580,7 @@ sirf::cSTIR_setScatterEstimatorParameter
}
else if (sirf::iequals(name, "setAttenuationCorrectionFactors"))
{
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_ad, hv);
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_ad, hv);
obj.set_attenuation_correction_factors_sptr(sptr_ad);
}
else if (sirf::iequals(name, "setASM"))
Expand Down Expand Up @@ -679,7 +679,7 @@ sirf::cSTIR_setPoissonLogLikelihoodWithLinearModelForMeanAndProjDataParameter
//else if (sirf::iequals(name, "max_segment_num_to_process"))
// obj_fun.set_max_segment_num_toa_process(dataFromHandle<int>((void*)hv));
else if (sirf::iequals(name, "acquisition_data")) {
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_ad, hv);
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_ad, hv);
obj_fun.set_acquisition_data(sptr_ad);
}
else if (sirf::iequals(name, "acquisition_model")) {
Expand Down Expand Up @@ -715,7 +715,7 @@ sirf::cSTIR_setReconstructionParameter
if (sirf::iequals(name, "output_filename_prefix"))
recon.set_output_filename_prefix(charDataFromDataHandle(hv));
else if (sirf::iequals(name, "input_data")) {
SPTR_FROM_HANDLE(PETAcquisitionData, sptr_ad, hv);
SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_ad, hv);
recon.set_input_data(sptr_ad->data());
}
else if (sirf::iequals(name, "disable_output")) {
Expand Down Expand Up @@ -890,7 +890,7 @@ sirf::cSTIR_setFBP2DParameter(DataHandle* hp, const char* name, const DataHandle
xSTIR_FBP2DReconstruction& recon =
objectFromHandle<xSTIR_FBP2DReconstruction >(hp);
if (sirf::iequals(name, "input")) {
PETAcquisitionData& acq_data = objectFromHandle<PETAcquisitionData>(hv);
STIRAcquisitionData& acq_data = objectFromHandle<STIRAcquisitionData>(hv);
recon.set_input(acq_data);
}
else if (sirf::iequals(name, "zoom")) {
Expand Down
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