Merge pull request #1263 from KrisThielemans/revert_1241

Revert "Moving SyneRBI-Challenge nema-data utilities to SIRF (#1241)"

CHANGES.md

@@ -21,11 +21,6 @@
   - provided prior and objective function objects with methods for computing
     the product of the Hessian and a vector.
 
-* PET:
-  - incorporated into SIRF data processing utilities from SyneRBI-Challenge.
-
-## v3.7.0
-
 * CMake/building:
   - add `DISABLE_Gadgetron_TOOLBOXES` option (defaults to `OFF`) to be
     able to cope with compilation problems with older Gadgetron versions.

src/iUtilities/include/sirf/iUtilities/DataHandle.h

@@ -279,23 +279,6 @@ getObjectSptrFromHandle(const void* h, std::shared_ptr<Object>& sptr) {
 	sptr = *ptr_sptr;
 }
 
-template<class Object>
-void
-setHandleObjectSptr(void* h, std::shared_ptr<Object>& sptr) {
-	auto handle = reinterpret_cast<ObjectHandle<Object>*>(h);
-	//ObjectHandle<Object>* handle = (ObjectHandle<Object>*)h;
-#if defined(USE_BOOST)
-	if (handle->uses_boost_sptr())
-		THROW("cannot cast boost::shared_ptr to std::shared_ptr");
-#endif
-	void* ptr = handle->data();
-	if (ptr == 0)
-		THROW("zero data pointer cannot be dereferenced");
-	CAST_PTR(std::shared_ptr<Object>, ptr_sptr, ptr);
-	//delete ptr_sptr;
-	*ptr_sptr = sptr;
-}
-
 #if defined(USE_BOOST)
 template<class Object>
 void

src/xSTIR/cSTIR/cstir.cpp

@@ -39,8 +39,6 @@ using namespace sirf;
 #define NEW_OBJECT_HANDLE(T) new ObjectHandle<T >(std::shared_ptr<T >(new T))
 #define SPTR_FROM_HANDLE(Object, X, H) \
   std::shared_ptr<Object> X; getObjectSptrFromHandle<Object>(H, X);
-#define HANDLE_FROM_SPTR(Object, X, H) \
-  setHandleObjectSptr<Object>(H, X);
 
 static void*
 unknownObject(const char* obj, const char* name, const char* file, int line)
@@ -493,42 +491,6 @@ void* cSTIR_convertListmodeToSinograms(void* ptr)
 	CATCH;
 }
 
-extern "C"
-void* cSTIR_promptsFromListmode(void* ptr_lm2s, void* ptr_lmdata,
-	const float start, const float stop,
-	void* ptr_templ, void* ptr_sino, const char* prefix)
-{
-	try {
-		ListmodeToSinograms& lm2s = objectFromHandle<ListmodeToSinograms>(ptr_lm2s);
-		STIRListmodeData& lm_data = objectFromHandle<STIRListmodeData>(ptr_lmdata);
-		STIRAcquisitionData& templ = objectFromHandle<STIRAcquisitionData>(ptr_templ);
-		SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_sino, ptr_sino);
-		lm2s.prompts_from_listmode(lm_data, start, stop, templ, sptr_sino, prefix);
-		HANDLE_FROM_SPTR(STIRAcquisitionData, sptr_sino, ptr_sino);
-		return new DataHandle;
-	}
-	CATCH;
-}
-
-extern "C"
-void* cSTIR_promptsAndRandomsFromListmode(void* ptr_lm2s, void* ptr_lmdata,
-	const float start, const float stop,
-	void* ptr_templ, void* ptr_sino, void* ptr_rand, const char* prefix)
-{
-	try {
-		ListmodeToSinograms& lm2s = objectFromHandle<ListmodeToSinograms>(ptr_lm2s);
-		STIRListmodeData& lm_data = objectFromHandle<STIRListmodeData>(ptr_lmdata);
-		STIRAcquisitionData& templ = objectFromHandle<STIRAcquisitionData>(ptr_templ);
-		SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_sino, ptr_sino);
-		SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_rand, ptr_rand);
-		lm2s.prompts_and_randoms_from_listmode(lm_data, start, stop, templ, sptr_sino, sptr_rand, prefix);
-		HANDLE_FROM_SPTR(STIRAcquisitionData, sptr_sino, ptr_sino);
-		HANDLE_FROM_SPTR(STIRAcquisitionData, sptr_rand, ptr_rand);
-		return new DataHandle;
-	}
-	CATCH;
-}
-
 extern "C"
 void* cSTIR_scatterSimulatorFwd
 (void* ptr_am, void* ptr_im)
@@ -679,23 +641,6 @@ void* cSTIR_createPETAttenuationModel(const void* ptr_img, const void* ptr_am)
 	CATCH;
 }
 
-extern "C"
-void* cSTIR_computeACF(const void* ptr_sino,
-    const void* ptr_att, void* ptr_af, void* ptr_acf)
-{
-	try {
-		STIRAcquisitionData& sino = objectFromHandle<STIRAcquisitionData>(ptr_sino);
-		PETAttenuationModel& att = objectFromHandle<PETAttenuationModel>(ptr_att);
-		SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_af, ptr_af);
-		SPTR_FROM_HANDLE(STIRAcquisitionData, sptr_acf, ptr_acf);
-		PETAttenuationModel::compute_ac_factors(sino, att, sptr_af, sptr_acf);
-		HANDLE_FROM_SPTR(STIRAcquisitionData, sptr_af, ptr_af);
-		HANDLE_FROM_SPTR(STIRAcquisitionData, sptr_acf, ptr_acf);
-		return (void*) new DataHandle;
-	}
-	CATCH;
-}
-
 extern "C"
 void* cSTIR_chainPETAcquisitionSensitivityModels
 (const void* ptr_first, const void* ptr_second)

src/xSTIR/cSTIR/include/sirf/STIR/cstir.h

@@ -63,12 +63,6 @@ extern "C" {
 		(void* ptr_lm2s, const char* flag, int v);
 	void* cSTIR_setupListmodeToSinogramsConverter(void* ptr);
 	void* cSTIR_convertListmodeToSinograms(void* ptr);
-	void* cSTIR_promptsFromListmode(void* ptr_lm2s, void* ptr_lmdata,
-		const float start, const float stop,
-		void* ptr_templ, void* ptr_sino, const char* prefix);
-	void* cSTIR_promptsAndRandomsFromListmode(void* ptr_lm2s, void* ptr_lmdata,
-		const float start, const float stop,
-		void* ptr_templ, void* ptr_sino, void* ptr_rand, const char* prefix);
 	void* cSTIR_computeRandoms(void* ptr);
     void* cSTIR_lm_num_prompts_exceeds_threshold(void* ptr, const float threshold);
     void* cSTIR_objFunListModeSetInterval(void* ptr_f, size_t ptr_data);
@@ -82,8 +76,6 @@ extern "C" {
 		(const void* ptr_src, const char* src);
 	void* cSTIR_createPETAttenuationModel
 		(const void* ptr_img, const void* ptr_am);
-	void* cSTIR_computeACF
-		(const void* ptr_sino, const void* ptr_att, void* ptr_acf, void* ptr_iacf);
 	void* cSTIR_chainPETAcquisitionSensitivityModels
 		(const void* ptr_first, const void* ptr_second);
 	void* cSTIR_setupAcquisitionSensitivityModel(void* ptr_sm, void* ptr_ad);
@@ -100,7 +92,7 @@ extern "C" {
 		int subset_num, int num_subsets);
 	void* cSTIR_acquisitionModelBwdReplace(void* ptr_am, void* ptr_ad,
 		int subset_num, int num_subsets, void* ptr_im);
-	void* cSTIR_get_MatrixInfo(void* ptr);
+        void* cSTIR_get_MatrixInfo(void* ptr);
 
     // Acquisition Model Matrix
     void* cSTIR_setupSPECTUBMatrix(const void* h_smx, const void* h_acq, const void* h_img);