Merge pull request #1120 from SyneRBI/set_modality

Implement set/get modality methods for SIRF STIR.ImageData

CHANGES.md

@@ -2,23 +2,22 @@
 
 ## v3.3.0
 
-* SPECTUBMatrix for (simple) usage in SPECT added.
+* Added a new acquisition model `SPECTUBMatrix` for (simple) usage in SPECT.
+  `sirf.STIR.ImageData` has now a way to set/get the modality.
 
 * interactive Python demos superseded by SIRF-Exercises notebooks removed.
 
 * arguments setting number of CG iterations and verbosity of output
-  of acquisition models method norm() added.
+  of acquisition models method `norm()` added.
 
 * path for ISMRMRD shared library when generating MR data fixed.
 
-* extension processing in ISMRMRDImageData::write fixed.
+* extension processing in `ISMRMRDImageData::write` fixed.
 
 * Python int array check/conversion ensuring C++ compatibility added.
 
 * C/Python interfaces for computing prior value added.
 
-* STIR spect matrix added.
-
 * Zenodo citation file added.
 
 

src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadgetron_data_containers.h

@@ -42,7 +42,7 @@ limitations under the License.
 #include <ismrmrd/dataset.h>
 
 #include "sirf/common/DataContainer.h"
-#include "sirf/common/MRImageData.h"
+#include "sirf/common/ImageData.h"
 #include "sirf/common/multisort.h"
 #include "sirf/Gadgetron/cgadgetron_shared_ptr.h"
 #include "sirf/Gadgetron/gadgetron_image_wrap.h"
@@ -612,7 +612,7 @@ namespace sirf {
 
 	*/
 
-	class ISMRMRDImageData : public MRImageData {
+	class ISMRMRDImageData : public ImageData {
 	public:
 		//ISMRMRDImageData(ISMRMRDImageData& id, const char* attr, 
 		//const char* target); //does not build, have to be in the derived class
@@ -894,7 +894,7 @@ namespace sirf {
 			ImageWrapIter;
 		typedef std::vector<gadgetron::shared_ptr<ImageWrap> >::const_iterator 
 			ImageWrapIter_const;
-		class Iterator : public MRImageData::Iterator {
+		class Iterator : public ImageData::Iterator {
 		public:
 			Iterator(ImageWrapIter iw, int n, int i, const ImageWrap::Iterator& it) :
 				iw_(iw), n_(n), i_(i), iter_(it), end_((**iw).end())
@@ -966,7 +966,7 @@ namespace sirf {
 			gadgetron::shared_ptr<Iterator> sptr_iter_;
 		};
 
-		class Iterator_const : public MRImageData::Iterator_const {
+		class Iterator_const : public ImageData::Iterator_const {
 		public:
 			Iterator_const(ImageWrapIter_const iw, int n, int i, 
 				const ImageWrap::Iterator_const& it) :

src/xSTIR/cSTIR/cstir.cpp

@@ -167,7 +167,9 @@ void* cSTIR_setParameter
 	try {
 		CAST_PTR(DataHandle, hs, ptr_s);
 		CAST_PTR(DataHandle, hv, ptr_v);
-		if (sirf::iequals(obj, "ListmodeToSinograms"))
+		if (sirf::iequals(obj, "ImageData"))
+			return cSTIR_setImageDataParameter(ptr_s, name, ptr_v);
+		else if (sirf::iequals(obj, "ListmodeToSinograms"))
 			return cSTIR_setListmodeToSinogramsParameter(ptr_s, name, ptr_v);
 		else if (sirf::iequals(obj, "SeparableGaussianImageFilter"))
 			return cSTIR_setSeparableGaussianImageFilterParameter(ptr_s, name, ptr_v);
@@ -242,6 +244,8 @@ void* cSTIR_parameter(const void* ptr, const char* obj, const char* name)
 		else if (sirf::iequals(obj, "TruncateToCylindricalFOVImageProcessor"))
 			return cSTIR_truncateToCylindricalFOVImageProcessorParameter
 			(handle, name);
+		else if (sirf::iequals(obj, "ImageData"))
+			return cSTIR_ImageDataParameter(handle, name);
 		else if (sirf::iequals(obj, "RayTracingMatrix"))
 			return cSTIR_rayTracingMatrixParameter(handle, name);
 		else if (sirf::iequals(obj, "SPECTUBMatrix"))

src/xSTIR/cSTIR/cstir_p.cpp

@@ -94,6 +94,27 @@ wrongFloatParameterValue
 	return wrongParameterValue(name, buff, file, line);
 }
 
+void*
+sirf::cSTIR_setImageDataParameter(void* hp, const char* name, const void* hv)
+{
+	STIRImageData& id = objectFromHandle<STIRImageData>(hp);
+	if (sirf::iequals(name, "modality"))
+		id.set_modality(charDataFromHandle(hv));
+	else
+		return parameterNotFound(name, __FILE__, __LINE__);
+	return new DataHandle;
+}
+
+void*
+sirf::cSTIR_ImageDataParameter(void* hp, const char* name)
+{
+	STIRImageData& id = objectFromHandle<STIRImageData>(hp);
+	if (sirf::iequals(name, "modality"))
+		return charDataHandleFromCharData(id.modality().c_str());
+	else
+		return parameterNotFound(name, __FILE__, __LINE__);
+}
+
 void*
 sirf::cSTIR_setListmodeToSinogramsParameter(void* hp, const char* name, const void* hv)
 {

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

@@ -26,6 +26,12 @@ limitations under the License.
 
 namespace sirf {
 
+	void*
+		cSTIR_setImageDataParameter(void* hp, const char* name, const void* hv);
+
+	void*
+		cSTIR_ImageDataParameter(void* hp, const char* name);
+
 	void*
 		cSTIR_setListmodeToSinogramsParameter(void* hp, const char* name, const void* hv);
 

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

@@ -45,7 +45,7 @@ limitations under the License.
 #include "sirf/common/JacobiCG.h"
 #include "sirf/common/DataContainer.h"
 #include "sirf/common/ANumRef.h"
-#include "sirf/common/PETImageData.h"
+#include "sirf/common/ImageData.h"
 #include "sirf/common/GeometricalInfo.h"
 #include "stir/ZoomOptions.h"
 
@@ -735,11 +735,8 @@ namespace sirf {
 	additioanally, implements the linear algebra functionality specified by the
 	abstract base class aDatacontainer.
 	*/
-	//class STIRImageData : public aDataContainer < float > {
-	class STIRImageData : public PETImageData { //<Iterator, Iterator_const> {
+	class STIRImageData : public ImageData {
 	public:
-		//typedef PETImageData<Iterator, Iterator_const>::Iter BaseIter;
-		//typedef PETImageData<Iterator, Iterator_const>::Iter_const BaseIter_const;
 		typedef ImageData::Iterator BaseIter;
 		typedef ImageData::Iterator_const BaseIter_const;
 		class Iterator : public BaseIter {
@@ -893,12 +890,24 @@ namespace sirf {
 		{
 			return false;
 		}
-
 		unsigned int items() const
 		{
 			return 1;
 		}
-        /// Write to file
+
+		std::string modality() const
+		{
+			ExamInfo ex_info = data().get_exam_info();
+			return ex_info.imaging_modality.get_name();
+		}
+		void set_modality(const std::string& mod)
+		{
+			ExamInfo ex_info = data().get_exam_info();
+			ex_info.imaging_modality = ImagingModality(mod);
+			data().set_exam_info(ex_info);
+		}
+
+		/// Write to file
         virtual void write(const std::string &filename) const;
         /// Write to file using format file.
         /*! This allows speciyfing the output file format used by STIR using a text file.

src/xSTIR/cSTIR/tests/test1.cpp

@@ -33,6 +33,7 @@ limitations under the License.
 
 #include "stir/common.h"
 #include "stir/IO/stir_ecat_common.h"
+#include "stir/ExamData.h"
 
 #include "sirf/common/iequals.h"
 #include "sirf/STIR/stir_x.h"
@@ -113,11 +114,25 @@ int test1()
 		std::cout << geom_info.get_info().c_str();
 		ok = (geom_info == geom_info_copy);
 		if (ok)
-			std::cout << "== ok\n";
+			std::cout << "geom_info == ok\n";
 		else
-			std::cout << "== failed \n";
+			std::cout << "geom_info == failed \n";
 		fail = fail || !ok;
 
+		// show and change modality demo
+		std::string mod = image_data.modality();
+		std::cout << '\n' << "modality: " << mod << '\n';
+		image_data.set_modality("NM");
+		std::cout << "new modality set: " << image_data.modality() << '\n';
+		ok = sirf::iequals(image_data.modality(), "NM");
+		if (ok)
+			std::cout << "set_modality ok\n";
+		else
+			std::cout << "set_modality failed \n";
+		fail = fail || !ok;
+		// restore
+		image_data.set_modality(mod);
+
 		// create additive term
 		shared_ptr<PETAcquisitionData> sptr_a = acq_data.new_acquisition_data();
 		PETAcquisitionData& at = *sptr_a;

src/xSTIR/pSTIR/STIR.py

@@ -323,6 +323,17 @@ def same_object(self):
         """See DataContainer method."""
         return ImageData()
 
+    def modality(self):
+        """Returns imaging modality as Python string."""
+        return parms.char_par(self.handle, 'ImageData', 'modality')
+
+    def set_modality(self, mod):
+        """Sets imaging modality.
+
+        mod: "PT" or "NM" or "MR" or "CT" or "US" or "Optical"
+        """
+        return parms.set_char_par(self.handle, 'ImageData', 'modality', mod)
+
     def initialise(self, dim, vsize=(1., 1., 1.), origin=(0., 0., 0.)):
         """
         Sets image size and geometric information.