introduced a quick fix for dicom output failure #1128

src/xGadgetron/cGadgetron/cgadgetron.cpp

@@ -154,6 +154,8 @@ void* cGT_newObject(const char* name)
 		NEW_GADGET(PhysioInterpolationGadget);
 		NEW_GADGET(GPURadialSensePrepGadget);
 		NEW_GADGET(GPUCGSenseGadget);
+		NEW_GADGET(FFTGadget);
+		NEW_GADGET(CombineGadget);
 		NEW_GADGET(ExtractGadget);
 		NEW_GADGET(AutoScaleGadget);
 		NEW_GADGET(ComplexToFloatGadget);
@@ -1041,14 +1043,16 @@ cGT_imageParameter(void* ptr_im, const char* name)
 
 extern "C"
 void*
-cGT_reconstructImages(void* ptr_recon, void* ptr_input)
+cGT_reconstructImages(void* ptr_recon, void* ptr_input, const char* dcm_prefix)
 {
 	try {
 		CAST_PTR(DataHandle, h_recon, ptr_recon);
 		CAST_PTR(DataHandle, h_input, ptr_input);
 		ImagesReconstructor& recon = objectFromHandle<ImagesReconstructor>(h_recon);
 		MRAcquisitionData& input = objectFromHandle<MRAcquisitionData>(h_input);
-		recon.process(input);
+		if (strlen(dcm_prefix) < 1)
+			dcm_prefix = 0;
+		recon.process(input, dcm_prefix);
 		return new DataHandle;
 	}
 	CATCH;

src/xGadgetron/cGadgetron/gadgetron_x.cpp

@@ -236,13 +236,8 @@ AcquisitionsProcessor::process(MRAcquisitionData& acquisitions)
 }
 
 void 
-ImagesReconstructor::process(MRAcquisitionData& acquisitions)
+ImagesReconstructor::process(MRAcquisitionData& acquisitions, const char* dcm_prefix)
 {
-	//check_gadgetron_connection(host_, port_);
-
-	std::string config = xml();
-	//std::cout << "config:\n" << config << std::endl;
-
 	uint32_t nacquisitions = 0;
 	nacquisitions = acquisitions.number();
 	//std::cout << nacquisitions << " acquisitions" << std::endl;
@@ -254,6 +249,19 @@ ImagesReconstructor::process(MRAcquisitionData& acquisitions)
 	conn().register_reader(GADGET_MESSAGE_ISMRMRD_IMAGE,
 		shared_ptr<GadgetronClientMessageReader>
 		(new GadgetronClientImageMessageCollector(sptr_images_)));
+	if (dcm_prefix) {
+		add_gadget("extract", gadgetron::shared_ptr<aGadget>(new ExtractGadget));
+		add_gadget("autoscale", gadgetron::shared_ptr<aGadget>(new AutoScaleGadget));
+		add_writer("writer_dcm", writer_dcm_);
+		gadgetron::shared_ptr<DicomFinishGadget> endgadget(new DicomFinishGadget);
+		set_endgadget(endgadget);
+		conn().register_reader(GADGET_MESSAGE_DICOM_WITHNAME,
+			shared_ptr<GadgetronClientMessageReader>
+			(new GadgetronClientBlobMessageReader(std::string(dcm_prefix), std::string("dcm"))));
+	}
+	std::string config = xml();
+	//std::cout << "config:\n" << config << std::endl;
+
 	for (int nt = 0; nt < N_TRIALS; nt++) {
 		try {
 			conn().connect(host_, port_);
@@ -288,6 +296,7 @@ ImagesProcessor::process(const GadgetronImageData& images)
 		THROW("DICOM writer does not support complex images");
 
 	std::string config = xml();
+	std::cout << xml() << '\n';
 	GTConnector conn;
 	sptr_images_ = images.new_images_container();
 	if (dicom_)

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

@@ -97,7 +97,7 @@ extern "C" {
 		int from, int till, int n, PTR_FLOAT values);
 
 	// image methods
-	void* cGT_reconstructImages(void* ptr_recon, void* ptr_input);
+	void* cGT_reconstructImages(void* ptr_recon, void* ptr_input, const char* dcm_prefix);
 	void* cGT_reconstructedImages(void* ptr_recon);
     void* cGT_readImages(const char* file);
 	void* cGT_ImageFromAcquisitiondata(void* ptr_acqs);

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

@@ -356,7 +356,29 @@ namespace sirf {
 		}
 	};
 
-    class GenericReconCartesianFFTGadget : public Gadget {
+	class FFTGadget : public Gadget {
+	public:
+		FFTGadget() :
+			Gadget("FFT", "gadgetron_mricore", "FFTGadget")
+		{}
+		static const char* class_name()
+		{
+			return "FFTGadget";
+		}
+	};
+
+	class CombineGadget : public Gadget {
+	public:
+		CombineGadget() :
+			Gadget("Combine", "gadgetron_mricore", "CombineGadget")
+		{}
+		static const char* class_name()
+		{
+			return "CombineGadget";
+		}
+	};
+
+	class GenericReconCartesianFFTGadget : public Gadget {
 	public:
 		GenericReconCartesianFFTGadget() :
 			Gadget("Recon", "gadgetron_mricore", "GenericReconCartesianFFTGadget")

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

@@ -213,12 +213,14 @@ namespace sirf {
 			, file_prefix(fileprefix)
 			, file_suffix(filesuffix)
 		{
+			//std::cout << fileprefix << '.' << filesuffix << '\n';
 		}
 
 		virtual ~GadgetronClientBlobMessageReader() {}
 
 		virtual void read(boost::asio::ip::tcp::socket* socket)
 		{
+			//std::cout << "in GadgetronClientBlobMessageReader::read...\n";
 			// MUST READ 32-bits
 			uint32_t nbytes;
 			boost::asio::read(*socket, boost::asio::buffer(&nbytes, sizeof(uint32_t)));
@@ -255,7 +257,7 @@ namespace sirf {
 			filename << "." << file_suffix;
 			filename_attrib.append("_attrib.xml");
 
-			std::cout << "Writing image " << filename.str() << std::endl;
+			//std::cout << "Writing image " << filename.str() << std::endl;
 
 			std::ofstream outfile;
 			outfile.open(filename.str().c_str(), std::ios::out | std::ios::binary);

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

@@ -239,9 +239,9 @@ namespace sirf {
 
 		ImagesReconstructor() :
 			reader_(new IsmrmrdAcqMsgReader),
-			writer_(new IsmrmrdImgMsgWriter)
+			writer_(new IsmrmrdImgMsgWriter),
+			writer_dcm_(new DicomImageMessageWriter)
 		{
-			//class_ = "ImagesReconstructor";
 			sptr_images_.reset();
 			add_reader("reader", reader_);
 			add_writer("writer", writer_);
@@ -253,7 +253,7 @@ namespace sirf {
 			return "ImagesReconstructor";
 		}
 
-		void process(MRAcquisitionData& acquisitions);
+		void process(MRAcquisitionData& acquisitions, const char* dcm_prefix = "image");
 		gadgetron::shared_ptr<GadgetronImageData> get_output()
 		{
 			return sptr_images_;
@@ -262,6 +262,7 @@ namespace sirf {
 	private:
 		gadgetron::shared_ptr<IsmrmrdAcqMsgReader> reader_;
 		gadgetron::shared_ptr<IsmrmrdImgMsgWriter> writer_;
+		gadgetron::shared_ptr<DicomImageMessageWriter> writer_dcm_;
 		gadgetron::shared_ptr<GadgetronImageData> sptr_images_;
 	};
 

src/xGadgetron/pGadgetron/Gadgetron.py

@@ -1415,7 +1415,7 @@ class Reconstructor(GadgetChain):
     Class for a chain of gadgets that has AcquisitionData on input and 
     ImageData on output.
     '''
-    def __init__(self, list = None):
+    def __init__(self, list=None):
         self.handle = None
         self.handle = pygadgetron.cGT_newObject('ImagesReconstructor')
         check_status(self.handle)
@@ -1435,14 +1435,21 @@ def set_input(self, input_data):
         '''
         assert isinstance(input_data, AcquisitionData)
         self.input_data = input_data
-    def process(self):
+    def process(self, dcm_prefix=None):
         '''
         Processes the input with the gadget chain.
+        dcm_prefix: Python text string.
+        If dcm_prefix is not None, the reconstructed images are written to
+        files <dcm_prefix>_<image number>.dcm.
+        Otherwise, they are stored in memory and can be retrieved by
+        get_output().
         '''
         if self.input_data is None:
             raise error('no input data')
+        if dcm_prefix is None:
+            dcm_prefix = ""
         try_calling(pygadgetron.cGT_reconstructImages\
-             (self.handle, self.input_data.handle))
+             (self.handle, self.input_data.handle, dcm_prefix))
     def get_output(self, subset = None):
         '''
         Returns specified subset of the output ImageData. If no subset is