More updates to the waveform format

ismrmrd · Mar 5, 2018 · 45168d8 · 45168d8
1 parent 78892e0
commit 45168d8
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Showing 13 changed files with 273 additions and 74 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -68,7 +68,7 @@ set(ISMRMRD_VERSION_PATCH 0)
 set(ISMRMRD_VERSION_STRING ${ISMRMRD_VERSION_MAJOR}.${ISMRMRD_VERSION_MINOR}.${ISMRMRD_VERSION_PATCH})
 set(ISMRMRD_SOVERSION ${ISMRMRD_VERSION_MAJOR}.${ISMRMRD_VERSION_MINOR})
 
-set(ISMRMRD_XML_SCHEMA_SHA1 "a18ff3aeaa35aab79e405329d45a99229a996287")
+set(ISMRMRD_XML_SCHEMA_SHA1 "f9e6c0f867bd6395642d56cdf0a51b08ee6a636f")
 
 #Remove line breaks and white space that does not change the meaning of the schema
 file(STRINGS ${CMAKE_SOURCE_DIR}/schema/ismrmrd.xsd SCHEMA_STRINGS) #Read all strings from file

diff --git a/include/ismrmrd/dataset.h b/include/ismrmrd/dataset.h
@@ -183,6 +183,10 @@ class EXPORTISMRMRD Dataset {
     template <typename T> void readNDArray(const std::string &var, uint32_t index, NDArray<T> &arr);
     uint32_t getNumberOfNDArrays(const std::string &var);
 
+    //Waveforms
+    void appendWaveform(const Waveform &wav);
+    void readWaveform(uint32_t index, Waveform & wav);
+    uint32_t getNumberOfWaveforms();
 protected:
     ISMRMRD_Dataset dset_;
 };

diff --git a/include/ismrmrd/waveform.h b/include/ismrmrd/waveform.h
@@ -42,19 +42,26 @@ typedef struct ISMRMRD_Waveform
 
 
 EXPORTISMRMRD int ismrmrd_make_consistent_waveform(ISMRMRD_Waveform* wav);
-EXPORTISMRMRD int ismrmrd_size_of_waveform_data(ISMRMRD_Waveform* wav);
+EXPORTISMRMRD int ismrmrd_size_of_waveform_data(const ISMRMRD_Waveform* wav);
 EXPORTISMRMRD ISMRMRD_Waveform* ismrmrd_create_waveform();
 EXPORTISMRMRD int ismrmrd_free_waveform(ISMRMRD_Waveform*);
 EXPORTISMRMRD int ismrmrd_init_waveform(ISMRMRD_Waveform*);
+EXPORTISMRMRD int ismrmrd_init_waveformheader(ISMRMRD_WaveformHeader* header);
+EXPORTISMRMRD int ismrmrd_copy_waveform(ISMRMRD_Waveform* dest, const ISMRMRD_Waveform* src);
 
 #ifdef __cplusplus
 }
-    struct Waveform : public ISMRMRD_Waveform {
+    struct EXPORTISMRMRD Waveform : public ISMRMRD_Waveform {
+        Waveform();
+        Waveform(const Waveform &other);
+        Waveform(Waveform&& other);
         Waveform(uint16_t number_of_samples, uint16_t available_channels);
         ~Waveform();
+        Waveform & operator=(const Waveform &other);
+        Waveform & operator=(Waveform &&other);
 
     };
-};
-};
+}
+
 #endif
 #endif //ISMRMRD_WAVEFORM_H_H
diff --git a/include/ismrmrd/waveformdata.h b/include/ismrmrd/waveformdata.h
diff --git a/include/ismrmrd/xml.h b/include/ismrmrd/xml.h
@@ -289,12 +289,21 @@ namespace ISMRMRD
     Optional<std::string> interleavingDimension;
   };
 
+  enum class TrajectoryType {
+      CARTESIAN,
+      EPI,
+      RADIAL,
+      GOLDENANGLE,
+      SPIRAL,
+      OTHER
+  };
+
   struct Encoding
   {
     EncodingSpace encodedSpace;
     EncodingSpace reconSpace;
     EncodingLimits encodingLimits;
-    std::string trajectory;
+    TrajectoryType trajectory;
     Optional<TrajectoryDescription> trajectoryDescription;
     Optional<ParallelImaging> parallelImaging;
     Optional<long> echoTrainLength;
@@ -310,6 +319,19 @@ namespace ISMRMRD
     Optional<std::vector<float> > echo_spacing;
   };
 
+  enum class WaveformType {
+      ECG,
+      PULSE,
+      RESPIRATORY,
+      TRIGGER,
+      GRADIENTWAVEFORM,
+      OTHER
+  };
+  struct WaveformInformation{
+      std::string waveformName;
+      WaveformType waveformType;
+  };
+
   struct IsmrmrdHeader
   {
     Optional<long> version;
@@ -320,7 +342,8 @@ namespace ISMRMRD
     ExperimentalConditions experimentalConditions;
     std::vector<Encoding> encoding;
     Optional<SequenceParameters> sequenceParameters;
-    Optional<UserParameters> userParameters;    
+    Optional<UserParameters> userParameters;
+    std::vector<WaveformInformation> waveformInformation;
   };
 
 

diff --git a/libsrc/dataset.c b/libsrc/dataset.c
@@ -456,6 +456,12 @@ static hid_t get_hdf5type_waveformheader(void) {
     vartype = H5Tarray_create2(H5T_NATIVE_CHAR, 1, arraydims);
     h5status = H5Tinsert(datatype, "type", HOFFSET(ISMRMRD_AcquisitionHeader, position), vartype);
     H5Tclose(vartype);
+
+    /* Clean up */
+    if (h5status < 0) {
+        ISMRMRD_PUSH_ERR(ISMRMRD_FILEERROR, "Failed get imageheader data type");
+    }
+
     return  datatype;
 
 }

diff --git a/libsrc/dataset.cpp b/libsrc/dataset.cpp
@@ -29,10 +29,7 @@ Dataset::Dataset(const char* filename, const char* groupname, bool create_file_i
 // Destructor
 Dataset::~Dataset()
 {
-    int status = ismrmrd_close_dataset(&dset_);
-    if (status != ISMRMRD_NOERROR) {
-        throw std::runtime_error(build_exception_string());
-    }
+    ismrmrd_close_dataset(&dset_);
 }
 
 // XML Header
@@ -93,6 +90,25 @@ void Dataset::appendImage(const std::string &var, const ISMRMRD_Image *im)
         throw std::runtime_error(build_exception_string());
     }
 }
+
+
+void Dataset::appendWaveform(const Waveform &wav) {
+    int status = ismrmrd_append_waveform(&dset_,&wav);
+    if (status != ISMRMRD_NOERROR){
+        throw std::runtime_error(build_exception_string());
+    }
+}
+
+void Dataset::readWaveform(uint32_t index, Waveform &wav) {
+    int status = ismrmrd_read_waveform(&dset_,index,&wav);
+    if (status != ISMRMRD_NOERROR){
+        throw std::runtime_error(build_exception_string());
+    }
+}
+
+uint32_t Dataset::getNumberOfWaveforms() {
+    return ismrmrd_get_number_of_waveforms(&dset_);
+}
 // Specific instantiations
 template EXPORTISMRMRD void Dataset::appendImage(const std::string &var, const Image<uint16_t> &im);
 template EXPORTISMRMRD void Dataset::appendImage(const std::string &var, const Image<int16_t> &im);

diff --git a/libsrc/waveform.c b/libsrc/waveform.c
@@ -12,39 +12,85 @@
 #include <string.h>
 #include <stdlib.h>
 #include <stdio.h>
+#include <ismrmrd/version.h>
+
 #endif /* __cplusplus */
-int ismrmrd_make_consistent_waveform(ISMRMRD_Waveform* wav){
+
+#ifdef __cplusplus
+namespace ISMRMRD {
+extern "C" {
+#endif
+
+int ismrmrd_make_consistent_waveform(ISMRMRD_Waveform *wav) {
     size_t data_size;
 
     data_size = ismrmrd_size_of_waveform_data(wav);
 
-    if (data_size > 0){
-        uint32_t* newPtr = (uint32_t *)(realloc(wav->data,data_size));
+    if (data_size > 0) {
+        uint32_t *newPtr = (uint32_t *) (realloc(wav->data, data_size));
         if (newPtr == NULL) {
             return ISMRMRD_PUSH_ERR(ISMRMRD_MEMORYERROR,
-                          "Failed to realloc acquisition data array");
+                                    "Failed to realloc acquisition data array");
         }
         wav->data = newPtr;
     }
 
     return ISMRMRD_NOERROR;
 }
 
-int ismrmrd_size_of_waveform_data(ISMRMRD_Waveform* wav){
-    return wav->head.available_channels*wav->head.number_of_samples*sizeof(uint32_t);
+int ismrmrd_size_of_waveform_data(const ISMRMRD_Waveform *wav) {
+    return wav->head.available_channels * wav->head.number_of_samples * sizeof(uint32_t);
+}
+
+
+ISMRMRD_Waveform *ismrmrd_create_waveform() {
+    ISMRMRD_Waveform *wav = (ISMRMRD_Waveform *) malloc(sizeof(ISMRMRD_Waveform));
+    if (wav == NULL) {
+        ISMRMRD_PUSH_ERR(ISMRMRD_MEMORYERROR, "Failed to malloc new ISMRMRD_Waveform.");
+        return NULL;
+    }
+    if (ismrmrd_init_waveform(wav) != ISMRMRD_NOERROR) {
+        ISMRMRD_PUSH_ERR(ISMRMRD_RUNTIMEERROR, "Failed to initialize waveform.");
+        return NULL;
+    }
+    return wav;
+}
+
+int ismrmrd_init_waveformheader(ISMRMRD_WaveformHeader *hdr) {
+    memset(hdr, 0, sizeof(ISMRMRD_WaveformHeader));
+    hdr->available_channels = 1;
+    hdr->version = ISMRMRD_VERSION_MAJOR;
+    return ISMRMRD_NOERROR;
+
+}
+
+int ismrmrd_init_waveform(ISMRMRD_Waveform *wav) {
+
+    ismrmrd_init_waveformheader(&wav->head);
+    wav->data = NULL;
+    return ISMRMRD_NOERROR;
+
 }
 
+int ismrmrd_copy_waveform(ISMRMRD_Waveform *dest, const ISMRMRD_Waveform *src) {
+
+    if (src == NULL) {
+        return ISMRMRD_PUSH_ERR(ISMRMRD_RUNTIMEERROR, "Source pointer should not NULL.");
+    }
+    if (dest == NULL) {
+        return ISMRMRD_PUSH_ERR(ISMRMRD_RUNTIMEERROR, "Destination pointer should not NULL.");
+    }
+
+    memcpy(&dest->head, &src->head, sizeof(ISMRMRD_WaveformHeader));
+    ismrmrd_make_consistent_waveform(dest);
+
+    memcpy(dest->data, src->data, ismrmrd_size_of_waveform_data(src));
 
-ISMRMRD_Waveform * ismrmrd_create_waveform() {
-	ISMRMRD_Waveform *wav = (ISMRMRD_Waveform *)malloc(sizeof(ISMRMRD_Waveform));
-	if (wav == NULL) {
-		ISMRMRD_PUSH_ERR(ISMRMRD_MEMORYERROR, "Failed to malloc new ISMRMRD_Waveform.");
-		return NULL;
-	}
-	if (ismrmrd_init_waveform(wav) != ISMRMRD_NOERROR)
-	{
-		ISMRMRD_PUSH_ERR(ISMRMRD_RUNTIMEERROR, "Failed to initialize waveform.");
-		return NULL;
-	}
-	return wav;
-}
+    return ISMRMRD_NOERROR;
+
+}
+
+#ifdef __cplusplus
+}
+}
+#endif
diff --git a/libsrc/waveform.cpp b/libsrc/waveform.cpp
@@ -2,12 +2,33 @@
 // Created by dch on 27/02/18.
 //
 
+#include <cstring>
 #include "ismrmrd/waveform.h"
 
 
 ISMRMRD::Waveform::Waveform(uint16_t number_of_samples, uint16_t available_channels) {
 
+    ismrmrd_init_waveform(this);
     this->data = new uint32_t[number_of_samples*available_channels];
+    this->head.available_channels = available_channels;
+    this->head.number_of_samples = number_of_samples;
+    this->head.waveform_id =0;
+
+
+}
+
+ISMRMRD::Waveform::Waveform() {
+    ismrmrd_init_waveform(this);
+}
+
+ISMRMRD::Waveform::Waveform(const Waveform &other) {
+    ismrmrd_copy_waveform(this,&other);
+}
+
+ISMRMRD::Waveform::Waveform(Waveform &&other) {
+    memcpy(&this->head,&other.head,sizeof(ISMRMRD_WaveformHeader));
+    this->data = other.data;
+    other.data = nullptr;
 
 
 }
@@ -17,5 +38,16 @@ ISMRMRD::Waveform::~Waveform() {
 
 }
 
+ISMRMRD::Waveform & ISMRMRD::Waveform::operator=(Waveform &&other) {
+    memcpy(&this->head,&other.head,sizeof(ISMRMRD_WaveformHeader));
+    this->data = other.data;
+    other.data = nullptr;
+    return *this;
+}
+
+ISMRMRD::Waveform & ISMRMRD::Waveform::operator=(const Waveform &other) {
+    ismrmrd_copy_waveform(this,&other);
+    return *this;
+}
 
 
diff --git a/libsrc/waveformdata.cpp b/libsrc/waveformdata.cpp