/usr/include/ismrmrd/dataset.h is in libismrmrd-dev 1.3.3-1build2.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 | /* ISMRMRD Data Set */
/**
* @file dataset.h
*/
#pragma once
#ifndef ISMRMRD_DATASET_H
#define ISMRMRD_DATASET_H
#include "ismrmrd/ismrmrd.h"
#include <hdf5.h>
#ifdef __cplusplus
#include <string>
namespace ISMRMRD {
extern "C" {
#endif
/**
* Interface for accessing an ISMRMRD Data Set stored on disk in HDF5 format.
*
* A given ISMRMRD dataset if assumed to be stored under one group name in the
* HDF5 file. To make the datasets consistent, this library enforces that the
* XML configuration is stored in the variable groupname/xml and the
* Acquisitions are stored in the variable groupname/data.
*
*/
typedef struct ISMRMRD_Dataset {
char *filename;
char *groupname;
hid_t fileid;
} ISMRMRD_Dataset;
/**
* Initializes an ISMRMRD dataset structure
*
*/
EXPORTISMRMRD int ismrmrd_init_dataset(ISMRMRD_Dataset *dset, const char *filename, const char *groupname);
/**
* Opens an ISMRMRD dataset.
*
*/
EXPORTISMRMRD int ismrmrd_open_dataset(ISMRMRD_Dataset *dset, const bool create_if_neded);
/**
* Closes all references to the underlying HDF5 file.
*
*/
EXPORTISMRMRD int ismrmrd_close_dataset(ISMRMRD_Dataset *dset);
/**
* Writes the XML header string to the dataset.
*
* @warning There is no check of whether the string is a valid XML document at this point.
*
*/
EXPORTISMRMRD int ismrmrd_write_header(const ISMRMRD_Dataset *dset, const char *xmlstring);
/**
* Reads the XML configuration header from the dataset.
*
* @warning There is no check of whether the string is a valid XML document at this point.
*
*/
EXPORTISMRMRD char * ismrmrd_read_header(const ISMRMRD_Dataset *dset);
/**
* Appends and NMR/MRI acquisition to the dataset.
*
* Please consult @See ISMRMRD_Acquisition struct for details.
*/
EXPORTISMRMRD int ismrmrd_append_acquisition(const ISMRMRD_Dataset *dset, const ISMRMRD_Acquisition *acq);
/**
* Reads the acquisition with the specified index from the dataset.
*/
EXPORTISMRMRD int ismrmrd_read_acquisition(const ISMRMRD_Dataset *dset, uint32_t index, ISMRMRD_Acquisition *acq);
/**
* Return the number of acquisitions in the dataset.
*/
EXPORTISMRMRD uint32_t ismrmrd_get_number_of_acquisitions(const ISMRMRD_Dataset *dset);
/**
* Appends an Image to the variable named varname in the dataset.
*
* Please consult @See ISMRMRD_Image struct for details.
*
* Headers and attribute strings are stored separately from the data.
* This allows for easy viewing and reading in other applications.
*
* Images of the same size can be appended to "grow" an array.
* e.g. 20 images of size (256, 256, 4, 16), i.e. 4 slice and 16 channels, can be appended
* one at a time to make a (256, 256, 4, 16, 20) array in the file.
*
*/
EXPORTISMRMRD int ismrmrd_append_image(const ISMRMRD_Dataset *dset, const char *varname,
const ISMRMRD_Image *im);
/**
* Reads an image stored with appendImage.
* The index indicates which image to read from the variable named varname.
*/
EXPORTISMRMRD int ismrmrd_read_image(const ISMRMRD_Dataset *dset, const char *varname,
const uint32_t index, ISMRMRD_Image *im);
/**
* Return the number of images in the variable varname in the dataset.
*/
EXPORTISMRMRD uint32_t ismrmrd_get_number_of_images(const ISMRMRD_Dataset *dset, const char *varname);
/**
* Appends an NDArray to the variable named varname in the dataset.
*
* Please consult @See NDArray struct for details.
*
* Arrays contain simple data elements such as float, double, etc.
*
* Arrays of the same size can be appended to "grow" an array,
* e.g. 3D arrays of size (K,L,M) can be appended to grow a 4D array of size (K,L,M,N).
*
*/
EXPORTISMRMRD int ismrmrd_append_array(const ISMRMRD_Dataset *dset, const char *varname,
const ISMRMRD_NDArray *arr);
/**
* Reads an array from the data file.
*/
EXPORTISMRMRD int ismrmrd_read_array(const ISMRMRD_Dataset *dataset, const char *varname,
const uint32_t index, ISMRMRD_NDArray *arr);
/**
* Return the number of arrays in the variable varname in the dataset.
*/
EXPORTISMRMRD uint32_t ismrmrd_get_number_of_arrays(const ISMRMRD_Dataset *dset, const char *varname);
#ifdef __cplusplus
} /* extern "C" */
// ISMRMRD Dataset C++ Interface
class EXPORTISMRMRD Dataset {
public:
// Constructor and destructor
Dataset(const char* filename, const char* groupname, bool create_file_if_needed = true);
~Dataset();
// Methods
// XML Header
void writeHeader(const std::string &xmlstring);
void readHeader(std::string& xmlstring);
// Acquisitions
void appendAcquisition(const Acquisition &acq);
void readAcquisition(uint32_t index, Acquisition &acq);
uint32_t getNumberOfAcquisitions();
// Images
template <typename T> void appendImage(const std::string &var, const Image<T> &im);
void appendImage(const std::string &var, const ISMRMRD_Image *im);
template <typename T> void readImage(const std::string &var, uint32_t index, Image<T> &im);
uint32_t getNumberOfImages(const std::string &var);
// NDArrays
template <typename T> void appendNDArray(const std::string &var, const NDArray<T> &arr);
void appendNDArray(const std::string &var, const ISMRMRD_NDArray *arr);
template <typename T> void readNDArray(const std::string &var, uint32_t index, NDArray<T> &arr);
uint32_t getNumberOfNDArrays(const std::string &var);
protected:
ISMRMRD_Dataset dset_;
};
} /* ISMRMRD namespace */
#endif
#endif /* ISMRMRD_DATASET_H */
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