ISMRMRD
ISMRM Raw Data Format
ismrmrd.h
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1 /* ISMRMRD MR Raw Data Strutures */
2 /* DRAFT */
3 /* Authors: */
4 /* Michael S. Hansen (michael.hansen@nih.gov) */
5 /* Brian Hargreaves (bah@stanford.edu) */
6 /* Sebastian Kozerke (kozerke@biomed.ee.ethz.ch) */
7 /* Kaveh Vahedipour (k.vahedipour@fz-juelich.de) */
8 /* Hui Xue (hui.xue@nih.gov) */
9 /* Souheil Inati (souheil.inati@nih.gov) */
10 /* Joseph Naegele (joseph.naegele@nih.gov) */
11 
18 #pragma once
19 #ifndef ISMRMRD_H
20 #define ISMRMRD_H
21 
22 /* Language and cross platform section for defining types */
23 /* integers */
24 #ifdef _MSC_VER /* MS compiler */
25 #ifndef HAS_INT_TYPE
26 typedef __int16 int16_t;
27 typedef unsigned __int16 uint16_t;
28 typedef __int32 int32_t;
29 typedef unsigned __int32 uint32_t;
30 typedef __int64 int64_t;
31 typedef unsigned __int64 uint64_t;
32 #endif
33 #else /* non MS C or C++ compiler */
34 #include <stdint.h>
35 #include <stddef.h> /* for size_t */
36 #endif /* _MSC_VER */
37 
38 /* Complex numbers */
39 #ifdef __cplusplus
40 #include <complex>
41 typedef std::complex<float> complex_float_t;
42 typedef std::complex<double> complex_double_t;
43 #else
44 #ifdef _MSC_VER /* MS C compiler */
45 typedef struct complex_float_t{
46  float real;
47  float imag;
48 }complex_float_t;
49 typedef struct complex_double_t{
50  double real;
51  double imag;
52 }complex_double_t;
53 #else /* C99 compiler */
54 #include <complex.h>
55 typedef float complex complex_float_t;
56 typedef double complex complex_double_t;
57 #endif /* _MSC_VER */
58 #endif /* __cplusplus */
59 
60 /* Booleans - part of C++ */
61 #ifndef __cplusplus
62 #ifdef _MSC_VER /* MS C compiler */
63 typedef int bool;
64 #define false 0
65 #define true 1
66 #else /* C99 compiler */
67 #include <stdbool.h>
68 #endif /* _MSC_VER */
69 #endif /* __cplusplus */
70 
71 /* Vectors */
72 #ifdef __cplusplus
73 #include <vector>
74 #endif /* __cplusplus */
75 
76 /* Exports needed for MS C++ */
77 #include "ismrmrd/export.h"
78 
79 #pragma pack(push, 2) /* Use 2 byte alignment */
80 
81 #ifdef __cplusplus
82 namespace ISMRMRD {
83 extern "C" {
84 #endif
85 
90  ISMRMRD_USER_INTS = 8,
91  ISMRMRD_USER_FLOATS = 8,
92  ISMRMRD_PHYS_STAMPS = 3,
93  ISMRMRD_CHANNEL_MASKS = 16,
94  ISMRMRD_NDARRAY_MAXDIM = 7,
95  ISMRMRD_POSITION_LENGTH = 3,
96  ISMRMRD_DIRECTION_LENGTH = 3
97 };
98 
99 
104  ISMRMRD_BEGINERROR=-1,
105  ISMRMRD_NOERROR,
106  ISMRMRD_MEMORYERROR,
107  ISMRMRD_FILEERROR,
108  ISMRMRD_TYPEERROR,
109  ISMRMRD_RUNTIMEERROR,
110  ISMRMRD_HDF5ERROR,
111  ISMRMRD_ENDERROR
112 };
113 
126 };
127 
129 size_t ismrmrd_sizeof_data_type(int data_type);
130 
135  ISMRMRD_ACQ_FIRST_IN_ENCODE_STEP1 = 1,
136  ISMRMRD_ACQ_LAST_IN_ENCODE_STEP1 = 2,
137  ISMRMRD_ACQ_FIRST_IN_ENCODE_STEP2 = 3,
138  ISMRMRD_ACQ_LAST_IN_ENCODE_STEP2 = 4,
139  ISMRMRD_ACQ_FIRST_IN_AVERAGE = 5,
140  ISMRMRD_ACQ_LAST_IN_AVERAGE = 6,
141  ISMRMRD_ACQ_FIRST_IN_SLICE = 7,
142  ISMRMRD_ACQ_LAST_IN_SLICE = 8,
143  ISMRMRD_ACQ_FIRST_IN_CONTRAST = 9,
144  ISMRMRD_ACQ_LAST_IN_CONTRAST = 10,
145  ISMRMRD_ACQ_FIRST_IN_PHASE = 11,
146  ISMRMRD_ACQ_LAST_IN_PHASE = 12,
147  ISMRMRD_ACQ_FIRST_IN_REPETITION = 13,
148  ISMRMRD_ACQ_LAST_IN_REPETITION = 14,
149  ISMRMRD_ACQ_FIRST_IN_SET = 15,
150  ISMRMRD_ACQ_LAST_IN_SET = 16,
151  ISMRMRD_ACQ_FIRST_IN_SEGMENT = 17,
152  ISMRMRD_ACQ_LAST_IN_SEGMENT = 18,
153  ISMRMRD_ACQ_IS_NOISE_MEASUREMENT = 19,
154  ISMRMRD_ACQ_IS_PARALLEL_CALIBRATION = 20,
155  ISMRMRD_ACQ_IS_PARALLEL_CALIBRATION_AND_IMAGING = 21,
156  ISMRMRD_ACQ_IS_REVERSE = 22,
157  ISMRMRD_ACQ_IS_NAVIGATION_DATA = 23,
158  ISMRMRD_ACQ_IS_PHASECORR_DATA = 24,
159  ISMRMRD_ACQ_LAST_IN_MEASUREMENT = 25,
160  ISMRMRD_ACQ_IS_HPFEEDBACK_DATA = 26,
161  ISMRMRD_ACQ_IS_DUMMYSCAN_DATA = 27,
162  ISMRMRD_ACQ_IS_RTFEEDBACK_DATA = 28,
163  ISMRMRD_ACQ_IS_SURFACECOILCORRECTIONSCAN_DATA = 29,
164 
165  ISMRMRD_ACQ_COMPRESSION1 = 53,
166  ISMRMRD_ACQ_COMPRESSION2 = 54,
167  ISMRMRD_ACQ_COMPRESSION3 = 55,
168  ISMRMRD_ACQ_COMPRESSION4 = 56,
169  ISMRMRD_ACQ_USER1 = 57,
170  ISMRMRD_ACQ_USER2 = 58,
171  ISMRMRD_ACQ_USER3 = 59,
172  ISMRMRD_ACQ_USER4 = 60,
173  ISMRMRD_ACQ_USER5 = 61,
174  ISMRMRD_ACQ_USER6 = 62,
175  ISMRMRD_ACQ_USER7 = 63,
176  ISMRMRD_ACQ_USER8 = 64
177 };
178 
183  ISMRMRD_IMTYPE_MAGNITUDE = 1,
184  ISMRMRD_IMTYPE_PHASE = 2,
185  ISMRMRD_IMTYPE_REAL = 3,
186  ISMRMRD_IMTYPE_IMAG = 4,
187  ISMRMRD_IMTYPE_COMPLEX = 5
188 };
189 
194  ISMRMRD_IMAGE_IS_NAVIGATION_DATA = 1,
195  ISMRMRD_IMAGE_USER1 = 57,
196  ISMRMRD_IMAGE_USER2 = 58,
197  ISMRMRD_IMAGE_USER3 = 59,
198  ISMRMRD_IMAGE_USER4 = 60,
199  ISMRMRD_IMAGE_USER5 = 61,
200  ISMRMRD_IMAGE_USER6 = 62,
201  ISMRMRD_IMAGE_USER7 = 63,
202  ISMRMRD_IMAGE_USER8 = 64
203 };
204 
208 typedef struct ISMRMRD_EncodingCounters {
211  uint16_t average;
212  uint16_t slice;
213  uint16_t contrast;
214  uint16_t phase;
215  uint16_t repetition;
216  uint16_t set;
217  uint16_t segment;
218  uint16_t user[ISMRMRD_USER_INTS];
220 
225  uint16_t version;
226  uint64_t flags;
227  uint32_t measurement_uid;
228  uint32_t scan_counter;
230  uint32_t physiology_time_stamp[ISMRMRD_PHYS_STAMPS];
231  uint16_t number_of_samples;
233  uint16_t active_channels;
234  uint64_t channel_mask[ISMRMRD_CHANNEL_MASKS];
235  uint16_t discard_pre;
236  uint16_t discard_post;
237  uint16_t center_sample;
241  float position[3];
242  float read_dir[3];
243  float phase_dir[3];
244  float slice_dir[3];
245  float patient_table_position[3];
247  int32_t user_int[ISMRMRD_USER_INTS];
248  float user_float[ISMRMRD_USER_FLOATS];
250 
257 
259 typedef struct ISMRMRD_Acquisition {
261  float *traj;
262  complex_float_t *data;
264 
268 EXPORTISMRMRD ISMRMRD_Acquisition * ismrmrd_create_acquisition();
269 EXPORTISMRMRD int ismrmrd_free_acquisition(ISMRMRD_Acquisition *acq);
270 EXPORTISMRMRD int ismrmrd_init_acquisition(ISMRMRD_Acquisition *acq);
271 EXPORTISMRMRD int ismrmrd_cleanup_acquisition(ISMRMRD_Acquisition *acq);
272 EXPORTISMRMRD int ismrmrd_copy_acquisition(ISMRMRD_Acquisition *acqdest, const ISMRMRD_Acquisition *acqsource);
273 EXPORTISMRMRD int ismrmrd_make_consistent_acquisition(ISMRMRD_Acquisition *acq);
274 EXPORTISMRMRD size_t ismrmrd_size_of_acquisition_traj(const ISMRMRD_Acquisition *acq);
275 EXPORTISMRMRD size_t ismrmrd_size_of_acquisition_data(const ISMRMRD_Acquisition *acq);
278 /**********/
279 /* Images */
280 /**********/
281 
285 typedef struct ISMRMRD_ImageHeader {
286  uint16_t version;
287  uint16_t data_type;
288  uint64_t flags;
289  uint32_t measurement_uid;
290  uint16_t matrix_size[3];
291  float field_of_view[3];
292  uint16_t channels;
293  float position[3];
294  float read_dir[3];
295  float phase_dir[3];
296  float slice_dir[3];
297  float patient_table_position[3];
298  uint16_t average;
299  uint16_t slice;
300  uint16_t contrast;
301  uint16_t phase;
302  uint16_t repetition;
303  uint16_t set;
305  uint32_t physiology_time_stamp[ISMRMRD_PHYS_STAMPS];
306  uint16_t image_type;
307  uint16_t image_index;
309  int32_t user_int[ISMRMRD_USER_INTS];
310  float user_float[ISMRMRD_USER_FLOATS];
313 
315 EXPORTISMRMRD int ismrmrd_init_image_header(ISMRMRD_ImageHeader *hdr);
316 
321 typedef struct ISMRMRD_Image {
322  ISMRMRD_ImageHeader head;
323  char *attribute_string;
324  void *data;
325 } ISMRMRD_Image;
326 
327 
331 EXPORTISMRMRD ISMRMRD_Image * ismrmrd_create_image();
332 EXPORTISMRMRD int ismrmrd_free_image(ISMRMRD_Image *im);
333 EXPORTISMRMRD int ismrmrd_init_image(ISMRMRD_Image *im);
334 EXPORTISMRMRD int ismrmrd_cleanup_image(ISMRMRD_Image *im);
335 EXPORTISMRMRD int ismrmrd_copy_image(ISMRMRD_Image *imdest, const ISMRMRD_Image *imsource);
336 EXPORTISMRMRD int ismrmrd_make_consistent_image(ISMRMRD_Image *im);
337 EXPORTISMRMRD size_t ismrmrd_size_of_image_attribute_string(const ISMRMRD_Image *im);
338 EXPORTISMRMRD size_t ismrmrd_size_of_image_data(const ISMRMRD_Image *im);
341 /************/
342 /* NDArrays */
343 /************/
344 
348 typedef struct ISMRMRD_NDArray {
349  uint16_t version;
350  uint16_t data_type;
351  uint16_t ndim;
352  size_t dims[ISMRMRD_NDARRAY_MAXDIM];
353  void *data;
355 
359 EXPORTISMRMRD ISMRMRD_NDArray * ismrmrd_create_ndarray();
360 EXPORTISMRMRD int ismrmrd_free_ndarray(ISMRMRD_NDArray *arr);
361 EXPORTISMRMRD int ismrmrd_init_ndarray(ISMRMRD_NDArray *arr);
362 EXPORTISMRMRD int ismrmrd_cleanup_ndarray(ISMRMRD_NDArray *arr);
363 EXPORTISMRMRD int ismrmrd_copy_ndarray(ISMRMRD_NDArray *arrdest, const ISMRMRD_NDArray *arrsource);
364 EXPORTISMRMRD int ismrmrd_make_consistent_ndarray(ISMRMRD_NDArray *arr);
365 EXPORTISMRMRD size_t ismrmrd_size_of_ndarray_data(const ISMRMRD_NDArray *arr);
368 /*********/
369 /* Flags */
370 /*********/
374 EXPORTISMRMRD bool ismrmrd_is_flag_set(const uint64_t flags, const uint64_t val);
375 EXPORTISMRMRD int ismrmrd_set_flag(uint64_t *flags, const uint64_t val);
376 EXPORTISMRMRD int ismrmrd_set_flags(uint64_t *flags, const uint64_t val);
377 EXPORTISMRMRD int ismrmrd_clear_flag(uint64_t *flags, const uint64_t val);
378 EXPORTISMRMRD int ismrmrd_clear_all_flags(uint64_t *flags);
381 /*****************/
382 /* Channel Masks */
383 /*****************/
387 EXPORTISMRMRD bool ismrmrd_is_channel_on(const uint64_t channel_mask[ISMRMRD_CHANNEL_MASKS], const uint16_t chan);
388 EXPORTISMRMRD int ismrmrd_set_channel_on(uint64_t channel_mask[ISMRMRD_CHANNEL_MASKS], const uint16_t chan);
389 EXPORTISMRMRD int ismrmrd_set_channel_off(uint64_t channel_mask[ISMRMRD_CHANNEL_MASKS], const uint16_t chan);
390 EXPORTISMRMRD int ismrmrd_set_all_channels_off(uint64_t channel_mask[ISMRMRD_CHANNEL_MASKS]);
393 /******************/
394 /* Error Handling */
395 /******************/
399 typedef void (*ismrmrd_error_handler_t)(const char *file, int line,
400  const char *function, int code, const char *msg);
401 #define ISMRMRD_PUSH_ERR(code, msg) ismrmrd_push_error(__FILE__, __LINE__, \
402  __func__, (code), (msg))
403 int ismrmrd_push_error(const char *file, const int line, const char *func,
404  const int code, const char *msg);
406 EXPORTISMRMRD void ismrmrd_set_error_handler(ismrmrd_error_handler_t);
408 EXPORTISMRMRD char *ismrmrd_strerror(int code);
413 bool ismrmrd_pop_error(char **file, int *line, char **func,
414  int *code, char **msg);
415 
416 /*****************************/
417 /* Rotations and Quaternions */
418 /*****************************/
423 EXPORTISMRMRD int ismrmrd_sign_of_directions(float read_dir[3], float phase_dir[3], float slice_dir[3]);
424 
426 EXPORTISMRMRD void ismrmrd_directions_to_quaternion(float read_dir[3], float phase_dir[3], float slice_dir[3], float quat[4]);
427 
429 EXPORTISMRMRD void ismrmrd_quaternion_to_directions(float quat[4], float read_dir[3], float phase_dir[3], float slice_dir[3]);
432 #pragma pack(pop) /* Restore old alignment */
433 
434 #ifdef __cplusplus
435 } // extern "C"
436 
438 
440 std::string build_exception_string(void);
441 
444 
449 template <typename T> EXPORTISMRMRD ISMRMRD_DataTypes get_data_type();
451 
453 class EXPORTISMRMRD FlagBit
454 {
455 public:
456  FlagBit(unsigned short b)
457  : bitmask_(0)
458  {
459  if (b > 0) {
460  bitmask_ = 1;
461  bitmask_ = (bitmask_ << (b-1));
462  }
463  }
464 
465  bool isSet(const uint64_t& m) const {
466  return ((m & bitmask_)>0);
467  }
468 
469  uint64_t bitmask_;
470 
471 };
472 
474 class EXPORTISMRMRD AcquisitionHeader: public ISMRMRD_AcquisitionHeader {
475 public:
476  // Constructors
478 
479  // Flag methods
480  bool isFlagSet(const ISMRMRD_AcquisitionFlags val);
481  void setFlag(const ISMRMRD_AcquisitionFlags val);
482  void clearFlag(const ISMRMRD_AcquisitionFlags val);
483  void clearAllFlags();
484 
485  // Channel mask methods
486  bool isChannelActive(uint16_t channel_id);
487  void setChannelActive(uint16_t channel_id);
488  void setChannelNotActive(uint16_t channel_id);
489  void setAllChannelsNotActive();
490 
491 };
492 
494 class EXPORTISMRMRD Acquisition {
495  friend class Dataset;
496 public:
497  // Constructors, assignment, destructor
498  Acquisition();
499  Acquisition(uint16_t num_samples, uint16_t active_channels=1, uint16_t trajectory_dimensions=0);
500  Acquisition(const Acquisition &other);
501  Acquisition & operator= (const Acquisition &other);
502  ~Acquisition();
503 
504  // Accessors and mutators
505  const uint16_t &version();
506  const uint64_t &flags();
507  uint32_t &measurement_uid();
508  uint32_t &scan_counter();
509  uint32_t &acquisition_time_stamp();
510  uint32_t (&physiology_time_stamp())[ISMRMRD_PHYS_STAMPS];
511  const uint16_t &number_of_samples();
512  uint16_t &available_channels();
513  const uint16_t &active_channels();
514  const uint64_t (&channel_mask())[ISMRMRD_CHANNEL_MASKS];
515  uint16_t &discard_pre();
516  uint16_t &discard_post();
517  uint16_t &center_sample();
518  uint16_t &encoding_space_ref();
519  const uint16_t &trajectory_dimensions();
520  float &sample_time_us();
521  float (&position())[3];
522  float (&read_dir())[3];
523  float (&phase_dir())[3];
524  float (&slice_dir())[3];
525  float (&patient_table_position())[3];
527  int32_t (&user_int())[ISMRMRD_USER_INTS];
528  float (&user_float())[ISMRMRD_USER_FLOATS];
529 
530  // Sizes
531  void resize(uint16_t num_samples, uint16_t active_channels=1, uint16_t trajectory_dimensions=0);
532  size_t getNumberOfDataElements() const;
533  size_t getNumberOfTrajElements() const;
534  size_t getDataSize() const;
535  size_t getTrajSize() const;
536 
537  // Header, data and trajectory accessors
538  const AcquisitionHeader &getHead() const;
539  void setHead(const AcquisitionHeader &other);
540 
544  const complex_float_t * getDataPtr() const;
545  complex_float_t * getDataPtr();
546 
550  complex_float_t & data(uint16_t sample, uint16_t channel);
551 
555  void setData(complex_float_t * data);
556 
560  complex_float_t * data_begin() const;
561 
565  complex_float_t * data_end() const;
566 
570  const float * getTrajPtr() const;
571  float * getTrajPtr();
572 
576  float & traj(uint16_t dimension, uint16_t sample);
577 
581  void setTraj(float * traj);
582 
586  float * traj_begin() const;
587 
591  float * traj_end() const;
592 
593  // Flag methods
594  bool isFlagSet(const uint64_t val);
595  void setFlag(const uint64_t val);
596  void clearFlag(const uint64_t val);
597  void clearAllFlags();
598 
599  bool isFlagSet(const FlagBit &val) { return isFlagSet(val.bitmask_); }
600  void setFlag(const FlagBit &val) { setFlag(val.bitmask_); }
601  void clearFlag(const FlagBit &val) { clearFlag(val.bitmask_); }
602 
603  // Channel mask methods
604  bool isChannelActive(uint16_t channel_id);
605  void setChannelActive(uint16_t channel_id);
606  void setChannelNotActive(uint16_t channel_id);
607  void setAllChannelsNotActive();
608 
609 protected:
611 };
612 
614 class EXPORTISMRMRD ImageHeader: public ISMRMRD_ImageHeader {
615 public:
616  // Constructor
617  ImageHeader();
618 
619  // Flag methods
620  bool isFlagSet(const uint64_t val);
621  void setFlag(const uint64_t val);
622  void clearFlag(const uint64_t val);
623  void clearAllFlags();
624 
625 };
626 
628 template <typename T> class EXPORTISMRMRD Image {
629  friend class Dataset;
630 public:
631  // Constructors
632  Image(uint16_t matrix_size_x = 0, uint16_t matrix_size_y = 1,
633  uint16_t matrix_size_z = 1, uint16_t channels = 1);
634  Image(const Image &other);
635  Image & operator= (const Image &other);
636  ~Image();
637 
638  // Image dimensions
639  void resize(uint16_t matrix_size_x, uint16_t matrix_size_y, uint16_t matrix_size_z, uint16_t channels);
640  uint16_t getMatrixSizeX() const;
641  void setMatrixSizeX(uint16_t matrix_size_x);
642  uint16_t getMatrixSizeY() const;
643  void setMatrixSizeY(uint16_t matrix_size_y);
644  uint16_t getMatrixSizeZ() const;
645  void setMatrixSizeZ(uint16_t matrix_size_z);
646  uint16_t getNumberOfChannels() const;
647  void setNumberOfChannels(uint16_t channels);
648 
649  // Field of view
650  void setFieldOfView(float fov_x, float fov_y, float fov_z);
651  float getFieldOfViewX() const;
652  void setFieldOfViewX(float f);
653  float getFieldOfViewY() const;
654  void setFieldOfViewY(float f);
655  float getFieldOfViewZ() const;
656  void setFieldOfViewZ(float f);
657 
658  // Positions and orientations
659  void setPosition(float x, float y, float z);
660  float getPositionX() const;
661  void setPositionX(float x);
662  float getPositionY() const;
663  void setPositionY(float y);
664  float getPositionZ() const;
665  void setPositionZ(float z);
666 
667  void setReadDirection(float x, float y, float z);
668  float getReadDirectionX() const;
669  void setReadDirectionX(float x);
670  float getReadDirectionY() const;
671  void setReadDirectionY(float y);
672  float getReadDirectionZ() const;
673  void setReadDirectionZ(float z);
674 
675  void setPhaseDirection(float x, float y, float z);
676  float getPhaseDirectionX() const;
677  void setPhaseDirectionX(float x);
678  float getPhaseDirectionY() const;
679  void setPhaseDirectionY(float y);
680  float getPhaseDirectionZ() const;
681  void setPhaseDirectionZ(float z);
682 
683  void setSliceDirection(float x, float y, float z);
684  float getSliceDirectionX() const;
685  void setSliceDirectionX(float x);
686  float getSliceDirectionY() const;
687  void setSliceDirectionY(float y);
688  float getSliceDirectionZ() const;
689  void setSliceDirectionZ(float z);
690 
691  void setPatientTablePosition(float x, float y, float z);
692  float getPatientTablePositionX() const;
693  void setPatientTablePositionX(float x);
694  float getPatientTablePositionY() const;
695  void setPatientTablePositionY(float y);
696  float getPatientTablePositionZ() const;
697  void setPatientTablePositionZ(float z);
698 
699 
700  // Attributes
701  uint16_t getVersion() const;
702  ISMRMRD_DataTypes getDataType() const;
703 
704  // Counters and labels
705  uint32_t getMeasurementUid() const;
706  void setMeasurementUid(uint32_t measurement_uid);
707 
708  uint16_t getAverage() const;
709  void setAverage(uint16_t average);
710 
711  uint16_t getSlice() const;
712  void setSlice(uint16_t slice);
713 
714  uint16_t getContrast() const;
715  void setContrast(uint16_t contrast);
716 
717  uint16_t getPhase() const;
718  void setPhase(uint16_t phase);
719 
720  uint16_t getRepetition() const;
721  void setRepetition(uint16_t repetition);
722 
723  uint16_t getSet() const;
724  void setSet(uint16_t set);
725 
726  uint32_t getAcquisitionTimeStamp() const;
727  void setAcquisitionTimeStamp(uint32_t acquisition_time_stamp);
728 
729  uint32_t getPhysiologyTimeStamp(unsigned int stamp_id) const;
730  void setPhysiologyTimeStamp(unsigned int stamp_id, uint32_t value);
731 
732  uint16_t getImageType() const;
733  void setImageType(uint16_t image_type);
734 
735  uint16_t getImageIndex() const;
736  void setImageIndex(uint16_t image_index);
737 
738  uint16_t getImageSeriesIndex() const;
739  void setImageSeriesIndex(uint16_t image_series_index);
740 
741  // User parameters
742  float getUserFloat(unsigned int index) const;
743  void setUserFloat(unsigned int index, float value);
744 
745  int32_t getUserInt(unsigned int index) const;
746  void setUserInt(unsigned int index, int32_t value);
747 
748  // Flags
749  uint64_t getFlags() const;
750  void setFlags(const uint64_t flags);
751  bool isFlagSet(const uint64_t val) const;
752  void setFlag(const uint64_t val);
753  void clearFlag(const uint64_t val);
754  void clearAllFlags();
755 
756  // Header
757  ImageHeader & getHead();
758  const ImageHeader & getHead() const;
759  void setHead(const ImageHeader& head);
760 
761  // Attribute string
762  void getAttributeString(std::string &attr) const;
763  const char *getAttributeString() const;
764  void setAttributeString(const std::string &attr);
765  void setAttributeString(const char *attr);
766  size_t getAttributeStringLength() const;
767 
768  // Data
769  T * getDataPtr();
770  const T * getDataPtr() const;
772  size_t getNumberOfDataElements() const;
774  size_t getDataSize() const;
775 
777  T* begin();
778 
780  T* end();
781 
783  T & operator () (uint16_t x, uint16_t y=0, uint16_t z=0 , uint16_t channel =0);
784 
785 protected:
786  ISMRMRD_Image im;
787 };
788 
790 template <typename T> class EXPORTISMRMRD NDArray {
791  friend class Dataset;
792 public:
793  // Constructors, destructor and copy
794  NDArray();
795  NDArray(const std::vector<size_t> dimvec);
796  NDArray(const NDArray<T> &other);
797  ~NDArray();
798  NDArray<T> & operator= (const NDArray<T> &other);
799 
800  // Accessors and mutators
801  uint16_t getVersion() const;
802  ISMRMRD_DataTypes getDataType() const;
803  uint16_t getNDim() const;
804  const size_t (&getDims())[ISMRMRD_NDARRAY_MAXDIM];
805  size_t getDataSize() const;
806  void resize(const std::vector<size_t> dimvec);
807  size_t getNumberOfElements() const;
808  T * getDataPtr();
809  const T * getDataPtr() const;
810 
812  T * begin();
813 
815  T* end();
816 
818  T & operator () (uint16_t x, uint16_t y=0, uint16_t z=0, uint16_t w=0, uint16_t n=0, uint16_t m=0, uint16_t l=0);
819 
820 protected:
821  ISMRMRD_NDArray arr;
822 };
823 
824 
827 } // namespace ISMRMRD
828 
829 #endif
830 
831 #endif /* ISMRMRD_H */
uint16_t average
Definition: ismrmrd.h:211
uint16_t discard_pre
Definition: ismrmrd.h:235
uint16_t discard_post
Definition: ismrmrd.h:236
uint16_t version
Definition: ismrmrd.h:225
uint32_t scan_counter
Definition: ismrmrd.h:228
struct ISMRMRD::ISMRMRD_NDArray ISMRMRD_NDArray
uint16_t data_type
Definition: ismrmrd.h:350
ISMRMRD_Constants
Definition: ismrmrd.h:89
uint16_t channels
Definition: ismrmrd.h:292
struct ISMRMRD::ISMRMRD_Acquisition ISMRMRD_Acquisition
uint16_t phase
Definition: ismrmrd.h:301
uint16_t version
Definition: ismrmrd.h:349
ISMRMRD_AcquisitionFlags
Definition: ismrmrd.h:134
uint16_t image_series_index
Definition: ismrmrd.h:308
uint32_t acquisition_time_stamp
Definition: ismrmrd.h:229
uint16_t segment
Definition: ismrmrd.h:217
int ismrmrd_push_error(const char *file, const int line, const char *func, const int code, const char *msg)
Definition: ismrmrd.c:679
uint16_t data_type
Definition: ismrmrd.h:287
uint16_t phase
Definition: ismrmrd.h:214
uint16_t kspace_encode_step_1
Definition: ismrmrd.h:209
EXPORTISMRMRD void ismrmrd_quaternion_to_directions(float quat[4], float read_dir[3], float phase_dir[3], float slice_dir[3])
Definition: ismrmrd.c:658
uint16_t slice
Definition: ismrmrd.h:299
Definition: ismrmrd.h:125
Definition: ismrmrd.h:121
uint16_t active_channels
Definition: ismrmrd.h:233
uint16_t slice
Definition: ismrmrd.h:212
uint16_t contrast
Definition: ismrmrd.h:300
MR Acquisition type.
Definition: ismrmrd.h:494
Definition: ismrmrd.h:285
ISMRMRD_AcquisitionHeader head
Definition: ismrmrd.h:260
uint16_t center_sample
Definition: ismrmrd.h:237
uint16_t available_channels
Definition: ismrmrd.h:232
bool ismrmrd_pop_error(char **file, int *line, char **func, int *code, char **msg)
Definition: ismrmrd.c:708
struct ISMRMRD::ISMRMRD_EncodingCounters ISMRMRD_EncodingCounters
ISMRMRD_ImageFlags
Definition: ismrmrd.h:193
ISMRMRD_ImageTypes
Definition: ismrmrd.h:182
Definition: ismrmrd.h:120
uint32_t attribute_string_len
Definition: ismrmrd.h:311
uint16_t average
Definition: ismrmrd.h:298
EXPORTISMRMRD int ismrmrd_sign_of_directions(float read_dir[3], float phase_dir[3], float slice_dir[3])
Definition: ismrmrd.c:568
struct ISMRMRD::ISMRMRD_Image ISMRMRD_Image
uint16_t contrast
Definition: ismrmrd.h:213
Definition: ismrmrd.h:124
uint32_t acquisition_time_stamp
Definition: ismrmrd.h:304
uint16_t ndim
Definition: ismrmrd.h:351
std::string build_exception_string(void)
ISMRMRD C++ Interface.
Definition: ismrmrd.cpp:1202
struct ISMRMRD::ISMRMRD_ImageHeader ISMRMRD_ImageHeader
ISMRMRD_ErrorCodes
Definition: ismrmrd.h:103
uint16_t repetition
Definition: ismrmrd.h:215
float sample_time_us
Definition: ismrmrd.h:240
Header for MR Image type.
Definition: ismrmrd.h:614
Definition: ismrmrd.h:224
N-Dimensional array type.
Definition: ismrmrd.h:790
uint16_t trajectory_dimensions
Definition: ismrmrd.h:239
ISMRMRD_EncodingCounters EncodingCounters
Some typedefs to beautify the namespace.
Definition: ismrmrd.h:443
ISMRMRD_EncodingCounters idx
Definition: ismrmrd.h:246
uint16_t repetition
Definition: ismrmrd.h:302
Definition: dataset.h:144
Definition: ismrmrd.h:259
void * data
Definition: ismrmrd.h:353
uint16_t image_index
Definition: ismrmrd.h:307
EXPORTISMRMRD void ismrmrd_directions_to_quaternion(float read_dir[3], float phase_dir[3], float slice_dir[3], float quat[4])
Definition: ismrmrd.c:584
uint16_t version
Definition: ismrmrd.h:286
EXPORTISMRMRD int ismrmrd_init_acquisition_header(ISMRMRD_AcquisitionHeader *hdr)
Definition: ismrmrd.c:41
struct ISMRMRD::ISMRMRD_AcquisitionHeader ISMRMRD_AcquisitionHeader
Definition: ismrmrd.h:122
Definition: dataset.h:16
Definition: ismrmrd.h:208
Definition: ismrmrd.h:123
uint16_t encoding_space_ref
Definition: ismrmrd.h:238
Definition: ismrmrd.h:118
EXPORTISMRMRD char * ismrmrd_strerror(int code)
Definition: ismrmrd.c:744
uint16_t number_of_samples
Definition: ismrmrd.h:231
uint16_t image_type
Definition: ismrmrd.h:306
uint32_t measurement_uid
Definition: ismrmrd.h:227
Definition: ismrmrd.h:348
EXPORTISMRMRD void ismrmrd_set_error_handler(ismrmrd_error_handler_t)
Definition: ismrmrd.c:740
MR Image type.
Definition: ismrmrd.h:628
Header for MR Acquisition type.
Definition: ismrmrd.h:474
uint64_t flags
Definition: ismrmrd.h:226
uint64_t flags
Definition: ismrmrd.h:288
Convenience class for flags.
Definition: ismrmrd.h:453
size_t ismrmrd_sizeof_data_type(int data_type)
Definition: ismrmrd.c:445
Definition: ismrmrd.h:321
ISMRMRD_DataTypes
Definition: ismrmrd.h:117
Definition: ismrmrd.h:119
EXPORTISMRMRD int ismrmrd_init_image_header(ISMRMRD_ImageHeader *hdr)
Definition: ismrmrd.c:185
uint16_t kspace_encode_step_2
Definition: ismrmrd.h:210
EXPORTISMRMRD ISMRMRD_DataTypes get_data_type()
Allowed data types for Images and NDArrays.
uint32_t measurement_uid
Definition: ismrmrd.h:289