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;
41 typedef std::complex<float> complex_float_t;
42 typedef std::complex<double> complex_double_t;
45 typedef struct complex_float_t{
49 typedef struct complex_double_t{
55 typedef float complex complex_float_t;
56 typedef double complex complex_double_t;
77 #include "ismrmrd/export.h"
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
104 ISMRMRD_BEGINERROR=-1,
109 ISMRMRD_RUNTIMEERROR,
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,
165 ISMRMRD_ACQ_USER1 = 57,
166 ISMRMRD_ACQ_USER2 = 58,
167 ISMRMRD_ACQ_USER3 = 59,
168 ISMRMRD_ACQ_USER4 = 60,
169 ISMRMRD_ACQ_USER5 = 61,
170 ISMRMRD_ACQ_USER6 = 62,
171 ISMRMRD_ACQ_USER7 = 63,
172 ISMRMRD_ACQ_USER8 = 64
179 ISMRMRD_IMTYPE_MAGNITUDE = 1,
180 ISMRMRD_IMTYPE_PHASE = 2,
181 ISMRMRD_IMTYPE_REAL = 3,
182 ISMRMRD_IMTYPE_IMAG = 4,
183 ISMRMRD_IMTYPE_COMPLEX = 5
190 ISMRMRD_IMAGE_IS_NAVIGATION_DATA = 1,
191 ISMRMRD_IMAGE_USER1 = 57,
192 ISMRMRD_IMAGE_USER2 = 58,
193 ISMRMRD_IMAGE_USER3 = 59,
194 ISMRMRD_IMAGE_USER4 = 60,
195 ISMRMRD_IMAGE_USER5 = 61,
196 ISMRMRD_IMAGE_USER6 = 62,
197 ISMRMRD_IMAGE_USER7 = 63,
198 ISMRMRD_IMAGE_USER8 = 64
214 uint16_t
user[ISMRMRD_USER_INTS];
258 complex_float_t *data;
319 char *attribute_string;
332 EXPORTISMRMRD
int ismrmrd_make_consistent_image(
ISMRMRD_Image *im);
333 EXPORTISMRMRD
size_t ismrmrd_size_of_image_attribute_string(
const ISMRMRD_Image *im);
334 EXPORTISMRMRD
size_t ismrmrd_size_of_image_data(
const ISMRMRD_Image *im);
348 size_t dims[ISMRMRD_NDARRAY_MAXDIM];
360 EXPORTISMRMRD
int ismrmrd_make_consistent_ndarray(
ISMRMRD_NDArray *arr);
361 EXPORTISMRMRD
size_t ismrmrd_size_of_ndarray_data(
const ISMRMRD_NDArray *arr);
370 EXPORTISMRMRD
bool ismrmrd_is_flag_set(
const uint64_t flags,
const uint64_t val);
371 EXPORTISMRMRD
int ismrmrd_set_flag(uint64_t *flags,
const uint64_t val);
372 EXPORTISMRMRD
int ismrmrd_set_flags(uint64_t *flags,
const uint64_t val);
373 EXPORTISMRMRD
int ismrmrd_clear_flag(uint64_t *flags,
const uint64_t val);
374 EXPORTISMRMRD
int ismrmrd_clear_all_flags(uint64_t *flags);
383 EXPORTISMRMRD
bool ismrmrd_is_channel_on(
const uint64_t channel_mask[ISMRMRD_CHANNEL_MASKS],
const uint16_t chan);
384 EXPORTISMRMRD
int ismrmrd_set_channel_on(uint64_t channel_mask[ISMRMRD_CHANNEL_MASKS],
const uint16_t chan);
385 EXPORTISMRMRD
int ismrmrd_set_channel_off(uint64_t channel_mask[ISMRMRD_CHANNEL_MASKS],
const uint16_t chan);
386 EXPORTISMRMRD
int ismrmrd_set_all_channels_off(uint64_t channel_mask[ISMRMRD_CHANNEL_MASKS]);
395 typedef void (*ismrmrd_error_handler_t)(
const char *file,
int line,
396 const char *
function,
int code,
const char *msg);
397 #define ISMRMRD_PUSH_ERR(code, msg) ismrmrd_push_error(__FILE__, __LINE__, \
398 __func__, (code), (msg))
400 const int code,
const char *msg);
410 int *code,
char **msg);
457 bitmask_ = (bitmask_ << (b-1));
461 bool isSet(
const uint64_t& m)
const {
462 return ((m & bitmask_)>0);
479 void clearAllFlags();
482 bool isChannelActive(uint16_t channel_id);
483 void setChannelActive(uint16_t channel_id);
484 void setChannelNotActive(uint16_t channel_id);
485 void setAllChannelsNotActive();
495 Acquisition(uint16_t num_samples, uint16_t active_channels=1, uint16_t trajectory_dimensions=0);
501 const uint16_t &version();
502 const uint64_t &flags();
503 uint32_t &measurement_uid();
504 uint32_t &scan_counter();
505 uint32_t &acquisition_time_stamp();
506 uint32_t (&physiology_time_stamp())[ISMRMRD_PHYS_STAMPS];
507 const uint16_t &number_of_samples();
508 uint16_t &available_channels();
509 const uint16_t &active_channels();
510 const uint64_t (&channel_mask())[ISMRMRD_CHANNEL_MASKS];
511 uint16_t &discard_pre();
512 uint16_t &discard_post();
513 uint16_t ¢er_sample();
514 uint16_t &encoding_space_ref();
515 const uint16_t &trajectory_dimensions();
516 float &sample_time_us();
517 float (&position())[3];
518 float (&read_dir())[3];
519 float (&phase_dir())[3];
520 float (&slice_dir())[3];
521 float (&patient_table_position())[3];
523 int32_t (&user_int())[ISMRMRD_USER_INTS];
524 float (&user_float())[ISMRMRD_USER_FLOATS];
527 void resize(uint16_t num_samples, uint16_t active_channels=1, uint16_t trajectory_dimensions=0);
528 size_t getNumberOfDataElements()
const;
529 size_t getNumberOfTrajElements()
const;
530 size_t getDataSize()
const;
531 size_t getTrajSize()
const;
540 const complex_float_t * getDataPtr()
const;
541 complex_float_t * getDataPtr();
546 complex_float_t & data(uint16_t sample, uint16_t channel);
551 void setData(complex_float_t * data);
556 complex_float_t * data_begin()
const;
561 complex_float_t * data_end()
const;
566 const float * getTrajPtr()
const;
567 float * getTrajPtr();
572 float & traj(uint16_t dimension, uint16_t sample);
577 void setTraj(
float * traj);
582 float * traj_begin()
const;
587 float * traj_end()
const;
590 bool isFlagSet(
const uint64_t val);
591 void setFlag(
const uint64_t val);
592 void clearFlag(
const uint64_t val);
593 void clearAllFlags();
595 bool isFlagSet(
const FlagBit &val) {
return isFlagSet(val.bitmask_); }
596 void setFlag(
const FlagBit &val) { setFlag(val.bitmask_); }
597 void clearFlag(
const FlagBit &val) { clearFlag(val.bitmask_); }
600 bool isChannelActive(uint16_t channel_id);
601 void setChannelActive(uint16_t channel_id);
602 void setChannelNotActive(uint16_t channel_id);
603 void setAllChannelsNotActive();
616 bool isFlagSet(
const uint64_t val);
617 void setFlag(
const uint64_t val);
618 void clearFlag(
const uint64_t val);
619 void clearAllFlags();
624 template <
typename T>
class EXPORTISMRMRD
Image {
628 Image(uint16_t matrix_size_x = 0, uint16_t matrix_size_y = 1,
629 uint16_t matrix_size_z = 1, uint16_t channels = 1);
635 void resize(uint16_t matrix_size_x, uint16_t matrix_size_y, uint16_t matrix_size_z, uint16_t channels);
636 uint16_t getMatrixSizeX()
const;
637 void setMatrixSizeX(uint16_t matrix_size_x);
638 uint16_t getMatrixSizeY()
const;
639 void setMatrixSizeY(uint16_t matrix_size_y);
640 uint16_t getMatrixSizeZ()
const;
641 void setMatrixSizeZ(uint16_t matrix_size_z);
642 uint16_t getNumberOfChannels()
const;
643 void setNumberOfChannels(uint16_t channels);
646 void setFieldOfView(
float fov_x,
float fov_y,
float fov_z);
647 float getFieldOfViewX()
const;
648 void setFieldOfViewX(
float f);
649 float getFieldOfViewY()
const;
650 void setFieldOfViewY(
float f);
651 float getFieldOfViewZ()
const;
652 void setFieldOfViewZ(
float f);
655 void setPosition(
float x,
float y,
float z);
656 float getPositionX()
const;
657 void setPositionX(
float x);
658 float getPositionY()
const;
659 void setPositionY(
float y);
660 float getPositionZ()
const;
661 void setPositionZ(
float z);
663 void setReadDirection(
float x,
float y,
float z);
664 float getReadDirectionX()
const;
665 void setReadDirectionX(
float x);
666 float getReadDirectionY()
const;
667 void setReadDirectionY(
float y);
668 float getReadDirectionZ()
const;
669 void setReadDirectionZ(
float z);
671 void setPhaseDirection(
float x,
float y,
float z);
672 float getPhaseDirectionX()
const;
673 void setPhaseDirectionX(
float x);
674 float getPhaseDirectionY()
const;
675 void setPhaseDirectionY(
float y);
676 float getPhaseDirectionZ()
const;
677 void setPhaseDirectionZ(
float z);
679 void setSliceDirection(
float x,
float y,
float z);
680 float getSliceDirectionX()
const;
681 void setSliceDirectionX(
float x);
682 float getSliceDirectionY()
const;
683 void setSliceDirectionY(
float y);
684 float getSliceDirectionZ()
const;
685 void setSliceDirectionZ(
float z);
687 void setPatientTablePosition(
float x,
float y,
float z);
688 float getPatientTablePositionX()
const;
689 void setPatientTablePositionX(
float x);
690 float getPatientTablePositionY()
const;
691 void setPatientTablePositionY(
float y);
692 float getPatientTablePositionZ()
const;
693 void setPatientTablePositionZ(
float z);
697 uint16_t getVersion()
const;
701 uint32_t getMeasurementUid()
const;
702 void setMeasurementUid(uint32_t measurement_uid);
704 uint16_t getAverage()
const;
705 void setAverage(uint16_t average);
707 uint16_t getSlice()
const;
708 void setSlice(uint16_t slice);
710 uint16_t getContrast()
const;
711 void setContrast(uint16_t contrast);
713 uint16_t getPhase()
const;
714 void setPhase(uint16_t phase);
716 uint16_t getRepetition()
const;
717 void setRepetition(uint16_t repetition);
719 uint16_t getSet()
const;
720 void setSet(uint16_t set);
722 uint32_t getAcquisitionTimeStamp()
const;
723 void setAcquisitionTimeStamp(uint32_t acquisition_time_stamp);
725 uint32_t getPhysiologyTimeStamp(
unsigned int stamp_id)
const;
726 void setPhysiologyTimeStamp(
unsigned int stamp_id, uint32_t value);
728 uint16_t getImageType()
const;
729 void setImageType(uint16_t image_type);
731 uint16_t getImageIndex()
const;
732 void setImageIndex(uint16_t image_index);
734 uint16_t getImageSeriesIndex()
const;
735 void setImageSeriesIndex(uint16_t image_series_index);
738 float getUserFloat(
unsigned int index)
const;
739 void setUserFloat(
unsigned int index,
float value);
741 int32_t getUserInt(
unsigned int index)
const;
742 void setUserInt(
unsigned int index, int32_t value);
745 uint64_t getFlags()
const;
746 void setFlags(
const uint64_t flags);
747 bool isFlagSet(
const uint64_t val)
const;
748 void setFlag(
const uint64_t val);
749 void clearFlag(
const uint64_t val);
750 void clearAllFlags();
758 void getAttributeString(std::string &atrr)
const;
759 void setAttributeString(
const std::string &attr);
760 size_t getAttributeStringLength()
const;
764 const T * getDataPtr()
const;
766 size_t getNumberOfDataElements()
const;
768 size_t getDataSize()
const;
777 T & operator () (uint16_t x, uint16_t y=0, uint16_t z=0 , uint16_t channel =0);
784 template <
typename T>
class EXPORTISMRMRD
NDArray {
789 NDArray(
const std::vector<size_t> dimvec);
795 uint16_t getVersion()
const;
797 uint16_t getNDim()
const;
798 const size_t (&getDims())[ISMRMRD_NDARRAY_MAXDIM];
799 size_t getDataSize()
const;
800 void resize(
const std::vector<size_t> dimvec);
801 size_t getNumberOfElements()
const;
803 const T * getDataPtr()
const;
812 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);
uint16_t average
Definition: ismrmrd.h:207
struct ISMRMRD::ISMRMRD_NDArray ISMRMRD_NDArray
uint16_t data_type
Definition: ismrmrd.h:346
ISMRMRD_Constants
Definition: ismrmrd.h:89
struct ISMRMRD::ISMRMRD_Acquisition ISMRMRD_Acquisition
uint16_t version
Definition: ismrmrd.h:345
ISMRMRD_AcquisitionFlags
Definition: ismrmrd.h:134
uint16_t segment
Definition: ismrmrd.h:213
int ismrmrd_push_error(const char *file, const int line, const char *func, const int code, const char *msg)
Definition: ismrmrd.c:671
uint16_t phase
Definition: ismrmrd.h:210
uint16_t kspace_encode_step_1
Definition: ismrmrd.h:205
EXPORTISMRMRD void ismrmrd_quaternion_to_directions(float quat[4], float read_dir[3], float phase_dir[3], float slice_dir[3])
Definition: ismrmrd.c:650
Definition: ismrmrd.h:125
Definition: ismrmrd.h:121
uint16_t slice
Definition: ismrmrd.h:208
MR Acquisition type.
Definition: ismrmrd.h:490
ISMRMRD_AcquisitionHeader head
Definition: ismrmrd.h:256
uint16_t user[ISMRMRD_USER_INTS]
Definition: ismrmrd.h:214
bool ismrmrd_pop_error(char **file, int *line, char **func, int *code, char **msg)
Definition: ismrmrd.c:700
struct ISMRMRD::ISMRMRD_EncodingCounters ISMRMRD_EncodingCounters
ISMRMRD_ImageFlags
Definition: ismrmrd.h:189
ISMRMRD_ImageTypes
Definition: ismrmrd.h:178
Definition: ismrmrd.h:120
EXPORTISMRMRD int ismrmrd_sign_of_directions(float read_dir[3], float phase_dir[3], float slice_dir[3])
Definition: ismrmrd.c:560
struct ISMRMRD::ISMRMRD_Image ISMRMRD_Image
uint16_t contrast
Definition: ismrmrd.h:209
Definition: ismrmrd.h:124
uint16_t ndim
Definition: ismrmrd.h:347
std::string build_exception_string(void)
ISMRMRD C++ Interface.
Definition: ismrmrd.cpp:1187
struct ISMRMRD::ISMRMRD_ImageHeader ISMRMRD_ImageHeader
ISMRMRD_ErrorCodes
Definition: ismrmrd.h:103
uint16_t repetition
Definition: ismrmrd.h:211
N-Dimensional array type.
Definition: ismrmrd.h:784
ISMRMRD_EncodingCounters EncodingCounters
Some typedefs to beautify the namespace.
Definition: ismrmrd.h:439
Definition: dataset.h:143
Definition: ismrmrd.h:255
void * data
Definition: ismrmrd.h:349
EXPORTISMRMRD void ismrmrd_directions_to_quaternion(float read_dir[3], float phase_dir[3], float slice_dir[3], float quat[4])
Definition: ismrmrd.c:576
uint16_t set
Definition: ismrmrd.h:212
EXPORTISMRMRD int ismrmrd_init_acquisition_header(ISMRMRD_AcquisitionHeader *hdr)
Definition: ismrmrd.c:41
struct ISMRMRD::ISMRMRD_AcquisitionHeader ISMRMRD_AcquisitionHeader
Definition: ismrmrd.h:122
Definition: ismrmrd.h:204
Definition: ismrmrd.h:123
Definition: ismrmrd.h:118
EXPORTISMRMRD char * ismrmrd_strerror(int code)
Definition: ismrmrd.c:736
size_t dims[ISMRMRD_NDARRAY_MAXDIM]
Definition: ismrmrd.h:348
Definition: ismrmrd.h:344
EXPORTISMRMRD void ismrmrd_set_error_handler(ismrmrd_error_handler_t)
Definition: ismrmrd.c:732
MR Image type.
Definition: ismrmrd.h:624
Convenience class for flags.
Definition: ismrmrd.h:449
size_t ismrmrd_sizeof_data_type(int data_type)
Definition: ismrmrd.c:437
Definition: ismrmrd.h:317
ISMRMRD_DataTypes
Definition: ismrmrd.h:117
Definition: ismrmrd.h:119
EXPORTISMRMRD int ismrmrd_init_image_header(ISMRMRD_ImageHeader *hdr)
Definition: ismrmrd.c:183
uint16_t kspace_encode_step_2
Definition: ismrmrd.h:206
EXPORTISMRMRD ISMRMRD_DataTypes get_data_type()
Allowed data types for Images and NDArrays.