1 /* 2 % 3 % $Id$ 4 % Copyright (C) 2008,2009,2012 Alois Schloegl <alois.schloegl@ist.ac.at> 5 % This file is part of the "BioSig for C/C++" repository 6 % (biosig4c++) at http://biosig.sf.net/ 7 8 9 This program is free software; you can redistribute it and/or 10 modify it under the terms of the GNU General Public License 11 as published by the Free Software Foundation; either version 3 12 of the License, or (at your option) any later version. 13 14 This program is distributed in the hope that it will be useful, 15 but WITHOUT ANY WARRANTY; without even the implied warranty of 16 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 17 GNU General Public License for more details. 18 19 You should have received a copy of the GNU General Public License 20 along with this program. If not, see <http://www.gnu.org/licenses/>. 21 22 */ 23 24 25 // swig.i 26 27 %module biosig 28 %{ 29 #include "../biosig.h" 30 %} 31 32 33 %include <inttypes.i> 34 35 36 typedef int64_t gdf_time; /* gdf time is represented in 64 bits */ 37 38 typedef int64_t nrec_t; /* type for number of records */ 39 40 41 /* list of file formats */ 42 enum FileFormat { 43 noFile, unknown, 44 ABF, ACQ, ACR_NEMA, AIFC, AIFF, AINF, alpha, ARFF, 45 ASCII_IBI, ASCII, AU, ASF, ATES, ATF, AVI, Axona, 46 BCI2000, BDF, BESA, BIN, BKR, BLSC, BMP, BNI, BSCS, 47 BrainVision, BrainVisionVAmp, BrainVisionMarker, BZ2, 48 CDF, CFS, CFWB, CNT, CTF, DICOM, DEMG, 49 EBS, EDF, EEG1100, EEProbe, EEProbe2, EEProbeAvr, EGI, 50 EGIS, ELF, EMBLA, EMSA, ePrime, ET_MEG, ETG4000, EVENT, EXIF, 51 FAMOS, FEF, FITS, FLAC, GDF, GDF1, 52 GIF, GTF, GZIP, HDF, HL7aECG, HEKA, 53 ISHNE, ITX, JPEG, JSON, Lexicor, 54 Matlab, MFER, MIDI, MIT, MM, MSI, MSVCLIB, MS_LNK, 55 native, NeuroLoggerHEX, NetCDF, NEURON, NEV, NEX1, NIFTI, 56 OGG, OpenXDF, 57 PBMA, PBMN, PDF, PDP, Persyst, PGMA, PGMB, 58 PLEXON, PNG, PNM, POLY5, PPMA, PPMB, PS, 59 RDF, RIFF, 60 SASXPT, SCP_ECG, SIGIF, Sigma, SMA, SND, SQLite, 61 SPSS, STATA, SVG, SXI, SYNERGY, 62 TIFF, TMS32, TMSiLOG, TRC, UNIPRO, VRML, VTK, 63 WAV, WG1, WinEEG, WMF, XML, XPM, 64 Z, ZIP, ZIP2 65 }; 66 67 68 typedef struct CHANNEL_STRUCT { 69 double PhysMin; /* physical minimum */ 70 double PhysMax; /* physical maximum */ 71 double DigMin; /* digital minimum */ 72 double DigMax; /* digital maximum */ 73 double Cal; /* gain factor */ 74 double Off; /* bias */ 75 76 char OnOff; 77 char Label[MAX_LENGTH_LABEL+1]; /* Label of channel */ 78 uint16_t LeadIdCode; /* Lead identification code */ 79 char Transducer[MAX_LENGTH_TRANSDUCER+1]; /* transducer e.g. EEG: Ag-AgCl electrodes */ 80 // char PhysDim[MAX_LENGTH_PHYSDIM+1] ; /* physical dimension */ 81 /*PhysDim is now obsolete - use function PhysDim3(PhysDimCode) instead */ 82 uint16_t PhysDimCode; /* code for physical dimension */ 83 /* char* PreFilt; // pre-filtering */ 84 85 float TOffset; /* time delay of sampling */ 86 float LowPass; /* lowpass filter */ 87 float HighPass; /* high pass */ 88 float Notch; /* notch filter */ 89 float XYZ[3]; /* sensor position */ 90 // float Orientation[3]; // sensor direction 91 // float Area; // area of sensor (e.g. for MEG) 92 93 union { 94 /* context specific channel information */ 95 float Impedance; /* Electrode Impedance in Ohm, defined only if PhysDim = _Volt */ 96 float fZ; /* ICG probe frequency, defined only if PhysDim = _Ohm */ 97 }; 98 99 uint16_t GDFTYP; /* data type */ 100 uint32_t SPR; /* samples per record (block) */ 101 } CHANNEL_TYPE; 102 103 104 105 /* 106 This structure defines the general (fixed) header 107 */ 108 typedef struct { 109 float VERSION; /* GDF version number */ 110 char* FileName; 111 enum FileFormat TYPE; /* type of file format */ 112 113 struct { 114 size_t size[2]; /* size {rows, columns} of data block */ 115 biosig_data_type* block; /* data block */ 116 } data; 117 118 uint8_t IPaddr[16]; /* IP address of recording device (if applicable) */ 119 double SampleRate; /* Sampling rate */ 120 int64_t NRec; /* number of records/blocks -1 indicates length is unknown. */ 121 gdf_time T0; /* starttime of recording */ 122 uint32_t HeadLen; /* length of header in bytes */ 123 uint32_t SPR; /* samples per block (when different sampling rates are used, this is the LCM(CHANNEL[..].SPR) */ 124 uint32_t LOC[4]; /* location of recording according to RFC1876 */ 125 uint16_t NS; /* number of channels */ 126 int16_t tzmin; /* time zone (minutes of difference to UTC */ 127 128 #ifdef CHOLMOD_H 129 cholmod_sparse *Calib; /* re-referencing matrix */ 130 #endif 131 CHANNEL_TYPE *rerefCHANNEL; 132 133 /* Patient specific information */ 134 struct { 135 gdf_time Birthday; /* Birthday of Patient */ 136 // Age; /* the age is HDR.T0 - HDR.Patient.Birthday, even if T0 and Birthday are not known */ 137 uint16_t Headsize[3]; /* circumference, nasion-inion, left-right mastoid in millimeter; */ 138 char Name[MAX_LENGTH_NAME+1]; /* because for privacy protection it is by default not supported, support is turned on with FLAG.ANONYMOUS */ 139 // char* Name; /* because for privacy protection it is by default not supported, support is turned on with FLAG.ANONYMOUS */ 140 char Id[MAX_LENGTH_PID+1]; /* patient identification, identification code as used in hospital */ 141 uint8_t Weight; /* weight in kilograms [kg] 0:unkown, 255: overflow */ 142 uint8_t Height; /* height in centimeter [cm] 0:unkown, 255: overflow */ 143 // BMI; /* the body-mass index = weight[kg]/height[m]^2 */ 144 /* Patient classification */ 145 int Sex; /* 0:Unknown, 1: Male, 2: Female */ 146 int Handedness; /* 0:Unknown, 1: Right, 2: Left, 3: Equal */ 147 int Smoking; /* 0:Unknown, 1: NO, 2: YES */ 148 int AlcoholAbuse; /* 0:Unknown, 1: NO, 2: YES */ 149 int DrugAbuse; /* 0:Unknown, 1: NO, 2: YES */ 150 int Medication; /* 0:Unknown, 1: NO, 2: YES */ 151 struct { 152 int Visual; /* 0:Unknown, 1: NO, 2: YES, 3: Corrected */ 153 int Heart; /* 0:Unknown, 1: NO, 2: YES, 3: Pacemaker */ 154 } Impairment; 155 } Patient; 156 157 struct { 158 char Recording[MAX_LENGTH_RID+1]; /* HL7, EDF, GDF, BDF replaces HDR.AS.RID */ 159 char* Technician; 160 char* Hospital; 161 uint64_t Equipment; /* identifies this software */ 162 struct { 163 /* see 164 SCP: section1, tag14, 165 MFER: tag23: "Manufacturer^model^version number^serial number" 166 GDF: tag3: "Manufacturer\0model\0version\0number\0serial number\0" 167 */ 168 // char _field[MAX_LENGTH_MANUF+1]; /* buffer */ 169 char* Name; 170 char* Model; 171 char* Version; 172 char* SerialNumber; 173 } Manufacturer; 174 } ID; 175 176 /* position of electrodes; see also HDR.CHANNEL[k].XYZ */ 177 struct { 178 float REF[3]; /* XYZ position of reference electrode */ 179 float GND[3]; /* XYZ position of ground electrode */ 180 } ELEC; 181 182 /* EVENTTABLE */ 183 struct { 184 double SampleRate; /* for converting POS and DUR into seconds */ 185 uint16_t *TYP; /* defined at ../biosig4matlab/doc/eventcodes.txt */ 186 uint32_t *POS; /* starting position [in samples] */ 187 uint32_t *DUR; /* duration [in samples] */ 188 uint16_t *CHN; /* channel number; 0: all channels */ 189 #if (BIOSIG_VERSION >= 10500) 190 gdf_time *TimeStamp ATT_ALI; /* store time stamps */ 191 #endif 192 char **CodeDesc; /* describtion of "free text"/"user specific" events (encoded with TYP=0..255 */ 193 uint32_t N; /* number of events */ 194 uint16_t LenCodeDesc; /* length of CodeDesc Table */ 195 } EVENT; 196 197 struct { /* flags */ 198 char OVERFLOWDETECTION; /* overflow & saturation detection 0: OFF, !=0 ON */ 199 char UCAL; /* UnCalibration 0: scaling !=0: NO scaling - raw data return */ 200 char ANONYMOUS; /* 1: anonymous mode, no personal names are processed */ 201 char ROW_BASED_CHANNELS; /* 0: column-based data [default]; 1: row-based data */ 202 char TARGETSEGMENT; /* in multi-segment files (like Nihon-Khoden, EEG1100), it is used to select a segment */ 203 } FLAG; 204 205 CHANNEL_TYPE *CHANNEL; 206 207 struct { /* File specific data */ 208 #ifdef ZLIB_H 209 gzFile gzFID; 210 #endif 211 #ifdef _BZLIB_H 212 // BZFILE* bzFID; 213 #endif 214 FILE* FID; /* file handle */ 215 size_t POS; /* current reading/writing position [in blocks] */ 216 // int Des; /* file descriptor */ 217 uint8_t OPEN; /* 0: closed, 1:read, 2: write */ 218 uint8_t LittleEndian; 219 uint8_t COMPRESSION; /* 0: no compression 9: best compression */ 220 // int DES; /* descriptor for streams */ 221 } FILE; 222 223 /* internal variables (not public) */ 224 struct { 225 const char* B4C_ERRMSG; /* error message */ 226 // char PID[MAX_LENGTH_PID+1]; /* use HDR.Patient.Id instead */ 227 // char* RID; /* recording identification */ 228 // uint32_t spb; /* total samples per block */ 229 // uint32_t bpb; /* total bytes per block */ 230 // uint32_t bpb8; /* total bits per block */ 231 uint8_t* Header; 232 // uint8_t* rawEventData; 233 // uint8_t* rawdata; /* raw data block */ 234 // char flag_collapsed_rawdata; /*0 if rawdata contain obsolete channels, too. */ 235 // nrec_t first; /* first block loaded in buffer - this is equivalent to hdr->FILE.POS */ 236 // nrec_t length; /* number of block(s) loaded in buffer */ 237 uint8_t* auxBUF; /* auxillary buffer - used for storing EVENT.CodeDesc, MIT FMT infor */ 238 char* bci2000; 239 // uint32_t SegSel[5]; /* segment selection in a hirachical data formats, e.g. sweeps in HEKA/PatchMaster format */ 240 enum B4C_ERROR B4C_ERRNUM; /* error code */ 241 // char flag_collapsed_rawdata; /* 0 if rawdata contain obsolete channels, too. */ 242 } AS; 243 244 void *aECG; 245 246 } HDRTYPE; 247 248 HDRTYPE* constructHDR(const unsigned NS, const unsigned N_EVENT); 249 void destructHDR(HDRTYPE* hdr); 250 HDRTYPE* sopen(const char* FileName, const char* MODE, HDRTYPE* hdr); 251 int sclose(HDRTYPE* hdr); 252 size_t sread(biosig_data_type* data, size_t start, size_t length, HDRTYPE* hdr); 253 size_t swrite(const biosig_data_type *data, size_t nelem, HDRTYPE* hdr); 254 int seof(HDRTYPE* hdr); 255 void srewind(HDRTYPE* hdr); 256 int sseek(HDRTYPE* hdr, long int offset, int whence); 257 long int stell(HDRTYPE* hdr); 258 int serror2(HDRTYPE* hdr); 259 int hdr2ascii(HDRTYPE* hdr, FILE *fid, int verbosity); 260 261 int RerefCHANNEL(HDRTYPE *hdr, void *ReRef, char rrtype); 262 const char* GetFileTypeString(enum FileFormat FMT); 263 264 uint16_t PhysDimCode(char* PhysDim0); 265 char* PhysDim3(uint16_t PhysDimCode); 266 267 int fprintf_hdr2json(FILE *stream, HDRTYPE* hdr); 268 int asprintf_hdr2json(char **str, HDRTYPE* hdr); 269 270 271 int printf_hdr2json(HDRTYPE* hdr); 272 %{ printf_hdr2json(HDRTYPE * hdr)273 int printf_hdr2json(HDRTYPE* hdr) { 274 return ( fprintf_hdr2json(stdout, hdr) ); 275 }; 276 %} 277 278 char *display_header(const char *filename); 279 %{ display_header(const char * filename)280 int display_header(const char *filename) { 281 HDRTYPE *hdr = sopen(filename,"r",NULL); 282 if (serror()) return NULL; 283 284 char *str = NULL; 285 asprintf_hdr2json(&str, hdr); 286 destructHDR(hdr); 287 return str; 288 }; 289 %} 290 291 292 /* 293 HDRTYPE* sopen(char *filename); 294 %{ 295 HDRTYPE* sopen(char *filename) 296 { 297 HDRTYPE *hdr = constructHDR(0,0); 298 hdr = sopen(filename, "r", hdr); 299 return hdr; 300 } 301 %} 302 303 int sclose(HDRTYPE *hdr); 304 %{ 305 int sclose(HDRTYPE *hdr) 306 { 307 sclose(hdr); 308 destructHDR(hdr); 309 return 0; 310 } 311 %} 312 313 void serror(); 314 %{ 315 void _serror() { 316 fprintf(stderr,"Use of SERROR is deprecated - use serror2(HDR) instead"); 317 serror(); 318 } 319 %} 320 321 void hdr2ascii(HDRTYPE* hdr, int verbosity); 322 %{ 323 void hdr2ascii(HDRTYPE* hdr, int verbosity) 324 { 325 hdr2ascii(hdr, stdout, verbosity); 326 } 327 %} 328 329 */ 330 331