NMRPipe File Format - CONNJUR/CONNJUR_widgets GitHub Wiki

NMRPipe File Format

Mostly from fdatap.h

The NMRPipe header is 2048 bytes. It is essentially a 512 element array of 4-byte floats. However, some of the contiguous floats are actually recast into char's for storing strings. Integer metadata is simply recorded as floats. fdatap.h defines named constants to provide a key-value lookup using the array indices.

Two notes. One, the actual data sizes of the file appear to be given by array elements 99, 219, 15 and 32, corresponding to FDSIZE, FDSPECNUM, FDF3SIZE and FDF4SIZE. Two, the "correct first point" C1 value and the ZF sizes appear to be negated. (Array elements: 108, 404, 409, 418, 423, 437, 438 and 439)

Array Index Name Comment
0 FDMAGIC Should be zero in valid NMRPipe file
1 FDFLTFORMAT Constant defining floating point format. (IEEE or VAX).
2 FDFLTORDER Constant for determining endieness. 2.345 is correct.
3-8 unused
9 FDDIMCOUNT Number of dimensions in complete data
10 FDF3OBS Obs Freq MHz.
11 FDF3SW Sweep Width Hz.
12 FDF3ORIG Axis Origin (Last Point), Hz.
13 FDF3FTFLAG 1=Freq Domain 0=Time Domain.
14 FDPLANELOC Location of this plane; currently unused
15 FDF3SIZE Number of points in dimension.
16-17 FDF2LABEL 8-char Axis Label.
18-19 FDF1LABEL 8-char Axis Label.
20-21 FDF3LABEL 8-char Axis Label.
22-23 FDF4LABEL 8-char Axis Label.
24 FDDIMORDER1 Dimension stored in X-Axis.
25 FDDIMORDER2 Dimension stored in Y-Axis.
26 FDDIMORDER3 Dimension stored in Z-Axis.
27 FDDIMORDER4 Dimension stored in A-Axis.
28 FDF4OBS Obs Freq MHz.
29 FDF4SW Sweep Width Hz.
30 FDF4ORIG Axis Origin (Last Point), Hz.
31 FDF4FTFLAG 1=Freq Domain 0=Time Domain.
32 FDF4SIZE Number of points in dimension.
40 FDDMXVAL
41 FDDMXFLAG
42 FDDELTATR
45 FDNUSDIM Unexpanded NUS dimensions.
50 FDF3APOD Current valid time-domain size.
51 FDF3QUADFLAG
53 FDF4APOD Current valid time-domain size.
54 FDF4QUADFLAG
55 FDF1QUADFLAG
56 FDF2QUADFLAG
57 FDPIPEFLAG Dimension code of data stream.
58 FDF3UNITS
59 FDF4UNITS
60 FDF3P0
61 FDF3P1
62 FDF4P0
63 FDF4P1
64 FDF2AQSIGN
65 FDPARTITION Slice count for server mode. Added for NMRPipe
66 FDF2CAR
67 FDF1CAR
68 FDF3CAR
69 FDF4CAR
70 FDUSER1
71 FDUSER2
72 FDUSER3
73 FDUSER4
74 FDUSER5
75 FDPIPECOUNT Number of functions in pipe.
76 FDUSER6
77 FDFIRSTPLANE First Z-Plane in subset. Added for NMRPipe
78 FDLASTPLANE Last Z-Plane in subset. Added for NMRPipe
79 FDF2CENTER Point where carrier freq is referenced. May be outside datasize.
80 FDF1CENTER Point where carrier freq is referenced. May be outside datasize.
81 FDF3CENTER Point where carrier freq is referenced. May be outside datasize.
82 FDF4CENTER Point where carrier freq is referenced. May be outside datasize.
95 FDF2APOD Current valid time-domain size.
96 FDF2FTSIZE
97 FDREALSIZE Number of valid time-domain pts (obsolete).
98 FDF1FTSIZE
99 FDSIZE I.
100 FDF2SW Sweep Width Hz.
101 FDF2ORIG Axis Origin (Last Point), Hz.
106 FDQUADFLAG See Data Type codes below.
108 FDF2ZF
109 FDF2P0
110 FDF2P1
111 FDF2LB
119 FDF2OBS Obs Freq MHz.
135 FDMCFLAG Magnitude Calculation performed.
152 FDF2UNITS
153 FDNOISE Used to contain an RMS noise estimate.
157 FDTEMPERATURE Temperature, K.
158 FDPRESSURE Pressure, Pascal.
180 FDRANK Estimate of matrix rank; Added for NMRPipe.
199 FDTAU A Tau value (for spectral series).
200 FDF3FTSIZE
201 FDF4FTSIZE
218 FDF1OBS Obs Freq MHz.
219 FDSPECNUM Number of complex 1D slices in file.
220 FDF2FTFLAG 1=Freq Domain 0=Time Domain.
221 FDTRANSPOSED 1=Transposed, 0=Not Transposed.
222 FDF1FTFLAG 1=Freq Domain 0=Time Domain.
229 FDF1SW Sweep Width Hz.
234 FDF1UNITS
243 FDF1LB
245 FDF1P0
246 FDF1P1
247 FDMAX Max value in real part of data.
248 FDMIN Min value in real part of data.
249 FDF1ORIG Axis Origin (Last Point), Hz.
250 FDSCALEFLAG 1 if FDMAX and FDMIN are valid.
251 FDDISPMAX Max value, used for display generation.
252 FDDISPMIN Min value, used for display generation.
253 FDPTHRESH Positive threshold for peak detection.
254 FDNTHRESH Negative threshold for peak detection.
256 FD2DPHASE See 2D Plane Type codes below.
257 FDF2X1
258 FDF2XN
259 FDF1X1
260 FDF1XN
261 FDF3X1
262 FDF3XN
263 FDF4X1
264 FDF4XN
266 FDDOMINFO Spectral/Spatial Flags. Added for NMRPipe.
267 FDMETHINFO FT/Direct Flags. Added for NMRPipe.
283 FDHOURS Time: hours
284 FDMINS Time: minutes
285 FDSECS Time: seconds
286-289 FDSRCNAME char srcFile[16] (seems blank)
290-293 FDUSERNAME char uName[16] (seems blank)
294 FDMONTH Date: month
295 FDDAY Date: day
296 FDYEAR Date: year
297-311 FDTITLE char title[60] (seems blank)
312-351 FDCOMMENT char comment[160] (seems blank)
359 FDLASTBLOCK
360 FDCONTBLOCK
361 FDBASEBLOCK
362 FDPEAKBLOCK
363 FDBMAPBLOCK
364 FDHISTBLOCK
365 FD1DBLOCK
370 FDSCORE Added for screening score etc.
371 FDSCANS Number of Scans per 1D.
372 FDF3LB
373 FDF4LB
374 FDF2GB
375 FDF1GB
376 FDF3GB
377 FDF4GB
378 FDF2OBSMID
379 FDF1OBSMID
380 FDF3OBSMID
381 FDF4OBSMID
382 FDF2GOFF
383 FDF1GOFF
384 FDF3GOFF
385 FDF4GOFF
386 FDF2TDSIZE
387 FDF1TDSIZE
388 FDF3TDSIZE
389 FDF4TDSIZE
399 FD2DVIRGIN 0=Data never accessed, header never adjusted.
400 FDF3APODCODE
401 FDF3APODQ1
402 FDF3APODQ2
403 FDF3APODQ3
404 FDF3C1
405 FDF4APODCODE
406 FDF4APODQ1
407 FDF4APODQ2
408 FDF4APODQ3
409 FDF4C1
413 FDF2APODCODE GMB=7, SP=1
414 FDF1APODCODE
415 FDF2APODQ1
416 FDF2APODQ2
417 FDF2APODQ3
418 FDF2C1
419 FDF2APODDF
420 FDF1APODQ1
421 FDF1APODQ2
422 FDF1APODQ3
423 FDF1C1
428 FDF1APOD Current valid time-domain size.
437 FDF1ZF
438 FDF3ZF
439 FDF4ZF
442 FDFILECOUNT Number of files in complete data.
443 FDSLICECOUNT0 Encodes number of 1D slices in stream.
444 FDTHREADCOUNT Multi-Thread Mode: Number of Threads.
445 FDTHREADID Multi-Thread Mode: Thread ID, First = 0.
446 FDSLICECOUNT1 Encodes number of 1D slices in stream.
447 FDCUBEFLAG Data is 3D cube file series.
464-471 FDOPERNAME char oName[32] (seems blank)
475 FDF1AQSIGN
476 FDF3AQSIGN
477 FDF4AQSIGN
480 FDF2OFFPPM
481 FDF1OFFPPM
482 FDF3OFFPPM
483 FDF4OFFPPM
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