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  Frank Delaglio, Ph.D.

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  E-mail: delaglio@nmrscience.com

NMRPipe Processing Functions

This particular reference page lists the specific processing functions that can be used in an nmrPipe processing pipeline (via nmrPipe -fn ...), for example "FT", the Fourier Transform function.

Like FT, many of these functions frequently in typical processing schemes. Some functions and options, however, may rarely be used, were added only for development purposes, or may be superseded by other functions. In an attempt to indicate which functions and options are used most frequently, this reference list includes an instance count. In the current version of this reference list, the instance count tallies how often NMRPipe's developer Frank Delaglio has used a particular function or option in a script during both routine use and research and development of the software. Note that this scheme will underestimate the uses of functions such as SAVE which are primarily used interactively, and not within scripts.

NMRPipe Processing Functions

Function	Instances	Description	Common Arguments (Instances)
ADD	0	Add a Constant
APOD	11	Apply the Selected Window (Apodization)	`-inv (7)` `-hdr (7)` `-qName (4)` `-q1 (4)` `-q2 (4)` `-q3 (4)`
BASE	9	Linear Baseline Corrections	`-first (8)` `-last (8)` `-nw (8)` `-nl (6)`
CBF	20	Subtract Constant Baseline
COADD	31	Linear Combination of Data Vectors	`-cList (30)` `-axis (27)` `-time (25)`
CS	48	Circular Shift	`-rs (37)` `-sw (37)` `-neg (27)` `-ls (10)` `-1ppm (5)` `-inv (1)`
DX	0	Derivative
EM	35	Exponential Multiply Window	`-lb (34)` `-c (18)`
EXT	487	Extract Region	`-sw (455)` `-xn (317)` `-x1 (306)` `-left (157)` `-yn (7)` `-y1 (6)`
FSH	2	Frequency Shift via Fourier Transform	`-ls (1)` `-sw (1)`
FT	1597	Complex Fourier Transform	`-inv (178)` `-auto (111)` `-neg (53)` `-alt (25)` `-bruk (17)` `-real (11)`
GM	54	Lorentz-to-Gauss Window	`-g1 (53)` `-g2 (53)` `-c (53)` `-g3 (5)`
GMB	0	Gaussian Window
HA	0	Hadamard Transform
HT	155	Reconstruct Imaginary Data Via Hilbert Transform	`-auto (90)` `-ps90-180 (4)`
IMG	5	Image Processing Functions	`-median (3)` `-dx (2)` `-dy (2)` `-kern (1)` `-min (1)` `-thresh (1)`
INTEG	0	Integral
JMOD	0	Damped J-Modulation
LP	198	Linear Prediction	`-ord (148)` `-fb (93)` `-pred (74)` `-xn (46)` `-ps0-0 (28)` `-ps90-180 (18)`
LS	0	Left Shift
MAC	187	M-language MACRO Processing	`-macro (186)` `-all (67)` `-var (25)` `-str (14)` `-reg (9)` `-dif (6)`
MC	29	Modulus (Magnitude) Calculation for Complex Data	`-p0 (4)` `-p1 (4)`
MED	2	Baseline Correction via Local Median	`-nw (1)`
MEM	50	ND Maximum Entropy Reconstruction	`-sigma (49)` `-report (46)` `-ndim (42)` `-alpha (21)` `-zero (18)` `-xconv (17)`
MIR	2	Form Mirror Image
ML	22	Maximum Likelihood Frequency Map	`-xfSize (12)` `-ndim (11)` `-yfSize (10)` `-xlw (8)` `-sign (7)` `-report (5)`
MULT	92	Multiply by a Constant	`-xn (69)` `-c (63)` `-hdr (24)` `-inv (6)` `-r (4)` `-i (2)`
NULL	7	Null Function; Leave Data Unchanged
POLY	169	Polynomial Time-Domain Solvent Subtraction	`-time (169)`
POLY	562	Polynomial Frequency-Domain Baseline Correction	`-auto (390)` `-ord (134)` `-xn (20)` `-x1 (20)` `-window (3)` `-nw (3)`
PS	1333	Phase Correction	`-p0 (1176)` `-p1 (1167)` `-hdr (150)` `-inv (89)` `-ls (2)` `-rs (2)`
QART	6	Scale Quad Artifacts	`-a (5)` `-f (5)`
QMIX	5	General Linear Combination of Data Vectors	`-ic (5)` `-oc (5)` `-cList (5)` `-time (5)` `-0,1 (1)`
REV	17	Reverse Data	`-sw (2)`
RFT	0	Real Fourier Transform
RS	22	Right Shift	`-rs (21)` `-sw (11)`
SAVE	0	Save Current 1D Data Vector
SET	43	Set Data to Constant	`-r (25)` `-c (15)` `-x1 (9)` `-xn (8)`
SHUF	15	Shuffle Data (Exchange Reals and Imaginaries, etc)	`-exlr (7)` `-ri2c (2)` `-bswap (2)` `-swap (1)` `-c2ri (1)` `-r2i (1)`
SIGN	11	Sign Manipulation (Negate, etc)	`-alt (7)` `-i (3)`
SMO	3	Smooth Data via Convolution Filter
SOL	208	Solvent Filter	`-head (16)` `-mir (16)` `-fl (2)`
SP	1357	Adjustable Sine Bell Window	`-off (1204)` `-end (1160)` `-pow (1148)` `-c (1143)` `-inv (117)` `-hdr (117)`
TM	0	Trapezoid Window
TP	892	2D Transpose XY->YX (YTP)	`-hyper (47)` `-nohdr (7)` `-auto (2)`
TRI	2	Triangle Window	`-loc (1)`
ZD	0	Zero Diagonal Region
ZF	1580	Zero Fill	`-auto (941)` `-size (284)` `-zf (169)` `-inv (122)` `-mid (11)` `-pad (3)`
ZTP	35	3D Transpose XYZ->ZYX

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last updated: Apr 20, 2011 / big frank

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