NMRPipe Processing Functions
SP: Adjustable Sine Window.
Flag 
Argument 
Default 
Description 
off 
offset 
0.0 
Sine Start*PI (APOD Parameter Q1). 
end 
end 
1.0 
Sine End*PI (APOD Parameter Q2). 
pow 
exp 
1.0 
Sine Exponent (APOD Parameter Q3). 
size 
aSize 
TSIZE 
Number of Points in Apodize Window. 
start 
aStart 
1 
Start Location for Applying Apodize Window. 
c 
fScale 
1 
Scale Factor for First Point (C1 Parameter). 
one 


Set window points outside apodize region to 1. 
hdr 


Use Q1,Q2,Q3,C1 Values from Header as Defaults. 
inv 


Invert Window. 

SP applies a sinebell window with an adjustable
offset, endpoint, and exponent. The offset and endpoint are
specified in units of pi radians.
In the following formula tSize is the number of
timedomain points, which defines the length of the window
function; SP[i] is the SP window function from i = 0 (first
point) to i = tSize  1 (last point).
SP[i] = sin( (PI*off + PI*(endoff)*i/(tSize1) )^pow
In addition to functionspecific options, the SP
window provides the following features common
to all nmrPipe window functions:

Optional scaling of the first point of each FID.

Automatic recording of window parameters and first point
scaling in the data header during processing.

Automatic adjustment of the default size of the window
function to match the valid timedomain size recorded in
the header.

Optional extraction and use of window parameters recorded
in the header, rather than from the commandline.

An inverse mode, which divides by the window function and
first point scale rather than multiplying by them.

Options to adjust the size or starting point of the window
function via commandline arguments.
SP OPTIONS
off offset
(Q1) Specifies the starting point of the sinebell in
units of pi radians. Common
values are 0.0 (for a sine
window which starts height at 0.0) and 0.5 (for a
cosine window, which starts at height 1.0). The
default value is 0.0.
end end
(Q2) Specifies the ending point of the sinebell in
units of pi radians. Common values are
1.0 (for a window which goes to 0.0 height at the last
point) and
0.95 (for a window which doesn't go all the way to
0.0). The default value is 1.0.
pow pow
(Q3) Specifies the exponent of the sinebell;
Noninteger values are allowed. Common values are 1.0
(for ordinary sinebell) and 2.0 (for squaredbell
functions). The default value is 1.0.
GENERIC OPTIONS
size aSize
Specifies the number of points in the window function.
The default value is the valid timedomain size
recorded in the data header.
start aStart
Specifies the starting point of the window function.
The default value is 1, which means the window function
starts at the first point of the FID. This option is
intended for creation of composite windows by application
of different functions to different regions of the
FID.
c fScale
Specifies the scaling applied to the first point of the
FID, which influences the zeroorder offset in the
corresponding spectrum. The default value is 1.0,
which means no first point adjustment is applied. A
value of 0.5 is usually appropriate in cases where no
substantial firstorder phase correction will be
applied.
one
This flag influences the values used "outside" the window
function, in cases where the window size is smaller
than the actual number of data points. By default,
data values outside the window region are multiplied by
zero when the window is applied. However if the one
flag is used, data values outside the window region
will be multiplied by 1.0 when the window is applied.
This flag is intended to assist creation of composite
windows by application of different functions to different
regions of the FID.
hdr
When this flag is used, default window parameters
(Q1, Q2, Q3) will be extracted from the data header,
along with the first point scaling. This requires that
all of these parameters have already been recorded, for
instance during previous processing or format conversion
(see EXAMPLES below). Additional commandline can
be used to override values restored from the header.
The window parameters stored in the data header can be
viewed using the showhdr program, for example:
showhdr verb test.ft2
inv
When this flag is used, the inverse (1/window) of the
selected window and first point scale will be applied.
This option is intended for removing a
previouslyapplied window in inverse processing
schemes. This option should generally only be used on
window functions which have no values close or equal to
zero. In cases where the window does have a zero
value, the inverse window is also given as zero.
EXAMPLES
Two ways of specifying an ordinary cosine bell:
nmrPipe fn SP off 0.5
nmrPipe fn SP off 0.5 end 1.0
Three ways of specifying an ordinary sine bell; note that
this is the default function for SP:
nmrPipe fn SP
nmrPipe fn SP off 0.0
nmrPipe fn SP off 0.0 end 1.0
A cosinesquared bell:
nmrPipe fn SP off 0.5 end 1.0 pow 2
A 60degree shifted sine bell with scaling of the first
point by 0.5; offset = 60/180, roughly 0.33:
nmrPipe fn SP off 0.33 end 1.0
A cosine bell which does not decrease all the way to zero;
this window function can usually be inverted safely for
inverse processing schemes, because its smallest height is
about 0.16:
nmrPipe fn SP off 0.5 end 0.95
A cosinesquared rolloff function; the cosine function is
set to span 100 points starting from point 257 in the data,
so that the window region extends from point 257 to point
356. Since the one flag is included, the data will be multiplied
by 1.0 outside of this region. Therefore, the
result is a window which is uniformly 1.0 over points 1 to
256, and decays to 0.0 as a cosinesquare over points 257 to
356:
nmrPipe fn SP off 0.5 pow 2 start 257 size 100 one
The following scheme shows window parameters (APOD, Q1, Q2,
and Q3), first point scale (C1), and phasing (P0, P1) specified
during conversion. The values are then extracted and
used during processing by including the hdr option with
processing functions APOD and PS:
#!/bin/csh
bruk2pipe in hsqcn.ser \
xN 2048 yN 256 \
xT 1024 yT 128 \
xMODE Complex yMODE Complex \
xSW 9090.91 ySW 2500.00 \
xOBS 600.138 yOBS 60.8108 \
xCAR 4.73 yCAR 118.0 \
xLAB HN yLAB N \
xAPOD SP yAPOD SP \
xQ1 0.50 yQ1 0.50 \
xQ2 0.98 yQ2 0.95 \
xQ3 2.0 yQ3 1.0 \
xC1 0.5 yC1 1.0 \
xP0 0.0 yP0 90.0 \
xP1 0.0 yP1 180.0 \
ndim 2 aq2D States \
out hsqcn.fid verb ov
nmrPipe in hsqcn.fid \
 nmrPipe fn SOL \
 nmrPipe fn APOD hdr \
 nmrPipe fn ZF auto \
 nmrPipe fn FT \
 nmrPipe fn PS p0 22 p1 0.0 di \
 nmrPipe fn EXT left sw verb \
 nmrPipe fn TP \
 nmrPipe fn APOD hdr \
 nmrPipe fn ZF auto \
 nmrPipe fn FT \
 nmrPipe fn PS hdr di \
verb ov out test.ft2
In this inverse processing scheme, a spectrum is inverse
transformed, and the SP window applied in a previous scheme
is removed (SP inv hdr ) in order to apply Linear Prediction
(LP). After LP, the window is reapplied (SP hdr ):
xyz2pipe in lp/test%03d.ft3 z verb \
 nmrPipe fn HT auto \
 nmrPipe fn PS inv hdr \
 nmrPipe fn FT inv \
 nmrPipe fn ZF inv \
 nmrPipe fn SP inv hdr \
 nmrPipe fn LP fb \
 nmrPipe fn SP hdr \
 nmrPipe fn ZF auto \
 nmrPipe fn FT \
 nmrPipe fn PS hdr di \
 pipe2xyz out lp/test%03d.ft3 z inPlace
HEADER VALUES
The nmrPipe window functions use the recorded timedomain
size (NDAPOD) to establish their default length.
When the hdr flag is used, default window parameters are
extracted from header values NDAPODCODE, NDAPODQ1, NDAPODQ2,
NDAPODQ3, and NDC1.
The header values NDAPODCODE, NDAPODQ1, NDAPODQ2, NDAPODQ3,
and NDC1 are updated according to the values applied during
processing.
