NMRPipe Processing Functions
GM: LorentztoGauss Window.
Flag 
Argument 
Default 
Description 
g1 
expHz 
0.0 
Inverse Exponential Width, Hz (APOD Parameter Q1). 
g2 
gaussHz 
0.0 
Gaussian Broaden Width, Hz (APOD Parameter Q2). 
g3 
center 
0.0 
Location of Gauss Maximum, 0.0 to 1.0 (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. 

GM applies a LorentztoGauss window,
which is a combination
of an inverse exponential and a Gaussian. The purpose of
the window is to replace the exponential decay of the original
data with a Gaussian decay, so that the corresponding
spectral lineshape will be more like a Gaussian rather
than a Lorentzian.
The exponential term is
specified as a Lorentzian line sharpening in Hz. The Gaussian
term is specified as a Gaussian line broadening in Hz,
and a center position (location of the Gaussian maximum).
The Gaussian center position is specified as a value ranging
from 0.0 (Gaussian maximum at the first point of the FID) to
1.0 (Gaussian maximum at the last point of the FID).
In a usual application,
the Lorentzian line sharpening is chosen to match the intrinsic decay of
the timedomain data, and the Gaussian broadening is chosen to provide
a suitable degree of decay. In most cases, this means that the Gaussian
broadening will be substantially larger than the Lorentzian sharpening.
In the following formula for GM, tSize is th number of
timedomain points, which defines the length of the window
function; GM[i] is the window function from i = 0 (first
point) to i = tSize  1 (last point); and sw
is the sweep width in Hz.
GM[i] = exp( e  g*g )
where
e = PI*i*g1/sw
g = 0.6*PI*g2*(g3*(tSize1)  i)/sw
In addition to functionspecific options, the GM window function
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.
GM OPTIONS
g1 invExpHz
(Q1) Specifies the inverse exponential to apply in
terms of a line sharpening in Hz. It is usually
adjusted to match the natural linewidth. The default
value is 0.0, which means no exponential term will be
applied, and the window will be a pure Gaussian function.
g2 gaussHz
(Q2) Specifies the Gaussian to apply in terms of a line
broadening in Hz. It is usually adjusted to be
larger (x 1.25  4.0) than the line sharpening
specified by the g1 option.
g3 gCenter
(Q3) Specifies the position of the Gaussian function's
maximum on the FID. It is specified as a value ranging
from 0.0 (Gaussian maximum at the first point of the
FID) to 1.0 (Gaussian maximum at the last point of the
FID). It most applications, the default value of 0.0
is used.
GENERIC WINDOW 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, and 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
A typical usage of a LorentztoGauss window:
nmrPipe fn GM g1 20 g2 35
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 GM yAPOD GM \
xQ1 20 yQ1 10 \
xQ2 35 yQ2 15 \
xQ3 0.0 yQ3 0.0 \
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
HEADER VALUES
GM and the other 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.
