NMRPipe Processing Functions
GMB: Another Version of the Gauss Window.
GMB applies a Gauss-like window, inspired by a similar window function found on Bruker spectrometers. It is somewhat similar to the GM function, and like this function, it also applies a combination of an exponential and a Gaussian.
In the following formula for GMB,
tSize is th number of
time-domain points, which defines the length of the window
function; GMB[i] is the window function from
i = 0 (first
i = tSize - 1 (last point); and
is the sweep width in Hz.
Given the GMB adjustable parameters
GMB[i] = exp( -a*t - b*t*t )where
t = i/sw aq = tSize/sw a = PI*lb b = -a/(2.0*gb*aq)In addition to function-specific options, the GMB window function provides the following features common to all NMRPipe window functions:
(Q1) Specifies an exponential factor
as used in the
formula given above. This value is usually specified
as a negative number which is about the same size as
the natural linewidth in Hz. The default value is 0.0,
which means no exponential term will be applied.
(Q2) Specifies a Gaussian factor
as used in the formula
given above. It is usually specified as a positive
number which is a fraction of 1.0. The default
value is 0.0, which leads to an undefined window function
according to the formula; for this reason, the
Gaussian term is omitted from the calculation
-gb 0.0 is given.
GENERIC WINDOW OPTIONS
Specifies the number of points in the window function. The default value is the valid time-domain size recorded in the data header.
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.
Specifies the scaling applied to the first point of the FID, which influences the zero-order 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 first-order phase correction will be applied.
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
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.
When this flag is used, default window parameters (Q1 and Q2) will be extracted from the data header, along with the first point scaling (C1). This requires that all of these parameters have already been recorded, for instance during previous processing or format conversion (see EXAMPLES below). Additional command-line 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
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 previously-applied 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.
A typical usage of a GM and GMB window:
nmrPipe -fn GM -g1 20 -g2 35 nmrPipe -fn GMB -lb -20 -gb 0.25
GMB and the other nmrPipe window functions use the recorded time-domain size (NDAPOD) to establish their default length.
-hdr flag is used, default window parameters are
extracted from header values NDAPODCODE, NDAPODQ1, NDAPODQ2,
The header values NDAPODCODE, NDAPODQ1, NDAPODQ2, and NDC1 are updated according to the values applied during processing.