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NMRPipe Processing Functions
APOD: Generic Apodization Window.
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APOD applies one of the nmrPipe apodize windows, as specified by command-line arguments or header values. It can be used to apply a window function which was specified during format conversion or during previous processing.
In addition to function-specific options, each of the nmrPipe window functions provides the following features in common:
APOD OPTIONS
-qName apodName
Specifies the name of the window function to apply:
EM
GM
GMB
JMOD
SP
TM
TRI. See the section on a given window function for more information.
-q1 apodQ1
Specifies the first parameter (Q1) of the selected window
function.
See the section on a given window function for information
on which window parameter corresponds with Q1.
-q2 apodQ2
Specifies the second parameter (Q2) of the selected
window function.
See the section on a given window function for information
on which window parameter corresponds with Q2.
-q3 apodQ3
Specifies the third parameter (Q3) of the selected window function.
See the section on a given window function for information
on which window parameter corresponds with Q3.
GENERIC WINDOW OPTIONS
-size aSize
Specifies the number of points in the window function.
The default value is the valid time-domain 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 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.
-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 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
-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
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.
EXAMPLES
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 window applied in a previous scheme
is removed (APOD -inv -hdr) in order to apply Linear Prediction
(LP). After LP, the window is re-applied (APOD -hdr).
The inverse window will only work well if the original window did not have
any values equal or close to zero.
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 APOD -inv -hdr \
| nmrPipe -fn LP -fb \
| nmrPipe -fn APOD -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 time-domain 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.