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NMRPipe Processing Functions
SP: Adjustable Sine Window.
SP applies a sine-bell 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
time-domain points, which defines the length of the window
function; SP[i] is the SP window function from
i = 0 (first
i = tSize - 1 (last point).
SP[i] = sin( (PI*off + PI*(end-off)*i/(tSize-1) )^pow
In addition to function-specific options, the SP window provides the following features common to all nmrPipe window functions:
(Q1) Specifies the starting point of the sine-bell 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.
(Q2) Specifies the ending point of the sine-bell 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.
(Q3) Specifies the exponent of the sine-bell; Non-integer values are allowed. Common values are 1.0 (for ordinary sine-bell) and 2.0 (for squared-bell functions). The default value is 1.0.
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, 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 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.
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 cosine-squared bell:
nmrPipe -fn SP -off 0.5 -end 1.0 -pow 2
A 60-degree 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 cosine-squared roll-off 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 cosine-square over points 257 to
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 re-applied (
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
The 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,
NDAPODQ3, and NDC1.
The header values NDAPODCODE, NDAPODQ1, NDAPODQ2, NDAPODQ3, and NDC1 are updated according to the values applied during processing.