NMRPipe Processing Functions
TM: Trapezoid Multiply Window.
| Flag |
Argument |
Default |
Description |
-t1 |
leftPts |
0 |
Left Ramp Length (APOD Parameter Q1). |
-t2 |
rightPts |
0 |
Right Ramp Length (APOD Parameter Q2). |
-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,C1 Values from Header as Defaults. |
-inv |
|
|
Invert Window. |
|
TM applies a trapezoid window. The window is
specified in terms of the lengths of the left and right edges
of the trapezoid. The lengths are specified in points.
The window is seldom if ever used with biomolecular NMR spectra,
but might be of use for time-domain data which has its
largest amplitudes near the center, as is commonly found in
time-domain image data.
In addition to function-specific options, each of the
nmrPipe window functions provides the following features:
-
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 time-domain size recorded in
the header.
-
Optional extraction and use of window parameters recorded
in the header, rather than from the command-line.
-
An inverse mode, which divides by the window function and
first point scale rather than multiplying by them. However,
since the TM function always has zero values at the start and
end, it is unlikely that the inverse mode would be used for
this particular type of window.
-
Options to adjust the size or starting point of the window
function via command-line arguments.
TM OPTIONS
-t1 leftPts
(Q1) Specifies the number of points in the left edge of
the trapezoid window. The window function will
increase from 0.0 to 1.0 over this point range.
-t2 rightPts
(Q2) Specifies the number of points in the right edge
of the trapezoid window. The window function will
decrease from 1.0 to 0.0 over this point range.
GENERIC 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
TM is commonly applied with equal lengths for the legs of
the trapezoid:
| nmrPipe -fn TM -t1 32 -t2 32 \
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,
and NDC1.
The header values NDAPODCODE, NDAPODQ1, NDAPODQ2,
and NDC1 are updated according to the values applied during
processing.
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