Frank Delaglio, Ph.D.

19804 Maycrest Way
Germantown MD 20876 USA

301 806-0867
delaglio@nmrscience.com



NMRPipe Processing Functions
APOD: Generic Apodization Window.

Flag Argument Default Description
 -qName apName None Apodize Function Name: SP EM GM GMB TM TRI JMOD.
 -q1 parm1 0.0 Apodize Parameter 1 (APOD Parameter Q1).
 -q2 parm2 0.0 Apodize Parameter 2 (APOD Parameter Q2).
 -q3 parm3 0.0 Apodize Parameter 3 (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.

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:

  • 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.
  • Options to adjust the size or starting point of the window function via command-line arguments.

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.