NMRPipe:POLY and BASE baseline correction

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Relevant functions: POLY (polynomial baseline correction) and BASE (linear baseline correction)


Function POLY

Function POLY calculates a polynomial fitting selected points (which are contained in the user- or automatically defined nodes) on the vector. If the data is complex, fitting is done independently on the real and imaginary data components using the same node coordinates. Values of that polynomial(s) are then subtracted from the data vector thus giving the baseline-corrected spectrum. Function accepts additional optional parameters that are listed in the "options" section below.

Either -time (for time domain data), -auto, or -nl option must be provided. Last two options can be used toghether or separately, but cannot be used toghether with -time.


Point coordinates that are to be provided with -nl, -x1, -xn, -sx, -sxn, -fx, -fxn options can be specified in different units. Default unit is pts - i.e. 5 and 5pts have same meaning.

pts5ptspoint number of the data point in data vector; numbering of data points starts at 1
%5.5%by percent offset from the beginning of data vector
ppm10.35ppmby ppm coordinate
hz1603.5hzby offset of the point in hertz from the beginning of the data vector

node - a group of odd number of adjacent data points (node center + equal number of extra points as specified by the -nw paramater)


optiontype of valuedefault valuemeaning
-ordintegerorder of fitting polynomial
-autono valueturns on automatic determination of baseline nodes; nodes are automatically determined for separately each data vector; -auto function should only be used in the frequency domain
parameter -nl can be used together with -auto in order to force certain points into the baseline definition.
If the data is complex, node points are searched in the real component, but fitting and baseline substraction is performed in both real and imaginary parts
-nllist of point coordinates separated by empty space characterno default value, user must specify listlist of node center coordinates; parameter -nw can be used together with -nl to add more points to each node on either side of each point specified with -nl
-timeno valuemust be used when POLY is applied to the time domain data
-sx1 point coordinate 1 (i.e. first data point)Subtract Region
-sxn point coordinate size of data vector, i.e. last data pointSubtract Region
-fx1 point coordinate 1Initial Fit Region
-fxn point coordinate size of data vector Initial Fit Region
-x1point coordinate1sets beginning of the region where POLY is applied
-xnpoint coordinatesize of data vector sets the end of region where POLY is applied
-nwinteger1adds specified number of points to each node on the left and right side of node center point; i.e. by default, each node contains three adjacent points


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