NMRPipe:POLY and BASE baseline correction
From NMR Wiki
Relevant functions: POLY (polynomial baseline correction) and BASE (linear baseline correction)
Contents |
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.
Concepts
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.
| unit | example | meaning |
| pts | 5pts | point 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 |
| ppm | 10.35ppm | by ppm coordinate |
| hz | 1603.5hz | by 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)
Options
| option | type of value | default value | meaning |
| -ord | integer | order of fitting polynomial | |
| -auto | no value | turns 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 | |
| -nl | list of point coordinates separated by empty space character | no default value, user must specify list | list 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 |
| -time | no value | must 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 point | Subtract Region |
| -fx1 | point coordinate | 1 | Initial Fit Region |
| -fxn | point coordinate | size of data vector | Initial Fit Region |
| -x1 | point coordinate | 1 | sets beginning of the region where POLY is applied |
| -xn | point coordinate | size of data vector | sets the end of region where POLY is applied |
| -nw | integer | 1 | adds 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 |
Examples
No examples yet.
