# Alignpeaks

### Purpose

Calibrates wavelength scale using standard peaks.

### Synopsis

- s = alignpeaks(x0,x1,ax,options)
- y = alignpeaks(s,y1)

### Description

ALIGNPEAKS calibrates a wavelength scale using standard peak positions. Ideally, the axis scale (x0) would apply to a single instrument at time *t* = 0 and *t* > 0 or for two different instruments. However, (x1) at *t* > 0 doesn't typically match (x0) at *t* = 0 even though the numbers in the scales are identical. The result is that a plot of (x0,y0) and (x0,y1) appear shifted from one another.

The inputs to ALIGNPEAKS are (x0) a 1x*K* vector containing the axis locations of *K* peaks on the standard instrument at *t* = 0 (e.g., the true wavelengths), (x1) a 1x*K* vector containing the axis locations of the corresponding peaks on the field / test instrument at *t* > 0 (e.g., the peak positions on the field instrument), and ax a 1x*N* vector containing the axis scale where *N* > *K*. ALIGNPEAKS finds a polynomial fit between (x0) and (x1) and outputs the result in the structure array (s). The output (y) is a fit of (x1).

### Options

Optional input (options) is a structure array with the following fields:

**name**: 'options', name indicating that this is an options structure,

**plots**: [ 'none' | {'final'} ] governs level of plotting, and

**order**: [ {2} ] integer giving the polynomial order.

Executing options = alignpeaks('options'); gives an empty options structure.

### Example

A measurements at *t* = 0 gives a spectrum (y0) with axis (ax), and measurements at *t* > 0 of the same sample yields a spectrum (y1) with the same axis (ax) but with peaks shifted. Therefore

- plot(ax,y0,'b',ax,y1,'r')

shows a shift in the peaks. The peak positions at *t* = 0 are listed in (x0) and the peak positions at *t* > 0 are listed in (x1). The polynomial fit is given by

- s = alignpeaks(x0,x1,ax);

and the transformed spectrum is obtained with

- y10 = alignpeaks(s,y1);

so that

- plot(ax,y0,'b',ax,y1,'r')

shows less of a peak shift. See alignpeaksdemo.