Alignpeaks: Difference between revisions
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===Purpose=== | ===Purpose=== | ||
Calibrates wavelength scale using standard peaks. | Calibrates wavelength scale using standard peaks. | ||
===Synopsis=== | ===Synopsis=== | ||
:s = alignpeaks(x0,x1,ax,options) | :s = alignpeaks(x0,x1,ax,options) | ||
:y = alignpeaks(s,y1) | :y = alignpeaks(s,y1) | ||
===Description=== | ===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. | 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. | 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=== | ===Options=== | ||
Optional input options is a structure array with the following fields: | 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 | * '''plots''': [ 'none' | {'final'} ] governs level of plotting, and | ||
* '''order''': [ {2} ] integer giving the polynomial order. | * '''order''': [ {2} ] integer giving the polynomial order. | ||
Executing options = alignpeaks('options'); gives an empty options structure. | Executing options = alignpeaks('options'); gives an empty options structure. | ||
===Example=== | ===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 | 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 | 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 | and the transformed spectrum is obtained with | ||
:y10 = alignpeaks(s,y1); | |||
so that | so that | ||
shows less of a peak shift. See | :plot(ax,y0,'b',ax,y1,'r') | ||
shows less of a peak shift. See alignpeaksdemo. | |||
===See Also=== | ===See Also=== | ||
[[alignmat]], [[alignspectra]], [[registerspec]], [[stdgen]] | [[alignmat]], [[alignspectra]], [[registerspec]], [[stdgen]] | ||
Revision as of 14:24, 3 September 2008
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 1xK vector containing the axis locations of K peaks on the standard instrument at t = 0 (e.g., the true wavelengths), x1 a 1xK 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 1xN 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.