biospecnorway / biospectools Goto Github PK
View Code? Open in Web Editor NEWTools for working with spectral data https://biospectools.readthedocs.io/en/latest/
Tools for working with spectral data https://biospectools.readthedocs.io/en/latest/
Also class MeEMSCDetails
needs to be documented.
The simplest way would be to use as a template documentation of the EMSC
method.
biospectools/src/biospectools/preprocessing/emsc.py
Lines 72 to 113 in 2e2c3e5
Rename and support old kwargs until version 0.6.0
@JohanneSolheim spotted a problem that when EMSC is used with several non-connected regions of spectra, then the established polynomial components look to be off center. In the image below you can see that the red line (linear polynomial) is shifted more towards left region.
Indeed, current implementation defines the middle point of spectrum as a mean of all wavenumbers (np.mean(wavenumbers)
), what essentially means that the middle point lies in the center of mass of wavenumbers. This approach seems to be invalid when used with several non-connected spectral regions, because the middle point will depend on the number of points in each region. The edge case is when one region contains 1000 wavenumbers and another region contains only 1 wavenumber. In that case the mid-point will be placed in the first region.
The suggested improvement is to calculate the middle point as the average of min and max wavenumber ((wns.min() + wns.max()) / 2
). In that case mid point will not depend on number of points in regions.
This improvement may change results of correction of spectra with glued multi-regions, for example lipid peaks around 3000 cm-1 and 1700 cm-1. For a single region it should work the same as previously.
For orange-spectroscopy extension of Orange3 it is important to have possibility to add progress callbacks into long running function to be more responsible for users. Although, it is also useful to see a progress for other users of the package.
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