Apodization: Apodization of the FID

Description Usage Arguments Details Value Author(s) References Examples

View source: R/Apodization.R

Description

The function multiplies the FID by a defined factor to increase the sensibility and/or resolution of the spectra.

Usage

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Apodization(Fid_data, Fid_info = NULL, DT = NULL, type.apod = c("exp","cos2", 
            "blockexp","blockcos2","gauss","hanning","hamming"), phase = 0,
            rectRatio = 1/2, gaussLB = 1, expLB = 0.3, plotWindow = FALSE, 
            returnFactor = FALSE, verbose=FALSE)

Arguments

Fid_data

Matrix containing the FIDs, one row per signal, as outputted by ReadFids.

Fid_info

Matrix containing the info about the FIDs, one row per signal, as outputted by ReadFids.

DT

If given, used instead of Fid_info to give the Dwell Time, the time between 2 points of the FID.

type.apod

Type of apodization, see details.

phase

Phase at which the apodization window is maximum for cos2, hanning and hamming types. For example, if phase is 0.2, the maximum is at 20% of the signal.

rectRatio

If there is a rectangular window, ratio between the width of the window and the width of the signal.

gaussLB

Line Broadening for the gaussian window, see details.

expLB

Line Broadening for the exponential window, see details.

plotWindow

If TRUE, a plot of the signal applied to the FID is displayed.

returnFactor

If TRUE, returns a list with the final FIDs and the apodization function.

verbose

If"TRUE", will print processing information.

Details

The apodization is usually performed in order to increase the sensitivity, i.e. the Signal-to-Noise Ratio (SNR) of the spectra. This is based on the fact that the signal intensity is decreasing over time unlike the noise that keeps a constant amplitude, leaving a noisy tail at the end of the FID. Multiplying the FID with a decaying signal will then increase the SNR. Since the area under the spectral peak remains unchanged, a faster decay will also result in a reduced peak height in spectra, lowering the spectral resolution. Optimal trade-off parameters for the apodization signal are thus needed to prevent high losses in sensitivity/resolution.

A FID of the form s0 exp(i*2*pi*nu*t) exp(-t/T) has a peak in its spectrum at the frequency nu of width that is inversely proportional to T. This peak is called a spectral line and its width a spectral width.

In the case of the exponential multiplication ("exp"), which is the default apodization, the decaying exponential becomes:

exp(-t(1/T + LB))

The new decay T* which satisfies 1/T* = 1/T + LB is therefore smaller so the spectral line is broader. That is why we call this parameter the Line Broadening.

If LB increases, the SNR increases but at the expense of the spectral resolution. Usual values in proton NMR for “LB” found in the literature are 0.3 for the NOESY presat pulse sequence and -0.01 for the CMPG presat pulse sequence. It should not exceed the value of 1 to avoid information loss.

The different types of apodization are:

exp

The signal is multiplied by a decreasing exponential exp(-t/expLB).

cos2

The signal is multiplied by the value of a cosinus squared from 0 (where its value is 1) until pi/2 (where its value is 0).

blockexp

The first part of the signal (defined by rectRatio) is left unchanged and the second is multiplied by exp(-t/expLB) starting at value 1.

blockcos2

the first part is left unchanged as with blockexp and the second part is multiplied by a cosinus squared where its value starts at 1 at the end of the block and ends at 0 at the end of the signal.

gauss

The signal is multiplied by a gaussian window centered at the beginning of the FID and with sigma=1/gaussLB.

hanning

The signal is multiplied by a hanning window : 0.5 + 0.5 cos.

hamming

The signal is multiplied by a hamming window : 0.54 + 0.46 cos.

Value

If returnFactor is TRUE, will return a list with the following elements: Fid_data and Factor. Otherwise, the function will just return Fid_data.

Fid_data

The apodized FIDs.

Factor

The apodization signal.

Author(s)

Benoît Legat & Manon Martin

References

Inspired from the matNMR library.

Martin, M., Legat, B., Leenders, J., Vanwinsberghe, J., Rousseau, R., Boulanger, B., & Govaerts, B. (2018). PepsNMR for 1H NMR metabolomic data pre-processing. Analytica chimica acta, 1019, 1-13.

Rousseau, R. (2011). Statistical contribution to the analysis of metabonomics data in 1H NMR spectroscopy (Doctoral dissertation, PhD thesis. Institut de statistique, biostatistique et sciences actuarielles, Université catholique de Louvain, Belgium).

Examples

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require(PepsNMRData)
Apod_res <- Apodization(Data_HS_sp$FidData_HS_2, 
                          FidInfo_HS, plotWindow=FALSE)

#or
Apod_res <- Apodization(Data_HS_sp$FidData_HS_2, 
                          FidInfo_HS, plotWindow=FALSE, returnFactor=TRUE)
Apod_fid = Apod_res[["Fid_data"]]
plot(Apod_res[["Factor"]], type="l")

ManonMartin/PepsNMR documentation built on Nov. 28, 2021, 6:22 p.m.