---
title: "Pre-processing spectral data"
author:
  - name: Antoine Stevens and Leonardo Ramirez-Lopez
    email: ramirez.lopez.leo@gmail.com
date: today
bibliography: prospectr.bib
csl: elsevier-harvard.csl
format:
  html:
    toc: true
    toc-depth: 3
    number-sections: true
    toc-location: left
    code-overflow: wrap
    smooth-scroll: true
    html-math-method: mathjax
vignette: >
  %\VignetteIndexEntry{Pre-processing spectral data}
  %\VignetteEncoding{UTF-8}
  %\VignetteEngine{quarto::html}
---

:::: {.columns}
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> *Organism is opposed to chaos... as message is to noise.* -- [@wiener1954human]
:::
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<img src="logo.jpg" style="width: 150%; max-width: 150px;">
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# Introduction

The aim of spectral pre-treatment is to improve signal quality before modelling
as well as remove physical information from the spectra. Applying a
pre-treatment can increase the repeatability/reproducibility of the method,
model robustness and accuracy, although there are no guarantees this will
actually work. The pre-processing functions currently available in the package
are listed in @tbl-preprocessing.

```{r}
#| label: tbl-preprocessing
#| tbl-cap: "Pre-processing functions available in the package."
#| echo: false

library(prospectr)

preprocessing_fns <- data.frame(
  `Function` = c(
    "`movav`", "`savitzkyGolay`", "`gapDer`", "`baseline`",
    "`continuumRemoval`", "`detrend`", "`standardNormalVariate`",
    "`msc`", "`binning`", "`resample`", "`resample2`",
    "`blockScale`", "`blockNorm`"
  ),
  `Description` = c(
    "Simple moving (or running) average filter",
    "Savitzky--Golay smoothing and derivative",
    "Gap--segment derivative",
    "Baseline removal (similar to `continuumRemoval`)",
    "Computes continuum--removed values",
    "Detrend normalisation",
    "Standard Normal Variate (SNV) transformation",
    "Multiplicative Scatter Correction",
    "Average a signal in column bins",
    "Resample a signal to new band positions",
    "Resample a signal using new FWHM values",
    "Block scaling",
    "Sum of squares block weighting"
  ),
  check.names = FALSE
)

knitr::kable(preprocessing_fns)
```

We show below how they can be used, using the Near-Infrared (NIR) dataset
(`NIRsoil`) included in the package [@fernandez2008]. Observations should be
arranged row-wise.

```{r}
#| label: load-NIRsoil
#| message: false

library(prospectr)
data(NIRsoil)
# NIRsoil is a data.frame with 825 observations and 5 variables:
# Nt (Total Nitrogen), Ciso (Carbon), CEC (Cation Exchange Capacity),
# train (0/1 indicator for training (1) and validation (0) samples),
# spc (spectral matrix)
str(NIRsoil)
```

# Noise removal

Noise represents random fluctuations around the signal that can originate from
the instrument or environmental laboratory conditions. The simplest solution is
to perform $n$ repeated measurements and average the individual spectra; noise
decreases by a factor of $\sqrt{n}$. When this is not possible, or if residual
noise remains, it can be removed mathematically.

## Moving average

A moving average filter is a column-wise operation that averages contiguous
wavelengths within a given window size, as illustrated in @fig-movav.

```{r}
#| label: fig-movav
#| fig-cap: "Effect of a moving average with window size of 11 bands on a raw spectrum."
#| fig-height: 4
#| fig-width: 6
#| echo: true

# Add some noise
noisy <- NIRsoil$spc + rnorm(length(NIRsoil$spc), 0, 0.001)

# Plot the first spectrum
plot(
  x = as.numeric(colnames(NIRsoil$spc)),
  y = noisy[1, ],
  type = "l",
  lwd = 1.5,
  xlab = "Wavelength",
  ylab = "Absorbance"
)

# Window size of 11 bands; note the 5 first and last bands are lost
X <- movav(X = noisy, w = 11)
lines(x = as.numeric(colnames(X)), y = X[1, ], lwd = 1.5, col = "red")
grid()
legend(
  "topleft",
  legend = c("Raw", "Moving average"),
  lty = 1,
  col = c("black", "red")
)
```

## Savitzky-Golay filtering

Savitzky-Golay filtering [@savitzky1964] is a widely used pre-processing
technique. It fits a local polynomial regression on the signal and requires
**equidistant** bandwidth. Mathematically, it operates as a weighted sum of
neighbouring values:

$$x_j^* = \frac{1}{N}\sum_{h=-k}^{k} c_h x_{j+h}$$

where $x_j^*$ is the smoothed value, $N$ is a normalising coefficient, $k$ is
the number of neighbouring values on each side of $j$, and $c_h$ are
pre-computed coefficients that depend on the chosen polynomial order, window
size, and derivative degree (0 = smoothing, 1 = first derivative, 2 = second derivative).

```{r}
#| label: savitzky-golay
#| echo: true

# p = polynomial order
# w = window size (must be odd)
# m = m-th derivative (0 = smoothing)
# Accepts vectors, data frames, or matrices (observations row-wise)
sgvec <- savitzkyGolay(X = NIRsoil$spc[1, ], p = 3, w = 11, m = 0)
sg <- savitzkyGolay(X = NIRsoil$spc, p = 3, w = 11, m = 0)

# Bands at the edges of the spectral matrix are lost
dim(NIRsoil$spc)
dim(sg)
```


# Derivatives

Taking numerical derivatives of the spectra can remove both additive and
multiplicative effects and has further consequences summarised in @tbl-derivatives.

```{r}
#| label: tbl-derivatives
#| tbl-cap: "Advantages and drawbacks of derivative spectra."
#| echo: false

der_table <- data.frame(
  Advantage = c(
    "Reduces baseline offset",
    "Can resolve overlapping absorptions",
    "Compensates for instrumental drift",
    "Enhances small spectral absorptions",
    "Often increases predictive accuracy for complex datasets"
  ),
  Drawback = c(
    "Risk of overfitting the calibration model",
    "Increases noise; smoothing required",
    "Increases uncertainty in model coefficients",
    "Complicates spectral interpretation",
    "Removes the baseline"
  )
)

knitr::kable(der_table)
```

First and second derivatives can be computed with the finite difference method
(difference between two subsequent data points), provided that bandwidth is
constant:

$$x_i' = x_i - x_{i-1}$$

$$x_i'' = x_{i-1} - 2 \cdot x_i + x_{i+1}$$

In R this can be achieved with the `diff` function from `base`, as shown in
@fig-derivatives:

```{r}
#| label: fig-derivatives
#| fig-cap: "First and second derivatives of a raw spectrum."
#| fig-height: 4
#| fig-width: 6
#| echo: true

d1 <- t(diff(t(NIRsoil$spc), differences = 1))  # first derivative
d2 <- t(diff(t(NIRsoil$spc), differences = 2))  # second derivative

plot(
  as.numeric(colnames(d1)), d1[1, ],
  type = "l", lwd = 1.5,
  xlab = "Wavelength", ylab = ""
)
lines(as.numeric(colnames(d2)), d2[1, ], lwd = 1.5, col = "red")
grid()
legend(
  "topleft",
  legend = c("1st derivative", "2nd derivative"),
  lty = 1, col = c("black", "red")
)
```

Derivatives tend to amplify noise. The gap derivative and the Savitzky-Golay
algorithm both address this. The gap derivative is computed as:

$$x_i' = x_{i+k} - x_{i-k}$$

$$x_i'' = x_{i-k} - 2 \cdot x_i + x_{i+k}$$

where $k$ is the gap size. This can be achieved using the `lag` argument of
`diff` (see @fig-gap-derivative):

```{r}
#| label: fig-gap-derivative
#| fig-cap: "Comparison of first derivative (finite difference) and
#|   gap derivative (lag = 10 bands) for the first spectrum."
#| fig-height: 4
#| fig-width: 6
#| echo: true

# m = derivative order; w = gap size; s = segment size
gsd1 <- gapDer(X = NIRsoil$spc, m = 1, w = 11, s = 5)

plot(
  as.numeric(colnames(d1)), d1[1, ],
  type = "l", lwd = 1.5,
  xlab = "Wavelength (nm)", ylab = "1st derivative"
)
par(new = TRUE)
plot(
  as.numeric(colnames(gsd1)), gsd1[1, ],
  type = "l", lwd = 1.5, col = "red",
  xaxt = "n", yaxt = "n",
  xlab = "", ylab = ""
)
axis(4, col = "red")
mtext("Gap-segment derivative", side = 4, line = 3, col = "red")
grid()
legend(
  "topleft",
  legend = c("1st derivative", "Gap-segment 1st derivative"),
  lty = 1, col = c("black", "red")
)
par(new = FALSE)
```

For greater control over smoothing, the Savitzky-Golay (`savitzkyGolay`) and
gap-segment derivative (`gapDer`) functions are preferable. The gap-segment
algorithm first smooths the signal over a given segment size, then computes a
derivative of a given order over a given gap size. See @luo2005properties and
@hopkins2001norris for details on these methods.


# Scatter and baseline corrections

Undesired spectral variations due to light *scatter* effects and variations in
effective *path length* can be removed using scatter corrections.

## Standard Normal Variate (SNV)

The *Standard Normal Variate* (SNV) transformation [@barnes1989] is a
row-wise standardisation that corrects for light *scatter* by centering and
scaling each spectrum individually (@fig-snv):

$$\text{SNV}_i = \frac{x_i - \bar{x}_i}{s_i}$$

where $\bar{x}_i$ is the mean and $s_i$ the standard deviation of the $i$-th
spectrum (i.e. computed across all bands of that observation).

```{r}
#| label: fig-snv
#| fig-cap: "Raw absorbance spectra (left) and SNV-transformed spectra (right)
#|   for the first five observations."
#| fig-height: 4
#| fig-width: 8
#| echo: true

snv <- standardNormalVariate(X = NIRsoil$spc)
wav <- as.numeric(colnames(NIRsoil$spc))

par(mfrow = c(1, 2))

matplot(
  wav, t(NIRsoil$spc[1:5, ]),
  type = "l", lty = 1, lwd = 1.5,
  col = c("black", "grey20", "grey40", "grey60", "grey80"),
  xlab = "Wavelength (nm)", ylab = "Absorbance",
  main = "Raw"
)
grid()

matplot(
  wav, t(snv[1:5, ]),
  type = "l", lty = 1, lwd = 1.5,
  col = c("red", "tomato", "coral", "salmon", "lightsalmon"),
  xlab = "Wavelength (nm)", ylab = "SNV (Absorbance)",
  main = "SNV"
)
grid()

par(mfrow = c(1, 1))
```

According to @fearn2008, SNV should be applied *after* filtering (e.g.
Savitzky-Golay) rather than before.




## Multiplicative Scatter Correction (MSC)

Along with SNV, MSC [@geladi1985linearization] is one of the most widely used
pre-processing techniques in NIR spectroscopy [@rinnan2009review]. It is a
scatter correction method that accounts for additive and multiplicative effects
by regressing each spectrum ($x_i$) against a reference spectrum ($x_r$,
typically the mean spectrum, @fig-msc):

$$x_i = m_i x_r + a_i$$

$$\text{MSC}(x_i) = \frac{x_i - a_i}{m_i}$$

where $a_i$ and $m_i$ are the additive and multiplicative scatter coefficients,
respectively, estimated by ordinary least squares for each spectrum.

```{r}
#| label: fig-msc
#| fig-cap: "Effect of MSC on a raw spectrum (reference = mean spectrum)."
#| fig-height: 4
#| fig-width: 6
#| echo: true

# Reference spectrum is the column mean of the full matrix
msc_spc <- msc(X = NIRsoil$spc, ref_spectrum = colMeans(NIRsoil$spc))

plot(
  as.numeric(colnames(NIRsoil$spc)), NIRsoil$spc[1, ],
  type = "l", lwd = 1.5,
  xlab = "Wavelength (nm)", ylab = "Absorbance"
)
lines(as.numeric(colnames(msc_spc)), msc_spc[1, ], lwd = 1.5, col = "red")
grid()
legend(
  "topleft",
  legend = c("Raw", "MSC"),
  lty = 1, col = c("black", "red")
)
```

Because MSC correction depends on a reference spectrum, that reference must be
stored and reused when processing new spectra. The following example shows how
to apply the correction estimated on a training set to a separate validation
set:

```{r}
#| label: msc-transfer
#| eval: false
#| echo: true

# Training and validation partitions
Xr <- NIRsoil$spc[NIRsoil$train == 1, ]
Xu <- NIRsoil$spc[NIRsoil$train == 0, ]

# Fit MSC on the training set (reference = mean of Xr by default)
Xr_msc <- msc(Xr)

# Apply the same reference spectrum to the validation set
Xu_msc <- msc(Xu, ref_spectrum = attr(Xr_msc, "Reference spectrum"))
```

## SNV-Detrend

The *SNV-Detrend* transformation [@barnes1989] extends SNV by additionally
correcting for wavelength-dependent scattering effects, i.e. residual
curvature remaining after SNV. After the SNV transformation, a second-order
polynomial is fitted to each spectrum and subtracted from it (@fig-detrend).

```{r}
#| label: fig-detrend
#| fig-cap: "Effect of SNV-Detrend on a raw spectrum. Note the different
#|   y-axis scales: raw absorbance (left) and detrended signal (right)."
#| fig-height: 4
#| fig-width: 6
#| echo: true

wav <- as.numeric(colnames(NIRsoil$spc))
dt  <- detrend(X = NIRsoil$spc, wav = wav)

# Dual y-axis: raw and detrended spectra are on different scales
plot(
  wav, NIRsoil$spc[1, ],
  type = "l", lwd = 1.5,
  xlab = "Wavelength (nm)", ylab = "Absorbance"
)
par(new = TRUE)
plot(
  wav, dt[1, ],
  type = "l", lwd = 1.5, col = "red",
  xaxt = "n", yaxt = "n",
  xlab = "", ylab = ""
)
axis(4, col = "red")
mtext("Detrended", side = 4, line = 3, col = "red")
grid()
legend(
  "topleft",
  legend = c("Raw", "SNV-Detrend"),
  lty = 1, col = c("black", "red")
)
par(new = FALSE)
```


## Baseline removal

The `baseline` function estimates and removes the baseline of each spectrum in
three steps, with the result illustrated in @fig-baseline:

1. The convex hull points of each spectrum are identified using
   `grDevices::chull`.
2. The convex hull points are linearly interpolated to the wavelength positions
   of the original spectrum to produce the baseline.
3. The baseline is subtracted from the original spectrum.

```{r}
#| label: fig-baseline
#| fig-cap: "Raw absorbance spectra (left) and baseline-corrected spectra (right)
#| for the first three observations."
#| fig-height: 4
#| fig-width: 8
#| echo: true

wav <- as.numeric(colnames(NIRsoil$spc))
bs <- baseline(NIRsoil$spc, wav)
fitted_baselines <- attr(bs, "baselines")

par(mfrow = c(1, 2))

# Raw spectra with fitted baselines
matplot(
  wav, t(NIRsoil$spc[1:3, ]),
  type = "l", lty = 1, lwd = 1.5,
  col = c("black", "grey40", "grey70"),
  xlab = "Wavelength (nm)", ylab = "Absorbance",
  main = "Raw and baseline"
)
matlines(wav, t(fitted_baselines[1:3, ]), lty = 2, col = c("black", "grey40", "grey70"))
grid()

# Baseline-corrected spectra
matplot(
  wav, t(bs[1:3, ]),
  type = "l", lty = 1, lwd = 1.5,
  col = c("red", "tomato", "salmon"),
  xlab = "Wavelength (nm)", ylab = "Absorbance",
  main = "Baseline corrected"
)
grid()

par(mfrow = c(1, 1))
```

# Centering and scaling

Centering and scaling transform a given matrix so that columns have zero mean
(*centering*), unit variance (*scaling*), or both (*auto-scaling*):

$$Xc_{ij} = X_{ij} - \bar{X}_{j}$$

$$Xs_{ij} = \frac{X_{ij} - \bar{X}_{j}}{s_{j}}$$

where $Xc$ and $Xs$ are the mean-centred and auto-scaled matrices, $\bar{X}_j$
and $s_j$ are the mean and standard deviation of variable $j$. In R these
operations are obtained with the `scale` function.

Spectroscopic models can often be improved by incorporating ancillary data
(e.g. temperature) alongside the spectra [@fearn2010]. However, due to the
high dimensionality of spectral data, ancillary variables risk being dominated
by the spectral block and contributing negligibly to the model
[@eriksson2006]. *Block scaling* addresses this by applying different scaling
weights to different blocks of variables. With *soft block scaling*, each block
is divided by a constant such that the sum of its column variances equals
$\sqrt{p}$, where $p$ is the number of variables in the block. With *hard block
scaling*, the block is scaled so that the sum of its column variances equals 1.

```{r}
#| label: block-scale
#| echo: true

# type = "soft" or "hard"
# Returns a list with the scaled matrix (Xscaled) and the divisor (f)
bsc <- blockScale(X = NIRsoil$spc, type = "hard")$Xscaled
sum(apply(bsc, 2, var))  # should equal 1
```

A limitation of block scaling is that all variables within a block are brought
to the same variance. When this is undesirable, *sum-of-squares block
weighting* (`blockNorm`) provides an alternative: the spectral matrix is
multiplied by a scalar to achieve a pre-specified sum of squares.

```{r}
#| label: block-norm
#| echo: true

# targetnorm = desired Frobenius norm (sum of squares) for X
bn <- blockNorm(X = NIRsoil$spc, targetnorm = 1)$Xscaled
sum(bn^2)  # should equal 1
```

# Resampling

To match the spectral response of one instrument to another, a signal can be
resampled to new band positions by interpolation (`resample`) or by convolution
using full-width at half-maximum (FWHM) values (`resample2`). @fig-resample
shows an example of resampling a NIR spectrum to a coarser resolution of 10 nm
using `resample`.

```{r}
#| label: fig-resample
#| fig-cap: "Original NIR spectrum and resampled spectrum at a coarser
#|   resolution (every 10 nm) using interpolation."
#| fig-height: 4
#| fig-width: 6
#| echo: true

wav <- as.numeric(colnames(NIRsoil$spc))
wav_coarse <- seq(min(wav), max(wav), by = 10)

rs <- resample(X = NIRsoil$spc, wav = wav, new.wav = wav_coarse)

plot(
  wav, NIRsoil$spc[1, ],
  type = "l", lwd = 1.5,
  xlab = "Wavelength (nm)", ylab = "Absorbance"
)
lines(
  wav_coarse, rs[1, ], lwd = 1.5, col = "red", type = "b", pch = 19, cex = 0.5
)
grid()
legend(
  "topleft",
  legend = c("Original", "Resampled (10 nm)"),
  lty = 1, col = c("black", "red")
)
```

# Other transformations

## Continuum removal

The continuum removal technique was introduced by @clark1984 to highlight
absorption features by removing the effect of the overall spectral shape
(albedo). The method identifies the convex-hull envelope (continuum) of each
spectrum and normalises the original values against it (@fig-continuum-removal):

$$\phi_{i} = \frac{x_{i}}{c_{i}}, \quad i = \{1, \ldots, p\}$$

where $x_i$ and $c_i$ are the original and continuum values at the $i$-th
wavelength of a set of $p$ wavelengths. The result $\phi_i$ is dimensionless
and bounded in $[0, 1]$ for reflectance spectra, where values close to 1
indicate no absorption relative to the continuum.

The `continuumRemoval` function handles both reflectance (`type = "R"`,
default) and absorbance (`type = "A"`) spectra. For absorbance data, spectra
are first converted to reflectance ($1/X$) before computing the continuum,
and the result is back-transformed afterwards. This means that for absorbance
data, `continuumRemoval` and `baseline` are not equivalent: they compute the
convex-hull envelope on different scales. For reflectance data the two
functions are more directly comparable, differing only in the final step:
`baseline` subtracts the continuum ($x_i - c_i$), whereas `continuumRemoval`
divides by it ($x_i / c_i$).

```{r}
#| label: fig-continuum-removal
#| fig-cap: "Raw absorbance spectra (left) and continuum-removed spectra (right)
#|   for the first three observations."
#| fig-height: 4
#| fig-width: 8
#| echo: true

# type = "A" for absorbance, "R" for reflectance (default)
cr  <- continuumRemoval(X = NIRsoil$spc, type = "A")
wav <- as.numeric(colnames(NIRsoil$spc))

par(mfrow = c(1, 2))

matplot(
  wav, t(NIRsoil$spc[1:3, ]),
  type = "l", lty = 1, lwd = 1.5,
  col = c("black", "grey40", "grey70"),
  xlab = "Wavelength (nm)", ylab = "Absorbance",
  main = "Raw"
)
grid()

matplot(
  wav, t(cr[1:3, ]),
  type = "l", lty = 1, lwd = 1.5,
  col = c("red", "tomato", "salmon"),
  xlab = "Wavelength (nm)", ylab = "Continuum-removed",
  main = "Continuum removal"
)
grid()

par(mfrow = c(1, 1))
```

# References {-}
