README.md

Overview

Chemometrics and machine learning offer a large set of mathematical tooling to extract and (re)apply chemical and physical knowledge from spectra and minimal analytical lab data in automated fashion. For this, spectra are typically preprocessed as part of the workflow. This is mostly to reduce light scattering and other optical artefacts.

The goal of {specprepper} is not only to wrap different signal processing methods and make them more accessible, but also to offer some of the exisiting algorithms with faster code implementations. It features a recipe-like interface, which also makes it possible to chain different methods in sequence. I will soon add support to save preprocessed spectra as chunked multimensional arrays on disk using the zarr format.

This is open source, so if you want to help me improving it:

Scope of application

This meta package provides both data-dependent and data independent preprocessing methods that are useful for infrared spectral data. For example, multiplicative scatter correction (MSC) needs special teatment in training, evaluation and prediction workflows. This is mainly because of overfitting and the need of data independence to avoid such effects. To mediate overfitting, such methods require application to data within the resampling units.

Goals

To schedule prepreprocessing operations, we aim for simple and efficient data structures. We make use of the "data.table" class to provide a recipe-like interface to configure methods and its parameters to be applied to data.

Many base algorithms are provided by excellent {prospectr}. On top, we use {data.table} plus the {future.apply} map-reduce API to provide memory-efficient computations.

{specprepper} also with sticky attributes that are pinned to matrix or data.tables via {sticky}. This means that processing function respect all preexisting attributes and do not strip them in the returned output.

The roadmap of this package might is subject to change, because it is still maturing.

This R meta library that is also spiced up with rust code in the back is made with a focus on containerized environments for preprocessing.

Currently supported methods

• Savitzky-Golay smoothing: sg_apply()
• Standard Normal Variate: snv_apply()

Planned methods

• Different wavelet transforms
• Binning/bucketing
• Bruker Inc custom vector normalization
• 1-D Gaussian pyramid (armadillo binding) aka weighted moving average filter
• Ordination methods
• Splice correction agross different sensor ranges

Getting started

Installation

if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("spectral-cockpit/specprepper")

Prepare test data

library("data.table")
# load example data
spec_dt <- qs::qread(file = file.path("inst", "extdata", "spec_dt"))
spec <- spec_dt$.predictor_values[[1]]
# x-values as wavenumbers

Glue sticky attributes

library("sticky")
sticky(spec)

Inspect the data quickly.

r$> spec_dt
         .dims        .idx_row        .predictor_values                                         .predictor_labels
1: 10874, 3578 1,2,3,4,5,6,... <data.table[10874x3578]> 7497.969,7496.041,7494.112,7492.184,7490.255,7488.327,...
r$> dim(spec)
[1] 10874  3578

Parameterize Savitzky-Golay filters

We create a custom list and expand it to a preprocessing plan.

make_sg_param_list <- function(sg_windows = c(5L, 9L, 13L, 15L, 17L, 19L, 21L,
                                              23L, 25L, 27L, 35L)) {
  param_list <- list(
    sg_1 = list(m = 1L, p = c(2L, 3L), w = sg_windows),
    sg_2 = list(m = 2L, p = c(3L, 4L), w = sg_windows)
  )
  return(param_list)
}

make_preproc_plan <- function() {
  param_list <- make_sg_param_list()
  preproc_plan <- specprepper::sg_make_plan(param_list = param_list)
  return(preproc_plan)
}

preproc_plan <- make_preproc_plan()

We now inspect the plan.

r$> preproc_plan
    prep_set   prep_label m p  w
 1:     sg_1  sg_m1_p2_w5 1 2  5
 2:     sg_1  sg_m1_p2_w9 1 2  9
 3:     sg_1 sg_m1_p2_w13 1 2 13
 4:     sg_1 sg_m1_p2_w15 1 2 15
 5:     sg_1 sg_m1_p2_w17 1 2 17
 6:     sg_1 sg_m1_p2_w19 1 2 19
 7:     sg_1 sg_m1_p2_w21 1 2 21
 8:     sg_1 sg_m1_p2_w23 1 2 23
 9:     sg_1 sg_m1_p2_w25 1 2 25
10:     sg_1 sg_m1_p2_w27 1 2 27
11:     sg_1 sg_m1_p2_w35 1 2 35
12:     sg_1  sg_m1_p3_w5 1 3  5
13:     sg_1  sg_m1_p3_w9 1 3  9
14:     sg_1 sg_m1_p3_w13 1 3 13
15:     sg_1 sg_m1_p3_w15 1 3 15
16:     sg_1 sg_m1_p3_w17 1 3 17
17:     sg_1 sg_m1_p3_w19 1 3 19
18:     sg_1 sg_m1_p3_w21 1 3 21
19:     sg_1 sg_m1_p3_w23 1 3 23
20:     sg_1 sg_m1_p3_w25 1 3 25
21:     sg_1 sg_m1_p3_w27 1 3 27
22:     sg_1 sg_m1_p3_w35 1 3 35
23:     sg_2  sg_m2_p3_w5 2 3  5
24:     sg_2  sg_m2_p3_w9 2 3  9
25:     sg_2 sg_m2_p3_w13 2 3 13
26:     sg_2 sg_m2_p3_w15 2 3 15
27:     sg_2 sg_m2_p3_w17 2 3 17
28:     sg_2 sg_m2_p3_w19 2 3 19
29:     sg_2 sg_m2_p3_w21 2 3 21
30:     sg_2 sg_m2_p3_w23 2 3 23
31:     sg_2 sg_m2_p3_w25 2 3 25
32:     sg_2 sg_m2_p3_w27 2 3 27
33:     sg_2 sg_m2_p3_w35 2 3 35
34:     sg_2  sg_m2_p4_w5 2 4  5
35:     sg_2  sg_m2_p4_w9 2 4  9
36:     sg_2 sg_m2_p4_w13 2 4 13
37:     sg_2 sg_m2_p4_w15 2 4 15
38:     sg_2 sg_m2_p4_w17 2 4 17
39:     sg_2 sg_m2_p4_w19 2 4 19
40:     sg_2 sg_m2_p4_w21 2 4 21
41:     sg_2 sg_m2_p4_w23 2 4 23
42:     sg_2 sg_m2_p4_w25 2 4 25
43:     sg_2 sg_m2_p4_w27 2 4 27
44:     sg_2 sg_m2_p4_w35 2 4 35
    prep_set   prep_label m p  w

Prepare futures

library("future")
plan(multisession)

Launch the preprocessing prepper

spec_proc <- sg_apply(
  X = spec,
  dt_sg_plan = preproc_plan
)

Inspect the results

r$> spec_proc
    prep_set   prep_label       prep_params                 spc_prep
 1:     sg_1  sg_m1_p2_w5 <data.table[1x3]> <data.table[10874x3574]>
 2:     sg_1  sg_m1_p2_w9 <data.table[1x3]> <data.table[10874x3570]>
 3:     sg_1 sg_m1_p2_w13 <data.table[1x3]> <data.table[10874x3566]>
 4:     sg_1 sg_m1_p2_w15 <data.table[1x3]> <data.table[10874x3564]>
 5:     sg_1 sg_m1_p2_w17 <data.table[1x3]> <data.table[10874x3562]>
 6:     sg_1 sg_m1_p2_w19 <data.table[1x3]> <data.table[10874x3560]>
 7:     sg_1 sg_m1_p2_w21 <data.table[1x3]> <data.table[10874x3558]>
 8:     sg_1 sg_m1_p2_w23 <data.table[1x3]> <data.table[10874x3556]>
 9:     sg_1 sg_m1_p2_w25 <data.table[1x3]> <data.table[10874x3554]>
10:     sg_1 sg_m1_p2_w27 <data.table[1x3]> <data.table[10874x3552]>
11:     sg_1 sg_m1_p2_w35 <data.table[1x3]> <data.table[10874x3544]>
12:     sg_1  sg_m1_p3_w5 <data.table[1x3]> <data.table[10874x3574]>
13:     sg_1  sg_m1_p3_w9 <data.table[1x3]> <data.table[10874x3570]>
14:     sg_1 sg_m1_p3_w13 <data.table[1x3]> <data.table[10874x3566]>
15:     sg_1 sg_m1_p3_w15 <data.table[1x3]> <data.table[10874x3564]>
16:     sg_1 sg_m1_p3_w17 <data.table[1x3]> <data.table[10874x3562]>
17:     sg_1 sg_m1_p3_w19 <data.table[1x3]> <data.table[10874x3560]>
18:     sg_1 sg_m1_p3_w21 <data.table[1x3]> <data.table[10874x3558]>
19:     sg_1 sg_m1_p3_w23 <data.table[1x3]> <data.table[10874x3556]>
20:     sg_1 sg_m1_p3_w25 <data.table[1x3]> <data.table[10874x3554]>
21:     sg_1 sg_m1_p3_w27 <data.table[1x3]> <data.table[10874x3552]>
22:     sg_1 sg_m1_p3_w35 <data.table[1x3]> <data.table[10874x3544]>
23:     sg_2  sg_m2_p3_w5 <data.table[1x3]> <data.table[10874x3574]>
24:     sg_2  sg_m2_p3_w9 <data.table[1x3]> <data.table[10874x3570]>
25:     sg_2 sg_m2_p3_w13 <data.table[1x3]> <data.table[10874x3566]>
26:     sg_2 sg_m2_p3_w15 <data.table[1x3]> <data.table[10874x3564]>
27:     sg_2 sg_m2_p3_w17 <data.table[1x3]> <data.table[10874x3562]>
28:     sg_2 sg_m2_p3_w19 <data.table[1x3]> <data.table[10874x3560]>
29:     sg_2 sg_m2_p3_w21 <data.table[1x3]> <data.table[10874x3558]>
30:     sg_2 sg_m2_p3_w23 <data.table[1x3]> <data.table[10874x3556]>
31:     sg_2 sg_m2_p3_w25 <data.table[1x3]> <data.table[10874x3554]>
32:     sg_2 sg_m2_p3_w27 <data.table[1x3]> <data.table[10874x3552]>
33:     sg_2 sg_m2_p3_w35 <data.table[1x3]> <data.table[10874x3544]>
34:     sg_2  sg_m2_p4_w5 <data.table[1x3]> <data.table[10874x3574]>
35:     sg_2  sg_m2_p4_w9 <data.table[1x3]> <data.table[10874x3570]>
36:     sg_2 sg_m2_p4_w13 <data.table[1x3]> <data.table[10874x3566]>
37:     sg_2 sg_m2_p4_w15 <data.table[1x3]> <data.table[10874x3564]>
38:     sg_2 sg_m2_p4_w17 <data.table[1x3]> <data.table[10874x3562]>
39:     sg_2 sg_m2_p4_w19 <data.table[1x3]> <data.table[10874x3560]>
40:     sg_2 sg_m2_p4_w21 <data.table[1x3]> <data.table[10874x3558]>
41:     sg_2 sg_m2_p4_w23 <data.table[1x3]> <data.table[10874x3556]>
42:     sg_2 sg_m2_p4_w25 <data.table[1x3]> <data.table[10874x3554]>
43:     sg_2 sg_m2_p4_w27 <data.table[1x3]> <data.table[10874x3552]>
44:     sg_2 sg_m2_p4_w35 <data.table[1x3]> <data.table[10874x3544]>
    prep_set   prep_label       prep_params                 spc_prep

r$> format(object.size(spec_proc), units = "GB")
[1] "12.7 Gb"

Credits

The main idea for this package came while working at the Swiss Competence Center for Soils (KOBO). I have as well used internally some early prototype of this package in my own research.