Morphological Baseline Correction (Erosion/Dilation)

step_measure_baseline_morphological() creates a specification of a recipe step that applies morphological erosion followed by dilation for baseline estimation.

Usage

step_measure_baseline_morphological(
  recipe,
  measures = NULL,
  window_size = 50L,
  iterations = 1L,
  role = NA,
  trained = FALSE,
  skip = FALSE,
  id = recipes::rand_id("measure_baseline_morphological")
)

Arguments

recipe

A recipe object.

measures

An optional character vector of measure column names.

window_size

Size of the structuring element. Default is 50.

iterations

Number of erosion iterations. Default is 1.

role

Not used.

trained

Logical indicating if the step has been trained.

skip

Logical. Should the step be skipped when baking?

id

Unique step identifier.

Value

An updated recipe with the new step added.

Details

This morphological approach uses erosion (local minimum) to push the baseline down below peaks, followed by dilation (local maximum) to smooth the result.

Multiple erosion iterations can be used for signals with tall peaks that require more aggressive baseline estimation.

See also

Other measure-baseline: step_measure_baseline_airpls(), step_measure_baseline_als(), step_measure_baseline_arpls(), step_measure_baseline_aspls(), step_measure_baseline_auto(), step_measure_baseline_custom(), step_measure_baseline_fastchrom(), step_measure_baseline_gpc(), step_measure_baseline_iarpls(), step_measure_baseline_minima(), step_measure_baseline_morph(), step_measure_baseline_poly(), step_measure_baseline_py(), step_measure_baseline_rf(), step_measure_baseline_rolling(), step_measure_baseline_snip(), step_measure_baseline_tophat(), step_measure_detrend()

Examples

library(recipes)

# \donttest{
rec <- recipe(water + fat + protein ~ ., data = meats_long) |>
  update_role(id, new_role = "id") |>
  step_measure_input_long(transmittance, location = vars(channel)) |>
  step_measure_baseline_morphological(window_size = 50) |>
  prep()

bake(rec, new_data = NULL)
#> # A tibble: 215 × 6
#>       id water   fat protein .measures channel    
#>    <int> <dbl> <dbl>   <dbl>    <meas> <list>     
#>  1     1  60.5  22.5    16.7 [100 × 2] <int [100]>
#>  2     2  46    40.1    13.5 [100 × 2] <int [100]>
#>  3     3  71     8.4    20.5 [100 × 2] <int [100]>
#>  4     4  72.8   5.9    20.7 [100 × 2] <int [100]>
#>  5     5  58.3  25.5    15.5 [100 × 2] <int [100]>
#>  6     6  44    42.7    13.7 [100 × 2] <int [100]>
#>  7     7  44    42.7    13.7 [100 × 2] <int [100]>
#>  8     8  69.3  10.6    19.3 [100 × 2] <int [100]>
#>  9     9  61.4  19.9    17.7 [100 × 2] <int [100]>
#> 10    10  61.4  19.9    17.7 [100 × 2] <int [100]>
#> # ℹ 205 more rows
# }