def_features: Define features

In OpenSpecy: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra

Define features

Description

Functions for analyzing features, like particles, fragments, or fibers, in spectral map oriented OpenSpecy object.

Usage

collapse_spec(x, ...)

## Default S3 method:
collapse_spec(x, ...)

## S3 method for class 'OpenSpecy'
collapse_spec(x, ...)

def_features(x, ...)

## Default S3 method:
def_features(x, ...)

## S3 method for class 'OpenSpecy'
def_features(x, features, ...)

Arguments

x	an OpenSpecy object
features	a logical vector or character vector describing which of the spectra are of features (TRUE) and which are not (FALSE). If a character vector is provided, it should represent the different feature types present in the spectra.
...	additional arguments passed to subfunctions.

Details

def_features() accepts an OpenSpecy object and a logical or character vector describing which pixels correspond to particles. collapse_spec() takes an OpenSpecy object with particle-specific metadata (from def_features()) and collapses the spectra to median intensities for each unique particle. It also updates the metadata with centroid coordinates, while preserving the feature information on area and Feret max.

Value

An OpenSpecy object appended with metadata about the features or collapsed for the features.

Author(s)

Win Cowger, Zacharias Steinmetz

Examples

tiny_map <- read_extdata("CA_tiny_map.zip") |> read_any()
identified_map <- def_features(tiny_map, tiny_map$metadata$x == 0)
collapse_spec(identified_map)

OpenSpecy documentation built on Nov. 26, 2023, 1:09 a.m.