[Feature]: Automated Matching

[wincowgerDEV]

Guidelines

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Description

Garth C created this routine for automated matching with the standard package. Hopefully there are somethings we can reuse from that.

Problem

No

Proposed Solution

library(dplyr)
library(OpenSpecy)
library(stringr)
library(ggplot2)
library(foreach)

analyze_particles <-
  function(spectra) {
    spec_lib <-
      load_lib(which = "raman")  # load the spectral library

    output <- list()  # initialize lists and vectors for the loops
    wavenumber <- numeric()
    intensity <- numeric()
    identity <- numeric()
    rsq <- numeric()
    match <- data.frame()

    for (i in 1:(nrow(spectra) - 1)) {
      for (j in 1:(ncol(spectra) - 1)) {
        wavenumber[j] = spectra[1, j + 1]
        intensity[j] = spectra[i + 1, j + 1]
      }
      data <- data.frame(wavenumber,
                         intensity)
      output[[i]] <- data
    }

    ## Now loop over all particles and output summary data

    parallel::detectCores()

    n.cores <- parallel::detectCores() - 1  # set core number

    #create the cluster
    my.cluster <- parallel::makeCluster(n.cores,
                                        type = "PSOCK")

    #register it to be used by %dopar%
    doParallel::registerDoParallel(cl = my.cluster)

    match <- foreach(i = 1:length(output)) %dopar% {
      match <- OpenSpecy::match_spec(
        output[[i]],
        library = spec_lib,
        which = "raman",
        type = "full",
        top_n = 1
      )
    }

    parallel::stopCluster(my.cluster)

    identity <- unlist(lapply(match, function(x)
      x[1, 2]))
    rsq <- unlist(lapply(match, function(x)
      x[1, 3]))

    spec_summary <-
      data.frame(particle_number = seq(1, length(identity)),
                 identity, rsq)

    ## Add indicators for whether particles are PE, PS, PET, PC, or something else
    ## PE
    spec_summary$PE <- ifelse(str_detect(spec_summary$identity, 
                                         "LDPE|olyeth"),
                              1,
                              0)
    ## PS
    spec_summary$PS <- ifelse(str_detect(spec_summary$identity, 
                                         "PS|tyrene"),
                              1,
                              0)
    ## PET
    spec_summary$PET <- ifelse(str_detect(spec_summary$identity, 
                                          "PET|terephtalate"),
                               1,
                               0)
    ## Remove PE that is actually PET
    spec_summary$PE[spec_summary$PET == 1] <- 0
    ## PC 
    spec_summary$PC <- ifelse(str_detect(spec_summary$identity, 
                                         "olycarb"),
                              1,
                              0)

    spec_summary$other <- with(spec_summary, ifelse(PE == 1 |
                                                      PS == 1|
                                                      PET == 1|
                                                      PC == 1,
                                                    0,
                                                    1))
    return(spec_summary)
  }

Alternatives Considered

With the new open specy file format we may not be able to reproduce this exactly.

[wincowgerDEV]

Implemented in package now! Thanks Garth for the inspiration!