R/getLightDiff.R

In TIMP: Fitting Separable Nonlinear Models in Spectroscopy and Microscopy

"getLightDiff" <-
  function(theta, x, kinscal, kmat, jvec, fixedkmat = FALSE,
           kinscalspecial = list(), kinscalspecialspec = list(),
           lightregimespec = list()) {
    depkIn <- lightregimespec$depkIn
    br <- lightregimespec$lightBreaks
    br <- append(br, tail(x, 1))
    inten <- lightregimespec$intensity

    ## depkIn is 1 for those rates where there is intensity dependence
    depkin <- as.logical(depkIn)

    dimk <- ncol(kmat)

    # get eigen for the case that the light is off
    theta1 <- theta
    theta1[which(depkin)] <- 0

    K1 <- fillK(theta1, kinscal, kmat, fixedkmat, kinscalspecial,
      kinscalspecialspec,
      nocolsums = TRUE
    )
    eigenlijk1 <- eigen(K1, only.values = FALSE)
    V1 <- eigenlijk1$vectors
    gamma1 <- solve(V1)
    k1 <- -eigenlijk1$values
    cat("eigen dark", k1, "\n")

    # get eigen for the case that the light is on
    theta2 <- theta
    theta2[which(depkin)] <- theta[which(depkin)] * inten
    K2 <- fillK(theta2, kinscal, kmat, fixedkmat, kinscalspecial,
      kinscalspecialspec,
      nocolsums = TRUE
    )
    eigenlijk2 <- eigen(K2, only.values = FALSE)
    V2 <- eigenlijk2$vectors
    gamma2 <- solve(V2)
    k2 <- -eigenlijk2$values
    cat("eigen light", k2, "\n")

    A <- matrix(nrow = dimk, ncol = dimk)

    ## start with light off
    break2 <- 0

    for (i in 1:(length(br))) {
      break1 <- break2 + 1
      break2 <- which(x >= br[i])[1]

      if (is.na(break2)) break2 <- length(x)
      if (break1 > break2) break
      if (break2 < length(x)) break2 <- break2 - 1

      cat("times are from", break1, "to", break2, "\n")

      xtemp <- x[break1:break2]
      if (i %% 2 != 0) {
        k <- k1
        V <- V1
        gamma <- gamma1
      } else {
        k <- k2
        V <- V2
        gamma <- gamma2
      }

      if (i > 1) {
        # take the last concentrations
        finalcon <- c.tempA[nrow(c.tempA), ]
      } else {
        finalcon <- jvec
      }

      finalcon <- finalcon / max(finalcon)
      cat("finalcon", finalcon, "\n")
      gamma <- gamma %*% finalcon
      for (j in 1:dimk) {
        A[j, ] <- V[, j] * gamma[j]
      }

      c.temp <- calcC(k, xtemp)
      c.temp <- c.temp %*% A

      if (i == 1) {
        c.tempA <- c.temp
      } else {
        c.tempA <- rbind(c.tempA, c.temp)
      }
    }
    c.tempA
  }