R/wf_net.r

In mlpeck/zernike: Zernike Polynomials and Fringe Analysis tools

## calculate net and zernike fit wavefronts from any of psifit, fftfit, vortexfit

wf_net <- function(phi, mod, cp, options) {

  if (is.null(cp)) {
    cp <- circle.pars(mod, plot=options$plots)
  }
  cp.orig <- cp
  if (options$crop) {
    mod <- crop(mod, cp)$im
    phi <- crop(phi, cp)
    cp <- phi$cp
    phi <- phi$im
  }
  nr <- nrow(phi)
  nc <- ncol(phi)
  prt <- pupil.rhotheta(nr, nc, cp)
  phi[is.na(prt$rho)] <- NA
  class(phi) <- "pupil"
  wf.raw <- switch(options$puw_alg,
                   qual = qpuw(phi, mod),
                   brcut = zernike::brcutpuw(phi),
                   lpbrcut = lppuw::brcutpuw(phi),
                   lp = lppuw::netflowpuw(phi, mod),
                   qpuw(phi, mod)
  )
  wf.raw <- options$fringescale*wf.raw
  class(wf.raw) <- "pupil"
  rho <- prt$rho
  theta <- prt$theta
  wfok <- !is.na(rho) & !is.na(wf.raw)
  wf.v <- wf.raw[wfok]
  rho.v <- rho[wfok]
  th.v <- theta[wfok]
  fit <- fitzernikes(wf.v, rho.v, th.v,
                     eps=cp$obstruct,
                     maxorder=options$maxorder, 
                     nthreads=options$nthreads, 
                     isoseq=options$isoseq,
                     usecirc=options$usecirc,
                     ext_prec=options$ext_prec)
  if (options$isoseq) {
    ind.ptf <- c(1:3, 5)
    ind.sa4 <- 13
    ind.sa6 <- 25
    ind.astig <- c(6, 4)
    ind.coma <- 8:9
    zc.low <- numeric(28)
  } else {
    ind.ptf <- 1:4
    ind.sa4 <- 9
    ind.sa6 <- 16
    ind.astig <- 5:6
    ind.coma <- 7:8
    zc.low <- numeric(16)
  }
  if (sign(fit[ind.sa4])*sign(options$satarget[1]) < 0) {
    fit <- -fit
    wf.raw <- -wf.raw
  }
  
  zc.low[ind.ptf] <- fit[ind.ptf]
  zc.low[c(ind.sa4, ind.sa6)] <- zc.low[c(ind.sa4, ind.sa6)] + options$satarget
  zc.low[ind.astig] <- zc.low[ind.astig] + options$astig.bath
  if (is.element(6, options$zc0)) {
    zc.low[ind.coma] <- fit[ind.coma]
  }
  wf.net <- wf.raw - pupil(zcoef=zc.low, maxorder=6, 
                           isoseq=options$isoseq, usecirc=options$usecirc,
                           nrow=nr, ncol=nc, cp=cp)
  if (options$plots) {
    if (tolower(.Platform$OS.type) == "windows") {
      windows(width=18, height=6)
    } else {
        x11(width=18, height=6)
    }
    split.screen(figs=c(1,3))
    screen(1)
    plot(wf.net, cp=cp, col=options$colors, addContours=FALSE)
    mtext(paste("RMS = ", format(pupilrms(wf.net),digits=3)))
  }
  zcoef.net <- fit
  zcoef.net[1:length(zc.low)] <- zcoef.net[1:length(zc.low)] - zc.low
  wf.smooth <- pupil(zcoef=zcoef.net, maxorder=options$maxorder, 
                     isoseq=options$isoseq, usecirc=options$usecirc,
                     cp=cp, nrow=nr, ncol=nc)
  if (options$plots) {
    screen(2)
    plot(wf.smooth, cp=cp, col=options$colors)
    mtext(paste("RMS = ", format(pupilrms(wf.smooth),digits=3)))
  }
  wf.residual <- wf.net - wf.smooth
  if (options$plots) {
    screen(3)
    plot(wf.residual, cp=cp, col=grey256, addContours=FALSE)
    mtext(paste("RMS = ", format(pupilrms(wf.residual),digits=3)))
    close.screen(all.screens=TRUE)
  }
  outs <- list(phi=phi, mod=mod, cp=cp, cp.orig=cp.orig, 
               wf.net=wf.net, wf.smooth=wf.smooth, wf.residual=wf.residual, 
               fit=fit, zcoef.net=zcoef.net[-1])
  class(outs) <- c(class(outs), "wf_zfit")
  outs
}

#' Methods for class "wf_zfit"
#' 
#' Summary, print, plot, report, and invert methods for the returned list of values
#'  from [psifit()], [fftfit()], or [vortexfit()]
#'
#' @param wffit the return values from one of the fringe analysis routines or [wf_net()]
#' @param digits number of digits to display in print and summary methods
#' @param printnow send output to console?
#' @param ... values passed to [plot.pupil()]
#'
#' @details The report method combines the plot, summary, and print methods into an html document and displays it in a browser.
#' The invert method negates the values of wavefronts and Zernike coefficients and returns the adjusted input
#'
#' @return summary and print methods return data frame with wavefront summaries and Zernike coefficients
summary.wf_zfit <- function(wffit, digits=3, printnow=TRUE) {
  df.sum <- data.frame(Name    = c("Current time      : ",
                                   "Run time          : ",
                                   "Algorithm         : ",
                                   "Image size(s)     : ",
                                   "Unsmoothed RMS    : ",
                                   "Zernike fit RMS   : ",
                                   "Zernike fit Strehl: ",
                                   "Zernike fit P-V   : ",
                                   "PVr               : "),
                       Value  = c(date(),
                                  if (!is.null(wffit$rundate)) wffit$rundate else "",
                                  if (!is.null(wffit$algorithm)) wffit$algorithm else "unknown",
                                  paste(nrow(wffit$wf.smooth), "x", ncol(wffit$wf.smooth)),
                                  format(pupilrms(wffit$wf.net),digits=digits),
                                  format(hypot(wffit$zcoef.net),digits=digits),
                                  format(strehlratio(hypot(wffit$zcoef.net)),digits=digits),
                                  format(pupilpv(wffit$wf.smooth),digits=digits),
                                  format(PVr(wffit$wf.smooth, wffit$wf.residual),digits=digits))
  )
  if (printnow) {
    print(df.sum, digits=digits, right=FALSE, justify="left", row.names=FALSE)
  }
  invisible(df.sum)
}

print.wf_zfit <- function(wffit, digits=3, abnames=TRUE, printnow=TRUE) {
  fit <- wffit$fit
  nz <- length(fit)
  sqnz <- sqrt(nz)
  if (sqnz %% 1 > sqrt(.Machine$double.eps)) {
    ## Zernikes are (probably) in ISO sequence
    maxorder <- (-3 + sqrt(1+8*nz))/2
    zlist <- makezlist.iso(maxorder=maxorder)
  } else {
    maxorder <- 2*(sqnz-1)
    zlist <- makezlist(maxorder=maxorder)
  }
  znames <- paste("Z", 0:(nz-1), sep="")
  mmult <- 1 - 2*as.numeric(zlist$t == "s")
  n <- zlist$n
  m <- zlist$m * mmult
  if (abnames) {
    ab <- rep("", nz)
    ab[n==0 & m==0] <- "piston"
    ab[n==2 & m==0] <- "defocus"
    ab[n>=4 & m==0] <- paste("spherical ", n[n>=4 & m==0], "'th", sep="")
    
    ab[n==1 & m==1] <- "x tilt"
    ab[n==1 & m==-1] <- "y tilt"
    cond <- n>=3 & m==1
    ab[cond] <- paste("x coma ", n[cond] + 1, "'th", sep="")
    cond <- n>=3 & m== -1
    ab[cond] <- paste("y coma ", n[cond] + 1, "'th", sep="")
    
    ab[m==2] <- paste("cos astigmatism ", n[m==2] + 2, "'th", sep="")
    ab[m== -2] <- paste("sin astigmatism ", n[m== -2] + 2, "'th", sep="")
    
    ab[m==3] <- paste("cos trefoil ", n[m==3] + 3, "'th", sep="")
    ab[m== -3] <- paste("sin trefoil ", n[m== -3] + 3, "'th", sep="")
    
    df.zernikes <- data.frame(Z = znames, n=n, m=m, aberration=ab,
                              zcoef.raw = fit, zcoef.net = c(0, wffit$zcoef.net))
  } else {
    df.zernikes <- data.frame(Z = znames, n=n, m=m,
                              zcoef.raw = fit, zcoef.net = c(0, wffit$zcoef.net))
  }
  if (printnow) {
    summary(wffit, digits=digits)
    cat("\n")
    print(df.zernikes, digits=digits, row.names=FALSE)
  }
  invisible(df.zernikes)
}

plot.wf_zfit <- function(wffit, wftype="smooth", ...) {
  wf <- get(paste("wf", wftype, sep="."), wffit)
  plot.pupil(wf, cp=wffit$cp, ...)
}

report <- function(wffit, ...) UseMethod("report", wffit)

report.wf_zfit <- function(wffit, digits=3, col=rev(rygcb(400)), figheight=30, ...) {
  if (!require(tinytable)) {
    stop("report method requires package tinytable\n")
  }
  fname <- file.path(tempdir(), "report.html")
  fwfnet <- file.path(tempdir(), "wf_net.png")
  fwfz <- file.path(tempdir(), "wf_zfit.png")
  df.plot <- data.frame("wf.net" = "", "wf.zernike" = "")
  wf.net <- wffit$wf.net
  wf.smooth <- wffit$wf.smooth
  if (exists("cp", wffit)) {
    cp <- wffit$cp
  } else {
    cp <- NULL
  }
  grDevices::png(file=fwfnet, width=512, height=512, bg="white")
  zernike::plot.pupil(wf.net, cp=cp, col=col, addContours=FALSE, ...)
  mtext(paste("RMS =", format(zernike::pupilrms(wf.net), digits=3)))
  dev.off()
  grDevices::png(file=fwfz, width=512, height=512, bg="white")
  zernike::plot.pupil(wf.smooth, cp=cp, col=col, addContours=TRUE, ...)
  mtext(paste("RMS =", format(zernike::pupilrms(wf.smooth), digits=3)))
  dev.off()
  
  img <- c("wf_net.png", "wf_zfit.png")
  
  df.plot.tt <- tt(df.plot) |>
  plot_tt(i=1, j=1:2, images=img, height=figheight, asp=1)
  
  df.sum <- summary(wffit, digits=digits, printnow=FALSE)
  colnames(df.sum) <- NULL
  df.det <- print(wffit, digits=digits, printnow=FALSE)
  nc.det <- ncol(df.det)
  nr.det <- nrow(df.det)
  
  df.sum.tt <- tt(df.sum) |> 
  group_tt(j = list("Metadata and Wavefront summary" = 1:2))
  
  df.det.tt <- tt(df.det) |>
  group_tt(j = list("Zernike coefficients" = 1:nc.det)) |>
  format_tt(j = c("zcoef.raw", "zcoef.net"), digits=digits, num_fmt="decimal") |>
    style_tt(j=1:nc.det, align="lrrlrr")
    str.plot.tt <- save_tt(df.plot.tt, output="html")
    str.sum.tt <- save_tt(df.sum.tt, output="html")
    str.det.tt <- save_tt(df.det.tt, output="html")
    cat(c(str.plot.tt, str.sum.tt, str.det.tt), file=fname)
    browseURL(fname)
    invisible(fname)
}

invert <- function(wffit) UseMethod("invert", wffit)

invert.wf_zfit <- function(wffit) {
  if (exists("phi", wffit)) {
    wffit$phi <- -wffit$phi
  }
  if (exists("phases", wffit)) {
    wffit$phases <- -wffit$phases
  }
  wffit$wf.net <- -wffit$wf.net
  wffit$wf.smooth <- -wffit$wf.smooth
  wffit$wf.residual <- -wffit$wf.residual
  wffit$zcoef.net <- -wffit$zcoef.net
  wffit$fit <- -wffit$fit

  wffit
}