R/estimate_template.methods.R

In templateICAr: Estimate Brain Networks and Connectivity with ICA and Empirical Priors

#' Summarize a \code{"template.cifti"} object
#'
#' Summary method for class \code{"template.cifti"}
#'
#' @param object Object of class \code{"template.cifti"}.
#' @param ... further arguments passed to or from other methods.
#' @export
#' @return A list summarizing the template: data dimensions, options used for
#'  template estimation, etc.
#' @method summary template.cifti
summary.template.cifti <- function(object, ...) {
  tmean <- struct_template(object$template$mean, "CIFTI", object$dat_struct, object$params)
  x <- c(
    summary(tmean),
    list(has_DR="DR" %in% names(object)),
    object$params
  )

  class(x) <- "summary.template.cifti"
  return(x)
}

#' Summarize a \code{"template.gifti"} object
#'
#' Summary method for class \code{"template.gifti"}
#'
#' @param object Object of class \code{"template.gifti"}.
#' @param ... further arguments passed to or from other methods.
#' @export
#' @return A list summarizing the template: data dimensions, options used for
#'  template estimation, etc.
#' @method summary template.gifti
summary.template.gifti <- function(object, ...) {
  x <- c(
    list(
      nV=nrow(object$template$mean),
      nL=ncol(object$template$mean),
      hemisphere=object$dat_struct$hemisphere,
      hasDR="DR" %in% names(object)
    ),
    object$params
  )

  class(x) <- "summary.template.gifti"
  return(x)
}

#' Summarize a \code{"template.nifti"} object
#'
#' Summary method for class \code{"template.nifti"}
#'
#' @param object Object of class \code{"template.nifti"}.
#' @param ... further arguments passed to or from other methods.
#' @export
#' @return A list summarizing the template: data dimensions, options used for
#'  template estimation, etc.
#' @method summary template.nifti
summary.template.nifti <- function(object, ...) {
  x <- c(
    list(
      mask_dims=dim(object$dat_struct),
      nV=nrow(object$template$mean),
      nL=ncol(object$template$mean),
      hasDR="DR" %in% names(object)
    ),
    object$params
  )

  class(x) <- "summary.template.nifti"
  return(x)
}

#' Summarize a \code{"template.matrix"} object
#'
#' Summary method for class \code{"template.matrix"}
#'
#' @param object Object of class \code{"template.matrix"}.
#' @param ... further arguments passed to or from other methods.
#' @export
#' @return A list summarizing the template: data dimensions, options used for
#'  template estimation, etc.
#' @method summary template.matrix
summary.template.matrix <- function(object, ...) {
  x <- c(
    list(
      nV=nrow(object$template$mean),
      nL=ncol(object$template$mean),
      hasDR="DR" %in% names(object)
    ),
    object$params
  )

  class(x) <- "summary.template.matrix"
  return(x)
}

#' @rdname summary.template.cifti
#' @export
#'
#' @param x The template from \code{estimate_template.cifti}
#' @param ... further arguments passed to or from other methods.
#' @return Nothing, invisibly.
#' @method print summary.template.cifti
print.summary.template.cifti <- function(x, ...) {
  # Get DCT output.
  dct <- x$detrend_DCT
  if (!is.null(dct)) {
    dct <- as.numeric(x$detrend_DCT)
    dct <- if (dct>1) {
      paste(dct, "DCT bases")
    } else if (dct > 0) {
      paste(dct, "DCT basis")
    } else {
      "None"
    }
  }

  cat("====TEMPLATE INFO====================\n")
  cat("# Subjects:      ", x$num_subjects, "\n")
  cat("Detrending:      ", dct, "\n")
  cat("Spatial scaling: ", x$scale, "\n")
  cat("A normalization: ", x$normA, "\n")
  cat("Q2 and Q2_max:   ", paste0(x$Q2, ", ", x$Q2_max), "\n")
  cat("Pseudo retest:   ", x$pseudo_retest, "\n")
  cat("\n")

  class(x) <- "summary.xifti"
  print(x)
  invisible(NULL)
}

#' @rdname summary.template.gifti
#' @export
#'
#' @param x The template from \code{estimate_template.gifti}
#' @param ... further arguments passed to or from other methods.
#' @return Nothing, invisibly.
#' @method print summary.template.gifti
print.summary.template.gifti <- function(x, ...) {
  # Get DCT output.
  dct <- x$detrend_DCT
  if (!is.null(dct)) {
    dct <- as.numeric(x$detrend_DCT)
    dct <- if (dct>1) {
      paste(dct, "DCT bases")
    } else if (dct > 0) {
      paste(dct, "DCT basis")
    } else {
      "None"
    }
  }

  cat("====TEMPLATE INFO====================\n")
  cat("# Subjects:      ", x$num_subjects, "\n")
  cat("Detrending:      ", dct, "\n")
  cat("Spatial scaling: ", x$scale, "\n")
  cat("A normalization: ", x$normA, "\n")
  cat("Q2 and Q2_max:   ", paste0(x$Q2, ", ", x$Q2_max), "\n")
  cat("Pseudo retest:   ", x$pseudo_retest, "\n")
  cat("-------------------------------------\n")
  cat("# Locations:     ", x$nV, "\n")
  cat("# Template ICs:  ", x$nL, "\n")
  cat("Hemisphere:      ", x$hemisphere, "\n")
  cat("\n")

  invisible(NULL)
}

#' @rdname summary.template.nifti
#' @export
#'
#' @param x The template from \code{estimate_template.nifti}
#' @param ... further arguments passed to or from other methods.
#' @return Nothing, invisibly.
#' @method print summary.template.nifti
print.summary.template.nifti <- function(x, ...) {
  # Get DCT output.
  dct <- x$detrend_DCT
  if (!is.null(dct)) {
    dct <- as.numeric(x$detrend_DCT)
    dct <- if (dct>1) {
      paste(dct, "DCT bases")
    } else if (dct > 0) {
      paste(dct, "DCT basis")
    } else {
      "None"
    }
  }

  cat("====TEMPLATE INFO====================\n")
  cat("# Subjects:      ", x$num_subjects, "\n")
  cat("Detrending:      ", dct, "\n")
  cat("Spatial scaling: ", x$scale, "\n")
  cat("A normalization: ", x$normA, "\n")
  cat("Q2 and Q2_max:   ", paste0(x$Q2, ", ", x$Q2_max), "\n")
  cat("Pseudo retest:   ", x$pseudo_retest, "\n")
  cat("-------------------------------------\n")
  cat("Mask dims:       ", paste0(x$mask_dims, collapse=" x "), "\n")
  cat("Vectorized dims:\n")
  cat("# Locations:     ", x$nV, "\n")
  cat("# Template ICs:  ", x$nL, "\n")
  cat("\n")

  invisible(NULL)
}

#' @rdname summary.template.matrix
#' @export
#'
#' @param x The template from \code{estimate_template.cifti}
#' @param ... further arguments passed to or from other methods.
#' @return Nothing, invisibly.
#' @method print summary.template.matrix
print.summary.template.matrix <- function(x, ...) {
  # Get DCT output.
  dct <- x$detrend_DCT
  if (!is.null(dct)) {
    dct <- as.numeric(x$detrend_DCT)
    dct <- if (dct>1) {
      paste(dct, "DCT bases")
    } else if (dct > 0) {
      paste(dct, "DCT basis")
    } else {
      "None"
    }
  }

  cat("====TEMPLATE INFO====================\n")
  cat("# Subjects:      ", x$num_subjects, "\n")
  cat("Detrending:      ", dct, "\n")
  cat("Spatial scaling: ", x$scale, "\n")
  cat("A normalization: ", x$normA, "\n")
  cat("Q2 and Q2_max:   ", paste0(x$Q2, ", ", x$Q2_max), "\n")
  cat("Pseudo retest:   ", x$pseudo_retest, "\n")
  cat("-------------------------------------\n")
  cat("Dimensions:      \n")
  cat("# Locations:     ", x$nV, "\n")
  cat("# Template ICs:  ", x$nL, "\n")
  cat("\n")

  invisible(NULL)
}

#' @rdname summary.template.cifti
#' @export
#'
#' @return Nothing, invisibly.
#' @method print template.cifti
print.template.cifti <- function(x, ...) {
  print.summary.template.cifti(summary(x))
}

#' @rdname summary.template.gifti
#' @export
#'
#' @return Nothing, invisibly.
#' @method print template.gifti
print.template.gifti <- function(x, ...) {
  print.summary.template.gifti(summary(x))
}

#' @rdname summary.template.nifti
#' @export
#'
#' @return Nothing, invisibly.
#' @method print template.nifti
print.template.nifti <- function(x, ...) {
  print.summary.template.nifti(summary(x))
}

#' @rdname summary.template.matrix
#' @export
#'
#' @return Nothing, invisibly.
#' @method print template.matrix
print.template.matrix <- function(x, ...) {
  print.summary.template.matrix(summary(x))
}

#' Plot template
#'
#' @param x The template from \code{estimate_template.cifti}
#' @param stat \code{"mean"}, \code{"sd"}, or \code{"both"} (default). By
#'  default the square root of the variance template is shown; another option is 
#'  \code{stat="var"} to instead display the variance template directly.
#' @param var_method \code{"non-negative"} (default) or \code{"unbiased"}
#' @param ... Additional arguments to \code{view_xifti}
#' @return The plot
#' @export
#' @method plot template.cifti
plot.template.cifti <- function(x, stat=c("both", "mean", "sd", "var"),
  var_method=c("non-negative", "unbiased"), ...) {
  stopifnot(inherits(x, "template.cifti"))

  if (!requireNamespace("ciftiTools", quietly = TRUE)) {
    stop("Package \"ciftiTools\" needed to read NIFTI data. Please install it.", call. = FALSE)
  }

  var_method <- match.arg(var_method, c("non-negative", "unbiased"))

  # Check `...`
  args <- list(...)
  has_title <- "title" %in% names(args)
  has_idx <- "idx" %in% names(args)
  has_fname <- "fname" %in% names(args)

  # Check `stat`
  stat <- tolower(stat)
  if (has_idx && length(args$idx)>1 && !("fname" %in% names(args))) {
    if (identical(stat, c("both", "mean", "sd", "var"))) {
      stat <- "mean"
    } else {
      stat <- match.arg(stat, c("both", "mean", "sd", "var"))
    }
    if (stat == "both") {
      if (!("fname" %in% names(args))) {
        warning(
          "For multiple `idx`, use one call to plot() ",
          "for the mean template, ",
          "and a separate call for the variance template. ",
          "Showing the mean template now."
        )
        stat <- "mean"
      }
    }
  }
  stat <- match.arg(stat, c("both", "mean", "sd", "var"))

  # Print message saying what's happening.
  msg1 <- ifelse(has_idx,
    "Plotting the",
    "Plotting the first component's"
  )
  msg2 <- switch(stat,
    both="mean and sqrt(variance) template.",
    mean="mean template.",
    sd="sqrt(variance) template.",
    var="variance template."
  )
  cat(msg1, msg2, "\n")

  # Plot
  out <- list(mean=NULL, var=NULL)
  if (stat == "both") { stat <- c("mean", "sd") }
  for (ss in stat) {
    ssname <- if (ss == "mean") {
      ss
    } else if (var_method=="non-negative") {
      "varNN"
    } else {
      "varUB"
    }
    if (ss=="var" && var_method=="unbiased") { x$template[[ssname]][] <- pmax(0, x$template[[ssname]]) }
    if (ss=="sd") { 
      x$template[[ssname]] <- sqrt(x$template[[ssname]])
    }
    tss <- struct_template(x$template[[ssname]], "CIFTI", x$dat_struct, x$params)
    if (ss=="sd") { 
      ssname <- paste0("sqrt ", ssname)
    }
    
    args_ss <- args
    # Handle title and idx
    if (!has_title && !has_idx) {
      c1name <- if (!is.null(tss$meta$cifti$names)) {
        tss$meta$cifti$names[1]
      } else {
        "First component"
      }
      args_ss$title <- paste0(c1name, " (", ssname, ")")
    } else if (!has_idx) {
      args_ss$title <- paste0(args_ss$title, "(", ssname, ")")
    }
    # Handle fname
    if (has_fname) {
      fext <- if (grepl("html$", args_ss$fname[1])) {
        "html"
      } else if (grepl("pdf$", args_ss$fname[1])) {
        "pdf"
      } else {
        "png"
      }
      args_ss$fname <- gsub(paste0(".", fext), "", args_ss$fname, fixed=TRUE)
      args_ss$fname <- paste0(args_ss$fname, "_", ss, ".", fext)
    }
    out[[ss]] <- do.call(
      ciftiTools::view_xifti, c(list(tss), args_ss)
    )
  }

  invisible(out)
}

#' Plot template
#'
#' @param x The template from \code{estimate_template.gifti}
#' @param stat \code{"mean"}, \code{"sd"}, or \code{"both"} (default). By
#'  default the square root of the variance template is shown; another option is 
#'  \code{stat="var"} to instead display the variance template directly.
#' @param var_method \code{"non-negative"} (default) or \code{"unbiased"}
#' @param ... Additional arguments to \code{view_xifti}
#' @return The plot
#' @export
#' @method plot template.gifti
plot.template.gifti <- function(x, stat=c("both", "mean", "sd", "var"),
  var_method=c("non-negative", "unbiased"), ...) {
  stopifnot(inherits(x, "template.gifti"))

  if (!requireNamespace("ciftiTools", quietly = TRUE)) {
    stop("Package \"ciftiTools\" needed to read NIFTI data. Please install it.", call. = FALSE)
  }

  if (x$dat_struct$hemisphere == "left")  {
    y <- ciftiTools::as_cifti(cortexL=x$template$mean[,1,drop=FALSE] * 0)
  } else {
    y <- ciftiTools::as_cifti(cortexR=x$template$mean[,1,drop=FALSE] * 0)
  }
  y <- ciftiTools::move_from_mwall(y)
  x$dat_struct <- y; class(x) <- "template.cifti"
  plot.template.cifti(x, stat, var_method, ...)
}

#' Plot template
#'
#' Based on \code{oro.nifti::image}.
#'
#' Consider using \code{struct_template} to obtain the 3D volumes to plot with a different
#'  viewer function (e.g. from \code{oro.nifti}) if desired.
#'
#' @param x The template from \code{estimate_template.nifti}
#' @param stat \code{"mean"} (default), \code{"sd"}, or \code{"var"}. 
#'  (\code{"sd"} will show the square root of the variance template.)
#' @param var_method \code{"non-negative"} (default) or \code{"unbiased"}
#' @param plane,n_slices,slices Anatomical plane and which slice indices to 
#'  show.
#'  Default: 9 axial slices.
#' @param ... Additional arguments to \code{oro.nifti::image}
#' @return The plot
#' @export
#' @method plot template.nifti
plot.template.nifti <- function(x, stat=c("mean", "sd", "var"),
  plane=c("axial", "sagittal", "coronal"), n_slices=9, slices=NULL,
  var_method=c("non-negative", "unbiased"), ...) {
  stopifnot(inherits(x, "template.nifti"))

  if (!requireNamespace("oro.nifti", quietly = TRUE)) {
    stop("Package \"oro.nifti\" needed to read NIFTI data. Please install it.", call. = FALSE)
  }

  var_method <- match.arg(var_method, c("non-negative", "unbiased"))

  # Check `...`
  args <- list(...)
  has_title <- "title" %in% names(args)
  has_idx <- "idx" %in% names(args)
  has_fname <- "fname" %in% names(args)

  # Check `idx`
  if (has_idx) {
    stopifnot(length(args$idx)==1)
    stopifnot(is.numeric(args$idx) && args$idx==round(args$idx))
    stopifnot(args$idx %in% seq(ncol(x$template$mean)))
  } else {
    args$idx <- 1
  }
  idx <- args$idx; args$idx <- NULL

  # Check `stat`
  stat <- tolower(stat)
  if (has_idx && length(args$idx)>1 && !("fname" %in% names(args)) && identical(stat, c("mean", "sd", "var"))) {
    stat <- "mean"
  }
  stat <- match.arg(stat, c("mean", "sd", "var"))

  # Print message saying what's happening.
  msg1 <- ifelse(has_idx,
    "Plotting the",
    "Plotting the first component's"
  )
  msg2 <- switch(stat,
    mean="mean template.",
    sd="sqrt(variance) template.",
    var="variance template."
  )
  cat(msg1, msg2, "\n")

  # Plot
  out <- list(mean=NULL, var=NULL)

  plane <- match.arg(plane, c("axial", "sagittal", "coronal"))
  args$plane <- plane
  plane_dim <- switch(plane, axial=3, coronal=2, sagittal=1)
  if (is.null(slices)) {
    if (is.null(n_slices)) { warning("Using 9 slices."); n_slices <- 9 }
    n_slices <- as.numeric(n_slices)
    if (length(n_slices) > 1) { warning("Using the first entry of `slice`."); n_slices <- n_slices[1] }
    # Pick slices that are spaced out, and with many voxels.
    mask_count <- apply(x$dat_struct, plane_dim, sum)
    ns_all <- length(mask_count)
    slices <- seq(ns_all)
    # Remove slices with zero voxels.
    slices <- slices[mask_count != 0]
    mask_count <- mask_count[mask_count != 0]
    ns_all <- length(mask_count)
    if (n_slices > length(slices)) {
      warning(
        "`n_slices` is larger than the number of non-empty slices (",
        length(slices), "). Showing all non-empty slices."
      )
      n_slices <- length(slices)
    }
    # Remove slices with few voxels.
    if (n_slices < (ns_all / 2)) {
      slices <- slices[mask_count > quantile(mask_count, .33)]
    }
    slices <- slices[round(seq(1, length(slices), length.out=n_slices))]
  } else {
    slices <- as.numeric(slices)
    stopifnot(all(slices %in% seq(dim(x$dat_struct)[plane_dim])))
  }

  ssname <- if (stat == "mean") {
    stat
  } else if (var_method=="non-negative") {
    "varNN"
  } else {
    "varUB"
  }
  if (stat=="var" && var_method=="unbiased") { x$template[[ssname]][] <- pmax(0, x$template[[ssname]]) }
  tss <- struct_template(x$template[[ssname]], "NIFTI", x$dat_struct, x$params)
  tss <- tss[,,,idx]

  if (plane=="axial") {
    tss <- tss[,,slices,drop=FALSE]
  } else if (plane=="coronal") {
    tss <- tss[,slices,,drop=FALSE]
  } else if (plane=="sagittal") {
    tss <- tss[slices,,,drop=FALSE]
  } else { stop() }

  if (stat=="sd") { 
    tss <- sqrt(tss)
    ssname <- paste0("sqrt ", ssname)
  }

  args_ss <- args
  args_ss$plane <- plane
  # Handle title and idx
  if (!has_title && !has_idx) {
    c1name <- "First component"
  }
  if (has_title) { stop("Not supported yet.") }
  if (has_fname) { stop("Not supported yet. Call `pdf` or `png` beforehand, and then `dev.off`.") }
  do.call(
    oro.nifti::image,
    c(list(oro.nifti::as.nifti(tss)), args_ss)
  )
}

#' Plot template
#'
#' @param x The template from \code{estimate_template.matrix}
#' @param ... Additional arguments
#' @return The plot
#' @export
#' @method plot template.matrix
plot.template.matrix <- function(x, ...) {
  stop("Not supported yet.")
}