showinf: Displaying images and metadata

In neuroconductor-releases/bftools: BioFormats Tools

Description

Displaying images and metadata

Usage

showinf(
  file,
  pixel_data = FALSE,
  series = NULL,
  range = NULL,
  crop = NULL,
  autoscale = FALSE,
  ome_xml = FALSE,
  opts = c("-no-upgrade", "-novalid"),
  debug = FALSE,
  verbose = TRUE,
  run = TRUE
)

showinf.help()

bf_showinf(
  file,
  pixel_data = FALSE,
  series = NULL,
  range = NULL,
  crop = NULL,
  autoscale = FALSE,
  ome_xml = FALSE,
  opts = c("-no-upgrade", "-novalid"),
  debug = FALSE,
  verbose = TRUE,
  run = TRUE
)

bf_show_info(
  file,
  pixel_data = FALSE,
  series = NULL,
  range = NULL,
  crop = NULL,
  autoscale = FALSE,
  ome_xml = FALSE,
  opts = c("-no-upgrade", "-novalid"),
  debug = FALSE,
  verbose = TRUE,
  run = TRUE
)

showinf_version()

bf_meta_subset(file)

Arguments

file	File to display
pixel_data	Should the image/pixel data be read in? If FALSE, the -nopix is passed.
series	All images in the input file are converted by default. To convert only one series, set this to a numeric
range	To convert images between certain indices (inclusive), set 0 to first
crop	of the format x,y,width,height. The (x, y) coordinate (0, 0) is the upper-left corner of the image; x + width must be less than or equal to the image width and y + height must be less than or equal to the image height.
autoscale	Adjusts the display range to the minimum and maximum pixel values.
ome_xml	should this populate OME-XML metadata
opts	Additional options to pass to showinf
debug	Enables debugging output if more information is needed
verbose	Should the command be printed
run	Should the command be run? Useful for diagnostics.

Value

The output file name

Examples

file = "~/Downloads/2017_08_03__0006.czi"
if (file.exists(file)) {
res = showinf(file = file, run = FALSE)
res
}
showinf_version()

neuroconductor-releases/bftools documentation built on Oct. 30, 2020, 11:06 p.m.