showinf: Displaying images and metadata

Description Usage Arguments Value Examples

View source: R/showinf.R

Description

Displaying images and metadata

Usage

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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

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

neuroconductor/bftools documentation built on Sept. 18, 2019, 3:15 a.m.