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Convert Specialized TIF Formats to Basic TIF

Source: R/images.R
to_simple_tif.Rd

Simple converter from specialized formats to .tif format. Utilizes the python tifffile package. Performs image conversions one page at a time. Wrap this in a for loop or lapply for more than one image or page. Used when image formats are unsupported by terra. This is implementation may change in the future. Currently tested to work with .ome.tif and qptiff

Usage

to_simple_tif(
  input_file,
  output_dir = file.path(dirname(input_file), "tif_exports"),
  page,
  overwrite = FALSE
)

ometif_to_tif(
  input_file,
  output_dir = file.path(dirname(input_file), "tif_exports"),
  page,
  overwrite = FALSE
)

Arguments

input_file

character. Filepath to tif to convert

output_dir

character. Directory to write .tif to. Defaults to a new folder in the directory called "tif_exports"

page

numeric. Which page of the tif to open (if needed). If provided, a "_%04d" formatted suffix will be added to the output filename.

overwrite

logical. Default = FALSE. Whether to overwrite if the filename already exists.

Value

returns the written filepath invisibly

Functions

  • ometif_to_tif(): deprecated.

See also

Other tif utility functions: tif_metadata()