ExtractImages_toMulti: Shortcut for Batch Images Extraction to Multichannel Tiff

In gitdemont/IFC: Tools for Imaging Flow Cytometry

Shortcut for Batch Images Extraction to Multichannel Tiff

Description

Function to shortcut extraction images to multichannel tiff ! excludes mask.

Usage

ExtractImages_toMulti(
  ...,
  objects,
  offsets,
  display_progress = TRUE,
  write_to,
  overwrite = FALSE
)

Arguments

...	arguments to be passed to objectExtract with the exception of 'ifd' and 'bypass'(=TRUE). /!\ If not any of 'fileName', 'info' and 'param' can be found in '...' then attr(offsets, "fileName_image") will be used as 'fileName' input parameter to pass to objectParam.
objects	integer vector, IDEAS objects ids numbers to use. This argument is not mandatory, if missing, the default, all objects will be used.
offsets	object of class 'IFC_offset'. This argument is not mandatory but it may allow to save time for repeated image export on same file. If 'offsets' are not provided, extra arguments can also be passed with '...' to getOffsets.
display_progress	whether to display a progress bar. Default is TRUE.
write_to	used to compute respectively exported file name. Exported "multi" extension will be deduced from this pattern. Allowed export are ".tif", ".tiff". Placeholders, if found, will be substituted: -%d: with full path directory, -%p: with first parent directory, -%e: with extension (without leading .), -%s: with shortname (i.e. basename without extension), -%o: with object_id, A good trick is to use: "%d/%s/%s_%o.tiff".
overwrite	whether to overwrite file or not. Default is FALSE.

Details

If 'param' is provided in '...':
-'param$export'<-"multi", 'param$mode'<-"raw" and 'param$overwrite'<-'overwrite' will be overwritten.
-if 'write_to' is not missing, 'param$write_to'<-'write_to' will be overwritten. Otherwise, 'param$write_to' will be used only if 'param$export' was "multi".

'write_to' has to be provided if 'param' can't be found in '...' or if 'param$export' was not "multi".

Value

It invisibly returns a list of exported file path of corresponding to objects extracted.

Note

Arguments of objectExtract will be deduced from ExtractImages_toMulti input arguments.

gitdemont/IFC documentation built on Feb. 20, 2025, 12:55 a.m.