ExtractMasks_toFile: Shortcut for Batch Masks Extraction to Files

In IFC: Tools for Imaging Flow Cytometry

Shortcut for Batch Masks Extraction to Files

Description

Function to shortcut extraction, normalization and eventually colorization of masks to file ! excludes image.

Usage

ExtractMasks_toFile(
  ...,
  objects,
  offsets,
  display_progress = TRUE,
  mode = c("rgb", "gray")[1],
  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.
mode	(objectParam argument) color mode export. Either "rgb", "gray". Default is "rgb".
write_to	used to compute respectively exported file name. Exported "file" extension will be deduced from this pattern. Allowed export are ".bmp", ".jpg", ".jpeg", ".png", ".tif", ".tiff". Note that ".bmp" is faster but files are not compressed producing bigger data. 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 -%c: with channel_id A good trick is to use: "%d/%s/%s_%o_%c.tiff".
overwrite	whether to overwrite file or not. Default is FALSE.

Details

If 'param' is provided in '...':
-'param$export'<-"file", 'param$mode'<-'mode' 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 "file".

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

Value

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

Note

Arguments of objectExtract will be deduced from ExtractMasks_toFile input arguments.

IFC documentation built on Sept. 14, 2023, 1:08 a.m.