ExtractImages_toFile: Shorcut for Batch Images Extraction to Files

Description

Function to shortcut extraction, normalization and eventually colorization of images to matrix ! excludes mask.

Usage

ExtractImages_toFile(
  ...,
  objects,
  offsets,
  display_progress = TRUE,
  mode = c("rgb", "gray")[1],
  write_to
)

Arguments

...

arguments to be passed to objectExtract with the exception of 'ifd' and 'bypass'(=TRUE). If 'param' is provided 'export'(="file"), 'write_to' and 'mode' will be overwritten. If 'offsets' are not provided extra arguments can also be passed with ... getOffsets. /!\ 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.

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

(objectParam argument) used to compute exported file name. Exported "file" extension will be deduced from this pattern. Allowed export are '.bmp', '.jpg', '.jpeg', '.png', '.tif', '.tiff'. Note that '.bmp' are faster but 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".

Value

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

Details

arguments of objectExtract will be deduced from ExtractImages_toFile input arguments.