DisplayGallery: Gallery Display

In IFC: Tools for Imaging Flow Cytometry

Gallery Display

Description

Displays gallery of 'IFC_img' / 'IFC_msk' objects

Usage

DisplayGallery(
  ...,
  objects,
  offsets,
  image_type = "img",
  layout,
  name = "DisplayGallery",
  caption = FALSE,
  pageLength = 10L,
  pdf_pageSize = "A2",
  pdf_pageOrientation = "landscape",
  pdf_image_dpi = 96,
  extract_max = 10,
  sampling = FALSE,
  display_progress = TRUE,
  mode = c("rgb", "gray")[1]
)

Arguments

...	arguments to be passed to objectExtract with the exception of 'ifd' and 'bypass'(=TRUE). If 'param' is provided 'export'(="base64") and the above parameters will be overwritten. If 'offsets' are not provided extra arguments can also be passed with ... to 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.
image_type	image_type of desired offsets. Either "img" or "msk". Default is "img".
layout	a character vector of [acquired channels + 'composite' images] members to export. Default is missing to export everything. Note that members can be missing to be removed from final display. Note that members not found will be automatically removed and a warning will be thrown.
name	id of the datatable container. Default is DisplayGallery.
caption	whether to display caption name or not. Default is FALSE.
pageLength	integer, number of objects to display per page. Default is 10.
pdf_pageSize	string, page dimension when exporting to pdf. Default is "A2".
pdf_pageOrientation	string, page orientation when exporting to pdf. Default is "landscape". Allowed are "landscape" or "portrait".
pdf_image_dpi	integer, desired image resolution. Default is 96, for full resolution.
extract_max	maximum number of objects to extract. Default is 10. Use +Inf to extract all.
sampling	whether to sample objects or not. Default is FALSE.
display_progress	whether to display a progress bar. Default is TRUE.
mode	(objectParam argument) color mode export. Either "rgb" or "gray". Default is "rgb".

Details

arguments of objectExtract will be deduced from DisplayGallery input arguments.
Please note that PDF export link will be available if 'write_to' will not result in a "bmp".
Please note that exporting to "tiff" may depend on browser capabilities.
Please note that a warning may be sent if gallery to display contains large amount of data. This is due to use of datatable() from DT.
Warning message:
In instance$preRenderHook(instance) :
It seems your data is too big for client-side DataTables. You may consider server-side processing: http://rstudio.github.io/DT/server.html
For these reasons, it may be better to use "png" extension to display images.

Value

it invisibly returns a list whose members are:
-data, data for DT::datatable(),
-args, associated arguments to pass to DT::datatable().

Examples

if(requireNamespace("IFCdata", quietly = TRUE)) {
  ## use a cif file
  file_cif <- system.file("extdata", "example.cif", package = "IFCdata")
  cif <- ExtractFromXIF(fileName = file_cif)
  info <- getInfo(fileName = file_cif, from = "analysis")
  ## randomly show at most 10 "img" objects from file
  DisplayGallery(info = info, image_type = "img", extract_max = 10,
                 sampling = TRUE, write_to = "example.bmp")
} else {
  message(sprintf('Please run `install.packages("IFCdata", repos = "%s", type = "source")` %s',
                  'https://gitdemont.github.io/IFCdata/',
                  'to install extra files required to run this example.'))
}

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