checkImages | R Documentation |
Check validity of paired DNA and a fluorescent images
appropriate for parseImages()
.
checkImages(
source,
type = "tiff",
which.images = c(1, 2, 2),
pattern = NULL,
method = c("none", "raster", "browser"),
ask = TRUE,
separate = FALSE,
nx = 2
)
source |
A character vector identifying the source of images.
The source can be a directory with subdirectories, each of which
contains images organized as specified by |
type |
A character string identifying the type of image files to parse ("tif", tiff", jpeg", jpg or png"). |
which.images |
An integer of length 2 or 3 or |
pattern |
Optional grep pattern as character string used by
|
method |
Character string specifying the method of displaying images.
Default of |
ask |
Logical value to use |
separate |
Logical value to normalize each frame separately if
|
nx |
Integer value passed to the |
If which.images
is not NULL
, the images specified in
source
will be evaluated with the same logic in
getImages
to determine if the proper number of files are
present and report on the number and form of the image files. If
which.images
is NULL
, no check will be performed.
Images associated with each multiplicity of infection can be individual
files in a single directory where each directory is named for the well
such as A1
, A2
, etc. and the files within are identified as
A1/file001.tif
, A1/file002.tif
, etc. The well identifier
can be in upper or lower case and can contain leading zeros such as
c0003/file12.tif
/ The well identifier also can contain a leading
prefix designating the plate such as in 1A2
or Plate_1B6
.
Alternatively, each group of images associated with a given moi can be
a multi-layered tiff file where the sequence of images in the file is
specified by the argument which.images
.
If 'source'
is one or more zip files, files in the temporary directory
(tempdir
) will be deleted in order to receive the compressed
files.
An invisible
character vector of image files, diagnostic messages
are printed on the console with the option to display normalized image pairs.
# Example with data organized by folder or well
path.by.folder <- system.file("extdata", "by_folder", package = "virustiter")
checkImages(path.by.folder)
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