View source: R/cellid_wrapper.R
arguments | R Documentation |
Obtener argumentos para CellID
arguments( path, parameters = rcell2::parameters.write(), BF.pattern = "^BF", file.pattern = "^(BF|[A-Z]FP)_Position(\\d+)_time(\\d+).tif$", file.pattern.groups.order = c("ch", "pos", "t.frame"), tiff.ext = "tif$" )
path |
directory where images are stored, full path. |
parameters |
path to the parameters file or a data.frame with "pos" (position number) and "parameter" (path) columns. Defaults to |
BF.pattern |
regex pattern to detect BF images only. Defaults to: |
file.pattern |
regex pattern for all tif files, with one group for each of |
file.pattern.groups.order |
a character vector of components |
tiff.ext |
regex pattern for the tif file extension |
All 4 regex groups are mandatory, 't.frame' may be left as empty parenthesis, while also preserving group order defined by 'file.pattern.groups.order'.
The "channel" and "pos" regex groups _must always_ match pos and channel identifiers in the file name.
Example 'file.pattern' regex, when 'file.pattern.groups.order = c("ch", "pos", "t.frame")':
With Z planes time: file.pattern = "^(BF|[TYR]FP|[TYR]\d{2})_Position(\d+)_time(\d+).tif$"
No Z planes, with time (note the empty parentheses): file.pattern = "^(BF|[A-Z]FP)_Position(\d+)_time(\d+).tif$"
No Z planes, no time: file.pattern = "^(BF|[TYR]FP)_Position(\d+)().tif$"
a data.frame with all the information needed to run CellID
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.