zie: ZIE (ZooImage Extension) manipulate .zie files to add custom...
In zooimage: Analysis of Numerical Plankton Images

Description Usage Arguments Value Author(s) See Also Examples

A .zie file describes sequentially images and tells how to convert and rename them and automates creation of associated metadata (.zim files). At the end of the process, one ends with complete and fully usable information (both the images with correct format/name and the metadata), so that you can proceed in ZooImage with imported data.

zieMake(path = ".", Filemap = "Import_Table.zie", check = TRUE, replace = FALSE,
    move.to.raw = TRUE, zip.images = "[.]tif$")

zieCompile(path = ".", Tablefile = "Table.txt", Template = "ImportTemplate.zie",
    Filemap = paste("Import_", noExtension(Tablefile), ".zie", sep = ""),
    Nrange = c(1, 1000), replace = TRUE, make.it = FALSE,
    zip.images = "[.]tif$")
zieCompileFlowCAM(path = ".", Tablefile, Template = "ImportTemplate.zie",
    check.names = TRUE)

ZIE(title, filter, description, pattern, command, author, version, date,
    license, url, depends = "R (>= 2.4.0), zooimage (>= 1.0-0)",
    type = c("import", "export"))
## S3 method for class 'ZIE'
print(x, ...)

`path`	path where the images and the .zie file are located.
`check.names`	do wr check names in the .zie and .txt files?
`Filemap`	name of the .zie file mapping images to convert.
`check`	do we check if conversion programs (if any needed) are available?
`replace`	do we replace existing files (not used yet)?
`move.to.raw`	do we move processed files to the '_raw' subdirectory (currently, it is always the case)?
`zip.images`	the pattern to use for images extension in the zipped file.
`Tablefile`	a tab-delimited ASCII file containing a table defining samples and samples characteristics used to compile .zim files and to convert/rename images.
`Template`	a template to use for creating the .zie file.
`Nrange`	A range (two integers) giving min and max number of images for each sample/fraction.
`make.it`	do we make the .zie (run its commands) after compiling it?
`title`	the title of the ZooImage Extension.
`filter`	a filter to apply to select concerned files.
`description`	a short description of the ZooImage Extension.
`pattern`	a regular expression to use to select concerned files.
`command`	a string holding the R command to run to convert images.
`author`	who wrote and maintains the ZooImage Extension? Please, provide also an email address.
`version`	version of the ZooImage Extension as x.y-z, in a string.
`date`	date at which the extension was compiled as yyyy-mm-dd.
`license`	which are the license terms for this ZooImage Extension?
`url`	a link to a web page dedicated to this ZooImage Extension.
`depends`	which R packages does this ZooImage Extension requires?
`type`	type of ZooImage extension; currently, only "import" or "export".
`x`	a ZIE object.
`...`	further arguments passes to the function (currently not in use).

zieMake(), zieCompile() and zieCompileFlowCAM() are invoked for their side-effects of importing images and metadata into a format that ZooImage can use. The first two functions return TRUE or FALSE, depending if the importation was done without errors, or not. More information is issued as warnings. The last function returns the name of the .zie file resulting from the compilation. It returns NULL in case it failed to compile the .zie file.

ZIE() creates a 'ZIE' object that describes a ZooImage Extension and allows to plug it in transparently inside the ZooImage GUI. print.ZIE() nicely formats the content of this objects when using the generic function print().

Philippe Grosjean <Philippe.Grosjean@umons.ac.be>

zimMake

##TODO...

### For programmers ###
# Adding a new import filter is just a mather of writing the importation function
# and making it available to users by means of a ZIEimport object.

zooimage documentation built on May 2, 2019, 3:43 p.m.