R: ZIE (ZooImage Extension) manipulate .zie files to add custom...
zie
R Documentation
ZIE (ZooImage Extension) manipulate .zie files to add custom import, export, etc. routines to ZooImage
Description
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.
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).
Value
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().
Author(s)
Philippe Grosjean <Philippe.Grosjean@umons.ac.be>
See Also
zimMake
Examples
##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.