An OMERO client for downloading data in bulk from the server. The -h
option prints a brief summary of command-line options.
From the source repository mvn builds and packages the downloader.
OMERO.downloader has not yet seen much use. One should therefore expect both bugs and breaking changes. However, it is hoped that even in its early state there are use cases for which it offers significant help.
For testing, make a new scratch directory, say /tmp/repo/, to specify
to the -b option below. In general one should use a separate download
directory for each OMERO server from which one fetches data.
./download.sh -b /tmp/repo -s <server host> -u <user name> -w <password> -f binary Image:<image ID>
downloads an image's binary files into the scratch directory. To include
companion files use -f binary,companion.
Repeating a download resumes any interrupted files and skips files that are already present.
Within /tmp/repo/Image/ it may seem inconvenient to have each image's
downloaded files sorted into separate Binary and Companion
directories. However, these are simply symbolic links that can be
followed to find the files together within the Repository directory.
When binary and companion files should be used together the realpath
utility from GNU coreutils can be helpful, e.g.,
showinf -autoscale `realpath /tmp/repo/Image/123/Binary/myimage`
Instead of using Image as a target, containers such as dataset or
screens may be specified to target all their images. However, note that
for plates the default server configuration disables file download.
Additionally, specifying -a extends the targeted images to include all
that are in the same fileset as any targeted image.
Image metadata is available as OME-XML without pixel data.
The included metadata can be limited with the -x option.
ome-xml-parts downloads metadata for images, ROIs and some simple
annotations on them as many standalone XML files. For example, with,
./download.sh -b /tmp/repo -s <server host> -u <user name> -w <password> -f ome-xml-parts Image:123
the ROIs on image 123 can then be found as
/tmp/repo/Image/123/Roi/*/Metadata/roi-*.ome.xml. Note that these
numbered Roi/* directories are themselves symbolic links into
/tmp/repo/Roi/.
ome-xml-whole assembles OME-XML export files from the standalone XML
files. ome-xml is shorthand for both the parts and whole. So, to
export image 123's metadata into one file, simply omit the -parts from
the above then check /tmp/repo/Image/123/Export/image-123.ome.xml.
It is possible to directly target annotations and ROIs for metadata export regardless of images.
Available as Open Source: see the license for details.
Copyright (C) 2016-2018 University of Dundee & Open Microscopy Environment. All rights reserved.