Import images ------------- The |CLI| import command allows you to import images to an OMERO.server from the command line, and is ideally suited for anyone wanting to use a shell-scripted or web-based front-end interface for importing. Based upon the same set of libraries as the standard importer, the command line version supports the same file formats and functions in much the same way. Visit :bf_doc:`Supported Formats ` for a detailed list of supported formats. Import command ^^^^^^^^^^^^^^ .. program:: omero import To import a file :file:`image.tif`, use:: $ bin/omero import image.tif Some of the options available to the import command are: .. option:: -h, --help Display the help for the import command .. option:: --java-help Display the help for the Java options of the import command Java options can be passed after ``--``, e.g.:: bin/omero import image.tif -- --name=test --description=description .. option:: --advanced-help Display the advanced help for the import command Some advanced import options are described in the :ref:`inplace_import` section. .. option:: -f Display all the files that would be imported, then exit:: $ bin/omero import -f image.tif $ bin/omero import -f images_folder This will output a list of all the files which would be imported in groups separated by "#" comments. Note that this usage does not require a running server to be available. .. option:: --depth DEPTH Set the number of directories to scan down for files (default: 4):: $ bin/omero import --depth 1 images_folder .. option:: --skip SKIP Specify optional step to skip during import. The import of very large datasets like High-Content Screening data or SPIM data can be time and resource consuming both at the client and at the server level. This option allows the disabling of some non-critical steps and thus faster import of such datasets. The caveat associated with its usage is that some elements are no longer generated at import time. Some of these elements, like thumbnails, will be generated at runtime during client access. Available options that can be skipped are currently: all Skip all optional steps described below checksum Skip checksum calculation on image files before and after transfer This option effectively sets the :option:`--checksum_algorithm` to use a fast algorithm, ``File-Size-64``, that considers only file size, not the actual file contents. minmax Skip calculation of the minima and maxima pixel values This option will also skip the calculation of the pixels checksum. Recalculating minima and maxima pixel values post-import is currently not supported. See :ref:`minmax_limitation` for more information. thumbnails Skip generation of thumbnails Thumbnails will usually be generated when accessing the images post-import via the OMERO clients. upgrade Skip upgrade check for Bio-Formats Example of usage:: $ bin/omero import large_image --skip all $ bin/omero import large_image --skip minmax Multiple import steps can be skipped by supplying multiple arguments:: $ bin/omero import large_image --skip checksum --skip minmax .. option:: -T, --target TARGET Select an import target. See :doc:`import-target` for more information. .. option:: --debug DEBUG Set the debug level for the command line import output:: $ bin/omero import images_folder --debug WARN .. option:: --report Report emails to the OME team. This flag is mandatory for the :option:`--upload` and :option:`--logs` arguments. .. option:: --email EMAIL Set the contact email to use when reporting errors. This argument should be used in conjunction with the :option:`--report` and :option:`--upload` or :option:`--logs` arguments. .. option:: --upload Upload broken files and log file (if any) with report The following command would import a broken image and upload it together with the import log if available in case of failure:: $ bin/omero import broken_image --report --upload --email my.email@domain.com .. option:: --logs Upload log file (if any) with report The following command would import a broken image and upload only the import log if available in case of failure:: $ bin/omero import broken_image --report --logs --email my.email@domain.com Command Line Importer ^^^^^^^^^^^^^^^^^^^^^ The |CLI| import plugin calls the ``ome.formats.importer.cli.CommandLineImporter`` Java class. The Linux OMERO.importer also includes an :file:`importer-cli` shell script allowing calls to the importer directly from Java. Using :file:`importer-cli` might look like this:: ./importer-cli -s localhost -u user -w pass image.tif To use the ``ome.formats.importer.cli.CommandLineImporter`` class from java on the command line you will also need to include a classpath to the required support jars. Please inspect the ``importer-cli`` script for an example of how to do this. The Command Line Importer tool takes a number of mandatory and optional arguments to run. These options will also be displayed on the command line by passing no arguments to the importer: .. literalinclude:: /downloads/cli/help.out .. seealso:: :doc:`/sysadmins/import-scenarios`