ome admin
OME commander, version 2.7.0
Usage:
ome admin <command> [<options>]
ome admin commands are:
users Commands for administering OME users
groups Commands for administering OME groups
configure Utility for modifying configuration variables
uninstall Command for removing your OME installation
help <command> Display help information about a specific command
Note that most of these commands will require you to log in as an
already-existing OME administrative user.
ome admin configure
OME commander, version 2.7.0
Usage:
ome admin configure [<options>]
This utility allows you to modify configuration variables that are critical to
your OME installation. Exercise care when using it. It is a good practise to note
the current configuration so you can revert to it if your changes have ill-effects.
N.B: This doesn't move the OME db, it just changes the pointer to it.
Options to configure the database connection:
-d, --database
Database name.
-u, --user
User name to connect as.
-h, --host
Host name of the database server.
-p, --port
port number to use for connection.
-c, --class
Delegate class to use for connection (default OME::Database::PostgresDelegate).
N.B: This command only modifies the URL to your OMEIS. The OMEIS at the new url
MUST contain exactly the same data as the OMEIS at the old URL. If you want to
move OMEIS to another server, you must compile + install the omeis executable
under Apache cgi-bin and copy the Files / Pixels directory structure manually.
Changing the LSID authority is an experimental feature. Attributes that were
issued with the previous LSID authority will not be updated when the LISD
authority is renamed.
Options to configure OME server URLS:
--omeis_url
FQDN of your OMEIS Authority
--lsid_url
FQDN of your LSID Authority
N.B: This does not move, create, or verify Web-UI's HTML templates. If the
templates structure is mutilated or doesn't exist in the directory pointed by
this configuration variable, the Web-UI will be severely broken.
Options to configure Web-UI's HTML templates:
--templates-path
Path to HTML templates used by Web-UI
N.B: You cannot use this tool to modify settings pursuant to your MATLAB
installation. For example, if you installed a new version of MATLAB you must
re-run the OME installer in order that the OME/MATLAB connector be properly compiled.
If the user specified here is not licensed to run MATLAB then the analysis
engine will be unable to execute OME MATLAB modules. The m-files-path is
recursively searched by the MATLAB connector to find .m files referenced in
the XML MATLAB analysis module definitions.
Options to configure MATLAB connection:
--matlab-user
System user that islicensed to run MATLAB.
--m-files-path
Path searched by MATLAB Handler for relevent .m interpreted scripts.
N.B: The analysis engine is used every time images are imported into OME.
Configuring the Analysis Engine for anything other than "Unthreaded" module
execution is experimental. Configure local worker processes only if OME
with distributed analysis engine is installed on your network. Read for more info:
http://cvs.openmicroscopy.org.uk/tiki/tiki-index.php?page=Distributed+Analysis+Engine
Options to configure Analysis Engine connection:
--max-local-workers
How many local worker processes should be allowed to execute on this machine
ome admin groups
OME commander, version 2.7.0
Usage:
ome admin groups <command> [<options>]
Available group-related commands are:
add Create a new OME group
edit Edit an existing OME group
list List existing OME group
ome admin groups add
OME commander, version 2.7.0
Usage:
ome admin groups add [<options>]
Creates a new OME group. You can specify the information about the
new user on the command line, or type it in at the prompts. There is
also a batch mode which allows you to type in several new groups with
a single execution of this command.
Options:
-b, --batch
Allows you to type in several group in one execution of this
command. If you specify this option, you cannot specify any
of other data options.
-n, --name <name>
Specify the name of the new group.
-l, --leader (<user ID> | <username>)
Specify the leader of the group as either an integer user ID,
or as a username.
-c, --contact (<user ID> | <username>)
Specify the contact of the group as either an integer user ID,
or as a username.
ome admin groups edit
OME commander, version 2.7.0
Usage:
ome admin groups edit [<options>]
Edits an existing OME group. You specify the group to edit with the
-i option. You must specify the modified values for the group on the
command line; no prompting is done. The edit is performed atomically;
if there is any database error or inconsistency in the data, none of
the other (possibly valid) changes are saved.
Options:
-g, --group (<group ID> | <group name>)
Specify the group to edit by its database ID or name. If the parameter
is an integer, it will be assumed to be a group ID.
Edit options:
-n, --name <name>
Change the group's name.
-l, --leader (<user ID> | <username>)
Change the group's leader. The leader is specified as either
an integer user ID, or as a username.
-c, --contact (<user ID> | <username>)
Change the group's contact. The contact is specified as
either an integer user ID, or as a username.
-a, --addUser (<user ID> | <username>)
Add the specified user to the group.
-d, --deleteUser (<user ID> | <username>)
Delete the specified user from the group.
ome admin groups list
OME commander, version 2.7.0
Usage:
ome admin groups list [<options>]
Lists all of the groups matching the specified criteria. For each one
that is found, displays the group ID and name, and names of the group
leader and contact person.
Filter options:
-u, --user (<user ID> | <username>)
Lists the groups that the given user belongs to.
-n, --name <name>
Lists the groups with a matching name. You can specify a
partial name; any groups containing the specified string will
be returned.
-l, --leader (<user ID> | <username>)
List the groups with the specified leader. The leader can be
specified either by an integer user ID, or a username.
-c, --contact (<user ID> | <username>)
List the groups with the specified contact. The contact can
be specified either by an integer user ID, or a username.
Output options:
-t, --tabbed
Causes the groups to be printed with no headers, in
tab-separated form, suitable for automatic parsing. The
output columns will be, in order:
ID, Name, Leader ID, Contact ID
ome admin uninstall
OME commander, version 2.7.0
Usage:
ome admin uninstall [<options>]
This will effortlessly remove the OME installation from your system. All data
will be destroyed.
Options:
-a This flag signals to remove everything.
ome admin users
OME commander, version 2.7.0
Usage:
ome admin users <command> [<options>]
Available user-related commands are:
add Create a new OME user
edit Edit an existing OME user
list List existing OME users
passwd Change an OME user's password
ome admin users add
OME commander, version 2.7.0
Usage:
ome admin users add [<options>]
Creates a new OME user. You can specify the information about the new
user on the command line, or type it in at the prompts.
You can also simultaneously create a new group and its leader/contact.
Options:
-u, --username <name>
Specify the username for the new user.
-f, --first-name <name>
Specify the first name for the new user.
-l, --last-name <name>
Specify the last name for the new user.
-e, --email <name>
Specify the email address for the new user.
-d, --directory <name>
Specify the data directory for the new user.
-p, --password <password>
Supplies the user's password on the command line rather than
prompting for it. This is pretty insecure, since the
command-line is publicly available to other processes, but we
still provide it for convenience.
-g, --group (<id> | <name>)
Specify the group for the new user. If the group doesn't exist, a new
one can be made with the specified user as its leader/contact.
ome admin users edit
OME commander, version 2.7.0
Usage:
ome admin users edit [<options>]
Edits an existing OME user.
If you don't want to use this utility in interactive mode, specify the user with the
-u flag and use the edit options.
The edit is performed atomically; if there is any database error or
inconsistency in the data, none of the other (possibly valid) changes are
saved.
Options:
-u, --user (<user ID> | <user name>)
Specify the user by their username or database ID.
-f, --first-name <name>
Change the user's first name.
-l, --last-name <name>
Change the user's last name.
-e, --email <email address>
Change the user's email address.
-d, --directory <path>
Change the user's data directory.
-g, --group (<id> | <name>)
Change the user's main group.
ome admin users list
OME commander, version 2.7.0
Usage:
ome admin users list [<options>]
Lists all of the users matching the specified criteria. Displays the
user ID, username, and full name for any that are found.
Filter options:
-g, --group (<id> | <name>)
Lists only those users who belong to the specified group.
-p, --primary-group (<id> | <name>)
Lists only those users who's primary group is the specified group.
-u, --username <name>
Lists the user which has the given username.
-f, --first-name <name>
Lists the users with a matching first name. You can specify a
partial name; any users containing the specified string will
be returned.
-l, --last-name <name>
Lists the users with a matching last name. You can specify a
partial name; any users containing the specified string will
be returned.
Output options:
-t, --tabbed
Causes the users to be printed with no headers, in tab-separated
form, suitable for automatic parsing. The output columns will
be, in order:
ID, Username, FirstName, LastName, Email
ome admin users passwd
OME commander, version 2.7.0
Usage:
ome admin users passwd [<options>]
Changes the password for an existing OME user. Prompts for the new
password if it is not specific on the command line via the --pasword
option. Note that you must specify exactly one of the -i or -u
options.
Note that you might first be prompted to log into OME as an
administrative user. This is *not* the user whose password you want
to change.
Options:
-u, --user (<username> | <ID>)
Specify the user by their username or database ID.
-p, --password <password>
Supplies the new password on the command line rather than
prompting for it. This is pretty insecure, since the
command-line is publicly available to other processes, but we
still provide it for convenience.
ome annotate
OME commander, version 2.7.0
Usage:
ome annotate <command> [<options>]
ome annotate commands are:
wizard Various wizards to help users define image annotations based
on their directory structure.
spreadsheet Command for doing bulk annotations based on Excel or tsv
spreadsheets (e.g. created by the OME annotation wizards)
help <command> Display help information about a specific command
ome annotate spreadsheet
OME commander, version 2.7.0
Usage:
ome annotate spreadsheet [<options>]
This command parses Excel or tsv spreadsheets (e.g. created by the OME
annotation wizards) to create bulk annotations.
Options:
-f, --file
The Excel or tsv spreadsheet that will be parsed to generate annotations.
-n, --noop
Do not create any annotations, just report what would be created.
ome annotate wizard
OME commander, version 2.7.0
Usage:
ome annotate wizard <command> [<options>]
These wizards programatically generate image annotations by interpreting
directory structure under the guidance of the user.
ome annotate wizard commands are:
PDI Wizard for organising images into a projects/datasets/images heirarchy
CGC Wizard for organising images into a category-group/category/images
heirarchy
SPW Wizard for organising images into a screens/plates/wells/images
heirarchy [NOT IMPLEMENTED]
help <command> Display help information about a specific command
ome annotate wizard CGC
OME commander, version 2.7.0
Usage:
ome annotate wizard CGC [<options>]
This command examines a directory structure to associate images with CategoryGroups and
and Categories. A tsv spreadsheet is written that can be parsed by OME using
e.g. the command-line tool "ome annotate spreadsheet".
All directories one level under the root directory become CategoryGroups. All
directories two levels under the root become Categories and their files the
images. N.B: The previous rules are superseded in so far as no empty Categories or
CategoryGroups will be created.
E.G:
Suppose the file structure is:
/
/TestImages/
/Worms/Day1/
/Worms/Day2/
/Worms/Day3/ImageA
/Worms/Day3/ImageB
/Worms/Day3/etc/
/Worms/Day3/etc/README
/Worms/Day4
If the root is pointed at / then the CategoryGroup-Category-Image heirarchy will be:
Worms
\_ Day 3
\_ ImageA
\_ ImageB
the same heirarchy will be constructed if the -s flag is used and the root is
pointed at /Worms
Options:
-f, --file
The name of the tsv spreadsheet that will be written.
-s, --short
This signifies that the root directory name is used to form the CategoryGroup.
-r, --root
Path to the root directory.
-x, --exclude
Ignore the specified root subdirectories.
ome annotate wizard PDI
OME commander, version 2.7.0
Usage:
ome annotate wizard PDI [<options>]
This command examines a directory structure to associate images with datasets and
and projects. A tsv spreadsheet is written that can be parsed by OME using
e.g. the command-line tool "ome annotate spreadsheet".
All directories one level under the root directory become projects. All
directories two levels under the root become datasets and their files the
images. N.B: The previous rules are superseded in so far as no empty projects or
datasets will be created.
E.G:
Suppose the file structure is:
/
/Proj1/
/Proj2/
/Proj2/Dataset1/
/Proj2/Dataset2/
/Proj2/Dataset2/ImageA
/Proj2/Dataset2/ImageB
/Proj2/Dataset2/etc/
/Proj2/Dataset2/etc/funny
/Proj3/Dataset3
If the root is pointed at / then the Project-Dataset-Image heirarchy will be:
Proj2
\_ Dataset 2
\_ ImageA
\_ ImageB
if the command is called with the -s parameter and the root is pointed at /Proj2
then the Dataset-Image heirarchy will be:
Dataset 2
\_ ImageA
\_ ImageB
Options:
-f, --file
The name of the tsv spreadsheet that will be written.
-s, --short
This signifies that the root points to the Dataset-Image heirarchy.
-r, --root
Path to the root directory.
-x, --exclude
Ignore the specified root subdirectories.
ome data
OME commander, version 2.7.0
Usage:
ome data [command] [options]
Available OME database related commands are:
backup Backup OME data to an (optionally) compressed tar archive.
restore Restore OME data from an (optionally) compressed tar archive.
export Export objects as XML files.
delete Delete objects in the OME DB.
chown Change ownership of objects and MEXes in the DB.
ome data backup
OME commander, version 2.7.0
Usage:
ome data backup [<options>]
Backs up OMEIS's image repository and OME's postgress db to a tar archive of
the specified name. If compression is prescribed, the archive will have a
.gz or .bz2 suffix.
The default naming convention is
ome_backup_YYYY-MM-DD.tar*
where YYYY-MM-DD is the date, in ISO-8601, when the backup was performed.
Options:
-a, --archive
Specify path to archive that will be created.
-c, --compression
Specify compression algorithm that will be applied to archive.
"none" [default], "gzip", "bzip2"
-q, --quick
If set, only OME's postgress db (and not OMEIS) is backed up.
-f, --force
If set, there will be no further user confirmations.
ome data chown
OME commander, version 2.7.0
Usage:
ome data chown [<options>] [<project <ID|name>> | <dataset <ID|name>> | <image <ID|name>> | MEXes]...
Change user and group ownership.
Options:
-g, --group (<group ID> | <group name>)
Specify group to change ownership to.
Use #undefined# (with the #'s) to set it to NULL (make it public).
-u, --user (<user ID> | <username>)
Specify user to change ownership to
-p, --project
Parameters are project IDs or names
-d, --dataset
Parameters are dataset IDs or names
-i, --image
Parameters are dataset IDs or names
-m, --MEX
Parameters are Module Execution IDs (MEXes)
ome data delete
OME commander, version 2.7.0
Usage:
ome data delete [command] [options]
Available OME database deletion related commands are:
CHEX Delete a Chain Execution and all of its dependencies.
MEX Delete a Module Execution and all of its dependencies.
Image Delete an Image and all of its dependencies.
Dataset Delete a dataset and all of its dependencies, optionally deleting Images.
ST Delete a Semantic Type and all of its descendents.
ome data delete CHEX
OME commander, version 2.7.0
Usage:
ome data delete CHEX [<options>] [CHEX_ID]+
Delete one or more CHEXes and all of their descendents. This can potentially delete a lot.
Images, Datasets, the whole lot potentially. By default, this doesn't delete constituent MEXs
just the NEXs. It is suggested to try -n first to see what will happen.
And once its gone, its gone. You can only get it back from a backup.
You do have a backup, right?
Options:
-o, --orph Keep orphaned Original Files even if they are not used by any other MEX
-n, --noop Do not delete anything, just report what would be deleted.
-d, --delete Actually delete the CHEX(es). Nothing will happen unless -n or -d is specified.
-c, --chain Delete all CHEXes for the specified chain (ID if numeric, otherwise by name).
-m, --mexs Delete CHEXes' constituant MEXs too.
-f, --keep-files Keep orphaned OMEIS Files.
-p, --keep-pixels Keep orphaned OMEIS Pixels.
-g, --graph Generate a graph of the dependencies using GraphViz, and save in specified file.
ome data delete Dataset
OME commander, version 2.7.0
Usage:
ome data delete Dataset [<options>] [Dataset ID | Name]+
Delete one or more Datasets and all of their descendents. This can potentially delete a lot.
Images, Datasets, the whole lot potentially.
It is suggested to try -n first to see what will happen.
And once its gone, its gone. You can only get it back from a backup.
You do have a backup, right?
Options:
-i, --images Delete all images (and their dependencies) in each dataset.
-o, --orph Keep orphaned Original Files even if they are not used by any other MEX
-n, --noop Do not delete anything, just report what would be deleted.
-d, --delete Actually delete the Datasets. Nothing will happen unless -n or -d is specified.
-f, --keep-files Keep orphaned OMEIS Files.
-p, --keep-pixels Keep orphaned OMEIS Pixels.
-g, --graph Generate a graph of the dependencies using GraphViz, and save in specified file.
ome data delete Image
OME commander, version 2.7.0
Usage:
ome data delete Image [<options>] [Image ID | Name]+
Delete one or more Images and all of their descendents. This can potentially delete a lot.
Images, Datasets, the whole lot potentially.
It is suggested to try -n first to see what will happen.
And once its gone, its gone. You can only get it back from a backup.
You do have a backup, right?
Options:
-o, --orph Keep orphaned Original Files even if they are not used by any other MEX
-n, --noop Do not delete anything, just report what would be deleted.
-d, --delete Actually delete the Images. Nothing will happen unless -n or -d is specified.
-f, --keep-files Keep orphaned OMEIS Files.
-p, --keep-pixels Keep orphaned OMEIS Pixels.
-g, --graph Generate a graph of the dependencies using GraphViz, and save in specified file.
ome data delete MEX
OME commander, version 2.7.0
Usage:
ome data delete MEX [<options>] [MEX_ID]+
Delete one or more MEXes and all of their descendents. This can potentially delete a lot.
Images, Datasets, the whole lot potentially.
It is suggested to try -n first to see what will happen.
And once its gone, its gone. You can only get it back from a backup.
You do have a backup, right?
Options:
-o, --orph Keep orphaned Original Files even if they are not used by any other MEX
-n, --noop Do not delete anything, just report what would be deleted.
-d, --delete Actually delete the MEX(es). Nothing will happen unless -n or -d is specified.
-m, --module Delete all MEXes for the specified module (ID if numeric, otherwise by name).
-f, --keep-files Keep orphaned OMEIS Files.
-p, --keep-pixels Keep orphaned OMEIS Pixels.
-g, --graph Generate a graph of the dependencies using GraphViz, and save in specified file.
ome data delete ST
OME commander, version 2.7.0
Usage:
ome data delete ST [<options>] [ST]+
Delete an ST definition.
This utility can only deal with a small subset of ST deletions. It can only
delete STs that are not referenced by other STs or Module Formal Inputs/Outputs
(therefore there can be no attributes in the DB).
Options:
-n, --noop Do not delete anything, just report what would be deleted.
-d, --delete Actually delete the STs(es). Nothing will happen unless -n or -d is specified.
ome data export
OME commander, version 2.7.0
Available commands:
chains
ome data export chains
OME commander, version 2.7.0
Usage:
ome data export chains [<options>] [<list of chains>]
This utility exports analysis chains into OME XML files.
Analysis chains can be specified by ID or by name
Options:
-f Specify a filename for the OME XML file. Otherwise all output goes
to STDOUT
--no_compress Do not compress the output file. (disabled by default)
ome data restore
OME commander, version 2.7.0
Usage:
ome data restore [<options>] archive-name
Restores OMEIS's image repository and OME's postgress db from a .tar archive of
specified name. This utility, as applicable, decompresses the archive.
By default, it looks in the current directory for an ome_backup file of this form:
ome_backup_YYYY-MM-DD.tar*
The ome_backup file with the latest YYYY-MM-DD is selected.
Options:
-a, --archive
Specify path to existing archive.
-q, --quick
If set, only OME's postgress db (and not OMEIS) is extracted from archive.
-f, --force
If set, there will be no further user confirmations.
ome dev
OME commander, version 2.7.0
Usage:
ome dev <command> [<options>]
ome commands are:
chex_stats Command for getting information about a Chain Execution
finish_execute Command for clearing up a Chain Execution with errors.
classifier Commands that facilitate the computation of Image Signatures
lint Command for checking/correcting syntax of OME XML files
templates Command for displaying progress info about OME tasks
help <command> Display help information about a specific command
ome dev chex_stats
OME commander, version 2.7.0
Usage:
ome dev chex_stats [<options>]
This command displays statistics about a chain execution.
Options:
-c | --chex <id>
ID of Analysis chain executions
-v | --verbose
print more information
ome dev classifier
OME commander, version 2.7.0
Available commands:
compile_chain
compile_sigs
import_test_train_dataset
make_predictions
stitch_prediction_chain
stitch_training_chain
ome dev classifier compile_sigs
OME commander, version 2.7.0
Usage:
ome dev classifier compile_sigs [<options>]
This will compile a signature matrix for a matlab Trainer. It needs a
complete signature chain (e.g. a chain generated by 'stitch_chain'), and
a dataset that has exactly one classification per image. It will execute
the signature chain if necessary. There will be one row per image in the
matrix. Each column represents another image. Each row represents one
signature, and the last row is the image class. If the image has no
classification, the class will be 0.
Img 1 Img 2 ...
Sig 1 [ x, x, ... ]
Sig 2 [ x, x, ... ]
... [ ..., ..., ... ]
Sig n [ x, x, ... ]
Class [ x, x, ... ]
The original signature chain must already be imported into the database.
Options:
-a Signature analysis chain name or ID.
-d Dataset name or ID.
-e Analysis Chain Execution ID. This Optional parameter takes precedence over
the -a and -d flags. If you specify this then you don't need to specify
-a and -d. This is especially useful if the analysis chain was executed
multiple times against the dataset.
-o Output filename.
-f, --force
Force re-execution of chain (i.e. do not reuse previous module execution
results).
ome dev classifier import_test_train_dataset
OME commander, version 2.7.0
Usage:
ome dev classifier import_test_train_dataset [<options>]
Given a set of images, this function randomly chooses to import half of
the images into the specified datset.
-d Name of Dateset to import images into
--test or --train (one of these options need to be specified)
ome dev classifier make_predictions
OME commander, version 2.7.0
Usage:
ome dev classifier make_predictions [<options>]
-x Classifier Training Chain Execution ID
-a ID/name of the Image Prediction Chain corresponding to the Classifier
Training Chain with CHEX -x
-d ID/name of Dataset containing images that are going to be classified
ome dev classifier stitch_chain
OME commander, version 2.7.0
Usage:
ome dev classifier stitch_chain [<options>]
This will create a custom Signature Stitcher module for a signature
chain. Additionally, it will copy the chain and attach the stitcher
module to the copy. The newly created module and chain will be imported
to the database and saved to disk.
The original signature chain must already be imported into the database.
Options:
-a the id or name of the signature chain to stitch
-x path of xml source directory
-o output directory
-compress Compress the output file.
ome dev classifier stitch_prediction_chain
ome dev classifier stitch_training_chain
OME commander, version 2.7.0
Usage:
ome dev classifier stitch_training_chain [<options>]
This will create a custom Signature Stitcher module for a signature
chain. Additionally, it will copy the chain and attach the stitcher
module to the copy. The newly created module and chain will be imported
to the database and saved to disk.
The original signature chain must already be imported into the database.
Options:
-a the id or name of the signature chain to stitch
-x path of xml source directory
-o output directory
-compress Compress the output file.
ome dev finish_execute
OME commander, version 2.7.0
Usage:
ome dev finish_execute [<options>] [<flags>]
This command attempts to finish an analysis chain execution that was initiated
before, continued till completetion, but left some MEX's with ERROR or UNREADY
status. This commend re-executes these MEXs.
Options:
-x, --chex (<id>)
Analysis Chain Execution ID
ome dev lint
OME commander, version 2.7.0
Available commands:
uc
untangle_chains
ome dev lint uc
OME commander, version 2.7.0
Usage:
ome dev lint uc [<options>]
This utility will parse an OME file containing chains, check for
multiple nodes feeding a single input, correct those if found, and save
the untangled chains back to file.
Options:
-f Specify filename for the input file.
-o Specify a filename for the OME XML file. Otherwise all output goes
to STDOUT
-v Verbose. Print out a topologically sorted view of the chain nodes.
-c Compress the output file.
ome dev lint untangle_chains
OME commander, version 2.7.0
Usage:
ome dev lint untangle_chains [<options>]
This utility will parse an OME file containing chains, check for
multiple nodes feeding a single input, correct those if found, and save
the untangled chains back to file.
Options:
-f Specify filename for the input file.
-o Specify a filename for the OME XML file. Otherwise all output goes
to STDOUT
-v Verbose. Print out a topologically sorted view of the chain nodes.
-c Compress the output file.
ome dev templates
OME commander, version 2.7.0
Available commands:
update
ome dev templates update
OME commander, version 2.7.0
Usage:
ome dev templates update [<options>]
This utility will scan the html template directory and register each
template file in the database by creating template attributes. Files
already registered will be ignored.
Options:
-u all Update all template directories.
-u Display/One Update the Display/One directory
-u Display/Many Update the Display/Many directory
-u Actions/Annotator Update the Actions/Annotator directory
-u Browse Update the Browse directory
ome execute
OME commander, version 2.7.0
Usage:
ome execute [<options>] [<flags>]
This command uses the Analysis Engine to execute the analysis chain against
a dataset.
Options:
-a, --analysis-chain (<name> | <id>)
Analysis chain
-d, --dataset (<name> | <id>)
Dataset name
-s, --skip_optional_inputs
-i, --inputs
specify User inputs by id and source MEX(s)
ex. -i 551:17,21-552:114
means supply formal input 551 with source MEXs 17 & 21
supply formal input 552 wiht source MEX 114
-f, --force
Force re-execution of chain (i.e. do not reuse previous module execution
results).
-c, --caching
Enable DBObject caching.
ome import
OME commander, version 2.7.0
Usage:
ome import [<options>] [<list of files>]
This utility imports files into OME database and runs the import analysis
chain against them.
The files can be proprietary format image files or OME XML files that define
OME objects.
Options:
-d, --dataset (<id> | <name>)
Specify which dataset images should be imported into. If you don't
own an unlocked dataset with the specified name, a new one will be
created for you. If you are importing OME Semantic Type Definitions,
Analysis Modules, or Chains this parameter is unnecessary. If you
import images, but don't specify a dataset, a new dataset called
'<time_stamp> Import Dataset' will be created for you.
-D, --description
Use this flag if you want to give a description to your new dataset.
-i, --format
Suggests the image formats. The Import Engine first checks if the images
are of the specified format, if not it reverts to default behaviour and
tries to discover the image formats. This speeds up import times for
common images such as TIFFs.
Permitted Values:
OME::ImportEngine::OMETIFFreader
OME::ImportEngine::MetamorphHTDFormat
OME::ImportEngine::DVreader
OME::ImportEngine::STKreader
OME::ImportEngine::BioradReader
OME::ImportEngine::LSMreader
OME::ImportEngine::TIFFreader
OME::ImportEngine::BMPreader
OME::ImportEngine::DICOMreader
OME::ImportEngine::XMLreader
OME::ImportEngine::BioFormats
-r, --reimport
Reimports images which are already in the database. This should
only be used for testing purposes. This flag is ignored for OME
XML files.
ome top
OME commander, version 2.7.0
Usage:
ome top
This utility prints out detailed information about OME Tasks that are executing
or finished execution.
Options:
-w , --wait optional flag specifying how many seconds to wait before updating
