Metadata-Version: 2.1
Name: omero-metadata
Version: 0.10.0
Summary: Metadata plugin for use in the OMERO CLI.
Home-page: https://github.com/ome/omero-metadata/
Author: The Open Microscopy Team
Author-email: ome-devel@lists.openmicroscopy.org.uk
License: GPL-2.0+
Download-URL: https://github.com/ome/omero-metadata//v0.10.0.tar.gz
Keywords: OMERO.CLI,plugin
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Plugins
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: End Users/Desktop
Classifier: License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=3
License-File: LICENSE.txt

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    :target: https://github.com/ome/omero-metadata/actions

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OMERO metadata plugin
=====================

Plugin for use in the OMERO CLI. Provides tools for bulk
management of annotations on objects in OMERO.

Requirements
============

* OMERO 5.6.0 or newer
* Python 3.6 or newer


Installing from PyPI
====================

This section assumes that an OMERO.py is already installed.

Install the command-line tool using `pip <https://pip.pypa.io/en/stable/>`_:

::

    $ pip install -U omero-metadata

Note the original version of this code is still available as deprecated code in
version 5.4.x of OMERO.py. When using the CLI metadata plugin, the
`OMERO_DEV_PLUGINS` environment variable should not be set to prevent
conflicts when importing the Python module.

Usage
=====

The plugin is called from the command-line using the `omero` command::

    $ omero metadata <subcommand>

Help for each command can be shown using the ``-h`` flag.
Objects can be specified as arguments in the format ``Class:ID``, such
as ``Project:123``.

Bulk-annotations are HDF-based tables with the NSBULKANNOTATION
namespace, sometimes referred to as OMERO.tables.

Available subcommands are:

- ``allanns``: Provide a list of all annotations linked to the given object
- ``bulkanns``: Provide a list of the NSBULKANNOTATION tables linked to the given object
- ``mapanns``: Provide a list of all MapAnnotations linked to the given object
- ``measures``: Provide a list of the NSMEASUREMENT tables linked to the given object
- ``original``: Print the original metadata in ini format
- ``pixelsize``: Set physical pixel size
- ``populate``: Add metadata (bulk-annotations) to an object (see below)
- ``rois``: Manage ROIs
- ``summary``: Provide a general summary of available metadata
- ``testtables``: Tests whether tables can be created and initialized

populate
--------

This command creates an ``OMERO.table`` (bulk annotation) from a ``CSV`` file and links 
the table as a ``File Annotation`` to a parent container such as Screen, Plate, Project
Dataset or Image. It also attempts to convert Image, Well or ROI names from the ``CSV`` into
object IDs in the ``OMERO.table``.

The ``CSV`` file must be provided as local file with ``--file path/to/file.csv``.

If you wish to ensure that ``number`` columns are created for numerical data, this will
allow you to make numerical queries on the table.
Column Types are:

- ``d``: ``DoubleColumn``, for floating point numbers
- ``l``: ``LongColumn``, for integer numbers
- ``s``: ``StringColumn``, for text
- ``b``: ``BoolColumn``, for true/false
- ``plate``, ``well``, ``image``, ``dataset``, ``roi`` to specify objects

These can be specified in the first row of a ``CSV`` with a ``# header`` tag (see examples below).
The ``# header`` row is optional. Default column type is ``String``.

NB: Column names should not contain spaces if you want to be able to query
by these columns.

**Project / Dataset**

To add a table to a Project, the ``CSV`` file needs to specify ``Dataset Name``
and ``Image Name`` or ``Image ID``::

    $ omero metadata populate Project:1 --file path/to/project.csv

project.csv::

    # header s,s,d,l,s
    Image Name,Dataset Name,ROI_Area,Channel_Index,Channel_Name
    img-01.png,dataset01,0.0469,1,DAPI
    img-02.png,dataset01,0.142,2,GFP
    img-03.png,dataset01,0.093,3,TRITC
    img-04.png,dataset01,0.429,4,Cy5

This will create an OMERO.table linked to the Project like this with
a new ``Image`` column with IDs:

========== ============ ======== ============= ============ =====
Image Name Dataset Name ROI_Area Channel_Index Channel_Name Image
========== ============ ======== ============= ============ =====
img-01.png dataset01    0.0469   1             DAPI         36638
img-02.png dataset01    0.142    2             GFP          36639
img-03.png dataset01    0.093    3             TRITC        36640
img-04.png dataset01    0.429    4             Cy5          36641
========== ============ ======== ============= ============ =====

If the target is a Dataset instead of a Project, the ``Dataset Name`` column is not needed.


**Screen / Plate**

To add a table to a Screen, the ``CSV`` file needs to specify ``Plate`` name and ``Well``.
If a ``# header`` is specified, column types must be ``well`` and ``plate``.

screen.csv::

    # header well,plate,s,d,l,d
    Well,Plate,Drug,Concentration,Cell_Count,Percent_Mitotic
    A1,plate01,DMSO,10.1,10,25.4
    A2,plate01,DMSO,0.1,1000,2.54
    A3,plate01,DMSO,5.5,550,4
    B1,plate01,DrugX,12.3,50,44.43

This will create an OMERO.table linked to the Screen, with the
``Well Name`` and ``Plate Name`` columns added and the ``Well`` and
``Plate`` columns used for IDs:

===== ====== ====== ============== =========== ================ =========== ===========
Well  Plate  Drug   Concentration  Cell_Count  Percent_Mitotic  Well Name   Plate Name
===== ====== ====== ============== =========== ================ =========== ===========
9154  3855   DMSO   10.1           10          25.4             a1          plate01
9155  3855   DMSO   0.1            1000        2.54             a2          plate01
9156  3855   DMSO   5.5            550         4.0              a3          plate01
9157  3855   DrugX  12.3           50          44.43            b1          plate01
===== ====== ====== ============== =========== ================ =========== ===========

If the target is a Plate instead of a Screen, the ``Plate`` column is not needed.

**ROIs**

If the target is an Image or a Dataset, a ``CSV`` with ROI-level or Shape-level data can be used to create an
``OMERO.table`` (bulk annotation) as a ``File Annotation`` linked to the target object.
If there is an ``roi`` column (header type ``roi``) containing ROI IDs, an ``Roi Name``
column will be appended automatically (see example below). If a column of Shape IDs named ``shape``
of type ``l`` is included, the Shape IDs will be validated (and set to -1 if invalid).
Also if an ``image`` column of Image IDs is included, an ``Image Name`` column will be added.
NB: Columns of type ``shape`` aren't yet supported on the OMERO.server.

Alternatively, if the target is an Image, the ROI input column can be
``Roi Name`` (with type ``s``), and an ``roi`` type column will be appended containing ROI IDs.
In this case, it is required that ROIs on the Image in OMERO have the ``Name`` attribute set.

image.csv::

    # header roi,l,l,d,l
    Roi,shape,object,probability,area
    501,1066,1,0.8,250
    502,1067,2,0.9,500
    503,1068,3,0.2,25
    503,1069,4,0.8,400
    503,1070,5,0.5,200

This will create an OMERO.table linked to the Image like this:

=== ===== ====== =========== ==== ========
Roi shape object probability area Roi Name
=== ===== ====== =========== ==== ========
501 1066  1      0.8         250  Sample1
502 1067  2      0.9         500  Sample2
503 1068  3      0.2         25   Sample3
503 1069  4      0.8         400  Sample3
503 1070  5      0.5         200  Sample3
=== ===== ====== =========== ==== ========

Note that the ROI-level data from an ``OMERO.table`` is not visible
in the OMERO.web UI right-hand panel under the ``Tables`` tab,
but the table can be visualized by clicking the "eye" on the bulk annotation attachment on the Image.

Developer install
=================

This plugin can be installed from the source code with::

    $ cd omero-metadata
    $ pip install .


License
-------

This project, similar to many Open Microscopy Environment (OME) projects, is
licensed under the terms of the GNU General Public License (GPL) v2 or later.

Copyright
---------

2018-2021, The Open Microscopy Environment


