ezomero

A module with convenience functions for writing Python code that interacts with OMERO.

Installation

Just pip install ezomero and you should be good to go! The repo contains the specific package versions we test ezomero with in setup.py, but any Python>=3.8 and latest omero-py and numpy should work - note that this package is in active development!

If you want to use get_table and post_table to/from Pandas dataframes, you need to install ezomero[tables] - that install an optional pandas dependency. Installing ezomero without this will default get_table and post_table to use lists of row lists as their default.

Usage

In general, you will need to create a BlitzGateway object using ezomero.connect(), then pass the conn object to most of these helper functions along with function-specific parameters.

Documentation

Documentation is available at https://thejacksonlaboratory.github.io/ezomero/

Issues

moving `fill_color`, `stroke_color` and `stroke_width` to be `Shape` attributes

opened on 2023-02-13 18:02:05 by erickmartins

Description

This work covers issue #65. We have moved those parameters to the Shape object instead of ROI, so that a single ROI with shapes of differing colors and widths can exist.

Checklist

Docstrings updated, passing test, flake8 and type hinting

For reviewers

• Check that the PR title is short, concise, and will make sense 1 year later.
• Check that new functions are imported in corresponding __init__.py.

[BUG] Documentation errors due to how sphinx wants to handle dataclasses

opened on 2023-02-03 17:17:05 by mellertd

Sphinx is "double documenting" attributes of certain classes using dataclasses.

This can be fixed by editing Sphinx's conf.py, specifically autodoc_default_options = {'exclude-members'} should include all double-counted attributes.

[FEATURE] Verbose option for ezomero.connect

opened on 2023-02-03 17:00:54 by mellertd

It would be useful to have a verbose option for connect that tells you (i.e. stdout) from where the login information is coming.

Maybe also print the values (besides password)

[FEATURE] Add DOI

opened on 2023-01-23 14:49:42 by erickmartins

ezomero should have a DOI!

[FEATURE] Implement `fill_color`, `stroke_color` and `stroke_width` as `Shape` parameters

opened on 2023-01-13 17:22:31 by erickmartins

Is your feature request related to a problem? Please describe. Right now, we only set these parameters at the ROI level, where they could potentially be different between Shapes.

Describe the solution you'd like Extra few parameters for every ezShape class.

[FEATURE] add cross-group functionality to `post_table`

opened on 2022-09-12 13:45:59 by erickmartins

Is your feature request related to a problem? Please describe. Right now (as of PR #58), post_table() cannot do cross-group posting - that is specifically because the OriginalFile created for the file annotation that contains the table seems to always be created on the original group for the conn object, ignoring the conn.SERVICE_OPTS.setOmeroGroup() from set_group() and leading to a group mismatch between FileAnnotation and OriginalFile.

Describe the solution you'd like Just make it work!

Describe alternatives you've considered One alternative is trying a different solution for switching groups such as conn.setGroupForSession() and see if it makes any difference.

Releases

1.2.1 - bugfix for import errors 2022-12-21 18:24:21

What's Changed

• quick fix for pandas types on function signatures by @erickmartins in https://github.com/TheJacksonLaboratory/ezomero/pull/61

Full Changelog: https://github.com/TheJacksonLaboratory/ezomero/compare/1.2.0...1.2.1

1.2.0 - added support to tables and type hints 2022-12-20 20:43:31

What's Changed

• Adding support to tables by @erickmartins in https://github.com/TheJacksonLaboratory/ezomero/pull/58
• Typed functions by @erickmartins in https://github.com/TheJacksonLaboratory/ezomero/pull/60

Full Changelog: https://github.com/TheJacksonLaboratory/ezomero/compare/1.1.1...1.2.0

ezomero 1.1.1 - fixes `ezimport` on Windows, adds tests to `ezimport` 2022-07-21 20:19:35

What's Changed

• fixing imports with weird chars in path by @erickmartins in https://github.com/TheJacksonLaboratory/ezomero/pull/56
• Adding tests to ezimport by @erickmartins in https://github.com/TheJacksonLaboratory/ezomero/pull/57

Full Changelog: https://github.com/TheJacksonLaboratory/ezomero/compare/1.1.0...1.1.1

ezomero 1.1.0 - extra ID functions, experimental import 2022-06-08 17:16:41

What's Changed

• Get id functions (get_project_ids, get_dataset_ids) by @erickmartins in https://github.com/TheJacksonLaboratory/ezomero/pull/51
• adding EXPERIMENTAL ezomero.ezimport by @erickmartins in https://github.com/TheJacksonLaboratory/ezomero/pull/52

Full Changelog: https://github.com/TheJacksonLaboratory/ezomero/compare/1.0.1...1.1.0

ezomero 1.0.1 - a few extra ROI types 2022-02-15 20:07:33

What's Changed

• Added new ROI types (Label, Polyline) and extended Line to allow start/end markers by @erickmartins in https://github.com/TheJacksonLaboratory/ezomero/pull/50

Full Changelog: https://github.com/TheJacksonLaboratory/ezomero/compare/1.0.0...1.0.1

ezomero 1.0.0 - the big one! 2022-01-21 15:34:46

New in this release:

API changes

• Introduces get_roi_ids, get_shape_ids and get_shape, plus relevant tests.
• Added get_pyramid_levels and the pyramid_level parameter to get_image, allowing an user to see which pyramid levels are available for an image and then request pixels at a specific level.
• Added the json_api submodule, with create_json_session and get_rendered_jpeg functions, and tests to go with them.
• Added the dim_order parameter to get_image and post_image.

Bug fixes and improvements

• Solves #38 by including parameters validation to functions in ezomero. Type errors, and value errors are raised accordingly.
• Added a LOT of tests and made some small changes in main repo to make sure tests are passing.
• post_dataset and post_image now honor the group from the conn argument when creating orphan datasets/images, rather than using whatever group is a user's default.