Create labels from map annotations

ome / omero-figure

An OMERO.web app for creating Figures from images in OMERO

http://figure.openmicroscopy.org

GNU Affero General Public License v3.0

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Create labels from map annotations #323

Closed will-moore closed 5 years ago

will-moore commented 5 years ago

See https://trello.com/c/TT47EiZH/185-labels-from-map-annotations

And requested again at the BioImage Analysis Satellite Symposium at Light Microscopy Australia 2019, Brisbane.

Demo at https://twitter.com/will_j_moore/status/1105389170065899522

To test:

Select some image panels in Figure that have some Map Annotations (Key-Value pairs)
In the "Add Labels" form, choose Key-Value Pairs in the drop-down menu
Dialog should load all map annotations on the images and allow you to choose the Key. Numbers for each should indicate how many of the selected images have that Key (see screenshot)
The Example Label at the bottom should give you an idea of what the label will look like Key: Value.
The Include Key in Label checkbox and choosing a new Key from the list should update the example label
Clicking OK should create labels on the selected images (If each image has that key).
NB: If an image has multiple Key: Value pairs for a chosen key, then multiple labels will be created for that image.

jburel commented 5 years ago

This feature was also mentioned during last week training in Singapore

pwalczysko commented 5 years ago

All works as described. Ready to merge FMPOV

joshmoore commented 5 years ago

Is there an idea of a target version for this?

jburel commented 5 years ago

We have not focussed much effort on figure recently. This feature could be included in a point release

evenhuis commented 5 years ago

Hi Will,

that looks awesome.

What would be great is to have the option to add the key as group-level label over the set of value labels.

Tools for adding group-level labels or arbitrary labels on figure would be great.

Maybe easy to understand in pictures:

Cheers,

Chris

Screen Shot 2019-03-15 at 12 46 10 pm

Screen Shot 2019-03-15 at 12 58 02 pm

will-moore commented 5 years ago

@evenhuis Thanks for the feedback. This is another use-case for "standalone labels" (labels not on panels) https://trello.com/c/wtu7IVuN/10-stand-alone-labels.

If you want to test this PR locally, you need to clone the repo, and put the omero-figure directory on your PYTHONPATH.

cd path/to/figure
git clone git@github.com:ome/omero-figure.git
export PYTHONPATH=/path/to/figure/omero-figure:$PYTHONPATH

You'll need to pip uninstall the figure you've already got there (if you haven't got figure on that server, you'll need to at least do the $ bin/omero config append omero.web.apps '"omero_figure"' step.

Then checkout my branch and you'll need npm install and grunt build as described at https://github.com/ome/omero-figure#development That should create the JavaScript files you need. Let us know if that works...

jburel commented 5 years ago

Thanks

will-moore commented 5 years ago

@evenhuis This just got released. Sorry it took so long. https://www.openmicroscopy.org/2019/10/28/figure-4-1-0.html

evenhuis commented 5 years ago

Hi Will,

Great work. It will be a greatly appreciated functionality.

Cheers,

Chris

On 28 Oct 2019, at 11:14 pm, Will Moore notifications@github.com wrote:

@evenhuis This just got released. Sorry it took so long. https://www.openmicroscopy.org/2019/10/28/figure-4-1-0.html

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