polygon support #253

will-moore · 2017-11-20T09:29:06Z

Supports adding of Polygons from OMERO to figure and editing them in Figure.

NB: creation of NEW polygons in figure is not supported in this PR.

To test:

Create and save Polygons AND Polylines in:
- iviewer
- Insight
- ImageJ.
Open image in Figure
Add ROIs -> Load from OMERO -> Pick Polygon / Polyline
Once added, can edit (drag shape or corner handles)
Test Copy and Paste of Polygons/Polylines, between panels AND within 1 panel
Save figure, reload etc - check Polygons/Polylines saved OK.
Export to TIFF and PDF *NB: Polyline not supported here yet

jburel · 2017-11-20T10:13:38Z

let's put that onhold, we will do without for training.
We need to discuss the future of our own drawing library
ROI handling in figure in general needs to be reviewed.

jburel · 2017-12-18T09:29:04Z

To add to the description:
polygon should be created from different source: minimally insight and imageJ
since I noticed some difference between applications see ome/openmicroscopy#5597

manics · 2017-12-18T10:55:59Z

Don't forget there's the really old format too: https://github.com/openmicroscopy/openmicroscopy/blob/v5.4.1/components/tools/OmeroPy/test/unit/test_rois.py#L32 which should be either tested or an appropriate error message shown.

will-moore · 2017-12-18T11:24:52Z

Thanks @manics - That should be handled by the webgateway marshalling: https://github.com/openmicroscopy/openmicroscopy/blob/develop/components/tools/OmeroWeb/omeroweb/webgateway/marshal.py#L357

jburel · 2018-01-11T16:33:01Z

The same should be done for Polyline

jburel · 2018-01-11T16:36:06Z

The changes in shape-editor must go to its repository https://github.com/ome/shape-editor
A new version will be released prior to adding the feature in figure

jburel · 2018-03-01T20:51:24Z

Gruntfile.js

+            expand: true,
+            cwd: 'node_modules/ome-shape-editor/dist/js',
+            src: 'shape-editor.js',
+            dest: 'omero_figure/static/figure/3rdparty/shape-editor-3.1.0'


The version of shape-editor should ideally be retrieved from package.json

Hmm - that might be kinda tricky.
This version number is also in index.html

<script src="{% static 'figure/3rdparty/shape-editor-3.1.0/shape-editor.js' %}"></script>

Having that version number in multiple places is not new, but now we don't have the shape-editor.js code itself.

will-moore · 2018-03-01T21:45:38Z

@jburel Any idea what's going on here? Even when I remove the small change I made to setup.py, travis is still failing here with

+ python setup.py sdist
running sdist
running grunt
running npm_install
npm install
unable to execute npm: No such file or directory
error: command 'npm' failed with exit status 1

pwalczysko · 2018-03-08T12:17:25Z

2 problems detected #253 (comment) and #253 (comment), otherwise works as expected

rgozim · 2018-03-08T14:26:18Z

Tested locally and working is working fine for editing an iviewer image with ROIs.

Small issue with copying an image with shapes that lie outside the image viewport, as @pwalczysko mentioned before me.

joshmoore · 2018-03-12T11:48:56Z

Raising the limit to 500 seems fairly arbitrary and likely to require your testers to increase the number of ROIs they have to add before they see a potential problem, no?

will-moore · 2018-03-14T06:54:58Z

Not entirely arbitrary, but this was a quick fix I needed for the iviewer demo movie and could certainly be improved.
500 is the default max limit of the JSON API allows, so setting it higher than that here would not allow you to load any more ROIs.
I could get the max limit from api and use that, so that if someone were to config a higher value then it would allow more to be loaded here too.
Unfortunately there is only 1 API_MAX_LIMIT setting which applies to all objects, so it's not possible to allow loading of 1000 ROIs while keeping the limit lower for e.g. Wells or Images (which tend to be more verbose).

joshmoore · 2018-03-14T07:56:30Z

was a quick fix I needed for the iviewer demo movie

understood.

500 is the default max limit of the JSON API allows, so setting it higher than that here would not allow you to load any more ROIs.

understood. Was having it at 200 causing issues because it was different from the API's 500 or is there another underlying issue? i.e. must the values be the same?

jburel · 2018-03-14T08:11:59Z

I reckon 200 was an arbitrary value set since figure did not use the json api to load roi.

will-moore · 2018-03-14T09:19:04Z

On the image I used in the movie, the ImageJ Analyse-Particles created over 200 polygons on the image, so that the Arrow I added in iviewer was not included in the first 200 shapes I loaded into figure (so it didn't show up in figure).
200 is the default API_LIMIT of the json api.

joshmoore · 2018-03-15T12:20:23Z

Sorry for derailing this PR. Assuming the summary is correct, happy for "figure should load more than 1 page of ROIs" to be captured somewhere.

will-moore · 2018-03-16T16:08:57Z

That should fix the 2 problems reported by @pwalczysko above.

jburel · 2018-03-21T09:20:31Z

omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py

+            h = sqrt(dx * dx + dy * dy)
+            # and the angle (avoid division by zero!)
+            if dy == 0:
+                dy = 0.000001


what is the rationale?

You can't divide by zero, but dividing by a number close to zero works very well and is the simplest workaround (the previous workaround was not working).

Isn't this the case we you want to use math.atan2 rather than math.atan?

Yep, that works. Thanks

pwalczysko · 2018-03-21T15:17:46Z

That should fix the 2 problems reported by @pwalczysko above.

Yes, both problems are fixed. Ready to merge FMPOV

jburel · 2018-03-27T16:51:36Z

Could you open a PR against shape-editor?
We first need to tag shape-editor before moving forward with this PR

snoopycrimecop · 2018-03-27T23:53:50Z

Conflicting PR. Removed from build FIGURE-merge#677. See the console output for more details.
Possible conflicts:

PR Big images #243 will-moore 'Big images'
- omero_figure/templates/figure/index.html

~~--conflicts~~ Conflict resolved in build FIGURE-merge#678. See the console output for more details.

will-moore · 2018-03-28T08:25:40Z

Doh - conflict was bound to happen sometime I guess with these two big PRs.
But shape-editor PR is open in the meantime...

jburel · 2018-03-29T17:58:23Z

No problem noticed with handling of polygons/polylines
next steps are:

clean up code in https://github.com/ome/shape-editor
tag and push a 3.1.1 version to npm using the openmicroscopy scope Add scope shape-editor#9
update the version of shape-editor used in this PR

will-moore · 2018-04-05T06:27:47Z

I have deprecated shape-editor from npm (couldn't unpublish).

$ npm deprecate -f 'ome-shape-editor@3.1.0' "To be replaced by openmicroscopy/shape-editor"

Can you now publish openmicroscopy/shape-editor so I can use that?

jburel · 2018-04-05T06:34:24Z

package has now been published under the organisation
https://www.npmjs.com/settings/openmicroscopy/packages

will-moore · 2018-04-05T06:45:52Z

Thanks. Hopefully with a final test to check this is working, we should be good to merge?

jburel · 2018-04-05T08:04:03Z

I would think so. Added chat to standup

jburel · 2018-04-05T09:59:54Z

Retested with the latest change on web-dev-merge
Still not great to have the version in 3 different places with it
Merging so we can move forward with the Big images review

Initial support for adding Polygon shape from OMERO

9bbe338

will-moore added 2 commits December 17, 2017 23:16

shape-editor.js supports Polygon editing (not creation)

f585ba9

Merge remote-tracking branch 'origin/master' into polygon_support

9b1e52b

will-moore added 2 commits December 18, 2017 12:37

Fix Polygon intersectRegion() to ignore zoom level

ea33268

Add Polygon support for PDF and TIFF export

14dce0d

jburel added this to the 3.2.0 milestone Jan 4, 2018

jburel removed this from the 3.2.0 milestone Jan 11, 2018

will-moore added 11 commits January 23, 2018 11:10

Started using new JSON /api/rois/

d083ed4

Improve parse(shape) to handle more attributes

ac326f5

Fix color handling in parse(shape)

067883a

Fix Crop dialog to use new JSON Shapes

92d9af0

Merge branch 'rois_from_new_api' into polygon_support

ad78204

Delete static shape-editor.js

64c48fb

Add ome-shape-editor to package.json dependencies

8713f74

Add Grunt task to copy shape-editor from node_modules to static

53bd3ee

Add shape-editor to .gitignore

f74c244

Add 'grunt build' task and updated README

b99e641

polyline-icon-16.png

f7d8863

jburel reviewed Mar 1, 2018

View reviewed changes

will-moore added 4 commits March 1, 2018 21:08

Merge remote-tracking branch 'origin/master' into polygon_support

c9210f5

Add polyline-icon to figure.css

2327a61

Roll back adding grunt copy:shapeEditor to setup.py

9b7b127

Add Polyline to supported shapes in roi_loader_view.js

7cb1b20

Raise limit on /api/rois/ to 500

a6c7d64

will-moore added 3 commits March 16, 2018 15:30

Fix polygon handling in PDF export

c4a38c9

Fix polygon handling in TIFF export

c53f7ff

Fix pasting of ROIs to panels in right panel

0396f2e

jburel reviewed Mar 21, 2018

View reviewed changes

Use atan2 to get_panel_coords() of shapes in export script

63bd676

will-moore mentioned this pull request Mar 27, 2018

Polygon support ome/shape-editor#8

Merged

will-moore mentioned this pull request Mar 28, 2018

Big images #243

Merged

10 tasks

Update to use @openmicroscopy/shape-editor 3.1.1

ae6429d

jburel merged commit 715aeb0 into ome:master Apr 5, 2018

jburel added this to the 4.0.0 milestone May 22, 2018

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polygon support #253

polygon support #253

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polygon support #253

polygon support #253

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