Fill rois #577

Rdornier · 2024-07-09T15:05:41Z

Hello,

This PR should fiy the issue #485 about ROI filling.
If you load ROIs from OMERO, the fill-color is read correctly but not the transparency. I wasn't able to get it from the imported json object. So, the current transparency is set to the loaded ROI.

Rémy.

will-moore · 2024-07-10T21:48:00Z

You shouldn't commit any files under omero_figure/static/figure/... - They should be ignored by .gitignore.

The following change should give you FillOpacity (and StrokeOpacity) from Shapes loaded from OMERO:

diff --git a/src/js/models/roi_model.js b/src/js/models/roi_model.js
index eb8411b4..f8fe3b54 100644
--- a/src/js/models/roi_model.js
+++ b/src/js/models/roi_model.js
@@ -14,6 +14,12 @@ var ShapeModel = Backbone.Model.extend({
             intAsHex = ("00000000" + intAsHex).slice(-8);
             return '#' + intAsHex.substring(0,6);
         }
+        var rgbint_to_opacity = function(signed_integer) {
+            if (signed_integer < 0) signed_integer = signed_integer >>> 0;
+            var intAsHex = signed_integer.toString(16);
+            intAsHex = ("00000000" + intAsHex).slice(-2);
+            return parseInt(intAsHex, 16) / 255;
+        }
         shape.id = shape['@id'];
         shape.type = shape['@type'].split('#')[1];
         delete shape['@id']
@@ -27,6 +33,9 @@ var ShapeModel = Backbone.Model.extend({
         _.each(["StrokeColor", "FillColor", ], function(attr) {
             if (shape[attr] !== undefined) {
                 shape[lowerFirst(attr)] = rgbint_to_css(shape[attr]);
+                // strokeColor -> strokeOpacity, fillColor -> fillOpacity
+                let opacityAttr = lowerFirst(attr).replace("Color", "Opacity")
+                shape[opacityAttr] = rgbint_to_opacity(shape[attr]);
                 delete shape[attr];
             }
         });

However, the opacity needs formatting to e.g. 2 decimal places to avoid this layout issue:

Even without that, it would be nice to avoid the Load ROIs button wrapping:

(e.g. move it to the top of the right column)

will-moore · 2024-07-10T21:58:35Z

NB: I'm away for holidays after tomorrow so it may be a while before I can look at this again...

snoopycrimecop · 2024-07-11T00:47:25Z

Conflicting PR. Removed from build OMERO-plugins-push#118. See the console output for more details.
Possible conflicts:

PR Inset feature #549 will-moore 'Inset feature'
- src/js/shape_editor/rect.js

--conflicts

will-moore · 2024-07-11T07:45:25Z

I've removed the include label to avoid the "Conflicting PR" messages every day. #549 isn't quite ready to merge just yet so I'm afraid we'll have to wait a bit.

Rdornier · 2024-07-12T09:12:49Z

Hi @will-moore

Thanks for the feedback and the suggestion

You shouldn't commit any files under omero_figure/static/figure/... - They should be ignored by .gitignore.

It has been included in the gitignore

I added the rounding with 2 decimales

NB: I'm away for holidays after tomorrow so it may be a while before I can look at this again...

No worries, enjoy your holidays !

I've removed the include label to avoid the "Conflicting PR" messages every day.

OK

Rémy

will-moore · 2024-08-26T14:41:31Z

@Rdornier This is looking pretty good now. I haven't tested the PDF/Tiff export yet. I seem to remember there were some issues there, which is why I removed the fillOpacity code from the ShapeEditor code when I ported it over. I'll give that a go anyway...
I had a go at fixing the toolbar wrapping above. See last commit at https://github.com/will-moore/figure/commits/fill-rois/ which gives the toolbar the whole top row of the dialog.

Rdornier · 2024-08-27T12:19:23Z

Hi @will-moore

I haven't tested the PDF/Tiff export yet. I seem to remember there were some issues there

True, I have to check as well
I tried to build the app, as described in the readme but it gives me this output

$ npm run build

 >[email protected] build
 >vite build --emptyOutDir && ./deploy_build.sh

vite v3.2.10 building for production...
transforming...
✓ 139 modules transformed.
rendering chunks...
../omero_figure/static/omero_figure/assets/luts_10.863786e7.png   18.12 KiB
../omero_figure/static/omero_figure/index.html                    63.62 KiB
../omero_figure/static/omero_figure/assets/index.3fe885b4.css     251.65 KiB / gzip: 42.17 KiB
../omero_figure/static/omero_figure/assets/index.05660f14.js      659.28 KiB / gzip: 206.62 KiB
../omero_figure/static/omero_figure/assets/index.05660f14.js.map  2277.14 KiB
'.' is not recognized as an internal or external command,
operable program or batch file.

I don't know if this is expected, probably not. But then, how can I use this output to test the save/export ?

I had a go at fixing the toolbar wrapping above. See last commit at https://github.com/will-moore/figure/commits/fill-rois/ which gives the toolbar the whole top row of the dialog.

Ok

Rdornier · 2024-08-27T15:32:54Z

I've updated the Figure_to_pdf script acording to what I understood from the code and from what was missing to fit with the new feature.
I didn't manage yet to make and use the figure build, so, I didn't test if the changes worked or not.

will-moore · 2024-08-27T15:44:48Z

This is what I see:

$ npm run build

> [email protected] build
> vite build --emptyOutDir && ./deploy_build.sh

vite v3.2.10 building for production...
✓ 139 modules transformed.
../omero_figure/static/omero_figure/assets/luts_10.863786e7.png   18.12 KiB
../omero_figure/static/omero_figure/index.html                    61.77 KiB
../omero_figure/static/omero_figure/assets/index.676c7de2.css     251.38 KiB / gzip: 42.09 KiB
../omero_figure/static/omero_figure/assets/index.c141c1a9.js      656.93 KiB / gzip: 206.49 KiB
../omero_figure/static/omero_figure/assets/index.c141c1a9.js.map  2418.04 KiB

(!) Some chunks are larger than 500 KiB after minification. Consider:
- Using dynamic import() to code-split the application
- Use build.rollupOptions.output.manualChunks to improve chunking: https://rollupjs.org/guide/en/#outputmanualchunks
- Adjust chunk size limit for this warning via build.chunkSizeWarningLimit.
Deploying built resources to plugin directory...

It looks like the JS build worked OK. I guess you see the various assets under ../omero_figure/static/omero_figure/assets/ ?
Can you just try running the ./deploy_build.sh script manually to copy those assets into the correct place?

$ ./deploy_build.sh
Deploying built resources to plugin directory...

Rdornier · 2024-08-28T08:13:44Z

I guess you see the various assets under ../omero_figure/static/omero_figure/assets/ ?

Yes, I do.

Can you just try running the ./deploy_build.sh script manually to copy those assets into the correct place?

It works, thanks. Now, I'm able to fully build and test

will-moore · 2024-08-29T10:31:58Z

omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py

@@ -771,7 +777,9 @@ def draw_ellipse(self, shape):
        # Draw outer ellipse, then remove inner ellipse with full opacity
        rgba = ShapeToPdfExport.get_rgba_int(shape['strokeColor'])
        ellipse_draw.ellipse((0, 0, width, height), fill=rgba)
-        rgba = self.get_rgba_int(shape.get('fillColor', '#00000000'))
+        r,g,b,a = self.get_rgba_int(shape.get('fillColor', '#00000000'))


This line (and others above) are causing flake8 build failures:

flake8.main.application MainProcess 652 INFO Found a total of 99 violations and reported 9 ./omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py:651:10: E231 missing whitespace after ',' ./omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py:651:12: E231 missing whitespace after ',' ./omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py:651:14: E231 missing whitespace after ',' ./omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py:709:10: E231 missing whitespace after ',' ./omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py:709:12: E231 missing whitespace after ',' ./omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py:709:14: E231 missing whitespace after ',' ./omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py:780:10: E231 missing whitespace after ',' ./omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py:780:12: E231 missing whitespace after ',' ./omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py:780:14: E231 missing whitespace after ','

snoopycrimecop · 2024-09-23T01:07:52Z

Conflicting PR. Removed from build OMERO-plugins-push#192. See the console output for more details.
Possible conflicts:

PR Points in shape editor #555 will-moore 'Points in shape editor'
- omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py

--conflicts

snoopycrimecop · 2024-09-24T01:07:38Z

Conflicting PR. Removed from build OMERO-plugins-push#193. See the console output for more details.
Possible conflicts:

PR Points in shape editor #555 will-moore 'Points in shape editor'
- omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py

--conflicts

snoopycrimecop · 2024-09-25T00:42:48Z

Conflicting PR. Removed from build OMERO-plugins-push#194. See the console output for more details.
Possible conflicts:

PR Points in shape editor #555 will-moore 'Points in shape editor'
- omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py

--conflicts

snoopycrimecop · 2024-09-26T05:43:35Z

Conflicting PR. Removed from build OMERO-plugins-push#195. See the console output for more details.
Possible conflicts:

PR Points in shape editor #555 will-moore 'Points in shape editor'
- omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py

--conflicts

snoopycrimecop · 2024-09-26T11:32:30Z

Conflicting PR. Removed from build OMERO-plugins-push#196. See the console output for more details.
Possible conflicts:

PR Points in shape editor #555 will-moore 'Points in shape editor'
- omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py

--conflicts

snoopycrimecop · 2024-09-27T04:44:22Z

Conflicting PR. Removed from build OMERO-plugins-push#197. See the console output for more details.
Possible conflicts:

PR Points in shape editor #555 will-moore 'Points in shape editor'
- omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py

--conflicts

snoopycrimecop · 2024-10-01T00:44:01Z

Conflicting PR. Removed from build OMERO-plugins-push#198. See the console output for more details.
Possible conflicts:

PR Points in shape editor #555 will-moore 'Points in shape editor'
- omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py

--conflicts

snoopycrimecop · 2024-10-02T01:02:25Z

Conflicting PR. Removed from build OMERO-plugins-push#199. See the console output for more details.
Possible conflicts:

PR Points in shape editor #555 will-moore 'Points in shape editor'
- omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py

--conflicts

snoopycrimecop · 2024-10-03T00:46:47Z

Conflicting PR. Removed from build OMERO-plugins-push#200. See the console output for more details.
Possible conflicts:

PR Points in shape editor #555 will-moore 'Points in shape editor'
- omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py

--conflicts

snoopycrimecop · 2024-10-04T00:45:21Z

Conflicting PR. Removed from build OMERO-plugins-push#201. See the console output for more details.
Possible conflicts:

PR Points in shape editor #555 will-moore 'Points in shape editor'
- omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py

--conflicts

snoopycrimecop · 2024-10-05T00:51:05Z

Conflicting PR. Removed from build OMERO-plugins-push#202. See the console output for more details.
Possible conflicts:

Upstream changes
- omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py

--conflicts

snoopycrimecop · 2024-10-06T00:42:39Z

Conflicting PR. Removed from build OMERO-plugins-push#203. See the console output for more details.
Possible conflicts:

Upstream changes
- omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py

~~--conflicts~~ Conflict resolved in build OMERO-plugins-push#208. See the console output for more details.

…into fill-rois

will-moore · 2024-10-10T10:04:17Z

Thanks for the updates on this and other PRs. Just a heads up that I'm pretty tied up over the next week or so - Afraid I might not get time to review etc for a bit...

will-moore · 2024-10-22T21:40:24Z

A couple of issues:

The drop-down for choosing Opacity above looks strange with the 2 decimal places. E.g. 0, 0.1, 0.2, 0.3.. would look better.
With Points PR now merged, when I try to select points on the Image in the ROI dialog, I get a console error:

shape_manager.js:679 Uncaught TypeError: l.getFillColor is not a function
   at shape_manager.js:679:27

It seems that when I pick a Shape loaded from OMERO (with fill Color rgba 255, 255, 255, 0) and "Add" it to the Figure panel, it seems that the Opacity that is applied to it is the current value of the Fill-Opacity select option. E.g. here the current value is 0.20 and when I add the Ellipse, that's the Opacity it gets (not the 0 opacity loaded from OMERO)

It would be nice to fix the toolbar wrapping. Here's a commit where I tried this above - hopefully this will still work: will-moore@7da63a6

Rdornier · 2024-10-24T08:20:55Z

Hi @will-moore

Thanks for your feedback.

The drop-down for choosing Opacity above looks strange with the 2 decimal places. E.g. 0, 0.1, 0.2, 0.3.. would look better.

Ok, I'll correct it

With Points PR now merged, when I try to select points on the Image in the ROI dialog, I get a console error:

I think this is normal, as Point ROI doesn't have yet the methods to get fill etc. I'll add them.

It seems that when I pick a Shape loaded from OMERO (with fill Color rgba 255, 255, 255, 0) and "Add" it to the Figure panel, it seems that the Opacity that is applied to it is the current value of the Fill-Opacity select option. E.g. here the current value is 0.20 and when I add the Ellipse, that's the Opacity it gets (not the 0 opacity loaded from OMERO)

Yes, it is the current behavior. I don't remember why I didn't read the opacity from OMERO. I'll check it.

I'm a bit busy this and next week. So, I'll most probably do the corrections at the beginning of November.

Rémy.

Rdornier · 2024-11-04T14:13:02Z

Hi @will-moore ,

I fixed all the points you mentionned above.
Thanks for your careful review !

Rémy.

Rdornier added 7 commits July 3, 2024 11:24

handle roi filling

55438c4

handle opacity

e2d88d2

fix bug with color picker

735a5ee

handle ellipse

e6663e6

handle polygon/polyline

06012fb

handle line to avoid errors

42fbff0

update css

0fb5f26

will-moore added the include label Jul 10, 2024

will-moore removed the include label Jul 11, 2024

Rdornier added 4 commits July 12, 2024 10:28

remove static files

ace4591

update gitignore

ea2a045

read opacity for loaded rois

dcd6dae

format opacity to 2 decimal places

6d5d511

Rdornier added 3 commits August 12, 2024 11:06

Merge branch 'ome:master' into fill-rois

df540f6

Merge branch 'ome:master' into fill-rois

7ce2ce9

Merge branch 'ome:master' into fill-rois

b088368

will-moore added the include label Aug 26, 2024

updating figure to pdf

df6f353

Fix bug on export tiff

3c605ca

will-moore reviewed Aug 29, 2024

View reviewed changes

Merge branch 'ome:master' into fill-rois

1535381

will-moore added this to the 7.2.0 milestone Oct 3, 2024

jburel mentioned this pull request Oct 4, 2024

Points in shape editor #555

Merged

Rdornier added 2 commits October 10, 2024 10:54

Merge branch 'master' into fill-rois

6208bcd

Merge branch 'fill-rois' of https://github.com/Rdornier/omero-figure …

6fee74b

…into fill-rois

snoopycrimecop mentioned this pull request Oct 11, 2024

Image outline #578

Open

Rdornier added 2 commits October 11, 2024 08:37

Fix snoopycrimecop conflict

2a35068

update gitignore

4069931

Merge branch 'ome:master' into fill-rois

c03b871

Rdornier added 5 commits November 4, 2024 13:41

fix decimal places on opacities

c7b731c

Handle points

f3277f8

fix decimal places on opacity where selecting shapes again

237b88b

fix toolbar wrapping thanks to will

3e71003

correctly read opacity from rois coming from omero

fc8e383

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Fill rois #577

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Fill rois #577

Are you sure you want to change the base?

Fill rois #577

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