Get ROI count by dominikl · Pull Request #4550 · ome/openmicroscopy

dominikl · 2016-03-31T13:16:50Z

At the moment Insight loads all ROIs and counts them on the client side for showing the number of ROIs in the right hand side meta data panel. This PR adds a method for directly getting the number of ROIs via an HQL query.

Test: Check some images with ROIs, make sure the ROI count (right hand side metadata panel) is correct.

(based on #4549 to avoid merge conflicts)

gusferguson · 2016-04-01T07:49:41Z

@dominikl

Tested using OMERO.insight-5.3.0-m1-153-53a0751-ice35-b82-mac regions-omero.docker.openmicroscopy.org DB: user-14

Multiselected 16 of 18 existing ROIs on image - added to newly created folder - count correct.
Multiselected remaining 2 ROIs and tried to add to newly created folder - on clicking “Save” received error message shown below.
Error window re-opened every time tried to close - had to quit Insight to escape.

On logging back in I could see the second ROI folder had been created and the ROIs added despite the error.

I tried to delete the first folder to free up some ROIs for retesting and received the same error message as below. This time the error window closed and Insight crashed.

Reproducible on another image with both existing and newly created ROIs.

Log entry shows repeated error:

2016-04-01 07:40:35,100 INFO  [   o.o.s.env.data.login.LoginServiceImpl] (nitializer) Logged onto OMERO at: regions-omero.docker.openmicroscopy.org
User Name: user-14 -- Password: ***

2016-04-01 07:40:35,677 WARN  [     o.o.s.a.m.editor.AnnotationTaskPane] (nitializer) UI for displaying ROIS annotations not implemented yet!
2016-04-01 07:40:36,022 DEBUG [       omero.gateway.facility.Facility$1] ( Thread-12) Created new BrowseFacility
2016-04-01 07:40:50,529 DEBUG [       omero.gateway.facility.Facility$1] ( Thread-24) Created new ROIFacility
2016-04-01 07:40:50,546 DEBUG [       omero.gateway.facility.Facility$1] ( Thread-24) Created new DataManagerFacility
2016-04-01 07:40:52,368 WARN  [     o.o.s.a.m.editor.AnnotationTaskPane] (entQueue-0) UI for displaying ROIS annotations not implemented yet!
2016-04-01 07:43:12,283 ERROR [      o.o.s.a.m.view.MeasurementViewerUI] (entQueue-0) An unexpected error occurred while handling ROI null
2016-04-01 07:45:23,776 ERROR [      o.o.s.a.m.view.MeasurementViewerUI] (entQueue-0) An unexpected error occurred while handling ROI null
2016-04-01 07:45:27,276 ERROR [      o.o.s.a.m.view.MeasurementViewerUI] (entQueue-0) An unexpected error occurred while handling ROI null
2016-04-01 07:45:28,508 ERROR [      o.o.s.a.m.view.MeasurementViewerUI] (entQueue-0) An unexpected error occurred while handling ROI null
2016-04-01 07:45:29,507 ERROR [      o.o.s.a.m.view.MeasurementViewerUI] (entQueue-0) An unexpected error occurred while handling ROI null
2016-04-01 07:45:31,076 ERROR [      o.o.s.a.m.view.MeasurementViewerUI] (entQueue-0) An unexpected error occurred while handling ROI null

Error message:

java.lang.Exception: java.lang.NullPointerException
    at org.jdesktop.swingx.treetable.AbstractMutableTreeTableNode.remove(AbstractMutableTreeTableNode.java:114)
    at org.openmicroscopy.shoola.agents.measurement.util.roitable.ROINode.remove(ROINode.java:343)
    at org.openmicroscopy.shoola.agents.measurement.view.ROITable.removeROIShape(ROITable.java:713)
    at org.openmicroscopy.shoola.agents.measurement.view.ObjectManager.removeFigure(ObjectManager.java:824)
    at org.openmicroscopy.shoola.agents.measurement.view.MeasurementViewerUI.removeROI(MeasurementViewerUI.java:975)
    at org.openmicroscopy.shoola.agents.measurement.view.MeasurementViewerControl.figureRemoved(MeasurementViewerControl.java:605)
    at org.jhotdraw.draw.AbstractDrawing.fireFigureRemoved(AbstractDrawing.java:226)
    at org.jhotdraw.draw.AbstractDrawing.remove(AbstractDrawing.java:142)
    at org.openmicroscopy.shoola.util.ui.drawingtools.DrawingComponent.removeAllFigures(DrawingComponent.java:205)
    at org.openmicroscopy.shoola.agents.measurement.view.MeasurementViewerModel.removeAllROI(MeasurementViewerModel.java:943)
    at org.openmicroscopy.shoola.agents.measurement.view.MeasurementViewerComponent.setUpdateROIComponent(MeasurementViewerComponent.java:940)
    at org.openmicroscopy.shoola.agents.measurement.ROIFolderSaver.handleResult(ROIFolderSaver.java:170)
    at org.openmicroscopy.shoola.env.data.events.DSCallAdapter.eventFired(DSCallAdapter.java:90)
    at org.openmicroscopy.shoola.env.data.views.BatchCallMonitor$1.run(BatchCallMonitor.java:124)
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
    at java.awt.EventQueue.access$500(EventQueue.java:97)
    at java.awt.EventQueue$3.run(EventQueue.java:709)
    at java.awt.EventQueue$3.run(EventQueue.java:703)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

    at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showErrorDialog(UserNotifierImpl.java:189)
    at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:289)
    at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:257)
    at org.openmicroscopy.shoola.agents.measurement.view.MeasurementViewerUI.handleROIException(MeasurementViewerUI.java:1118)
    at org.openmicroscopy.shoola.agents.measurement.view.MeasurementViewerUI.removeROI(MeasurementViewerUI.java:980)
    at org.openmicroscopy.shoola.agents.measurement.view.MeasurementViewerControl.figureRemoved(MeasurementViewerControl.java:605)
    at org.jhotdraw.draw.AbstractDrawing.fireFigureRemoved(AbstractDrawing.java:226)
    at org.jhotdraw.draw.AbstractDrawing.remove(AbstractDrawing.java:142)
    at org.openmicroscopy.shoola.util.ui.drawingtools.DrawingComponent.removeAllFigures(DrawingComponent.java:205)
    at org.openmicroscopy.shoola.agents.measurement.view.MeasurementViewerModel.removeAllROI(MeasurementViewerModel.java:943)
    at org.openmicroscopy.shoola.agents.measurement.view.MeasurementViewerComponent.setUpdateROIComponent(MeasurementViewerComponent.java:940)
    at org.openmicroscopy.shoola.agents.measurement.ROIFolderSaver.handleResult(ROIFolderSaver.java:170)
    at org.openmicroscopy.shoola.env.data.events.DSCallAdapter.eventFired(DSCallAdapter.java:90)
    at org.openmicroscopy.shoola.env.data.views.BatchCallMonitor$1.run(BatchCallMonitor.java:124)
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
    at java.awt.EventQueue.access$500(EventQueue.java:97)
    at java.awt.EventQueue$3.run(EventQueue.java:709)
    at java.awt.EventQueue$3.run(EventQueue.java:703)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

gusferguson · 2016-04-01T07:50:23Z

@dominikl

Another issue seen on testing.

Created a number of new ROIs on an image and all of the previously created ROIs remained selected despite clicking on toolbar and creation of new ROIs - see screenshot.

dominikl · 2016-04-01T08:04:23Z

I just realized that you're actually testing #4549 as well, as I based this PR on it, sorry. The errors are probably caused by #4549, will fix them in that PR. Thanks for spotting them.

gusferguson · 2016-04-05T07:05:35Z

@dominikl

Tested with OMERO.insight-5.3.0-m1-229-2b1e3eb-ice35-b86-win Win 8.1 regions-omero.docker.openmicroscopy.org DB: user-14

Test: Check some images with ROIs, make sure the ROI count (right hand side metadata panel) is correct.

The counts are correct for existing ROIs on selecting image in data tree - both in Right Hand Pane General tab of main viewer and in General tab of rendering settings pane in Full Viewer.
However if I then add ROIs to the image - save and refresh using green arrows in the full image viewer the rendering settings General Tab ROI Count does not update - see screenshot.
If ROIs are saved and Full Viewer closed the ROI count does not update In the Main window General Tab.
Have to refresh data tree using green arrows before ROI Count updates to reflect added ROIs.
If re-open image ROI count is now correct in Rendering Settings General tab.

Previous NullPointerException

Not occurring any more - no problem creating new folder with multi-selected ROIs

Previous issue with persistent selection of ROIs created in Measurement Tool

Not occurring any more - behaves as expected.

dominikl · 2016-04-06T15:19:46Z

Review: Only last two commits; check that the ROI count (right hand side metadata panel) is updated when ROIs are created or deleted (Note: if single ROIs are deleted they are actually just removed from the view, the real deletion happens in that case after clicking on the "save" button, that's when the ROI count gets updated in these cases).

gusferguson · 2016-04-07T07:09:49Z

@dominikl

Tested using OMERO.insight-5.3.0-m1-248-0ddee08-ice35-b90-mac regions-omero.docker.openmicroscopy.org DB: user-14

Adding ROIs to folder gives correct number in Folder title.
Delete of single ROI causes immediate update of ROI count in General pane of both Full Viewer and main window.
Delete of all ROIs triggers immediate update.
Addition of ROI does not update ROI count until “Save” triggered - then updates correctly in both places.
Behaves as expected. No issues.
Good to merge.

dominikl · 2016-04-07T07:50:26Z

Thanks @gusferguson . This PR might also be worth rebasing to develop, as it's also a problem in 5.2.2, and it doesn't contain any 'regions' branch specific things. Your thougths @jburel ?

dominikl mentioned this pull request Mar 31, 2016

Get ROI count #4548

Closed

jburel added the regions label Apr 1, 2016

pwalczysko mentioned this pull request Apr 1, 2016

Roifolders improvements #4549

Merged

dominikl force-pushed the get_roi_count_regions branch from f4e9284 to bbb2e31 Compare April 1, 2016 10:35

dominikl added 3 commits April 4, 2016 13:56

Added getROICount method to gateway

12802c6

Use getROICount method in insight

5b97d55

Just modified comment

8b0f2cb

dominikl force-pushed the get_roi_count_regions branch from bbb2e31 to 8b0f2cb Compare April 4, 2016 12:56

dominikl added 2 commits April 6, 2016 15:15

Reload ROI count

e099128

Update ROI count after ROI deletion

3f26654

sbesson merged commit a345e89 into ome:regions Apr 7, 2016

dominikl deleted the get_roi_count_regions branch April 15, 2016 09:35

sbesson added this to the 5.3.0 milestone Apr 20, 2016

dominikl mentioned this pull request Apr 22, 2016

Get ROI count #4602

Merged

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Get ROI count#4550

Get ROI count#4550
sbesson merged 5 commits intoome:regionsfrom
dominikl:get_roi_count_regions

dominikl commented Mar 31, 2016

Uh oh!

gusferguson commented Apr 1, 2016

Uh oh!

gusferguson commented Apr 1, 2016

Uh oh!

dominikl commented Apr 1, 2016

Uh oh!

gusferguson commented Apr 5, 2016

Uh oh!

dominikl commented Apr 6, 2016

Uh oh!

gusferguson commented Apr 7, 2016

Uh oh!

dominikl commented Apr 7, 2016

Uh oh!

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dominikl commented Mar 31, 2016

Uh oh!

gusferguson commented Apr 1, 2016

Uh oh!

gusferguson commented Apr 1, 2016

Uh oh!

dominikl commented Apr 1, 2016

Uh oh!

gusferguson commented Apr 5, 2016

Uh oh!

dominikl commented Apr 6, 2016

Uh oh!

gusferguson commented Apr 7, 2016

Uh oh!

dominikl commented Apr 7, 2016

Uh oh!

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