Roi annotations

[jburel]

Replace gh-3928

Initial changes to allow tagging of shapes.
To tag a shape

• Select the shape
• right-clik on shape, select the tag option
• The standard tagging dialog will pop up
• Select a tag and/or create a new one
• The tags are displayed in the Inspector tab (for now)
• Tag can be added or removed from the shapes
• Shapes need to be saved before tagging can occur.

[gusferguson]

@jburel

Tested using OMERO.insight-5.2.0-m0-417-5513811-ice35-b63-mac eel user-3 read-only-1

Noted that when ROI selected (not shape) - no information appears in Inspector tab

Add single rectangle to plane

• add tag - warning ROI not saved
• save ROI - then add tag successfully
• visible in Inspector
• as expected

Propagate shape to other planes

• save
• select ROI (not shapes) add tag - existing tags shown in tag dialogue - add tags
• appears to succeed
• no tags visible in Inspector

Add tags individually to single shapes (rectangle and elipse)

• works as expected
• tags show in Inspector
• multiple tags to single shape works as expected

Multiselect shapes (elipse)

• add tags
• not shown in inspector

Create text shape

• save
• add existing tag
• not visible in inspector
• add new tag
• not visible in inspector
• new tag not visible in tag dialogue (i.e. never created)
• no error message

Propagate shape to other planes (rectangle)

• did not save
• select ROI (not shapes) add tag - no existing tags shown in tag dialogue - previously applied tag not visible on left or right side - create new tag and add - fatal crash

Stopped testing there for this round.

Error message:
java.lang.Exception: Abnormal termination due to an uncaught exception.
java.lang.NullPointerException
at org.openmicroscopy.shoola.agents.measurement.view.MeasurementViewerComponent.setROIAnnotations(MeasurementViewerComponent.java:1149)
at org.openmicroscopy.shoola.agents.measurement.ROIAnnotationLoader.handleResult(ROIAnnotationLoader.java:93)
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$1.doIntersectionPrivilege(ProtectionDomain.java:75)
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)
Abnormal termination due to an uncaught exception.
java.lang.NullPointerException
at org.openmicroscopy.shoola.agents.measurement.view.MeasurementViewerComponent.setROIAnnotations(MeasurementViewerComponent.java:1149)
at org.openmicroscopy.shoola.agents.measurement.ROIAnnotationLoader.handleResult(ROIAnnotationLoader.java:93)
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$1.doIntersectionPrivilege(ProtectionDomain.java:75)
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)
Exception in thread "AWT-EventQueue-0"

at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showErrorDialog(UserNotifierImpl.java:191)
at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:291)
at org.openmicroscopy.shoola.env.AbnormalExitHandler.doTermination(AbnormalExitHandler.java:147)
at org.openmicroscopy.shoola.env.AbnormalExitHandler.terminate(AbnormalExitHandler.java:85)
at org.openmicroscopy.shoola.env.RootThreadGroup.uncaughtException(RootThreadGroup.java:69)
at java.awt.EventDispatchThread.processException(EventDispatchThread.java:223)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:215)
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]

@jburel
Using image ID: 23053
Double checking adding tags to ROIs rather than shapes.

• add rectangular ROI
• save
• propagate to 6 planes
• save
• add tag to ROI - appears successful
• click on inspector - ROI still selected - see details as if for shape - tag added
• select shape - click on inspector - details as expected - tag added
• tags on all shapes as expected
• select ROI - click on inspector - blank as expected

Save and add elipse and save

• close viewer
• reopen image in viewer
• rectangle shows on image - eclipse not visible on image (this is intermittent - appears sometimes when rectangle selected)
• rectangle is visible in manager and expanded with previously selected shape still selected
• select elipse in manager - shape in rectangle remains selected
• select shape in eclipse
• add multiple tags
• fail to add - not visible in inspector
• add tag again - tags still in LHP of tag dialog - none in RHP
• check rectangle - tags disappeared from shapes.

Did more selection and deselection

• checked shapes in rectangle again - now have the multiple tags added to elipse on them.

Very difficult to work out what is happening.

[jburel]

@gusferguson: I figured out why annotations show up and sometimes do not... Now need to fix it ;-)

[gusferguson]

@jburel

Tested using OMERO.insight-5.2.0-m0-479-f740b93-ice35-b65-mac user-3 read-only 1
Images: ID: 23056

Draw rectangular ROI on 1 Z and T

• select ROI
• add tag
• click on Inspector tab - see information for shape not ROI i.e. not blank as expected
• select shape - Inspector tab shows expected information
• select ROI again - Inspector tab blank - as expected
• appears to be refresh issue

With existing shape - already tagged

• propagate ROI to Z and T planes
• shape propagated successfully
• all new shapes have tag attached
• as expected.

Create new ROI - ellipse

• propagate shape to Z and T
• add tag to 1 shape
• Inspector tab as expected
• tag only added to single selected shape
• multiselect shapes - add tag
• tags on all shapes - as expected
• add multiple tags to single and multi-selected shapes - successful
• behaves as expected

Created text ROI

• tag added
• tag and comment remain in correct fields
• no weirdness with other ROIs
• tagging of text ROIs as such now behaving as expected

Removing tags from ROIs works as expected.

Noticed quite a bit of lag selecting shapes - accessing from home but a lot of performance fall off as more shapes and tags added.
A slight lag occurs with un-annotated ROIs as their numbers increase.
Comparing similar numbers of propagated ROIs with no tags attached and tags attached - I estimate the tags are more than doubling the performance lag.

May be time to get @pwalczysko to start tearing it apart as well.

[jburel]

@gusferguson: Thanks for the report. It seems that the general weirdness has been fixed.
I think I can improve the tagging refresh a bit.
Adding tags to rois implies that we need an extra call to load the annotations,

[jburel]

removing exclude label. conflicts have now been fixed.

[jburel]

@gusferguson: I will probably do the performance improvement in a follow up PR, mainly to avoid further
conflicts
Are you happy with the functionalities?

[gusferguson]

@jburel - yes - happy with functionalities.
Good to merge from that POV.

[sbesson]

Note this is causing new Javadoc warnings

Standard Doclet version 1.8.0_51
Building tree for all the packages and classes...
/opt/hudson/workspace/OMERO-DEV-merge-build/src/components/insight/SRC/org/openmicroscopy/shoola/agents/metadata/editor/Editor.java:297: warning - @param argument "file" is not a parameter name.
/opt/hudson/workspace/OMERO-DEV-merge-build/src/components/insight/SRC/org/openmicroscopy/shoola/env/data/OmeroMetadataService.java:770: warning - @return tag cannot be used in method with void return type.
/opt/hudson/workspace/OMERO-DEV-merge-build/src/components/insight/SRC/org/openmicroscopy/shoola/env/data/views/calls/ArchivedImageLoader.java:225: warning - @param argument "imageID" is not a parameter name.
/opt/hudson/workspace/OMERO-DEV-merge-build/src/components/insight/SRC/org/openmicroscopy/shoola/env/data/views/calls/ArchivedImageLoader.java:225: warning - @param argument "name" is not a parameter name.
/opt/hudson/workspace/OMERO-DEV-merge-build/src/components/insight/SRC/org/openmicroscopy/shoola/agents/measurement/view/ROITable.java:840: warning - Tag @see: can't find loadTag() in org.openmicroscopy.shoola.agents.measurement.util.roitable.ROIActionController
/opt/hudson/workspace/OMERO-DEV-merge-build/src/components/insight/SRC/org/openmicroscopy/shoola/util/roi/model/ROIShape.java:181: warning - @return tag cannot be used in method with void return type.

See https://ci.openmicroscopy.org/view/DEV/job/OMERO-DEV-merge-build/ICE=3.5,jdk=8_LATEST,label=octopus/77/consoleText

[jburel]

2 warnings are not related to this PR

• Editor
• ArchivedImageLoader

[jburel]

--no-rebase