Code

Support NGFF using n5-universe#328

Code

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tinevez merged 134 commits intomastodon-sc:devmastodon-sc/mastodon:devfrom elephant-track:n5universeelephant-track/mastodon:n5universeCopy head branch name to clipboardOct 10, 2024

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Commits

Commits on Aug 8, 2023

• Move project related class to io sub-package.

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Commits on Aug 9, 2023

• MamutProjectIO has only static methods now.

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Commits on Aug 15, 2023

• WIP: rework the app model and the project IO.

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Commits on Aug 16, 2023

• Add missing classes from the WIP.

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• Rework project loading / saving.

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• Rename appActions and globalAppActions.

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• Remove unused fields.

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• Remove duplicate fields in WindowManager.

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Commits on Aug 17, 2023

• Rename MamutAppModel in ProjectModel.

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• Fix deprecation of addTimePointListeners()

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• Fix depracation warnings with some YAML constructors.

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• Remove the use of deprecated BDV classes.

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• Do not try to load GUI settings when creating new projects.

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• Fix minor warnings.

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• Add and use convenience methods for opening / creating projects.

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• Move the importer package into the io package.

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• Store style managers in a common map.

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• Make an interface for views that have and use a context chooser.

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• Manage views and branch views in a common fields.

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• Remoe unused import.

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• Rework a bit the forEeach methods of the window manager.

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• Remove the now empty settings menu in bdv views.

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• Fix the size of the feature color mode panel.

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Commits on Aug 18, 2023

• Move ColorBarOverlay in a more suitable package.

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• Interface for views that some special components.

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• Use the right opn() method when opening a project from the launcher.

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• Tentative factory design for mamut views.

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• Tentative factory for BDV views.

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• Rework the mother interfaces for Mastodon and Mamut views.

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• The mamut view factory uses MamutViewI.

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• A factory for branch bdv views.

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• Use the common MamutViewI interface in WindowManager.

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• Let MamutBranchViewBdv implements HasColorBarOverlay & HasColoringModel.

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• Factory pattern for trackscheme views.

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• Factory pattern for the table views.

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Commits on Aug 19, 2023

• Use a separate class for selection tables.

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• Factory pattern for grapher views.

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• Move mamut view classes in the respective views subpackages.

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Commits on Aug 20, 2023

• Use the new view factories everywhere in Mastodon.

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Commits on Aug 21, 2023

• Make the createView() method synchronized.

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• Use a discoverable pattern for style managers and settings page.

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• Remove unused class.

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• Use a common utility to discover plugins.

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• Remove unused method.

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• Add TODO.

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• Replace KeyMap and associated classes by upstream implementations.

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• Add some javadoc.

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Commits on Aug 22, 2023

• Recompute min & max timepoint everytime they are queried.

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• Code style changes.

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Commits on Aug 23, 2023

• An intermediate abstract class for style managers with YAML.

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• Use the YAML style manager as mother class for Mastodon style managers.

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• Offer facilities to deserialize from YAML with catchable errors.

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Commits on Aug 24, 2023

• Better error messages when we cannot open the project.xml file.

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• The launcher log panel should not be editable.

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• Make it possible to recuperate when we cannot find the image data file.

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• Rework interactive project opening, local or remote.

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• Determine physical units if missing when creating new projects.

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• Ask for a file to save to if one was not set before.

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• When creating a view, returns null if the view type is unknown.

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• Do not close the project if we failed to save it when converting to BDV.

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• Close the main window when a project is closed.

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• Do not run saveProjectAs on multiple forking threads.

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• Show the project name on the main window.

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• Some javadoc.

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• The ProjectModel can return a suitable project name.

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• The window manager manages a list of extra windows.

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• Update all the window names when a project change name.

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Commits on Aug 25, 2023

• The interactive LauncherUtils methods should not throw exceptions.

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• Fix javadoc errors.

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• Fix javadoc warnings.

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• Remove superficious type in the FocusModel.

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• Save BDV settings when we save a Mastodon file.

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• Add the colorbar overlay to the trackscheme branch view.

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• Make the color bar overlay listenable.

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• Use a dedicated menu class for the colorbar overlay menu.

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• When loading a project, build the branch graph.

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• Have a launcher main class that exits gracefully.

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• When restoring a BDV view, wait a bit before restoring the transform.

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Commits on Aug 27, 2023

• Less gigantic size for the tag-set editor.

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Commits on Aug 29, 2023

• FeatureSpecsService must have EXTREMELY_LOW priority.

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• Be more cautious when meeting an error we don't know about.

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Commits on Aug 30, 2023

• Merge branch 'rework-app-model' of github.com:mastodon-sc/mastodon into rework-app-model

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• Add description for the online doc action.

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• Fix keystroke context for ShowSelectedTracksActions.

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• In the preferences dialog, make a sub-category for core settings page.

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• Add a method to handle legacy config files for styles.

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Commits on Sep 8, 2023

• Add commonly useful lazy features.

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• Make sure the projections() method of feature is called only once,

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Commits on Oct 14, 2023

• Update parent to pom-scijava v37.0.0

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• Depend on beta-25 for mastodon-collection and mastodon-graph.

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• Depend on bdv-core v10.4.8

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• Remove opening of remote datasets (S3) for now.

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• Fix bogus import of Font from itext.

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• Cleanup pom.xml.

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• Make WindowsManager.getViewList( final Class< T > klass ) public

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• Don't let a piublic method mofify the state of the window manager.

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Commits on Nov 18, 2023

• Add n5-universe

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Commits on Nov 25, 2023

• Merge remote-tracking branch 'upstream/dev' into n5universe

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• Remove vscode related files from index

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Commits on Jan 12, 2024

• Merge remote-tracking branch 'upstream/dev' into n5universe

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Commits on Jan 22, 2024

• Remove old ome.zarr test data

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• Add new ome.zarr test data

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• Update n5-universe version to 1.3.0

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• Update N5Universe loader

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• Fix imports

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• Update test dataset xml files

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Commits on Feb 24, 2024

• Merge remote-tracking branch 'upstream/dev' into n5universe

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• Update LICENSE

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• Update the version of n5-universe to 1.3.2-SNAPSHOT

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• Add an example settings file for S3 stored data

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Commits on Apr 16, 2024

• Merge remote-tracking branch 'upstream/dev' into n5universe

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Commits on Apr 18, 2024

• work in progress

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• Remove double slashes

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Commits on Apr 19, 2024

• Minor fixes

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Commits on Jul 30, 2024

• Work in progress

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Commits on Sep 2, 2024

• Merge remote-tracking branch 'upstream/dev' into n5universe

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Commits on Sep 3, 2024

• Use stored credentials if exits

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Commits on Sep 4, 2024

• Keep FeatureSpecsService updated

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• Update pom.xml

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Commits on Sep 10, 2024

• Add xml file for n5 in s3

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• Implement getNumSetups and update test files

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• Organize packages to separate mobie-derived modules

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Commits on Sep 14, 2024

• Update pom-scijava version to 38.0.1

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• Implement getMetadata

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Commits on Sep 18, 2024

• Use n5-viewer_fiji as backend

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Commits on Sep 28, 2024

• Update pom-scijava version to 37.0.0

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• Make compatible with both N5 and OME-Zarr

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• Keep the dependencies updated with the latest version available in Fiji

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• Use IJ's current directory for the default directory for saving xml

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Commits on Oct 4, 2024

• Update dependencies

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• Minor fixes

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• Fix issues

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• Merge remote-tracking branch 'upstream/dev' into n5universe

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• Remove old test data

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