Update pom scijava to 37 to dev #260
Closed
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Not used anywhere in the code. And itext caused a licensing problem. Fix mastodon-sc#221
…able * In case of no image data available the user may decide, if he wants to load the project anyway to inspect the meta data / cell lineages or if he does not want to open the project at all * When projects are saved, a copy the spim data xml is saved within the project
Windows, Linux & MacOS use different slashes in file paths. Windows uses backward slashes, Linux & MacOS use forward slashes. If a Mastodon project is saved on Windows, the project.xml will have a dataset path with backward slashes like: ..\dataset.xml. On Linux this path is not interpreted correctly. We need to manually replace the backward slashes with forward slashes. This commit moves the code that replaces the slashes into the class MamutProjectIO. This makes a lot of sense, as the backward slashes are introduced when reading the project.xml.
* Add new classes ExampleGraph1, ExampleGraph2 * Add javadoc and unit test for BranchNSpotsFeature * Add javadoc and unit test for BranchDisplacementDurationFeature * Add javadoc and unit test for BranchDepthFeature * Make feature projection of BranchNSpotsFeature package protected
The Mastodon launcher has a list of recently opened projects. This commit makes the entries is this list editable. A user can now modify a path in the list before opening the project. Resolves mastodon-sc#181
The "show track downward" action got stuck, whenever there's a loop in the ModelGraph. This is because the "show track downward" action uses the DepthFirstIteration class to iterate over the ModelGraph when searching for the correct new roots. The DepthFirstIteration class itself does not detect loops and hangs if loops are present in the graph. The commit adds the required tests to that keep track of visited nodes and breaks the loop during iteration.
This will introduce deployment of SNAPSHOT version if changes are merged into the dev branch
Add dev branch to build PR workflow
* Method saveAndReload returns the reloaded Feature * Separate mamut projects are used for saving and reloading
…erService() methods
Some classes had a timepointModel and a fadingTimepointModel but both where functionally equivalent. After the last changes there is no reason left to have a fadingTimepointModel. This also simplifies the TrackSchemeFrame, because there is no more need to have the two different timepoint models there.
When transitioning (appear/disappear) the color including its alpha value needs to be set with alpha value. Before, the new color was missing the alpha bits, when generated, which caused wrong visualisation in some transition animations.
…lues should be used with java.util.Color objects
…ings panel. Its size was too big to accomodate the default width of TrackScheme windows. Now we need to center and shrink the other widgets.
So that - we have some space to display them all with the default window width, - their texts are all aligned vertically on the same baseline, - the font used is the same everywhere.
* Add a tooltip with some explanation of the function of the button
* On a windows machine the group lock ids (the numbers) where not shown, but "..." instead * I think only preferred size is need to set the size
* I think it is better to avoid abbreviations in user interfaces. What might be clear to us (t = timepoint) may not be so clear for a newbie user.
* The class contains some convenience methods to deal with tag sets * This class is moved from: https://github.com/mastodon-sc/mastodon-tomancak/blob/master/src/main/java/org/mastodon/mamut/tomancak/lineage_registration/TagSetUtils.java * A new method tagSpotAndLinks() is added * A unit test testing tagSpotAndLinks() and addNewTagSetToModel() is added
…or_to_color_utils Add glasbey color palette to color utils
- Rename tagSpotAndLinks to tagSpotAndOutgoingEdges. - Rename testTagSpotAndLinks to testTagSpotAndOutgoingEdges - Add more similar methods tagSpot, tagSpotAndIncomingEdges, tagSpots, tagLinks - Remove the tagSetAsMap method - Add a findTag method, that is similar to findTagSet
* Intention is to improve readability of this variable
Adds a new class TagSetUtils and new class TagHelper
The TagHelper constructor checks the arguments an throws an exception if something is wrong.
Replace HashSet used for projections() by LinkedHashSet, since the order of entry needs to be stable in process using this method.
* KeymapManager, MastodonDebugSettings, WorkaroundConstructor and WorkaroundRepresenter needed to be adapted as well
|
Replaced by #261 |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.