diff --git a/README.md b/README.md index f911a499..f7a6fc50 100644 --- a/README.md +++ b/README.md @@ -143,12 +143,35 @@ place. ### Locate tags -### Copy tag +* Menu Location: `Plugins > Tags > Locate tags` +* Opens a window with a list showing tracks and tags assigned to them. + The time point and the spot (identified via its label) of the first occurrence of the tag in a track are shown. +* The user can select a tag-track combination in the list and linked views will navigate to the corresponding spot. + The spot will be selected and highlighted. +* Tags can be removed from the selected spots. +* Example: ![locate_tags.gif](doc/tags/locate_tags.gif) + +### Copy tags + +* Menu Location: `Plugins > Tags > Copy tag` +* Allows the user to assign a tag to spots under the condition that the spots already have a certain tag that can be + specified by the user. +* Example: ![copy_tag.gif](doc/tags/copy_tag.gif) ### Add tag set to highlight cell divisions +* Menu Location: `Plugins > Tags > Add tag set to highlight cell divisions` +* The command creates a tag set that highlights cell divisions. The user interface allows to specify the number of spots + to highlight before and after a division. +* The colors for highlight background can be selected. +* Example: ![add_tag_set_to_highlight_cell_divisions.gif](doc/tags/add_tag_set_to_highlight_cell_divisions.gif) + ### Create Dummy Tag Set +* Menu Location: `Plugins > Tags > Create Empty Tag Set` +* Creates a tag set with a specified number of tags in random colors. +* Example: ![dummy_tagset.png](doc/tags/dummy_tagset.png) + ## Trees management ### Flip descendants diff --git a/doc/tags/add_tag_set_to_highlight_cell_divisions.gif b/doc/tags/add_tag_set_to_highlight_cell_divisions.gif new file mode 100644 index 00000000..ada03e99 Binary files /dev/null and b/doc/tags/add_tag_set_to_highlight_cell_divisions.gif differ diff --git a/doc/tags/copy_tag.gif b/doc/tags/copy_tag.gif new file mode 100644 index 00000000..319e4ba6 Binary files /dev/null and b/doc/tags/copy_tag.gif differ diff --git a/doc/tags/dummy_tagset.png b/doc/tags/dummy_tagset.png new file mode 100644 index 00000000..e7ade735 Binary files /dev/null and b/doc/tags/dummy_tagset.png differ diff --git a/doc/tags/locate_tags.gif b/doc/tags/locate_tags.gif new file mode 100644 index 00000000..a57d9010 Binary files /dev/null and b/doc/tags/locate_tags.gif differ diff --git a/pom.xml b/pom.xml index b0792102..d62a2527 100644 --- a/pom.xml +++ b/pom.xml @@ -46,6 +46,19 @@ mpicbg + + + ch.qos.logback + logback-classic + test + + + + ch.qos.logback + logback-core + test + + junit diff --git a/src/main/java/org/mastodon/mamut/tomancak/CopyTagDialog.java b/src/main/java/org/mastodon/mamut/tomancak/CopyTagDialog.java index 74e486be..a556f36e 100644 --- a/src/main/java/org/mastodon/mamut/tomancak/CopyTagDialog.java +++ b/src/main/java/org/mastodon/mamut/tomancak/CopyTagDialog.java @@ -78,7 +78,8 @@ public class CopyTagDialog extends JDialog public CopyTagDialog( final Frame owner, final Model model ) { - super( owner, "Copy Tag...", false ); + super( owner, "Copy Tag", false ); + setLocationRelativeTo( null ); this.model = model; model.getTagSetModel().listeners().add( this::tagSetStructureChanged ); diff --git a/src/main/java/org/mastodon/mamut/tomancak/resolve/LocateTagsFrame.java b/src/main/java/org/mastodon/mamut/tomancak/resolve/LocateTagsFrame.java index 9bab3246..2d9aff31 100644 --- a/src/main/java/org/mastodon/mamut/tomancak/resolve/LocateTagsFrame.java +++ b/src/main/java/org/mastodon/mamut/tomancak/resolve/LocateTagsFrame.java @@ -156,6 +156,7 @@ public LocateTagsFrame( final ProjectModel projectModel ) groupHandle = this.projectModel.getGroupManager().createGroupHandle(); setTitle( "Locate Tags" ); setLayout( new MigLayout( "insets dialog", "[grow]", "[][][grow]" ) ); + setLocationRelativeTo( null ); add( new GroupLocksPanel( groupHandle ), "split" ); add( new Label( "Tag Set:" ) ); tagSetComboBox = new JComboBox<>(); diff --git a/src/test/resources/logback-test.xml b/src/test/resources/logback-test.xml new file mode 100644 index 00000000..b7fd67d4 --- /dev/null +++ b/src/test/resources/logback-test.xml @@ -0,0 +1,153 @@ + + + + + + + + + + + %highlight(%-5level) %d{yyyy-MM-dd HH:mm:ss.SSS} [%blue(%t)] \(%file:%line\) - %m%n + + + + DEBUG + + + + + %highlight(%-5level) %d{yyyy-MM-dd HH:mm:ss.SSS} [%blue(%t)] \(%file:%line\) - %m%n + + + + WARN + + + + ${LOGS}/trace.log + + %d{yyyy-MM-dd HH:mm:ss.SSS} [%t] %-5p [%c{1}:%M:%L] - %m%n + + + + ${LOGS}/trace.%d{yyyy-MM-dd}.%i.log.zip + + 20MB + 60 + 1GB + + + TRACE + + + + ${LOGS}/debug.log + + %d{yyyy-MM-dd HH:mm:ss.SSS} [%t] %-5p [%c{1}:%M:%L] - %m%n + + + + ${LOGS}/debug.%d{yyyy-MM-dd}.%i.log.zip + + 20MB + 60 + 1GB + + + DEBUG + + + + ${LOGS}/info.log + + %d{yyyy-MM-dd HH:mm:ss.SSS} [%t] %-5p [%c{1}:%M:%L] - %m%n + + + + ${LOGS}/info.%d{yyyy-MM-dd}.%i.log.zip + + 20MB + 60 + 1GB + + + INFO + + + + ${LOGS}/warn.log + + %d{yyyy-MM-dd HH:mm:ss.SSS} [%t] %-5p [%c{1}:%M:%L] - %m%n + + + + ${LOGS}/warn.%d{yyyy-MM-dd}.%i.log.zip + + 20MB + 60 + 1GB + + + WARN + + + + ${LOGS}/error.log + + %d{yyyy-MM-dd HH:mm:ss.SSS} [%t] %-5p [%c{1}:%M:%L] - %m%n + + + + ${LOGS}/error.%d{yyyy-MM-dd}.%i.log.zip + + 20MB + 60 + 1GB + + + ERROR + + + + + + + + + + + + + + + + +