Merge pull request #74 from mastodon-sc/tags-docs

Add documentation for Tag related functions of mastodon tomancak
mastodon-sc · Dec 11, 2024 · 93fa42f · 93fa42f
2 parents 0729b84 + a4433ab
commit 93fa42f
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diff --git 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
diff --git a/doc/tags/copy_tag.gif b/doc/tags/copy_tag.gif
diff --git a/doc/tags/dummy_tagset.png b/doc/tags/dummy_tagset.png
diff --git a/doc/tags/locate_tags.gif b/doc/tags/locate_tags.gif
diff --git a/pom.xml b/pom.xml
@@ -46,6 +46,19 @@
 			<artifactId>mpicbg</artifactId>
 		</dependency>
 
+		<!-- include logback-classic at test runtime -->
+		<dependency>
+			<groupId>ch.qos.logback</groupId>
+			<artifactId>logback-classic</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<!-- include logback-core at test runtime -->
+		<dependency>
+			<groupId>ch.qos.logback</groupId>
+			<artifactId>logback-core</artifactId>
+			<scope>test</scope>
+		</dependency>
+
 		<!-- Test dependencies -->
 		<dependency>
 			<groupId>junit</groupId>

diff --git 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
@@ -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
@@ -0,0 +1,153 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+  #%L
+  mastodon-deep-lineage
+  %%
+  Copyright (C) 2022 - 2024 Stefan Hahmann
+  %%
+  Redistribution and use in source and binary forms, with or without
+  modification, are permitted provided that the following conditions are met:
+  
+  1. Redistributions of source code must retain the above copyright notice,
+     this list of conditions and the following disclaimer.
+  2. Redistributions in binary form must reproduce the above copyright notice,
+     this list of conditions and the following disclaimer in the documentation
+     and/or other materials provided with the distribution.
+  
+  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+  AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+  IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+  ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+  LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+  CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+  SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+  INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+  CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+  POSSIBILITY OF SUCH DAMAGE.
+  #L%
+  -->
+
+
+<configuration debug="false">
+
+    <property name="LOGS" value="./logs"/>
+
+    <appender name="stdout" class="ch.qos.logback.core.ConsoleAppender">
+        <encoder>
+            <pattern>%highlight(%-5level) %d{yyyy-MM-dd HH:mm:ss.SSS} [%blue(%t)] \(%file:%line\) - %m%n
+            </pattern>
+        </encoder>
+        <filter class="ch.qos.logback.classic.filter.ThresholdFilter">
+            <level>DEBUG</level>
+        </filter>
+    </appender>
+    <appender name="stderr" class="ch.qos.logback.core.ConsoleAppender">
+        <encoder>
+            <pattern>%highlight(%-5level) %d{yyyy-MM-dd HH:mm:ss.SSS} [%blue(%t)] \(%file:%line\) - %m%n
+            </pattern>
+        </encoder>
+        <filter class="ch.qos.logback.classic.filter.ThresholdFilter">
+            <level>WARN</level>
+        </filter>
+    </appender>
+    <appender name="file-trace" class="ch.qos.logback.core.rolling.RollingFileAppender">
+        <File>${LOGS}/trace.log</File>
+        <encoder>
+            <Pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%t] %-5p [%c{1}:%M:%L] - %m%n</Pattern>
+        </encoder>
+        <rollingPolicy class="ch.qos.logback.core.rolling.SizeAndTimeBasedRollingPolicy">
+            <!-- rollover daily -->
+            <fileNamePattern>${LOGS}/trace.%d{yyyy-MM-dd}.%i.log.zip</fileNamePattern>
+            <!-- each file should be at most 10MB, keep 60 days worth of history, but at most 1GB-->
+            <maxFileSize>20MB</maxFileSize>
+            <maxHistory>60</maxHistory>
+            <totalSizeCap>1GB</totalSizeCap>
+        </rollingPolicy>
+        <filter class="ch.qos.logback.classic.filter.ThresholdFilter">
+            <level>TRACE</level>
+        </filter>
+    </appender>
+    <appender name="file-debug" class="ch.qos.logback.core.rolling.RollingFileAppender">
+        <File>${LOGS}/debug.log</File>
+        <encoder>
+            <Pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%t] %-5p [%c{1}:%M:%L] - %m%n</Pattern>
+        </encoder>
+        <rollingPolicy class="ch.qos.logback.core.rolling.SizeAndTimeBasedRollingPolicy">
+            <!-- rollover daily -->
+            <fileNamePattern>${LOGS}/debug.%d{yyyy-MM-dd}.%i.log.zip</fileNamePattern>
+            <!-- each file should be at most 10MB, keep 60 days worth of history, but at most 1GB-->
+            <maxFileSize>20MB</maxFileSize>
+            <maxHistory>60</maxHistory>
+            <totalSizeCap>1GB</totalSizeCap>
+        </rollingPolicy>
+        <filter class="ch.qos.logback.classic.filter.ThresholdFilter">
+            <level>DEBUG</level>
+        </filter>
+    </appender>
+    <appender name="file-info" class="ch.qos.logback.core.rolling.RollingFileAppender">
+        <File>${LOGS}/info.log</File>
+        <encoder>
+            <Pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%t] %-5p [%c{1}:%M:%L] - %m%n</Pattern>
+        </encoder>
+        <rollingPolicy class="ch.qos.logback.core.rolling.SizeAndTimeBasedRollingPolicy">
+            <!-- rollover daily -->
+            <fileNamePattern>${LOGS}/info.%d{yyyy-MM-dd}.%i.log.zip</fileNamePattern>
+            <!-- each file should be at most 10MB, keep 60 days worth of history, but at most 1GB-->
+            <maxFileSize>20MB</maxFileSize>
+            <maxHistory>60</maxHistory>
+            <totalSizeCap>1GB</totalSizeCap>
+        </rollingPolicy>
+        <filter class="ch.qos.logback.classic.filter.ThresholdFilter">
+            <level>INFO</level>
+        </filter>
+    </appender>
+    <appender name="file-warn" class="ch.qos.logback.core.rolling.RollingFileAppender">
+        <File>${LOGS}/warn.log</File>
+        <encoder>
+            <Pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%t] %-5p [%c{1}:%M:%L] - %m%n</Pattern>
+        </encoder>
+        <rollingPolicy class="ch.qos.logback.core.rolling.SizeAndTimeBasedRollingPolicy">
+            <!-- rollover daily -->
+            <fileNamePattern>${LOGS}/warn.%d{yyyy-MM-dd}.%i.log.zip</fileNamePattern>
+            <!-- each file should be at most 10MB, keep 60 days worth of history, but at most 1GB-->
+            <maxFileSize>20MB</maxFileSize>
+            <maxHistory>60</maxHistory>
+            <totalSizeCap>1GB</totalSizeCap>
+        </rollingPolicy>
+        <filter class="ch.qos.logback.classic.filter.ThresholdFilter">
+            <level>WARN</level>
+        </filter>
+    </appender>
+    <appender name="file-error" class="ch.qos.logback.core.rolling.RollingFileAppender">
+        <File>${LOGS}/error.log</File>
+        <encoder>
+            <Pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%t] %-5p [%c{1}:%M:%L] - %m%n</Pattern>
+        </encoder>
+        <rollingPolicy class="ch.qos.logback.core.rolling.SizeAndTimeBasedRollingPolicy">
+            <!-- rollover daily -->
+            <fileNamePattern>${LOGS}/error.%d{yyyy-MM-dd}.%i.log.zip</fileNamePattern>
+            <!-- each file should be at most 10MB, keep 60 days worth of history, but at most 1GB-->
+            <maxFileSize>20MB</maxFileSize>
+            <maxHistory>60</maxHistory>
+            <totalSizeCap>1GB</totalSizeCap>
+        </rollingPolicy>
+        <filter class="ch.qos.logback.classic.filter.ThresholdFilter">
+            <level>ERROR</level>
+        </filter>
+    </appender>
+
+    <!-- Set root log level to INFO -->
+    <root level="INFO">
+        <appender-ref ref="stdout"/>
+        <appender-ref ref="file-trace"/>
+        <appender-ref ref="file-debug"/>
+        <appender-ref ref="file-info"/>
+        <appender-ref ref="file-warn"/>
+        <appender-ref ref="file-error"/>
+    </root>
+
+    <!-- Example how to change log level for certain packages -->
+    <logger name="org.mastodon.mamut" level="DEBUG"/>
+
+</configuration>