Update CLEM collection table example

mobie · Oct 4, 2024 · 9a0e954 · 9a0e954
1 parent 5a4ffe9
commit 9a0e954
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Showing 5 changed files with 23 additions and 9 deletions.
diff --git a/src/main/java/org/embl/mobie/command/context/SourcesInfoCommand.java b/src/main/java/org/embl/mobie/command/context/SourcesInfoCommand.java
@@ -97,6 +97,7 @@ public void run()
 
             if ( showTransformationHistory )
             {
+                IJ.log( "## Transformation history" );
                 transformations.forEach( transformation ->
                 {
                     IJ.log( transformation.toString() );

diff --git a/src/main/java/org/embl/mobie/command/open/OpenCollectionTableCommand.java b/src/main/java/org/embl/mobie/command/open/OpenCollectionTableCommand.java
@@ -56,12 +56,12 @@ public static enum DataRoot{
 	public File table;
 
 	@Parameter( label = "Data Root",
-			description = "Use this is if the paths to the images and labels in the table are relative." )
+			description = "Specify whether the data URIs in the table are absolute or relative." )
 	public DataRoot dataRoot = DataRoot.PathsInTableAreAbsolute;
 
-	@Parameter( label = "Data Root Folder",
+	@Parameter( label = "( Data Root Folder )",
 			style = "directory",
-			description = "The root folder of the data (i.e., images and labels) in the table.",
+			description = "Optional. Use this is if the paths to the images and labels in the table are relative.",
 			required = false )
 	public File dataRootFile;
 

diff --git a/src/main/java/org/embl/mobie/lib/serialize/transformation/AffineTransformation.java b/src/main/java/org/embl/mobie/lib/serialize/transformation/AffineTransformation.java
@@ -68,7 +68,7 @@ public String toString()
 	{
 		List<String> lines = new ArrayList<>();
 
-		lines.add( "## Affine transformation: " + getName() );
+		lines.add( "Affine transformation: " + getName() );
 
 		String affineString = MoBIEHelper.print( parameters, 3 );
 

diff --git a/src/test/java/org/embl/mobie/command/open/OpenCollectionTableCommandTest.java b/src/test/java/org/embl/mobie/command/open/OpenCollectionTableCommandTest.java
@@ -10,7 +10,7 @@ public class OpenCollectionTableCommandTest
     static { net.imagej.patcher.LegacyInjector.preinit(); }
 
     @Test
-    public void simpleTable( )
+    public void blobsTable( )
     {
         final ImageJ imageJ = new ImageJ();
         imageJ.ui().showUI();
@@ -22,6 +22,19 @@ public void simpleTable( )
         command.run();
     }
 
+
+    @Test
+    public void clemTable( )
+    {
+        final ImageJ imageJ = new ImageJ();
+        imageJ.ui().showUI();
+
+        OpenCollectionTableCommand command = new OpenCollectionTableCommand();
+        command.table = new File( "src/test/resources/collections/clem-table.txt" );
+        command.dataRoot = OpenCollectionTableCommand.DataRoot.PathsInTableAreAbsolute;
+        command.run();
+    }
+
     @Test
     public void gridTable( )
     {
@@ -37,6 +50,6 @@ public void gridTable( )
 
     public static void main( String[] args )
     {
-        new OpenCollectionTableCommandTest().gridTable();
+        new OpenCollectionTableCommandTest().clemTable();
     }
 }
diff --git a/src/test/resources/collections/clem-table.txt b/src/test/resources/collections/clem-table.txt
@@ -1,3 +1,3 @@
-uri	type	affine	color
-https://s3.embl.de/yeast-clem/hela/images/ome-zarr/em-overview.ome.zarr	intensities	(-0.102, -0.971, 0, 483.043, -0.985, 0.119, 0, 487.003, 0, 0, 29.308, 0)	white
-https://raw.githubusercontent.com/mobie/clem-example-project/main/data/hela/images/bdv-n5-s3/fluorescence-a2-FMR-c2.xml	intensities	(-0.377, 0.951, 0, 193.574, 0.974, 0.359, 0, -39.55, 0, 0, 15.546, 0)	green
+uri	view	type	affine	color
+https://s3.embl.de/yeast-clem/hela/images/ome-zarr/em-overview.ome.zarr	CLEM	intensities	(-0.102, -0.971, 0, 483.043, -0.985, 0.119, 0, 487.003, 0, 0, 29.308, 0)	white
+https://raw.githubusercontent.com/mobie/clem-example-project/main/data/hela/images/bdv-n5-s3/fluorescence-a2-FMR-c2.xml	CLEM	intensities	(-0.377, 0.951, 0, 193.574, 0.974, 0.359, 0, -39.55, 0, 0, 15.546, 0)	green