Add tests for 2d and 3d spots opening

mobie · Dec 2, 2024 · fc00784 · fc00784
1 parent 1d7c722
commit fc00784
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Showing 6 changed files with 51 additions and 5 deletions.
diff --git a/src/main/java/org/embl/mobie/lib/table/saw/TableOpener.java b/src/main/java/org/embl/mobie/lib/table/saw/TableOpener.java
@@ -119,7 +119,8 @@ private static Table openTableFile( StorageLocation storageLocation, String chun
 		}
 		else
 		{
-			final String path = resolveTablePath( IOHelper.combinePath( storageLocation.absolutePath, chunk ) );
+			String tablePath = chunk != null ? IOHelper.combinePath( storageLocation.absolutePath, chunk ) : storageLocation.absolutePath;
+			final String path = resolveTablePath( tablePath );
 			final Character separator = tableDataFormat.getSeparator();
 			return openDelimitedTextFile( numSamples, path, separator );
 		}

diff --git a/src/test/java/org/embl/mobie/command/open/OpenCollectionTableCommandTest.java b/src/test/java/org/embl/mobie/command/open/OpenCollectionTableCommandTest.java
@@ -11,7 +11,7 @@ public class OpenCollectionTableCommandTest
     static { net.imagej.patcher.LegacyInjector.preinit(); }
 
     @Test
-    public void blobsTable( )
+    public void blobs( )
     {
         final ImageJ imageJ = new ImageJ();
         imageJ.ui().showUI();
@@ -25,7 +25,7 @@ public void blobsTable( )
     }
 
     @Test
-    public void clemTable( )
+    public void clem( )
     {
         final ImageJ imageJ = new ImageJ();
         imageJ.ui().showUI();
@@ -37,21 +37,52 @@ public void clemTable( )
     }
 
     @Test
-    public void gridTable( )
+    public void grid( )
     {
         final ImageJ imageJ = new ImageJ();
         imageJ.ui().showUI();
 
         OpenCollectionTableCommand command = new OpenCollectionTableCommand();
         command.table = new File( "src/test/resources/collections/blobs-grid-table.txt" );
+        // FIXME: Make this work with relative paths
         command.dataRoot = OpenCollectionTableCommand.DataRoot.UseBelowDataRootFolder;
         command.dataRootFile = new File( "/Users/tischer/Documents/mobie-viewer-fiji/src/test/resources/collections" );
         command.bdvViewingMode = BdvViewingMode.TwoDimensional;
         command.run();
     }
 
+    @Test
+    public void spots2D( )
+    {
+        final ImageJ imageJ = new ImageJ();
+        imageJ.ui().showUI();
+
+        OpenCollectionTableCommand command = new OpenCollectionTableCommand();
+        command.table = new File( "src/test/resources/collections/spots-2d-collection.txt" );
+        // FIXME: Make this work with relative paths
+        command.dataRoot = OpenCollectionTableCommand.DataRoot.UseBelowDataRootFolder;
+        command.dataRootFile = new File( "/Users/tischer/Documents/mobie-viewer-fiji/src/test/resources/collections" );
+        command.bdvViewingMode = BdvViewingMode.TwoDimensional;
+        command.run();
+    }
+
+    @Test
+    public void spots3D( )
+    {
+        final ImageJ imageJ = new ImageJ();
+        imageJ.ui().showUI();
+
+        OpenCollectionTableCommand command = new OpenCollectionTableCommand();
+        command.table = new File( "src/test/resources/collections/spots-3d-collection.txt" );
+        // FIXME: Make this work with relative paths
+        command.dataRoot = OpenCollectionTableCommand.DataRoot.UseBelowDataRootFolder;
+        command.dataRootFile = new File( "/Users/tischer/Documents/mobie-viewer-fiji/src/test/resources/collections" );
+        command.bdvViewingMode = BdvViewingMode.ThreeDimensional;
+        command.run();
+    }
+
     public static void main( String[] args )
     {
-        new OpenCollectionTableCommandTest().gridTable();
+        new OpenCollectionTableCommandTest().spots3D();
     }
 }
diff --git a/src/test/resources/collections/spots-2d-collection.txt b/src/test/resources/collections/spots-2d-collection.txt
@@ -0,0 +1,2 @@
+uri	name	type
+spots-2d.txt	spots	spots
diff --git a/src/test/resources/collections/spots-2d.txt b/src/test/resources/collections/spots-2d.txt
@@ -0,0 +1,5 @@
+spot_id	x	y
+1	10	0
+2	0	10
+3	0	0
+4	10	10
diff --git a/src/test/resources/collections/spots-3d-collection.txt b/src/test/resources/collections/spots-3d-collection.txt
@@ -0,0 +1,2 @@
+uri	name	type
+spots-3d.txt	spots	spots
diff --git a/src/test/resources/collections/spots-3d.txt b/src/test/resources/collections/spots-3d.txt
@@ -0,0 +1,5 @@
+spot_id	x	y	z
+1	10	0	0
+2	0	10	0.25
+3	0	0	0
+4	10	10	0.25