Improve opening OME-Zarr files as a grid view

mobie · Jun 7, 2024 · 6bed6f9 · 6bed6f9
1 parent eedee2a
commit 6bed6f9
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Showing 8 changed files with 17 additions and 8 deletions.
diff --git a/src/main/java/org/embl/mobie/command/open/OpenImageAndLabelsFilesCommand.java b/src/main/java/org/embl/mobie/command/open/OpenImageAndLabelsFilesCommand.java
@@ -32,6 +32,7 @@
 import org.embl.mobie.MoBIESettings;
 import org.embl.mobie.command.CommandConstants;
 import org.embl.mobie.command.SpatialCalibration;
+import org.embl.mobie.lib.MoBIEHelper;
 import org.embl.mobie.lib.transform.GridType;
 import org.scijava.command.Command;
 import org.scijava.plugin.Parameter;
@@ -59,7 +60,7 @@ public class OpenImageAndLabelsFilesCommand implements Command {
 	@Parameter( label = "Spatial Calibration" )
 	public SpatialCalibration spatialCalibration = SpatialCalibration.FromImage;
 
-	@Parameter( label = "Grid type", description = "If the images are different and not too many, use Transformed; otherwise use Stitched for better performance.")
+	@Parameter( label = "Grid type", description = MoBIEHelper.GRID_TYPE_HELP )
 	public GridType gridType = GridType.Transformed;
 
 	@Override

diff --git a/src/main/java/org/embl/mobie/command/open/OpenImageAndLabelsURIsCommand.java b/src/main/java/org/embl/mobie/command/open/OpenImageAndLabelsURIsCommand.java
@@ -32,6 +32,7 @@
 import org.embl.mobie.MoBIESettings;
 import org.embl.mobie.command.CommandConstants;
 import org.embl.mobie.command.SpatialCalibration;
+import org.embl.mobie.lib.MoBIEHelper;
 import org.embl.mobie.lib.transform.GridType;
 import org.scijava.command.Command;
 import org.scijava.plugin.Parameter;
@@ -57,7 +58,7 @@ public class OpenImageAndLabelsURIsCommand implements Command {
 	@Parameter( label = "Spatial Calibration" )
 	public SpatialCalibration spatialCalibration = SpatialCalibration.FromImage;
 
-	@Parameter( label = "Grid type", description = "If the images are different and not too many, use Transformed; otherwise use Stitched for better performance.")
+	@Parameter( label = "Grid type", description = MoBIEHelper.GRID_TYPE_HELP )
 	public GridType gridType = GridType.Transformed;
 
 	@Override

diff --git a/src/main/java/org/embl/mobie/command/open/OpenMultipleImagesAndLabelsFilesCommand.java b/src/main/java/org/embl/mobie/command/open/OpenMultipleImagesAndLabelsFilesCommand.java
@@ -32,6 +32,7 @@
 import org.embl.mobie.MoBIESettings;
 import org.embl.mobie.command.CommandConstants;
 import org.embl.mobie.command.SpatialCalibration;
+import org.embl.mobie.lib.MoBIEHelper;
 import org.embl.mobie.lib.transform.GridType;
 import org.scijava.command.Command;
 import org.scijava.plugin.Parameter;
@@ -73,7 +74,7 @@ public class OpenMultipleImagesAndLabelsFilesCommand implements Command {
 	@Parameter( label = "Spatial Calibration" )
 	public SpatialCalibration spatialCalibration = SpatialCalibration.FromImage;
 
-	@Parameter( label = "Grid type", description = "If the images are different and not too many, use Transformed; otherwise use Stitched for better performance.")
+	@Parameter( label = "Grid type", description = MoBIEHelper.GRID_TYPE_HELP )
 	public GridType gridType = GridType.Transformed;
 
 	@Override

diff --git a/src/main/java/org/embl/mobie/command/open/OpenMultipleImagesAndLabelsURIsCommand.java b/src/main/java/org/embl/mobie/command/open/OpenMultipleImagesAndLabelsURIsCommand.java
@@ -32,6 +32,7 @@
 import org.embl.mobie.MoBIESettings;
 import org.embl.mobie.command.CommandConstants;
 import org.embl.mobie.command.SpatialCalibration;
+import org.embl.mobie.lib.MoBIEHelper;
 import org.embl.mobie.lib.transform.GridType;
 import org.scijava.command.Command;
 import org.scijava.plugin.Parameter;
@@ -72,7 +73,7 @@ public class OpenMultipleImagesAndLabelsURIsCommand implements Command {
 	@Parameter( label = "Spatial Calibration" )
 	public SpatialCalibration spatialCalibration = SpatialCalibration.FromImage;
 
-	@Parameter( label = "Grid type", description = "If the images are different and not too many, use Transformed; otherwise use Stitched for better performance.")
+	@Parameter( label = "Grid type", description = MoBIEHelper.GRID_TYPE_HELP )
 	public GridType gridType = GridType.Transformed;
 
 	@Override

diff --git a/src/main/java/org/embl/mobie/command/open/OpenTableCommand.java b/src/main/java/org/embl/mobie/command/open/OpenTableCommand.java
@@ -33,6 +33,7 @@
 import org.embl.mobie.MoBIESettings;
 import org.embl.mobie.command.CommandConstants;
 import org.embl.mobie.command.SpatialCalibration;
+import org.embl.mobie.lib.MoBIEHelper;
 import org.embl.mobie.lib.transform.GridType;
 import org.scijava.command.Command;
 import org.scijava.plugin.Parameter;
@@ -74,7 +75,7 @@ public class OpenTableCommand implements Command {
 	@Parameter( label = "Spatial Calibration" )
 	public SpatialCalibration spatialCalibration = SpatialCalibration.FromImage;
 
-	@Parameter( label = "Grid type", description = "If the images are different and not too many, use \"Transformed\"; otherwise use \"Stitched\" for better performance.")
+	@Parameter( label = "Grid type", description = MoBIEHelper.GRID_TYPE_HELP )
 	public GridType gridType = GridType.Transformed;
 
 	@Override

diff --git a/src/main/java/org/embl/mobie/lib/MoBIEHelper.java b/src/main/java/org/embl/mobie/lib/MoBIEHelper.java
@@ -62,6 +62,8 @@
 
 public abstract class MoBIEHelper
 {
+	public static final String GRID_TYPE_HELP = "If the images are different and not too many, use Transformed; otherwise use Stitched for better performance.";
+
 	static { net.imagej.patcher.LegacyInjector.preinit(); }
 
 	public static String print(double[] array, int numSignificantDigits) {

diff --git a/src/test/java/develop/OpenAutoMicTable.java b/src/test/java/develop/OpenAutoMicTable.java
@@ -29,6 +29,7 @@
 package develop;
 
 import net.imagej.ImageJ;
+import org.embl.mobie.command.open.OpenTableCommand;
 import org.embl.mobie.lib.transform.GridType;
 
 import java.io.File;
@@ -40,15 +41,15 @@ public static void main( String[] args )
         final ImageJ imageJ = new ImageJ();
         imageJ.ui().showUI();
 
-        OpenTableAdvancedCommand command = new OpenTableAdvancedCommand();
+        OpenTableCommand command = new OpenTableCommand();
         //command.table = new File( "/Volumes/almf/group/Aliaksandr/User_data/Furlong_CrispR/test_data_20231018/20231004/20231004-172458/summary_calculated1.txt" );
         //command.table = new File( "/Volumes/almf/group/Aliaksandr/User_data/Furlong_CrispR/test_data_20231018/20231004/20231004-172458/summary_calculated1_subset.txt" );
         command.table = new File( "/Users/tischer/Desktop/teresa/summary_calculated1_subset.txt" );
         //command.table = new File( "/Volumes/cba/exchange/furlong_test/summary_calculated1_subset_zarr.txt" );
         //command.images = "Result.Image.Zarr"; // Result.Image.Zarr
         command.root = command.table.getParentFile();
         command.images = "FileName_Result.Image_IMG"; // Result.Image.Zarr
-        command.gridType = GridType.Transformed; // FIXME: not working with Stitched!
+        command.gridType = GridType.Transformed;
         command.run();
     }
 }
diff --git a/src/test/java/projects/muscle_patterning_drosophila/OpenTeresaData.java b/src/test/java/projects/muscle_patterning_drosophila/OpenTeresaData.java
@@ -29,6 +29,7 @@
 package projects.muscle_patterning_drosophila;
 
 import net.imagej.ImageJ;
+import org.embl.mobie.command.open.OpenTableCommand;
 import org.embl.mobie.lib.transform.GridType;
 
 import java.io.File;
@@ -40,7 +41,7 @@ public static void main( String[] args )
         final ImageJ imageJ = new ImageJ();
         imageJ.ui().showUI();
 
-        OpenTableAdvancedCommand command = new OpenTableAdvancedCommand();
+        OpenTableCommand command = new OpenTableCommand();
         //command.table = new File( "/Volumes/almf/group/Aliaksandr/User_data/Furlong_CrispR/test_data_20231018/20231004/20231004-172458/summary_calculated1.txt" );
         //command.table = new File( "/Volumes/almf/group/Aliaksandr/User_data/Furlong_CrispR/test_data_20231018/20231004/20231004-172458/summary_calculated1_subset.txt" );
         command.table = new File( "/Users/tischer/Desktop/teresa/summary_calculated1_subset.txt" );