diff --git a/pom.xml b/pom.xml
index 3fca8a11b..0d19f2283 100644
--- a/pom.xml
+++ b/pom.xml
@@ -9,7 +9,7 @@
org.embl.mobie
mobie-viewer-fiji
- 5.0.4
+ 5.0.6-SNAPSHOT
diff --git a/src/main/java/org/embl/mobie/command/SpatialCalibration.java b/src/main/java/org/embl/mobie/command/SpatialCalibration.java
index 5cbf25c67..729d59bca 100644
--- a/src/main/java/org/embl/mobie/command/SpatialCalibration.java
+++ b/src/main/java/org/embl/mobie/command/SpatialCalibration.java
@@ -30,7 +30,7 @@ public void setVoxelDimensions( MoBIESettings settings, String tablePath )
if ( rows.columnNames().contains( PixelSizeColumns.PIXEL_SIZE ) )
{
FinalVoxelDimensions voxelDimensions = new FinalVoxelDimensions(
- rows.textColumn( PixelSizeColumns.PIXEL_UNIT ).get( 0 ),
+ rows.stringColumn( PixelSizeColumns.PIXEL_UNIT ).get( 0 ),
rows.doubleColumn( PixelSizeColumns.PIXEL_SIZE ).get( 0 ),
rows.doubleColumn( PixelSizeColumns.PIXEL_SIZE ).get( 0 ),
rows.doubleColumn( PixelSizeColumns.PIXEL_SIZE ).get( 0 )
@@ -40,7 +40,7 @@ public void setVoxelDimensions( MoBIESettings settings, String tablePath )
else
{
FinalVoxelDimensions voxelDimensions = new FinalVoxelDimensions(
- rows.textColumn( PixelSizeColumns.PIXEL_UNIT ).get( 0 ),
+ rows.stringColumn( PixelSizeColumns.PIXEL_UNIT ).get( 0 ),
rows.doubleColumn( PixelSizeColumns.PIXEL_SIZE_X ).get( 0 ),
rows.doubleColumn( PixelSizeColumns.PIXEL_SIZE_Y ).get( 0 ),
rows.doubleColumn( PixelSizeColumns.PIXEL_SIZE_Z ).get( 0 )
diff --git a/src/main/java/org/embl/mobie/command/context/ManualTransformationCommand.java b/src/main/java/org/embl/mobie/command/context/ManualTransformationCommand.java
index 81c57d85e..8c0fded11 100644
--- a/src/main/java/org/embl/mobie/command/context/ManualTransformationCommand.java
+++ b/src/main/java/org/embl/mobie/command/context/ManualTransformationCommand.java
@@ -34,6 +34,7 @@
import org.embl.mobie.command.MoBIEManualTransformationEditor;
import org.embl.mobie.lib.image.Image;
import org.embl.mobie.lib.image.RegionAnnotationImage;
+import org.scijava.ItemVisibility;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
import org.scijava.widget.Button;
@@ -46,6 +47,9 @@
@Plugin(type = BdvPlaygroundActionCommand.class, menuPath = CommandConstants.CONTEXT_MENU_ITEMS_ROOT + "Transform>Registration - Manual")
public class ManualTransformationCommand extends AbstractTransformationCommand
{
+
+ public static final String INACTIVE = "Status: Manual transform inactive.";
+
static { net.imagej.patcher.LegacyInjector.preinit(); }
@Parameter ( label = "Start manual transform", callback = "startManualTransform" )
@@ -57,6 +61,9 @@ public class ManualTransformationCommand extends AbstractTransformationCommand
@Parameter ( label = "Cancel manual transform", callback = "cancelManualTransform" )
public Button cancelManualTransform;
+ @Parameter( visibility = ItemVisibility.MESSAGE )
+ private final String status = INACTIVE;
+
private MoBIEManualTransformationEditor transformationEditor;
@Override
@@ -71,6 +78,9 @@ public void startManualTransform()
transformationEditor = new MoBIEManualTransformationEditor( bdvHandle.getViewerPanel(), bdvHandle.getKeybindings() );
transformationEditor.setTransformableSources( movingSacs );
transformationEditor.setActive( true );
+
+ getInfo().getMutableInput( "status", String.class )
+ .setValue( this, "Status: You are transforming " + selectedSourceName + "...");
}
private void acceptManualTransform()
@@ -83,6 +93,9 @@ private void acceptManualTransform()
// but this is intended as the transformed image is now a new image that is stored as a new view.
// And this new transformed image will also be shown by the above applyTransform function.
transformationEditor.setActive( false );
+
+ getInfo().getMutableInput( "status", String.class )
+ .setValue( this, INACTIVE );
}
private void cancelManualTransform()
@@ -90,5 +103,8 @@ private void cancelManualTransform()
if ( transformationEditor == null ) return;
transformationEditor.setActive( false );
+
+ getInfo().getMutableInput( "status", String.class )
+ .setValue( this, INACTIVE );
}
}
diff --git a/src/main/java/org/embl/mobie/lib/files/FileSourcesDataSetter.java b/src/main/java/org/embl/mobie/lib/files/FileSourcesDataSetter.java
index 8dc035de3..b064ab524 100644
--- a/src/main/java/org/embl/mobie/lib/files/FileSourcesDataSetter.java
+++ b/src/main/java/org/embl/mobie/lib/files/FileSourcesDataSetter.java
@@ -90,7 +90,7 @@ public void addDataAndDisplaysAndViews( Dataset dataset )
List< String > imageNames = sources.getSources();
ImageDataFormat imageDataFormat = ImageDataFormat.fromPath( sources.getPath( imageNames.get( 0 ) ) );
- IJ.log(sources.name + " file type: " + imageDataFormat );
+ IJ.log( "\""+ sources.name + "\" file type: " + imageDataFormat );
for ( String imageName : imageNames )
{
@@ -339,7 +339,15 @@ else if ( sources.getGridType().equals( GridType.Transformed ) )
// construct and add the view
//
final ImageZoomViewerTransform viewerTransform = new ImageZoomViewerTransform( fileSourcesList.get( 0 ).getSources().get( 0 ), 0 );
- final View view = new View( "all images", "data", displays, transformations, viewerTransform, false, null );
+ final View view = new View(
+ "all images",
+ "data",
+ displays,
+ transformations,
+ viewerTransform,
+ false,
+ null );
+ view.overlayNames( true );
dataset.views().put( view.getName(), view );
}
}
diff --git a/src/test/java/projects/microbial_predation/MicrobialPredation.java b/src/test/java/projects/microbial_predation/MicrobialPredation.java
index 61d871081..35ee2545b 100644
--- a/src/test/java/projects/microbial_predation/MicrobialPredation.java
+++ b/src/test/java/projects/microbial_predation/MicrobialPredation.java
@@ -14,10 +14,16 @@ public static void main( String[] args )
OpenImageAndLabelsCommand command = new OpenImageAndLabelsCommand();
- String root = "/Users/tischer/Documents/microbial-predation-data/";
- command.image = new File( root + "test_timelapse_subset/.*.tif" );
- command.labels = new File( root + "test_timelapse_results/.*_labels.tif" );
- command.table = new File( root + "test_timelapse_results/.*_measurements.csv" );
+// String root = "/Users/tischer/Documents/microbial-predation-data/";
+// command.image = new File( root + "test_timelapse_subset/.*.tif" );
+// command.labels = new File( root + "test_timelapse_results/.*_labels.tif" );
+// command.table = new File( root + "test_timelapse_results/.*_measurements.csv" );
+// command.spatialCalibration = SpatialCalibration.FromTable;
+
+ String root = "/Volumes/Microbial_Predation_Analysis_Dev/Interval_output";
+ command.image = new File( root, "Source/.*.tif" );
+ command.labels = new File( root , ".*_profile_labels.tif" );
+ command.table = new File( root, ".*_measurements.csv" );
command.spatialCalibration = SpatialCalibration.FromTable;
command.run();