Set voxel units to pixel in BioFormatsImageData, mobie/mobie-viewer-fiji#1247

Author: tischi

src/main/java/org/embl/mobie/io/imagedata/BioFormatsImageData.java

@@ -5,11 +5,16 @@
 import ch.epfl.biop.bdv.img.bioformats.BioFormatsHelper;
 import ch.epfl.biop.bdv.img.opener.OpenerSettings;
 import mpicbg.spim.data.generic.AbstractSpimData;
+import mpicbg.spim.data.generic.sequence.BasicViewSetup;
+import mpicbg.spim.data.sequence.FinalVoxelDimensions;
+import mpicbg.spim.data.sequence.VoxelDimensions;
 import net.imglib2.type.NativeType;
 import net.imglib2.type.numeric.NumericType;
 
 import java.io.File;
+import java.lang.reflect.Method;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 public class BioFormatsImageData< T extends NumericType< T > & NativeType< T > > extends SpimDataImageData< T >
@@ -48,16 +53,49 @@ public BioFormatsImageData( String uri, SharedQueue sharedQueue )
                             .setSerie( i )
                             .useBFMemo( false );
 
-                    if ( usePixelUnits )
-                        settings.unit( "pixel" );
+                    // Throws NPE, https://github.com/mobie/mobie-viewer-fiji/issues/1247
+                    // if ( usePixelUnits )
+                    //    settings.unit( "pixel" );
 
                     settingsList.add( settings );
                 }
 
-                return OpenersToSpimData.getSpimData( settingsList );
+                AbstractSpimData< ? > spimData = OpenersToSpimData.getSpimData( settingsList );
+
+                // Since the above throws a NPE, we resort to
+                if ( usePixelUnits )
+                    setAllVoxelUnitsToPixel( spimData );
+
+                return spimData;
             }
         } );
         this.uri = uri;
         this.sharedQueue = sharedQueue;
     }
+
+    private static void setAllVoxelUnitsToPixel(AbstractSpimData<?> spimData) {
+
+        spimData.getSequenceDescription().getViewSetupsOrdered().forEach(setup -> {
+            final Method setVoxelSize;
+            try
+            {
+                setVoxelSize = BasicViewSetup.class.getDeclaredMethod("setVoxelSize", VoxelDimensions.class);
+            }
+            catch ( NoSuchMethodException ex )
+            {
+                throw new RuntimeException( ex );
+            }
+            setVoxelSize.setAccessible(true);
+
+            try {
+                final double[] dims = new double[setup.getVoxelSize().numDimensions()];
+                Arrays.fill(dims,1.0);
+                setVoxelSize.invoke(setup, new FinalVoxelDimensions("pixel", dims));
+            }
+            catch ( Exception e )
+            {
+                throw new RuntimeException("Failed to set voxel size for setup " + setup.getId(), e);
+            }
+        });
+    }
 }

src/test/java/org/embl/mobie/io/imagedata/BioFormatsImageDataTest.java

@@ -20,7 +20,7 @@ public void openPNG()
                 ImageDataFormat.fromPath( "src/test/resources/images/boats.png" ),
                 new SharedQueue( 1 ) );
         VoxelDimensions voxelDimensions = imageData.getSourcePair( 0 ).getB().getVoxelDimensions();
-        assertEquals( "px", voxelDimensions.unit() );
+        assertEquals( "pixel", voxelDimensions.unit() );
     }
 
     @Test