Use pixel units for PNG and JPG, mobie/mobie-viewer-fiji#1247

Author: tischi

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

@@ -27,16 +27,33 @@ public BioFormatsImageData( String uri, SharedQueue sharedQueue )
             public AbstractSpimData< ? > open( String uri )
             {
                 final File file = new File( uri );
-                List< OpenerSettings > openerSettings = new ArrayList<>();
+
+                String lowerCaseUri = uri.toLowerCase();
+
+                boolean usePixelUnits =
+                        (          lowerCaseUri.endsWith( ".png" )
+                                || lowerCaseUri.endsWith( ".jpg" )
+                                || lowerCaseUri.endsWith( ".jpeg" ) )
+                        ? true : false;
+
+                usePixelUnits = false;
+
+                List< OpenerSettings > settingsList = new ArrayList<>();
                 int numSeries = BioFormatsHelper.getNSeries(file);
+
                 for (int i = 0; i < numSeries; i++) {
-                    openerSettings.add(
-                            OpenerSettings.BioFormats()
-                                    .location(file)
-                                    .setSerie(i) );
+                    OpenerSettings settings = OpenerSettings.BioFormats()
+                            .location( file )
+                            .setSerie( i )
+                            .useBFMemo( false );
+
+                    if ( usePixelUnits )
+                        settings.unit( "pixel" );
+
+                    settingsList.add( settings );
                 }
 
-                return OpenersToSpimData.getSpimData( openerSettings );
+                return OpenersToSpimData.getSpimData( settingsList );
             }
         } );
         this.uri = uri;

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

@@ -0,0 +1,41 @@
+package org.embl.mobie.io.imagedata;
+
+import bdv.cache.SharedQueue;
+import mpicbg.spim.data.sequence.VoxelDimensions;
+import org.embl.mobie.io.ImageDataFormat;
+import org.embl.mobie.io.ImageDataOpener;
+import org.junit.jupiter.api.Test;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+
+class BioFormatsImageDataTest
+{
+    @Test
+    public void openPNG()
+    {
+        ImageData< ? > imageData = ImageDataOpener.open(
+                "src/test/resources/images/boats.png",
+                ImageDataFormat.fromPath( "src/test/resources/images/boats.png" ),
+                new SharedQueue( 1 ) );
+        VoxelDimensions voxelDimensions = imageData.getSourcePair( 0 ).getB().getVoxelDimensions();
+        assertEquals( "px", voxelDimensions.unit() );
+    }
+
+    @Test
+    public void openIlastikSavedByIlastik()
+    {
+        ImageData< ? > imageData = ImageDataOpener.open(
+                "src/test/resources/ilastik/probabilities-from-ilastik.h5",
+                ImageDataFormat.fromPath( "src/test/resources/ilastik/probabilities-from-ilastik.h5" ),
+                new SharedQueue( 1 ));
+        VoxelDimensions voxelDimensions = imageData.getSourcePair( 0 ).getB().getVoxelDimensions();
+        assertNotNull( voxelDimensions );
+    }
+
+    public static void main( String[] args )
+    {
+        new BioFormatsImageDataTest().openPNG();
+    }
+
+}