Merge pull request #30 from BIOP/pom-scijava-39

Update to pom scijava 39

pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>38.0.1</version>
+		<version>39.0.0-SNAPSHOT</version>
 		<relativePath />
 	</parent>
 

src/main/java/ch/epfl/biop/bdv/img/OpenersToSpimData.java

@@ -49,6 +49,7 @@
 import org.slf4j.LoggerFactory;
 import spimdata.util.Displaysettings;
 
+import java.io.File;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -208,7 +209,7 @@ protected AbstractSpimData<?> getSpimDataInstance(List<OpenerSettings> openerSet
             // create spimdata
             SequenceDescription sd = new SequenceDescription(new TimePoints(timePoints), viewSetups, null, new MissingViews(missingViews));
             sd.setImgLoader(new OpenersImageLoader(openerSettings, openers, sd));
-            return new SpimData(null, sd, new ViewRegistrations(registrations));
+            return new SpimData((File) null, sd, new ViewRegistrations(registrations));
         }
         catch (Exception e) {
             e.printStackTrace();

src/main/java/ch/epfl/biop/bdv/img/bioformats/BioFormatsArrayLoaders.java

@@ -195,6 +195,75 @@ public int getBytesPerElement() {
 		}
 	}
 
+	/**
+	 * Class explaining how to read and load pixels of type : unsigned short (16 bits)
+	 */
+	public static class BioFormatsShortArrayLoader extends
+			BioformatsArrayLoader implements CacheArrayLoader<VolatileShortArray>
+	{
+
+		final ByteOrder byteOrder;
+
+		protected BioFormatsShortArrayLoader(ResourcePool<IFormatReader> readerPool,
+													 int channel, int iSeries, boolean littleEndian)
+		{
+			super(readerPool, channel, iSeries);
+			if (littleEndian) {
+				byteOrder = ByteOrder.LITTLE_ENDIAN;
+			}
+			else {
+				byteOrder = ByteOrder.BIG_ENDIAN;
+			}
+		}
+
+		@Override
+		public VolatileShortArray loadArray(int timepoint, int setup, int level,
+											int[] dimensions, long[] min) throws InterruptedException
+		{
+			try {
+				// get the reader
+				IFormatReader reader = readerPool.acquire();
+				reader.setSeries(iSeries);
+				reader.setResolution(level);
+				int minX = (int) min[0];
+				int minY = (int) min[1];
+				int minZ = (int) min[2];
+				int maxX = Math.min(minX + dimensions[0], reader.getSizeX());
+				int maxY = Math.min(minY + dimensions[1], reader.getSizeY());
+				int maxZ = Math.min(minZ + dimensions[2], reader.getSizeZ());
+				int w = maxX - minX;
+				int h = maxY - minY;
+				int d = maxZ - minZ;
+				int nElements = (w * h * d);
+
+				// read pixels
+				ByteBuffer buffer = ByteBuffer.allocate(nElements * 2);
+				for (int z = minZ; z < maxZ; z++) {
+					byte[] bytes = reader.openBytes(reader.getIndex(z, channel, timepoint), minX, minY,
+							w, h);
+					buffer.put(bytes);
+				}
+
+				// release the reader
+				readerPool.recycle(reader);
+
+				// unsigned short specific transform
+				short[] shorts = new short[nElements];
+				buffer.flip();
+				buffer.order(byteOrder).asShortBuffer().get(shorts);
+				return new VolatileShortArray(shorts, true);
+			}
+			catch (Exception e) {
+				throw new InterruptedException(e.getMessage());
+			}
+		}
+
+		@Override
+		public int getBytesPerElement() {
+			return 2;
+		}
+	}
+
 	/**
 	 * Class explaining how to read and load pixels of type : float (32 bits)
 	 */

src/main/java/ch/epfl/biop/bdv/img/bioformats/BioFormatsOpener.java

@@ -53,6 +53,7 @@
 import net.imglib2.type.numeric.ARGBType;
 import net.imglib2.type.numeric.NumericType;
 import net.imglib2.type.numeric.integer.IntType;
+import net.imglib2.type.numeric.integer.ShortType;
 import net.imglib2.type.numeric.integer.UnsignedByteType;
 import net.imglib2.type.numeric.integer.UnsignedIntType;
 import net.imglib2.type.numeric.integer.UnsignedShortType;
@@ -564,6 +565,9 @@ private static Type<? extends NumericType<?>> getBioformatsBdvSourceType(int pt,
 			if (pt == FormatTools.UINT32) {
 				return new UnsignedIntType();
 			}
+			if (pt == FormatTools.INT16) {
+				return new ShortType();
+			}
 		}
 		throw new UnsupportedOperationException("Unhandled pixel type for serie " +
 				image_index + ": " + pt);

src/main/java/ch/epfl/biop/bdv/img/bioformats/BioFormatsSetupLoader.java

@@ -44,6 +44,7 @@
 import net.imglib2.type.numeric.NumericType;
 import net.imglib2.type.numeric.integer.AbstractIntegerType;
 import net.imglib2.type.numeric.integer.IntType;
+import net.imglib2.type.numeric.integer.ShortType;
 import net.imglib2.type.numeric.integer.UnsignedByteType;
 import net.imglib2.type.numeric.integer.UnsignedIntType;
 import net.imglib2.type.numeric.integer.UnsignedShortType;
@@ -183,8 +184,18 @@ else if (t instanceof UnsignedShortType) {
 						(CacheArrayLoader<A>) new BioFormatsArrayLoaders.BioFormatsUnsignedShortArrayLoader(
 								readerPool, iChannel, iSeries, isLittleEndian);
 			}
-		}
-		else if (t instanceof FloatType) {
+		} else if (t instanceof ShortType) {
+			if (opener.to16bit()) {
+				// the data is originally 8 bits
+				throw new UnsupportedOperationException("Pixel type " + t.getClass()
+						.getName() + " conversion to 16 bits unsupported in " + BioFormatsSetupLoader.class
+						.getName());
+			} else {
+				loader =
+						(CacheArrayLoader<A>) new BioFormatsArrayLoaders.BioFormatsShortArrayLoader(
+								readerPool, iChannel, iSeries, isLittleEndian);
+			}
+		} else if (t instanceof FloatType) {
 			loader =
 				(CacheArrayLoader<A>) new BioFormatsArrayLoaders.BioFormatsFloatArrayLoader(
 					readerPool, iChannel, iSeries, isLittleEndian);

src/main/java/ch/epfl/biop/bdv/img/legacy/bioformats/BioFormatsToSpimData.java

@@ -286,7 +286,7 @@ protected AbstractSpimData<?> getSpimDataInstance(
 			sd.setImgLoader(new BioFormatsImageLoader(openers, sd, openers.get(
 				0).nFetcherThread, openers.get(0).numPriorities));
 
-			return new SpimData(null, sd, new ViewRegistrations(registrations));
+			return new SpimData((File) null, sd, new ViewRegistrations(registrations));
 		}
 		catch (Exception e) {
 			e.printStackTrace();

src/main/java/ch/epfl/biop/bdv/img/legacy/qupath/QuPathToSpimData.java

@@ -493,7 +493,7 @@ public AbstractSpimData<?> getSpimDataInstance(URI quPathProject,
 			sd.setImgLoader(new QuPathImageLoader(quPathProject, openerModel, sd,
 				openerModel.nFetcherThread, openerModel.numPriorities));
 
-			final SpimData spimData = new SpimData(null, sd, new ViewRegistrations(
+			final SpimData spimData = new SpimData((File) null, sd, new ViewRegistrations(
 				registrations));
 			return spimData;
 		}

src/main/java/ch/epfl/biop/bdv/img/omero/OmeroOpener.java

@@ -185,7 +185,7 @@ public OmeroOpener(
 
 		List<Long> imageIDs = OmeroHelper.getImageIDs(datalocation, gateway, securityContext);
 
-		if (imageIDs.size()==0) throw new IllegalStateException("Could not found an image ID in url "+datalocation);
+		if (imageIDs.isEmpty()) throw new IllegalStateException("Could not found an image ID in url "+datalocation);
 		if (imageIDs.size()>1) throw new UnsupportedOperationException("Could not open multiple Omero IDs in a single URL, split them.");
 
 		long imageID = imageIDs.get(0);