Import sofima's non-rigid deformation fields

render-app/pom.xml

@@ -164,6 +164,28 @@
             <artifactId>n5-hdf5</artifactId>
         </dependency>
 
+        <!-- n5-universe aggregates the n5 backends (filesystem, zarr, aws-s3, google-cloud, hdf5, blosc).  Managed by pom-scijava. -->
+        <dependency>
+            <groupId>org.janelia.saalfeldlab</groupId>
+            <artifactId>n5-universe</artifactId>
+        </dependency>
+
+        <!-- Neuroglancer-precomputed backend used by DisplacementFieldTransform to read SOFIMA warp fields. -->
+        <dependency>
+            <groupId>org.janelia</groupId>
+            <artifactId>n5-ng-precomputed</artifactId>
+            <version>0.1.0</version>
+        </dependency>
+
+        <!-- PrecomputedTestVolumes writes tiny precomputed volumes; reused by DisplacementFieldTransformTest. -->
+        <dependency>
+            <groupId>org.janelia</groupId>
+            <artifactId>n5-ng-precomputed</artifactId>
+            <version>0.1.0</version>
+            <classifier>tests</classifier>
+            <scope>test</scope>
+        </dependency>
+
         <!-- Version comes from the jackson.version property in the root pom, which keeps jackson-databind
              in sync with jackson-core, jackson-annotations and the jaxrs provider. -->
         <dependency>

render-app/src/main/java/org/janelia/alignment/loader/N5SliceLoader.java

@@ -9,9 +9,11 @@
 import java.net.URI;
 import java.net.URLDecoder;
 import java.nio.charset.Charset;
+import java.util.Optional;
 
 import net.imglib2.loops.LoopBuilder;
 import net.imglib2.type.numeric.integer.UnsignedShortType;
+import org.janelia.alignment.util.QueryKeyValueParameters;
 import org.janelia.saalfeldlab.n5.DataType;
 import org.janelia.saalfeldlab.n5.DatasetAttributes;
 import org.janelia.saalfeldlab.n5.N5FSReader;
@@ -67,44 +69,19 @@ public ImageProcessor load(final String urlString)
 
             final String defaultCharsetName = Charset.defaultCharset().name();
             final String basePath = URLDecoder.decode(uri.getPath(), defaultCharsetName);
-            final String query = uri.getQuery();
-            final String[] queryKeyValuePairs = query.split("&"); // note: uses "fastpath" for simple regex
-            String dataSet = null;
-            Long x = null;
-            Long y = null;
-            Long z = null;
-            Integer width = null;
-            Integer height = null;
-            for (final String keyValuePair : queryKeyValuePairs) {
-                final String[] keyValue = keyValuePair.split("=");
-                if (keyValue.length == 2) {
-                    final String key = keyValue[0];
-                    if ("x".equals(key)){
-                        x = Long.valueOf(keyValue[1]);
-                    } else if ("y".equals(key)) {
-                        y = Long.valueOf(keyValue[1]);
-                    } else if ("z".equals(key)) {
-                        z = Long.valueOf(keyValue[1]);
-                    } else if ("w".equals(key)) {
-                        width = Integer.valueOf(keyValue[1]);
-                    } else if ("h".equals(key)) {
-                        height = Integer.valueOf(keyValue[1]);
-                    } else if ("dataSet".equals(key)) {
-                        dataSet = URLDecoder.decode(keyValue[1], defaultCharsetName);
-                    }
-                }
-            }
+            final QueryKeyValueParameters query = new QueryKeyValueParameters(uri.getQuery(), urlString);
 
-            long[] xAndYOffsets = null;
-            if (x != null) {
-                if (y != null) {
-                    xAndYOffsets = new long[] { x, y };
-                } else {
-                    xAndYOffsets = new long[] { x, 0 };
-                }
-            } else if (y != null) {
-                xAndYOffsets = new long[] { 0, y };
-            }
+            final Optional<String> rawDataSet = query.getString("dataSet");
+            final String dataSet = rawDataSet.isPresent() ? URLDecoder.decode(rawDataSet.get(), defaultCharsetName) : null;
+            final Long z = query.getLong("z").orElse(null);
+            Integer width = query.getInt("w").orElse(null);
+            Integer height = query.getInt("h").orElse(null);
+
+            final Optional<Long> x = query.getLong("x");
+            final Optional<Long> y = query.getLong("y");
+            final long[] xAndYOffsets = (x.isPresent() || y.isPresent())
+                                        ? new long[] { x.orElse(0L), y.orElse(0L) }
+                                        : null;
 
             if ((basePath != null) && (dataSet != null)) {
 
@@ -128,20 +105,13 @@ public ImageProcessor load(final String urlString)
                     height = (int) dimensions[1];
                 }
 
-                switch(dataType) {
-                    case UINT8:
-                        imageProcessor = UNSIGNED_BYTE_HELPER.load(reader, dataSet, width, height, xAndYOffsets, z);
-                        break;
-                    case INT16:
-                        imageProcessor = SHORT_HELPER.load(reader, dataSet, width, height, xAndYOffsets, z);
-                        break;
-                    case FLOAT32:
-                        imageProcessor = FLOAT_HELPER.load(reader, dataSet, width, height, xAndYOffsets, z);
-                        break;
-                    default:
-                        // case INT8: case INT32: case INT64: case FLOAT64: case OBJECT: case UINT16: case UINT32: case UINT64:
-                        throw new IllegalArgumentException("dataType " + dataType + " is not supported");
-                }
+                imageProcessor = switch (dataType) {
+                    case UINT8 -> UNSIGNED_BYTE_HELPER.load(reader, dataSet, width, height, xAndYOffsets, z);
+                    case INT16 -> SHORT_HELPER.load(reader, dataSet, width, height, xAndYOffsets, z);
+                    case FLOAT32 -> FLOAT_HELPER.load(reader, dataSet, width, height, xAndYOffsets, z);
+                    // case INT8: case INT32: case INT64: case FLOAT64: case OBJECT: case UINT16: case UINT32: case UINT64:
+                    default -> throw new IllegalArgumentException("dataType " + dataType + " is not supported");
+                };
 
             } else {
                 throw new IllegalArgumentException(