Review previously generated code

Author: minnerbe

render-ws-java-client/src/main/java/org/janelia/render/client/StackStraighteningClient.java

@@ -23,8 +23,6 @@
  *
  * The offset is linearly interpolated across layers:
  * layer z is moved by (z - zmin) / (zmax - zmin) * offset
- *
- * @author Michael Innerberger
  */
 public class StackStraighteningClient {
 
@@ -39,35 +37,11 @@ public static class Parameters extends CommandLineParameters {
                 required = true)
         public String stack;
 
-        @Parameter(
-                names = "--targetOwner",
-                description = "Name of target stack owner (default is same as source stack owner)")
-        public String targetOwner;
-
-        @Parameter(
-                names = "--targetProject",
-                description = "Name of target stack project (default is same as source stack project)")
-        public String targetProject;
-
         @Parameter(
                 names = "--targetStack",
                 description = "Name of target stack",
                 required = true)
         public String targetStack;
-
-        @Parameter(
-                names = "--completeTargetStack",
-                description = "Complete the target stack after processing all layers",
-                arity = 0)
-        public boolean completeTargetStack = false;
-
-        public String getTargetOwner() {
-            return targetOwner == null ? renderWeb.owner : targetOwner;
-        }
-
-        public String getTargetProject() {
-            return targetProject == null ? renderWeb.project : targetProject;
-        }
     }
 
     public static void main(final String[] args) {
@@ -81,51 +55,33 @@ public void runClient(final String[] args) throws Exception {
                 LOG.info("runClient: entry, parameters={}", parameters);
 
                 final StackStraighteningClient client = new StackStraighteningClient(parameters);
-
-                client.setupDerivedStack();
                 client.straightenStack();
-
-                if (parameters.completeTargetStack) {
-                    client.completeTargetStack();
-                }
             }
         };
         clientRunner.run();
     }
 
     private final Parameters parameters;
-    private final RenderDataClient sourceDataClient;
-    private final RenderDataClient targetDataClient;
+    private final RenderDataClient renderDataClient;
     private final List<Double> zValues;
 
     private StackStraighteningClient(final Parameters parameters)
             throws IOException {
 
         this.parameters = parameters;
-
-        this.sourceDataClient = parameters.renderWeb.getDataClient();
-        this.targetDataClient = new RenderDataClient(parameters.renderWeb.baseDataUrl,
-                                                     parameters.getTargetOwner(),
-                                                     parameters.getTargetProject());
-
-        this.zValues = sourceDataClient.getStackZValues(parameters.stack);
+        this.renderDataClient = parameters.renderWeb.getDataClient();
+        this.zValues = renderDataClient.getStackZValues(parameters.stack);
 
         if (zValues.size() < 2) {
             throw new IllegalArgumentException("Stack must have at least 2 layers for straightening");
         }
     }
 
-    private void setupDerivedStack() throws IOException {
-        final StackMetaData sourceStackMetaData = sourceDataClient.getStackMetaData(parameters.stack);
-        targetDataClient.setupDerivedStack(sourceStackMetaData, parameters.targetStack);
-    }
-
-    private void completeTargetStack() throws Exception {
-        targetDataClient.setStackState(parameters.targetStack, StackMetaData.StackState.COMPLETE);
-    }
-
     private void straightenStack() throws Exception {
 
+        final StackMetaData sourceStackMetaData = renderDataClient.getStackMetaData(parameters.stack);
+        renderDataClient.setupDerivedStack(sourceStackMetaData, parameters.targetStack);
+
         final double zMin = zValues.get(0);
         final double zMax = zValues.get(zValues.size() - 1);
 
@@ -151,11 +107,13 @@ private void straightenStack() throws Exception {
             straightenLayer(z, zMin, zRange, totalOffsetX, totalOffsetY);
         }
 
+        renderDataClient.setStackState(parameters.targetStack, StackMetaData.StackState.COMPLETE);
+
         LOG.info("straightenStack: exit, processed {} layers", zValues.size());
     }
 
     private double[] getLayerBoundingBoxMidpoint(final double z) throws Exception {
-        final ResolvedTileSpecCollection tiles = sourceDataClient.getResolvedTiles(parameters.stack, z);
+        final ResolvedTileSpecCollection tiles = renderDataClient.getResolvedTiles(parameters.stack, z);
         final Bounds layerBounds = tiles.toBounds();
 
         if (layerBounds == null || layerBounds.getMinX() == null) {
@@ -180,7 +138,7 @@ private void straightenLayer(final Double z,
 
         LOG.info("straightenLayer: entry, z={}", z);
 
-        final ResolvedTileSpecCollection tiles = sourceDataClient.getResolvedTiles(parameters.stack, z);
+        final ResolvedTileSpecCollection tiles = renderDataClient.getResolvedTiles(parameters.stack, z);
 
         if (tiles.getTileCount() == 0) {
             LOG.info("straightenLayer: no tiles for z={}, skipping", z);
@@ -193,27 +151,22 @@ private void straightenLayer(final Double z,
         final double factor = (z - zMin) / zRange;
 
         // The translation needed to straighten this layer
-        // We negate the offset because we want to move layers back toward the first layer's position
         final double translateX = -factor * totalOffsetX;
         final double translateY = -factor * totalOffsetY;
 
-        if (Math.abs(translateX) > 0.001 || Math.abs(translateY) > 0.001) {
-            final AffineModel2D translationModel = new AffineModel2D();
-            translationModel.set(1, 0, 0, 1, translateX, translateY);
+        final AffineModel2D translationModel = new AffineModel2D();
+        translationModel.set(1, 0, 0, 1, translateX, translateY);
 
-            final LeafTransformSpec translationTransform = new LeafTransformSpec(
-                    translationModel.getClass().getName(),
-                    translationModel.toDataString());
+        final LeafTransformSpec translationTransform = new LeafTransformSpec(
+                translationModel.getClass().getName(),
+                translationModel.toDataString());
 
-            tiles.preConcatenateTransformToAllTiles(translationTransform);
+        tiles.preConcatenateTransformToAllTiles(translationTransform);
 
-            LOG.info("straightenLayer: applied translation ({}, {}) to {} tiles for z={}",
-                     translateX, translateY, tiles.getTileCount(), z);
-        } else {
-            LOG.info("straightenLayer: no significant translation needed for z={}", z);
-        }
+        LOG.info("straightenLayer: applied translation ({}, {}) to {} tiles for z={}",
+                 translateX, translateY, tiles.getTileCount(), z);
 
-        targetDataClient.saveResolvedTiles(tiles, parameters.targetStack, z);
+        renderDataClient.saveResolvedTiles(tiles, parameters.targetStack, z);
 
         LOG.info("straightenLayer: exit, saved {} tiles for z={}", tiles.getTileCount(), z);
     }